title: ChIP-Input FUS

first: kenian

last: chen

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: SingleRun 101bp with P2-100 cycle kit

data_processing:
Basecalls performed using CASAVA version 1.8.2
For RNA-seq analysis,reads were aligned to the mouse reference genome  GRCm38 (mm10) using the Hisat (version 2.0.0) aligner using default settings. Aligned reads were counted using featureCounts (version 1.4.6) per gene ID.
For ChIP-seq analysis, raw sequencing reads with > 30% nucleotide with phred quality scores < 20 were filtered. Single-end sequencing reads were then aligned to the mouse reference genome GRCm38 (mm10) using bowtie2 aligner (v 2.3.4.3) with default parameters. For transcription factor ChIP-seq data, peaks were called using HOMER software package (version 4.9) findpeaks command, with parameter ‘-style factor’, peaks were called with >2 fold enrichment over input controls and > 4 fold enrichment over local tag counts and FDR threshold was set to 10-3. For histone marker ChIP-Seq data, peaks were called by findpeaks command with parameter ‘–style histone’, peaks were called with >2 fold enrichment over input controls and > 4 fold enrichment over local tag counts and FDR threshold set to 10-3. ChIP-seq peaks within a 1000 bp range were stitched together to form broad regions.
Assembly: GRCh38/mm10
Supplementary files format and content: Bigwig for ChIPseq, RNAseq Genome Tracks. Bed file for ChIP Peaks, TXT file for RNAseq RawCount

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagents and Direct-zol RNA Miniprep Kits (Zymo Research, R2052) according to manufacturer’s protocol. For ChIP-seq, cells were fixed and crosslinked with 4% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
For RNA-seq, stranded mRNA-Seq libraries were generated using KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol. For ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB (NEB, E6177S). 10 ng of DNA was used as starting material for Input samples and 1 ng for IP samples. Libraries were amplified using 12 cycles for Input samples and 15 cycles for IP samples on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

value: Fibroblast-like cells from C3H mouse embryo

value: WT

value: MYOCD-FUS retroviral transduction, SMC differentiation


title: ChIP-Input CDT1

status: Public on Feb 08 2024

type: SRA

city: Dallas

state: TX

country: USA

description: SingleRun 101bp with P2-100 cycle kit

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: MYOCD-CDT1 retroviral transduction, SMC differentiation


title: PB01009_liver_roi005_Fibrosis

type: protein

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: protein detected by antibody

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

label: fluorescent barcode

molecule: protein

organism: Homo sapiens

treatment_protocol: Pre-treatment tumor and liver biopsy tissues were obtained from patients with unresectable hepatocellular carcinoma trated with bavituximab and pembrolizumab.

tag: patient id

tag: tissue type

value: liver

tag: region of interest (roi) number

tag: segment type

value: fibrous tissue enriched

tag: positive immuno-fluorescent morphology marker

value: SMA

tag: radiographic objective response

value: partial response (PR)


title: PB01009_tumor_roi004_Fibrosis

description: protein detected by antibody

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: tumor


title: ChIP-Input deltaTAD

description: SingleRun 101bp with P2-100 cycle kit

value: MYOCD-deltaTAD retroviral transduction, SMC differentiation


title: PB01009_liver_roi005_nonTumorLiver

description: protein detected by antibody

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: non-tumor liver


title: ChIP-Input MYOCD

description: SingleRun 101bp with P2-100 cycle kit

value: MYOCD retroviral transduction, SMC differentiation


title: ChIP-H3K27ac CDT1

description: SingleRun 101bp with P2-100 cycle kit


title: ChIP-H3K27ac FUS

description: SingleRun 101bp with P2-100 cycle kit


title: ChIP-H3K27ac GFP

description: SingleRun 101bp with P2-100 cycle kit

value: GFP retroviral transduction, SMC differentiation


title: ChIP-H3K27ac MYOCD

description: SingleRun 101bp with P2-100 cycle kit


title: ChIP-GFP CDT1

description: SingleRun 101bp with P2-100 cycle kit


title: PB01009_liver_roi007_ImmuneCell

description: protein detected by antibody

extract_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: immune cell enriched


title: ChIP-GFP deltaTAD

description: SingleRun 101bp with P2-100 cycle kit


title: ChIP-GFP FUS

description: SingleRun 101bp with P2-100 cycle kit


title: PB02009_tumor_roi004_CancerCell

description: protein detected by antibody

value: cancer cell enriched

value: stable disease (SD)


title: PB02009_tumor_roi004_ImmuneCell

description: protein detected by antibody


title: ChIP-GFP MYOCD

description: SingleRun 101bp with P2-100 cycle kit


title: Photoconverted brain endothelial cells, rep2

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic single cell

data_processing:
Demultiplexing with bcl2fastq
Alignment against the zebrafish Danio_rerio.GRCz11.95 build using Bowtie2
Removal of adapter sequencing with TrimGalore
Removal of duplets using samtools
Generation of a count matrix with FeatureCounts from the SubRead package
Assembly: Danio.Rerio.GRCz11
Supplementary files format and content: Count files, with every column a cell and every row a gene.

molecule: total RNA

organism: Danio rerio

source_name: Brain

growth_protocol: Standard

extract_protocol:
Photoconversion ofTg(fli1:Gal4)ubs3;(UAS:Kaede)rk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope (Carl Zeiss, objective lenses: Plan-Apochromat ×20/0.8 M27). Briefly, anesthetised embryos were mounted laterally in 1% low-melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405 nm laser (five iterations of 50 s). After isolation from the agarose, embryos were washed in Ca2+/Mg2+-free HBSS (Hank’s Balanced Salt Solution, Gibco) and dissociated at 28.5 °C for 30 min in TrypLE select (Thermo Fischer Scientific, 12563011). Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS, filtered, and submitted to FACS (BD Biosciences FACSAria III).
Single-cell cDNA libraries were prepared according to the established protocol for Smart-Seq2. In brief, poly-adenylated mRNA was transcribed to cDNA using oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific). Synthesis of second strand cDNA was achieved using a template switching oligo, and the double stranded cDNA was then amplified using polymerase chain reaction (PCR) for 23 – 26 cycles. After bead purification, overall cDNA quality was controlled (QC) by analyzing randomly selected single cell samples (wells) on a 2100 Bioanalyzer with a DNA High sensitivity chip (Agilent Biotechnologies). When the sample (plate) passed the QC, the cDNA was fragmented and tagged (tagmented) using Tn5 transposase, and each single cell sample (well) was uniquely indexed using Illumina Nextera XT index kits (set A-D). Thereafter, the indexed single-cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer (Illumina), using dual indexing and 50 base read-length.
ScRNA-Seq with Smart-seq2

treatment_protocol: Morpholino injection

tag: tissue

value: Brain

tag: age

value: 30 hpf

value: Endothelial cells

value: WT and gpr124 morpholino


title: Photoconverted brain endothelial cells, rep1


title: ChIP-Input GFP

description: SingleRun 101bp with P2-100 cycle kit

value: Fibroblast-like cells from C3H mouse embryo

value: WT


title: PB02009_tumor_roi003_Fibrosis

description: protein detected by antibody

value: fibrous tissue enriched


title: PB02009_tumor_roi003_CancerCell

description: protein detected by antibody


title: HFD+MEC1-4

city: High Education Mega Center, SCUT, Building B2, Room 404

first: min

last: ma

state: guangzhou

address: Panyu Square

department: medical division

country: China

institute: south china university of technology

library_source: transcriptomic

data_processing:
Raw sequene data were processed on STAR_2.7.10a
Assembly: mm10
Supplementary files format and content: tab-delimited text files include rpkm values for each Sample .

source_name: Liver

extract_protocol:
liver tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver


title: PB02009_tumor_roi002_CancerCell

description: protein detected by antibody


title: ChIP-GFP GFP

description: SingleRun 101bp with P2-100 cycle kit


title: HFD+MEC1-2


title: ChIP-H3K27ac deltaTAD

description: SingleRun 101bp with P2-100 cycle kit


title: PB01009_liver_roi006_ImmuneCell

description: protein detected by antibody

value: liver

value: partial response (PR)


title: PB01009_liver_roi006_BileDuct

description: protein detected by antibody

value: bile duct

value: PanCK


title: HFD+MEC1-1


title: RNA MYOCD_3 WT

molecule: polyA RNA

value: MYOCD retroviral transduction, SMC differentiation


title: HFD-4


title: PB01009_tumor_roi004_ImmuneCell

description: protein detected by antibody

value: tumor


title: PB02009_tumor_roi002_Fibrosis

description: protein detected by antibody

value: SMA


title: RNA MYOCD_2 WT


title: PB02009_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: RNA MYOCD_1 WT


title: ND-4


title: HFD-1


title: HFD-2


title: HFD-3


title: PB02009_tumor_roi003_ImmuneCell

description: protein detected by antibody

value: stable disease (SD)


title: RNA GFP_3

value: GFP retroviral transduction, SMC differentiation


title: PB02009_tumor_roi001_Fibrosis

description: protein detected by antibody


title: HFD+MEC1-3


title: PB02009_tumor_roi001_CancerCell

description: protein detected by antibody

value: cancer cell enriched


title: E10NEW_D5

city: Rochester

first: Fergus

last: Couch

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
FASTQ files of sequenced samples from Illumina MiSeq were trimmed for adapter sequences using cutadapt (v3.5).
SeqPrep (v1.2) converted the paired-end reads into single reads.
The single reads were aligned to the human reference genome (GRCh38) utilizing bwa-mem (v0.7.17).
Following alignment, a custom-developed tool `CountReads` was used for the analysis of DNA sequencing data, with a particular focus on mutation identification and characterization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited files for each variant from the library, day 5 and day 20 for each replicate
Library strategy: amplicon-seq

source_name: blood

growth_protocol: HAP1 cell (Horizon discovery) were maintained in IMDM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Harvested cell pellets were thawed and genomic DNA were extracted by using Monarch Genomic DNA purification kit (NEB). Target region specific primer were used for PCR using Q5 High-Fidelity 2X Master Mix (NEB). Addaptor and index were added for each target region PCR product and samples were purified using AMPure XP beads and sent for sequencing.
Homologous arms (HA) that are 600-1000bp upstream and downstream flanking each target region were amplied from HAP1 cells and cloned into TOPO vector; site-directed mutagenesis PCR were performed in the HA arm vector to introduce target region saturation mutations with the PAM or sgRNA recognition site -destroying to avoind re-cutting by Cas9. Pooled mutagenesis PCR product was phosphorylated and transformed into MaxEfficient DH5a competent cells, grow overnight at 37 degree and library plasmids were extracted by ZymoPUREII MaxiPrep kit.
amplicon based sequencing (AMPLN)

treatment_protocol: day -1: 2 million HAP1 cells seeded; day 0: transfection with library and sgRNA/Cas9 counstruct; day 1: 1ug/ml puromycin treatment; day 4: change back to regular medium; day 5: half of the cells were harvested for genomic DNA extraction, remaining cells continue culturing and passaged at 3-day interval; day 20: 5 million cells were harvested.

