title: ML-2 sgC1.1, ATAC-seq

data_processing:
Raw reads were trimmed and filtered using Skewer v0.2.2.
Clean reads were aligned to hg19 using BWA v0.7.12-r1039 with the parameters -T 25 -k 18.
Mitochondrial reads were removed prior to subsequent analysis.
Normalized bigWig files were generated using bamCoverage from deepTools v3.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized (RPM) bigWig tracks

extract_protocol:
We performed ATAC-seq as previously described (Buenrostro et al., Curr Protoc Mol Biol 2015, Buenrostro et al., Nat Methods 2013). On day 3 post-transduction, 50K cells were sorted and processed via the Illumina Tagment DNA Enzyme and Buffer Kit (20034197).
Illumina libraries were constructed from the transposed DNA as previously described (Buenrostro et al., Curr Protoc Mol Biol 2015, Buenrostro et al., Nat Methods 2013), and sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).


title: noInh_soft_s4

status: Public on Oct 04 2023

type: SRA

city: Philadelphia

first: Richard

middle: K

last: Assoian

address: 421 Curie Blvd

department: Systems Pharmacology

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Salmon (https://combine-lab.github.io/salmon/) was used to count the data against the transcriptome defined inGencodevM28, which was built on the genome GRCm39.
Assembly: Genecode vM28
Supplementary files format and content: csv file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: mouse embryo fibroblasts

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and further purified with an RNeasy kit (74106, Qiagen)
TruSeq RNA Stranded mRNA (Illumina) and PE100

treatment_protocol: Spontaneously immortalized MEFs pre-incubated with EHT1864 (Rac inhibitor), CT04 (Rho inhibitor), or vehicle (untreated control) were plated on soft (2-4 kPa) or stiff (20-25 kPa) fibroenctin-coated polyacrylamide hydrogels for 1 hr before collection, isolation of total RNA and analysis of the transcriptomes by RNASeq.

tag: group

value: control

tag: cell type

value: mouse embryo fibroblasts

tag: strain

tag: treatment

value: soft hydrogel-no inhibitor


title: B27-S1, Bd infected, Utah, Skin_rep5

city: Las Vegas

first: Sarah

last: Corey-Rivas

state: New Mexico

address: PO BOX 9000

department: Biology

institute: New Mexico Highlands University

data_processing:
Trimmomatic (ver. 0.33) was used to remove residual adapter/index sequences and quality trimming of paired reads.
Trinity (ver. 2.4.0) was used to de novo assemble trimmed read data from all forty-eight libraries. After filtering transcripts with lengths less than 500 bp from the primary assembly, the filtered transcriptome was used as the mapping reference for subsequent RNA-Seq analysis and as input for Blast analyses.
Trinity was used to align reads from each sample to the transcriptome with Bowtie2 and to determine count values using RSEM.
Supplementary files format and content: Tab-delimited txt file, raw count for each sample, from RSEM

organism: Anaxyrus boreas boreas

source_name: Skin

extract_protocol:
Tissue was harvested in RNA-later and stored at -80C. RNA was isolated from liver using the RNeasy Plus Mini Kit and isolated RNA from ventral skin using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) and homogenized tissue using a Polytron PT1600E (Kinematica AG, Bohemia, NY) or liquid nitrogen and mortar and pestle following the kit protocols. RNA quality was quantified using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and verified a minimum RIN>8 and quantity >1ug.
Stranded sequence libraries were prepared from total RNA (KAPA Stranded mRNA-Seq kit, Kappa Biosystems) and fragmentation was performed to select for larger sized inserts.

treatment_protocol: Bd challenge group was innoculated with 10^6 Bd zoospores (JEL 275) for 24 hours in Holfreter’s solution and control animals were treated with Holfreter’s solution, alone, for 24 hours. The experiment ran for 34 days before tissue was collected from euthanized animals.

tag: tissue

value: Skin

tag: Sex

value: F

tag: location

value: Utah

value: Bd infected


title: GFP+ cells, organoid, Day 20

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger pipeline (v7.0.1) was applied to generate a data matrix
Assembly: custom mm10 with EGFP and tdTomodo sequence added
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Lung

growth_protocol: Sorted GFP+ cells were seeded with 100,000 MLg fibroblasts in growth factor-reduced Matrigel on Transwell filter inserts in DMEM/F-12 containing 10% fetal bovine serum, insulin transferrin, glutamine, penicillin/streptomycin and SB 431542.

extract_protocol:
Flow cytometry sorted GFP+ cells were defined as day 0. On days 8, 13, and 20 of 3D culture, to obtain single cells, colonies were dissociated with dispase and TrypLE express. Biotinylated EpCAM Ab, anti-biotin microbeads, and MS columns were used to enrich for epithelial cells. For each time point, cells were counted, and viability was measured using an automated cell counter.
Single-cell suspensions were processed for library construction using Chromium Single Cell 3’ Reagent Kits v3.1. Briefly, cells resuspended in the reaction mix were loaded into the Chromium Single Cell Chip G, as well as the 10x Barcoded Gel Beads and the partitioning oil. The Chip G was placed into the 10x Chromium controller for cell partitioning, targeting a final number of 10 thousand cells per sample. After partition was concluded, the Gel Bead-In Emulsions were transferred to the C1000 Touch Thermal Cycler for the first phase of reverse transcription and samples proceed to library preparation following manufacturer’s instructions.

value: Lung

value: Alveolar epithelial cells

tag: genotype

tag: time

value: Day 20


title: B36-S2, Bd infected, Utah, Skin_rep6


title: ML-2 sgLUC, ATAC-seq

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: ML-2 cell line

treatment_protocol: Stable Cas9-expressing K562 and ML-2 cells were transduced with sgRNAs targeting either MYNRL15 cis-regulatory region C1 (sgC1.1) or the firefly luciferase gene (sgLUC; non-targeting control).

tag: cell line

value: Myelomonocytic leukemia

value: sgRNA against LUC (control)


title: GFP+ cells, organoid, Day 13

description: 10x Genomics

value: Day 13


title: noInh_soft_s2


title: GFP+ cells, organoid, Day 8

description: 10x Genomics

value: Day 8


title: K562 sgC1.1, ATAC-seq

source_name: K562 cell line

value: Erythroleukemia

value: sgRNA against MYNRL15 C1


title: B23-S1, Bd infected, Utah, Skin_rep4


title: B24-L1, Control group, Utah, Liver_rep4

source_name: Liver

value: Liver

value: Control


title: GFP+ cells, Day 0

description: 10x Genomics

value: Day 0


title: 311E, DMSO 96hr bio rep 2

city: Boston

first: Chris

last: French

state: MA

address: 77 avenue louis Pasteur, NRB 652

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Quality-controlled reads are aligned to the human genome (GRCh38/hg38) and to ERCC92 spike-in sequences using a splice-aware aligner (STAR89) with Ensembl. transcriptome annotations.
Differential expression (DE) analysis is performed using RUVSeq to identify unwanted variation followed by edgeR91 and/or DESeq2
Assembly: GRCm39/mm39 and GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 311E cell line

growth_protocol: HBSS + 10% FBS + 1% pen/strep + 1x glutamax

extract_protocol:
RNA was harvested using RNAeasy (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. ERCC92 spike-in RNA is added to normalize reads.
RNA libraries for RNA-seq were prepared using the Roche KAPA HyperPrep RNA RiboErase Kit following manufacturer's protocols.

value: 311E cell line

value: GEMM, esophagus mNC tumor

value: DMSO


title: K562 sgLUC, ATAC-seq


title: B22-S1, Bd infected, Utah, Skin_rep3

value: Skin

value: M

value: Utah


title: noInh_stiff_s3

value: control

value: mouse embryo fibroblasts

value: stiff hydrogel-no inhibitor


title: IH 2w, scRNAseq

city: Changsha

first: Xuejing

last: Sun

state: Hunan

address: Ton-zi po road

department: Department of Cardiology

country: China

institute: Third Xinagya Hospital

description: 10x Genomics

data_processing:
Sequencing data were processed into transcript count tables using the Cell Ranger Single Cell Software Suite version 2.2.0 by 10× Genomics (http://www.10xgenomics.com/).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every single cell

source_name: carotid artery

extract_protocol:
For isolation of single cells from remodeled vessel, mice with a murine model of intimal hyperplasia were sacrificed. To avoid and limit the blood contamination, we cut the control side of carotid artery, and transcardially perfused the mice with PBS, which flush the blood out of the aortic grafts, followed by aortic grafts harvesting from the mice. Adventitial layer of the grafts was first dissected from the medial and neointimal layers. After three times washes of PBS, grafts were cut into fine pieces and digested in digestion solutions (which consist of 1 mg/ml papain (Sigma, P4762), 0.5 mg/ml 1,4-Dithioerythritol (Sigma, D8255), 0.156 mg/ml Taurine (Sigma, T8691); 0.25 mg/ml bovine serum albumin (Sigma, A2058) in PBS) at 37 ć with reciprocal shaking for a total 40 min. Detached cells were then collected through a 40 μm cell strainer and suspended in DMEM with 10% FBS (Gibco, 10270). Cells were further stained with LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (Invitrogen, L34975) and Hoechst 33342 (Invitrogen, H3570) for 20 mins. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+/Dead Cell Stain-) were sorted into PBS with 0.04% BSA using a BD FACS ARIA II Flow Cytometer (BD Biosciences).
Libraries generated using the 10× Genomics Chromium system require a conversion step using the MGIEasy Universal Library Conversion kit (App-A) (Part Number: 1000004155) before sequencing can be performed.

treatment_protocol: Carotid artery wire injury was induced just proximal to the carotid bifurcation. Briefly, mice were anesthetized with isoflurane. The left carotid artery was exposed on the ventral side of the neck via a midline incision. The bifurcation of the right carotid artery was located, and two ligatures (surgical silk, size 6-0, Deknatel, Queens Village, NY) were placed around the external carotid artery, which was then tied off with the distal ligature. After temporarily occlusion of the internal carotid artery, a small incision was made between the two ligatures placed around the external carotid artery, and a curved, 0.014-inch (= 0.38 mm) guide wire (C-SF-15-15, Cook Belgium, NV) was passed toward the aortic arch and withdrawn three times with a rotating motion to denude endothelial cells. Ligation of the external carotid artery was applied after withdrawal of the guide wire to increase the neointimal area. The skin incision was closed with a single suture. Animals were allowed to recover and carotid arteries were harvested 14 or 28 days after the injury.

