title: mRNA-seq-Siadat2-replicate_2

first: xueliang

last: lyu

address: 6001 Forest Park Road

department: Physiology

data_processing:
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using tophat2 with parameters --library-type fr-firststrand --min-intron-length 20 --max-intron-length 50000 --read-mismatches 4.
Fragments Per Kilobase Million (FPKM) were calculated using cufflinks with parameters --library-type fr-firststrand --multi-read-correct --min-intron-length 20 --max-intron-length 50000 --frag-bias-correct
Genome_build: For the ribosome profiling, the reference sequences are all mRNAs with uptream and dowmstream 100 bp respectively; for the mRNA-seq, the reference sequence is whole genome sequence with gtf annotation file from NCBI database.
Supplementary_files_format_and_content: For the mRNA-seq, tab-delimited text files include FPKM values for each sample; for the ribosome profiling, tab-delimited text file includes absolute codon occupancy values.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: For the ribosome profiling and accompanying mRNA-seq, fresh conidia (one week post inoculation on slants) of adat2-silenced mutant and wild-type strain were cultured in plates with 50 ml growth medium (1 × Vogel’s, 0.1% glucose, 10-2 M QA) at room temperate for three days. The cultures were cut into small discs with a diameter of 1 cm and then were transferred into flasks with the same medium and grown with orbital shaking (200 rpm) under constant light for one day. For the independent mRNA-seq, the culture condition was identical to that described above, except that CHX was not added.

extract_protocol:
For the ribosome profiling and accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq™ Ribosome Profiling Kit(Catalog Number: RPYSC12116). For the independent mRNA-seq, total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase (Turbo DNase, Ambion) accoding to standard RNA extraction protocal.
For the ribosomal profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq™ Ribosome Profiling Kit(Catalog Number: RPYSC12116). For the independent mRNA-seq, libraries were constucted using Illumina TruSeq reagents. All RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the ribosome profiling and accompanying mRNA-seq, CHX (final concentration of 50 g/ml) was added 10 min before collecting the samples. For the mRNA-seq, no special treatment was performed.

value: mycelia

value: adat2-silenced mutant

tag: molecule

value: mRNA


title: mRNA-seq-Siadat2-replicate_1

status: Public on May 22 2020

type: SRA

city: Dallas

state: Texas

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: tissue

tag: genotype/variation


title: iMG_Chol [AGGCAGAA]

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

data_processing:
Sabre for demultiplexing based on 8bp sample barcode
RNAsik for alignment, deduplication and counting (Tsyganov, K., Perry, A., Archer, S. and Powell, D. (2018). RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease. Journal of Open Source Software 3.)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts of transcripts are provided as .txt files. Gene lists are provided as excel spreadsheets.
Supplementary_files_format_and_content: Text file of RNA-seq gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: iPS-derived microglia like cells

