title: WT_out

data_processing:
raw reads were trimmed with trimmomatic (V 0.39) and quality control of fragments was done with FastQC (V 0.11.09)
mapping on the chromosomes with bowtie2 (V 2.5.2) and turned into SAM files with samtools (V 1.8)
Peak calling was done with MACS2 (V 2.2.9.1)
Assembly: ASM22609v1
Supplementary files format and content: wig files containing peaks

growth_protocol: 10^6 conidia/mL were grown in VMM medium for  16 h

extract_protocol:
fresh mycelial samples were PBS washed, formaldehyde fixed and flash frozen. Samples were dounced and ultrasonicated in the corresponding buffers
Kapa Biosystems library prep

tag: chip antibody

value: α-V5 antibody (Rabbit Polyclonal (14440-1-AP), Thermo


title: WT 11.5h biol rep 3

status: Public on Oct 28 2024

type: SRA

city: Berkeley

first: Louise

middle: N

last: Glass

state: CA

address: Koshland Hall

department: PMB

country: USA

institute: UC California

library_source: transcriptomic

data_processing:
raw reads were trimmed with trimmomatic (V 0.39) and quality control of fragments was done with FastQC (V 0.11.09)
mapping on the chromosomes with HiSat2 (V 2.1.0) and turned into SAM files with samtools (V 1.8)
counts per million were counted with a custom R script and further processed
Assembly: ASM22609v1
Supplementary files format and content: RData file containing the  mapped reads

molecule: total RNA

organism: Thermothelomyces thermophilus

growth_protocol: 10^6 conidia/mL were grown in pre-culture medium for the described periods of time

extract_protocol:
Frozen mycelial samples were mixed with 1 mL TRIzol (Thermo Fisher Scientific) and processed for 1 minute on a beadbeater with 250 mg silica beads (0.5mm Zirconia). Samples were then centrifuged and the supernatant mixed with 200 µL chloroform and centrifuged again. The aqueous phase was mixed with isopropanol and RNA was precipitated, centrifuged, and washed with ethanol. RNA was resuspended in RNase free water and DNaseI (NEB) digested and purified on Monarch®
Kapa Biosystems library prep

treatment_protocol: timecourse

tag: tissue

tag: cell line

tag: cell type

value: fungal

tag: genotype

value: WT

tag: treatment

value: time course


title: WT 11.5h biol rep 2


title: WT_in

library_source: genomic

molecule: genomic DNA


title: ∆res1 Pres1::res1-V5_in

value: {delta}res1 Pres1::res1-V5


title: WT 14h biol rep 3


title: ∆res1 Pres1::res1-V5_out


title: R. tolerans EL-164, after AHL spike-in, NAME-spiked cultures, 53 h incubation time, replicate B

city: Oldenburg

first: Janina

last: Leinberger

address: Ammerländer Heerstraße 114-118

department: Institute for Chemistry and Biology of the Marine Environment

country: Germany

institute: University of Oldenburg

data_processing:
Reads were preprocessed with fastp (version 0.20.1)
Trimmed reads were mapped to the reference genome (GCF_028885395.1) using BWA-MEM (version 0.7.12) and SAMtools (version 0.1.19)
Reads mapping to genes were counted with HTSeq-count with mode union and stranded reverse (version 0.13.5)
Read counts were normalized and filtered with DESeq2 (version 1.32.0)
Assembly: GCF_028885395.1
Supplementary files format and content: tab-delimited files (.tsv) include raw read counts per gene for each sample
Supplementary files format and content: tab-delimited text file (.txt) includes read counts per gene (rows) and per sample (columns) after DESeq2 normalization

organism: Roseovarius tolerans

source_name: bacterial cell

growth_protocol: EL-164  was cultivated in marine broth medium with modifications given by Beyersmann et al. (2017). Incubations were carried out in the dark, at 20 °C and 100 rpm.

extract_protocol:
For RNA sampling, 2 ml EL-164 culture were removed aseptically, snap frozen in liquid nitrogen and subsequently stored at -80 °C until RNA extraction. The latter was performed as described earlier (Leinberger et al. (2022)), omitting the DNA extraction steps.
Libraries for transcriptomics were generated according to Shishkin et al., 2015 including rRNA removal with the RiboZero Kit (Illumina Inc., San Diego, CA, US).

treatment_protocol: The experiment was set up with an OD600nm = 0.01 with three biological replicates (B-D) and three different test conditions: (N) Cultures were spiked with synthetic C16:1-NAME at tS1=26 h, (A) Cultures were spiked with synthetic C14:1-AHL at tS2=49 h, (NA) Cultures were spiked with NAME and AHL at tS1 and tS2 respectively

tag: strain

value: bacterial cell

value: NAME-spiked


title: R. tolerans EL-164, after AHL spike-in, AHL-spiked cultures, 53 h incubation time, replicate D

value: AHL-spiked


title: R. tolerans EL-164, after AHL spike-in, NAME- and AHL-spiked cultures, 53 h incubation time, replicate B

value: NAME- and AHL-spiked


title: R. tolerans EL-164, prior to AHL spike-in, NAME- and AHL-spiked cultures, 49 h incubation time, replicate D


title: ∆res1 PH2A::res1-V5_out

value: {delta}res1 PH2A::res1-V5


title: ∆res1 PH2A::res1-V5_in


title: R. tolerans EL-164, prior to AHL spike-in, AHL-spiked cultures, 49 h incubation time, replicate C


title: R. tolerans EL-164, after AHL spike-in, NAME-spiked cultures, 53 h incubation time, replicate C


title: WT 11.5h biol rep 1


title: R. tolerans EL-164, after AHL spike-in, NAME- and AHL-spiked cultures, 53 h incubation time, replicate D


title: R. tolerans EL-164, prior to AHL spike-in, NAME- and AHL-spiked cultures, 49 h incubation time, replicate B


title: R. tolerans EL-164, after AHL spike-in, AHL-spiked cultures, 53 h incubation time, replicate B


title: R. tolerans EL-164, after AHL spike-in, NAME- and AHL-spiked cultures, 53 h incubation time, replicate C


title: R. tolerans EL-164, prior to AHL spike-in, AHL-spiked cultures, 49 h incubation time, replicate B


title: R. tolerans EL-164, prior to AHL spike-in, NAME-spiked cultures, 49 h incubation time, replicate C


title: R. tolerans EL-164, after NAME spike-in, NAME-spiked cultures, 26 h incubation time, replicate B


title: R. tolerans EL-164, prior to AHL spike-in, NAME- and AHL-spiked cultures, 49 h incubation time, replicate C


title: R. tolerans EL-164, after NAME spike-in, NAME- and AHL-spiked cultures, 26 h incubation time, replicate B


title: R. tolerans EL-164, prior to AHL spike-in, AHL-spiked cultures, 49 h incubation time, replicate D


title: R. tolerans EL-164, after NAME spike-in, AHL-spiked cultures, 26 h incubation time, replicate B


title: R. tolerans EL-164, after NAME spike-in, NAME-spiked cultures, 26 h incubation time, replicate D


title: ymoA mutant_replicate 3

city: Uppsala

first: Helen

last: Wang

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
Data analysis was done by Novogene Bioinformatics Institute. Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by trimming reads containing adapter and removing poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Yersini_pseudotuberculosis_GCF_000020085.1_ASM2008v1
Supplementary files format and content: Raw data for each samples in FASTQ format

organism: Yersinia pseudotuberculosis

source_name: Bacteria

extract_protocol:
Strains were grown overnight  at 26°C and subsequently diluted 1:25 into fresh media and cultured for 5h at 26°C at which point samples were taken.
Total RNA was extracted using a Trizol RNA isolation kit according to the manufacturer’s protocol. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA was sent to Novogene Bioinformatics Institute, there, RNA degradation and contamination was monitored on 1 % agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

value: Bacteria


title: ymoA mutant_replicate 2


title: R. tolerans EL-164, after NAME spike-in, NAME- and AHL-spiked cultures, 26 h incubation time, replicate D


title: ∆res1 mutant 11.5h biol rep 2


title: ymoA mutant_replicate 1


title: tomB mutant_replicate 2


title: R. tolerans EL-164, after NAME spike-in, AHL-spiked cultures, 26 h incubation time, replicate D


title: R. tolerans EL-164, after NAME spike-in, NAME-spiked cultures, 26 h incubation time, replicate C


title: R. tolerans EL-164, after NAME spike-in, AHL-spiked cultures, 26 h incubation time, replicate C


title: R. tolerans EL-164, after AHL spike-in, AHL-spiked cultures, 53 h incubation time, replicate C


title: tomB mutant_replicate 3


title: shLinc_rep3

city: Beijing

first: longtao

last: huangfu

address: No.52, Fucheng Road, Haidian District, Beijing, China

department: Cancer Hospital

country: China

institute: Peking University

data_processing:
Illumina HiSeq 2000 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg38 whole genome using STAR with parameters --readFilesCommand zcat --outSAMtype BAM  SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Hg38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample
Supplementary_files_format_and_content: Raw counts

organism: Homo sapiens

source_name: BGC823 (gastric cancer cells)

growth_protocol: The cells were seeded in Roswell Park Memorial Institute 1640 medium (RPMI 1640; GIBCO, USA), and were cultured at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA from the BGC823 cells with LINC00205 knockdown and negative control were isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq RNA Sample Preparation Kit (Illumina, USA) following TruSeq RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Purified libraries were quantified by Qubit 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq X-ten (Illumina, USA).

treatment_protocol: For viral transductions, 1 mL of the scrambled shControl or shLINC00205 lentiviruses were incubated with BGC823 and MKN28 cells overnight at 37°C in the cell culture incubator. Stable knockdown of LINC00205 were selected with puromycin (0.8 μg/mL) in the culture media.

value: gastric cancer cells

value: stable transfected with LINC00207 shRNA


title: shCtl_rep1

value: stable transfected with negative control


title: WT_replicate 3


title: embryo-ev, control7, mirna

city: Budapest

first: Bence

last: Nagy

state: Pest

address: Nagyvárad tér 4

department: Institute of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

data_processing:
Pseudoalignment was generated by the Kallisto v0.46.1 software
Summarizing the abundances of the transcripts and the identification of their genes were performed by the featureCounts program within the Rsubread v2.16 package
A first QC check on raw sequence data provided by FASTQC software
DeSeq2 v1.42 software was used for differential expression analysis
Gene ontology enrichment analysis was completed with ClusterProfiler v4.10 software
GeneTonic  v2.6  R package was used for the visualization of the results
miRNA reads were trimmed for adaptor sequences by Seed 2.0 software
For functional interpretation of miRNA-target interaction networks, we used the miRNET 2.0 platform
Assembly: GRCm39
Supplementary files format and content: comma-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: embryo

extract_protocol:
For RNA sequencing, total RNA was isolated from murine embryos using the RNeasy MiniKit (Qiagen, Venlo, Netherlands) according to the recommendations of the manufacturer.
For library preparation, multiplex Small RNA Library Prep Kit (Illumina, Inc., UK) was used according to the manufacturer’s instructions.

value: embryo

value: control


title: embryo-ev, white light, mirna

description: R2 file is missing because of issues during the sequencing process

value: white light


title: shLinc_rep2

value: stable transfected with LINC00206 shRNA


title: shLinc_rep1

value: stable transfected with LINC00205 shRNA


title: embryo-ev, red light3, mirna

value: red light


title: embryo-ev, white light2, mirna


title: embryo-ev, control5, mirna


title: shCtl_rep3


title: embryo-ev, white light3, mirna


title: tomB mutant_replicate 1


title: embryo-ev, control4, mirna


title: embryo-ev, control3, mirna


title: embryo-ev, control6, mirna


title: EMPTY_Ebf1–/– Lin–_rep1

type: RNA

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

description: Gene expression of Ebf1–/– Lin– cells after B cell developing stimulation