value: carotid artery

value: mouse primary tissue cells

value: male

tag: condition

value: intimal hyperplasia model

tag: Stage

value: early stage (IH 2w)


title: HO-OFT, E12.5, 5

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Sequencing reads were mapped to the reference genome (mm10, rno6) using the STAR aligner (v2.5.0c)
The mean read insert sizes and their standard deviations were calculated using Picard tools 6 (v.1.126)
The read count tables were generated using HTSeq (v0.6.0)35, normalized based on their library size factors using DESeq2. (v3.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read counts for each Sample

source_name: cardiac outflow tract

extract_protocol:
total RNAs were extracted from disected outflow tract using the RNeasy kit (Qiagen) according to the manufacture's protocol.
Sequencing libraries were prepared using low input Clontech SMART-Seq HT with Nxt HT and SMART-Seq Library Prep Kit

value: cardiac outflow tract

tag: strain background

tag: developmental stage

value: embryonic day 12.5


title: B20-S1, Bd infected, Utah, Skin_rep2

value: Bd infected


title: noInh_soft_s3

value: soft hydrogel-no inhibitor


title: wing_w1118_H3K4me2_rep2_(220614_JA_Dm_JA858)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Whole-mount CUT&Tag profiling H3K4me2 in w1118 wing discs

data_processing:
Genome_build: dm6
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked dm6 Drosophila melanogaster reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the D. melanogaster alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count dm6 track which is the fraction of counts at each base pair scaled by the size of the dm6 reference sequence (137567484) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .dm6.bw)

organism: Drosophila melanogaster

source_name: CUT&Tag

extract_protocol:
https://www.protocols.io/view/cut-amp-tag-direct-with-cutac-x54v9mkmzg3e/v3
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: whole wing disc, permeabilized with 0.1% Triton

tag: antibody

value: H3K4me2 Epicypher 13-0027


title: B27-L2, Bd infected, Utah, Liver_rep5

value: Liver

value: F


title: HO-OFT, E12.5, 3


title: wing_hephGFP_uH2A_rep1_(221109_JA_Dm_JA944)

description: CUT&Tag profiling uH2A in dissociated heph-GFP wing discs

value: wing disc from heph-GFP

value: uH2A Cell Signaling Technology 8240S


title: rhoInh_stiff_s4

value: test sample

value: mouse embryo fibroblasts

value: stiff hydrogel-CT04


title: HO-OFT, E12.5, 4


title: B23-L2, Bd infected, Utah, Liver_rep4

value: Utah


title: rhoInh_stiff_s3


title: wing_hephGFP_RNAPolIIser2phos_rep1_(221024_JA_Dm_JA924)

description: CUT&Tag profiling RNAPolIIser2phos in dissociated heph-GFP wing discs

value: RNAPolIIser2phos Cell Signaling Technology E1Z3G


title: noInh_stiff_s4

value: control

value: stiff hydrogel-no inhibitor


title: HO-OFT, E12.5, 2

value: cardiac outflow tract


title: Tau PFF treatment with PI103, D2

city: Bethesda

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

institute: NIH

data_processing:
Data quality check-a step where low confidence nucleotide base-calls can be identified and removed
Map data to reference genome – a suitable genome was chosen from publicly available genomic repositories, such as the NCBI/UCSC/Ensembl databases.
Differential gene expression analysis, where results visualize the distribution of differentially expressed genes across the samples using high-resolution and publication ready volcano plots and heatmaps.
Functional analysis by mapping the reads against publicly available protein databases, such as the Gene Ontology db (GO enrichment analysis), Kyoto Encyclopedia of Genes and Genomes db (KEGG enrichment analysis), or perform a Gene Set Enrichment Analysis (GSEA) and Protein-Protein interaction studies.
Supplementary files format and content: Excel file reporting counts and fpkms.

source_name: Brain

growth_protocol: Isolated astrocytes were cultured in a defined, serum-free base medium containing 50% neurobasal, 50% DMEM, 100 U/ml penicillin, 100 μg/ml streptomycin, 1 mM sodium pyruvate, 292 μg/ml L-glutamine, 1 x G5 supplement, and the astrocyte-required survival factor HBEGF at 5 ng/ml.

extract_protocol:
RNA isolation was performed using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was measured using Nanodrop-1000.
The polyA enrichment library preparation procedure is used for RNA library construction and it results in the construction of 250-300 bp insert cDNA library
PE150 bp strategy

treatment_protocol: Astrocytes were treated with tau PFF 200 nM together with the inhibitors specified in the sample section. Cells were incubated with a serum free medium containing 0.05% trypsin for 10 min at 25 °C. Cells were washed at least three times to remove the remaining tau. Cells were then incubated with a serum-free and protein-free medium at 37 °C in the incubator for the indicated time periods.

value: Brain

value: astrocyte

value: wt

value: Tau PFF+PI103


title: wing_hephGFP_H4K16Ac_rep2_(221109_JA_Dm_JA951)

description: CUT&Tag profiling H4K16Ac in dissociated heph-GFP wing discs

value: H4K16Ac Abcam ab109463


title: IH 4w, scRNAseq

description: 10x Genomics

value: carotid artery

value: mouse primary tissue cells

value: male

value: intimal hyperplasia model

value: late stage (IH 4w)


title: B22-L2, Bd infected, Utah, Liver_rep3

value: Liver

value: M

value: Bd infected


title: HO-OFT, E12.5, 1

value: embryonic day 12.5


title: noInh_stiff_s2

value: control

value: mouse embryo fibroblasts


title: rhoInh_stiff_s2

value: test sample

value: stiff hydrogel-CT04


title: rhoInh_stiff_s1


title: wing_w1118_H3K4me2_rep3_(220614_JA_Dm_JA859)

value: whole wing disc, permeabilized with 0.1% Triton

value: H3K4me2 Epicypher 13-0027


title: wing_hephGFP_H4K16Ac_rep1_(221109_JA_Dm_JA941)

value: wing disc from heph-GFP


title: B17-S2, Bd infected, Utah, Skin_rep1

value: Skin

value: Utah


title: noInh_stiff_s1

value: stiff hydrogel-no inhibitor


title: wing_hephGFP_uH2A_rep2_(221109_JA_Dm_JA945)

value: uH2A Cell Signaling Technology 8240S


title: B36-L1, Bd infected, Utah, Liver_rep6

value: F


title: WT-OFT, E12.5, 4

value: cardiac outflow tract


title: B20-L1, Bd infected, Utah, Liver_rep2

value: Liver


title: wing_hephGFP_H3K9me2_rep2_(221109_JA_Dm_JA947)

description: CUT&Tag profiling H3K9me2 in dissociated heph-GFP wing discs

value: H3K9me2 EMD Millipore 05-1249


title: WT-OFT, E12.5, 3


title: racInh_stiff_s3

value: stiff hydrogel-EHT1864


title: WT-OFT, E12.5, 2

value: embryonic day 12.5


title: wing_hephGFP_H3K9me2_rep1_(221109_JA_Dm_JA946)


title: E7-S1, Control group, Colorado, Skin_rep6

value: Colorado

value: Control


title: racInh_stiff_s2

value: test sample

value: mouse embryo fibroblasts


title: wing_hephGFP_H3K27me3_rep2_(221109_JA_Dm_JA949)

description: CUT&Tag profiling H3K27me3 in dissociated heph-GFP wing discs

value: H3K27me3 Cell Signaling Technology C3611B


title: WT-OFT, E12.5, 1


title: E34-S1, Control group, Colorado, Skin_rep5


title: wing_hephGFP_H3K27me3_rep1_(221109_JA_Dm_JA948)


title: testis_hephGFP_dissociated_testis_RNAPolIIser2phos_rep6_(220606_JA_Dm_JA843)

description: CUT&Tag profiling RNAPolIIser2phos in dissociated heph-GFP testis

value: sorted testis cells from heph-GFP testis dissociated with collagenase

value: RNAPolIIser2phos Cell Signaling Technology E1Z3G


title: Microglia treated with IFNgamma, LPS, SCH 58261 and 2-Cl-IB-MECA, 4

city: Barcelona

first: Rafael

last: Franco

address: Avinguda Diagonal, 643

country: Spain

institute: Universitat de Barcelona

data_processing:
Feature Counts v1.5.0-p3 software
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Microglia

extract_protocol:
extraction of total RNA with the Trizol-based method using chloroform and isopropanol to purify the RNA. Quality control was assessed by measuring the 280/260 absorption ratio and the RIN in the Services of the University of Barcelona (CCiTUB: Scientific and technological centers of the Universitat de Barcelona).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Microglia

value: Primary culture

value: WT

value: Proinflammatory components

value: Day 3


title: E16-S1, Control group, Colorado, Skin_rep2

value: Skin

value: M


title: Microglia treated with IFNgamma, LPS, SCH 58261 and 2-Cl-IB-MECA, 3


title: OPN treatment for 24 hours 3

data_processing:
Data quality check-a step where low confidence nucleotide base-calls can be identified and removed
Map data to reference genome – a suitable genome was chosen publicly available genomic repositories, such as the NCBI/UCSC/Ensembl databases.
Differential gene expression analysis, where results visualize the distribution of differentially expressed genes across the samples using high-resolution and publication ready volcano plots and heatmaps.
Functional analysis by mapping the reads against publicly available protein databases, such as the Gene Ontology db (GO enrichment analysis), Kyoto Encyclopedia of Genes and Genomes db (KEGG enrichment analysis), or perform a Gene Set Enrichment Analysis (GSEA) and Protein-Protein interaction studies.

extract_protocol:
RNA isolation was performed using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was measured using Nanodrop-1000.
The polyA enrichment library preparation procedure is used for RNA library construction and it results in the construction of 250-300 bp insert cDNA library

treatment_protocol: Astrocytes were treated with tau PFF 200 nM or 20ug/ml OPN for 6 hours or 24 hours. Cells were incubated with a serum free medium containing 0.05% trypsin for 10 min at 25 °C. Cells were washed at least three times to remove the remaining tau. Cells were then incubated with a serum-free and protein-free medium at 37 °C in the incubator for the indicated time periods.

value: Brain

value: astrocyte

value: wt

value: OPN 24h


title: OPN treatment for 24 hours 1


title: racInh_stiff_s4

value: stiff hydrogel-EHT1864


title: E12-S1, Control group, Colorado, Skin_rep1

value: Colorado

value: Control


title: testis_hephGFP_dissociated_testis_RNAPolIIser2phos_rep4_(220414_JA_Dm_JA766)


title: testis_hephGFP_dissociated_testis_RNAPolIIser2phos_rep5_(220421_JA_Dm_JA813)


title: Microglia treated with IFNgamma, LPS, SCH 58261 and 2-Cl-IB-MECA, 2


title: Microglia treated with IFNgamma, LPS, SCH 58261 and 2-Cl-IB-MECA, 1


title: B17-L1, Bd infected, Utah, Liver_rep1

value: Liver

value: Utah

value: Bd infected


title: OPN treatment for 6 hours 3

value: OPN  6h


title: testis_hephGFP_dissociated_testis_RNAPolIIser2phos_rep3_(220317_JA_Dm_JA745)

value: sorted testis cells from heph-GFP testis dissociated with collagenase

value: RNAPolIIser2phos Cell Signaling Technology E1Z3G


title: Microglia treated with IFNgamma, LPS and SCH 58261, 4

value: Microglia

value: Primary culture

value: WT

value: Proinflammatory components + 2-Cl-IB-MECA


title: E3-S1, Control group, Colorado, Skin_rep4

value: Skin

value: F


title: racInh_stiff_s1

value: test sample

value: mouse embryo fibroblasts


title: testis_hephGFP_dissociated_testis_RNAPolIIser2phos_rep2_(220224_JA_Dm_JA675)


title: Microglia treated with IFNgamma, LPS and SCH 58261, 3

value: Day 3


title: E7-L1, Control group, Colorado, Liver_rep6

value: Colorado


title: OPN treatment for 6 hours 1

value: Brain

value: astrocyte

value: wt


title: testis_hephGFP_dissociated_testis_RNAPolIIser2phos_rep1_(220224_JA_Dm_JA674)


title: E28-S1, Control group, Colorado, Skin_rep3

value: M

value: Control


title: E3-L1, Control group, Colorado, Liver_rep4

value: Liver


title: Microglia treated with IFNgamma, LPS and SCH 58261, 2


title: OPN treatment for 6 hours 2

value: OPN  6h


title: PFF treatment for 24 hours 3

value: Tau PFF 24h


title: E28-L1, Control group, Colorado, Liver_rep3


title: OPN treatment for 24 hours 2

value: OPN 24h


title: Microglia treated with IFNgamma, LPS and SCH 58261, 1

value: Microglia

value: Primary culture

value: WT


title: E16-L1, Control group, Colorado, Liver_rep2


title: testis_hephGFP_spermatocyte_uH2A_rep8_(220304_JA_Dm_JA688)

description: FACS-CUT&Tag profiling uH2A in sorted spermatocytes from heph-GFP testis

value: sorted testis cells from heph-GFP testis dissociated with collagenase

value: uH2A Cell Signaling Technology 8240S


title: testis_hephGFP_spermatocyte_uH2A_rep9_(220414_JA_Dm_JA761)


title: testis_hephGFP_spermatocyte_uH2A_rep13_(221031_JA_Dm_JA932)


title: MLL-AF9_KO2_BMSC_RNA-seq

city: Shanghai

first: Jiaying

last: Zhang

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

description:
KO2
MLL-AF9_BMSC_result.xlsx

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to mm10 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.(RNA-seq)
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).(RNA-seq)
Assembly: mm10
Supplementary files format and content: normalized files were calculated by DEseq2(1.32.0).(RNA-seq)

source_name: Bone marrow

growth_protocol: BMSC isolation and culture was performed using the whole bone marrow and bone adhesion method.

