title: From_SID_4_PreTreat_Biopsy_TMb

data_processing:
75-base single reads average 20M reads per sample (3.5B reads total).
Raw counts were generated based on Ensembl genes (Ensembl release 91) with HTSeq (ver.0.11)
Reads from T cell RNA-seq were mapped to the human genome (GRCh38) using STAR (ver.2.5.0) aligner
Fold changes of differential expression were estimated through DESeq2(1.22.2)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: RawGeneCounts.xlsx

value: CD


title: BL6, Proximal colon, rep1

status: Public on Aug 23 2022

type: SRA

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

country: USA

institute: Vanderbilt University Medical Center

description:
Read length 150
BL6_pC_1

library_source: transcriptomic

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Alignments were parsed using Tophat program.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al. 2008).
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include readcount for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Proximal colon

extract_protocol:
Epithelial cells were mechanically isolated from colon using micro forceps in ice-cold PBS containing 30 mM EDTA and immersed in TRIzol Reagent (Invitrogen 15596018).
Libraries were prepared by Novogene Corporation Inc. (Sacramento, CA). mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented  randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and  RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified doublestranded  cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA  fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select  cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system  (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR  products by AMPure XP beads.

tag: tissue

value: Proximal colon

tag: tissue preparation

value: fresh tissue

tag: cell type

value: epithelial cells

tag: genotype

value: wild type

tag: treatment


title: FIP2, Distal colon, rep1

description:
Read length 150
FIP2_dC_1

source_name: Distal colon

value: Distal colon

value: Rab11-FIP2 KO


title: BL6, Distal colon, rep3

description:
Read length 150
BL6_dC_3


title: MerR_2

city: Buenos Aires

first: Sieira

last: Rodrigo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
Low-quality reads were removed using Trimmomatic v0.39
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
RNA-seq counts were determined using FeatureCounts
RNA-seq differential expression analysis was performed using DESeq2
RNA-seq reads were aligned to sequences of the contigs of Bizionia argentinensis JUB59 genome sequencing project (https://www.ncbi.nlm.nih.gov/genome/?term=Bizionia+argentinensis+JUB59).
Genome_build: BizArg_1.0
Supplementary_files_format_and_content: tsv file generated by DESeq2 provides gene ID, base mean reads, log2 fold-change, log2 fold-change standard error, Wald statistic, Wald test p-value, and Bonferroni Hochberg corrected p-value for the expression of each gene.

organism: Bizionia argentinensis JUB59

source_name: MerR cells

growth_protocol: B. argentinensis JUB59 strains were cultured in marine broth at 22 °C until the optical density at 600 nm (OD600) reached 1.4 (exponential phase).

extract_protocol:
Total RNA was isolated using Trizol Max Bacterial RNA Isolation Kit  (Ambion – Life Technologies) and then treated with TURBO DNAse (Ambion – Life Technologies)
RNA samples were submitted to NEB Microbe rRNA depletion kit, TruSeq stranded mRNA library preparation and 100-bp paired-end Illumina NovaSeq6000 sequencing.

value: delta merR

tag: biological replicate


title: WT_2

source_name: WT cells

value: Wild-type


title: From_SID_3_PreTreat_Biopsy_TMb

city: Miami

first: Maria

middle: T

last: Abreu

state: Florida

address: 1475 NW 12th Ave floor 1

department: Gastroenterology

institute: University of Miami

organism: Homo sapiens

source_name: Biopsy

extract_protocol:
Total RNA was extracted via miRNAeasy Micro Kit (Qiagen, Germantown, MD)
Libraries were individually indexed and pooled in groups of 20. Each pool was run on a NextSeq500 flow cell (9 flow cells total)

treatment_protocol: Mucosal biopsies from UC and CD were digested for single cells and FAC sorted for Treg and Tmem subset  sorted from PBMCs and biopsies

value: control

tag: time

value: Pre-treatment

tag: disease state

tag: sample type

value: Biopsy

value: Tmen

tag: location collected

value: Colon


title: BL6, Distal colon, rep2

description:
Read length 150
BL6_dC_2


title: From_SID_2_PreTreat_Blood_TMb

source_name: Blood (PBMC)

value: Blood (PBMC)


title: P5_CD_Inflamed_ileum_1

data_processing:
4.18 billion paired-end reads (2.09 billion clusters) were generated, and 472 million paired-end reads (236 million clusters) were unindexed.
Reads were mapped to the GRCh38 reference sequence using STAR (ver 2.5.0,  Durbin et al, 2013) aligner.
Raw counts were generated based on Ensembl genes (GENCODE version 26) with featureCounts (version 1.5.0).
Fold changes of differential expression were estimated through DESeq2 (ver.3.11, Love et al. 2014)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: csv format

source_name: Ileum

extract_protocol:
Cells were lysed with RLT buffer and RNA was extracted via RNeasy Mini Kit (Qiagen, Germantown, MD)
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR; Roche Life Science, Wilmington, MA) and then using standard Illumina protocols

treatment_protocol: Mucosal biopsies were digested for single cells and sorted for CD11b+ cells via magnetic column cell sorting.

value: Ileum

tag: biologics


title: Hi-C_Stag2f/y_rep2

city: Dallas

first: Hongtao

last: Yu

address: 6001 Forest Park Rd

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
The read-pairs were aligned and filtered using the HiC-Bench pipeline (https://github.com/NYU-BFX/hic-bench) with the following parameters: Genome-build=mm10; –very-sensitive-local –local; mapq=20; –min-dist 25000 –max-offset 500
Juicer “pre” tool (https://github.com/aidenlab/juicer) was used to generate the .hic file with default parameters.
The compartments analysis was done using the HOMER tool (http://homer.ucsd.edu/homer/index.html) by 100kb bins. H3K27ac ChIP-seq data was used to assign compartment sign.
Topological associated domains (TAD) and boundaries were identified with the Hicratio method with the follow parameters: –min-lambda=0.0 –max-lambda=1.0 –n-lambda=6 –gamma=0 –distance=500kb –fdr=0.1.
The loops were classified into group-specific loops and common-loops by using the significance cutoffs provided by Fit-HiC
Genome_build: mm10
Supplementary_files_format_and_content: indexed binary format files for access to chromatin contact matrix heatmaps
Supplementary_files_format_and_content: HDF container format files for high resolution genomic interaction matrices
Supplementary_files_format_and_content: track format files including continuous-valued data for house-keeping gene fixed eigenvector-1 at 100kb genomic bins
Supplementary_files_format_and_content: browser extensible data paired-end format files including "loops" from fit-hic

molecule: genomic DNA

source_name: Oligodendrocytes

extract_protocol:
3.5 to 4μg of DNA containing cells were cross-linked with 2% formaldehyde at RT for 10 minutes. Arima Hi-C kit (Arima Genomics, San Diego, CA) was usded for the Hi-C sample preparation
Illumina-compatible sequencing libraries were prepared by using a modified version of KAPA HyperPrep library kit (KAPA BioSystems, Willmington, MA).

tag: strain

tag: cell types

value: isolated primary oligodendrocytes

tag: age

value: post natal day 11-13


title: P4_UC_Uninflamed_colon_1

source_name: Colon

value: UC


title: P4_UC_Inflamed_colon_2


title: Wild_type-48h-HT115-400uM_tamoxifen-2

city: Worcester

first: Hefei

last: Zhang

state: Massachusetts

address: 4 Miles Ave

department: Department of Systems Biology

institute: University of Massachusetts Chan Medical School

data_processing:
Homemade python script was used for demultiplexing
Sequenced reads were trimmed using trimmomatic-0.32
Trimmed reads were aligned to the reference genome using STAR with the following parameters: —runThreadN 4 --alignIntronMax 25000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Features were counted by ESAT (Derr et al Genome Res. 2016) with parameter “-task score3p -wLen 100 -wOlap 50 -wExt 1000 -sigTest .01 -multimap normal -scPrep -umiMin 1”. Features in “c_elegans.PRJNA13758.WS271.canonical_geneset.gtf” were used as the annotation table input for ESAT, but pseudogenes were discard
Genome_build: c_elegans.PRJNA13758 (WormBase WS271)
Supplementary_files_format_and_content: tab dilimeted file containing TPM matrix for all samples and all genes

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were maintained on NGM-agar on an E. coli OP50 diet prior to experiment. They were synchronized by an 18 hour L1 arrest post-buffered bleach treatment.

extract_protocol:
A minumum of 200 staged animals were collected and washed thrice in M9 buffer. Total RNA was extracted via Trizol followed Zymo Direct-zol RNA miniprep kit extraction. DNAse I treatment was realized during the Zymo Direct-zol RNA miniprep kit extraction.
Cel-seq2

treatment_protocol: Synchronized animals were grown on NGM-agar 400 µM Citrate or 400 µM tamoxifen and seeded with E. coli HT115

value: wild-type

tag: Stage

value: grown on NGM + 400 uM tamoxifen + E. coli HT115


title: MerR_3


title: Hi-C_Stag2f/y_rep1


title: P3_CD_Uninflamed_colon_1

value: CD

value: anti-integrin


title: BL6, Distal colon, rep1

description:
Read length 150
BL6_dC_1

value: Distal colon

value: fresh tissue

value: epithelial cells

value: wild type


title: P1_UC_Inflamed_colon_2


title: Hi-C_Stag2f/y; Cre_rep2

value: Stag2f/y; Cre


title: BCSP4, experiment 4

type: RNA

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

state: California

address: 2700 Stockton Blvd

institute: UC Davis

description: Fracture BCSP4

hyb_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix 430-2.0 arrays (Affymetrix).