value: blood

value: HAP1(a near-haploid human cell line derived from the KBM-7 chronic myelogenous leukemia (CML) cell line)


title: E10NEW_pUCSSMmu_lib

value: chronic myelogenous leukemia (CML) cell line


title: RNA GFP_2

value: Fibroblast-like cells from C3H mouse embryo

value: WT


title: ND-2

value: Liver


title: RNA GFP_1


title: ND-1


title: E10NEW_Cis_pUCSSMmu_lib


title: E10NEW_D20


title: PB02009_liver_roi007_Rest_F

description: protein detected by antibody

value: liver

value: fibrous tissue enriched


title: RNA FUS_2

value: MYOCD-FUS retroviral transduction, SMC differentiation


title: Total RNA from lung, Gdf15-/- animal, 20 hours post innoculation with PA supernatant, KO5

city: Pittsburgh

first: William

last: Bain

state: PA

address: 3459 Fifth Ave., MUH NW 628

department: Medicine

institute: University of Pittsburgh

data_processing:
Raw fastq file quality was verified with fastQC and the first 10 nucleotides were trimmed.
Reads were aligned to mouse genome using STAR. Raw counts were determined using the GeneCounts option in STAR.
Assembly: mm39
Supplementary files format and content: Tab-delimited text file with raw read counts for each sample

source_name: whole lung

extract_protocol:
Lung was homogenized using a tissue homogenizer in trizol. RNA was extracted from Trizol/homogenate according to manufacturer's protocol. RNA was subsequently purified on an RNAeasy column according to manufacturer's protocol.
RNA quality control and library contruction was performed at Novagene (non-directional library)

treatment_protocol: Animals were treated with PA supernatant 20 hours prior to collection.

value: whole lung

value: PA supernatant


title: RNA FUS_3


title: PB02009_tumor_roi001_ImmuneCell

description: protein detected by antibody

value: tumor


title: PB02009_tumor_roi005_ImmuneCell

description: protein detected by antibody


title: PB02009_tumor_roi005_BileDuct

description: protein detected by antibody

value: bile duct

value: PanCK


title: E10NEW_Cis_D5


title: Total RNA from lung, WT animal, 20 hours post innoculation with PA supernatant, WT5


title: E10NEW_Cis_D20


title: Total RNA from lung, WT animal, 20 hours post innoculation with PA supernatant, WT4


title: RNA deltaTAD_3

value: MYOCD-deltaTAD retroviral transduction, SMC differentiation


title: Total RNA from lung, WT animal, 20 hours post innoculation with PA supernatant, WT3


title: ND-3


title: TKO chromatin MNase 0.75 U

city: Srinagar

first: Ajaz ul Hamid

last: Wani

state: Jammu and Kashmir

address: Hazratbal

department: Biotechnology

country: India

institute: University of Kashmir

data_processing:
Using Bowtie aligner2 the sequenced paired-end reads were mapped to the Saccharomyces cerevisiae reference genome((as described in earlier Mieczkowski et al., 2016)
Supplementary files format and content: biwig

organism: Saccharomyces cerevisiae

source_name: TKO chromatin

growth_protocol: Both wildtype and triple knockout strains were grown at 30◦C in YPD media upto OD-2 to 2.5.

extract_protocol:
DNA was extracted by using phenol: chloroform
Library was prepared as per protocol described in Bowman et al., BMC Genomics (2013)

treatment_protocol: After spheroplast and nuclei isolation chromatin was extracted and digested with 0.75 U of MNase.

value: Triple knockout

value: MNase 0.75 U


title: WT Chromatin MNase 0.75 U

source_name: WT chromatin

value: Wildtype


title: RNA deltaTAD_2


title: Total RNA from lung, Gdf15-/- animal, 20 hours post innoculation with PA supernatant, KO4


title: PB02009_liver_roi006_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

value: stable disease (SD)


title: PB02009_tumor_roi005_Rest_F

description: protein detected by antibody


title: Hi-C Triple knockout-Replicate 2

description: TKO- Replicate 2

data_processing:
Reads were aligned with the reference genome using bowtie aligner2
Valid interaction products were detected, filtered, and binned in equal size genome fragments to generate contact maps
The contact matrices were normalized and visualized using Juicebox
Supplementary files format and content: mcool

source_name: Saccharomyces cerevisiae

growth_protocol: Both wildtype and knockout strains were grown at 30◦C in YPD media upto OD-1 and crosslinked chromatin with 3% formaldehyde.

extract_protocol:
DNA was extracted by using phenol: chloroform
Biotin was removed from free ends and DNA was sonicated. Size selection was done by Ampure beads and NGS library was prepared as per Rao et al., Cell (2014) with some modifications

treatment_protocol: After spheroplast preparation and nuclei isolation chromatin was digested with DpnII, labelled with biotin and ligated.

value: Saccharomyces cerevisiae

value: DpnII Digestion


title: PB02009_liver_roi006_nonTumorLiver

description: protein detected by antibody

value: non-tumor liver


title: PB02009_liver_roi007_ImmuneCell

description: protein detected by antibody

value: liver


title: RNA deltaTAD_1

value: Fibroblast-like cells from C3H mouse embryo

value: WT


title: Total RNA from lung, Gdf15-/- animal, 20 hours post innoculation with PA supernatant, KO3

value: whole lung


title: PB02009_liver_roi007_BileDuct

description: protein detected by antibody


title: Hi-C Wildtype-Replicate2

description: WT- Replicate 2


title: RNA CDT1_3

value: MYOCD-CDT1 retroviral transduction, SMC differentiation


title: Total RNA from lung, Gdf15-/- animal, 20 hours post innoculation with PA supernatant, KO2

value: PA supernatant


title: Hi-C Triple knockout-Replicate 1

description: TKO- Replicate 1


title: RNA FUS_1

value: MYOCD-FUS retroviral transduction, SMC differentiation


title: Total RNA from lung, Gdf15-/- animal, 20 hours post innoculation with PA supernatant, KO1


title: RNA CDT1_1


title: Hi-C Wildtype-Replicate1

description: WT- Replicate 1


title: Total RNA from lung, WT animal, 20 hours post innoculation with PA supernatant, WT2


title: Triple knockout-Replicate 2

description: TKO- Replicate 2

data_processing:
Reads were aligned with the reference genome using bowtie aligner2
Valid interaction products were detected, filtered, and binned in equal size genome fragments to generate contact maps
The contact matrices were normalized and visualized using HiGlass
Supplementary files format and content: MCOOL
Library strategy: Micro-C

source_name: Triple knockout

growth_protocol: Both wildtype and knockout strains were grown at 30◦C in YPD media upto OD-0.55. Crosslinked chromatin first with 3% formaldehyde and after spheroplast preparation with second crosslinker EGS .

extract_protocol:
DNA was extracted by using phenol: chloroform
After size selection of dinucleosomal band, NGS library was prepared as per Rao et al., Cell (2014) with some modifications

treatment_protocol: Chromatin was digested with MNase, ends were repaired and after biotin labelling ligation was done.

tag: strain

value: MNase Digestion


title: PB01011_tumor_roi001_ImmuneCell

description: protein detected by antibody

value: tumor

value: progressive disease (PD)


title: PB01011_tumor_roi001_Fibrosis

description: protein detected by antibody

value: fibrous tissue enriched

value: SMA


title: Exp2 4E-T (Neurosphere)

city: Toronto

first: Adelaida

last: Kolaj

state: Ontario

address: 27 King's College Circle

country: Canada

institute: University of Toronto

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 High Throughput flowcell paired-end 2x125bp or Novaseq SP flowcell paired-end 2x150bp with ~60 million reads per sample . Data quality was assessed by FastQC v.0.11.5, adaptors were trimmed using TrimGalore v. 0.5.0. , raw trimmed reads were aligned using STAR aligner, v.2.6.0c, and alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2. Two-condition differential gene expression analysis was performed with DESeq2 v. 1.26.0. Where applicable, normalization/batch correction was performed by initial minimal filtering of 10 read counts per gene in at least 2 samples was applied to the datasets. More strict filtering to increase power is automatically applied via independent filtering on the mean of normalized counts within the DESeq results() function. All samples for each project were filtered and normalized together. Normalization is performed using the "median ratio method" (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106), implemented by the estimateSizeFactors function. The raw counts are divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene. Differential expression testing was performed using the default Wald test. To control for batch effect the batch variable was added to the design formula.
Assembly: mm10
Supplementary files format and content: Deseq2 differential gene expression analysis, excel file

source_name: Neurospheres from P7/P8 V-SVZ

extract_protocol:
RNA was isolated as described in Kolaj et al 2023 using the MAGNA RIP kit
cDNA was generated using the Takara Bio SMART-Seq® v4 Low Input RNA Kit for Sequencing, and libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit.

value: V-SVZ neurosphere

tag: rip antibody

tag: fraction

value: IP'd RNA

tag: time

value: 7 days


title: Exp2 IgG control (Neurosphere)

value: anti-IgG


title: Triple knockout-Replicate 1

description: TKO- Replicate 1

value: Triple knockout


title: Total RNA from lung, WT animal, 20 hours post innoculation with PA supernatant, WT1


title: Exp1 IgG control (Neurosphere)


title: Wildtype-Replicate2

description: WT- Replicate 2

source_name: Wildtype

value: Wildtype


title: Exp1 4E-T (Neurosphere)


title: PB01011_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: Wildtype-Replicate1

description: WT- Replicate 1


title: PB01011_tumor_roi002_PanCK_T

description: protein detected by antibody

value: cancer cell enriched

value: PanCK


title: PB01011_tumor_roi002_Rest_F

description: protein detected by antibody


title: Exp2 4E-T (V-SVZ)

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 High Throughput flowcell paired-end 2x125bp or Novaseq SP flowcell paired-end 2x150bp with ~60 million reads per sample . Data quality was assessed by FastQC v.0.11.5, adaptors were trimmed using TrimGalore v. 0.5.0. , raw trimmed reads were aligned using STAR aligner, v.2.6.0c, and alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2. Two-condition differential gene expression analysis was performed with DESeq2 v. 1.26.0. Where applicable, normalization/batch correction was performed by initial minimal filtering of 10 read counts per gene in at least 2 samples was applied to the datasets. More strict filtering to increase power is automatically applied via independent filtering on the mean of normalized counts within the DESeq results() function. All samples for each project were filtered and normalized together. Normalization is performed using the "median ratio method" (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106), implemented by the estimateSizeFactors function. The raw counts are divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene. Differential expression testing was performed using the default Wald test. To control for batch effect the batch variable was added to the design formula.
Assembly: mm10
Supplementary files format and content: Deseq2 differential gene expression analysis, Excel file

source_name: V-SVZ

value: V-SVZ

value: WT


title: Exp2 IgG (VSVZ)


title: RNA CDT1_2

value: Fibroblast-like cells from C3H mouse embryo

value: MYOCD-CDT1 retroviral transduction, SMC differentiation


title: PB01011_tumor_roi003_ImmuneCell

description: protein detected by antibody

value: tumor


title: PB01011_tumor_roi005_ImmuneCell

description: protein detected by antibody

value: progressive disease (PD)


title: TD 100 U MNase Replicate-2

description:
H5
TD- Replicate 2

data_processing:
Using Bowtie aligner2 the sequenced paired-end reads were mapped to the Saccharomyces cerevisiae reference genome((as described in earlier Mieczkowski et al., 2016)
Read frequencies were calculated in non-overlapping bins of 200 bp size for each titration point individually.
Linear regression was fitted on the normalized frequencies in bins and the obtained regression coefficients were used as MACC scores.
Supplementary files format and content: biwig, wig
Supplementary files format and content: bedgraph

source_name: yeast

growth_protocol: Both wildtype and triple deletion strains were grown at 30◦C in YPD media upto OD-2 and crosslinked with 1% formaldehyde.