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized using Gene Expression Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner ( G2600D SG13164306) using one color scan setting for 4x44k array slides using scan protocol AgilentHD_HiSen_GX_1Color.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 026655_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: empty virus infected Ebf1–/– Lin– cells, replicate1

label_protocol: 100 ng RNA were labeled with Cyanine-3 (Cy3) using Agilent Whole Mouse Genome Microarray 4x44K v2 (Agilent) according to the manufacturer’s instructions.

extract_protocol: RNA was prepared using the Rneasy(Qiagen) following the manufacturer's recommendations.

treatment_protocol: cultured with each 10ng/mL SCF, IL-7 and Flt-ligand

value: Fetal liver Lin– cells

tag: developmental stage

value: early B cell (around pro B cell)


title: WT_replicate 1


title: embryo-ev, red light2, mirna


title: embryo-ev, red light1, mirna


title: embryo-ev, white light1, mirna


title: miR-195_Ebf1–/– Lin–_rep2

description: Gene expression of miR-195 transduced Ebf1–/– Lin– cells after B cell developing stimulation

source_name: miR-195 virus infected Ebf1–/– Lin– cells, replicate2


title: embryo-ev, control1, mirna


title: embryo, red light1, mirna


title: WT_replicate 2


title: embryo, control1, mirna


title: miR-195_Ebf1–/– Lin–_rep1

source_name: miR-195 virus infected Ebf1–/– Lin– cells, replicate1


title: embryo, white4, mirna


title: EMPTY_Ebf1–/– Lin–_rep2

source_name: empty virus infected Ebf1–/– Lin– cells, replicate2


title: embryo, control2, mirna


title: shCtl_rep2


title: embryo, white3, mirna


title: embryo, control3, mrna


title: embryo, control2, mrna


title: embryo, control1, mrna


title: embryo, red2, mrna


title: embryo, white2, mrna


title: Pl_LFDxC_-+_2

city: Munich

first: Tim

last: Hasenbein

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

description: DEseq2_output_placenta, AP_ARmedian_placenta

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.6.0c). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
Assembly: mm10
Supplementary files format and content: Excel (.xlsx) sheets with DESeq2 output from differential gene expression analysis.

molecule: polyA RNA

source_name: extraembryonic placenta

extract_protocol:
RNA was extracted from TRIzol using standard protocols.
The Illumina TruSeq kit was used to create polyA+ libraries from total RNA. We generated strand-specific libraries for tissues collected form the F1 crosses (TruSeq stranded Illumina) and non-strand-specific TruSeq libraries for the adult organs. All the libraries were run on a Bioanalyzer to assess purity, fragment size, and concentration and sequenced on a HiSeq 2500 at Harvard University’s Bauer Sequencing Core (75 bp paired end).

value: extraembryonic placenta

tag: age

tag: background

tag: Sex

value: F


title: embryo, red3, mrna


title: embryo, red1, mrna


title: res1OE mutant 6h biol rep 3

value: fungal

value: time course


title: Pl_CxLFD_+-_3


title: Pl_LFDxC_-+_1


title: Pl_LFDxC_-+_3


title: embryo, red ligh2, mirna


title: Pl_CxLF_+-_3

value: Crossfirre-Firre


title: Pl_LFxC_-+_2


title: Pl_LFxC_-+_3


title: Pl_CxLF_+-_2


title: Pl_XFLxC_-+_1

value: Crossfirre


title: Pl_XFLxC_-+_2


title: Sp_LFxLF_--_1

source_name: adult spleen

value: adult spleen

value: 6 weeks


title: Sp_XFLxXFL_--_2


title: embryo, white1, mrna


title: Pl_CxLFD_+-_1


title: Pl_CxLF_+-_1


title: Pl_CxXFL_+-_3


title: Pl_CxXFL_+-_1


title: embryo-ev, control2, mirna


title: Pl_CxXFL_+-_2


title: Sp_XFLxXFL_--_1


title: Sp_LFDxLFD_--_3

description: DEseq2_output_bodymap, DEseq2_output_adult_spleen


title: Lu_LFDxLFD_--_1

source_name: adult lung

value: adult lung


title: Sp_LFDxLFD_--_1


title: Ki_LFDxLFD_--_3

source_name: adult kidney

value: adult kidney


title: Ki_LFDxLFD_--_1


title: Li_LFDxLFD_--_3

source_name: adult liver

value: adult liver


title: Sp_LFDxLFD_--_2


title: Pl_LFxC_-+_1


title: Pl_CxLFD_+-_2


title: Ki_LFDxLFD_--_2


title: He_LFDxLFD_--_3

source_name: adult heart

value: adult heart


title: Li_LFDxLFD_--_1


title: He_LFDxLFD_--_1


title: Lu_LFDxLFD_--_3


title: Br_LFDxLFD_--_2

source_name: adult brain

value: adult brain


title: Sp_XFLxXFL_--_3


title: Li_LFDxLFD_--_2


title: Br_LFDxLFD_--_1


title: He_LFDxLFD_--_2


title: Pl_XFLxC_-+_3


title: Immortalized pericytes, NAMPT+PDGF-BB, biol rep 5

city: Novara

first: Grolla

middle: A

last: Ambra

address: Bovio street, 6

department: Department of Pharmaceutical Sciences

country: Italy

institute: University of Eastern Piedmont

description: Sample 20_988

data_processing:
Quality check of RNA-seq reads was performed using fastQC v0.11.7
The alignment was generated with STAR tool v2.6.1a
Number of read counts per gene and exon were determined from the mapped RNA-seq reads in a strand-specific manner using featureCounts v1.6.4
Differential gene expression analysis was performed using DESeq2 v1.18.1
Assembly: RNA-seq reads were mapped against the human genome hsa_GRCh38.94
Supplementary files format and content: Tab-delimited .tsv.gz summary file includes base mean and log2 fold change for each sample
Supplementary files format and content: Tab-delimited .tsv summary file includes Raw_counts for each sample

source_name: CL 05008-CLTH

growth_protocol: Immortalized pericytes were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using SPLIT RNA Extraction Kit (Lexogen, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Immortalized pericytes were treated for 4 hours respectively with the recombinant form of human eNAMPT [500 ng/ml] (Peprotech, Cat. 130-09), PDGF-BB [20 ng/ml] (Peprotech, Cat. 100-14B) or the two cytokines together.

value: CL 05008-CLTH

value: Immortalized pericytes

value: Wild-type

value: NAMPT+PDGF-BB


title: Immortalized pericytes, PDGF-BB, biol rep 4

description: Sample 15_983

value: PDGF-BB


title: Immortalized pericytes, PDGF-BB, biol rep 5

description: Sample 19_987


title: Immortalized pericytes, NAMPT, biol rep 4

description: Sample 14_982

value: NAMPT


title: Immortalized pericytes, NAMPT, biol rep 5

description: Sample 18_986


title: Immortalized pericytes, NAMPT+PDGF-BB, biol rep 4

description: Sample 16_984


title: Lu_LFDxLFD_--_2

value: F


title: Immortalized pericytes, ctrl, biol rep 4

description: Sample 13_981

value: Ctrl


title: Sp_LFxLF_--_2

value: Crossfirre-Firre


title: Immortalized pericytes, PDGF-BB, biol rep 3

description: Sample 11_979


title: Immortalized pericytes, NAMPT, biol rep 3

description: Sample 10_978


title: Br_LFDxLFD_--_3


title: Immortalized pericytes, NAMPT+PDGF-BB, biol rep 2

description: Sample 8_976


title: Immortalized pericytes, PDGF-BB, biol rep 2

description: Sample 7_975


title: Immortalized pericytes, ctrl, biol rep 3

description: Sample 9_977


title: Immortalized pericytes, NAMPT, biol rep 2

description: Sample 6_974


title: Immortalized pericytes, ctrl, biol rep 2

description: Sample 5_973


title: Immortalized pericytes, ctrl, biol rep 5

description: Sample 17_985


title: Immortalized pericytes, NAMPT+PDGF-BB, biol rep 1

description: Sample 4_972


title: Immortalized pericytes, NAMPT, biol rep 1

description: Sample 2_970


title: Immortalized pericytes, PDGF-BB, biol rep 1

description: Sample 3_971


title: Immortalized pericytes, ctrl, biol rep 1

description: Sample 1_969


title: Y79 cells, treated, rep3

city: Hong Kong

first: Dan

last: WANG

address: Lo Kwee-Seong Integrated Biomedical Sciences Building

institute: the Chinese University of Hong Kong

data_processing:
SOAPnuke software developed by BGI
raw data with adapter sequences or low-quality sequences was filtered
SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim"
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: retinoblastoma

growth_protocol: Y79 cells were maintained in RPMI medium 1640 containing 10% fetal bovine serum and 1% penicillin–streptomycin in humidified  atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was extracted from the cells according to the protocol for the RNA extraction mini kit (Favorgen Biotech Cooperation. Taiwan).
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit / BGI / LR00R96

treatment_protocol: 2U/mL of recombinant human arginase is added plus the growth medium

value: retinoblastoma

value: retinoblatoma cell line

value: WT

value: complete medium with recombinant human arginase


title: Y79 cells, control, rep3

value: complete medium


title: Y79 cells, treated, rep1


title: Y79 cells, treated, rep2


title: Y79 cells, control, rep1


title: Y79 cells, control, rep2


title: Immortalized pericytes, NAMPT+PDGF-BB, biol rep 3

description: Sample 12_980


title: PolyU library, bulk RNA, rep2

city: Cambridge

first: Emma

middle: Joanna Katharina

last: Kowal

email: emmajkkowal@gmail.com, ejkk@mit.edu

state: MA

address: 21 St Mary Road Apt 2

department: Biology

institute: MIT

description: amplicon generated by gene-specific RT-PCR

data_processing:
Fastq files were analyzed with custom python scripts to extract sample id, reporter gene, barcode and splicing status of each read and summed to totals per sample per barcode. Reads were filtered to those with an exact or close match to expected sample, reporter, and barcode sequences, and otherwise discarded.
Assembly: N/A
Supplementary files format and content: tab-delimited text file includes raw read counts for spliced GFP, unspliced GFP, and dTomato, for each barcode and each bulk RNA sample
Supplementary files format and content: tab-delimited text file includes raw read counts for spliced GFP, unspliced GFP, and dTomato, for each barcode and each iterative FACS RNA sample
Supplementary files format and content: excel spreadsheet includes raw read counts for both replicates of polyU validation library, as well as intron and barcode sequences

source_name: HEK293T A2

growth_protocol: HEK293T A2 HILO-RMCE cells were grown in DMEM, with high glucose and pyruvate, supplemented with 10% fetal bovine serum and 10% penicillin/streptomycin. Cells were passaged 1:10 every 2-3 days by washing with PBS and treated with 0.25% Trypsin following standard procedures.

extract_protocol:
Total RNA was extracted from the pooled cells using Zymo Quick RNA Miniprep kits. For each RNA-seq sample, 2µg RNA extracted from the pooled random intron library was treated with Turbo DNase (Thermo) to remove any residual genomic DNA before further processing. We removed DNase using Zymo RNA clean & concentrate kit.
The amplicon library was constructed via gene-specific RT using SuperScript IV (Thermo) and two primers, complementary to the GFP and dTomato N-termini, respectively, in order to generate cDNA of the two reporter gene 5ʹUTRs only. After first strand synthesis we treated the samples with RNase cocktail (Thermo) to avoid interference with downstream PCR. The cDNA was amplified with 16 cycles of PCR using Q5 polymerase (NEB) and custom sample-specific indexing primers. The PCR product was purified by a double-sided SPRI purification, first removing genomic DNA with 0.55x volumes of beads and then adding 85µL beads for a final 1.4x volume.