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.

data_processing: Raw microarray data were submitted to Gene Expression Commons (http://gexc.riken.jp) where data normalization was computed against the Common Reference, a large collection (n = 11,939) of publicly available microarray data from the National Center for Biotechnology Information Gene Expression Omnibus. Meta-analysis of the Common Reference also provides the dynamic range of each probe set on the array.

label: biotin

source_name: Gene expression data from BCSPs isolated from day-7 femoral fracture callus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: No in vitro culture, direct sort from freshly harvested fracture tissue.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Bicortical femoral fractures with an intramedullary pin were established in 10-12 week-old male C57/Bl6 mice. Callus tissue was harvested seven days after injury and processed for flow cytometric sorting for 10,000 SSCs and BCSPs for each experiment. Cells were directly sorted into Trizol.

value: Femur day-7 fracture callus

value: BCSP

value: 10-12 weeks

tag: Sex

value: Male


title: SSC4, experiment 4

description: Fracture SSC4

source_name: Gene expression data from SSCs isolated from day-7 femoral fracture callus

value: SSC


title: Hi-C_Stag2f/y; Cre_rep1

value: isolated primary oligodendrocytes


title: MerR_1

value: delta merR


title: RBP95-HTP

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

country: France

institute: Université Paris Descartes

description: cDNA librairies obtained after reverse transcription and PCR amplification of associated RNAs after digestion (Rnace it)

data_processing:
library strategy: Cross-Linking and cDNA (CRAC)
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using Flexbar with a barcode and an adaptor file using --adapter-trim-end RIGHT option.
Alignement was performed using Novoalign and -r Random option.
Aligned reads were analyzed using pyCRAC software.
Genome_build: R64 (S.cerevisiae)
Supplementary_files_format_and_content: One of the sequence analysis corresponds to the numbert of hits in each genes per 1000000 reads.
Supplementary_files_format_and_content: *_overview: Hits repartition; *35S: Hits pileup on 35S rRNA; *snoRNAs: Detailed hits repartition on snoRNAs

organism: Saccharomyces cerevisiae

source_name: Total extract

growth_protocol: Yeast were gorwn in YMM, -trp + glucose, until final OD=0.6

extract_protocol:
Cell lysis was perfomed using Zirconium beads (5x 1minutes, with 1 minutes intervals on ice). Complex was isolated by two succesive IPs.
Library was constructed by linking to digested RNA illumina compatible 5' Adaptaters and 3' linkers. Then, those modified RNA were extracted and a Reverse Transcription was performed using Superscript III followed by a final moderate PCR enrichement (16 cycles). This was then analyzed on MiSeq plateform from illumina.

treatment_protocol: Protein were cross-linked to RNA using Megatron

tag: strain background

value: HTP (His-Tev-ProtA)

tag: cross-link

value: Megatron (100 secondes)


title: Wild_type-48h-HT115-400uM_citrate-2

value: wild-type

value: grown on NGM + 400 uM citrate + E. coli HT115


title: P3_CD_Uninflamed_ileum_1

tag: tissue

value: Ileum

value: CD

value: anti-integrin


title: Wild_type-48h-HT115-400uM_tamoxifen-3

value: grown on NGM + 400 uM tamoxifen + E. coli HT115


title: P2_CD_Uninflamed_colon_1

value: Colon

tag: cell type


title: BY4741_control_1

tag: genotype

value: no Tag


title: P2_CD_Uninflamed_ileum_1


title: P4_UC_Uninflamed_ileum_1

value: UC


title: Wild_type-48h-HT115-400uM_tamoxifen-1

tag: treatment


title: SSC2, experiment 2

description: Fracture SSC2

value: Femur day-7 fracture callus


title: TID_3IAA_C (RNA-seq)

status: Public on Aug 22 2022

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
Signal per gene was normalized by the number of all S. pombe reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: acCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed CSV files contain normalized signal for all analyzed features (5797 mRNA coding genes).

source_name: whole organism

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Newly synthesized RNA molecules were labeled for 5 minute with 4-thioU.

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 med14DORF::KanMX pGPD1-OSTIR::HIS3 pSH1933 (ars cen TRP1 pRGR1-med14DTID) pSH1940 (ars cen LEU2 pRGR1-med14 TID-3xV5-degron)


title: TID_3IAA_B (RNA-seq)


title: TID_3IAA_A (RNA-seq)


title: SSC3, experiment 3

description: Fracture SSC3

value: 10-12 weeks

value: Male


title: TID_DMSO_A (RNA-seq)

value: DMSO


title: P1_UC_Uninflamed_colon_1


title: P1_UC_Uninflamed_ileum_1


title: Wild_type-48h-HT115-400uM_citrate-1


title: TID_DMSO_B (RNA-seq)


title: BCSP3, experiment 2

description: Fracture BCSP2

value: BCSP


title: Med7_WT_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1970 (ars cen LEU2 MED7)


title: Med9_3IAA_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED9-3xV5 IAA7 mini degron::KanMX


title: Med9_DMSO_B (RNA-seq)


title: Med9_DMSO_A (RNA-seq)


title: Med7N_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1991 (ars cen LEU2 mini degron-med7DC) pSH1986 (ars cen TRP1 med7DN)


title: TID_DMSO_C (RNA-seq)


title: Med7_WT_C (RNA-seq)


title: Med9_DMSO_C (RNA-seq)


title: BCSP3, experiment 3

description: Fracture BCSP3


title: SSC1, experiment 1

description: Fracture SSC1

value: SSC


title: Splenic CD19+ B cells, ApoE KO and ApoE/Gpr55 DKO

city: Munich

first: Sabine

last: Steffens

state: Bayern

address: Pettenkoferstrasse 9b

department: Clinical Pathobiochemistry

country: Germany

institute: Institute for Cardiovascular Prevention-LMU Klinikum

library_source: transcriptomic single cell

data_processing:
The reads were demultiplexed using deML and then filtered.
The reads were mapped to the mouse genome (mm10, GRCm38), and counted using zUMIs (version 2.5.5) with STAR.
Differential gene expression analysis was performed using DESeq2 and then the characterization of the molecular functions or pathways in which differentially expressed genes (DEGs) are involved was performed using gene set enrichment analysis (GSEA).
In addition, GSEA software was used to find immunological gene set annotations by using the ImmuneSigDB subset (C7) Molecular Signature Database (MSigDB).
Other resources used were such as Gene Ontology, Bioconductor, Gorilla and DAVID.
Assembly:  GRCm38 (mm10)
Supplementary files format and content: WT-GPR55.dgecounts.rds, WT-GPR55-sample_info.csv

source_name: spleen

extract_protocol:
Splenic single cell suspensions were obtained by mashing the spleens through a 70-µm cell strainer. Then stained with labelled antibodies and sort B cells for CD19. RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
Libraries were then constructed with the NEB Next Ultra II FS kit (E6177S, NEB) using the prime-seq specifications

value: female

value: spleen

value: Splenic CD19+ B cells

value: ApoE-/- and ApoE-/- GPR55-/-

value: untreated


title: Med7N_3IAA_A (RNA-seq)


title: Med7N_3IAA_C (RNA-seq)


title: med7N_del_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1986 (ars cen TRP1 med7DN)


title: Med7_EWE3_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1998 (ars cen LEU2 med7 EWE3)


title: BCSP1, experiment 1

description: Fracture BCSP1

value: Femur day-7 fracture callus


title: Med9_3IAA_A (RNA-seq)


title: Med7_WT_B (RNA-seq)


title: Med9_3IAA_C (RNA-seq)


title: med7N_del_A (RNA-seq)


title: Med7N_DMSO_A (RNA-seq)


title: Med7C_3IAA_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1989 (ars cen LEU2 med7DC) pSH1990 (ars cen TRP1 med7DN-mini degron)


title: Med7_3IAA_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED7-3xV5 IAA7::KanMX


title: Med7N_DMSO_B (RNA-seq)


title: med7N_del_C (RNA-seq)


title: Med6_delH1_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med6D::KanMX pSH2009 (ars cen LEU2 med6D Helix 1 residues 13-20)


title: Med7_EWE3_A (RNA-seq)


title: Med7_DMSO_C (RNA-seq)

value: DMSO


title: Med5_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3  MED5-3xV5 IAA7::KanMX


title: HUVEC-FUCCI - S-G2-M 2 [SG2M-2]

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

data_processing:
Raw read data was quality-control checked using FastQC v0.11.9.
Raw read data was aligned to either human genome hg38 or mouse genome GRCm38 using Kallisto v0.46.2.
Aligned data was normalized using Sleuth v0.30.0.
Assembly: hg38 or m38
Supplementary files format and content: TPM

source_name: Human Umbilical Vein Endothelial Cells

extract_protocol:
QIAGEN RNeasy MinElute Kit was used to purify RNA.
Low cell isolation numbers required cDNA amplification for RNA sequencing. RNA preparation and cDNA amplification for Illumina next-generation sequencing was performed with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.). Retinal endothelial cell samples were transferred to the University of Virginia Genome Analysis and Technology Core, which performed cDNA library preparation with the DNA Prep, (M) Tagmentation kit (Illumina Cat #20018704). HUVEC-FUCCI samples were transferred to the Yale Center for Genomic Analysis, which performed cDNA library preparation and amplification.

tag: cell line

value: Human Umbilical Vein Endothelial Cells

value: Endothelial Cell


title: HUVEC-FUCCI - G1-S 3 [G1S-3]


title: HUVEC-FUCCI - S-G2-M 3 [SG2M-3]


title: Med7_DMSO_B (RNA-seq)


title: Med7C_DMSO_C (RNA-seq)


title: Med5_3IAA_C (RNA-seq)


title: Med7_DMSO_A (RNA-seq)


title: Med7C_DMSO_B (RNA-seq)


title: Med5_3IAA_B (RNA-seq)


title: Med7C_DMSO_A (RNA-seq)


title: Med7C_3IAA_C (RNA-seq)


title: Med7_3IAA_C (RNA-seq)


title: Med7_3IAA_B (RNA-seq)


title: Med7C_3IAA_B (RNA-seq)


title: Med6_WT_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med6D::KanMX pSH2008 (ars cen LEU2 MED6)


title: Med7N_3IAA_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1991 (ars cen LEU2 mini degron-med7DC) pSH1986 (ars cen TRP1 med7DN)


title: Med31_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED19-3xV5 IAA7::KanMX


title: Med5_3IAA_A (RNA-seq)


title: Med6_WT_A (RNA-seq)


title: Med6_delH1_B (RNA-seq)


title: Med6_WT_B (RNA-seq)


title: Med31_DMSO_A (RNA-seq)


title: HUVEC-FUCCI - G1-S 2 [G1S-2]


title: Med5_DMSO_B (RNA-seq)


title: Med31_DMSO_B (RNA-seq)


title: HUVEC-FUCCI - Late G1 3 [LG1-3]


title: Med6_delH1_A (RNA-seq)


title: HUVEC-FUCCI - early G1 2 [EG1-2]


title: HUVEC-FUCCI - Early G1 3 [EG1-3]


title: HUVEC-FUCCI - G1-S 1 [G1S-1]


title: HUVEC-FUCCI - Late G1 2 [LG1-2]


title: Med5_DMSO_A (RNA-seq)


title: Med31_3IAA_A (RNA-seq)


title: HUVEC-FUCCI - Late G1 1 [LG1-1]


title: Med31_3IAA_C (RNA-seq)


title: A549C2, scATACseq

city: Beijing

first: Xiaofei

last: Zheng

state: Beijing

address: No.27, Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

description: 10x Genomics

library_source: genomic single cell

data_processing:
Sample demultiplexing, barcode processing, and unique molecular identifers (UMI) counting were performed by using the 10x Genomics pipeline CellRanger v.2.1.0 with default parameters. Specifcally, for each library, raw reads were demultiplexed using the pipeline command ‘cellranger mkfastq’ in conjunction with ‘bcl2fastq’ (v2.17.1.14, Illumina) to produce two fastq fles: the read 1 fle contains 26-bp reads, each consists of a cell barcode and a unique molecule identifer (UMI), and the read 2 file contains 96-bp reads including cDNA sequences. Reads then were aligned to the human reference genome (GRCh38), fltered, and counted using ‘cellranger count’ to generate the gene-barcode matrix.
For scRNA-seq data, expression matrices were processed using scCANCER (v2.2.1) . Briefly, the droplets having low transcripts diversity, capturing lysed cells or doublets were filtered based on five matrices: the number of total unique molecular identifiers (UMIs), the number of expressed genes and the percentages of UMIs from mitochondrial, ribosomal and  dissociation-associated genes per cell. Doublet score was performed by scCANCER using binary classification-based and co-expression-based algorithm, scds (v.1.2.0). After quality control, downstream analyses were performed based on Seurat (v4.1.0) in which canonical correlation analysis (CCA) was applied to integrate scRNA-seq data and remove the batch effect between different samples.
For scATAC-seq data, we computed per-cell quality control metrics using the DNA accessibility assay, including the strength of the nucleosome banding pattern and transcriptional start site (TSS) enrichment score and removed low-quality cells based on these metrics.
Assembly: GRCh38
Supplementary files format and content: .gz files including filtered tab-separated values files and matrix files

growth_protocol:
Purified A549 cells were monoclonally cultured in DMEM medium.
Irradiated A549 cells for scRNA-seq were harvested after continued culturing for 2 h and 6 h after irradiation; irradiated A549 cells for scATAC-seq were harvested at immediate and after continued culturing for 2 h after irradiation; A549 cells in control group for scRNA-seq and scATAC-seq were all harvest at the same time with 2h post-irradiation goups.