extract_protocol:
DNA was extracted by using phenol: chloroform
Size selection was done to exclude fragments of larger size and then the library was prepared as per protocol described in Bowman et al., BMC Genomics (2013)

treatment_protocol: After spheroplast and nuclei isolation chromatin was digested with increasing concentrations of MNase (0.39, 1.56, 6.25, 25 and 100 U )

value: Triple deletion

value: MNase 100 U


title: PB01011_tumor_roi005_Fibrosis

description: protein detected by antibody

value: fibrous tissue enriched

value: SMA


title: TD 25 U MNase Replicate-2

description:
H4
TD- Replicate 2

value: MNase 25 U


title: Exp1 4E-T (VSVZ)

value: IP'd RNA


title: TD 6.25 U MNase Replicate-2

description:
H3
TD- Replicate 2

value: MNase 6.25 U


title: Exp1 IgG (VSVZ)

value: anti-IgG


title: Exp2 Cpeb4 (V-SVZ)

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 High Throughput flowcell paired-end 2x125bp or Novaseq SP flowcell paired-end 2x150bp with ~60 million reads per sample . Data quality was assessed by FastQC v.0.11.5, adaptors were trimmed using TrimGalore v. 0.5.0. , raw trimmed reads were aligned using STAR aligner, v.2.6.0c, and alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2. Two-condition differential gene expression analysis was performed with DESeq2 v. 1.26.0. Where applicable, normalization/batch correction was performed by initial minimal filtering of 10 read counts per gene in at least 2 samples was applied to the datasets. More strict filtering to increase power is automatically applied via independent filtering on the mean of normalized counts within the DESeq results() function. All samples for each project were filtered and normalized together. Normalization is performed using the "median ratio method" (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106), implemented by the estimateSizeFactors function. The raw counts are divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene. Differential expression testing was performed using the default Wald test. To control for batch effect the batch variable was added to the design formula.
Assembly: mm10
Supplementary files format and content: Deseq2 differential gene expression analysis, tsv file


title: PB01011_tumor_roi003_PanCK_T

description: protein detected by antibody


title: Exp2 IgG control (VSVZ)


title: WT 100 U MNase Replicate-2

description:
G5
WT- Replicate 2

value: Wildtype


title: PB01014_tumor_roi005_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: PB01014_tumor_roi005_BileDuct

description: protein detected by antibody

value: bile duct

value: PanCK


title: Exp1 Cpeb4 (VSVZ)

value: V-SVZ

value: WT


title: WT 25 U MNase Replicate-2

description:
G4
WT- Replicate 2


title: WT 6.25 U MNase Replicate-2

description:
G3
WT- Replicate 2


title: WT 1.56 U MNase Replicate-2

description:
G2
WT- Replicate 2

value: MNase 1.56 U


title: PB01014_tumor_roi006_ImmuneCell

description: protein detected by antibody

value: tumor


title: EXP3 Cpeb4 (Neurosphere)

source_name: V-SVZ precursors neurosphere

value: V-SVZ precursors neurosphere

value: Day 7


title: PB01014_tumor_roi006_BileDuct

description: protein detected by antibody

value: progressive disease (PD)


title: Exp2 Cpeb4 (Neurosphere)


title: WT 0.39 U MNase Replicate-2

description:
G1
WT- Replicate 2

value: MNase 0.39 U


title: Exp1 IgG control (VSVZ)


title: TD 100 U MNase Replicate-1

description:
B5
TD- Replicate 1

value: Triple deletion

value: MNase 100 U


title: Exp2 IgG (Neurosphere)

value: IP'd RNA


title: PB01014_tumor_roi006_Rest_F

description: protein detected by antibody

value: fibrous tissue enriched


title: PB01014_liver_roi007_nonTumorLiver

description: protein detected by antibody

value: liver

value: non-tumor liver


title: Exp1 Cpeb4 (Neurosphere)


title: PB01014_liver_roi007_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: TD 25 U MNase Replicate-1

description:
B4
TD- Replicate 1

value: MNase 25 U


title: PB01014_tumor_roi004_PanCK_T

description: protein detected by antibody

value: cancer cell enriched

value: PanCK


title: PB01014_liver_roi008_nonTumorLiver

description: protein detected by antibody


title: TD 1.56 U MNase Replicate-2

description:
H2
TD- Replicate 2


title: TD 6.25 U MNase Replicate-1

description:
B3
TD- Replicate 1

value: MNase 6.25 U


title: Exp1 IgG (Neurosphere)

value: WT

value: anti-IgG


title: PB01014_tumor_roi004_ImmuneCell

description: protein detected by antibody

value: tumor


title: TD 1.56 U MNase Replicate-1

description:
B2
TD- Replicate 1

value: MNase 1.56 U


title: TD 0.39 U MNase Replicate-2

description:
H1
TD- Replicate 2


title: EXP3 RT IgG

data_processing:
CLC Genomics Workbench v 11.0.1
Libraries were sequenced on the Illumina HiSeq 2500 High Throughput flowcell paired-end 2x125bp or Novaseq SP flowcell paired-end 2x150bp with ~60 million reads per sample . Data quality was assessed by FastQC v.0.11.5, adaptors were trimmed using TrimGalore v. 0.5.0. , raw trimmed reads were aligned using STAR aligner, v.2.6.0c, and alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2. Two-condition differential gene expression analysis was performed with DESeq2 v. 1.26.0. Where applicable, normalization/batch correction was performed by initial minimal filtering of 10 read counts per gene in at least 2 samples was applied to the datasets. More strict filtering to increase power is automatically applied via independent filtering on the mean of normalized counts within the DESeq results() function. All samples for each project were filtered and normalized together. Normalization is performed using the "median ratio method" (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-10-r106), implemented by the estimateSizeFactors function. The raw counts are divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene. Differential expression testing was performed using the default Wald test. To control for batch effect the batch variable was added to the design formula.
Assembly: mm10
Supplementary files format and content: Deseq2 differential gene expression analysis, excel file
Library strategy: Ribo-Tag

extract_protocol:
RNA was isolated as described in Kolaj et al 2023
cDNA was generated using the Takara Bio SMART-Seq® v4 Low Input RNA Kit for Sequencing, and libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit.

value: V-SVZ precursors neurosphere

value: NestinCreERT2(+/-); RPL22HA/HA

value: Tamoxifen

value: Day 7.5


title: 2-DG nanoparticles sample 2- Day 7

city: Omaha

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: University of Nebraska Medical Center

data_processing:
The RNAseq data analysis was performed by standard pipeline including quanlity control, trimming, aligment, and qualtification in Partek Flow v11.0.23.1105
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with normalized gene TPM expression values for every gene and every sample

source_name: infected joint tissue

growth_protocol: To model infectious complications following prosthetic joint surgery, a mouse model of S. aureus PJI was used. Mice were anesthetized using ketamine/xylazine prior to an initial incision made through the quadriceps. A secondary incision was then created to laterally displace the patellar tendon prior to generating a burr hole in the distal end of the femur using a 26-gauge needle. An orthopedic-grade nickel-titanium Kirschner wire (0.6 mm diameter; Custom Wire Technologies) was inserted through the burr hole into the medullary canal, whereupon 10^3 colony-forming units (CFUs) of S. aureus were inoculated at the tip of the wire. Slow-release Buprenex was administered subcutaneously following surgery to provide analgesia for 72 h. Mice were monitored daily to ensure normal ambulatory function and the lack of discernable pain behaviors. For 2-DG nanoparticle delivery, mice were placed in an induction chamber without restraint and anesthetized with 2.5% isoflurane. A single dose of 2-DG-containing (25 μL of 3.5 mg/mL 2-DG in 1X PBS) or empty nanoparticles was administered by injection into the soft tissue surrounding the infected joint on day 3 post-infection. Animals were sacrificed 4 days later (day 7 post-infection) to isolate Ly6G+ cells by FACS for bulk RNA-seq analysis.

extract_protocol:
To recover CD45+ cells from the soft tissue surrounding the infected joint by FACS, tissue homogenates were filtered, and red blood cells (RBCs) were eliminated by treating cells with 1X RBC lysis buffer. Next, cells were incubated with TruStain FcX (BioLegend) prior to staining with CD45-APC (RRID: AB_312977) and Ly6G-PE (RRID: AB_1186099). Dead cells were excluded from analysis using a Zombie UV fixable Live/Dead stain (Cat. #423108; BioLegend).
TruSeq V2 RNA sequencing library kit from Illumina following recommended procedures (Illumina Inc., San Diego, CA)

value: infected joint tissue

value: Ly6G+ cells


title: PB01014_tumor_roi003_PanCK_T

description: protein detected by antibody

value: progressive disease (PD)


title: 2-DG nanoparticles sample 1- Day 7


title: Exp3 RT HA

value: anti-HA

value: IP'd RNA


title: WT 100 U MNase Replicate-1

description:
A5
WT- Replicate 1

value: Wildtype

value: MNase 100 U


title: Exp3 IgG (Neurosphere)

value: Day 7


title: PB01014_tumor_roi002_CancerCell

description: protein detected by antibody

value: cancer cell enriched


title: WT 25 U MNase Replicate-1

description:
A4
WT- Replicate 1

value: MNase 25 U


title: Exp2 RT IgG

value: anti-IgG


title: Empty nanoparticles sample 2- Day 7

value: Vehicle


title: Exp2 RT HA


title: Exp1 RT IgG


title: Empty nanoparticles sample 1- Day 7


title: PB01014_tumor_roi002_Fibrosis

description: protein detected by antibody

value: tumor

value: fibrous tissue enriched

value: SMA


title: WT 1.56 U MNase Replicate-1

description:
A2
WT- Replicate 1

value: MNase 1.56 U


title: KO-UUO4

city: chengdu

first: Ting

last: Xiang

address: chengdu

institute: West China Hospital of Medicine: Sichuan Universit

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
Assembly: mm10
Supplementary files format and content: raw count

source_name: kidney

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: kidney

value: UUO+ACSS2 knockout

value: Unilateral Ureteral Obstruction


title: PB01014_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

value: progressive disease (PD)


title: WT 6.25 U MNase Replicate-1

description:
A3
WT- Replicate 1

value: MNase 6.25 U


title: Exp1 RT HA

value: V-SVZ precursors neurosphere

value: NestinCreERT2(+/-); RPL22HA/HA

value: Tamoxifen

value: Day 7.5

value: anti-HA

value: IP'd RNA


title: PB01014_tumor_roi001_Fibrosis

description: protein detected by antibody


title: WT-UUO3

value: UUO


title: KO-UUO3


title: Yuuki_24

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

description: Panc 10.05 LMO3 transgene

data_processing:
mRNA-Seq samples were pooled and sequenced on NextSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 32 to 60 million pass filter reads with more than 93% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Pancreatic cancer cell line