treatment_protocol: The intron reporter cassettes were integrated by following authors’ recommendations: briefly, we first plated 1.5×105 cells per well on a 12-well plate coated with 0.1mg/mL Poly-d -Lysine. After culturing the cells for 24 hours in antibiotic-free media, the cells in each well were co-transfected using Lipofectamine 2000 with 500 ng of a reporter plasmid plus 0.5% wt/wt Cre recombinase vector pEM784 (Khandelia et al., 2011), and allowed them 24–48 hours before selection with 4–8µg/mL Puromycin for two weeks to ensure genomic integration. Cells were monitored throughout for surviving colony formation and wells were split and pooled before becoming overconfluent.

value: HEK293T A2

value: library transfected


title: Random intron library, iterative FACS RNA, second red sort, rep 2

value: library integrated via recombinase-mediated cassette exchange


title: Random intron library, iterative FACS RNA, third red sort, rep 1


title: Random intron library, iterative FACS RNA, first green sort, rep 2


title: Random intron library, iterative FACS RNA, first green sort, rep 1


title: Random intron library, iterative FACS RNA, second green sort, rep 1


title: Random intron library, iterative FACS RNA, first red sort, rep 2


title: Random intron library, iterative FACS RNA, third red sort, rep 2


title: Random intron library, iterative FACS RNA, second red sort, rep 1


title: PolyU library, bulk RNA, rep1


title: Random intron library, iterative FACS RNA, second green sort, rep 2


title: Random intron library, bulk RNA, rep8


title: Random intron library, bulk RNA, rep10


title: Random intron library, bulk RNA, rep9


title: Random intron library, iterative FACS RNA, third green sort, rep 2


title: Random intron library, iterative FACS RNA, third green sort, rep 1


title: Random intron library, bulk RNA, rep6


title: R2-M2

city: guangzhou

first: cuicui

last: wang

state: guangdong

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software,version 1.8 ) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Cutadapt software
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.10.0)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: synovial tissues

extract_protocol:
The RNA of  rheumatoid fibroblast-like synoviocytes was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit(Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: synovial tissues

value: Primary cell

value: rheumatoid fibroblast-like synoviocytes

value: MSMP siRNA(siMSMP-2)

value: Transfected with siMSMP for  48h


title: R3-NC

value: control siRNA(siC)

value: Transfected with siC for  48h


title: R3-M2


title: Random intron library, bulk RNA, rep7


title: R2-NC


title: R1-M2


title: Random intron library, iterative FACS RNA, first red sort, rep 1


title: lip SCC_PanCK_23

city: Seoul

first: Myoung Eun

last: Choi

address: Song-pa gu

country: South Korea

institute: Asan medical center

library_source: other

data_processing:
Nanostring GeoMx Digital Spatial Profiling (DSP) Platform
QC and probeQC were performed using DSP platform.
Probe count extraction and Q3 normalization were performed using DSP platform.
Assembly: Human WTA
Supplementary files format and content: tab-delimited text files include normalization values for each Sample
Library strategy: GeoMX

molecule: other

source_name: Human lip

extract_protocol:
FFPE tissue sections were mounted on positively charged histology slides. FFPE tissue sections were subjected to in situ hybridization with GeoMX RNA Detection probe (WTA or CTA). Nuclear stain marker and antibodies of target protein were applied to each section. Slides were load on the GeoMX DSP. ROIs were selected and the GeoMX software was used to define AOIs with in each ROIs as one segment containing positive immonofluorescent signals. Once AOIs were defined, the DSP then exposed AOIs to 365nm light (UV), releasing the indexing oligonucleotides, which were collected with a microcapillary.
The GeoMX libraries for NGS were prepared using GeoMX Library Prep Kit following maufacture's protocols.

value: Human lip

value: lip SCC

value: PanCK


title: lip SCC_PanCK_22


title: lip SCC_PanCK_24


title: lip SCC_CD45_17


title: lip SCC_CD45_16


title: lip SCC_PanCK_18


title: lip SCC_PanCK_21


title: lip SCC_PanCK_19


title: lip SCC_CD45_13


title: lip SCC_PanCK_17


title: lip SCC_PanCK_14


title: lip SCC_CD45_10


title: lip SCC_CD45_12


title: lip SCC_PanCK_13


title: lip SCC_PanCK_16


title: lip SCC_CD45_11


title: lip SCC_CD45_8


title: lip SCC_PanCK_20


title: lip SCC_CD45_15


title: lip SCC_CD45_7


title: lip SCC_PanCK_11


title: lip SCC_PanCK_12


title: lip SCC_CD45_9


title: lip SCC_PanCK_10


title: lip cheilosis_PanCK_11

value: lip cheilosis


title: lip cheilosis_CD45_8


title: lip cheilosis_PanCK_10


title: lip SCC_CD45_6


title: lip SCC_PanCK_8


title: lip cheilosis_PanCK_9


title: lip SCC_CD45_14


title: lip SCC_PanCK_15


title: R1-NC


title: lip cheilosis_PanCK_8


title: lip SCC_PanCK_5


title: lip SCC_PanCK_9


title: lip cheilosis_PanCK_5


title: lip SCC_PanCK_6


title: lip SCC_PanCK_3


title: lip SCC_CD45_4


title: lip cheilosis_CD45_5


title: lip cheilosis_CD45_6


title: lip cheilosis_CD45_7


title: lip cheilosis_PanCK_6


title: lip cheilosis_CD45_3


title: lip cheilosis_PanCK_3


title: lip SCC_CD45_3


title: lip SCC_PanCK_4


title: lip cheilosis_CD45_1


title: lip cheilosis_CD45_4


title: lip cheilosis_CD45_2


title: lip cheilosis_PanCK_4


title: lip SCC_CD45_5


title: lip cheilosis_PanCK_7


title: lip SCC_PanCK_7


title: lip cheilosis_PanCK_2


title: lip cheilosis_PanCK_1


title: lip SCC_CD45_2


title: lip SCC_PanCK_2


title: lip SCC_CD45_1


title: lip SCC_PanCK_1


title: organoid, Fenebrutinib Aggregated IgG, F4

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description:
brain_organoid_count.gct
brain_organoid_tpm.gct

data_processing:
Basecalls and sample de-multiplexing performed by bcl2fastq conversion with default parameters
Sequenced reads were quality check with fastqc default parameters and then mapped with STAR using default algorithm parameters against hg38
The resulting BAM files were processed with FeatureCounts (Subreads) to yield count data for RefSeq transcript annotations
Transcripts Per Million (TPM) were calculated.
RefSeq annotations from NCBI Homo sapiens Annotation Release 110
Assembly: hg38
Supplementary files format and content: brain_organoid_count.gct contains raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format for the brain organoid samples
Supplementary files format and content: brain_organoid_tpm.gct contains normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format for the brain organoid samples
Supplementary files format and content: triculture_count.gct contains raw read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format for the tri-culture samples
Supplementary files format and content: triculture_tpm.gct contains normalized read counts per RefSeq gene (Entrezgene ID and gene symbol) in gct format for the triculture samples

source_name: central nervous system

growth_protocol: Brain tricultures: 96-well plates (PerkinElmer) were coated with dendritic polyglycerol amine (dPGA, 100 µg/ml, Dendrotek, overnight) and laminin (10 µg/ml, Sigma, 2 h). On day 1, Neurobasal media supplemented with B27 (Gibco), Glutamax (Gibco), penicillin-streptomycin (ThermoFisher), brain-derived neurotrophic factor (BDNF; 10 ng/ml, Bio-Techne), doxycycline (0.4 ng/ml) and ROCK inhibitor (10 µM, Y-27632 Tocris) was added to each well (50 µl per well). iAstrocytes and iNGN2 (DIV3) were thawed and seeded into the coated plate (0.5 x 10^4 iAstrocytes/well and 1.5 x 10^4 iNGN2/well; 50 µl per well). After 1 h, all media was exchanged with Neurobasal media containing all supplements except for ROCK inhibitor. On day 3, all media was exchanged with supplemented Neurobasal media containing laminin (1 µg/ml; Roche) and ara-C (0.5 µM, Sigma). On day 5, iMicroglia were thawed and plated at 1.5 x 104 cells/well in supplemented Neurobasal media and CMM (1:1 ratio). 50% media exchanges were performed on days 7, 10 and 12. All treatments were added on day 15.  Neural stem cell culture and generation of immunocompetent brain organoids (IMHBOs): The iPSC line BIONI037-A was differentiated into neural stem cells (NSC), expanded, quality controlled, and biobanked as per established protocols (Costa et al. 2016). Culture conditions for all cells were 37°C with 5% CO2, and the media used are detailed in Supplementary Table 1. NSCs were cultured to 70-90% confluence in neural basal medium (NBM) and accutase was used to detach NSC cultures. In order to initiate organoid formation, AggreWell 800 plates (StemCell Technologies), which were prepared according to the manufacturer's instructions, were used. Detached NSCs were resuspended in fresh NBM and adjusted to a concentration of 1.5 x 10^6 cells/ml. This suspension was added to the AggreWell plates containing 1 ml of NDM, centrifuged at 100 x g for 3 min and incubated for 48 h. Next, 1 ml of media was removed, 1.5 ml of fresh brain organoid medium (BOM) was added, and the organoids were transferred to 6-well plates (Corning 3471) on a gyratory shaker at 88 rpm. Media changes were performed every other day. For the integration of human iMicroglia into 8-week-old human brain organoids, individual organoids were transferred into 96-well round bottom plates (Corning 7007) in BOM supplemented with M-CSF (coBOM). Cell suspension of iMicroglia was prepared in coBOM with a final concentration of 2 x 10^3 iMicroglia/organoid and centrifuged to facilitate iMicroglia settling. The plates were incubated for at least one week with media changes every other day.

extract_protocol:
Total RNA was isolated from cell lysates of brain tricultures and IMHBOs using the Qiagen RNeasy Mini kit following manufacturer’s instructions. RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies).
RNA sequencing was performed by Azenta Life Sciences/Genewiz (Germany). Briefly, libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB). Sequencing libraries were validated using the NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies) and quantified by using Qubit 4.0 Fluorometer (Invitrogen). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument.

treatment_protocol: Heat-aggregated immunoglobulin G (Agg IgG) was prepared by resuspending human IgG (Sigma) in culture media at 25 mg/ml and heating at 63°C for 75 min. Agg IgG (1 mg/ml) was added to cells and supernatants and lysates were collected after 24 h. Lysophosphatidylcholine (LPC; 0.1 mM) was added to IMHBOs and supernatants and lysates collected after 72 h. DMSO or Fenebrutinib (1 µM) was added for 30 min prior to stimulus addition.

value: central nervous system

value: BIONi037-A, iMicroglia

tag: stimulus id

value: Aggregated IgG

tag: stimulus dose

tag: stimulus dose_unit

value: µg/ml

tag: treatment id

value: Fenebrutinib

tag: treatment dose

tag: treatment dose_unit

value: µM

tag: treatment time

tag: treatment time_unit

value: hours

tag: individual id


title: organoid, Lysophosphatidylcholine, G5

tag: tissue

tag: cell line

tag: cell type

value: Lysophosphatidylcholine

value: mM

value: DMSO


title: organoid, Aggregated IgG, E6


title: organoid, Aggregated IgG, E5


title: organoid, Fenebrutinib Aggregated IgG, F5


title: organoid, Fenebrutinib Aggregated IgG, F6


title: organoid, DMSO, C6

value: Unstimulated


title: organoid, Lysophosphatidylcholine, G4


title: organoid, Lysophosphatidylcholine Fenebrutinib, B7


title: organoid, Lysophosphatidylcholine Fenebrutinib, A7


title: organoid, DMSO, C4


title: triculture, DMSO, U1

description:
triculture_count.gct
triculture_tpm.gct

value: iMicroglia, iAstrocytes, iNGN2 neurons


title: triculture, DMSO, U2

description:
triculture_count.gct
triculture_tpm.gct


title: triculture, Aggregated IgG + Fenebrutinib, AgF2

description:
triculture_count.gct
triculture_tpm.gct


title: triculture, DMSO, U3

description:
triculture_count.gct
triculture_tpm.gct


title: B16-F1 cells, DKO, 24h, biol rep 2

city: Rochester

first: Adrian

middle: T.