extract_protocol:
After BMSC from AML mouse were harvested, the total RNA is extracted with TRIzol Reagent.
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina NovaSeq6000.(RNA-seq)

value: Bone marrow

value: mesenchymal cell

value: BMSC

value: Id1 knockout

value: BMSC from AML bone marrow microenvironment


title: PFF treatment for 6 hours 3

value: Brain

value: astrocyte

value: wt

value: Tau PFF 6h


title: PFF treatment for 24 hours 1


title: MLL-AF9_KO1_BMSC_RNA-seq

description:
KO1
MLL-AF9_BMSC_result.xlsx


title: E12-L1, Control group, Colorado, Liver_rep1

value: Liver

value: M

value: Colorado

value: Control


title: testis_hephGFP_spermatocyte_uH2A_rep12_(221024_JA_Dm_JA927)


title: E34-L1, Control group, Colorado, Liver_rep5

value: F


title: PFF treatment for 24 hours 2

value: Tau PFF 24h


title: E8-S1, Bd infected, Colorado, Skin_rep6

value: Skin

value: Bd infected


title: MLL-AF9_WT2_BMSC_RNA-seq

description:
WT2
MLL-AF9_BMSC_result.xlsx

value: Bone marrow

value: Id1 wild type


title: testis_hephGFP_spermatocyte_uH2A_rep11_(220509_JA_Dm_JA827)

value: sorted testis cells from heph-GFP testis dissociated with collagenase

value: uH2A Cell Signaling Technology 8240S


title: PFF treatment for 6 hours 2


title: E35-S1, Bd infected, Colorado, Skin_rep5


title: PFF treatment for 6 hours 1


title: MLL-AF9_WT1_BMSC_RNA-seq

description:
WT1
MLL-AF9_BMSC_result.xlsx

value: mesenchymal cell

value: BMSC

value: BMSC from AML bone marrow microenvironment


title: E31-S1, Bd infected, Colorado, Skin_rep4


title: testis_hephGFP_spermatocyte_uH2A_rep10_(220421_JA_Dm_JA808)


title: AE9a_KO2_BMSC_RNA-seq

description:
AE9a_KO-2
AE9a_BMSC_result.xlsx

value: Id1 knockout


title: testis_hephGFP_spermatocyte_RNAPolIIser2phos_rep4_(220224_JA_Dm_JA667)

description: FACS-CUT&Tag profiling RNAPolIIser2phos in sorted spermatocytes from heph-GFP testis

value: RNAPolIIser2phos Cell Signaling Technology E1Z3G


title: E29-S1, Bd infected, Colorado, Skin_rep3


title: PBS treated control 2

value: Brain

value: astrocyte

value: wt

value: PBS


title: AE9a_KO1_BMSC_RNA-seq

description:
AE9a_KO-1
AE9a_BMSC_result.xlsx


title: testis_hephGFP_spermatocyte_RNAPolIIser2phos_rep3_(220224_JA_Dm_JA666)


title: E27-S1, Bd infected, Colorado, Skin_rep2

value: F

value: Colorado


title: AE9a_WT1_BMSC_RNA-seq

description:
AE9a_WT-1
AE9a_BMSC_result.xlsx


title: E18-S1, Bd infected, Colorado, Skin_rep1

value: Skin

value: M


title: AE9a_WT2_BMSC_RNA-seq

description:
AE9a_WT-2
AE9a_BMSC_result.xlsx

value: Bone marrow


title: testis_hephGFP_spermatocyte_RNAPolIIser2phos_rep2_(220224_JA_Dm_JA665)


title: PBS treated control 1


title: E8-L1, Bd infected, Colorado, Liver_rep6

value: Liver

value: Bd infected


title: MS_Veh_rep2

city: durham

first: Yiping

last: He

state: NC

address: 199A MSRB1, Research Drive

institute: Duke University

description: treated with DMSO for 12days

data_processing:
fastq raw data were trimmed by Tim Galore!
aligned to mm10 by Hisat2
reassembled by Stringtie
defferentially expressed genes analyzed by Deseq2

source_name: Mouse GBM cell line

extract_protocol:
E.Z.N,A, Total RNA Kit (OMEGA R6834-02)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: treated with DMSO for 12days


title: testis_hephGFP_spermatocyte_RNAPolIIser2phos_rep1_(220224_JA_Dm_JA664)

value: sorted testis cells from heph-GFP testis dissociated with collagenase


title: MS_Veh_rep1

description: treated with DMSO for 12days


title: E35-L1, Bd infected, Colorado, Liver_rep5


title: testis_hephGFP_spermatocyte_H4K16Ac_rep2_(220527_JA_Dm_JA833)

description: FACS-CUT&Tag profiling H4K16Ac in sorted spermatocytes from heph-GFP testis

value: H4K16Ac Abcam ab109463


title: C57BL/6J Dhpsfl/fl;Vil1cre/+ mice rep2

city: Nashville

first: Alain

middle: P

last: Gobert

address: 2215B Garland Ave

institute: VUMC

data_processing:
Reads were trimmed of the adapter sequences and read quality was checked using fastp
Reads were mapped to the indexed transcriptome of the GRCm38 assembly and quantified using Salmon
Transcript-level quantification was summarized to the gene-level using tximeta
Raw transcript counts were determined using the R package DESeq2. Genes that had a sinlge count or less across samples were excluded
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts of each gene for each sample

source_name: isolated epithelial cells from the colon

growth_protocol: Age-matched (8-12 weeks) male C57BL/6J Dhpsfl/fl and C57BL/6J Dhpsfl/fl;Vil1cre/+ mice were house-bred in our animal facility.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (Qiagen).
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (BioLabs, Inc.)


title: C57BL/6J Dhpsfl/fl;Vil1cre/+ mice rep3


title: MS_CW_rep2

description: treated with 1uM CW3388(sigma-aldrich cat# SML2602) for 12days


title: testis_hephGFP_spermatocyte_H4K16Ac_rep1_(220421_JA_Dm_JA814)


title: C57BL/6J Dhpsfl/fl;Vil1cre/+ mice rep1


title: E31-L1, Bd infected, Colorado, Liver_rep4


title: PBS treated control 3


title: E29-L1, Bd infected, Colorado, Liver_rep3


title: C57BL/6J Dhpsfl/fl rep3


title: MS_Cle_rep2

description: treated with 4uM clemastine (Cayman #14637)for 12days


title: testis_hephGFP_spermatocyte_H3K9me2_rep2_(220927_JA_Dm_JA909)

description: FACS-CUT&Tag profiling H3K9me2 in sorted spermatocytes from heph-GFP testis

value: H3K9me2 EMD Millipore 05-1249


title: E27-L1, Bd infected, Colorado, Liver_rep2


title: E18-L1, Bd infected, Colorado, Liver_rep1


title: C57BL/6J Dhpsfl/fl rep2


title: testis_hephGFP_spermatocyte_H3K27me3_rep1_(220317_JA_Dm_JA712)

description: FACS-CUT&Tag profiling H3K27me3 in sorted spermatocytes from heph-GFP testis

value: H3K27me3 Cell Signaling Technology C3611B


title: GN192_Vg4_biol_rep_4

status: Public on Oct 03 2023

city: London

first: Adrian

last: Hayday

address: Great Maze Pond

department: Immunobiology

country: United Kingdom

institute: King's  College London

data_processing:
The quality of the sequencing reads was examined using FastQC (v0.11.4) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Raw sequencing reads (100-nt, paired-end) were trimmed using Trimgalore (v0.4.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Traces of ribosomal DNA and mitochondrial DNA were removed using the Bowtie2 (v2.2.5) (Langmead et al., 2012).
Reads were aligned to the human reference genome GRCh38 using STAR (v2.5.3a) (Dobin et al., 2013) default setting. Duplicate reads were removed using theMarkDuplicates function of the Picard tools (v2.17.11) (http://broadinstitute.github.io/picard/).
Reads were annotated using the Partek E/M (Partek software) gene count. Differentially expressed genes (DEG) were identified using DESeq2 (v3.5)(Love et al., 2014). DEG with fold change >= 2 and FDR value <= 0.05 were used for pathway enrichment and gene ontology (GO) analysis. GO and pathway enrichment analysis was done using DAVID Bioinformatics Resources v6.8 (https://david.ncifcrf.gov/).
Assembly: GRCh38
Supplementary files format and content: Gene count and DEGs.xlsx, geme counts and DEG

source_name: Colon

extract_protocol:
Colonic biopsies from 1 donors (GN178) were used fresh. Colonic biopsies from 3 of the donors (GN188; GN190 and GN192) were defrosted. Biopsies were dissociated with Miltenyi Biotec's tumour dissociation kit, stained with  antibodies and sorted on BD FACS AriaII Cell Sorter.
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina

value: Colon

value: Vg4+ gd T cells

value: non-inflamed; non-transformed


title: GN190_Vg4_biol_rep_3


title: GN190_Vg589_biol_rep_3

value: Vg5/8/9+ gd T cells


title: GN192_Vg589_biol_rep_4


title: GN178_Vg589_biol_rep_1


title: GN188_Vg4_biol_rep_2


title: GN178_Vg4_biol_rep_1


title: Mouse_hippocampus

city: Cambridge

first: Andrew

middle: James Charles

last: Russell

address: 415 Main St

institute: Broad Institute of MIT and Harvard

description: 10x Genomics

data_processing:
We used Cell Ranger v6.1.22 mkfastq (10x Genomics, https://www.10xgenomics.com/support/software/cell-ranger) to generate demultiplexed FASTQ files from the raw sequencing reads. We aligned these reads to either the mouse mm10 genome whilst including intronic reads with --include-introns, and quantified gene counts as UMIs using Cell Ranger count (10x Genomics).
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Fresh frozen tissues were cryo-sectioned to 20 μm on a cryostat (CM1950, Leica) at -16 °C. Pre-cooled 2 mm circular (3331P/25, Integra), 3 mm circular (3332P/25, Integra), or 5.5 mm square custom-made biopsy punches were used to isolate regions of interest from tissue sections. The punched tissue regions were then placed on the puck, ensuring there were no folds. A finger was placed on the bottom of the puck to melt the tissue whilst trying to prevent rolling. Immediately this puck was placed on the glass slide and placed on ice, and 6-10 µL of dissociation buffer (82 mM Na2SO4 , 30 mM K2SO4 , 10 mM Glucose, 10mM HEPES, 5 mM MgCl2 ) was placed on top of the puck so that the buffer covered the whole puck. The puck was then placed under a UV (365 nm) light source (0.42 mW/mm2 , Thorlabs, M365LP1-C5, Thorlabs, LEDD1B) for 30 s (TAGS beads), or 3 mins (SLAC beads), in order to cleave the same amount of spatial barcode oligonucleotides between bead designs (Fig. S2h). After photo-cleavage, the puck was incubated for 7.5 mins (TAGS beads) or 5 mins (SLAC beads) and then placed into a 12-well plate (Corning, 3512). Using a 200 µL pipette, 10 x 200 µL aliquots of extraction buffer (Dissociation Buffer, 1% Kollidon VA64, 1% Triton X100, 0.01% BSA, 666 units/mL RNase-inhibitor (Biosearch technologies, 30281-1)) were dispensed onto the puck for a total volume of 2 mL. Dispensed extraction buffer was triturated up and down on the puck for 10-15 times to release the tissue. This step was repeated until the tissue was completely removed from the puck. The puck was removed, and mechanical dissociation of the supernatant was performed using 1 mL pipette 20-25 times trituration to fully dissociate the tissue. Dissociated nuclei were removed from the well and the well was rinsed twice with 1 mL of wash buffer (82 mM Na2SO4 , 30 mM K2SO4 , 10 mM Glucose, 10mM HEPES, 5 mM MgCl2 , 50 µl of RNase-inhibitor (Biosearch technologies, 30281-1)) which was added to nuclei suspension. Wash buffer was added to the tube to a final volume of 20 mL. This 20 mL was mixed and divided equally into another 50 mL falcon tube. Nuclei were spun in a pre-cooled swinging bucket centrifuge at 600 g for 10 min at 4 °C. After centrifugation, 19.5 mL of supernatant was removed, leaving 500 µL in each tube. The pellet was resuspended and pooled. This pooled suspension was then filtered using a pre-cooled 40 µm cell strainer (Corning, 431750). DAPI (Thermo Fisher Scientific, 62248) was added to the filtered solution at a 1:1000 dilution and incubated for 5-7 mins at 4 °C. This was then centrifuged at 200 g for 10 mins at 4 °C. The supernatant was removed, leaving 50 µL of pellet. The pellet was resuspended and nuclei were counted manually using a C-Chip Fuchs-Rosenthal disposable hemocytometer (INCYTO, DHC-F01-5).
For Slide-tags snRNA-seq experiments, 43.3 µL of counted nuclei were loaded into the 10x Genomics Chromium controller using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, PN-1000268). The Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein CG000317 was used according to the manufacturer’s recommendations with slight modifications. Spatial barcode libraries were prepared as Cell Surface Protein Library preparations. The number of PCR cycles used for the index PCR step in the Cell Surface Protein Library preparation (step 4.1f) for 5.5x5.5 mm TAGS arrays was 7; for 3 mm diameter TAGS arrays the number of cycles was 9. For the mouse brain sample, ligated pucks were used for spatial barcoding. For this sample, a custom PCR protocol was used instead of step 4.1: 10 uL of cleaned supernatant from step 2.3, 50 µL NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541S), 2.5 µL STAG_P701_NEX (10 uM), 2.5 µL 10 μM P5-Truseq Hybrid oligo, 35 µL UltraPure DNase/RNase-Free Distilled Water (Invitrogen, 10977015). In this sample, 10 PCR cycles were performed according to the manufacturer’s recommendations.

value: Brain


title: Mouse_E14

description: 10x Genomics


title: MT-1

city: Chapel Hill

first: Whitney

last: Edwards

address: 133 North Medical Drive

institute: University of North Carolina Chapel Hill

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
he trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: GRCm38-mm10 reference genome
Supplementary files format and content: Tab-delimited text files include raw hit counts

source_name: Heart

extract_protocol:
Embryonic hearts were dissected from embryos, cardiac RNA was harvested using RNAqueous™-Micro Total RNA Isolation Kit.
Rna-seq libraries were prepared by Azenta biosciences. Illumina, RNA with PolyA selection

value: Heart

value: Homozygous Tbx20EH1Mut

value: Collected entire heart at E9.5


title: MT-2


title: MS_CW_rep1

value: treated with 1uM CW3388(sigma-aldrich cat# SML2602) for 12days


title: MT-3


title: WT-4

value: WT


title: MT-4


title: WT-3


title: WT-1


title: sorted STINGgt/gt BMDCs, +Tem+anti-CD3 stimulated 1hr 2

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
FastQC, TrimGalore, cutadapt, STAR, sambamba, and subread were performed by the Informatics core at Cincinnati Children's Hospital Med Ctr to create a counts matrix and FPKM files
DESeq2 v1.36.0 used to normalize counts and run downstream analyses
Assembly: mm10
Supplementary files format and content: raw counts matrix in tab-delimited format

source_name: bone marrow derived

growth_protocol: BMDCs grown in 5% FCS containing RPMI for 7 days. Naïve CD4+ T cells expanded with anti-CD3, anti-CD28 coated plate + IL-2 for 5 days. Effector T cells then rested 2 days with IL-2 to create effector memory T (Tem) cell population.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was sent to Novogene and used for construction of sequencing libraries.
RNA libraries were constructed at Novogene (San Digeo) according to their RNA-seq protocols

treatment_protocol: BMDCs were treated with Tem cells +/- anti-CD3 for 1 hr, then sorted away from Tem cells for sequencing.

value: bone marrow derived

value: dendritic cells

value: Tem cells + anti-CD3


title: sorted STINGgt/gt BMDCs, +Tem+anti-CD3 stimulated 1hr 1


title: WT-2


title: testis_hephGFP_spermatocyte_H3K9me2_rep1_(220304_JA_Dm_JA706)

value: sorted testis cells from heph-GFP testis dissociated with collagenase


title: sorted STINGgt/gt BMDCs, +Tem unstimulated control 3

value: Tem cells unstimulated


title: sorted STINGgt/gt BMDCs, +Tem unstimulated control 1


title: sorted STINGgt/gt BMDCs, +Tem unstimulated control 2


title: MS_Cle_rep1

value: treated with 4uM clemastine (Cayman #14637)for 12days


title: C57BL/6J Dhpsfl/fl rep1


title: GN188_Vg589_biol_rep_2


title: sorted WT BMDCs, +Tem+anti-CD3 stimulated 1hr 1


title: sorted WT BMDCs, +Tem+anti-CD3 stimulated 1hr 3


title: sorted WT BMDCs, +Tem+anti-CD3 stimulated 1hr 2


title: sorted WT BMDCs, +Tem unstimulated control 3


title: sorted WT BMDCs, +Tem unstimulated control 1


title: CITE-seq sample of CSF immune cells from individual with postherpetic neuralgia ADT

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

description:
PHN_umap_005.Robj
integrated_umap
Heming&Zoe_integrated.Robj
5A_barcodes.tsv.gz
5A_features.tsv.gz
5A_matrix.mtx.gz

library_source: other

data_processing:
Bulk sequencing reads were pseudo-aligned with kallisto version 0.48.0 to the human genome: Homo Sapiens GCRh38, kallisto index version 10 (Bray et al., 2016).
Differential expression analyses were performed using DESeq2 (Love et al., 2014) or limma (Ritchie et al., 2015) in R.
CITE-sequencing reads were aligned using 10X Genomics CellRanger.
CITE-seq data were further processed using the R package Seurat (Hao et al., 2021).
Other packages we used were: SingleR (Aran et al., 2019) and SingleCellExperiment  (Amezquita et al., 2020).
Assembly: Homo Sapiens GCRh38
Supplementary files format and content: Seurat objects are provided for single cell data. Please see manuscript for detailed descriptions.
Supplementary files format and content: Excel files are provided for bulk sequencing data. Please see manuscript for detailed descriptions.
Library strategy: CITE-seq

molecule: protein

source_name: Cerebrospinal Fluid

extract_protocol:
For bulk sequencing,lysed cells were directly amplified into double stranded cDNA using the SMARTer protocol as described elsewhere (Picelli et al., 2014). All three cell types (CD4+ T cells, CD8+ T cells and monocytes) derived from one individual would be amplified at once. For single cell sequencing, we used a 10X Chromium Platform following manufacturer's protocols.
For bulk sequencing, library preparation from cDNA and sequencing were performed by an external company (Genewiz). For CITE-sequencing, the King's BRC Genomics facility followed the workflow recommended by 10X.

value: Cerebrospinal Fluid


title: CITE-seq sample of CSF immune cells from individual with failed low back surgery syndrome ADT

description:
FBSS_umap_011.Robj
integrated_umap
Heming&Zoe_integrated.Robj
11A_barcodes.tsv.gz
11A_features.tsv.gz
11A_matrix.mtx.gz


title: sorted STINGgt/gt BMDCs, +Tem+anti-CD3 stimulated 1hr 3


title: sorted WT BMDCs, +Tem unstimulated control 2


title: CITE-seq sample of CSF immune cells from individual with failed low back surgery syndrome GEX


title: RAP_XL_RNA_ALL_Rep1

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description: captured SARS-CoV-2 whole genome RNA; first replicate

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (v1.18). In the first run 5' and 3' adapters were clipped from both reads using the parameters: --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
RNA-seq reads were aligned to the concatenated genomes of hg38 (ensembl) and SARS-CoV-2 (ensembl MN908947.3) using STAR version 2.7.10a with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterType Normal --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --scoreDelOpen -1 --alignIntronMin 20 --alignIntronMax 3000 --alignMatesGapMax 3000
Using the python package pyBigWig, bigWig files were generated based on the SARS-Cov-2 genome and files were separately created for positive and negative sense mapped reads. Score represents the normalized coverage of positive and negative sense RNA fragments at a given genomic coordinate.
Assembly: hg38 and MN908947.3
Supplementary files format and content: bw

source_name: SARS-CoV-2 infected A549-ACE2 cells

growth_protocol: We maintained Huh-7 or A549-ACE2 cells in DMEM media (Thermo Fisher Scientific) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific), and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37°C and 5% CO2 atmosphere.

extract_protocol:
RAP-MS was carried out as described in Munschauer et al., Nature (2018). Covalent protein capture and sequencing of crosslinked RNA fragments for RAP-MS purified proteins was carried out as described in Schmidt et al., Nature Microbiology (2020).
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

treatment_protocol: For RAP-MS experiments Huh-7 or A549-ACE2 cells were infected with SARS-CoV-2 at MOI 5 PFU/cell. At 24 h post-infection, cells were washed with cold PBS and irradiated with 254 nm UV light on ice at a total dose of 800 mJ/cm2 in a GS Gene Linker (Bio-Rad Laboratories). Cells were lysed in 1 ml RAP lysis buffer (10 mM Tris pH 7.5, 500 mM LiCl, 0.5% dodecyl maltoside (DDM), 0.5% sodium dodecyl sulphate (SDS), 0.1% sodium deoxycholate, EDTA-free Protease Inhibitor Cocktail (Sigma Aldrich, 11873580001) and 300 U/ml Murine RNase Inhibitor (NEB, M0314L)) per 10 million cells, collected by scraping, and lysates were stored at -80°C.

tag: infection


title: RAP_XL_RNA_gRNA_Rep2

description: captured SARS-CoV-2 genomic RNA; second replicate


title: SMI_N_Rep2_XL

description: second replicate

data_processing:
Paired-end sequencing reads from cRIP experiments, were adapter- and quality trimmed by cutadapt (v1.18) in two runs according to the ENCODE eCLIP-seq processing pipeline v. 2.2 (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)). In the first run 5' and 3' adapters were clipped from both reads using the parameters: --match-read-wildcards --times 1 -e 0.1 -O 1 --quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
In the second run 3' adapters of read 2 were clipped to control for double ligation events. Cutadapt clipping was performed with the parameters:  --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT
RNA-seq reads were aligned to the concatenated genomes of hg38 (ensembl) and SARS-CoV-2 (ensembl MN908947.3) using STAR version 2.7.10a with parameters --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterType Normal --alignSoftClipAtReferenceEnds No --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --scoreDelOpen -1 --alignIntronMin 20 --alignIntronMax 3000 --alignMatesGapMax 3000 --alignEndsType EndToEnd
Using the python package pyBigWig, bigWig files were generated based on the SARS-Cov-2 genome and files were separately created for positive and negative sense mapped reads. Score represents the information content of IP over SMI of positive and negative sense RNA fragments at a given genomic coordinate.
Assembly: hg38 and MN908947.3
Supplementary files format and content: bw

growth_protocol: We maintained HuH-7 or A549-ACE2 cells in DMEM media (Thermo Fisher Scientific) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific), and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37°C and 5% CO2 atmosphere.