extract_protocol:
Irradiated A549 cells were harvested after continued culturing for 2 h and 6 h after irradiation. For scATAC-seq, irradiated A549 cells were harvested immediately and after continued culturing for 2 h after γ-ray treatment. Non-irradiated A549 cells for scRNA-seq and scATAC-seq were both harvested at 2 h after radiation. Single-cell sample preparation was conducted according to Sample Preparation Demonstrated Protocol provided by 10x Genomics as follows: 1mL of cell suspensions from each sample was pelleted in Eppendorf tubes by centrifugation (400 g, 5min). The supernatant was discarded, and the cells pellet was then resuspended in 1x PBS with 0.04% BSA, followed by two washing procedures by centrifugation (150 g, 3min). After the second wash, cells were resuspended in ~500 uL 1x PBS with 0.04% BSA followed by gently pipetting mix 10-15 times. Cells were counted using an Invitrogen Countess automated cell counter (LUNAⅡ) and the viability of cells was assessed by Trypan Blue staining (0.4%). After cell harvest, library and sequencing were completed by JingNeng company.
Libraries were prepared using the 10x Genomics Chromium Controller in conjunction with the single-cell 3′ v2 kit.

treatment_protocol: Purified A549 cells used in experimental groups were treated with Gy γ-ray.

value: lung cancer

value: IR immediately (purified)


title: Med31_3IAA_B (RNA-seq)


title: HUVEC-FUCCI - Early G1 1 [EG1-1]


title: Med21_EWE4_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med21D::KanMX pSH2001 (ars cen LEU2 med21 EWE4)


title: Med21_WT_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med21D::KanMX pSH1997 (ars cen LEU2 MED21)


title: A549C3, scATACseq

description: 10x Genomics

value: IR 2h (purified)


title: Med21_WT_A (RNA-seq)


title: Cybrid 16.184 European DM Hypoxia [AHD 32]

city: Irvine

middle: Cristina

last: Kenney

state: CA

address: 843 Health Science Rd

department: Ophthalmology

institute: University California Irvine

data_processing:
After acquiring the reads, the data were analyzed for quality control using FastQC. Reads were then quality and adaptor trimmed using Trimmomatic.Data were then aligned to the human hg19 reference genome using a short read sequence alignment tool that can account for splice variation, TopHat2. Gene expression was quantified by raw read counts using featureCounts and Reads-per-Kilobase-per-Million matched reads (RPKM) using Cufflinks.
Quantified data were then placed into 8 groups based on whether the cybrid from which the RNA originated had Euro or [Afr+Asi] mtDNA, was from a DM or Non-DM patient, or was grown in room-air or hypoxia. Differential gene expression between selected groups was performed using an R-based tool, DESeq2.
Assembly: hg38
Supplementary files format and content: tab-separated values text files include RPKM values for each Sample

source_name: ARPE19 Cybrid

extract_protocol:
isolating RNA using a PureLink RNA Mini Kit (Invitrogen, Waltham, MA) as per the manufacturer’s protocol.
For each sample, 500 ng of total RNA was use for library construction. Library construction was performed as per the TruSeq Stranded mRNA protocol (Illumina, San Diego, CA).

value: ARPE19 Cybrid

value: spontaneously immortalized cell line of human retinal pigment epithelium

value: European DM

value: Hypoxia

tag: time

value: 48 hours


title: Cybrid 16.184 European DM Normoxia [AHD 31]

value: Normoxia


title: Cybrid 15.176 Non European DM Hypoxia [AHD 28]

value: Non European DM


title: Cybrid 15.176 Non European DM Normoxia [AHD 27]


title: Cybrid 10.06 European Non-DM Normoxia [AHD 29]

value: European Non-DM


title: Cybrid 13.126 Non European Non DM Normoxia [AHD 25]

value: Non European Non-DM


title: Med2_15_3IAA_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED15-3xV5 IAA7::KanMX MED2-3xV5-IAA7::URA3


title: Cybrid 13.55 Non European DM Hypoxia [AHD 24]


title: Med2_15_DMSO_A (RNA-seq)

value: DMSO


title: Cybrid 10.06 European Non-DM Hypoxia [AHD 30]


title: Cybrid 13.126 Non European Non DM Hypoxia [AHD 26]


title: Med2_15_DMSO_C (RNA-seq)


title: Med2_15_DMSO_B (RNA-seq)


title: Med1_DMSO_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED1-3xV5 IAA7::KanMX


title: Med2_15_3IAA_A (RNA-seq)


title: Med2_15_3IAA_B (RNA-seq)


title: A549N1, scATACseq

description: 10x Genomics

value: lung cancer

value: Ctrl (purified)


title: Med21_EWE4_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med21D::KanMX pSH2001 (ars cen LEU2 med21 EWE4)


title: Med19_DMSO_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED19-3xV5 IAA7::KanMX


title: Med19_3IAA_C (RNA-seq)


title: Cybrid 13.55 Non European DM Normoxia [AHD 23]


title: Med1_DMSO_C (RNA-seq)


title: Cybrid 16.190 European DM Hypoxia [AHD 20]


title: Med1_DMSO_A (RNA-seq)


title: Cybrid 11.18 Non European Non DM Hypoxia [AHD 22]


title: Med19_DMSO_C (RNA-seq)


title: Med19_3IAA_B (RNA-seq)


title: Med19_3IAA_A (RNA-seq)


title: Cybrid 13.103 European DM Normoxia [AHD 15]


title: Cybrid 13.103 European DM Hypoxia [AHD 16]


title: Cybrid 11.08 European Non-DM Hypoxia [AHD 14]


title: Cybrid 14.135 European Non-DM Hypoxia [AHD 18]


title: Med17_3IAA_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED17-3xV5 IAA7 mini degron::KanMX


title: Med19_DMSO_A (RNA-seq)


title: Cybrid 14.135 European Non-DM Normoxia [AHD 17]

value: ARPE19 Cybrid


title: Cybrid 16.190 European DM Normoxia [AHD 19]

value: spontaneously immortalized cell line of human retinal pigment epithelium


title: Med17_DMSO_A (RNA-seq)


title: Med17_3IAA_B (RNA-seq)


title: Cybrid 11.18 Non European Non DM Normoxia [AHD 21]


title: Cybrid 11.08 European Non-DM Normoxia [AHD 13]


title: Cybrid 16.186 European DM Hypoxia [AHD 12]

value: European DM


title: Cybrid 16.186 European DM Normoxia [AHD 11]


title: Cybrid 13.45 European Non-DM Hypoxia [AHD 10]

value: Hypoxia


title: Med17_3IAA_A (RNA-seq)


title: Cybrid 13.124 Non European DM Hypoxia [AHD 8]

value: 48 hours


title: Cybrid 13.124 Non European DM Normoxia [AHD 7]

value: Normoxia


title: Cybrid 13.45 European Non-DM Normoxia [AHD 9]


title: Med16_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED16-3xV5 IAA7::KanMX


title: Med16_DMSO_A (RNA-seq)


title: Cybrid 11.30 Non European DM Hypoxia [AHD 4]

value: Non European DM


title: Med16_DMSO_B (RNA-seq)


title: Med15_Taf1_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED15-3xV5 IAA7::KanMX TAF1-3xV5-IAA7::LEU2


title: Cybrid 11.30 Non European DM Normoxia [AHD 3]


title: Cybrid 11.31 Non European Non DM Normoxia [AHD 1]

value: Non European Non-DM


title: Cybrid 11.38 Non European Non DM Normoxia [AHD 5]


title: Med15_Taf1_DMSO_B (RNA-seq)

value: DMSO


title: Med17_DMSO_C (RNA-seq)


title: Med16_3IAA_C (RNA-seq)


title: Cybrid 11.31 Non European Non DM Hypoxia [AHD 2]


title: Sorted 1 - Bulk RNA-seq - Composite 2

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Epidemiology

institute: University of Michigan

description:
Raw files are demultiplexed paired- or single-end fastq files. Processed file is a DESeq minimally prefiltered to genes with normalized counts greater than 10 per gene and detected in at least three individual samples. Genes represented by trimmed ENSEMBL IDs.
DESeq_prefiltered.rda

data_processing:
Single-cell RNA-sequencing read preprocessing and alignment: raw reads were processed, deconvoluted, droplet filtered, and aligned at the gene level with the CellRanger pipeline using default settings (v4.0.0), 10X Genomics)
Single-cell RNA-sequencing fetal/maternal identity and mosaic doublet removal: the freemuxlet function in the latest version (accessed 2021/12/05) of the ‘popscle’ package was used to assign fetal or maternal origin and identify 120 mosaic doublets for removal based on single nucleotide polymorphisms with minor allele frequency greater than 10% from the 1000 Genomes Phase 3 reference panel (released 2013/05/02).
Single-cell RNA-sequencing cell quality control: per cell quality control criteria were total RNA molecules, unique genes, and percentage of mitochondrial gene mapping reads. We excluded 1,398 low-quality outlier cells defined as cells that exceeded four median absolute deviations in samples 1 and 2 or three median absolute deviations in samples 3, 4, and 5 using the quickQCPerCell function in ‘scater’ (R package, version 1.18.6) with default settings.
Single-cell RNA-sequencing clustering and cluster annotation: maternal and fetal cells were split into separate datasets for clustering. Mutual nearest neighbor batch correction by biological replicate with default settings was used to identify cell type clusters and visualize clustering results via uniform manifold projection using FastMNN from ‘SeuratWrapper’ (R package, version 0.3.0). Iterative clustering and sub-clustering with ‘Seurat’ (R package, version 4.0.1) function FindClusters at different resolution parameters were evaluated using cluster stability via clustering trees in ‘clustree’. A priori canonical cell type marker gene expression patterns and cluster marker genes were used to assign cell types to cell clusters. Cells that fell outside cell type clusters and outlying in doublet density calculated with computeDoubletDensity were removed as putative doublets and doublet clusters.were identified with findDoubletClusters for removal in ‘scDblFinder’ (R package, version 1.4.0)
Bulk RNA-sequencing of placental tissue and cell types alignment and feature counts: Reads were aligned to the GRCh38.p12/ GENCODEv28 reference transcriptome using ‘STAR’ v2.6.0c with default settings [57]. featureCounts from ‘subread’ v1.6.1 was used to quantify and summarize gene expression with default settings [83]
Genome_build: For single-cell RNA-sequencing, reads were aligned to the GRCh38 GENCODEv32/Ensembl 98 reference transcriptome. For bulk RNA-sequencing, reads were aligned to the GRCh38.p12/ GENCODEv28 reference transcriptome
Supplementary_files_format_and_content: Processed files are .Rdata objects ready for analysis formatted as a Seurat object for the single-cell RNA-seq data or as DESeq object for the bulk RNA-sequencing data. Code used to generate these files is available (https://github.com/bakulskilab).