last: Ting

state: MN

address: 200 First St SW

department: Immunology

institute: Mayo Clinic

data_processing:
alignment of forward and reverse reads to index generated with Rsubread
generation of raw counts using featureCounts
normalization of raw counts using limma-voom
Assembly: GRCm38
Supplementary files format and content: .txt files containing raw counts (not yet normalized)

source_name: Skin

growth_protocol: B16-F1 cells were maintained in DMEM containing 10% fetal bovine serum (FBS) and 1% pen/strep in incubator at 37C and 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
Library preparation and sequencing at 100 bp read length were performed by BGI (Cambridge, MA)

treatment_protocol: Confluent cells were either treated with media alone as the 0 timepoint, or with 100 ng/mL recombinant murine IFNγ (PeproTech) for 16 or 24 hours

value: Skin

value: Melanoma

tag: genotype

value: TBK1/IKKE knockout

tag: treatment

value: 100 ng/mL IFNγ 24 h


title: triculture, Aggregated IgG + Fenebrutinib, AgF3

description:
triculture_count.gct
triculture_tpm.gct


title: B16-F1 cells, DKO, 0h, biol rep 3

value: Media


title: B16-F1 cells, DKO, 16h, biol rep 3

value: 100 ng/mL IFNγ 16 h


title: B16-F1 cells, DKO, 24h, biol rep 3


title: B16-F1 cells, DKO, 0h, biol rep 2


title: B16-F1 cells, DKO, 24h, biol rep 1


title: B16-F1 cells, DKO, 16h, biol rep 1


title: B16-F1 cells, DKO, 0h, biol rep 1


title: organoid, Aggregated IgG, E4

value: central nervous system

value: BIONi037-A, iMicroglia


title: triculture, Aggregated IgG, Ag3

description:
triculture_count.gct
triculture_tpm.gct

value: Aggregated IgG

value: µg/ml


title: triculture, Aggregated IgG + Fenebrutinib, AgF1

description:
triculture_count.gct
triculture_tpm.gct

value: Fenebrutinib

value: µM


title: organoid, Lysophosphatidylcholine Fenebrutinib, C7

value: Lysophosphatidylcholine

value: hours


title: organoid, DMSO, C5

value: DMSO


title: B16-F1 cells, DKO, 16h, biol rep 2


title: B16-F1 cells, NTNT, 24h, biol rep 3

value: WT


title: triculture, Aggregated IgG, Ag2

description:
triculture_count.gct
triculture_tpm.gct

value: iMicroglia, iAstrocytes, iNGN2 neurons


title: B16-F1 cells, NTNT, 16h, biol rep 3

value: Skin


title: B16-F1 cells, NTNT, 0h, biol rep 3

value: Melanoma


title: triculture, Aggregated IgG, Ag1

description:
triculture_count.gct
triculture_tpm.gct


title: B16-F1 cells, NTNT, 24h, biol rep 2


title: Diff LUHMES, TG, BG4+FLAG

city: Dallas

first: Peter

middle: M

last: Douglas

state: Tx

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description: bigwigCompare_BG4+Flag_norm_to_Flag_TG.bigwig

data_processing:
FASTQ files of the raw sequencing results were then uploaded to Galaxy and trimmed using TRIMMOMATIC 0.38.1 and the following command: ILLUMINACLIP:/usr/local/share/ trimmomatic-0.38-1/adapters/TruSeq2-PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25. Trimmed reads were then mapped to human genome hg38 using Bowtie2 and the following command: bowtie2 –local --very-fast-local --no-unal -hg38 --no-mixed --no-discordant -I 10 -X 500. Alignment BAM files were then sorted and merged with their duplicate using Samtools. Bigwig coverage files were then generated using bamCoverage (deeptools71 3.5.1) and normalized for read depth using counts per million. BG4+FLAG samples were then normalized to the FLAG only controls via bigwigCompare (deeptools71 3.5.1).
Assembly: Homo Sapiens (hg38)
Supplementary files format and content: CPM normalized coverages are provided as BIGWIG files
Library strategy: CUT&RUN

source_name: LUHMES

growth_protocol: LUHMES cells were differentiated using standard DIFF media for 6 days.

extract_protocol:
Differentiated LUHMES cells were treated with 10 nM TG or DMSO and collected 24 hours later. Cells were lifted via trypsinization, and triplicate conditions were mixed and counted.  Per sample 250,000 cells were aliquoted and washed two times using 1x wash buffer (+ spermidine and protease inhibitor cocktail). Cells were then immobilized with concanavalin A beads and incubated overnight at 4ºC with the BG4 antibody (MABE917) at a 1:50 dilution. The next day, the primary BG4 antibody was removed, cells were washed once using digitonin wash buffer, and the anti-FLAG secondary antibody (Sigma Aldrich F1804) was added at a 1:100 dilution for 1 hour at room temperature. Control samples that were not incubated with the BG4 primary received anti-FLAG only.
Following wash steps after anti-FLAG incubation, pAG-MNase mixture was added and incubated at 4ºC for 1 hour. After 3 washes with digitonin wash buffer cells were cooled on ice for 5 minutes and pAG-MNase was activated with cold calcium chloride and incubated at 4ºC for 30-minute. 1x stop buffer was added and diffused DNA-samples were purified using DNA spin columns. Input samples were prepared via sonication using 6x 15 seconds pulses with 30 seconds pauses. Input fragment size of ~300-400 bp was confirmed using agarose gel electrophoresis. Enriched DNA samples were then submitted for library prep and paired-end sequencing done by Novogene (Sacramento, CA).
Novogene library prep for CUT&RUN

treatment_protocol: Cells were treated with DMSO or 10 nM thapsigargin for 30 minutes and collected 24 hours later.

value: LUHMES

value: Neurons

tag: target

tag: antibody

value: BG4 (MABE917), anti-FLAG (F1804)

value: TG

tag: biological replicate

value: Biol rep 1-3


title: Diff LUHMES, TG, FLAG

value: FLAG

value: anti-FLAG (F1804)


title: Diff LUHMES, DMSO, BG4+FLAG

description: bigwigCompare_BG4+Flag_norm_to_Flag_VEH.bigwig


title: Diff LUHMES, DMSO, FLAG


title: B16-F1 cells, NTNT, 24h, biol rep 1

value: 100 ng/mL IFNγ 24 h


title: B16-F1 cells, NTNT, 0h, biol rep 2

value: Media


title: HEK293T 25uM U1 AMO PAS-seq Replicate 3

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

data_processing:
Library strategy: PAS-seq
We used Cutadapt (v2.10) to produce trimmed PAS-seq reads by: 1) trimming the 6 nucleotide linker sequence, 2) trimming the poly(A) tail sequence, and 3) removing any untrimmed reads. Trimmed reads were then mapped to a concatenated hg19 and mm9 genome using STAR (v2.7.3a) with the --alignEndsType EndToEnd parameter. The mapped reads were converted from a bam file to a bed file using bedtools (v2.29.2). Reads were removed as potential internal priming events if they mapped to a genomic region where 6 consecutive A's or 7 A's out of 10 nucleotides were observed in the 10 nucleotides downstream of the read using a custom python script. Samples treated with pLKO, U2AF1 KD, or U2AF2 KD were processed the same as above except that they did not contain spiked in mouse RNA and thus reads were mapped to an hg19 genome. To generate bigwig files, the remaining reads were first intersected using bedtools intersect with a master file of all annotated poly(A) sites, converted to a bam file, and bigwig files were generated using bedtools.
Assembly: hg19 and mm9 (concatenated) or hg19
Supplementary files format and content: bigwig

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and grown at 37˚C with 5% CO2

extract_protocol:
Total RNA was extracted from Trizol following the manufacturer's protocol
PAS-seq libraries were prepared as previously described (PMID: 34183125),  with the following minimal modifications. Purified mRNA was fragmented at 94˚C for 3 minutes using the NEBNext Magnesium RNA fragmentation module. In addition, the final libraries were run out on a 2.5% standard agarose gel and the region between 200-300 basepairs was gel extracted and sequenced.

value: U1 snRNA targeting AMO


title: B16-F1 cells, NTNT, 16h, biol rep 1

value: 100 ng/mL IFNγ 16 h


title: HEK293T 25uM U1 AMO PAS-seq Replicate 2


title: HEK293T PlaB PAS-seq Replicate 3

value: Pladienolide B


title: HEK293T 25uM Control AMO PAS-seq Replicate 1

value: 25uM Non-targeting Control AMO


title: HEK293T PlaB PAS-seq Replicate 2

value: WT


title: HEK293T PlaB PAS-seq Replicate 1


title: HEK293T 25uM Control AMO PAS-seq Replicate 2


title: 5448 (M1T1) in THY broth bulk RNA-seq 1

city: Saint Lucia

first: Johanna

last: Richter

state: Queensland

address: Institute for Molecular Bioscience, QBP, Building 80, Services Road

country: Australia

institute: The University of Queensland

data_processing:
QC raw reads using FastQC ver. 0.73
Mapping of reads against respective reference genomes using Bowtie2 ver. 2.5.0, special parameters: -very sensitive local
Read counting and filtering using FeatureCounts ver. 1.6.4, special parameters: -Minimum bases of overlap: 20
Differential rexpression analysis of SP1491 compared to SP1380 and SP1490 compared to 5448 using limma-voom ver. 3.50.1, special parameters: -apply voom with sample quality weights, -filter genes with CPM <1 in <4 samples
Assembly: GCF_028370295.1, GCF_001021955.1
Supplementary files format and content: limma-voom_SP1491-SP1380.tsv - Tab separated file - Differential gene expression of SP1380 covS mutant strain SP1491 compared to SP1380
Supplementary files format and content: limma-voom_SP1490-X5448.tsv  - Tab separated file - Differential gene expression of 5448 covS mutant strain SP1490 compared to 5448

organism: Streptococcus pyogenes

source_name: Bulk RNA-seq from mid-logarithmic phase from emm1 S. pyogenes M1global

growth_protocol: Bacteria were statically grown to mid-logarithmic growth phase in Todd Hewitt broth supplemented with 1% yeast extract (THY) at 37˚C

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to mid-logarithmic growth phase in THY and pelleted. RNA was isolated from the dry pellet as per the manufacturer’s instructions with an additional mechanical lysis step using Lysing Matrix B tubes (MP Biomedicals) on the FastPrep-2 5G bead beating grinder and lysis system (MP Biomedicals). On-column DNA extraction was also performed with RNase-Free DNAse Set (Qiagen) during RNA extraction according to manufacturer's instructions. To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNAseq analysis was performed at the Australian Genome Research Facility (Melbourne, VIC, Australia). cDNA libraries were prepared from total RNA using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Plus rRNA Depletion kit (Illumina). Sequencing of the cDNA libraries was performed on the NovaSeq 6000 System (Illumina) on a 2x150 bp SP flowcell run generating an average of 20 million reads per sample.