extract_protocol:
For immunoprecipitation procedures, lysates were combined with an equal amount of nuclease free water to adjust the lysis buffer to a 1x concentration. Subsequent steps were performed as described in the eCLIP protocol, with the following modifications. Immunoprecipitates were washed two times in 1 ml CLIP lysis buffer, two times in IP wash buffer (50 mM Tris-HCl pH 7.4, 300 mM NaCl, 1 mM EDTA, 1% (v/v) NP40, 0.5% sodium deoxycholate, 0.25 mM DTT), followed by two washes in 50 mM Tris-HCl pH 7.4, 1 mM EDTA, 0.5% (v/v) NP40. All other steps were carried out as described in the eCLIP method (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016)).
eCLIP-seq (Nostrand, E. L. V. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–14 (2016))

treatment_protocol:
For SND1 eCLIP, N eCLIP with UV crosslinking (+XL), and N eCLIP without UV crosslinking (noXL), we grew 24 million cells per condition and infected them with SARS-CoV-2 at MOI 3 PFU/cell. At 24 hpi, culture media was removed, cells were briefly rinsed with PBS and subjected to UV-irradiation with a total dose of 0.8 J/cm2, except N noXL samples, which were not UV crosslinked. Cells were scraped in PBS, pelleted at 200x g for 5 min and lysed by adding 2x CLIP lysis buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2 mM EDTA, 2% (v/v) IGEPAL CA-630, 1% sodium deoxycholate, 0.5 mM DTT, EDTA-free Protease Inhibitor Cocktail). Following a 30 min incubation at room temperature, fresh lysates were lysates were directly used for immunoprecipitation procedures or stored at -80°C.
For NSP9 cRIP experiments, we grew 24 million cells per condition and infected them with SARS-CoV-2 at MOI 3 PFU/cell. At 8 hpi and 12  hpi, culture media was removed and cells were scraped in cold PBS without UV crosslinking. Cells were pelleted by centrifugation (200 g, 8 min, 4°C) and lysed by adding 2x Co-IP buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2% (v/v) IGEPAL CA-630, 1% sodium deoxycholate, 0.5 mM TCEP, EDTA-free Protease Inhibitor Cocktail). Following a 30 min incubation at room temperature, fresh lysates were used for immunoprecipitation procedures.

tag: rip antibody

value: XL


title: RAP_XL_RNA_sgmRNA_Rep2

description: captured SARS-CoV-2 subgenomic RNA; second replicate


title: IP_N_Rep2_XL

description: second replicate

value: N


title: SMI_N_Rep2_noXL

description: second replicate

value: noXL


title: RAP_XL_RNA_gRNA_Rep1

description: captured SARS-CoV-2 genomic RNA; first replicate


title: IP_N_Rep1_XL

description: first replicate


title: IP_N_Rep2_noXL

description: second replicate


title: SMI_N_Rep1_XL

description: first replicate


title: SMI_NSP9_12h_KO_Rep2_cRIP

description: second replicate

source_name: SARS-CoV-2 infected A549-ACE2 SND1 knockout cells (KO)

value: SND1 knockout


title: IP_N_Rep1_noXL

description: first replicate


title: IP_NSP9_12h_KO_Rep2_cRIP

description: second replicate


title: SMI_NSP9_12h_CTRL_Rep2_cRIP

description: second replicate

source_name: SARS-CoV-2 infected A549-ACE2 control cells (CTRL)

value: control


title: IP_NSP9_12h_CTRL_Rep2_cRIP

description: second replicate


title: CITE-seq sample of CSF immune cells from individual with postherpetic neuralgia GEX


title: SMI_NSP9_8h_CTRL_Rep2_cRIP

description: second replicate


title: SMI_NSP9_8h_KO_Rep2_cRIP

description: second replicate


title: 254_RNA

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapping against human reference genome hs37d5 using STAR-2.5.3a
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region (Gencode29) associated with each gene.
To account for differences in library size between samples, Trimmed Mean of M values (TMM) normalization using calcNormFactors(), also from edgeR, was applied.
All data were then transformed using voom.
Assembly: hs37d5
Supplementary files format and content: tab-delimited text files include raw gene count for each sample or clinical data

source_name: ovarian tumors

extract_protocol:
RNA was harvested using the Qiagen All-Prep RNA isolation kit
RNA libraries were prepared by using Illumina TruSeqTM RNA Exome Library Preparation Kit (Illumina Inc., San Diego, CA) , following the manufacturer’s protocol

value: ovarian tumors

tag: analysis

value: Regular

tag: study

value: never


title: IP_NSP9_8h_CTRL_Rep2_cRIP

description: second replicate


title: 250_RNA


title: RAP_XL_RNA_sgmRNA_Rep1

description: captured SARS-CoV-2 subgenomic RNA; first replicate


title: 249_RNA


title: 247_RNA

value: Baby


title: 248_RNA

value: Both

value: current


title: SMI_N_Rep1_noXL

description: first replicate


title: 246_RNA


title: 245_RNA


title: 243_RNA


title: 242_RNA


title: 241_RNA


title: 240_RNA


title: 239_RNA


title: 233_RNA


title: 232_RNA


title: 234_RNA


title: 231_RNA


title: 238_RNA


title: RAP_XL_RNA_ALL_Rep2

description: captured SARS-CoV-2 whole genome RNA; second replicate


title: 229_RNA


title: 230_RNA


title: 228_RNA


title: 225_RNA


title: 219_RNA


title: 221_RNA


title: 218_RNA


title: 217_RNA


title: 212_RNA


title: 210_RNA


title: 211_RNA


title: 207_RNA


title: 213_RNA


title: 205_RNA


title: 204_RNA


title: 206_RNA


title: 200_RNA


title: 203_RNA


title: 199_RNA


title: 198_RNA


title: 194_RNA


title: 195_RNA


title: 192_RNA


title: 189_RNA


title: 190_RNA


title: 237_RNA


title: 183_RNA


title: 188_RNA


title: 184_RNA


title: 187_RNA


title: 185_RNA


title: 181_RNA


title: 186_RNA


title: 178_RNA


title: 180_RNA


title: 182_RNA


title: 179_RNA


title: 201_RNA


title: 177_RNA


title: 174_RNA


title: 172_RNA


title: 171_RNA


title: 175_RNA


title: 193_RNA


title: 170_RNA


title: 168_RNA


title: 166_RNA


title: 165_RNA


title: 162_RNA


title: 161_RNA


title: 191_RNA


title: 167_RNA


title: 160_RNA


title: 158_RNA


title: 157_RNA


title: 159_RNA


title: 154_RNA


title: 153_RNA


title: 144_RNA


title: 151_RNA


title: 150_RNA


title: 149_RNA


title: 152_RNA


title: 155_RNA


title: 156_RNA


title: 148_RNA


title: 143_RNA


title: 142_RNA


title: 141_RNA


title: 137_RNA


title: 139_RNA


title: 132_RNA


title: 135_RNA


title: 136_RNA


title: 131_RNA


title: 134_RNA


title: 130_RNA


title: 127_RNA


title: 124_RNA


title: 125_RNA


title: 126_RNA


title: 197_RNA


title: 123_RNA


title: 121_RNA


title: 115_RNA


title: 118_RNA


title: 113_RNA


title: 122_RNA


title: 117_RNA


title: 119_RNA


title: 116_RNA


title: 120_RNA


title: 110_RNA


title: 109_RNA


title: 129_RNA


title: 105_RNA


title: 108_RNA


title: 104_RNA


title: 101_RNA


title: 106_RNA


title: 099_RNA


title: 103_RNA


title: 098_RNA


title: 114_RNA


title: 095_RNA


title: 093_RNA


title: 112_RNA


title: 111_RNA


title: 089_RNA


title: 088_RNA


title: 091_RNA


title: 090_RNA


title: 092_RNA


title: 083_RNA


title: 084_RNA


title: 085_RNA


title: 087_RNA


title: 082_RNA


title: 100_RNA


title: 097_RNA


title: 081_RNA


title: 078_RNA


title: 077_RNA


title: 076_RNA


title: 068_RNA


title: 073_RNA


title: 094_RNA


title: 067_RNA


title: 066_RNA


title: 086_RNA


title: 063_RNA


title: 060_RNA


title: 065_RNA


title: IP_NSP9_8h_KO_Rep2_cRIP

description: second replicate


title: 059_RNA


title: 058_RNA


title: OT5_pelvis-day4

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: ICA001-00124A-001-E01-C01-NGS002_S18_L001_R1_001

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two mismatches
Reads per million mapped reads (RPM) method was used for normalization.
Assembly: miRbase 21

source_name: ascites

growth_protocol: Murine epithelial ovarian cancer cell line (ID8) were used. Then, we established the subclone of ID8 (ID8-T6), which has high metastatic ability in the peritoneal cavity. The cells were cultured in Dulbecco's modified Eagle medium (DMEM)-high glucose (Nacalai Tesque) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% antibiotics

extract_protocol:
The EV sheet was fabricated from cellulose nanofibers. The EV capture process from moistened organs using the EV sheet consists of the following steps: EV capture by absorption of ascites on organs, EV storage by drying, washing, and EV release. Then, total RNA was extracted using RNA purification kit (Norgen Biotek Corp, Thorold,  Canada). To obtain tissue RNA, tissues were shredded using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) and total RNAs was extracted by using the miRNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

treatment_protocol: Eight-week-old female BALB/cSlc-nu/nu mice were used. ID8-T6 cells were intraperitoneally (IP) or orthotopically (OT) transplanted into the left ovarian bursa.

tag: type

value: EV

value: pelvis

value: orthotopic transplantation, day4


title: 062_RNA


title: 057_RNA


title: OT4_diaphragm-day4

description: ICA001-00157A-001-E01-C01-NGS001_S5_L001_R1_001

value: diaphragm

tag: treatment


title: OT5_pelvis-day0

description: ICA001-00120A-001-E01-C01-NGS002_S14_L001_R1_001

tag: tissue

value: orthotopic transplantation, day0


title: 055_RNA


title: 054_RNA


title: OT4_pelvis-day4

description: ICA001-00156A-001-E01-C01-NGS001_S4_L001_R1_001


title: 053_RNA


title: OT4_diaphragm-day0

description: ICA001-00154A-001-E01-C01-NGS001_S2_L001_R1_001


title: 074_RNA


title: 052_RNA


title: OT4_pelvis-day0

description: ICA001-00153A-001-E01-C01-NGS001_S1_L001_R1_001


title: 051_RNA


title: 050_RNA


title: OT3_diaphragm-day4

description: ICA001-00135A-001-E01-C01-NGS001_S6_L001_R1_001


title: OT3_pelvis-day4

description: ICA001-00134A-001-E01-C01-NGS001_S5_L001_R1_001


title: OT3_diaphragm-day0

description: ICA001-00131A-001-E01-C01-NGS001_S2_L001_R1_001


title: 048_RNA


title: 047_RNA


title: OT5_diaphragm-day4

description: ICA001-00125A-001-E01-C01-NGS002_S19_L001_R1_001


title: 046_RNA


title: OT5_diaphragm-day0

description: ICA001-00121A-001-E01-C01-NGS002_S15_L001_R1_001


title: 044_RNA


title: 042_RNA


title: OT2_diaphragm-day0

description: ICA001-00108A-001-E01-C01-NGS002_S2_L001_R1_001


title: 040_RNA


title: OT3_pelvis-day0

description: ICA001-00130A-001-E01-C01-NGS001_S1_L001_R1_001


title: OT2_pelvis-day0

description: ICA001-00107A-001-E01-C01-NGS002_S1_L001_R1_001


title: 039_RNA


title: 037_RNA


title: OT1_diaphragm-day4

description: ICA001-00148A-001-E01-C01-NGS001_S19_L001_R1_001


title: OT2_diaphragm-day4

description: ICA001-00111A-001-E01-C01-NGS002_S5_L001_R1_001


title: OT1_pelvis-day4

description: ICA001-00147A-001-E01-C01-NGS001_S18_L001_R1_001


title: OT1_diaphragm-day0

description: ICA001-00145A-001-E01-C01-NGS001_S16_L001_R1_001


title: 035_RNA


title: OT1_pelvis-day0

description: ICA001-00144A-001-E01-C01-NGS001_S15_L001_R1_001


title: 034_RNA


title: 033_RNA


title: eIF4A-5000nM_b

first: Jon

middle: R.

last: Lorsch

address: BG 49 RM 2C08, 49 Convent Dr.