growth_protocol: Differentiation of iPS/ES cells to microglia-like cells  iHPC Differentiation Base Medium: IMDM (50% v/v, 12440053, ThermoFisher Scientific), F12 (50% v/v 11765054, ThermoFisher Scientific), ITS-X (2% v/v, 51500056, ThermoFisher Scientific), L-ascorbic acid 2-Phosphate magnesium (64 μg/ml, A8960, Sigma), monothioglycerol (400 μM, M6145, Sigma), PVA (10 μg/ml, P8136, Sigma), Glutamax (1X, 35050061, ThermoFisher Scientific), chemically-defined lipid concentrate (1X, 11905031, Thermo Fisher Scientific), non-essential amino acids (NEAA, 1X, 11140050, ThermoFisher Scientific), Penicillin/Streptomycin (P/S, 1% v/v, 15140122, ThermoFisher Scientific). Use 0.22 μm filter.     iMGLs Differentiation Medium: phenol-free DMEM/F12 (1:1, 11039021, ThermoFisher Scientific), ITS-G, (2% v/v, 41400045, ThermoFisher Scientific), B27 (2% v/v, 17504044, ThermoFisher Scientific), N2 (0.5% v/v, 17502048, ThermoFisher Scientific), monothioglycerol (200 μM, M6145, Sigma), Glutamax (1X, 35050061, ThermoFisher Scientific), NEAA (1X, 11140050, ThermoFisher Scientific), and additional insulin (5 μg/ml, I2643, Sigma), filtered through a 0.22 μm filter; supplemented with M-CSF (25 ng/ml, 130-096-492, Miltenyi biotec), IL-34 (100 ng/ml, 130-108-977, Miltenyi biotec), and TGF-1 (50 ng/ml, 130-108-969, Milteniy biotec) and cholesterol (1.5 μg/ml, 700000P, Avanti Polar Lipids).    The protocol for iMGL derivation was adapted from Abud et al. with modifications from the StemDiff Hematopoietic Kit (05310, Stem Cell Technologies). H9 CX3CR1-tdTomato cells were cultured on vitronectin (A14700, Thermo Fisher Scientific)-coated T25 flasks in E8 medium (A1517001, Thermo Fisher Scientific). 2 days prior to differentiation, cells were detached in 0.5mM EDTA and 40-80 colonies /well were seeded into a 12 well plate in E8 medium. On day 0, E8 medium was exchanged for 1 mL of supplemented iHPC Differentiation Base Medium per well. iHPC Differentiation Base Medium supplemented with FGF2 (50 ng/ml, 130-093-564, Miltenyi biotec), BMP4 (50 ng/ml, 130-111-165, Miltenyi biotec), Activin-A (12.5 ng/ml, 130-115-010, Miltenyi biotec), ROCKi (1 μM, 130-103-922, Milteniy biotec) and LiCl (2 mM, L7026, Sigma), and incubated in a hypoxic incubator. On day 2, medium was changed to 1 mL of iHPC Differentiation Base Medium supplemented with FGF2 (50 ng/ml) and VEGF (50 ng/ml, 130-109-385) and incubated in a hypoxic incubator. On day 4, medium was changed to 1 mL iHPC Differentiation Base medium containing humam FGF2 (50 ng/ml), VEGF (50 ng/ml), TPO (50 ng/ml, 130-095-752, Miltenyi biotec), SCF (10 ng/ml, 130-096-695, Miltenyi biotec), IL-6 (50 ng/ml, PHC0061, ThermoFisher Scientific), and IL-3 (10 ng/ml, PHC0031, ThermoFisher Scientific) and incubated under normoxia. Half the medium was replaced on days 5 and 7 with the same medium as day 4. On day 10, the supernatant containing the HPCs was collected, centrifuged (300 x g for 5 min at room temperature; RT), then 0.5ml cell-containing medium was replaced and supplemented with 0.5ml fresh medium. On day 12, the supernatant containing HPCs was collected and plated onto matrigel (1:40, 354277, hESC-qualified Matrix, LDEV-Free, Falcon)-coated 12 well plates at 1x105 cells/well in iMGL complete differentiation medium. Every two days, each well was supplemented with 0.5 ml per well of complete differentiation medium, and at day 22 a 50% media change was performed. From day 35, iMGLs were cultured in complete iMGL differentiation medium supplemented with human CD200 (100 ng/ml, C311, Novoprotein) and CX3CL1 (100 ng/ml, 300-31, Peprotech) for an additional three days.

extract_protocol:
RNA extraction from 1-10 x104 FACS-sorted CX3CR1+ iMGLs or from 2 wells of iMGLs harvested directly from 12 well plates, was performed on the QIAcube (Qiagen) using the RNeasy Micro Kit (Qiagen, Hilden, Germany) and RNA quality was assessed using the Bioanalyser (Agilent RNA 6000 Pico kit).
The libraries were prepared using 0.5-2 ng RNA with RIN value ≥ 8. An 8 bp sample index (Supplementary table 2) and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.

treatment_protocol: ReN cells (Millipore) were maintained and differentiated as previously described (Choi et al. 2014). Briefly, cells were maintained on Matrigel-coated flasks (BD Biosciences, San Jose, CA, USA) in DMEM/F12 (11320033, ThermoFisher Scientific) supplemented with 2 µg/ml heparin (07980, StemCell Technologies, 07980), 2% (v/v) B27, 20 µg/ml EGF (130-097-749, Miltenyi biotec), 20 µg/ml bFGF and 1% (v/v) P/S. Neuronal and glial differentiation was achieved by growth factor withdrawal, with twice-weekly half media changes. For co-culture assays, iMGLs were added to 21 d differentiated ReN cells for a further 21 d.

tag: treatment

value: iMG+cholesterol


title: iMG [CGTACTAG]

value: iMG


title: 24h_Acetic_JQ1_1

city: Montreal

first: Jason

last: Tanny

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Fastq files were trimmed with TrimGalore (v0.6.0)  with the settings --phred33 --length 36 -q 5 --stringency 1 -e 0.1
Fastq files were aligned rn6 genome assembly using STAR (v2.7.1a)
Transcript assembly was completed using StringTie (v1.3.4d)
The tximport (v1.12.3) R package was used to import into R (3.6.1) and summarize transcript abundance (t_data.ctab) to gene-level counts
Differential gene expression was completed with DESeq2 (v1.24.0)
Genome_build: Rattus_norvegicus.Rnor_6.0.94
Supplementary_files_format_and_content: StringTie transcript-level expression measurements for each sample are provided as tab-delimited files

organism: Rattus norvegicus

source_name: Cardiomyocytes

growth_protocol: Cardiomyocytes were isolated from 1-3 day old Sprague-Dawley rats and plated on 10 cm dishes coated with 0.1% gelatin and 10 μg/mL fibronectin at a density of 40 000 cells/cm2. Neonatal rat cardiomyocytes were cultured for 24 h in DMEM low glucose + 7% FBS + P/S + 10 μM cytosine β-d-arabinofuranoside (AraC). Media was changed and neonatal rat cardiomyocytes cultured for 24 h with DMEM low glucose + ITS + P/S +  10 μM AraC. Media was changed to DMEM low glucose + ITS + P/S for an additional 24 h before initiation of treatments.