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: Panc 10.05_LMO3 overexpression_4

value: PLMO3 transgene


title: TD 0.39 U MNase Replicate-1

description:
B1
TD- Replicate 1

value: Triple deletion

value: MNase 0.39 U


title: WT 0.39 U MNase Replicate-1

description:
A1
WT- Replicate 1

value: Wildtype


title: TD RNA replicate-2

description: TD- Replicate 2

data_processing:
Tophat software was used to align RNA-Seq tags.
RNA-Seq tag frequencies were normalized for GC content using bioconductor package EDASeq
Expression estimates for each gene were calculated using the bioconductor software DESeq.
Using the limma programme, differentially expressed genes were identified.
Supplementary files format and content: TDF File

source_name: yeast cells

growth_protocol: Both wildtype and triple deletion strains were grown at 30◦C in YPD media upto OD-1.

extract_protocol:
RNA was extracted by acidic phenol: chloroform.
Ribosomal RNA was depleted from total RNA by ribozero kit, cDNA was generated by kit, cDNA library were prepared for Next-generation sequencing and sequenced using Illlumina squencing platform 2500.

treatment_protocol: Cells were lncubated at 65° for 1 hour in TES buffer and acidic phenol : chloroform

value: yeast cells


title: PB01014_tumor_roi001_ImmuneCell

description: protein detected by antibody

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

value: tumor


title: PB01014_tumor_roi004_Rest_F

description: protein detected by antibody

value: fibrous tissue enriched


title: PB01014_tumor_roi003_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

value: progressive disease (PD)


title: WT-UUO2

value: kidney

value: Unilateral Ureteral Obstruction


title: Yuuki_23

description: Panc 10.05 LMO3 transgene

value: Panc 10.05_LMO3 overexpression_3

tag: cell line


title: Yuuki_22

description: Panc 10.05 LMO3 transgene

value: Panc 10.05_LMO3 overexpression_2


title: Yuuki_21

description: Panc 10.05 LMO3 transgene

value: Panc 10.05_LMO3 overexpression_1


title: TD RNA replicate-1

description: TD- Replicate 1

tag: cell type


title: PB01012_tumor_roi001_ImmuneCell

description: protein detected by antibody

value: stable disease (SD)


title: KO-C2

tag: genotype

value: ACSS2 knockout

value: shamoperated


title: KO-C1

tag: treatment


title: WT RNA replicate-1

description: WT- Replicate 1


title: PB01012_tumor_roi001_CancerCell

description: protein detected by antibody

tag: patient id

value: cancer cell enriched


title: PB01012_tumor_roi001_Fibrosis

description: protein detected by antibody

tag: tissue type

value: SMA


title: Yuuki_20

description: Panc 10.05 control

value: Panc 10.05_Ctrl_4

value: control


title: Yuuki_19

description: Panc 10.05 control

value: Panc 10.05_Ctrl_3


title: WT-C3

value: WT


title: PB01012_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: tumor

tag: region of interest (roi) number


title: PB01012_tumor_roi002_Fibrosis

description: protein detected by antibody

tag: segment type

value: fibrous tissue enriched


title: WT-C2


title: CTRL1T24_3, biol rep 3

city: Milan

first: Santo

last: Diprima

state: MI

address: Via Olgettina 58

department: COSR

country: Italy

institute: San Raffaele Hospital

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts.
Assembly: UCSC hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: induced pluripotent stem cells

growth_protocol: Proliferating iPSCs were cultured as a monolayer on matrigel-coated dishes in StemFlex medium (Thermo Fisher Scientific RRID:SCR_018018) with Penicillin/Streptomycin until they reached 70% confluence.

extract_protocol:
Total RNA was extracted using the High Pure RNA Isolation Kit (Roche RRID:SCR_004098)
Total RNA was extracted from each cell line at day 8 and day 24. RNA quality and integrity, checked by RNA Integrity Number (RIN), were evaluated on an Agilent 2100 Bioanalyzer

treatment_protocol: iPSCs were then switched to differentiating medium containing specific cocktails of cytokines (BMPs, FGF family members, Shh and Wnt family members) added at specific time points to induce first mid-hindbrain precursors and later cerebellar granule cells after 31 days of culture

value: induced pluripotent stem cells

value: cerebellar granule cells differentiation

value: day 24


title: WT RNA replicate-2

description: WT- Replicate 2

value: yeast cells

value: Wildtype


title: Yuuki_18

description: Panc 10.05 control

value: Panc 10.05_Ctrl_2


title: CTRL1T8_3, biol rep 3

value: day 8


title: CTRL1T24_2, biol rep 2


title: KO-C3

value: kidney

value: ACSS2 knockout


title: PB01012_tumor_roi003_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

tag: positive immuno-fluorescent morphology marker

value: stable disease (SD)


title: Yuuki_17

description: Panc 10.05 control

value: Panc 10.05_Ctrl_1


title: PB01012_tumor_roi003_Fibrosis

description: protein detected by antibody

value: SMA

tag: radiographic objective response


title: WTC1

tag: tissue

value: shamoperated


title: CC2D2AT24_3, biol rep 3

value: CC2D2A mutant:c.3856T>C;c.3856T>C


title: PB01012_tumor_roi003_CancerCell

description: protein detected by antibody

value: tumor

value: cancer cell enriched


title: Yale_mir708_INPUT_S20

city: New Haven

first: Carson

last: Bryant

state: CT

address: 333 Cedar Street

department: Molecular Biophysics and Biochemistry

institute: Yale University

data_processing:
UMI removal: UMIs were removed from reads and appended to the read name for PCR deduplication further downstream using umi_tools.
Adapter removal: Cutadapt was run on demultiplexed files to trim off 3' adapters and 3' UMIs.
STAR rmRep: STAR was used to map reads to a repetitive element database to remove repetitive elements like rRNA.
STAR genome mapping: STAR was used to map reads to the hg38 genome. Aligned reads represent non-chimeric RNA reads, while unaligned reads represent putative miRNA:RNA chimeras.
Deduplication: PCR duplicates were removed from aligned reads using umi_tools.
AGO2 binding site peak calling: CLIPper (Yeo lab) was used to identify clusters of aligned (non-chimeric) reads to define peaks representing AGO2 binding sites.
Unaligned reads remapping to find microRNA sequences: Bowtie was used to remap unmapped reads containing putative miRNA:mRNA chimeras to microRNAs. The best mapping microRNA was chosen, and the region of the read mapping to the microRNA was trimmed.
Unaligned reads remapping to find mRNA sequences: STAR was used to map the microRNA-trimmed chimeric reads to the genome.
Deduplication: PCR duplicates were removed from unaligned reads using umi_tools.
Peak calling: CLIPper was used to identify clusters of chimeric reads overlapping with AGO2 peaks, mapping microRNAs to their bound mRNAs. Number of reads for each miRNA:mRNA pair was counted.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes obtained chimeric interactions for the IP sample.
Supplementary files format and content: CombinedID.merged.r2.norm.[pos/neg].bw files are RPM-normalized genomic non-chimeric read coverage Bigwig files. Pos/neg indicates mapping to positive or negative strand.
Supplementary files format and content: reverse_mir_alignments.filtered.chimeric_candidates.STARAligned.outSo.rmDup.norm.[pos/neg].bw files are RPM-normalized coverage Bigwig files for the mRNA portion of chimeric reads. Pos/neg indicates mapping to positive or negative strand.
Supplementary files format and content: reverse_mir_alignments.filtered.chimeric_peaks.bed file includes locations of chimeric read clusters (“peaks”) called using the CLIPper algorithm (https://github.com/YeoLab/clipper). The BED file contains the following tab-separated columns: Chromosome, Start position, Stop position, miRNA name, RPM coverage of chimeric reads, Strand (+ or -)

source_name: miR-eCLIP size-matched input of human MCF10A cells treated with hsa-miR-28-5p and hsa-miR-708-5p mimics

growth_protocol: MCF10A cells were seeded at a density of 3.5 million cells into 15 cm dishes for 48 h.

extract_protocol:
Treated cells were washed with 1X PBS, then crosslinked using a using 254nm UV-C Mercury bulb at 400 mJ/cm^2. Cells were scraped, combined, flash frozen, and sent to Eclipse Bioinnovations (San Diego, 92121 CA, USA).
Library construction was performed by Eclise Bioinnovations. No modifications were made to the published miR-eCLIP methodology for this experiment. 30 ug of total RNA was used per sample.

treatment_protocol: Seeded MCF10A cells were transfected with 30 nM hsa-miR-28-5p or hsa-miR-708-5p microRNA mimics (Dharmacon/Horizon Discovery) for 27 h.

value: breast epithelial cells

tag: protocol

value: miR-eCLIP

value: MIR-28 mimics


title: Day 3 Null, Day3 Cre+, Day 14 Null, and Day14 Cre+ GEXPool

first: Sankarasubramanian

last: Jagadesan

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

description: 10X Genomics

data_processing:
The CellPlex data were demultiplexed using Cell Ranger software v7.0.0
The cell count were analyzed using cellranger multi (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi) using CMO constructs and associated barcodes (D3Null = CMO309, D3CRU = CMO308, D14Null = CMO307, D14CRU = CMO305)
Assembly: mm10
Supplementary files format and content: H5 files were created using cellranger multi to get the general multiplexing and demultiplexed output per samples

molecule: cytoplasmic RNA

growth_protocol: To model infectious complications following prosthetic joint surgery, a mouse model of S. aureus PJI was used. Mice were anesthetized using ketamine/xylazine prior to an initial incision made through the quadriceps. A secondary incision was then created to laterally displace the patellar tendon prior to generating a burr hole in the distal end of the femur using a 26-gauge needle. An orthopedic-grade nickel-titanium Kirschner wire (0.6 mm diameter; Custom Wire Technologies) was inserted through the burr hole into the medullary canal, whereupon 103 colony-forming units (CFUs) of S. aureus were inoculated at the tip of the wire. Slow-release Buprenex was administered subcutaneously following surgery to provide analgesia for 72 h. Mice were monitored daily to ensure normal ambulatory function and the lack of discernable pain behaviors.

extract_protocol: To recover CD45+ cells from the soft tissue surrounding the infected joint by FACS, tissue homogenates were filtered, and red blood cells (RBCs) were eliminated by rapid lysis in H2O, with isotonic conditions returned with the addition of 10X PBS. Next, cells were incubated with TruStain FcX (BioLegend) prior to staining with CD45-APC (RRID: AB_312977), Ly6G-PE (RRID: AB_1186099), CD11b-FITC (RRID: AB_312789), F4/80-PE-Cy7 (RRID: AB_893490), and Ly6C-PerCP-Cy 5.5 (Cat. #560525; BD). Dead cells were excluded from analysis using a Zombie UV fixable Live/Dead stain (Cat. #423108; BioLegend).