source_name: Placental Villous Tissue

extract_protocol:
Placentas were collected shortly after delivery from healthy, full term, singleton uncomplicated Cesarean sections at the University of Michigan Von Voigtlander Women’s Hospital. Villous placental tissue biopsies were collected and minced for dissociation after cutting away the basal and chorionic plates and scraping villous tissue from blood vessels. We subjected approximately 1g minced dissected villous tissue to the Miltenyi Tumor Dissociation Kit on the GentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) to yield single-cell suspensions of viable placental cells in 5μM StemMACS™ Y27632 (Miltenyi Biotec) in RPMI 1640 (Gibco) according to manufacturer’s instructions for “soft” tumor type. Red blood cells were depleted using RBC lysis buffer (Biolegend) according to manufacturer’s protocol A. Single-cell suspensions were size-filtered at 100μm and subsequently 40μm. To collect a syncytiotrophoblast-enriched fraction, the fraction between 40μm and 100μm was washed from the 40μm strainers. Single-cell suspensions <40μm were cryogenically stored in 5μM StemMACS™ Y27632 90% heat-inactivated fetal bovine serum (Gibco)/10% dimethyl sulfoxide (Invitrogen). For each placenta, additional whole villous tissue samples were stored in RNALater (Qiagen).
For single-cell RNA-sequencing, single cells were barcoded, and cDNA libraries constructed on the Chromium platform (10X Genomics, Single Cell 3' v2 chemistry).
For bulk RNA-sequencing, ribosomal RNAs were depleted with RiboGone (Takara) and libraries were prepared with the SMARTer Stranded RNA-Seq v2 kit (Takara).

value: Placental Villous Tissue


title: Med15_Taf1_DMSO_A (RNA-seq)


title: Med15_Taf1_3IAA_C (RNA-seq)


title: Med15_Taf1_3IAA_B (RNA-seq)


title: Med16_3IAA_A (RNA-seq)


title: Cybrid 11.38 Non European Non DM Hypoxia [AHD 6]


title: Med15_Taf1_3IAA_A (RNA-seq)


title: Sorted 4 - Bulk RNA-seq - Fibroblast


title: Med17_DMSO_B (RNA-seq)


title: Sorted 4 - Bulk RNA-seq - Extravilloustrophoblast


title: Sorted 4 - Bulk RNA-seq - Composite


title: Med15_Spt7_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED15-3xV5 IAA7::KanMX SPT7-3xV5-IAA7::LEU2


title: Sorted 4 - Bulk RNA-seq - Cytotrophoblast


title: Med15_Spt7_DMSO_B (RNA-seq)


title: Med16_3IAA_B (RNA-seq)


title: Sorted 4 - Bulk RNA-seq - Leukocyte


title: Sorted 4 - Bulk RNA-seq - Hofbauer


title: Med15_Spt7_DMSO_A (RNA-seq)


title: Sorted 2 - Bulk RNA-seq - Composite


title: Sorted 4 - Bulk RNA-seq - Syncytiotrophoblast


title: Med15_Med16_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED15-3xV5-IAA7::URA3 MED16-3xV5 IAA7 mini degron::KanMX


title: Med15_Med16_DMSO_B (RNA-seq)


title: Med15_Med16_3IAA_B (RNA-seq)


title: Med15_Med16_3IAA_A (RNA-seq)


title: Med15_Med16_3IAA_C (RNA-seq)


title: Sorted 2 - Bulk RNA-seq - Extravilloustrophoblast


title: Sorted 2 - Bulk RNA-seq - Leukocyte


title: Sorted 2 - Bulk RNA-seq - Fibroblast


title: Sorted 1 - Bulk RNA-seq - Composite


title: Med15_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED15-3xV5 IAA7::KanMX


title: Sorted 2 - Bulk RNA-seq - Endothelial


title: Sorted 1 - Bulk RNA-seq - Cytotrophoblast


title: Sorted 2 - Bulk RNA-seq - Hofbauer


title: Med15_DMSO_B (RNA-seq)


title: Sorted 1 - Bulk RNA-seq - Leukocyte


title: Sorted 1 - Bulk RNA-seq - Extravilloustrophoblast


title: Med1_5_DMSO_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED1-3xV5 IAA7::KanMX MED5-3xV5 IAA7::URA3


title: Med1_5_DMSO_B (RNA-seq)


title: Med15_DMSO_A (RNA-seq)


title: Med15_3IAA_C (RNA-seq)


title: Sorted 3 - Bulk RNA-seq - Composite


title: Sorted 1 - Bulk RNA-seq - Hofbauer


title: Sorted 1 - Bulk RNA-seq - Fibroblast


title: Med15_Med16_DMSO_A (RNA-seq)


title: Med1_5_DMSO_C (RNA-seq)


title: Med1_5_3IAA_C (RNA-seq)


title: Med15_3IAA_B (RNA-seq)


title: Med1_5_3IAA_A (RNA-seq)


title: Med15_3IAA_A (RNA-seq)


title: Sorted 3 - Bulk RNA-seq - Hofbauer


title: Med14_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX


title: Sorted 3 - Bulk RNA-seq - Syncytiotrophoblast


title: mNETseq_DRB_15min_R1

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Library strategy: mNET-seq
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d. For 3'seq, reads were mapped to the hg19 genome with Bowtie2.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: mNET-seq: hg38. 3'seq: hg19.
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: mNET-seq

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin. Nuclear RNAs were purified following cellular fractionation for 3'seq.
Libraries were prepared according to the protocol of TruSeq Small RNA Library Preparation Kit (Illumina) for mNET-seq. Libraries were prepared according to the protocol of NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB) for 3'seq.

treatment_protocol: Cells were treated with DMSO, DRB, or TNFα for the amount of time indicated in the sample's name.

value: HeLa

tag: agent

value: DRB

value: 15 min

tag: antibody

value: MABI0601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation.

tag: molecule subtype

value: nascent RNA


title: mNETseq_DRB_15min_R2


title: mNETseq_DRB_30min_R2

value: 30 min


title: Med1_5_3IAA_B (RNA-seq)


title: mNETseq_DMSO_15min_R1


title: Med14C_3IAA_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX pSH1936 (ars cen RGR1 / MED14 (D 2-704; TID2) LEU2) pSH1957 (ars cen MED14 (DTID)-mini degron TRP1)


title: HUVEC-FUCCI -S-G2-M 1 [SG2M-1]

value: Human Umbilical Vein Endothelial Cells

value: Endothelial Cell


title: Med14_DMSO_B (RNA-seq)


title: mNETseq_DMSO_30min_R1


title: mNETseq_DRB_10min

value: 10 min


title: mNETseq_DRB_30min_R1


title: S1049_D114

city: Bethesda

first: Robert

last: Morrison

state: MD

address: 29 Lincoln Drive

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to human genome GRC38.p2 using bowtie2 v2.3.4.3 with parameters  " -q --phred33-quals  --trim5 6  --trim3 4  --very-sensitive   -k 10  "
TPM values for each gene (Transcripts Per Million mapped reads) were calculated using R package DuffyNGS v1.9.1, using only reads landing within exon boundaries.
Assembly: GRCh38.p2
Supplementary files format and content: TPM

molecule: polyA RNA

source_name: Whole blood

extract_protocol:
Whole blood was collected in PAXgene tubes from vaccinees and controls and stored at -80C. Total RNA was extracted using the PAXgene miRNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole blood

tag: day

value: Day 114

tag: outcome

value: MoreProtected

value: PostVaccination

value: 3 doses of 1.8M PfSPZ sporozoites


title: Med14_3IAA_A (RNA-seq)

tag: strain


title: Med14C_DMSO_B (RNA-seq)

value: DMSO


title: Med14C_DMSO_A (RNA-seq)


title: S1047_D114


title: Med14_3IAA_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX


title: Med14_DMSO_A (RNA-seq)


title: S1045_D0

value: Day 0

value: LessProtected

value: PreVaccination


title: S1047_D0


title: Med12_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED12-3xV5 IAA7::KanMX


title: Sorted 3 - Bulk RNA-seq - Leukocyte

value: Placental Villous Tissue


title: Med14_3IAA_C (RNA-seq)


title: mNETseq_DMSO_15min_R2

value: HeLa

value: 15 min

value: MABI0601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation.

value: nascent RNA


title: S1043_D114


title: S1040_D0


title: mNETseq_DMSO_30min_R2

value: 30 min


title: Med14C_3IAA_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX pSH1936 (ars cen RGR1 / MED14 (D 2-704; TID2) LEU2) pSH1957 (ars cen MED14 (DTID)-mini degron TRP1)


title: mNETseq_DRB_5min

value: DRB

value: 5 min


title: S1049_D0

value: Whole blood

value: MoreProtected


title: Med1_3IAA_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED1-3xV5 IAA7::KanMX


title: Med12_3IAA_C (RNA-seq)


title: S1045_D114

value: Day 114

value: PostVaccination

value: 3 doses of 1.8M PfSPZ sporozoites


title: Med1_3IAA_A (RNA-seq)


title: Med14C_DMSO_C (RNA-seq)

value: DMSO


title: Med10_DMSO_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED10-3xV5 IAA7::KanMX


title: Med12_DMSO_A (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED12-3xV5 IAA7::KanMX


title: Med10_DMSO_A (RNA-seq)


title: Med10_3IAA_C (RNA-seq)


title: Med10_3IAA_B (RNA-seq)


title: S1037_D0

value: Day 0

value: LessProtected

value: PreVaccination


title: Med1_3IAA_C (RNA-seq)


title: Med12_DMSO_B (RNA-seq)


title: S1043_D0


title: Med14C_3IAA_B (RNA-seq)


title: CDK8_DMSO_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 SRB10-3xV5 IAA7::KanMX


title: CDK8_DMSO_C (RNA-seq)


title: S1038_D114


title: S1039_D0


title: S1040_D114


title: Med10_DMSO_C (RNA-seq)


title: CDK8_3IAA_C (RNA-seq)


title: Med12_3IAA_A (RNA-seq)


title: Med12_3IAA_B (RNA-seq)


title: S1019_D0

value: 5 doses of 270K PfSPZ sporozoites


title: S1037_D114


title: S1038_D0


title: S1035_D114


title: CDK8_3IAA_A (RNA-seq)


title: S1039_D114


title: CCL1_DMSO_B (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 CCL1-3xV5 IAA7::KanMX


title: CCL1_DMSO_A (RNA-seq)


title: Med10_3IAA_A (RNA-seq)


title: CCL1_3IAA_C (RNA-seq)


title: S1004_D142

value: Day 142


title: S1019_D142


title: S1034_D142


title: CCL1_3IAA_B (RNA-seq)


title: S1005_D0


title: S1034_D0


title: Med15_TFIIB_IAA_AI (ChIP-seq)

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all S. pombe reads mapped for the sample, multiplied by 10000 (arbitrarily chosen number) and multiplied by the ratio of S. pombe to S. cerevisiae reads in the corresponding input sample.
Genome_build: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

extract_protocol:
ChIP-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins.