treatment_protocol: No treatment

value: Bacterial culture

value: Bulk

tag: growth phase

value: Mid logarithmic


title: HEK293T 25uM Control AMO PAS-seq Replicate 3


title: B16-F1 cells, NTNT, 0h, biol rep 1

value: Skin

value: Melanoma


title: HEK293T 25uM U1 AMO PAS-seq Replicate 1


title: 5448 covS mutant strain in THY broth bulk RNA-seq 3


title: 5448 (M1T1) in THY broth bulk RNA-seq 2


title: 5448 (M1T1) in THY broth bulk RNA-seq 3


title: 5448 covS mutant strain in THY broth bulk RNA-seq 2


title: B16-F1 cells, NTNT, 16h, biol rep 2


title: 5448 covS mutant strain in THY broth bulk RNA-seq 1


title: HepG2 cells, wild type, ONT DRS

city: Tokyo

first: Boyi

last: Yu

address: 4-6-1 Komaba, Meguro-ku

institute: RCAST

description: pred.tsv contains site-level m6A prediction results in transcript-based coordination. Transcript: name of transcript, TranscriptStart: position of predicted site, Motif: 5-mer RNA motif of predicted site, Coverage: number of aligned reads, Probability: m6A modification probability, Ratio, m6A modification ratio.

data_processing:
Raw FAST5 files containing current intensity data were basecalled by Guppy basecalling software version 5.0.11 to generate FASTQ files of basecalled sequences. Reads scoring higher than a threshold of 7 in quality were used for alignment. Sequence alignment was performed against synthetic IVT sequences or GRCh38 reference transcriptome (cDNA and ncRNA) retrieved from the Ensembl project by Minimap2, and sorted BAM files and index files were prepared with Samtools. Preprocessed data containing m6A predictions were generated using our m6A detection tool m6ATM (https://github.com/poigit/m6ATM)
Assembly: hg38
Supplementary files format and content: bedGraph file including modification ratio information for m6A peaks
Supplementary files format and content: tab-delimited text file including Transcript, TranscriptStart, Motif, Coverage, Probability, Ratio information for predicted sites in each Sample

extract_protocol:
Total RNAs were extracted from HepG2 cells using the standard TRIzol (Invitrogen) protocol. Briefly, cells were homogenized in 1 ml of TRIzol reagent and incubated at 4°C for 10 minutes. Next, the total RNA precipitates were collected as pellets after appropriate centrifugation. RNA pellets were then washed with 75% ethanol and resuspended in RNase-free water for further use. To purify poly-adenylated RNAs, the kit NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S/L) was used. All steps were performed according to the manufacturer’s instructions to isolate intact poly(A)+ RNAs with Oligo dT Beads d(T)25. Last, concentrations and purity were measured by the NanoDrop ND1000 Spectrophotometer and the Qubit Fluorometer to ensure the quality of harvested RNAs.
500 ng of poly(A)+ RNAs from HepG2 samples were used to perform Direct RNA sequencing on the PromethION sequencers (Oxford Nanopore Technologies Ltd., ONT). All RNA libraries were prepared using the RNA-SQK002 Kit and sequenced on R9.4.1 flowcells, following the guidelines provided by ONT.


title: B220+_CD19-, Ebf1-/-_EMPTY transduced, #2

data_processing:
Short-read data were trimmed using sickle 1.33
trimmed data were mapped onto mm10 reference genome using bowtie2
Unmapped, multi, chrM mapping and duplicate reads were eliminated using samtools 1.16.1 and Picard Tools
Peak sumiits were determined using MACS3
Assembly: mm10
Supplementary files format and content: bed files of peak summits

source_name: Bone marrow

extract_protocol:
Cells were sorted from the bone marrow of NOG mice transplanted with miR-195-transduced Ebf1-/- Lin- cells. B220+ cells were also sorted from the empty transduced sample. The collected cells were resolved using CELLBANKER® (Takara Bio) and temporarily preserved at –20°C.
Libraries were prepared from the cryopreserved cells according to the Omni-ATAC protocol (M.R.Corces et al. Nat Methods. 14, 959–962 (2017).

value: Bone marrow

value: B220+ CD19- of engrafted FL Lin- cells

value: Ebf1-/- B6 in NOG

value: MDH1-PGK-GFP transduction


title: HEK293T OTS964 PAS-seq Replicate 2


title: SP1380 covS mutant strain in THY broth bulk RNA-seq 2

source_name: Bulk RNA-seq from mid-logarithmic phase from emm1 S. pyogenes M1uk


title: HEK293T OTS964 PAS-seq Replicate 3


title: B220+_CD19-, Ebf1-/-_EMPTY transduced, #1


title: SP1380 covS mutant strain in THY broth bulk RNA-seq 1


title: B220+_CD19-, Ebf1-/-_miR-195 transduced, #2

value: miR-195 transduction


title: HEK293T DMSO PAS-seq Replicate 3

value: DMSO


title: B220+_CD19-, Ebf1-/-_miR-195 transduced, #1


title: HEK293T DMSO PAS-seq Replicate 2


title: SP1380 (M1UK) in THY broth bulk RNA-seq 3


title: SP1380 covS mutant strain in THY broth bulk RNA-seq 3


title: HEK293T U2AF2 shRNA PAS-seq Replicate 3

value: U2AF2 targeting shRNA


title: HEK293T U2AF2 shRNA PAS-seq Replicate 1


title: SP1380 (M1UK) in THY broth bulk RNA-seq 1


title: SP1380 (M1UK) in THY broth bulk RNA-seq 2


title: HEK293T DMSO PAS-seq Replicate 1


title: Stressed_Mouse_No13

city: Shanghai

first: Xiaofei

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Raw fastq files were subjected to fastp software to trim adapters and remove low quality bases.
Filtered reads were aligned to mm10 reference genome using HISAT2.
Assembly: mm10
Supplementary files format and content: xlsx file containing raw counts of each sample.

source_name: Colon Tissue

extract_protocol:
RNA was extracted with an RNeasy Micro kit. RNA quality was determined by a Bioanalyzer 2000, and samples with RIN > 9 were used to prepare sequencing libraries.
mRNA was enriched by polyA selection and processed with a TruSeq Stranded mRNA LT kit under manufacturer's instruction.

treatment_protocol: Mice were treated with 30 min restraint stress for 3 days.

value: Colon Tissue

value: Wild-type

value: Stressed


title: non-TIS

city: Berlin

first: Zhiting

last: Shao

state: Berlin

address: Augustenburger Platz 1, Forum 4, 13353 Berlin

department: Hematology, Oncology, and Tumor Immunology Charité - Universitätsmedizin Berlin (CVK)

institute: Charité – Universitätsmedizin Berlin

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reference index building, gene counting were run by Cell Ranger - 7.1.0 software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/release-notes)
The matrices were merged, normalized, dimensionally reduced and clustered in Seurat 4.3.0 package (parameters- nVariableFeatures: 2000 FindNeighbors: dims 1:10 FindClusters: resolution 0.5 RunTSNE dims 1:10)
AUCell scores were calculated using AUCell 1.20.1 package
The t-SNE plots were drawn using t-SNE coordinates in SeuratObject and AUCell scores  were processed by Winsorize (parameters- 0.025,0.975) following z-score normalization
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Conditional senescence Eµ-myc;Suv39h1-;Bcl2;Suv39h1-ER; lymphoma model is generated as in previous publication (Milanovic el al., Nature 2018). Lymphoma cells were treated into TIS (1 uM 4-OHT+ 0.05 ug/ml ADR) or non-TIS (0.05 ug/ml ADR) and collected on day5 post-treatment. Dead-cell removal was performed according to manufacturer's protocol and proceeded with scRNAseq procedures.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lymph node

value: B cell lymphoma

value: Suv39h1-; Bcl2, Suv39h1-ER; E{mu}-myc

value: ADR


title: B220+_CD19+, Ebf1-/-_miR-195 transduced, #2

value: B220+ CD19+ of engrafted FL Lin- cells


title: B220+_CD19+, Ebf1-/-_miR-195 transduced, #1


title: UTSCC76a

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

description: BD Rhapsody

data_processing:
Raw FASTQ reads were quality trimmed using fastp (version 0.23.2 length cutoff 20, quality cutoff 15).
The UMI, complex barcode, and sample tags were extracted and demultiplexed using custom scripts.
We created a custom reference genome that adds eGFP and mCherry sequences to the human reference genome GRCh38. Gencode annotations v43 were filtered for protein-coding genes and lncRNAs, and entries for eGFP and mCherry were added manually. Reads were mapped using STAR version 2.7.10a (--soloType CB_UMI_Simple –soloCellFilter None –soloFeatures GeneFull_Ex50pAS –soloCBstart 1 –soloCBlen 27 –soloUMIstart 28 –soloUMIlen 8 –soloCBwhitelist rhapsody_whitelist.txt –soloMultiMappers EM)
Raw counts were imported as AnnData objects. We removed low complexity barcodes with the knee plot method (7000-8000 counts per cell), and further filtered out cells with a high mitochondrial mRNA percentage. Doublets were predicted with scrublet. Finally, each sample’s gene expression matrix was normalized using scran with Leiden clustering  input at resolution 0.5
At this stage samples were merged with scanpy. For 2D embedding, the expression matrix was subset to the 3,000 most highly variable genes (sc.pp.highly_variable_genes, flavor “seurat”). The top 100 principal components (PCs) were calculated. The PCs served as basis for k-nearest neighbor calculation (sc.pp.neighbors, n_neighbors=30), which were used as input for UMAP layout (sc.tl.umap, min_dist=0.3)
Assembly: hg38
Supplementary files format and content: fastq.gz: Demultiplexed FASTQ files
Supplementary files format and content: barcodes.tsv: Tab-separated values, BD Rhapsody barcodes
Supplementary files format and content: features.tsv: Tab-separated values, features/genes
Supplementary files format and content: matrix.mtx: MatrixMarket files with raw counts (Multimappers assigned with EM algorithm)
Supplementary files format and content: h5ad: AnnData file

growth_protocol: Human tongue squamous cell carcinoma cells UTSCC74a (isolated from a 31-year-old male with T3N1M0 G1-2 primary tumor) and UTSCC76a (isolated from a 52-year old male with T3N0M0 G2 primary tumor) were obtained from University of Turku. CAFs were isolated from a T2N2bM0 G1 primary tumor of the buccal mucosa. Cells were plated as single-cell suspensions into U-bottom ultra-low attachment 96-well plates (Corning 4520) in in DMEM (4500, mg/L glucose, 1x GlutaMAX, Gibco) supplemented with 1x non-essential amino acids (Gibco), 1x penicillin/streptomycin (Gibco) and 10% fetal bovine serum (Sigma-Aldrich). Cancer cells were cultured either alone or as co-cultures with CAFs. Cells were harvested after 48h.

extract_protocol:
Single cell suspensions were generated by incubation of spheroids with 0.5% Trypsin/0.5mM EDTA (Gibco). After washing with ice-cold DMEM, single cells were counted using Luna-II automated cell counter (Logos Biosystems) and loaded on a microwell cartridge of the BD Rhapsody Express system (BD) following the manufacturer’s instructions.
Single cell whole transcriptome analysis libraries were prepared according to the manufacturer’s instructions using BD Rhapsody WTA Reagent kit (BD, 633802) and sequenced on the Illumina NextSeq 500 using High Output Kit v2.5 (150 cycles, Illumina) for 2 × 75 bp paired-end reads with 8 bp single index aiming at sequencing depth of >20,000 reads per cell for each sample.