extract_protocol:
RNA isolated with Qiagen RNeasy kit with on-column DNAse I
Libraries were prepared using the NEBNext rRNA-depleted (HMR) stranded library kit

treatment_protocol: Neonatal rat cardiomyocytes were treated for 24 h with the indicated agonist and antagonist

tag: cell type

value: Cardiomyocytes

tag: age

value: Neonatal

tag: agonist

value: Acetic Acid (Vehicle)

tag: antagonist

value: 1 μM JQ1


title: BS_HS_BAL_916

type: genomic

city: Stockholm

first: Mikael

last: Ringh

state: Choose state (US & Canada)

address: Medical Epigenetics, CMM L8:00, Karolinska University Hospital Solna

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Conventional bisulfite conversion as well as oxidative bisulfite conversion using TrueMethyl conversion kit from Cambridge Epigenetix (CEGX). 250 ng of DNA per reaction followed by llumina MethylationEPIC BeadChip hybridization via Standard Illumina Protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina HiScan

data_processing: SQN normalisation

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Bronchoalveolar lavage cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol

tag: Sex

value: F

tag: diagnosis

value: H

tag: group

value: HS

value: S

tag: fvc


title: mRNA-seq-WT-replicate_2

value: wild type


title: BS_HS_BAL_913


title: BS_HS_BAL_920


title: 3342CA1

city: Gainesville

first: Tom

last: Foster

state: FL

address: 1149 Newell Drive

institute: University of Florida

data_processing:
ERCC analysis was performed with the ERCC analysis plugin in the Torrent. Spiked samples had an R2 above 0.9.
Ion Torrent derived reads were  aligned to the rattus norvegicus genome rn6 using STAR 2.5.3a in the in the Partek Flow servers Partek, Inc., St. Louis, MO.
Gene read counts were generated from Binary Alignment Map BAM files and annotated to the genome using Ensembl version 92; Partek, Inc..
Reads from FASTQ files produced by the Ion Torrent System were trimmed from both ends until all samples’ collective average Phred quality score was > 25. Reads shorter than 25 base pairs bps were also excluded.
Gene lists were filtered to exclude genes with an average count of 5 or less averaged across all samples included in a comparison.
Normalization and pairwise differential expression analysis were conducted using the DESeq2 package version 3.5 for comparisons by age, cognitive performance or hippocampal subregion. The threshold of significance was set at p<0.025 for differences by age.
Genome_build: Ensembl version 92; Partek, Inc..
Supplementary_files_format_and_content: Comma-separated values .csv files that contain the normalized counts for each sample

source_name: CA1 region of the hippocampus

extract_protocol:
Rats were briefly anesthetized with isoflurane Patterson Veterinary, Greenly, CO and swiftly decapitated. The brains were then rapidly removed, and the hippocampi were dissected according to previously described methods Lein 2004; Zeier 2011. The hippocampal regions DG, CA1, and CA3 were separated, placed in the tubes, and flash-frozen in liquid nitrogen. All samples were stored in at -80°C until processed. RNA was isolated from subregions of a hippocampus from a single hemisphere of each animal. RNA Isolation was performed according to methods previously described Ianov 2016; Barter 2019. Briefly, RNA was isolated using the RNeasy Lipid Tissue Mini kit Qiagen, catalog number 74804. Total RNA was treated with DNase using the RNase-Free DNase Set Qiagen, catalog number 79254. Concentration of total RNA was assessed using the NanoDrop 2000 spectrophotometer Thermo Fisher catalog number ND-2000 and the RNA integrity number RIN was quantified using the Agilent 2200 Tapestation system with High Sensitivity RNA Screen Tape Agilent Technologies, Santa Clara, CA. Mean RNA integrity across all samples was 9.05 SEM ± 0.02 with values ranging from 8.2 to 9.3. Poly-A-selection for mRNA was performed using 250 ng of isolated total RNA in the Dynabeads mRNA DIRECT Micro kit Thermo Fisher, catalog number 61021. External RNA Controls Consortium ERCC RNA Spike-In Control Mixes were included in all isolated mRNA samples Thermo Fisher, catalog number 4456740.
Library preparation was performed using the Ion Total RNA-seq Kit v2 Thermo Fisher, catalog number 4475936. Ion Xpress barcodes Thermo Fisher, catalog number 4475485 were included with libraries for multiplex sequencing. In summary, isolated mRNA was fragmented with RNase III then ligated to the Ion Adapter Mix v2. RNA samples were then reverse transcribed. cDNA from each biological replicate was uniquely barcoded and amplified with 16 PCR cycles. Library concentration from each sample was quantified using the Qubit dsDNA HS Assay Thermo Fisher, catalog number Q32851. DNA fragment size distribution was subsequently evaluated using High Sensitivity D1000 ScreenTape in the 2200 Tapestation system Agilent Technologies, Santa Clara, CA.   Templates were prepared using the Ion Chef system Thermo Fisher, catalog number 4484177 and sequencing was performed using the Ion Proton system Thermo Fisher, catalog number 4476610 or Ion GeneStudio S5 system Thermo Fisher, catalog number A38194.