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 SUA7-13x Myc::HPH MED15-3xV5 IAA7::KanMX

tag: sample type

value: input

tag: chip antibody


title: CDK8_DMSO_A (RNA-seq)


title: CDK8_3IAA_B (RNA-seq)


title: S1005_D142

value: Whole blood

value: MoreProtected


title: CCL1_3IAA_A (RNA-seq)


title: Med15_TFIIB_IAA_BI (ChIP-seq)


title: Knock-out (KO) 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Xbp1 deleted in intestinal epithelial cells

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 1.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Small intestinal tissue

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Villin-Cre Xbp1 fl/fl (KO) and Xbp1 fl/fl (WT) mice underwent lethal total body irradiation with 11 Gy und two equal-split doses 4 hours apart. After the second irradiation, mice received an i.v. injection with 5x10e6 bone marrow cells and 600 000 CD4+ and CD8+ T cells enriched from a BALB/c donor. Mice were monitored for 14 days. On day 14, the small intestine of recipient mice was isolated, cleaned and processed for RNA isolation.

extract_protocol: RNA was isolated using the miRNeasy Mini kit (Qiagen). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent 141 Technologies). RNA samples with an RNA integrity number (RIN) greater than 7 were further processed for Affymetrix microarrays.

treatment_protocol: The cells were not treated after isolation from the recipient mice.

tag: tissues

value: Small intestine

tag: cells

value: Whole lysate

tag: age

value: 8-12 weeks

value: Villin-Cre Xbp1 fl/fl


title: Wildtype (WT) 4

description: WT littermates withour Cre recombinase

value: Xbp1 fl/fl


title: Med15_TFIIB_IAA_A (ChIP-seq)

value: IP

value: IP antibody


title: S1004_D0

tag: tissue

value: Day 0

value: LessProtected


title: S1001_D142

value: PostVaccination


title: Wildtype (WT) 3

description: WT littermates withour Cre recombinase


title: S1002_D142

value: 5 doses of 270K PfSPZ sporozoites


title: Knock-out (KO) 4


title: Med14_TFIIB_IAA_B (ChIP-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 SUA7-13x Myc::HPH MED14-3xV5 IAA7::KanMX


title: Wildtype (WT) 2

description: WT littermates withour Cre recombinase


title: Med14_TFIIB_IAA_BI (ChIP-seq)


title: Med14_TFIIB_IAA_A (ChIP-seq)


title: Sample_9_KD_3, input

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

data_processing:
Reads were aligned to the human genome (hg38) using Bowtie2.
Alignments were sorted and indexed using Samtools for downstream processes. MACS2 was then used to identify significant peaks .
Peaks were annotated using the R package ChIPseeker [ref]. Peaks that overlapped a 4kb window centered at an annotated transcription start site were annotated as promoter peak
Differential enrichment analysis was performed using the R package DiffBind. Peaks with an FDR adjusted p-value of 0.1 or less were considered differentially enriched between the knockdown and control conditions
Motif enrichment analysis was performed on 3kb windows centered at the TSS of genes with differentially enriched promoter peaks using HOMER
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

growth_protocol: THP were cultivated in RPMI (ATCC) with 10% non-heat inactivated FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer.

tag: issue

value: monocytic cell line

value: transfection with gapmer targetting CHROME

tag: group

value: gapmer


title: Embryonic Stem Cells - H3K4me3

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Library strategy: CUT&Tag
Illumina Casava1.7 software used for basecalling
Supplementary_files_format_and_content: Peak text files. The data fles are the processed files using IgG control (S09-S9) sample.

source_name: Embryonic Stem Cells - H3K4me3

extract_protocol:
Samples were processed according to the CUT&Tag-IT™ assay Kit (Active motif) protocol. Instead of magnetic separation, centrifugation approach was used.
DNA libraries were prepared for sequencing using standard Illumina protocol

tag: cell type

value: mESC

value: C57BL/6 x CAST/EiJ

tag: Sex

value: male


title: Med14_TFIIB_IAA_AI (ChIP-seq)

tag: genotype

tag: treatment

value: input


title: IgG control

source_name: Embryonic Stem Cells


title: Sample_8_KD_2, input

tag: antibody


title: Med14_TFIIB_DMSO_B (ChIP-seq)

value: DMSO


title: Embryonic Stem Cells - H3K27ac

source_name: Embryonic Stem Cells - H3K27ac


title: Med14_TFIIB_DMSO_BI (ChIP-seq)


title: Med14_TFIIB_DMSO_A (ChIP-seq)


title: Med15_TFIIB_DMSO_A (ChIP-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 SUA7-13x Myc::HPH MED15-3xV5 IAA7::KanMX


title: Med15_TFIIB_DMSO_BI (ChIP-seq)


title: Med15_TFIIB_DMSO_B (ChIP-seq)


title: Sample_7_KD_1, input


title: Med14_TFIIB_DMSO_AI (ChIP-seq)


title: Sample_3_Control_3, input

value: transfection with control gapmer

value: control


title: Med15_TFIIB_IAA_B (ChIP-seq)

value: IP

value: IP antibody


title: Med15_TFIIB_DMSO_AI (ChIP-seq)


title: S1001_D0

value: Whole blood

value: Day 0

value: MoreProtected

tag: time

value: PreVaccination


title: Embryonic Stem Cells - H3K79me2

source_name: Embryonic Stem Cells - H3K79me2


title: Sample_2_Control_2, input

value: monocytic cell line


title: S1002_D0

tag: day

value: LessProtected

value: 5 doses of 270K PfSPZ sporozoites


title: Med10_TFIIB_IAA_AI (ChIP-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 SUA7-13x Myc::URA3 MED10-3xV5 IAA7::KanMX


title: Embryonic Stem Cells - H3K79me3

source_name: Embryonic Stem Cells - H3K79me3

value: mESC

value: C57BL/6 x CAST/EiJ


title: Med10_TFIIB_DMSO_BI (ChIP-seq)

value: input


title: Med10_TFIIB_DMSO_AI (ChIP-seq)

value: DMSO


title: Med10_TFIIB_IAA_B (ChIP-seq)


title: Swr1_C (ChEC-seq)

data_processing:
Library strategy: ChEC-seq
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins.

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 SWR1-MNase::TRP1


title: Swr1_A (ChEC-seq)


title: Med10_TFIIB_IAA_BI (ChIP-seq)


title: Med10_TFIIB_IAA_A (ChIP-seq)


title: input_3

data_processing:
Library strategy: ChIRP-seq
trim adapters using Trimmomatic
map reads using bwa
call peaks relative to input using macs
perform differential binding analysis using DiffBind from BioConductor
Assembly: hg19
Supplementary files format and content: base mean data was calculated from reads of three replicate samples. ChIRP results were analyzed as % enrichment relative to input DNA of respective experimental conditions.

extract_protocol:
DNA was eluted from hybridized magnetic beads and subjected for Illumina sequencing. In short, beads were washed at room temperature with ChIRP wash buffer (EMD Millipore, #17-10494). Beads were subsequently captured using a DynaMag magnet (Thermo Fisher Scientific) and DNA was eluted by suspending beads in elution buffer (20 mM Tris pH 7.4, 1% SDS, 50 mM NaHCO3, 1 mM EDTA). ChIRP eluates were reverse cross-linked at 65C for 4h, digested with Proteinase K (EMD Millipore) at 55C followed by incubation with RNase cocktail (Ambion). ChIRP purified DNA was cleaned using PCR purification columns (Zymo Research) and subjected to Illumina sequencing.
Illumina

treatment_protocol: 100 ng/mL PMA to differentiate into THP1 macrophages

tag: cell line


title: Med10_TFIIB_DMSO_B (ChIP-seq)

tag: strain


title: Embryonic Stem Cells - H3K4me1

source_name: Embryonic Stem Cells - H3K4me1

value: male


title: odd_3

tag: sample type

value: odd probes for CHROME


title: Sample_3_Control_3

value: transfection with control gapmer

value: control


title: Snf5_A (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 SNF5-MNase::TRP1


title: Sample_9_KD_3

value: transfection with gapmer targetting CHROME

value: gapmer


title: Med8_Mnase_Med14_deg_IAA_C (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX MED8-MNase::TRP1


title: Sample_8_KD_2

value: monocytic cell line


title: Med10_TFIIB_DMSO_A (ChIP-seq)

value: IP

tag: chip antibody

value: IP antibody


title: Sample_7_KD_1


title: Embryonic Stem Cells - H3K36me3

source_name: Embryonic Stem Cells - H3K36me3


title: Med8_Mnase_Med14_deg_IAA_A (ChEC-seq)


title: Med8_Mnase_Med14_deg_DMSO_B (ChEC-seq)


title: gapCHROME_3_polyIC

data_processing:
 RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
base mean data was calculated from reads of three replicate samples. Fold change was calculated as gapCHROME over gapctrl. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections.
Genome_build: hg19
Supplementary_files_format_and_content: 2021_11_30_gapmer_poly_Counts_all.xlsx

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x150bp configuration, single index, per lane