title: Resting_Mouse_No19

value: Resting


title: HEK293T U2AF1 shRNA PAS-seq Replicate 3

value: WT

value: U2AF1 targeting shRNA


title: Stressed_Mouse_No10


title: HEK293T U2AF1 shRNA PAS-seq Replicate 2


title: UTSCC74a + CAF

description: BD Rhapsody

value: Human tongue squamous cell carcinoma cells

value: Co-culture with cancer-associated fibroblasts


title: HEK293T OTS964 PAS-seq Replicate 1


title: HEK293T U2AF1 shRNA PAS-seq Replicate 1


title: UTSCC74a

description: BD Rhapsody


title: MFM-223 Input

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

data_processing:
ChIP-seq data was mapped using tools available on the public server at usegalaxy.org (Afgan et al. 2018). Adapters and poor quality reads were removed using Trimmomatic (Bolger et al. 2014) and  reads were aligned to human assembly GRCh37 (hg19) using Bowtie2 (Langmead & Salzberg 2012). PCR duplicates and poorly mapped reads were removed using SAMtools (Li et al. 2009).
AR peaks were called with MACS2 (Zhang et al. 2008), using default settings, against a total chromatin input corresponding to each cell line.
Peaks overlapping blacklisted regions were removed prior to downstream analysis using BEDTools (Quinlan & Hall 2010).  Consensus cistromes, representing peaks called in at least two replicates for any condition, were created using DiffBind (Ross Innes et al. 2012, Stark 2011). Reads were normalised by library size, and differential enrichment analysis was performed on the consensus cistromes using a generalized linear modelling function within DiffBind, modelling the effect of cell line and treatment, against a greylist background corresponding to the Input for each cell line.
The average AR enrichment signal for each condition was generated by merging replicate mapped reads. Merged reads were normalised by library size, and subject to background subtraction of Input reads using deepTools (Ramírez et al. 2016) on the public server at usegalaxy.org (Afgan et al. 2018).
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are provided for each replicate. Bigwig files are provided for visualization, corresponding to a merge of all replicates within a given condition. DiffBind results are available as Supplementary Data in the associated publication.

source_name: ER-negative breast cancer cell line

growth_protocol: MDA-MB-453 and MFM-223 cells were seeded into 15 cm2 tissue culture dishes (Corning) at a density to achieve approximately 75% confluence at harvest. Cells were seeded in normal maintenance media. After overnight incubation, the culture media was removed, cells were washed in DPBS, and cells were overlaid with serum-deplete media (where 10% (v/v) FBS is replaced with 10% (v/v) dextran coated, charcoal-stripped FBS). Serum-deplete media was washed and replenished daily for two days.

extract_protocol:
Treated cells were cross-linked with 1% formaldehyde for 10 min, quenched for 5 min with 0.1 M glycine (pH 7.5), washed briefly, and scraped into ice-cold DPBS supplemented with 1x protease inhibitor cocktail (Roche). Cell pellets were resuspended in LB1 cytoplasmic lysis buffer (50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 and 0.25% Triton X-100) at 4°C for 10 min. Nuclei were washed in LB2 buffer (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) at 4°C for 5 min, and subsequently resuspended in LB3 nuclear lysis buffer (10 mM Tris-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodiumdeoxycholate, 0.5% N-lauroylsarcosine). Lysates were sonicated using a Bioruptor Plus (Diagenode) to produce chromatin fragments of 200-1,000 bp. Trixon X-100 was spiked into sonicated lysates to a final of 1%, lysates were cleared of debris, and 5% of the sonicated chromatin was collected for an input control. Chromatin samples were immunoprecipitated overnight at 4°C with 100 µL of Protein A Dynabeads (Invitrogen) coupled to 5 µg of AR antibody (Abcam, ab108341 ). Three independent replicate experiments were performed, representing consecutive passages of cells. DNA was purified using phenol:chloroform:isoamyl alcohol extraction.
5 – 10 ng of AR-enriched DNA from each immunoprecipitation reaction, along with an even pool of input chromatin collected from all replicates and all samples, was provided to the South Australian Genomics Centre for library preparation and sequencing. Recovered DNA was amplified using the Ultra Low Library Prep Kit (Qiagen) and libraries were sequenced on the Illumina NextSeq 500 to a depth of a minimum ofapprox. 20 million  75 bp single-end reads per sample.
ChIP-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: Cells were treated for 4 hours with either a vehicle (ethanol) or 10 nM DHT.

tag: chip antibody

value: Input DNA

value: Pool

tag: replicate (passage)


title: Resting_Mouse_No15


title: Resting_Mouse_No17


title: IVT product, m6A 50%, ONT DRS

data_processing:
Barcoded FAST5 files of m6A-modified IVT products were first demultiplexed using DeePlexiCon.Demultiplexed FAST5 files containing current intensity data were basecalled by Guppy basecalling software version 5.0.11 to generate FASTQ files of basecalled sequences. Reads scoring higher than a threshold of 7 in quality were used for alignment. Sequence alignment was performed against synthetic IVT sequences or GRCh38 reference transcriptome (cDNA and ncRNA) retrieved from the Ensembl project by Minimap2, and sorted BAM files and index files were prepared with Samtools. Preprocessed data containing m6A predictions were generated using our m6A detection tool m6ATM (https://github.com/poigit/m6ATM)
Assembly: IVTR.fa
Supplementary files format and content: tab-delimited text file including Transcript, TranscriptStart, Motif, Coverage, Probability, Ratio information for predicted sites in each Sample

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
In-vitro transcribed RNAs were synthesized with different amounts of m6A-modified nulcelotides. The m6A-modified IVT products were prepared with either 20% or 50% m6A nucleotides, while the unmodified IVT products were prepared with unmodified adenosines only. To process samples for DRS, all IVT products were subjected to 5' capping and polyadenylation. For multiplex sequencing, the m6A-modified IVT products were additionally ligated to unique barcodes. Concentrations and purity were measured by the NanoDrop ND1000 Spectrophotometer and the Qubit Fluorometer to ensure the quality of RNAs.
500 ng of poly(A)+ RNAs from IVT samples were used to perform Direct RNA sequencing on the MinION sequencer (Oxford Nanopore Technologies Ltd., ONT). All RNA libraries were prepared using the RNA-SQK002 Kit and sequenced on R9.4.1 flowcells, following the guidelines provided by ONT.

value: synthetic construct

value: m6A 50percent


title: Stressed_Mouse_No11

value: Colon Tissue


title: HEK293T U2AF2 shRNA PAS-seq Replicate 2

value: U2AF2 targeting shRNA


title: UTSCC76a + CAF

description: BD Rhapsody


title: TIS

description: 10x Genomics

value: 4-OHT + ADR


title: IVT product, unmodified, ONT DRS

value: unmodified


title: HEK293T empty shRNA control vector PAS-seq Replicate 3

value: Empty shRNA vector


title: HEK293T empty shRNA control vector PAS-seq Replicate 1


title: HEK293T empty shRNA control vector PAS-seq Replicate 2


title: MFM-223 AR ChIP DHT 1

value: AR (Abcam Ab108341)

value: 10 nM DHT


title: IVT product, m6A 20%, ONT DRS

value: m6A 20percent


title: Sept_NBase_3, Septum base sample from septum_3, replicate 1

first: Stephen

middle: Jordan

last: Fleming

address: 415 Main St.

institute: Broad Institute

description: 10x Genomics 3' v2 chemistry

data_processing:
CellRanger v3.0.2 was used to run cellranger mkfastq in order to generate FASTQ files.
Assembly: rn6
Supplementary files format and content: Creation of the h5 count matrix files for each sample included the following: (1) FASTQ trimming using cutadapt. (2) Cellranger count was used to obtain h5 count matrices using a GTF file from our manuscript (supplementary file rn6.broad.cardiac.3.gtf.gz here). Note that these h5 files have not had CellBender run on them.

organism: Rattus norvegicus

source_name: Septum base

extract_protocol:
17-week-old animals were euthanized between 10am and 12pm using CO2, followed by perfusion with PBS to remove excess blood. Right ventricle, left ventricle and septum were immediately rinsed with ice cold PBS, then minced on ice by sterile razor blade, finally mixed with 4mL of nuclei isolation buffer (NIB). Left atria, right atria, SA node, AV node, aorta (from aortic root to iliac bifurcation), pulmonary vein, and pulmonary artery were immediately frozen in LN2 and stored at -80°C until use. Since AV nodes from rat have an approximate volume of 0.5mm3, we pooled 3-4 rat samples to obtain 1 sample for further processing. The same approach was used for SA node.
Frozen tissues were mounted on OCT and sectioned at 60μm at -20°C using a cryotome (Leica CM 1950). Tissue slices were transferred to 4mL of ice-cold NIB (Hepes 20 mM, Sucrose 0.25M, MgCl2 3mM, KCl 25mM, Igepal-630 0.01%, BSA 0.5%, pH 7.2). All tissue mixtures were dounce homogenized on ice with 10 strokes of a loose fit pestle followed by 10 minutes incubation, followed by 10 strokes of a tight fit pestle and 10 min incubation. Homogenate was transferred to a 15mL conical tube, filled to 8mL with nuclei wash buffer (NWB = NIB without detergent), and centrifuged at 40g x 4’, at 4°C (Beckman Coulter Allegra X-15R swinging bucket centrifuge). Supernatant was filtered through sequential 40μm and 10μm meshes (Pluriselect, Germany) in 50mL conical tube, filtrate topped up to 10mL with NWB and centrifuged at 600g x 5’, at 4°C. Supernatant was discarded and pellet resuspended, transferred to 15mL tube, topped up with 8mL NWB centrifuged (600g x 5’, 4°C). Final pellet was resuspended in 150μL nuclei resuspension buffer (NRB = NWB with 1:80 murine RNAse inhibitor, NEB). All procedures were performed on ice. Nuclei, stained with Trypan blue, were manually counted using a hemocytometer (inCyto.com). 7,000 nuclei input (5,000 calculated recovery) per sample were used for droplet generation and library construction according to the manufacturer's protocol (10x Genomics, single-cell 3-prime V2 chemistry), with minor modifications. First, after emulsion generation, nuclei were incubated on ice for 15 minutes to promote nuclear lysis. Second, the reverse transcription protocol was extended to enable the retention of longer transcripts. Libraries were multiplexed at an average of 4-5 libraries per flow cell. Sequencing was performed on an Illumina Nextseq550 in the Broad Institute’s Genomics Platform (genomics.broadinstitute.org).

treatment_protocol: 17-week-old healthy male Wistar rats

value: Septum base

tag: individual or_pool

tag: developmental stage

value: 17 week

tag: Sex

value: male

tag: strain

value: Wistar

tag: disease

value: healthy


title: Sept_NBase_1, Septum base sample from septum_1, replicate 1

description: 10x Genomics 3' v2 chemistry


title: DT40_H2A.Z_DKO/FLAG-H2A.Z-R80C

city: Sendai

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

description:
AR2281_03
Replicate 1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60 ºC for 30 min and hybridized by using Gene Expression Hybridization Kit (Agilent) according to the user guide.

scan_protocol: Slides were scanned by using Agilent DNA Microarray Scanner G2565CA.

data_processing: The scanned images were analyzed with Feature Extraction Software.

organism: Gallus gallus

source_name: DT40 H2A.Z DKO cells stably expressing H2A.Z-R80C mutant

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA by using Low Input Quick Amp labeling kit, one-color (Agilent) according to the provided protocol.

growth_protocol: DT40 cells were cultured at 38 ºC in Dulbecco's modified medium supplemented with 10% fetal bovine serum, 1% chicken serum, 2-mercaptoethanol, penicillin and streptomycin.

extract_protocol: Total RNAs were extracted with the RNeasy mini kit (QIAGEN) according to the manufacturer's protocol.

treatment_protocol: DT40 cells were cultured in the absence of tetracycline until semi-confluent.