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development,

institute: National Institutes of Health

description: 48S Preinitiaiton complex protected mRNA fragments

data_processing:
Remove sequencing adaptors sequence (AGATCGGAAGAGCAC) in the fastq files using cutadapt/4.4.
Demultiplex fastq sequences using Linux "grep" function to subset reads containing sample specific barcode at the 3' ends.
Remove non-coding RNA reads using STAR/2.7.10b
Map non-coding RNA removed reads to yeast genome using STAR/2.7.10b, and count 25-34 nt reads mapped to each transcript using "fp-count" function in RiboSeq (https://github.com/ingolia-lab/RiboSeq)
Map non-coding RNA removed reads to spike-in sequences using STAR/2.7.10b, and count 25-34 nt reads mapped to each transcript using "fp-count" function in RiboSeq (https://github.com/ingolia-lab/RiboSeq).
Wiggle files were produced from the alignment files using "wiggle-track" function in RiboSeq (https://github.com/ingolia-lab/RiboSeq), generating two wiggle files, each for genes on the Watson or Crick strand. Wiggle files were normalized by multiplying the size factor "q" (calculate using spike-in RPFs) in the wiggle-track function (-q).
Differential expression analysis of changes in RPF, recruitment efficiency (RE), or relative ribosome occupancy (RRO) values was performed using DESeq2 (Love et al., 2014) using custermerized Size-factors calculated from spike-in RPFs.
Assembly: R64-1-1 S288C Sac cer3 Genome Assembly
Supplementary files format and content: Wiggle files
Library strategy: Rec-Seq

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: WT yeast strain was cultured in Yeast Extract–Peptone–Dextrose (YPD) medium to OD600 of ~1. Harvested cells were washed with cold water and stored in -80°C before use.

extract_protocol:
The frozen cell pellet from a 500 ml culture was thawed on ice and mechanically disrupted by vortexing with glass beads three times for 2 min each at maximum speed in a cold room (4°C) in 2 ml of buffer RL (provided in the kit), 3 ml phenol:chloroform:isoamyl alcohol 25:24:1 (pH 5.2) and 3 ml ice cold glass beads. Following 5 min centrifugation at 14000 rpm in a Sorvall LYNX 6000 Superspeed centrifuge using a Fiberlite F14-14 x 50cy rotor, the supernatant was transferred to a fresh tube and total RNA was prepared using a GenElute total RNA purification Maxi kit (Sigma-Aldrich; RNB200) following the manufacturer’s protocol. 400 μg total RNA in 250 μl water was applied to a GeneElute mRNA miniprep kit (Sigma-Aldrich; MRN70-1KT), following the manufacturer’s protocol. The purified total mRNA was treated by 5’-Phosphate-Dependent Exonuclease (Lucigen, TER51020) to degrade RNAs with 5’ monophosphates, such as 18S and 25S ribosomal RNAs, at 0.3 μg/µl mRNA in 1X buffer A (provided in the kit), 1U/µl RiboGuard RNase Inhibitor (Lucigen; RG90925), 0.1 U/µl 5’-Phosphate-Dependent Exonuclease. Following a 1 h incubation at 30°C, the total mRNA was extracted using phenol:chloroform:isoamyl alcohol 25:24:1 (pH 5.2), ethanol precipitated, resuspended in 10 mM Tris (pH 8.0) and stored in -80 °C.
RecSeq sequencing library construction was conducted according to a previously described protocol (McGlincy and Ingolia 2017), with modifications, using identical barcoded linkers (NI-810 to NI-815), RT primer (NI-802) and PCR primers (NI-798, NI-799, NI-822 to NI-824). The RNA fragments purified from 48S PIC RPFs were dephosphorylated using T4 Polynucleotide Kinase (PNK) (NEB; M0201L) and ligated to pre-adenylated linkers (NI-810 to NI-815) containing 5 nt sample barcodes unique for each sample using truncated T4 RNA ligase 2 (K227Q) (NEB; M0351L). Ligated fragments were separated from free linkers on a 15% polyacrylamide TBE-Urea gel and then pooled and purified for reverse transcription using RT primer NI-802 and ProtoScript II Reverse Transcriptase (NEB; M0368S). The ~105 nt cDNAs were separated from free RT primers on a 15% TBE-Urea gel and circularized using CircLigaseII ssDNA Ligase (Biosearch Technologies; CL9021K). PCR was carried out using forward primer NI-798, and reverse primers (NI-799, NI-822 to 824) as already described (McGlincy and Ingolia 2017) .

treatment_protocol: No additional treatment for the cell.

tag: cell type

value: yeast strain

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


title: 036_RNA


title: Input-total_mRNA

description: RNA-Seq


title: 030_RNA


title: 031_RNA


title: eIF4A-500nM_b


title: OT2_pelvis-day4

description: ICA001-00110A-001-E01-C01-NGS002_S4_L001_R1_001


title: eIF4A-500nM_a


title: eIF4A-5000nM_a


title: Ded1-500nM_c


title: 029_RNA


title: Ded1-500nM_b


title: 022_RNA


title: Ded1-500nM_a


title: 027_RNA


title: 023_RNA


title: 024_RNA


title: 020_RNA


title: Ded1-100nM_c


title: Ded1-100nM_b


title: 018_RNA


title: 173_RNA


title: Ded1-100nM_a


title: Ded1-0nM_c


title: 016_RNA


title: Ded1-0nM_b


title: 014_RNA


title: Ded1-0nM_a


title: 012_RNA


title: 011_RNA


title: WT CD25lo Treg_1

city: San Francisco

first: K. Mark

last: Ansel

address: 513 Parnassus Ave. UCSF Box 0414

department: Microbiology & Immunology

institute: UCSF

data_processing:
Aligner: STAR_2.7.2b
Differential Expression Test: DESeq2 v1.24.0
Assembly: Ensembl Human GRCm38.78 alignment genome
Supplementary files format and content: Tab-delimited text file contains all statistics for all pairwise comparisons as well as read counts for each sample (in counts per million reads).

source_name: Spleen and inguinal, axillary, brachial lymph nodes pooled

extract_protocol:
Tregs were isolated fresh from tissues by FACS. 340,000-1,200,000 cells were lysed in QIAzol (Qiagen) and total RNA was isolated using miRNeasy Mini Kit (Qiagen) with on-column DNase digestion. RNA quality and yield was determined on an Agilent 2100 Bioanalyzer (Agilent BioTek).
cDNA was synthesized using the Nugen Universal Plus library kit (NuGen Technologies) following manufacturer's protocols.

value: T regulatory cell

value: WT

value: No treatment


title: WT CD25lo Treg_2

value: Spleen and inguinal, axillary, brachial lymph nodes pooled


title: WT CD25hi Treg_3


title: 009_RNA

value: ovarian tumors


title: 007_RNA


title: 006_RNA


title: 019_RNA


title: 005_RNA


title: 010_RNA


title: 004_RNA


title: WT Treg_3


title: WT Treg_2


title: WT CD25hi Treg_2


title: WT CD25hi Treg_1


title: 001_RNA

value: Regular


title: WT_SCoV2_12hpi_no4sU_rep2

data_processing:
SLAM-seq was performed in duplicates to identify newly synthesized RNA and total RNA using GRAND-SLAM. Sequencing adapters were trimmed using Cutadapt (version 3.4). Next, bowtie2 (version 2.3.0) (Langmead and Salzberg, 2012) with default parameters was used to discard reads mapping to rRNA (Genbank identifier U13369.1) and to verify the absence of mycoplasma contamination. STAR version 2.5.3a (REF) was used to map all remaining reads with length at least 18 nt against a combined index of the human genome (hg38/Ensembl version 90) and the SARS-CoV-2 genome (NC_045512) using STAR (version 2.5.3a) with the parameters –outFilterMismatchNmax 20 –outFilterScoreMinOverLread 0.4 –outFilterMatchNminOverLread 0.4 –alignEndsType Extend5pOfReads12 –outSAMattributes nM MD NH. We used GRAND-SLAM (version 2.0.6) to estimate the new-to-total RNA ratios. New RNA was computed by multiplying total RNA with the maximum a posteriori estimate of the new-to-total RNA ratio. Log2 fold-changes were estimated using PsiLFC (Erhard, 2018). Normalization factors were computed from total RNA such that the median log2 fold-change was 0 and applied to both total and new RNA.
Assembly: hg38 and NC_045512
Supplementary files format and content: comma separated file; log2 fold-changes with respect to corresponding WT sample

growth_protocol: We maintained A549-ACE2 cells in DMEM media (Thermo Fisher Scientific) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific), and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37°C and 5% CO2 atmosphere.

extract_protocol:
Cells were harvested in Trizol and RNA was extracted using the Direct-zol RNA microprep kit (Zymo Research) including DNase digest. From each sample, 2 μg of RNA were subjected to alkylation by incubating with 10 mM Iodoacetamide in PBS with 50% DMSO at 50°C for 15 min as previously described (Herzog, V.A., et al. Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods 14, 1198–1204 (2017). After adding an equal volume of H2O to the sample, the RNA was purified using the RNA Clean and Concentrator-5 kit (Zymo Research).
Approximately 800 ng of alkylated RNA was depleted of ribosomal RNA using the NEBNext rRNA Depletion Kit v2 (NEB) according to the manufacturer’s instructions. RNA was heat fragmented at 91°C for 3 min in 10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 100 mM KCl, 0.02% Triton X-100 and 0.1 mg/mL BSA. RNA was dephosphorylated using 1.75 U FastAP Thermosensitive Alkaline Phosphatase for 10 min at 37°C , and end-repaired using 15 U T4 PNK for 20 min at 37°C. Both reactions were performed in the presence of 10 U murine RNase inhibitor. RNA was cleaned up using Dynabeads MyOne Silane (Thermo Fisher Scientific). For this, 10 μl beads per sample were washed twice with RLT buffer (Qiagen) and beads were added to the RNA in 3x sample volumes RLT buffer. To bind the RNA to the beads, 4.5x volumes isopropanol were added and samples were incubated 5 min at room temperature. Beads were washed twice with 70% EtOH and RNA was eluted in 8 μl H2O. cDNA libraries were constructed from the recovered RNA as described in the Methods section of the accompanying paper.