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer and subsequent stimulated with polyIC (1000 ng/mL) or a control vehicle

tag: modification

value: transfection with gapmer targeting CHROME

value: CHROME depletion

value: polyIC


title: input_2


title: even_3

value: even probes for CHROME


title: Med8_Mnase_Med14_deg_DMSO_A (ChEC-seq)

value: DMSO


title: Knock-out (KO) 1

tag: tissues

value: Small intestine

tag: cells

value: Whole lysate

value: 8-12 weeks

value: Villin-Cre Xbp1 fl/fl


title: Snf5_C (ChEC-seq)


title: Knock-out (KO) 2

tag: age


title: Snf5_B (ChEC-seq)


title: Wildtype (WT) 1

description: WT littermates withour Cre recombinase

value: Xbp1 fl/fl


title: Swr1_B (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 SWR1-MNase::TRP1


title: S1035_D0

tag: tissue

value: Whole blood

value: Day 0

tag: outcome

value: LessProtected

value: PreVaccination

value: 3 doses of 1.8M PfSPZ sporozoites


title: Med8_A (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 MED8-MNase::TRP1


title: CCL1_DMSO_C (RNA-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 CCL1-3xV5 IAA7::KanMX


title: Med19_Mnase_kin28is_DMSO_B (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 kin28is MED19-3xFlag-MNase::TRP1


title: Sample_2_Control_2

tag: issue

value: monocytic cell line

value: transfection with control gapmer

tag: group

value: control


title: Med19_Mnase_kin28is_DMSO_A (ChEC-seq)

tag: genotype

value: DMSO


title: odd_2

value: odd probes for CHROME


title: input_1


title: gapCHROME_2_polyIC

tag: cell type

value: transfection with gapmer targeting CHROME

value: CHROME depletion

tag: treatment

value: polyIC


title: gapctrl_1_polyIC


title: odd_1


title: Med8_Mnase_Med14_deg_IAA_B (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX MED8-MNase::TRP1


title: gapCHROME_1_polyIC


title: Med8_Mnase_Med14_deg_DMSO_C (ChEC-seq)


title: even_2

value: even probes for CHROME


title: Med17_Mnase_TID2_deg_DMSO_C (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 med14DORF::KanMX pGPD1-OSTIR::HIS3 MED17-3xFlag-MNase::URA3 pSH1933 (ars cen TRP1 pRGR1-med14DTID) pSH1940 (ars cen LEU2 pRGR1-med14 TID-3xV5-degron)


title: Med17_Mnase_TID2_deg_DMSO_B (ChEC-seq)


title: Med17_Mnase_TID2_deg_IAA_A (ChEC-seq)


title: Med8_B (ChEC-seq)


title: gapctrl_2_polyIC


title: Med17_Mnase_TID2_deg_IAA_C (ChEC-seq)


title: even_1


title: EHT OCTN2 (N32S)

city: Hamburg

first: Arne

last: Hansen

address: Martinistraße 52

department: Institute of Experimental Pharmacology and Toxicology

institute: University Medical Center Hamburg-Eppendorf

description: 10x Genomics

data_processing:
Bcl files were converted to Fastq files by using bcl2fastq. Each sample was mapped to the human reference genome GRCh38 (GENCODE v32/Ensembl 98) using the CellRanger suite (v.5.0.0). Mapping quality was assessed using the cellranger summary statistics; Empty droplets were identified by Emptydrops, implemented in the CellRanger workflow, and subsequently removed, while doublets were identified and filtered using Solo.
Downstream analysis was performed using the Python Scanpy v1.5.1 toolkit. Single nuclei were filtered for counts (300 ≤ n_counts ≤20,000), genes (500 ≤ n_genes ≤5,500), mitochondrial genes (percent_mito ≤1%), ribosomal genes (percent_ribo ≤1%), and soft max score detected by Solo (solo_softmax_scores ≤0.5). After read count normalization and log-transformation, highly variable genes were selected. Principal components were computed, and elbow plots were used to define the appropriate number of principal components for neighbor graph construction. Prior to manifold construction using UMAP, selected principal components were harmonized by using Python Harmonypy. Finally, nuclei were clustered using the network-based Leiden algorithm.
Assembly: GRCh38_2020A
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, matrix.h5

molecule: nuclear RNA

source_name: Engineered heart tissue

extract_protocol:
Single nuclei were obtained from flash-frozen tissues using mechanical homogenization as previously described. Tissues were homogenized using a 7 ml glass Dounce tissue grinder set (Merck) with 8–10 strokes of a loose pestle (A) and 8–10 strokes of a tight pestle (B) in homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 1 mM dithiothreitol (DTT), 1× protease inhibitor, 0.4 U μl−1 RNaseIn, 0.2 U μl−1 SUPERaseIn, 0.1% Triton X-100 in nuclease-free water). Homogenate was filtered through a 40-μm cell strainer (Corning). After centrifugation (500g, 5 min, 4 °C) the supernatant was removed and the pellet was resuspended in storage buffer (1× PBS, 4% bovine serum albumin (BSA), 0.2 U μl−1 Protector RNaseIn). Nuclei were stained with NucBlue Live ReadyProbes Reagents (ThermoFisher) and Hoechst-positive single nuclei were purified by fluorescent activated cell sorting (FACS) using influx, XDP or FACSAria (BD Biosciences). Nuclei purification and integrity was verified under a microscope, and nuclei were further processed using the Chromium Controller (10X Genomics) according to the manufacturer’s protocol.
Single cells and nuclei were manually counted by Trypan blue exclusion or automatically using a Countess II (Life Technologies) using at least two separate counts. Cell or nuclei suspension was adjusted to 400–1,000 cells per microlitre and loaded on the Chromium Controller (10X Genomics) with a targeted cell or nuclei recovery of 4,000–10,000 per reaction. 3′ gene expression libraries were prepared according to the manufacturer’s instructions of the v2 or v3 Chromium Single Cell Reagent Kits (10X Genomics). Quality control of cDNA and final libraries was done using Bioanalyzer High Sensitivity DNA Analysis (Agilent) or 4200 TapeStation System (Agilent).

value: Engineered heart tissue

value: IPSC

value: IPSC-derived cardiac cells

value: SLC22A5 (OCTN2) homozygous point mutation (c.95A>G, p.N32S)


title: Med17_Mnase_TID2_deg_IAA_B (ChEC-seq)


title: gapctrl_3_polyIC


title: HepG2_LDB1ko_H3K27ac-rep1

first: GUOYOU

last: LIU

state: Maryland

address: 50 South Dr, Building 50, Room 3150

institute: NIH/NIDDK

data_processing:
Raw sequence reads were trimmed with cutadapt v2.7(Martin, 2011) to remove any adapters while performing light quality trimming with parameters "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 --minimum-length=25".
For RNAseq, Trimmed reads were mapped to the Homo sapiens hg38 or mouse mm10 reference genome  using hisat2 v2.1.0 (Kim et al., 2015) with default parameters. For ChIPseq, Reads were aligned to the human GENCODE release 25 assembly using Bowtie2 v2.3.5(Langmead and Salzberg, 2012).
For RNAseq, multimapping reads were filtered using samtools 1.9 (Li et al., 2009). For ChIPseq, Multimapping reads were removed with samtools v1.9 using the “view” subcommand and the additional argument “-q 20”, and duplicate reads were removed with the Picard v2.21.4 (Toolkit, 2019) Mark Duplicates tool.
For RNAseq, uniquely aligned reads were counted using subread featureCounts v1.6.4 with default parameters (Liao et al., 2014) except that “-s1” option for this sense-stranded library. For ChIPseq, BigWig signal tracks were created with deepTools v3.3.1 (Ramirez et al., 2016) using the bamCoverage tool with the additional arguments “–normalize Using CPM –extend Reads 300”.
For RNAseq, Differential expression between groups of samples was tested using R version 3.5.1 (R Core Team, 2018) (R Core Team) with DESeq2 1.22.1 (Love et al., 2014). For ChIPseq, peaks were called for each replicate individually using macs v2.2.7.1(Zhang et al., 2008). Pooled peaks were separately called by providing both replicates simultaneously to macs2. Final peaks for each antibody were selected as pooled peaks that also had a peak intersecting it by at least 1 bp in at least one of the replicates using BEDTools v2.29.0 (Quinlan and Hall, 2010) and pybedtools 0.8.0 (Dale et al., 2011).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Excel files.xlsx contain all gene TPM counts from RNAseq results. Excel files.xls contain peaks coordinates. Bigwig files are created with deepTools v3.3.1 using the bamCoverage tool.

growth_protocol: Mice were housed in a clean conventional vivarium at ~22 oC, with a 12:12-h dark-light cycle (lights on at 06:00). HepG2 cells (HB-8065, ATCC) were cultured in MEM medium (Corning, MT10010CV) with 10% FBS (ATLANTA Biologicals, s12450) and 1 ×Penicillin-Streptomycin (Gibco, 15140-122).

extract_protocol:
RNA was extracted by PureLink RNA mini kit (Invitrogen, 12183020), and DNA was removed by DNase digestion (Invitrogen, 12185-010).
For RNA sequencing, libraries were constructed from 1 mg total RNA by using the Truseq Stranded mRNA sample preparation kit (Illumina 20020493). ChIP-qPCR and ChIPmentatation were performed as described previously (Krivega and Dean, 2018a; Schmidl et al., 2015).

treatment_protocol: Mice were ad libitum access to water and chow (LabDiet, Advanced Protocol 5V0T, 12.5% kcal from fat) or high fat diet (HFD, 89067-469, 60% kcal fat, VWR). Ldb1 flox mice (Zhao et al., 2007) and Albumin-Cre mice (003574, The Jackson Laboratory) were mated to obtain control mice (Ldb1flox/flox) and liver-specific Ldb1 knockout mice Ldb1flox/flox; Alb-Cre+/-) on a C57Bl6 background. Only male littermates were used. To generate LDB1 knockout HepG2 clones, pSpCas9-2A-GFP plasmid (Addgene, Plasmid #4813) containing a guide RNA targeting the first exon of the LDB1 gene was electroporated into HepG2 cells by using Lonza nucleofector with kit V (VCA-1003).

value: LDB1 knockout cell

value: H3K27ac (Abcam 4729)


title: Med8_C (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 MED8-MNase::TRP1


title: HepG2_LDB1ko_H3K27ac_Input-rep2


title: HepG2_LDB1ko_H3K27ac_Input-rep1


title: Med17_Mnase_TID2_deg_DMSO_A (ChEC-seq)


title: Med15_Mnase_Med14_deg_IAA_C (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 RPB3-3xFlag::NATMX pGPD1-OSTIR::HIS3 MED14-3xV5 IAA7::KanMX MED15-MNase::TRP1


title: HepG2_LDB1ko_H3K27ac-rep2


title: EHT OCTN2 (-/-)

description: 10x Genomics

value: SLC22A5 (OCNT2) knockdown


title: Med15_Mnase_Med14_deg_IAA_A (ChEC-seq)


title: Med15_Mnase_Med14_deg_IAA_B (ChEC-seq)


title: Med15_Mnase_Med14_deg_DMSO_C (ChEC-seq)

value: DMSO


title: Med15_Mnase_Med14_deg_DMSO_B (ChEC-seq)


title: HepG2_control_H3K27ac_Input-rep2

value: control cell


title: HepG2_control_H3K27ac-rep2


title: Med15_C (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 MED15-MNase::TRP1


title: Med15_B (ChEC-seq)


title: Med15_Mnase_Med14_deg_DMSO_A (ChEC-seq)


title: Med15_A (ChEC-seq)


title: HepG2_control_H3K27ac-rep1


title: Hek293Phoenix cells transfected with pIRES2-EGFP empty_2

city: Salzburg

first: Emanuele

last: Bernardinelli

state: Salzburg

address: Strubergasse, 22

department: Institute for Pharmacology and Toxicology

country: Austria

institute: PMU - Salzburg

data_processing:
Raw reads were quality checked ( FastQC¨†MultiQC¨†minion¨†swan†), preprocessed ( setqk¨†Trimmomatic¨†FastQC¨†MultiQC†) and mapped ( STAR, ¨Samtools¨†MultiQC†) to the reference genome with gene annotation (genome version: Ensembl GRCh38, gene annotation: Ensembl v91)
Mapped reads were counted and summarized to genes ( featureCounts†)
Following checks were performed to estimate the overall sample quality: rRNA content estimate ( fastqﬂscreen†), Read duplication rate ( dupRadar†, Picard†tools†),n Sequenced (targeted) regions ( RSeQC†, Picard†tools†), Library strandedness ( RSeQC†)
Differential genes expression was calculated ( edgeR†, DESeq2†) by comparing all-vs-all
Assembly: (genome version: Ensembl GRCh38, gene annotation: Ensembl v91