value: infected joint tissue

value: CD45+ cells


title: Day 3 Null, Day3 Cre+, Day 14 Null, and Day14 Cre+ CMOPool

description: 10X Genomics


title: Yale_mir708_IP_S19

source_name: miR-eCLIP immunoprecipitation (IP) of human MCF10A cells treated with hsa-miR-28-5p and hsa-miR-708-5p mimics


title: Atrial_hPSC_CM_CUT&RUN_H3K4me3_2

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description: Ctrl_K4me3_2.ACACGATC_ATGGTATT.sam.tagdir.ucsc.bigWig

data_processing:
Reads were mapped to the human genome (GRCh38) using Bowtie2 with default paired-end settings. Next, all non-nuclear and unmapped paired reads were discarded. Duplicated reads were removed with the picard MarkDuplicates function, default settings. Visualization of ATAC-seq signals was done with Homer, and all reads were normalized by read count where scores represent read count per bp per 1 x 107 reads.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

source_name: hPSC-CM

extract_protocol:
50,000 Atrial iPS-CMs were used as input for ATAC-seq, following the OMNI-ATAC-seq protocol (PMID: 28846090). Transposed DNA was purified with a Qiagen PCR MinElute kit (Qiagen 28004).
And final ATAC-seq libraries were purified with a 1.8X SPRI purification using SPRISelect beads (Beckman Coulter) beads following PCR amplification. Libraries were sequenced on an Illumina Nextseq 500.

value: hPSC-CM

value: atrial cardiomyocyte

value: wt

tag: chip antibody


title: GM-MOI-36h-D4

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

description: RNA from monocyte-derived macrophages 36 hours after cultured with SARS-CoV-2

data_processing:
BGISEQ-500 platform
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 6 days in the presence of 1000 U/ml GM-CSF to generate GM-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Monocyte-derived macrophages were cultured with SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1), their VLPs or untrateated. After 4, 12 and 36 hours, cells were lysed and RNA isolated for transcriptional analysis.

value: macrophages

value: Monocyte-derived GM-CSF macrophages

value: Cultured with SARS-CoV-2


title: CC2D2AT8_2, biol rep 2

value: induced pluripotent stem cells

value: cerebellar granule cells differentiation

value: day 8


title: PB02011_tumor_roi001_Fibrosis

description: protein detected by antibody

extract_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: fibrous tissue enriched

value: SMA

value: progressive disease (PD)


title: GM-MOI-36h-D3


title: CC2D2AT24_1, biol rep 1

value: CC2D2A mutant:c.3856T>C;c.3856T>C

value: day 24


title: GM-MOI-36h-D2


title: GM-MOI-36h-D1


title: Atrial_hPSC_CM_CUT&RUN_H3K4me3_1


title: PB02011_tumor_roi007_Rest_F

description: protein detected by antibody

value: tumor


title: PB02011_liver_roi006_BileDuct

description: protein detected by antibody

value: liver

value: bile duct

value: PanCK


title: PB02011_tumor_roi007_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: GM-MOI-12h-D4

description: RNA from monocyte-derived macrophages 12 hours after cultured with SARS-CoV-2


title: CC2D2AT8_1, biol rep 1


title: Atrial_hPSC_CM_ATAC_1

data_processing:
Reads were mapped to the human genome (GRCh38) using Bowtie2 with default paired-end settings. Next, all non-nuclear and unmapped paired reads were discarded. Duplicated reads were removed with the picard MarkDuplicates function, default settings. Visualization of ATAC-seq signals was done with Homer, and all reads were normalized by read count where scores represent read count per bp per 1 x 107 reads.
Assembly: hg38
Supplementary files format and content: BigWig

value: hPSC-CM

value: atrial cardiomyocyte

value: wt


title: PB02011_liver_roi006_ImmuneCell

description: protein detected by antibody


title: GM-MOI-12h-D3

value: macrophages

value: Monocyte-derived GM-CSF macrophages

value: Cultured with SARS-CoV-2


title: PB02011_liver_roi006_Rest_F

description: protein detected by antibody


title: CTRL1T8_2, biol rep 2

value: induced pluripotent stem cells

value: WT

value: cerebellar granule cells differentiation

value: day 8


title: CC2D2AT8_3, biol rep 3

value: CC2D2A mutant:c.3856T>C;c.3856T>C


title: Atrial_hPSC_CM_ATAC_2


title: TMEM67T24_3, biol rep 3

value: TMEM mutant:c.755T>C;c.1769T>C

value: day 24


title: CC2D2AT24_2, biol rep 2


title: TMEM67T8_3, biol rep 3


title: OM (NCC+MK),  24 replicates, scRNA-seq 24

city: Boston

first: Safa

middle: F

last: Mohamad

address: 125 Park Drive, Apt 15

institute: Boston Children's Hospital/ Harvard Medical School

description:
Fluidigm single cell auto-prep system
024771_Plate-3-B7_S144_run568

data_processing:
Cluster analysis was conducted using Seurat with default parameters [25867923]. Differential gene expression analysis was conducted by an in-house method LTMG-DGE [https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz655/5542876] with p<0.001 as significance cutoff.
Assembly: UCSC mm10
Supplementary files format and content: Gene counts for each sample in spreadsheet

source_name: Primary osteomacs

growth_protocol: 1x105 NCC were cultured for 16hrs with or without 50,000 megakaryocytes in A-MEM supplemented with 10% FBS and 1% Penstrep

extract_protocol:
Cultured cells were trypsinized and sorted fo Osteomas which were CD45+F4/80+CD41-
Up to 0.4ng cDNA was used for library preparation and indexing with Nextera XT DNA Library Prep Kit

treatment_protocol: NCC were cultured with or without megakaryocytes

value: Primary osteomacs

value: without megakaryocytes


title: OM (NCC+MK),  24 replicates, scRNA-seq 22

description:
Fluidigm single cell auto-prep system
024769_Plate-3-E6_S142_run568


title: GM-MOI-12h-D2


title: PB02011_liver_roi005_nonTumorLiver

description: protein detected by antibody

value: liver

value: non-tumor liver

value: progressive disease (PD)


title: OM (NCC+MK),  24 replicates, scRNA-seq 23

description:
Fluidigm single cell auto-prep system
024770_Plate-3-F6_S143_run568


title: TMEM67T24_2, biol rep 2


title: GM-MOI-12h-D1


title: OM (NCC+MK),  24 replicates, scRNA-seq 20

description:
Fluidigm single cell auto-prep system
024767_Plate-3-C6_S140_run568


title: TMEM67T24_1, biol rep 1


title: OM (NCC+MK),  24 replicates, scRNA-seq 21

description:
Fluidigm single cell auto-prep system
024768_Plate-3-D6_S141_run568


title: PB02011_tumor_roi007_PanCK_T

description: protein detected by antibody

value: tumor

value: cancer cell enriched

value: PanCK


title: TMEM67T8_2, biol rep 2


title: OM (NCC+MK),  24 replicates, scRNA-seq 19

description:
Fluidigm single cell auto-prep system
024766_Plate-3-B6_S139_run568


title: TMEM67T8_1, biol rep 1


title: GM-MOI-4h-D3

description: RNA from monocyte-derived macrophages 4 hours after cultured with SARS-CoV-2

value: macrophages

value: Monocyte-derived GM-CSF macrophages


title: PB02011_liver_roi005_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: PB02011_tumor_roi004_Rest_F

description: protein detected by antibody

value: fibrous tissue enriched


title: PB02011_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB02011_tumor_roi004_ImmuneCell

description: protein detected by antibody


title: OM (NCC+MK),  24 replicates, scRNA-seq 17

description:
Fluidigm single cell auto-prep system
024764_Plate-3-D5_S137_run568


title: CPLANET8_3, biol rep 3

value: induced pluripotent stem cells

value: CPLANE mutant:c.3868T>C;c.C7477T

value: cerebellar granule cells differentiation


title: GM-MOI-4h-D2

value: Cultured with SARS-CoV-2


title: GM-MOCK-36h-D4

description: RNA from monocyte-derived macrophages 36 hours after cultured with VLPs

value: Cultured with VLPs


title: GM-MOI-4h-D1


title: CPLANET24_2, biol rep 2

value: day 24


title: GM-MOI-4h-D4


title: PB02011_tumor_roi003_CancerCell

description: protein detected by antibody


title: OM (NCC+MK),  24 replicates, scRNA-seq 15

description:
Fluidigm single cell auto-prep system
024762_Plate-3-F4_S135_run568

value: Primary osteomacs

value: without megakaryocytes


title: GM-MOCK-36h-D3


title: PB02011_tumor_roi002_Rest_F

description: protein detected by antibody


title: CPLANET8_2, biol rep 2

value: day 8


title: GM-MOCK-36h-D1


title: PB02011_tumor_roi002_PanCK_T

description: protein detected by antibody

value: progressive disease (PD)


title: OM (NCC+MK),  24 replicates, scRNA-seq 13

description:
Fluidigm single cell auto-prep system
024760_Plate-3-D4_S133_run568


title: OM (NCC+MK),  24 replicates, scRNA-seq 14

description:
Fluidigm single cell auto-prep system
024761_Plate-3-E4_S134_run568


title: PB02011_tumor_roi001_CancerCell

description: protein detected by antibody

value: tumor


title: CPLANET24_1, biol rep 1


title: GM-MOCK-12h-D4

description: RNA from monocyte-derived macrophages 12 hours after cultured with VLPs


title: PB02011_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: OM (NCC+MK),  24 replicates, scRNA-seq 18

description:
Fluidigm single cell auto-prep system
024765_Plate-3-E5_S138_run568


title: CPLANET8_1, biol rep 1


title: PB02012_tumor_roi001_ImmuneCell

description: protein detected by antibody

value: stable disease (SD)


title: GM-MOCK-12h-D3


title: CPLANET24_3, biol rep 3


title: CTRL1T24_1, biol rep 1

value: WT


title: OM (NCC+MK),  24 replicates, scRNA-seq 16

description:
Fluidigm single cell auto-prep system
024763_Plate-3-B5_S136_run568


title: OM (NCC+MK),  24 replicates, scRNA-seq 12

description:
Fluidigm single cell auto-prep system
024759_Plate-3-B4_S132_run568


title: OM (NCC+MK),  24 replicates, scRNA-seq 11

description:
Fluidigm single cell auto-prep system
024758_Plate-3-F3_S131_run568


title: GM-MOCK-12h-D2

value: macrophages


title: CTRL2T24_3, biol rep 3


title: OM (NCC+MK),  24 replicates, scRNA-seq 10

description:
Fluidigm single cell auto-prep system
024757_Plate-3-D3_S130_run568


title: CTRL2T8_3, biol rep 3


title: PB02012_tumor_roi001_Rest_F

description: protein detected by antibody


title: PB02012_tumor_roi001_PanCK_T

description: protein detected by antibody

value: cancer cell enriched

value: PanCK


title: GM-MOCK-12h-D1

value: Monocyte-derived GM-CSF macrophages


title: CTRL2T24_2, biol rep 2

value: induced pluripotent stem cells


title: OM (NCC+MK),  24 replicates, scRNA-seq 9

description:
Fluidigm single cell auto-prep system
024756_Plate-3-C3_S129_run568


title: GM-MOCK-4h-D4

description: RNA from monocyte-derived macrophages 4 hours after cultured with VLPs