treatment_protocol: A549-ACE2 SND1 knockout cells, control cells, or parental A549-ACE2 wild-type cells were infected with SARS-CoV-2 at MOI 3 PFU/cell. For each time point 4-Thiouridine was added to the cell culture medium to a final concentration of 200 μM and cells were returned to the incubator for 2 h.

value: wild type

value: infected with SARS-CoV-2

value: no 4sU


title: cKO Treg_5

value: miR-15/16 cKO


title: WT Treg_1


title: WT_SCoV2_12hpi_no4sU_rep1


title: cKO Treg_4


title: WT_mock_12hpi_no4sU_rep2

value: mock infected


title: cKO Treg_3


title: cKO Treg_2


title: cKO Treg_1


title: WT_SCoV2_4_6hpi_rep2

value: 2h 4sU


title: KCR18

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

data_processing:
Raw fastq files were aligned to mouse genome using HISAT2
RNA-seq QC and metrics were collected using Picard tools and gene counts were extracted using featureCounts
Genome_build: Mouse genome build GRCm38
Supplementary_files_format_and_content: Data matrix of raw counts

source_name: Tamoxifen treated iKCR mouse pancreas (P48-CreERT; LSL-KrasG12D ;Rbpjflox/flox)

extract_protocol:
RNA extraction was performed by QIAzol Lysis Reagent and RNeasy Mini Kit (Qiagen)
Directional mRNA library preparation (poly A enrichment); PE150, Q30≥80%; 15 G of raw data per sample

treatment_protocol: 6-8 weeks old mice were administered tamoxifen (iCR, iKC, and iKCR; n=6/group). Littermate control mice (iCR and iKCR; n=6/group) were injected with ClinOleic 20%. Pancreata were harvested at the 4 weeks.

value: RBPJ KO in context of KrasG12D expression in acinar cells (C57BL/6)

value: pancreatic cells (mainly acinar cells)


title: WT Treg_4


title: WT_mock_4_6hpi_rep2


title: WT_SCoV2_4_6hpi_rep1


title: KCR16


title: KCR15


title: KCR14


title: Pt6_normal-tissue3

description:
12-PT9-N3_S12_L001_R1_001
Pt6_data file(RPM).xlsx

source_name: normal

value: tissue


title: KCR17


title: Pt6_normal-tissue1

description:
10-PT9-N1_S10_L001_R1_001
Pt6_data file(RPM).xlsx


title: SND1_KO_SCoV2_10_12hpi_rep1

value: SND1 knockout cells


title: Pt6_tumor-tissue3

description:
09-PT9-T3_S9_L001_R1_001
Pt6_data file(RPM).xlsx

source_name: primary cancer


title: WT_mock_4_6hpi_rep1


title: SND1_KO_SCoV2_4_6hpi_rep2


title: Pt6_normal-tissue2

description:
11-PT9-N2_S11_L001_R1_001
Pt6_data file(RPM).xlsx


title: KCR12

source_name: Oil treated iKCR mouse pancreas (P48-CreERT; LSL-KrasG12D ;Rbpjflox/flox)

value: Control with one allele P48-creERT knock-in and LSL-KrasD12D knock-in (C57BL/6)


title: KCR13


title: KCR11


title: WT_SCoV2_10_12hpi_rep2


title: Pt6_tumor-tissue1

description:
07-PT9-T1_S7_L001_R1_001
Pt6_data file(RPM).xlsx


title: Pt5_normal-tissue3

description:
06-PT8-N3_S6_L001_R1_001
Pt5_data file(RPM).xlsx


title: SND1_KO_SCoV2_4_6hpi_rep1


title: WT_mock_12hpi_no4sU_rep1


title: WT_SCoV2_10_12hpi_rep1


title: KCR10


title: Pt5_normal-tissue2

description:
05-PT8-N2_S5_L001_R1_001
Pt5_data file(RPM).xlsx


title: KCR09


title: Pt5_normal-tissue1

description:
04-PT8-N1_S4_L001_R1_001
Pt5_data file(RPM).xlsx


title: SND1_KO_SCoV2_10_12hpi_rep2


title: SND1_KO_mock_4_6hpi_rep2


title: Pt5_tumor-tissue2

description:
02-PT8-T2_S2_L001_R1_001
Pt5_data file(RPM).xlsx


title: Pt5_tumor-tissue3

description:
03-PT8-T3_S3_L001_R1_001
Pt5_data file(RPM).xlsx


title: KCR08


title: Pt6_tumor-tissue2

description:
08-PT9-T2_S8_L001_R1_001
Pt6_data file(RPM).xlsx


title: KCR07


title: Ctrl2_SCoV2_10_12hpi_rep1

value: control


title: Ctrl2_SCoV2_10_12hpi_rep2


title: Pt4_tumor-tissue3

description:
09-PT7-T3_S9_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_normal-tissue3

description:
12-PT7-N3_S12_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_normal-tissue2

description:
11-PT7-N2_S11_L001_R1_001
Pt4_data file(RPM).xlsx


title: Ctrl2_SCoV2_4_6hpi_rep2


title: Pt4_normal-tissue1

description:
10-PT7-N1_S10_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_tumor-tissue2

description:
08-PT7-T2_S8_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_tumor-tissue1

description:
07-PT7-T1_S7_L001_R1_001
Pt4_data file(RPM).xlsx


title: KC05

source_name: Tamoxifen treated iKC mouse pancreas (P48-CreERT; LSL-KrasG12D)

value: KrasG12D expression  in acinar cells (C57BL/6)


title: KC04


title: Pt3_normal-tissue3

description:
06-PT6-N3_S6_L001_R1_001
Pt3_data file(RPM).xlsx


title: Ctrl2_SCoV2_4_6hpi_rep1


title: Pt3_normal-tissue2

description:
05-PT6-N2_S5_L001_R1_001
Pt3_data file(RPM).xlsx


title: Ctrl2_mock_4_6hpi_rep2


title: Pt3_normal-tissue1

description:
04-PT6-N1_S4_L001_R1_001
Pt3_data file(RPM).xlsx


title: KC03


title: SND1_KO_mock_4_6hpi_rep1


title: Ctrl2_mock_4_6hpi_rep1


title: Pt3_tumor-tissue2

description:
02-PT6-T2_S2_L001_R1_001
Pt3_data file(RPM).xlsx


title: Pt3_tumor-tissue3

description:
03-PT6-T3_S3_L001_R1_001
Pt3_data file(RPM).xlsx


title: Pt3_tumor-tissue1

description:
01-PT6-T1_S1_L001_R1_001
Pt3_data file(RPM).xlsx


title: KC02


title: Pt5_tumor-tissue1

description:
01-PT8-T1_S1_L001_R1_001
Pt5_data file(RPM).xlsx


title: KC01


title: Pt2_normal-tissue3

description:
PT2-N3_S6_L001_R1_001
Pt2_data file(RPM).xlsx


title: KC06


title: Pt2_normal-tissue2

description:
PT2-N2_S5_L001_R1_001
Pt2_data file(RPM).xlsx


title: Ctrl1_SCoV2_10_12hpi_rep1


title: CR18

source_name: Tamoxifen treated iCR mouse pancreas (P48-CreERT;Rbpjflox/flox)

value: RBPJ KO in acinar cells(C57BL/6)


title: Ctrl1_SCoV2_4_6hpi_rep2


title: Pt2_meta-tissue3

description:
PT2-M3_S12_L001_R1_001
Pt2_data file(RPM).xlsx

source_name: metastatic cancer


title: Pt2_meta-tissue2

description:
PT2-M2_S11_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_normal-tissue1

description:
PT2-N1_S4_L001_R1_001
Pt2_data file(RPM).xlsx


title: CR17


title: Pt2_meta-tissue1

description:
PT2-M1_S10_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_tumor-tissue3

description:
PT2-T3_S9_L001_R1_001
Pt2_data file(RPM).xlsx


title: CR16


title: Ctrl1_SCoV2_4_6hpi_rep1


title: Ctrl1_SCoV2_10_12hpi_rep2


title: CR15


title: Pt1_normal-tissue3

description:
06-PT1-EV-S6_S6_L001_R1_001
Pt1_data file(RPM).xlsx


title: Ctrl1_mock_4_6hpi_rep1


title: Pt1_normal-tissue2

description:
05-PT1-EV-S5_S5_L001_R1_001
Pt1_data file(RPM).xlsx


title: Pt1_normal-tissue1

description:
04-PT1-EV-S4_S4_L001_R1_001
Pt1_data file(RPM).xlsx


title: CR13


title: Pt1_tumor-tissue3

description:
PT1-T3_S3_L001_R1_001
Pt1_data file(RPM).xlsx


title: Pt1_tumor-tissue2

description:
PT1-T2_S2_L001_R1_001
Pt1_data file(RPM).xlsx


title: SMI_NSP9_12h_KO_Rep1_cRIP

treatment_protocol: For SND1 eCLIP experiments, we grew 24 million cells per condition and infected them with SARS-CoV-2 at MOI 3 PFU/cell. At 24 hpi, culture media was removed, cells were briefly rinsed with PBS and subjected to UV-irradiation with a total dose of 0.8 J/cm2. Cells were scraped in PBS, pelleted at 200x g for 5 min and lysed by adding 2x CLIP lysis buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2 mM EDTA, 2% (v/v) IGEPAL CA-630, 1% sodium deoxycholate, 0.5 mM DTT, EDTA-free Protease Inhibitor Cocktail). Following a 30 min incubation at room temperature, fresh lysates were lysates were directly used for immunoprecipitation procedures or stored at -80°C.    For NSP9 cRIP experiments, we grew 24 million cells per condition and infected them with SARS-CoV-2 at MOI 3 PFU/cell. At 8 hpi and 12  hpi, culture media was removed and cells were scraped in cold PBS without UV crosslinking. Cells were pelleted by centrifugation (200 g, 8 min, 4°C) and lysed by adding 2x Co-IP buffer (100 mM Tris-HCl pH 7.4, 300 mM NaCl, 2% (v/v) IGEPAL CA-630, 1% sodium deoxycholate, 0.5 mM TCEP, EDTA-free Protease Inhibitor Cocktail). Following a 30 min incubation at room temperature, fresh lysates were used for immunoprecipitation procedures.