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using polyA amplification

value: Human embryonic kidney cells


title: Hek293Phoenix cells transfected with pIRES2-EGFP empty_1


title: Hek293Phoenix cells transfected with pIRES2-EGFP POU3F4 C327X_3


title: EHT WT

description: 10x Genomics

value: Wildtype


title: Hek293Phoenix cells transfected with pIRES2-EGFP empty_3


title: Med10_Mnase_TID2_deg_IAA_B (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 med14DORF::KanMX pGPD1-OSTIR::HIS3 MED10-3xFlag-MNase::URA3 pSH1933 (ars cen TRP1 pRGR1-med14DTID) pSH1940 (ars cen LEU2 pRGR1-med14 TID-3xV5-degron)


title: Med10_Mnase_TID2_deg_IAA_C (ChEC-seq)


title: HepG2_control_LDB1-rep2

value: LDB1 (Abcam 96799)


title: Hek293Phoenix cells transfected with pIRES2-EGFP POU3F4 C327X_2


title: HepG2_control_H3K27ac_Input-rep1


title: Hek293Phoenix cells transfected with pIRES2-EGFP POU3F4 WT_3


title: Hek293Phoenix cells transfected with pIRES2-EGFP POU3F4 C327X_1


title: Hek293Phoenix cells transfected with pIRES2-EGFP POU3F4 WT_1


title: Med10_Mnase_Med14_deg_IAA_B (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 MED14-3xV5-IAA7::KanMX MED10-3xFlag-MNase::URA3


title: Med10_Mnase_Med14_deg_IAA_C (ChEC-seq)


title: Med10_Mnase_TID2_deg_DMSO_B (ChEC-seq)


title: Med10_Mnase_TID2_deg_DMSO_C (ChEC-seq)


title: Med10_Mnase_TID2_deg_DMSO_A (ChEC-seq)


title: CEM207_input_Rep1

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Reads from the sequencer were demultiplexed using bcl2fastq(v2.20.0). Sequencing adapters on reads were trimmed using cutadapt(v1.12) using options -a GATCGGAAGAGC -A GATCGGAAGAGC and --minimum-length 36 in paired mode. After trimming, reads were filtered for quality using the fastq_quality_filter in FASTX-Toolkit(v0.0.12), with options -Q 33, -p 90, and -q 20. In-house scripts were used to limit potential PCR duplicates by limiting reads with the same sequence to a maximum of five copies and discarding the copies beyond that limit. Once de-duplicated, read alignment was done using STAR(v2.5.2b) and options --outFilterMismatchNmax 2, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --outSAMtype BAM Unsorted, --outFilterType BySJout, --outFilterScoreMin 1, and --outFilterMultimapNmax 1. Post-alignment, SAMtools(v1.13) and BEDTools(v2.26) were used to generate bigWig files for downstream analyses. BRD4 signal was read depth normalized (per million mapped reads).
MACS2(v2.1.2) was used to call BRD4 peaks on each individual replicate using the input controls and default settings. BRD4 windows were created by taking the peak summits and adding 500 base pairs in both directions to create equal sized regions for even comparisons in subsequent analyses.
To create a union set of peaks, we used the “score per million” (SPM) method first described in https://www.science.org/lookup/doi/10.1126/science.aav1898. As sample quality or read depth increases, the number of peaks and their significance scores also increase which makes comparing peaks between samples difficult. To control for this, SPM creates relative peak (or region) scores for each sample that can more directly be compared. In brief, within each sample we calculated the per-region “score per million” by taking the individual peak score (-log(10)*adjusted p-value) and dividing by the total sum of all peak scores divided by one million. We then collected every region in every sample to make a cumulative union region set. When overlapping regions were found, only the region with the highest SPM value was kept. deepTools(v2.5.4) was used to calculate the mean BRD4 signal per region.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain read-depth normalized, genome-wide BRD4 ChIP-seq signal.
Supplementary_files_format_and_content: txt file contains the average read-depth normalized signal of each replicate in the union set of BRD4 peaks across all conditions (as described in the methods). Includes a header and is tab-delimited.
Supplementary_files_format_and_content: narrowPeak files are the peak calls returned by MACS2.

source_name: cells

extract_protocol:
Chromatin bound to BRD4 was immunoprecipitated from fixed and sheared nuclei, with or without CEM207 treatment, in HCT116 cells bearing sgNT or sgCXCR4 (promoter).
Enriched DNA from ChIP was barcoded and libraries were amplified, followed by size selection (fragment ranges between 250 and 1,000 bp), using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (E7103S) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (E6440S). Libraries were sequenced to a depth of 30 million base pairs (75-bp single-end reads) on an Illumina NextSeq 500.

tag: condition


title: Med10_Mnase_TID2_deg_IAA_A (ChEC-seq)

source_name: whole organism


title: Med10_Mnase_Med14_deg_DMSO_B (ChEC-seq)


title: sgCXCR4_CEM207_input_Rep1


title: Med10_Mnase_Med14_deg_DMSO_C (ChEC-seq)


title: sgNT_input_Rep1

value: sgNT


title: sgCXCR4_input_Rep1


title: Med10_Mnase_kin28is_CMK_B (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 kin28is MED10-3xFlag-MNase::TRP1

value: CMK


title: Med10_Mnase_kin28is_DMSO_B (ChEC-seq)


title: HepG2_control-rep1


title: Med10_Mnase_kin28is_DMSO_A (ChEC-seq)


title: HepG2_control_LDB1_Input-rep1


title: Hek293Phoenix cells transfected with pIRES2-EGFP POU3F4 WT_2


title: HepG2_control_LDB1_Input-rep2


title: freeMNase_C (ChEC-seq)

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pBDF2-Mnase::TRP1


title: CEM207_BRD4_ChIP_Rep3

tag: antibody


title: Med10_Mnase_Med14_deg_IAA_A (ChEC-seq)


title: HepG2_control-rep2


title: freeMNase_B (ChEC-seq)


title: freeMNase_D (ChEC-seq)


title: HepG2_LDB1ko-rep2

value: LDB1 knockout cell


title: CEM207_BRD4_ChIP_Rep2

tag: cell line


title: HepG2_control_LDB1-rep1


title: freeMNase_A (ChEC-seq)

tag: strain


title: Eaf5_C (ChEC-seq)

value: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 EAF5-MNase::TRP1


title: THP1_5

city: Bonn

first: Harald

last: Neumann

address: Venusberg-Campus 1

institute: University Hospital of Bonn

description:
Raw_gene_counts.csv
RUVSeq_normalized_gene_counts.csv
DESeq2_normalized_gene_counts.csv

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and base call file conversion.
Sequenced reads were corrected for low-quality sequences and adapter contamination, then mapped to hg38 whole genome with the ensembl gene annotation version 97 using STAR v2.7.3a with standard parameters.
Read count generation was performed using featureCounts/Subread v2.0.0 ignoring multimapping reads.
Batch effects were removed with R [v4.0.2 (R Core Team, 2021)] in RStudio [v1.3.1056 (RStudio Team, 2020) using the RUVSeq package [v1.22.0 (Risso et al, 2014)].
Differential expression analysis was performed using DESeq2 [v1.28.1 (Love et al, 2014)] with the individual groups as contrasts. The log2‐fold change (log2FC) shrinkage was performed using apeglm to preserve large effects of true positives [v1.10.0 (Zhu et al, 2019)]. Both, human primary microglia and iPSdMiG were individually compared to iPSCs and each data set was filtered for their specific microglia core signature with log2FC ≥ 3 and FDR-adjusted p value ≤ 0.001. These highly microglia-specific genes were then used to calculate transcription factor enrichment using ChEA3 (Keenan et al., 2019) and plotted with visNetwork [v2.0.9 (Almende et al. 2019)]. Further, a direct comparison of iPSdMiG to human primary microglia was performed and expression changes (|log2FC| ≥ 1 and FDR-adjusted p value ≤ 0.01) were identified by pathway enrichment analysis using clusterProfiler [v3.16.1 (Yu et al., 2012)] and reactomePA [v1.32.0 (Yu and He, 2016)]. Finally, weighted gene correlation network analysis was performed to identify co-expression of genes within the different cell types using WGCNA for R [v1.69 (Langfelder and Horvath, 2008)] and pathway enrichment for identified modules of interest was realized with clusterProfiler and ReactomePA.
Genome_build: hg38
Supplementary_files_format_and_content: [Raw_gene_counts.csv]  Matrix table with raw gene counts for every gene and every sample (39 microglia and 16 cortex samples from GSE99074 as well as 9 iPSC-derived microglia-like cell samples from GSE89189 included)
Supplementary_files_format_and_content: [RUVSeq_normalized_gene_counts.csv]  Matrix table with batch-corrected gene counts for every gene and every sample (39 microglia and 16 cortex samples from GSE99074 as well as 9 iPSC-derived microglia-like cell samples from GSE89189 included)
Supplementary_files_format_and_content: [DESeq2_normalized_gene_counts.csv]  Matrix table with DESeq2’s median of ratios-normalized counts for every gene and every sample (39 microglia and 16 cortex samples from GSE99074 as well as 9 iPSC-derived microglia-like cell samples from GSE89189 included)

source_name: THP1 Macrophages

growth_protocol: iPSCs were cultured in 2D adherent tissue culture formats. 2D expansion of iPSCs was carried out in 6-well tissue culture plates with geltrex coating (18 mg/ml, Thermo Fischer Scientific) and in StemMACS iPSbrew media (StemCell Technologies). Formation of multi-lineage embryoid bodies (EB) comprising neuroepithelial and microglial precursors was induced from evenly sized iPSC colonies in adherent culture. IPSC colonies were detached by incubating with Collagenase (Gibco, 1mg/ml) at 37°C for 30 minutes. The detached free-floating colonies were transferred out of collagenase solution and into EB basal media composed of 1 % N2 supplement (Gibco) and 2 % B27 supplement (Gibco) with respective small molecules in a stepwise manner (see publication). EBs were manually inoculated on macrocarriers in STEMdiff APELTM2 (Stemcell Technologies) supplemented with 10 % knock-out serum replacement, 1 % N2 supplement, 2 % B27 supplement (all from Gibco), and respective cytokines (see publication). IPSC-derived microglia (iPSdMiG) were produced into the supernatant of differentiation culture after 4 to 6 weeks of expansion. IPSdMiG were harvested from the supernatant and plated in 6-well plates in media containing cytokines (see publication). After 24 hours RNA extraction was performed.  THP1 monocytes were cultured in cell culture flasks with 5 % CO2 at 37 °C. The medium for maintaining THP1 monocytes consisted of RPMI (Gibco), 100 μM penicillin/streptomycin (Gibco), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 1 % human N2-supplement (Gibco) and 1 % heat-inactivated chicken serum (Gibco). For differentiation of THP1 monocytes into adherent macrophages, the monocytes were incubated with 10 ng/ml PMA (Sigma-Aldrich) in cell culture plates for 48 hours, and then the attached THP1 cells were washed three times with medium to remove residual PMA. Subsequently, THP1 cells were cultured in medium without PMA for another 48 hours for further maturation towards macrophage phenotype.