title: GM-MOCK-36h-D2


title: PB02012_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: CTRL2T8_2, biol rep 2

value: cerebellar granule cells differentiation


title: GM-MOCK-4h-D3


title: OM (NCC+MK),  24 replicates, scRNA-seq 7

description:
Fluidigm single cell auto-prep system
024753_Plate-3-C2_S126_run568


title: OM (NCC+MK),  24 replicates, scRNA-seq 8

description:
Fluidigm single cell auto-prep system
024754_Plate-3-D2_S127_run568


title: PB02012_tumor_roi003_PanCK_T

description: protein detected by antibody


title: PB02012_tumor_roi002_Rest_F

description: protein detected by antibody

value: fibrous tissue enriched


title: OM (NCC+MK),  24 replicates, scRNA-seq 6

description:
Fluidigm single cell auto-prep system
024752_Plate-3-B2_S125_run568


title: GM-MOCK-4h-D1

value: Cultured with VLPs


title: CTRL2T8_1, biol rep 1


title: OM (NCC+MK),  24 replicates, scRNA-seq 5

description:
Fluidigm single cell auto-prep system
024751_Plate-3-F1_S124_run568


title: PB02012_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: OM (NCC+MK),  24 replicates, scRNA-seq 4

description:
Fluidigm single cell auto-prep system
024750_Plate-3-E1_S123_run568


title: CTRL1T8_1, biol rep 1


title: GM-UNT-36h-D4

description: RNA from monocyte-derived macrophages 36 hours after cultured without virus

value: untreated


title: AHI1T24_3, biol rep 3

value: AHI1 mutant:c.1123A>C;c.1997A>T

value: day 24


title: GM-UNT-36h-D3


title: OM (NCC+MK),  24 replicates, scRNA-seq 3

description:
Fluidigm single cell auto-prep system
024749_Plate-3-D1_S122_run568

value: Primary osteomacs

value: without megakaryocytes


title: AHI1T8_3, biol rep 3

value: day 8


title: PB02012_tumor_roi003_Rest_F

description: protein detected by antibody

value: tumor

value: stable disease (SD)


title: OM (NCC+MK),  24 replicates, scRNA-seq 2

description:
Fluidigm single cell auto-prep system
024748_Plate-3-B1_S121_run568


title: GM-UNT-36h-D2

value: macrophages


title: AHI1T24_2, biol rep 2


title: PB02012_tumor_roi004_Rest_F

description: protein detected by antibody


title: PB02012_tumor_roi004_ImmuneCell

description: protein detected by antibody


title: GM-MOCK-4h-D2


title: CTRL2T24_1, biol rep 1

value: WT


title: GM-UNT-36h-D1


title: OM (NCC+MK),  24 replicates, scRNA-seq 1

description:
Fluidigm single cell auto-prep system
024755_Plate-3-E2_S128_run568


title: AHI1T8_2, biol rep 2


title: GM-UNT-12h-D4

description: RNA from monocyte-derived macrophages 12 hours after cultured without virus


title: OM (NCC+MK), 20 replicates, scRNA-seq 20

description:
Fluidigm single cell auto-prep system
024670_Plate-7-F5_S43_run568

value: with megakaryocytes


title: PB02012_liver_roi005_nonTumorLiver

description: protein detected by antibody

value: liver

value: non-tumor liver


title: PB02012_liver_roi006_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: AHI1T24_1, biol rep 1

value: induced pluripotent stem cells

value: cerebellar granule cells differentiation


title: GM-UNT-12h-D3

value: Monocyte-derived GM-CSF macrophages


title: OM (NCC+MK), 20 replicates, scRNA-seq 18

description:
Fluidigm single cell auto-prep system
024654_Plate-7-E1_S27_run568


title: cells sgMFSD7C4

city: JiNan

first: Kaige

last: Lyu

state: ShanDong

address: SCHOOL OF PHARMACY ROOM 612, NEW SCIENTIFIC RESEARCH BUILDING OF PHARMACY  NO.44 WENHUA XI ROAD JINAN SHANDONG 250012 CHINA

institute: ShanDong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Assembly: hg38 and GRCm38
Supplementary files format and content: gene_fpkm.text

source_name: HuLEC-5A cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: HuLEC-5A cells


title: GM-UNT-12h-D1

value: untreated


title: PB02012_liver_roi006_Rest_F

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

description: protein detected by antibody

value: fibrous tissue enriched


title: PB02003_tumor_roi004_CancerCell

description: protein detected by antibody

value: cancer cell enriched

value: progressive disease (PD)


title: OM (NCC+MK), 20 replicates, scRNA-seq 17

description:
Fluidigm single cell auto-prep system
024674_Plate-7-F6_S47_run568

value: Primary osteomacs


title: cells sgMFSD7C3


title: PB02012_liver_roi005_Fibrosis

description: protein detected by antibody

value: SMA


title: GM-UNT-4h-D4

description: RNA from monocyte-derived macrophages 4 hours after cultured without virus


title: PB02012_liver_roi005_ImmuneCell

description: protein detected by antibody

value: stable disease (SD)


title: OM (NCC+MK), 20 replicates, scRNA-seq 16

description:
Fluidigm single cell auto-prep system
024673_Plate-7-E6_S46_run568


title: cells sgMFSD7C2


title: OM (NCC+MK), 20 replicates, scRNA-seq 15

description:
Fluidigm single cell auto-prep system
024672_Plate-7-D6_S45_run568


title: PB02003_tumor_roi005_ImmuneCell

description: protein detected by antibody

value: tumor


title: cells sgControl4

value: WT


title: GM-UNT-4h-D3

value: macrophages


title: PB02003_tumor_roi005_Rest_F

description: protein detected by antibody


title: OM (NCC+MK), 20 replicates, scRNA-seq 14

description:
Fluidigm single cell auto-prep system
024671_Plate-7-B6_S44_run568

value: with megakaryocytes


title: GM-UNT-4h-D2


title: cells sgControl3


title: GM-UNT-4h-D1


title: cells sgControl2


title: GM-UNT-12h-D2


title: OM (NCC+MK), 20 replicates, scRNA-seq 19

description:
Fluidigm single cell auto-prep system
024662_Plate-7-E3_S35_run568


title: AHI1T8_1, biol rep 1

value: AHI1 mutant:c.1123A>C;c.1997A>T

value: day 8


title: M-CSF-derived macrophages 36 hours after transfection with MAFB-specific  siRNA and exposed to SARS-COV-2, rep3

data_processing:
BGISEQ-500 platform
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 6 days in the presence of 1000 U/ml GM-CSF or 10ng/ml M-CSF to generate GM- and M-CSF-polarized macrophages.

treatment_protocol: Monocyte-derived macrophages (at day 6 along the differentiation protocol) were transfected with MAFB-specific siRNA or control siRNA, kept in culture for 6 hours, and then cultured (or not) with SARS-CoV-2. After 36hours, cells were lysed and RNA isolated for transcriptional analysis.

value: Monocyte-derived M-CSF macrophages

value: MAFB knockdown

value: MAFB-specific siRNA; Cultured with SARS-CoV-2


title: PB02003_tumor_roi006_CancerCell

description: protein detected by antibody


title: PB02003_tumor_roi006_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: OM (NCC+MK), 20 replicates, scRNA-seq 12

description:
Fluidigm single cell auto-prep system
024667_Plate-7-C5_S40_run568


title: M-CSF-derived macrophages 36 hours after transfection with MAFB-specific  siRNA and exposed to SARS-COV-2, rep2


title: PB02003_tumor_roi006_Fibrosis

description: protein detected by antibody


title: PB02003_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: cells sgControl1

value: HuLEC-5A cells


title: M-CSF-derived macrophages 36 hours after transfection with MAFB-specific  siRNA and exposed to SARS-COV-2, rep1


title: hTERT RPE-1 cells (miR-708, BR3)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt

data_processing:
Adapters were trimmed using CutAdapat 1.12 with default parameters.
Trimmed reads were aligned to the hg38 genome assembly using HISAT 2.1.0 with default parameters.
Aligned reads were quantified with the RefSeq Transcripts 93 annotation using the Partek Flow E/M (expectation maximization) script with default parameters.
Quantified reads were subjected to differential expression analysis using the Partek Flow implementation of DESeq2 with default parameters.
Assembly: hg38
Supplementary files format and content: counts.txt: DESeq2 normalized read counts for indicated cell line samples.
Supplementary files format and content: gsa_result.txt: DESeq2 differential expression quantification/statistics for indicated cell line samples.

source_name: hTERT RPE-1

growth_protocol: Cells were seeded at a density of 100,000 cells/well in 6-well plates and grown in appropriate medium.

extract_protocol:
RNA was harvested using TRIzol according to the manufacturer's instructions.
The Yale Center for Genomic Analysis synthesized the PolyA+ mRNA library following Illumina mRNA sample preparation guidelines and also performed paired-end RNA sequencing using the Illumina HiSeq/NovaSeq sequencing system.

treatment_protocol: Cells were treated for 72 h with 30 nM non-targeting siRNA (siNT) or MIR-28 microRNA mimics (hsa-miR-28-5p or hsa-miR-708-5p) from Dharmacon/Horizon Discovery.

value: hTERT RPE-1

value: retinal pigment epithelial cells


title: PB02003_tumor_roi001_CancerCell

description: protein detected by antibody

value: cancer cell enriched

value: progressive disease (PD)


title: hTERT RPE-1 cells (miR-28, BR3)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: OM (NCC+MK), 20 replicates, scRNA-seq 9

description:
Fluidigm single cell auto-prep system
024664_Plate-7-D4_S37_run568

value: Primary osteomacs


title: GM-CSF-derived macrophages 36 hours after transfection with MAFB-specific  siRNA and exposed to SARS-COV-2, rep3

value: Monocyte-derived GM-CSF macrophages


title: OM (NCC+MK), 20 replicates, scRNA-seq 13

description:
Fluidigm single cell auto-prep system
024669_Plate-7-E5_S42_run568


title: OM (NCC+MK), 20 replicates, scRNA-seq 8

description:
Fluidigm single cell auto-prep system
024661_Plate-7-C3_S34_run568


title: GM-CSF-derived macrophages 36 hours after transfection with MAFB-specific  siRNA and exposed to SARS-COV-2, rep2


title: hTERT RPE-1 cells (siNT, BR3)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt

value: siNT


title: GM-CSF-derived macrophages 36 hours after transfection with MAFB-specific  siRNA and exposed to SARS-COV-2, rep1


title: PB02003_tumor_roi002_Fibrosis

description: protein detected by antibody

value: tumor

value: fibrous tissue enriched

value: SMA


title: cells sgMFSD7C1


title: hTERT RPE-1 cells (miR-708, BR2)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: OM (NCC+MK), 20 replicates, scRNA-seq 6

description:
Fluidigm single cell auto-prep system
024659_Plate-7-F2_S32_run568

value: with megakaryocytes


title: M-CSF-derived macrophages 36 hours after transfection with MAFB-specific siRNA, rep3