value: SND1 knockout (KO)


title: Pt1_tumor-tissue1

description:
PT1-T1_S1_L001_R1_001
Pt1_data file(RPM).xlsx


title: IP_NSP9_12h_KO_Rep1_cRIP


title: CR12

source_name: Oil treated iCR mouse pancreas (P48-CreERT;Rbpjflox/flox)

value: Control with one allele P48-creERT knock-in (C57BL/6)


title: CR11


title: Pt1_serum-postope1

description:
01-PT1-T4_S1_L001_R1_001
Pt1_data file(RPM).xlsx

source_name: serum

value: EV

value: post-operation


title: Pt1_serum-postope3

description:
03-PT1-T6_S3_L001_R1_001
Pt1_data file(RPM).xlsx


title: Pt1_ascites3

description:
N4_S8_L001_R1_001
Pt1_data file(RPM).xlsx

value: pre-operation


title: Pt1_ascites2

description:
N3_S7_L001_R1_001
Pt1_data file(RPM).xlsx


title: Ctrl1_mock_4_6hpi_rep2


title: CR10


title: Pt1_ascites1

description:
N2_S6_L001_R1_001
Pt1_data file(RPM).xlsx


title: Pt1_tumor-surface3

description:
T4_S5_L001_R1_001
Pt1_data file(RPM).xlsx

tag: location

value: surface


title: CR09

tag: genotype


title: Pt1_tumor-surface2

description:
T3_S4_L001_R1_001
Pt1_data file(RPM).xlsx


title: SMI_NSP9_8h_KO_Rep1_cRIP


title: CR14


title: IP_NSP9_8h_KO_Rep1_cRIP


title: Pt1_tumor-surface1

description:
T2_S3_L001_R1_001
Pt1_data file(RPM).xlsx


title: SMI_NSP9_8h_CTRL_Rep1_cRIP

value: control (CTRL)


title: CR07


title: IP_NSP9_8h_CTRL_Rep1_cRIP


title: SMI_NSP9_12h_CTRL_Rep1_cRIP


title: IP_NSP9_12h_CTRL_Rep1_cRIP


title: Pt1_serum-postope2

description:
02-PT1-T5_S2_L001_R1_001
Pt1_data file(RPM).xlsx


title: Gonad eif4e1b 2

city: Vienna

first: Marcus

last: Strobl

address: Campus Vienna Biocenter 1

country: Austria

institute: IMP

data_processing:
RNA-seq reads were trimmed using trim-galore v0.5.0, and reads mapping to abundant sequences (Dr mitochondrial chromosome, SILVA Dr ribosomal RNA, phiX174 genome) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts  (subread v1.6.2).
Differential gene expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1.
Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files with per gene read counts

organism: Danio rerio

source_name: Ovary

extract_protocol:
RNeasy Mini Kit (Qiagen)
SMARTerStrandedRNA library (Ribo-Zero)

value: Ovary

tag: Sex

value: female

value: Gonad

value: tg(ziwi:GFP), eif4e1b -/-


title: Gonad eif4e1b 3


title: SMI, SND1, eCLIP

source_name: SARS-CoV-2 infected Huh-7 cells

tag: cell line


title: Gonad eif4e1b 1


title: CR08

value: pancreatic cells (mainly acinar cells)


title: IP, SND1, eCLIP


title: Gonad WT 3

value: tg(ziwi:GFP), eif4e1b +/+


title: IP_normal-tissue2

value: tissue

value: control (PBS)


title: IP_normal-tissue3


title: IP_normal-tissue1


title: Gonad WT 2


title: Gonad WT 1


title: IP_tumor-tissue3

source_name: tumor

value: intraperitoneal transplantation


title: ADAR1KO_PKR_RIP

city: Stanford

first: Shibin

last: Hu

address: 240 pasteur drive, 4300

department: Genetics

institute: Stanford University

description: RNA IP enriched RNA

data_processing:
Basecalls performed using illumina RTA v2.
Reads were mapped using STAR v2.4.2a with the reference genome hg19 for human (paremeters: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10).
The expression of known genes (measured in Transcripts Per Kilobase Million, TPM) was quantified using RSEM v1.2.21.
Assembly: hg18
Supplementary files format and content: CSV file with TPM value for each gene

extract_protocol:
RNA was extracted by TriZol
Library was constructed using KAPA HyperPrep Kit

value: Human embryonic kidney

value: ADAR1 KO


title: IP_tumor-tissue2


title: WT_PKR_RIP

description: RNA IP enriched RNA

value: WT


title: Liver, Treatment_3

city: Guangzhou

first: Shengyun

last: Sun

state: Guangdong

address: 613 West Huangpu Avenue

institute: The First Affiliated Hospital of Jinan University

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research,2009
We calculated the differentially expressed  mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene FPKM values for every gene and sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according   to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2   mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The   mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a   new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for   15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper   aqueous phase where RNA remained was transferred into a new tube with equal volume of   supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After   deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix   was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the   pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated   water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using   a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented   into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was   generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA   synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end   repair. The cDNA fragments obtained from previous step were amplified by PCR, and products   were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on   the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products   from previous step were heated denatured and circularized by the splint oligo sequence to get the   final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The   final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300   copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases   reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Liver

tag: strain

value: Treatment


title: Liver, Treatment_2


title: IP_tumor-tissue1


title: IP_normal-peritonium3

value: EV

value: pelvis


title: Liver, Treatment_1


title: Anesthesia with sevoflurane

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Division of Biomedical Sciences, Research Center for Genomic Medicine

institute: Saitama Medical University

data_processing:
Terminal
Sequence reads were trimmed for adaptor sequence/low-quality sequence using sickle (parameter- -q 30 -l 20 )
Trimmed sequence reads were mapped to rn6 using hisat2 and samtools
Read count extraction and normalization were performed using Stringtie
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Total RNAs were harvested using RNeasy Midi Kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit (illumina) according to manufacturer’s instruction.

treatment_protocol: Rats were subjected to inhalational anesthesia using either sevoflurane (4.5%) or desflurane (6%) and rats were sacrificed by decapitation immediately after their loss of consciousness or after subjection of inhalational anesthesia for 6 hours and then portions of their livers were recovered and immersed in RNAlater until RNA preparation.

value: liver

value: wild type

value: Subjection of anesthesis with sevoflurane for 6h

tag: time

value: 6 hours


title: Liver, DEHP_2

value: DEHP


title: Control against anesthesia with desflurane

value: brief treatment with desflurane  until the loss of rats' consciousness

value: 0 hour


title: 0-week control - 2523

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Assembly: mm10
Supplementary files format and content: Text file including CPM for each sample (in columns) and gene (in rows)

source_name: Whole Lung

extract_protocol:
After sacrifice, lungs were immediately taken and flash frozen. RNA was isolated using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice underwent treatment with either L-NAME (0.5 g/L) in the water and high fat diet (60% lipid content) for 2 and 5 weeks, compared to 0 week controls.

value: Whole Lung

value: Control


title: Liver, DEHP_3


title: Liver, DEHP_1


title: Pt2_tumor-tissue2

description:
PT2-T2_S8_L001_R1_001
Pt2_data file(RPM).xlsx

value: tissue


title: Liver, Control_3


title: 0-week control - 2522


title: 0-week control - 2521


title: Pt2_tumor-tissue1

description:
PT2-T1_S7_L001_R1_001
Pt2_data file(RPM).xlsx


title: IP_cancerous-peritoneum2

source_name: ascites

value: intraperitoneal transplantation


title: Anesthesia with desflurane

value: Subjection of anesthesis with desflurane for 6h


title: 5-week LNAME/HFD - 2533

value: L-NAME/HFD for 5 weeks


title: ATAC-seq, naive_hESC_dCAS9-KRAB+sgRNA_rep2

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

data_processing:
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned with bowtie2. Mitochondrial reads were removed.
Accessible sites were called using MACS2, only peaks with a score higher than 5 (–log10 p-value) were kept. Then differential analysis between conditions was done using unique reads (filter for MAPQ > 10)
Assembly: hg19
Supplementary files format and content: A bed file containing the output of the peak called by MACS2

source_name: WIBR3dPE hESC

growth_protocol: Conventional (primed) human ESC lines were maintained in mTSER for H1 (Male) and IPS on Matrigel, for WIBR3 (Female) on irradiated inactivated mouse embryonic fibroblast (MEF) feeders in human ESC medium (hESM) and passaged with collagenase and dispase, followed by sequential sedimentation steps in hESM to remove single cells while naïve ES cells, primed H1 and IPS were passaged by Accutase in single cells. hES media composition: DMEM/F12 supplemented with 15% fetalbovine serum, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% nonessential amino acids, 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol and 4 ng/ml FGF2. Naïve media composition: 500 mL of medium was generated by including: 240 mL DMEM/F12, 240 mL Neurobasal, 5 mL N2 supplement, 10 mL B27 supplement, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin-streptomycin, 50 μg/ml BSA. In addition for 4i/LA:  PD0325901 (1 μM), SB590885 (0.5 μM), WH4-023 (1 μM), Activin A (10 ng/mL), 20 ng/ml hLIF, Y-27632 (10 μM) and IM-12 (0-1 μM). In addition for KN/2i media: PD0325901 (1 μM), CHIR99021 (1 μM), 20 ng/ml hLIF and Doxycycline (2 µg/ml). For conversion of primed human ESC lines (WIBR3), we seeded 2-3e105 trypsinized single cells on an MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (10 mM). Two days later, medium was switched to 4i/LA (+/- IM12)-containing naïve hESM (Theunissen et al., 2016). WIBR3dPE cells (OCT4 GFP knock-in depleted for its primed specific Proximal Enhancer (dPE) were converted in naïve with DOX-inducible KLF2 and NANOG transgenes and maintained in 2i/L/DOX (Theunissen et al., 2014).

extract_protocol:
ATAC-seq was performed as in (Buenrostro et al., 2013) on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs
Library were made using Nextera DNA Library Prep Kit (Illumina #FC-121-1030)

treatment_protocol: ATAC-seq was performed on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs

value: WIBR3dPE hESC

value: CRISPRi in naive

tag: media

value: KN/2iL media


title: IP_normal-peritonium2

value: EV

value: pelvis

value: control (PBS)


title: AC16 cells, IGF1_24h_2

type: genomic

city: Rochester

first: Hangchuan

last: Shi

address: 601 Elmwood Avenue

institute: University of Rochester

description: SAMPLE 15

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Illumina's GenomeStudio methylation module (v1.9.0)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from AC16 cells using Quick-DNA Isolation Kit according to standard instructions


title: AC16 cells, AngII_24h_2

description: SAMPLE 12

source_name: AC16 AngII 24h 2

value: AngII


title: Liver, Control_1

value: Liver


title: AC16 cells, AngII_24h_3

description: SAMPLE 13

source_name: AC16 AngII 24h 3


title: AC16 cells, Control_24h_2

description: SAMPLE 9

source_name: AC16 control 24h 2


title: IP_normal-peritonium1


title: Control against anesthesia with sevoflurane

value: liver

value: wild type

value: brief treatment with sevoflurane until the loss of rats' consciousness


title: ATAC-seq, naive_hESC_dCAS9-KRAB+sgRNA_rep1


title: AC16 cells, Control_24h_3

description: SAMPLE 10

source_name: AC16 control 24h 3


title: 5-week LNAME/HFD - 2531

value: Whole Lung


title: 0-week control - 2520

value: Control


title: AC16 cells, IGF1_24h_3

description: SAMPLE 16


title: IP_cancerous-peritoneum3


title: 5-week LNAME/HFD - 2530


title: AC16 cells, AngII_24h_1

description: SAMPLE 11

source_name: AC16 AngII 24h 1


title: AC16 cells, IGF1_24h_1

description: SAMPLE 14


title: ATAC-seq, naive_hESC_dCAS9-KRAB+sgRNA_rep3


title: LN-Negative-4

type: RNA

city: Kanazawa

first: Naohiro

last: Wakisaka

state: Ishikawa

institute: National Hospital Organization Kanazawa Medical Center

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LN4

hyb_protocol: Hybridization was performed using GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: The array was scanned using GeneChip Scanner 3000 7G, Affymetrix,.

data_processing: The data were analyzed with Transcriptome Analysis Console T hermo Fisher Scientific Inc.using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Lymph Node

label_protocol: cDNA synthesis, amplification and labeling were performed with WT Pico Reagent, and according to the standard Affymetrix protocol using Veriti 200, Life Technologies, Inc.

extract_protocol: Total RNA from FFPE block was isolated using RNeasyⓇ FFPE Kit.

tag: disease state

value: lymph node of oropharyngeal cancer


title: AC16 cells, AngII_12h_2

description: SAMPLE 3

source_name: AC16 AngII 12h 2


title: AC16 cells, AngII_12h_1

description: SAMPLE 2

source_name: AC16 AngII 12h 1


title: Liver, Control_2


title: 5-week LNAME/HFD - 2532

city: Nashville


title: AC16 cells, Control_24h_1

description: SAMPLE 8

source_name: AC16 control 24h 1