extract_protocol:
Cells were collected and lysed in RLT buffer containing beta-mercaptoethanol. RNA was isolated using the RNeasy RNA isolation kit (QIAgen) according to manufacturer’s extraction.
Library preparation was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) with an input of 100 ng total RNA according to manufacturer's instructions.

value: THP1 Monocytes

value: Macrophage


title: Med10_Mnase_Med14_deg_DMSO_A (ChEC-seq)


title: HepG2_LDB1ko-rep1


title: Med10_Mnase_kin28is_CMK_A (ChEC-seq)


title: Eaf5_B (ChEC-seq)


title: THP1_4


title: Eaf5_A (ChEC-seq)


title: THP1_6


title: THP1_3


title: sgCXCR4_CEM207_BRD4_ChIP_Rep2


title: sgNT_BRD4_ChIP_Rep2


title: THP1_2


title: sgCXCR4_CEM207_BRD4_ChIP_Rep1


title: sgNT_BRD4_ChIP_Rep1


title: sgCXCR4_BRD4_ChIP_Rep3


title: THP1_1


title: sgNT_BRD4_ChIP_Rep3

value: shNT


title: CEM207_BRD4_ChIP_Rep1


title: iPSC_3

source_name: iPSCs

value: ILB-C14m-S11 iPSCs

value: iPSC


title: iPSC_2


title: sgCXCR4_BRD4_ChIP_Rep2


title: C14_2

source_name: IPSC-derived microglia

value: Microglia


title: iPSC_1


title: RH30 cells - DDX5_IP_rep2

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Processing raw data for both format conversion and de-multiplexing by Bcl2Fastq 2.20 version of the Illumina pipeline
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute  Cambridge, UK) tool, then adapter sequences were masked with Cutadapt version 1.11 from raw fastq data using the following parameters: --anywhere (on both adapter sequences) --overlap 5 --times 2 --minimum-length 35 --mask-adapter
Reads were mapped to the human Ensembl GRCh38 build reference (release 96) using STAR (version 2.6.1d)
Each resulting BAM file were sorted using samtools 1.10 and then converted in scaled bigWig coverage tracks for visualization in the Integrative Genomics Viewer software.
DDX5 enriched regions were identified using MACS version 2.2.7.1 with Q-value cutoff of 0.05 by comparing the RIP-seq data to its matching input control.
Genome_build: hg38

source_name: rhabdomyosarcoma alveolar cell line

extract_protocol:
For RIP from nuclear extracts, RH30 cells were resuspended in buffer A/NT1 (20mM TrisHCl pH8.0, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 10% Glicerol, 0.2mM EDTA, 0.4mM PMSF, 1XPIC). In ice for 15 minutes and centrifuge at 2000 rpm for 5 minutes at 4°C to pellet the nuclei. The supernatant was collected as cytoplasmic extract. The pellet was rewashed with buffer A for 3 times. The pellet was resuspended in NT2/Wash buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2, 0,5% NP40, 20mM EDTA, 1X PIC, 1X PMSF, 1 mM DTT), break with 7ml dounce and centrifuged at 14000 rpm for 30 minutes at 4°C. Protein A/G Magnetic beads (Thermo Fisher Scientific) were incubate with IgG, DDX5 (ab126730) antibody on rotating wheel O/N at 4°C while the nuclear extract was precleared with the beads.
Trio RNA-Seq kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: unstranded). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA).

tag: gene fusion

value: pax3-foxo1 fusion positive cell line

tag: rip antibody

value: DDX5 (Abcam ab126730)


title: sgCXCR4_BRD4_ChIP_Rep1


title: RH30 cells - INPUT_rep3


title: RH30 cells - DDX5_IP_rep3


title: C133S4_3

value: ILB-C133bm-S4 iPSCs


title: C133S4_1


title: C133S4_2


title: C14_1


title: sgCXCR4_CEM207_BRD4_ChIP_Rep3


title: C14_3


title: RH30 cells - DDX5_IP_rep1


title: RH30 cells - INPUT_rep2


title: 31F_3

value: iLB-31f-r1 iPSCs


title: 31F_2


title: RH30 cells - INPUT_rep1


title: 31F_1


title: gapctrl_3_LPS

description:
gapctrl_LPS_3_63_S63
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv

data_processing:
 RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: base mean data was calculated from reads of three replicate samples. Fold change was calculated as gapCHROME over gapctrl. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections.

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer and subsequent stimulated with LPS (500 ng/mL) or a control vehicle

value: monocytic cell line

tag: modification

value: transfection with control gapmer


title: siG9a_rep4

data_processing:
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter and low-quality bases (Q < 20).
Then reads were mapped to the human Ensembl GRCh38 build reference genome using STAR version 2.5.0a using Gene annotations corresponding to the Ensembl annotation release 96
The same gene annotations were used to quantify the gene-level read counts using HTSeq-count version 0.8.0
Data normalization and differential analysis for gene expression were performed using Bioconductor R package edgeR version 3.28
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized cpm values for each Sample

extract_protocol:
Cells were harvested and centrifuged at 3000 rpm for 5 min at 4°C. Supernatant was then removed and cell pellet was resuspended in 1 ml of ice-cold PBS and centrifuged at 2000 rpm for 5 min at 4°C. After removing the supernatant, cell pellet was resuspended in 1 mL of TRIzol reagent (Invitrogen) and RNA extraction was carried out following Invitrogen protocol. RNA was then quantified using Nanodrop.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions. The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp.

tag: knockdown


title: gapCHROME_2_LPS

description:
gapmerCHROME_LPS_2_65_S65
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv

value: transfection with gapmer targetting CHROME


title: gapctrl_2_LPS

description:
gapctrl_LPS_2_62_S62
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: CTR_rep4

value: control


title: siG9a_rep3


title: scRNA_PLZF_RARA_RA

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

institute: CRCM

data_processing:
reads alignment, filtering, barcode counting anb unique molecular identifier (UMI) counting:
reads alignment to the mm10 genomes, filtering, barcode counting and unique molecular identifier (UMI) counting were performed with cellranger version 4.0.0 with Mouse reference dataset-2.1.0
(R1: 10X barcode (16 first bases) and UMI (from base 17 to 28); R2: biological read)
Genome_build: mm10 (genome-build GRCm38.p4,genome-version GRCm38,genome-date 2012-01,genome-build-accession NCBI:GCA_000001635.6)
Supplementary_files_format_and_content: Filtered gene-barcode matrix in MEX format (only detected cellular barcodes) stored in the Market Exchange Format (MEX) for sparse matrices with also gzipped TSV files for genes and barcode sequences corresponding to row and column indices respectively.

source_name: PLZF/RARA transformed progenitor cells

extract_protocol: PLZF/RARA transformed progenitors (late promyelocytes: Cd45.2+, C-Kit+, Gr1+, Cd34-, FcγR+) were purified using the FACS Aria III cell sorter (Beckman Dickinson). FACS purified  promyelocytes were loaded 30 min after the sorting onto a chromium Single Cell Chip and processed with the Chromium Controller (10x Genomics) according to the manufacturer’s instructions for single cell barcoding at a target capture rate of 6000 individual cells per sample.  Libraries were prepared using Chromium Single-Cell 3′ Reagent Kits v2 (10x Genomics).

treatment_protocol: A cohort of 3-5 mice was treated with retinoic acid or corn oil supplemented with 10% of DMSO for 7 days.

value: Late promyelocytes

value: Leukemic bone marrow

value: 0.8-1mg Retinoic Acid / Intraperitoneally injected


title: gapCHROME_3

description:
gapmerCHROME_3_60_S60
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: gapCHROME_3_LPS

description:
gapmerCHROME_LPS_3_66_S66
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapCHROME_2

description:
gapmerCHROME_2_59_S59
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: scRNA_PLZF_RARA_Ctrl

value: Corn Oil 10% DMSO / Intraperitoneally injected


title: CTR_rep3


title: siG9a_rep2


title: ATEV OM 2

city: Norfolk

first: Allison

middle: Heath

last: Mathiesen

state: VA

address: 700 W Olney Rd, Department of Physiology

institute: Eastern Virginia Medical School

description: miRNA was detected using the NanoString miRNA Array according to manufactuers instructions

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The NanoString RCC files were normalized in Rosalind and a threshold cutoff of 20 was applied for the normalized samples.

source_name: Adipose Tissue-Omental

label_protocol: not provided

growth_protocol: HAMVEC were cultured in endothelial cell media supplemented with growth factors and Pen/Strep until 70% confluency. Human adipose tissue was obtained from subjects undergoing bariatric surgery.

extract_protocol:
Conditioned media was collected and EV were isolated via serial ultracentrifugation and characterized using nanoparticle tracking analysis and electron microscopy.
Total RNA was collected using the GenElute single cell RNA purification kit (Sigma Life Sciences, Cat # RNB300)

treatment_protocol: HAMVEC PIC treatment was performed by supplementing media with TGF-beta, TNF-alpha, and IFN-gamma at 5ng/ml for 6 days.

value: Adipose Tissue-Omental


title: gapctrl_1_LPS

description:
gapctrl_LPS_1_61_S61
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: gapCHROME_1_LPS

description:
gapmerCHROME_LPS_1_64_S64
processed data file: gapmerCHROME_vs_gapCTRL_LPS.csv


title: CTR_rep1


title: ATEV OM 3


title: HAMVEC EV PIC 5

source_name: HAMVEC PIC Treated

value: HAMVEC PIC Treated


title: ATEV SC 3

source_name: Adipose Tissue-Subcutaneous

value: Adipose Tissue-Subcutaneous


title: ATEV OM 1


title: scATAC_PLZF_RARA_RA

data_processing:
reads alignment, filtering, barcode counting anb unique molecular identifier (UMI) counting:
reads alignment to the mm10 genomes, filtering, barcode counting and unique molecular identifier (UMI) counting were performed with cellranger version 4.0.0 with Mouse reference dataset-2.1.0
Genome_build: mm10 (genome-build GRCm38.p4,genome-version GRCm38,genome-date 2012-01,genome-build-accession NCBI:GCA_000001635.6)
Supplementary_files_format_and_content: Filtered gene-barcode matrix in MEX format (only detected cellular barcodes) stored in the Market Exchange Format (MEX) for sparse matrices with also gzipped TSV files for genes and barcode sequences corresponding to row and column indices respectively.

extract_protocol: NOT PROVIDED


title: ATEV SC 2


title: siG9a_rep1