value: macrophages

value: MAFB-specific siRNA; untreated


title: OM (NCC+MK), 20 replicates, scRNA-seq 7

description:
Fluidigm single cell auto-prep system
024660_Plate-7-B3_S33_run568


title: hTERT RPE-1 cells (miR-28, BR2)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: PB02003_tumor_roi003_Fibrosis

description: protein detected by antibody


title: PB02003_tumor_roi002_CancerCell

description: protein detected by antibody


title: PB02003_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: M-CSF-derived macrophages 36 hours after transfection with MAFB-specific siRNA, rep2

value: Monocyte-derived M-CSF macrophages

value: MAFB knockdown


title: OM (NCC+MK), 20 replicates, scRNA-seq 11

description:
Fluidigm single cell auto-prep system
024666_Plate-7-B5_S39_run568


title: OM (NCC+MK), 20 replicates, scRNA-seq 10

description:
Fluidigm single cell auto-prep system
024665_Plate-7-F4_S38_run568


title: OM (NCC+MK), 20 replicates, scRNA-seq 5

description:
Fluidigm single cell auto-prep system
024658_Plate-7-E2_S31_run568


title: hTERT RPE-1 cells (siNT, BR2)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: M-CSF-derived macrophages 36 hours after transfection with MAFB-specific siRNA, rep1


title: PB02003_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: hTERT RPE-1 cells (miR-708, BR1)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: GM-CSF-derived macrophages 36 hours after transfection with MAFB-specific siRNA, rep3


title: PB02003_tumor_roi003_CancerCell

description: protein detected by antibody


title: OM (NCC+MK), 20 replicates, scRNA-seq 3

description:
Fluidigm single cell auto-prep system
024655_Plate-7-F1_S28_run568


title: OM (NCC+MK), 20 replicates, scRNA-seq 4

description:
Fluidigm single cell auto-prep system
024657_Plate-7-D2_S30_run568


title: PB02003_tumor_roi004_ImmuneCell

description: protein detected by antibody


title: hTERT RPE-1 cells (miR-28, BR1)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: GM-CSF-derived macrophages 36 hours after transfection with MAFB-specific siRNA, rep2


title: OM (NCC+MK), 20 replicates, scRNA-seq 2

description:
Fluidigm single cell auto-prep system
024653_Plate-7-C1_S26_run568


title: hTERT RPE-1 cells (siNT, BR1)

description:
counts_RPE-1.txt
gsa_result_RPE-1.txt


title: PB02003_tumor_roi004_Fibrosis

description: protein detected by antibody


title: OM (NCC+MK), 20 replicates, scRNA-seq 1

description:
Fluidigm single cell auto-prep system
024652_Plate-7-B1_S25_run568


title: PB02015_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: AML5-S767_Rep3

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description: OCI-AML5 treated with 1 uM S767 - Replicate #3

data_processing:
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 32 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 32 using reverse strand orientation
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

growth_protocol: OCI-AML5 cell line was cultured in aMEM, 10% heat-inactivated FBS supplemented with 10 ng/mL GM-CSF.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy Micro columns (Qiagen)
ssRNA-seq; cDNA libraries were prepared from total RNA using a PolyA selection and the NEB mRNA stranded kit and were further amplified for sequencing.

treatment_protocol: OCI-AML5 cells were treated for 24 hours with DMSO or 1 uM of S767

value: Acute myeloid leukemia

value: 24 hours with 1 uM of S767


title: AML5-S767_Rep2

description: OCI-AML5 treated with 1 uM S767 - Replicate #2


title: M-CSF-derived macrophages 36 hours after transfection with a control siRNA and exposed to SARS-COV-2, rep3

value: WT

value: Control siRNA; Cultured with SARS-CoV-2


title: AML5-S767_Rep1

description: OCI-AML5 treated with 1 uM S767 - Replicate #1


title: Polycomb knockdownH3k4me3

city: Palo Alto

first: Sedona

middle: Eve

last: Murphy

state: California

address: 279 campus dr

institute: Stanford University

data_processing:
Libraries were demultiplexed with bcl2fastq
Libraries were concatenated.
Libraries were then aligned to mm10 using bowtie2
Coverage tracks were generated with bamCoverage
All analyses were performed on the Galaxy community platform.
Assembly: mm10
Supplementary files format and content: Aligned reads in BigWig format
Supplementary files format and content: n/a
Library strategy: CUT&RUN

source_name: embryonic

growth_protocol: Ring1b and EED dTAG cell lines were gifted to us from Christopher Weber and the Crabtree lab and cultured as previously described 1  with the following modifications. Cells were cultured in Knockout Dulbecco’s modified Eagle’s medium (Thermo Fisher, cat. No. 10829010), 15% qualified embryonic stem cell FBS (Thermo Fisher, cat. No. 16141079), 1x GlutaMAX™ Supplement (100x) (Thermo fisher, cat. No. 16141079), 1x Gibco™ Penicillin-Streptomycin (100X)(Thermo Fisher cat. No. 15140122), 1x MEM Non-Essential Amino Acids Solution (100X)(Thermo Fisher cat. No. 11140050), and 0.1mM β-mercaptoethanol (Thermo Fisher cat. No. 21985023). ESCs were grown on 0.1% gelatin coated dishes with EmbryoMax® Primary Mouse Embryonic Fibroblasts (Sigma, PMEF-CF). For assays, mES cells were depleted of feeder cells and plated on gelatin-coated dishes. Cells were passaged every 2 days and media was changed daily.

extract_protocol:
Cut and run was performed utilizing the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, 14-1048). In brief, 0.25 million cells per sample were collected via trypsinization and captured with activated ConA beads. Cells were permeabilized with 0.05% digitonin. 0.5ug antibody targeting the HA tag (Epicypher, cat. No. 13-2010) on Ring1B was used. IgG (negative) and H3k4me3 (positive) control antibodies were included in the kit.  DNA was cleaved with PAG-MNASE and released to solution.
Purified DNA was library prepped with the  CUTANA™ CUT&RUN Library Prep Kit (Epicypher, cat. No. 14-1001).

treatment_protocol: To degrade EED and RING1b, dTAG-13 was added for 8 h at 5 × 10−11 M.

value: embryonic

value: TC1(129) RING1B/EED degron

value: mESC

value: 8 hour dTAG


title: Polycomb knockdown IgG


title: Polycomb knockdown HA-RING1B


title: M-CSF-derived macrophages 36 hours after transfection with a control siRNA and exposed to SARS-COV-2, rep2


title: PB02015_tumor_roi002_Rest_F

city: Dallas

institute: University of Texas Southwestern Medical Center

description: protein detected by antibody

treatment_protocol: Pre-treatment tumor and liver biopsy tissues were obtained from patients with unresectable hepatocellular carcinoma trated with bavituximab and pembrolizumab.

value: tumor

value: progressive disease (PD)


title: M-CSF-derived macrophages 36 hours after transfection with a control siRNA and exposed to SARS-COV-2, rep1


title: Untreated HA-RING1B

value: NT


title: GM-CSF-derived macrophages 36 hours after transfection with a control siRNA and exposed to SARS-COV-2, rep3

value: Monocyte-derived GM-CSF macrophages


title: AML5-DMSO_Rep3

description: OCI-AML5 treated with DMSO (control) - Replicate #3

value: 24 hours with DMSO


title: AML5-DMSO_Rep2

description: OCI-AML5 treated with DMSO (control) - Replicate #2


title: Untreated H3k4me3


title: GM-CSF-derived macrophages 36 hours after transfection with a control siRNA and exposed to SARS-COV-2, rep2

value: macrophages


title: Untreated IgG


title: AML5-DMSO_Rep1

description: OCI-AML5 treated with DMSO (control) - Replicate #1


title: PB02015_tumor_roi002_BileDuct

description: protein detected by antibody

value: bile duct

value: PanCK


title: PB02004_tumor_roi002_ImmuneCell

description: protein detected by antibody

value: immune cell enriched

value: partial response (PR)


title: M-CSF-derived macrophages 36 hours after transfection with a control siRNA, rep3

value: Monocyte-derived M-CSF macrophages

value: Control siRNA; untreated


title: GM-CSF-derived macrophages 36 hours after transfection with MAFB-specific siRNA, rep1

value: MAFB knockdown

value: MAFB-specific siRNA; untreated


title: PB02004_tumor_roi001_PanCK_T

description: protein detected by antibody

value: cancer cell enriched


title: PB02004_liver_roi010_nonTumorLiver

description: protein detected by antibody

value: liver

value: non-tumor liver


title: Subject_5_Blood = 303, Subject_5_Tissue = 304 (GEX)

description: 10X Genomics

data_processing:
Cell Ranger software v7.0.0 was used for basecalling, demultiplexing and initial analyses to create the single cell count matrix (Subject_1_Blood, Subject_1_Tissue, Subject_2_Blood, Subject_2_Tissue). cellranger mkfastq and cellranger count were used for this purpose with default parameters.
H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample
The CellPlex data were demultiplexed using Cell Ranger software v7.0.0
The cell count were analyzed using cellranger multi (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi) using CMO constructs and associated barcodes (Subject_5_Blood = 303, Subject_5_Tissue = 304)
Assembly: GRCh38
Supplementary files format and content: H5 files were created using cellranger multi to get the general multiplexing and demultiplexed output per samples

source_name: Blood + Periprosthetic soft tissue

extract_protocol: Leukocytes were collected from whole blood using Histopaque and periprosthetic tissue was dissociated using a mortar and pestle in ice-cold HBSS + 10% FBS to obtain a single cell suspension. The resulting cell suspensions were passed through a 70um filter to remove aggregates and processed for FACS.

value: Blood + Periprosthetic soft tissue

value: Leukocytes


title: PB02004_tumor_roi002_CancerCell

description: protein detected by antibody

value: tumor


title: GM-CSF-derived macrophages 36 hours after transfection with a control siRNA and exposed to SARS-COV-2, rep1

value: Monocyte-derived GM-CSF macrophages

value: WT

value: Control siRNA; Cultured with SARS-CoV-2


title: PB02015_tumor_roi001_CancerCell

description: protein detected by antibody

value: progressive disease (PD)


title: Subject_5_Blood = 303, Subject_5_Tissue = 304 (CMO)

description: 10X Genomics


title: SMCTRAP-Athero_71_IP

city: Kuopio

first: Aarthi

last: Ravindran

address: Neulaniementie 2, 70150 Kuopio

country: Finland

institute: University of Eastern Finland

data_processing:
Sequencing reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with the mm10 mouse genome.
Assembly: mm10
Supplementary files format and content: raw count matrix

source_name: Thoracic aorta

growth_protocol: The mice were housed under standard conditions with a 12-hour light/dark cycle and were given access to a rodent chow diet (Teklad Global Rodent diet 2016 for maintenance and Teklad Global Rodent 2018s while breeding) and water ad libitum.