tag: cell line origin

value: B cell

tag: genotype/variation

value: H2A.Z double-knockout

tag: stable expression


title: HEK293T 50uM U2 AMO PAS-seq Replicate 3

tag: cell line

value: WT

value: U2 snRNA targeting AMO


title: MFM-223 AR ChIP Vehicle 2

value: Vehicle


title: Sept_NBase_2, Septum base sample from septum_2, replicate 1

description: 10x Genomics 3' v2 chemistry

tag: tissue


title: MFM-223 AR ChIP Vehicle 1

tag: treatment


title: MFM-223 AR ChIP Vehicle 3


title: Sept_Apex_3, Septum apex sample from septum_3, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Septum apex

value: Septum apex


title: MFM-223 AR ChIP DHT 2


title: HEK293T 50uM U2 AMO PAS-seq Replicate 2

tag: genotype


title: DT40_H2A.Z_DKO/FLAG-H2A.Z.1

description:
AR2281_02
Replicate 1

source_name: DT40 H2A.Z DKO cells stably expressing H2A.Z.1


title: BMDM_DRP1_HSS8_biol rep3_RNA-seq

city: Detroit

first: Yang

state: MI

address: 4100 John R St MM03BI

department: Karmanos Cancer Institute

institute: Wayne State University Schhol of Medicine

data_processing:
For mRNA sequencing, the Fastq files were quantified using kallisto (v0.46.1) with the transcriptome indices built on the cDNA FASTA files from mouse (Mus musculus) genome assembly GRCm39. Differential expression analysis was performed using DESeq2 (v1.44.0).
Assembly: GRCm39
Supplementary files format and content: For mRNA sequencing, processed data files are tab-delimited text files include read counts and TPM values for each sample generated from  kallisto (v0.46.1)

source_name: Mouse bone marrow macrophgaes

growth_protocol: BMDM cells were maintained in culture medium (DMEM with 4.5 g/L glucose, 2mM glutamine, 10% fetal bovine serum (FBS), 10% L929-cell culture supernatent and penicillin–streptomycin).

extract_protocol:
Total RNAs were extracted from cultured cells by using TRIzol® reagent (Invitrogen).
mRNA libraries were prepared using the Illumina TruSeq® Stranded mRNA library kit following manufacturer's protocols.

treatment_protocol: Day 7 BMDM culture media were replaced with endothelial starvation media without FBS and stimulated for 8h under 2.1% oxygen conc (HSS).

tag: cell type

value: Mouse bone marrow macrophgaes

value: Drp1 KO

value: Hypoxia serum starvation


title: BMDM_WT_HSS8_biol rep2_RNA-seq


title: BMDM_DRP1_HSS8_biol rep1_RNA-seq


title: BMDM_DRP1_HSS8_biol rep2_RNA-seq


title: BMDM_WT_HSS8_biol rep1_RNA-seq


title: MFM-223 AR ChIP DHT 3

value: AR (Abcam Ab108341)


title: BMDM_WT_HSS8_biol rep3_RNA-seq


title: MDA-MB-453 Input

value: Input DNA

value: Pool


title: Sept_Apex_2, Septum apex sample from septum_2, replicate 1

description: 10x Genomics 3' v2 chemistry


title: HEK293T 50uM Control AMO PAS-seq Replicate 3

value: 50uM Non-targeting Control AMO


title: HEK293T 50uM U2 AMO PAS-seq Replicate 1


title: MDA-MB-453 AR ChIP DHT 3

value: 10 nM DHT


title: Erythritol+High-Fat diet 40% 8

city: Daegu

first: Seong-su

address: Daehak-ro 9-gil, Buk-gu

institute: Kyungpook National Univ.

data_processing:
Following sequencing, pre-processing steps were applied to remove adapter sequences, contaminant DNA, and PCR duplicates to reduce bias.
Reads were aligned to the reference genome using HISAT2, and transcript assembly was conducted using StringTie.
Gene expression profiles were quantified using FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) values.
Assembly: mm10/NCBI_108/GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: liver

extract_protocol:
RNA was islolated from liver tissue using TRIzol reagent.
TruSeq Stranded mRNA Reference Guide

value: liver


title: Sept_Apex_1, Septum apex sample from septum_1, replicate 1

description: 10x Genomics 3' v2 chemistry

value: 17 week

value: male

value: Wistar


title: SAN3_a, Sinoatrial node sample from sa_3, replicate a

description: 10x Genomics 3' v2 chemistry

source_name: Sinoatrial node

value: Sinoatrial node

value: healthy


title: MDA-MB-453 AR ChIP DHT 2


title: UC8 colon

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
10X genomics
Seurat_object_scaled_data_integrated.rda

data_processing:
single cell RNA seq were processed with 10x Cell Ranger pipeline and downstream analysis was conducted using Seurat
Bulk RNA seq analysis was conducted in R
Assembly: hg19
Supplementary files format and content: RDS object

source_name: colon

extract_protocol:
human intestinal biopsies were collected in RPMI and processed fresh to ontain single cell suspension. Biopsies underwent two 20 minute rounds of dissociation to remove the epithelial layer (Dissociation media: 10 ml HBSS (free of calcium and magnesium) EDTA (0.5M, pH 8, Invitrogen) and HEPES (1M, Lonza)) was followed by transfer to 10 ml of digestion solution (containing RPMI, FBS (Corning 35-010-CV), 0.005 g of Type IV collagenase (Sigma-Aldrich, cat # C5138-1G) and DNAase I (Sigma Aldrich Fine Chemicals Biosciences cat # 10104159001)) and incubated for 40min at 37°C using gentle agitation (180 rpm). The digested tissue was then further mechanically broken down by aspirating 10-times with a 10ml syringe by sequentially filtering through a 100-µm and a 40-µm cell strainer and washed with RPMI twice to obtain a single cell suspension of the intestinal lamina propria.
For scRNASeq, Gene expression libraries were prepared as per 10x Genomics protocol. For RNA-seq Gene expression libraries were prepared as per SMART-Seq v4 Ultra Low Input Nextera XT or SureSelect XT RNA Direct v6 protocols

value: colon


title: Pulmonary_veins_2b, Pulmonary veins sample from pv_2, replicate b

city: Cambridge

description: 10x Genomics 3' v2 chemistry

source_name: Pulmonary veins

value: Pulmonary veins


title: UC7 colon


title: SAN3_b, Sinoatrial node sample from sa_3, replicate b

description: 10x Genomics 3' v2 chemistry


title: D-allulose+High-Fat diet 40% 7


title: Erythritol+High-Fat diet 40% 7


title: Pulmonary_veins_2a, Pulmonary veins sample from pv_2, replicate a

description: 10x Genomics 3' v2 chemistry


title: Erythritol+High-Fat diet 40% 4


title: HEK293T 50uM Control AMO PAS-seq Replicate 1

value: WT


title: HC3 colon


title: Pulmonary_veins_1b, Pulmonary veins sample from pv_1, replicate b

description: 10x Genomics 3' v2 chemistry


title: MDA-MB-453 AR ChIP DHT 1


title: Pulmonary_veins_1a, Pulmonary veins sample from pv_1, replicate a

description: 10x Genomics 3' v2 chemistry


title: MDA-MB-453 AR ChIP Vehicle 3

value: Vehicle


title: D-allulose+High-Fat diet 40% 2


title: HC2 ileum

source_name: ileum

value: ileum


title: D-allulose+High-Fat diet 40% 5


title: HEK293T 50uM Control AMO PAS-seq Replicate 2


title: MDA-MB-453 AR ChIP Vehicle 2


title: HC2 colon


title: M1 (3)

city: DAEGU

first: Daehoon

last: Kim

address: Buk-Gu

institute: Kyungpook National Univ

description: experimental group (3)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: peritoneal

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: LPS/IFNg

value: peritoneal

value: Primary cell

value: Macrophages

value: W/T

value: LPS/IFNg


title: D-allulose+High-Fat diet 40% 1


title: Erythritol+High-Fat diet 40% 2


title: HC1 ileum


title: M1 (2)

description: experimental group (2)


title: PV4_b, Pulmonary veins sample from pv_4, replicate b

description: 10x Genomics 3' v2 chemistry


title: M1

description: experimental group


title: HC1 colon


title: MDA-MB-453 AR ChIP Vehicle 1

value: AR (Abcam Ab108341)


title: PV3_b, Pulmonary veins sample from pv_3, replicate b

description: 10x Genomics 3' v2 chemistry


title: PV4_a, Pulmonary veins sample from pv_4, replicate a

description: 10x Genomics 3' v2 chemistry


title: M0 (3)

description: control group (3)

value: DW


title: NV162 colon


title: High-Fat diet 40% 5

value: liver


title: M0 (2)

description: control group (2)


title: PV3_a, Pulmonary veins sample from pv_3, replicate a

description: 10x Genomics 3' v2 chemistry

value: 17 week

value: male


title: PA2_c, Pulmonary arteries sample from pa_2, replicate c

description: 10x Genomics 3' v2 chemistry

source_name: Pulmonary arteries

value: Pulmonary arteries

value: Wistar


title: PA2_b, Pulmonary arteries sample from pa_2, replicate b

description: 10x Genomics 3' v2 chemistry

value: healthy


title: PA2_a, Pulmonary arteries sample from pa_2, replicate a

description: 10x Genomics 3' v2 chemistry


title: NV159 colon

value: colon


title: NV161 colon


title: M0

description: control group


title: NV161 ileum


title: ChIP-seq KAP1 1h Rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
*library strategy: calibrated ChIP-seq
We analyzed this human-calibrated ChIP dataset based on the strategy by Fursova et al. (2019) and Blackledge et al. (2020)
In summary, raw paired-end 41bp sequencing reads were aligned to a merged genome of mouse (mm10) and human (hg38) using Bowtie2 (v. 2.4.2), with prefixes Mm10 and Hg38 for mouse and human chromosome names, respectively.
We employed Picard (v. 2.23.7) SortSam and MarkDuplicates to sort and convert the SAM file to BAM files, marking duplicated reads. The Samtools view function was applied to separate human and mouse-mapped reads using the following commands: samtools view -h -L $bedfile_hg38Chrs or samtools view -h -L $bedfile_mm10Chrs.
We removed reads that mapped to both human and mouse and then separated the remaining reads based on whether they mapped to human or mouse. The downsampling factors (DFs) can be calculated based on this equation (Fursova et al., 2019)
DF=α×1/(N("spikeIn in ChIP"))×(N("spikeIn in Input" ))/(N("mouse in Input" ))
N (spikeIn in ChIP) - total number of reads aligning to the spike-in genome for each ChIP-seq sample;
N (spikeIn in Input) - total number of reads aligning to the spike-in genome in the corresponding Input sample;
N (mouse in Input) - total number of reads aligning to the mouse genome in the corresponding Input sample;
α - coefficient applied for all the files normalized together so the value of the largest downsampling factor equals 1.
Normalised bigwig files for ChIPs were generated based on the DFs calculated by the equation above using Deeptools (v.3.5.0) bamCoverage function with parameters -bl $blacklist_v1 --binSize 1 --extendReads --effectiveGenomeSize 2652783500 --scaleFactor $showDF.
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: B3 pre-B cells were maintained in IMDM with 10% heat inactivated FBS and 1x Pen/Strep (Gibco™ 15070063) and 1x L-glutamine (Gibco™ 25030081) between 0.5 – 2 million/ml. HEK293T cells were maintained in DMEM with 10% heat inactivated FBS and 1x Pen/Strep and 1x L-glutamine, and split every 2-3 days.

extract_protocol:
For calibrated ChIP-seq 2 million human HEK293T cells were mixed with 50 million B3 cells prior to fixation. Cells were fixed at room temperature in 10ml PBS with 1mM DSG (ThermoFisher 20593) for 30 min followed by addition of 1% formaldehyde (ThermoFisher 28908) and incubated for a further 10min. The reaction was quenched with 125mM glycine. Chromatin was digested by sonication or MNase to obtain fragments between 100-300bp. A small aliquot was reserved for the Input sample, and chromatin equivalent to 4 million cells was used per IP. HA-Ikaros-ERt2 ChIP performed using overnight incubation with Pierce magnetic anti-HA beads (Pierce 88836). For H3K27ac (Active Motif 39133) and CHD4 (Abcam ab70469), 4-6 mg of antibodies were incubated with each reaction overnight, followed by 2h of incubating with magnetic Prot A/G Dynabeads (ThermoFisher 10001D, 10003D). Washes were performed for 5 min rotating in the cold room twice with each buffer, Low Salt Buffer, High Salt Buffer, LiCl Buffer and TE. DNA was eluted with 1% SDS and 0.1M NaHCO3. For reverse crosslink, NaCl was added to a final concentration of 0.2M, and samples were incubated at 65°C shaking overnight, following by 2h of RNaseA and 2h of Proteinase K treatment.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645S) was used for all ChIP-seq libraries with PCR amplification of 5-8 cycles. Clean-up was performed with Ampure beads and quantification and quality control of libraries was performed using DNA Qubit and HS DNA Bioanalyser.

treatment_protocol: 500nM of 4-hydroxytamoxifen (Sigma-Aldrich H7904-5MG) was used to induce nuclear translocation of Ikaros for 1h

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2

value: 4-hydroxytamoxifen 1h

value: Abcam ab10483


title: ChIP-seq KAP1 0h Rep2


title: Normal diet 4


title: Normal diet 5


title: PA1_b, Pulmonary arteries sample from pa_1, replicate b

description: 10x Genomics 3' v2 chemistry


title: High-Fat diet 40% 3


title: High-Fat diet 40% 7


title: NV159 ileum

value: ileum


title: ChIP-seq Input 1h Rep2


title: High-Fat diet 40% 12


title: NV157 colon


title: NV162 ileum


title: ChIP-seq Input 0h Rep2


title: PA1_a, Pulmonary arteries sample from pa_1, replicate a

description: 10x Genomics 3' v2 chemistry


title: MPTP+PF4 #3

city: Chengdu

first: Haoran

last: Tai

state: Sichuan

address: #783 Xindu Avenue

department: Department of Histology and Embryology

institute: Chengdu Medical College

description: #ID gene_name nr_symbol con-1_FPKM con-1_count con-2_FPKM con-2_count con-3_FPKM con-3_count mptp-1_FPKM mptp-1_count mptp-2_FPKM mptp-2_count mptp-3_FPKM mptp-3_count pf4-1_FPKM pf4-1_count pf4-2_FPKM pf4-2_count pf4-3_FPKM pf4-3_count control_vs_mptp_DESeq2_Pvalue

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud (www.biocloud.net) online platform. KOBAS database and clusterProfiler software were used to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: mesencephalon

extract_protocol:
Collect fresh midbrain tissue samples and distribute them into 1.5 mL sterile centrifuge tubes. Each sample should be collected in triplicate and then stored at -80°C for preservation. For RNA extraction, thoroughly mix each sample with 1000 µL of Trizol reagent, ensuring complete homogenization. Allow the mixture to incubate for 5 to 15 minutes to facilitate the dissociation of nucleoprotein complexes. Following this incubation period, perform a brief centrifugation to remove any volatile components or let the mixture stand to allow for evaporation of such components. Utilize 1 μg of total RNA from each sample as the input material for subsequent RNA sample preparation procedures. This may include DNase treatment to eliminate contaminating DNA, followed by purification and quantification of the RNA to ensure high-quality material for downstream applications
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: mesencephalon

value: MPTP (i.p.); PF4 (i.v.)


title: Normal diet 1


title: MPTP+PF4 #2


title: ChIP-seq H3K9me3 1h Rep2

value: Diagenode C15410193


title: HIV066 ileum


title: Aorta_3b_06072019, Aorta sample from aorta_3, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Aorta

value: Aorta


title: ChIP-seq H3K9me3 0h Rep2


title: MPTP #3

value: MPTP (i.p.)


title: HIV064 colon


title: Aorta_4_06072019, Aorta sample from aorta_4, replicate 1

description: 10x Genomics 3' v2 chemistry


title: Aorta_3a_06072019, Aorta sample from aorta_3, replicate 1

description: 10x Genomics 3' v2 chemistry


title: Normal diet 6

value: liver


title: MPTP #2


title: ChIP-seq KAP1 1h Rep1


title: ChIP-seq Input 1h Rep1


title: HIV062 colon


title: HIV066 colon


title: MPTP #1


title: ChIP-seq Input 0h Rep1


title: ChIP-seq KAP1 0h Rep1


title: SA2d, Sinoatrial node sample from sa_2, replicate d

description: 10x Genomics 3' v2 chemistry

value: Sinoatrial node

value: 17 week


title: HIV062 ileum


title: HIV033 colon


title: SA2b, Sinoatrial node sample from sa_2, replicate b

description: 10x Genomics 3' v2 chemistry

value: male


title: ChIP-seq H3K9me3 1h Rep1


title: Control #2

value: Saline


title: SA2a, Sinoatrial node sample from sa_2, replicate a

description: 10x Genomics 3' v2 chemistry

value: Wistar

value: healthy


title: HIV064 ileum


title: HIV032 colon

value: colon


title: Control #1


title: SA1d, Sinoatrial node sample from sa_1, replicate d

description: 10x Genomics 3' v2 chemistry


title: ChIP-seq H3K9me3 0h Rep1

value: mouse pre-B

value: B3 transduced with Ikaros-ERt2


title: ChIPseq Input 30m Rep2

data_processing:
Raw paired-end 41bp sequencing reads were aligned against mouse genome (mm10) using Bowtie2 (v. 2.4.2; Langmead and Salzberg, 2012) with parameters: '--no-mixed --no-discordant'. Picard (v. 2.23.7; https://broadinstitute.github.io/picard/) SortSam and MarkDuplicates were applied for sorting and converting sam files to bam files and duplicated reads were marked. Peak calling was proceeded with MACS2 (v.2.2.7.1) callpeak function (with -f BAMPE -g mm for Ikaros and H3K27ac; with -f BAMPE --broad -g mm for CHD4).
Downsampling for generating bigwig files for Ikaros and CHD4:
We used the IP raw concentration at 2 hours from each ChIPs as the baseline to calculate the size factor (SF) for the downsampling analysis at each time point. The SF at each time point was calculated by dividing the IP raw concentration at time 0 hours or 1 hour by the IP raw concentration at 2 hours. Reads from raw fastq files were randomly selected based on the SF calculated for downsampling by using seqtk (v1.3; https://github.com/lh3/seqtk) with 'seqtk sample -s100 $ori.fastq.gz $sizeFactor - | gzip - > $DS_fastq.gz'. After downsampling the fastq files, we applied the same analytical pipeline described in this section for alignment, sorting, converting to BAM files, and marking duplicated reads. We generated downsampled BigWig files using Deeptools (v. 3.5.0) with the following command: 'bamCoverage -b ChIP.DupMark.bam -p 16 -bl mm10-blacklist_v1.bed --extendReads --effectiveGenomeSize 2652783500 -o ChIP_MarkedDup.bw'.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: Peak files (broad peaks for CHD4; narrow peaks for Ikaros and H3K27ac)

growth_protocol: B3 pre-B cells were maintained in IMDM with 10% heat inactivated FBS and 1x Pen/Strep (Gibco™ 15070063) and 1x L-glutamine (Gibco™ 25030081) between 0.5 – 2 million/ml. The inducible Ikaros-ERt2 construct was introduced in the B3 cell line using retroviral transduction.

extract_protocol:
Cells were fixed at room temperature in 10ml PBS with 1mM DSG (ThermoFisher 20593) for 30 min followed by addition of 1% formaldehyde (ThermoFisher 28908) and incubated for a further 10min. The reaction was quenched with 125mM glycine. Chromatin was digested by sonication or MNase to obtain fragments between 100-300bp. A small aliquot was reserved for the Input sample, and chromatin equivalent to 4 million cells was used per IP. HA-Ikaros-ERt2 ChIP performed using overnight incubation with Pierce magnetic anti-HA beads (Pierce 88836). For H3K27ac (Active Motif 39133) and CHD4 (Abcam ab70469), 4-6 mg of antibodies were incubated with each reaction overnight, followed by 2h of incubating with magnetic Prot A/G Dynabeads (ThermoFisher 10001D, 10003D). Washes were performed for 5 min rotating in the cold room twice with each buffer, Low Salt Buffer, High Salt Buffer, LiCl Buffer and TE. DNA was eluted with 1% SDS and 0.1M NaHCO3. For reverse crosslink, NaCl was added to a final concentration of 0.2M, and samples were incubated at 65°C shaking overnight, following by 2h of RNaseA and 2h of Proteinase K treatment.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645S) was used for all ChIP-seq libraries with PCR amplification of 5-8 cycles. Clean-up was performed with Ampure beads and quantification and quality control of libraries was performed using DNA Qubit and HS DNA Bioanalyser.

treatment_protocol: 500nM of 4-hydroxytamoxifen (Sigma-Aldrich H7904-5MG) was used to induce nuclear translocation of Ikaros for 30m, 1h, or 2h.

value: 4-hydroxytamoxifen 30m


title: HIV032 ileum

value: ileum


title: SA1c, Sinoatrial node sample from sa_1, replicate c

description: 10x Genomics 3' v2 chemistry


title: MPTP+PF4 #1

value: mesencephalon


title: Control #3


title: ChIPseq Input 2h Rep2

value: 4-hydroxytamoxifen 2h


title: HIV033 ileum


title: ChIPseq Input 1h Rep2

value: 4-hydroxytamoxifen 1h


title: RV7_2G, Right ventricle region 2G sample from chambers_7, replicate 1

description: 10x Genomics 3' v2 chemistry

source_name: Right ventricle region 2G

value: Right ventricle region 2G


title: HIV026 ileum


title: ChIPseq Input 0h Rep2


title: ISRIB treated M1 biol rep 1

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E 57th street

department: Medicine

institute: University of Chicago

data_processing:
Data was analyzed using Rosalind with a HyperScale architecture developed by ROSALIND, Inc.
Reads were trimmed using catadapt. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel files with raw counts
Supplementary files format and content: excel files with normalized counts

source_name: BMDM

growth_protocol: RPMI containing 10% FBS, 10 mM HEPES, and 100 U/ml penicillin/ streptomycin) supplemented with 10 ng/ml M-CSF

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: BMDMs were pre-treated with vehicle (DMSO) or 50 nM ISRIB followed with 10 ng/ml LPS and 25 ng/mL IFN-γ for M1-like polarization in the presence of vehicle or ISRIB.

value: BMDM

value: mouse macrophage

value: ISRIB 50nM


title: ISRIB treated M0 biol rep 3


title: ISRIB treated M1 biol rep 2


title: ISRIB treated M1 biol rep 3


title: HIV018 colon


title: RV6_2G, Right ventricle region 2G sample from chambers_6, replicate 1

description: 10x Genomics 3' v2 chemistry

value: 17 week


title: ChIPseq Ikaros 30m Rep2

value: anti-HA Pierce 88836


title: ISRIB treated M0 biol rep 2


title: RV5_2G, Right ventricle region 2G sample from chambers_5, replicate 1

description: 10x Genomics 3' v2 chemistry

value: male


title: HIV028 ileum


title: ChIPseq Ikaros 2h Rep2


title: HIV022 colon


title: HIV022 ileum


title: Vehicle treated M1 biol rep 3

value: Vehicle (DMSO)


title: ISRIB treated M0 biol rep 1


title: RV3_2G, Right ventricle region 2G sample from chambers_3, replicate 1

description: 10x Genomics 3' v2 chemistry

value: Wistar

value: healthy


title: RV4_2G, Right ventricle region 2G sample from chambers_4, replicate 1

description: 10x Genomics 3' v2 chemistry


title: ChIPseq Ikaros 1h Rep2

value: mouse pre-B


title: Vehicle treated M1 biol rep 2