extract_protocol:
Mice were euthanized in CO2 chamber (Metos) and the tissues were dissected while the mice were kept on ice after perfusing with ice-cold 1X PBS (Gibco). Aorta was snap-frozen using liquid nitrogen for TRAP-Seq. The frozen aortic tissue was pulverized using a TissueLyser II bead mill (QIAGEN) and added with low salt lysis buffer for homogenization. 5% of lysate was used for the bulk RNA extraction and the remaining lysate was immunoprecipitated with anti-GFP clone 19F7 and clone 19C8 antibodies. The Biotinylated Protein L (0.5 mg; Pierce #29997) and Dynabeads MyOne Streptavidin T1 (10mg/ml; Invitrogen 65602) are mixed to form bead-protein complex and capture the GFP antibodies in the samples. RNA from the lysate was extracted using RNeasy Micro Plus kit (QIAGEN, 74034).
The SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa, 634411, 634412) was used for library preparation, followed by single-end 76-bp sequencing on an Illumina NextSeq 500 instrument.

value: Thoracic aorta

tag: animal group

value: TRAP-Atherosclerosis

tag: Sex

value: Female

tag: rna fraction

value: smooth muscle cell specific ribosome-associated RNA (IP)


title: SMCTRAP-Athero_71_Input

value: total RNA extraction from the 5% of total lysate (Input)


title: M-CSF-derived macrophages 36 hours after transfection with a control siRNA, rep2

value: macrophages

value: Monocyte-derived M-CSF macrophages

value: Control siRNA; untreated

tag: time


title: PB02004_liver_roi010_ImmuneCell

description: protein detected by antibody

value: liver

value: immune cell enriched

value: partial response (PR)


title: SMCTRAP-Athero_69_IP


title: M-CSF-derived macrophages 36 hours after transfection with a control siRNA, rep1

tag: cell line


title: GM-CSF-derived macrophages 36 hours after transfection with a control siRNA, rep3

tag: cell type


title: SMCTRAP-Athero_69_Input

tag: genotype


title: PB02004_tumor_roi004_CancerCell

description: protein detected by antibody

value: cancer cell enriched


title: GM-CSF-derived macrophages 36 hours after transfection with a control siRNA, rep2

tag: treatment


title: PB02004_tumor_roi005_CancerCell

description: protein detected by antibody

tag: patient id

value: tumor


title: GM-CSF-derived macrophages 36 hours after transfection with a control siRNA, rep1

value: Monocyte-derived GM-CSF macrophages


title: PB02004_tumor_roi006_ImmuneCell

description: protein detected by antibody

tag: tissue type


title: PB02004_tumor_roi006_CancerCell

description: protein detected by antibody

tag: region of interest (roi) number


title: CDK12i.RNAseq_2

city: Guangzhou

first: Jingting

last: Li

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

institute: The First Affiliated Hospital, Sun Yat-sen University

description: RNA-Seq

data_processing:
NovaSeq S4 PE100 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek FLow, version 9.0.20.0202 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 93 2020-02-03). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Genome_build: hg19

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes and maintained in keratinocyte SFM medium (Life technologies).

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: CDK12 siRNA knockdown

tag: timepoints

value: 3 days

value: Ca2+ induced differentiation for 3 days


title: SMCTRAP-Athero_68_IP


title: OE FoxJ, repC

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
total RNA-seq
single-end

data_processing:
RNA-seq: Reads from the RNA-seq experiments were trimmed and filtered using the FASTX toolkit (v.0.10.1; http://hannonlab.cshl.edu/fastx_toolkit ). Mapping was performed using READemption (v.1.01) (Förstner et al., 2014) against the genome sequence for F. nucleatum subsp. nucleatum ATCC 23726 (NZ_CP028109.1) downloaded from the National Center for Biotechnology Information (NCBI). Differential gene expression analysis was carried using DEseq2 (v.1.18.01) (Love et al., 2014). All analysis for each was carried for biological triplicates and considered significant with a false-discovery rate ≤ 0.05.
dRNA-seq: Reads were processed and maps as described for the RNA-seq data excluding the DEseq analysis. For the prediction of transcriptional start sites (TSS) and small regulatory RNAs (sRNA), we used the modular, command-line tool ANNOgesic (Yu et al., 2018). All parameters were kept at the default setting, unless stated otherwise. Secondary TSSs were excluded if a primary TSS was within seven nucleotides distance. For annotation of 5’ untranslated regions (5’UTRs) the default settings for maximum length was corrected to 300 nt.
Term-seq: Reads were processed and maps as described for the RNA-seq data excluding the DEseq analysis.
Assembly: NZ_CP028109.1
Supplementary files format and content: wiggle files

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

source_name: bacterial culture

growth_protocol: All bacteria were grown in Columbia broth. Cells were grown to mid-exponential phase prior to harvest.

extract_protocol:
Total RNA-seq: Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95% ethanol, 5% phenol) and snap-frozen at –80°C if not directly processed. The bacterial solution was centrifuged for 20min, 4500rpm at 4°C and the supernatant was completely discarded. Cells were suspended in 600μl of 10mg/ml lysozyme in TE buffer (pH8.0) and incubated at 37°C for 10min. Next, 60μl of 10% w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64°C, 1-2min before adding 66μl 3MNaOAc, pH5.2. Next, 750μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5min. at 64°C. Samples were briefly placed on ice to cool before centrifugation for 15min, 13,000rpm at 4°C. The aqueous layer was transferred into a 2ml phase lock gel tube (Eppendorf), 750μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12min, 13,000rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3MNaOAc, pH6.5) was added and incubated overnight at -20°C. Precipitated RNA was harvested by centrifugation, washed with cold 75% v/v ethanol and air-dried. Purified RNA was resuspended in 50µl RNase-free water and stored at -80°C.
RNA-seq: For preparation cDNA library of the immunoprecipitated RNA samples, NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) was used. Briefly, 3.5 μl of RNA was mixed with 1 μl of 3’ SR Adaptor (diluted 1:10 in nuclease-free water) and incubated in a preheated thermal cycler for 2 min at 70 °C. The samples were transferred to ice and added with the premixed 3’ ligation mix (5 μl 3’ Ligation Reaction Buffer, 1.5 μl 3’ Ligation Enzyme Mix). The ligation mixture was then incubated for 1 h at 25 °C. 0.25 μl of SR RT Primer and 2.5 μl nuclease-free water were added to the mixture and incubated at 75 °C for 5 min, 37 °C for 15 min and followed by 25 °C for 15 min. To ligate the 5’ SR adaptor, the 5’ ligation mixture (0.5 μl 1:10 diluted 5’ SR Adaptor, 0.5 μl 10x 5’ ligation reaction buffer, 1.25 μl 5’ ligation enzyme mix) was added to each sample and incubated for 1 h at 25 °C. For synthesis first strand of cDNA, reverse transcription mix (4 μl first strand synthesis reaction buffer, 0.5 μl murine RNase inhibitor, 0.5 μl M-MLV reverse transcriptase) was added to each reaction and incubated for 1 h at 50 °C followed by 15 min at 70 °C to inactivate the reverse transcription reaction. 5 μl of cDNA was then proceeded to PCR amplification with the PCR mix (12.5 μl LongAmp Taq 2x master mix, 0.625 μl SR primer, 6.25 μl nuclease-free water) and 0.625 μl index (X) primer. PCR program (30s at 94°C, 15 s at 94 °C, 30 s at 62 °C and 15 s at 70 °C for 19 cycles, 5 s at 70 °C) was carried out. PCR products were mixed with 25 μl of GLII buffer and loaded on 6 % polyAcrylamide gel containing 8 M urea. After staining the gel for 10 min in 1x TBE buffer with a 1:10,000 dilution of SYBR Gold Nucleic Acid Gel Stain (Invitrogen), the bands in the range of 130- 1000 bp were cut into small pieces and transfer to a 2 ml LoBind tube. 500 μl of DNA elution buffer was added and incubated at the room temperature for 2 h. After transferring the elute and the gel debris to centrifuge tube filters (Sigma) and centrifugation (5000 rpm, 1 min), the elute was recovered by adding 1 μl liner acrylamide (NEB) and precipitating in ethanol at -80°C for 1 h. After precipitation, the pellet was washed with 80% ethanol and resuspended in 12 μl nuclease free water (NEB). 1 μl of the prepared cDNA library was subjected to Bioanalyzer analysis.  Amplified cDNAs were pooled and sequenced on an illumine NextSeq 2000 platform by the CoreUnit Sysmed from the University of Wuerzburg.
dRNA-seq: Library preparation for dRNA-seq was accomplished by Vertis Biotechnology AG. In brief, total RNA was analyzed on a Shimadzu MultiNA microchip electrophoresis system. 23S/16S ratio for all samples was 1.3. RNA was fragmented via ultrasound (4 pulses a 30 sec, 4 °C) and subsequently treated with T4 Polynucleotide Kinase (NEB). Half of the samples were then treated with terminator exonuclease (TEX) for dRNA-seq. For the cDNA synthesis, the RNA fragments were poly(A)-tailed and 5’PPP structures were removed with RNA 5’ Polyphosphatase (Epicentre). The RNA sequencing adapter with the barcodes were ligated to the 5’-monophosphate of the fragments. First strand cDNA was synthesized with an oligo(dT)-adapter primer and M-MLV reverse transcriptase. Amplification of cDNA was done via PCR to an approximate amount of 10 20 ng/µl. cDNA was purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed with Shimadzu MultiNA microchip electrophoresis. Equimolar amounts of the samples were pooled for sequencing. cDNAs had a size between 200 and 550 bp. The library pool was fractionated via differential clean-up with the Agencourt AMPure kit. The cDNA pool was checked with capillary electrophoresis as stated above.
Term-seq: The term-seq libraries were generated by first ligating the 5’ TruSeq Illumina adapter to 3’ hydroxyl ends of rRNA-depleted RNA via a probe-based approach. This RNA was used as input for first-strand cDNA synthesis using M-MLV reverse transcriptase. The cDNA was fragmented via ultrasound followed by the ligation of the 3’ TruSeq Illumina adapter. cDNA was PCR amplified with a high-fidelity DNA polymerase and purified with Agencourt AMPure XP beads (Catalogue number: A63881; Beckman Coulter Genomics). The resulting libraries were analyzed via capillary electrophoresis.

treatment_protocol: No specific treatment was applied.

tag: growth phase

value: Mid-exponential

value: WT carrying plasmid for FoxJ overexpression


title: CDK12i.RNAseq_1

description: RNA-Seq


title: CTLi.RNAseq_2

description: RNA-Seq


title: SMCTRAP-Athero_121_IP

value: Thoracic aorta

value: TRAP-Atherosclerosis


title: CTLi.RNAseq_1

description: RNA-Seq


title: OE FoxJ, repA

description:
total RNA-seq
single-end


title: PB02004_tumor_roi007_ImmuneCell

description: protein detected by antibody

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

tag: segment type

tag: positive immuno-fluorescent morphology marker

tag: radiographic objective response


title: OE ctrl, repC

description:
total RNA-seq
single-end

value: WT carrying control plasmid


title: PB02004_tumor_roi007_Rest_F

description: protein detected by antibody

value: fibrous tissue enriched


title: PB02004_tumor_roi008_ImmuneCell

description: protein detected by antibody