value: CA1 region of the hippocampus

value: 5 months

value: male


title: 24h_ET1_DMSO_2

value: DMSO (Vehicle)


title: mRNA-seq-WT-replicate_1

value: mycelia


title: iMGpChol [TAAGGCGA]


title: Vero m6A-IP viral genome RNA2

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

description:
m6A enriched mRNA
PEDV_readCount.txt

data_processing:
Seequencing reads were aligned to reference genome by Hisat2
Read counts in 50-bp consecutive bin were obtained using R package m6Amonster
Genome_build: KF272920.1 Porcine epidemic diarrhea virus strain USA/Colorado/2013, complete genome
Supplementary_files_format_and_content: Read counts in 50-bp consecutive bin on the PEDV geonme

organism: Porcine epidemic diarrhea virus

source_name: Vero

growth_protocol: Monkey kidney epithelial cell lines (MARC-145 and Vero [ATCC CCL-81]), a swine kidney epithelial cell line (LLC-PK1), and a swine intestinal epithelial cell line (IPEC-DQ) were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in a 37 °C incubator.

extract_protocol:
TRIzol (Invitrogen) + RiboMinus Eukaryote System v2
Kapa hyper RNA library kit
MeRIP-seq

treatment_protocol: RNAs were extracted from highly purified PEDV virions and purified with the RiboMinus Eukaryote System v2 kit (Thermo Fisher) to remove ribosome-derived RNA.

value: viral genome

tag: host cell line

value: Vero


title: IZ_rep2

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

description: Current project: combat between brown rot fungi was sptially acomplished by wafer design

data_processing:
RNA-seq data analysis was performed on the Galaxy platform (https://usegalaxy.org/) using described procedures for differential expression analysis (Trapnell et al., 2012). Raw reads were cleaned with Trimmomatic (v0.3) and mapped against the R. placenta MAD698-R (v1.0) and G. trabeum ATCC11539 (v1.0) genomes together as a concatenated genome using TopHat (v2.0.13). Previously generated RNA-seq data (GSE108189) from single-species cultures of both species grown on equivalent aspen wafers were used for comparison to data generated in this study (Zhang et al., 2016)(Zhang et al., 2019). In specific, these previouly geneated datasets are GSM2892065, GSM2892066 and GSM2892067 for R. placenta, and GSM2892074, GSM2892075 and GSM2892076 for G. trabeum. Expression levels found at the leading hyphal edge of fungal cultures on aspen and 5 mm outside of the IZ toward each species were compared to expression levels found at the IZ. Reference transcript models from the JGI mycocosm database were used to determine differences in expression levels as Reads Per Kilobase Per Million (RPKM) in pairwise comparisons among samples using Cuffdiff (Galaxy Tool Version 2.2.1.3) using geometric normalization. FDR was set at <0.05. Transcripts with 4-fold greater RPKM values in the IZ sample relative to other samples were identified.
Genome_build: Postia placenta MAD-698-R v1.0 and Gloeophyllum trabeum v1.0 from JGI (https://genome.jgi.doe.gov/programs/fungi/index.jsf)
Supplementary_files_format_and_content: Excel file (.xlsx) includes pairwise comparison and RPKM levels.

organism:
Rhodonia placenta
Gloeophyllum trabeum

source_name: brown rot decayed wood

growth_protocol: Gloeophyllum trabeum ATCC 11539 and Rhodonia (Postia) placenta MAD 698-R were maintained on malt extract agar and 1 cm diameter agar plugs were used to inoculate soil block microcosms as previously described (Presley and Schilling, 2017). Sterile 19 mm aspen blocks were degraded for 4 weeks in soil block jars for each species and then were used as inoculum for interaction microcosms. Interactions were simulated by placing one G. trabeum and one R. placenta block opposing one another in empty soil microcosms and laying a 60 x 23 x 3 mm aspen wafer (largest face in cross section) across the top of the two blocks (Figure 1). Fungal hyphae grew together until they met in the center of the wafer, forming an interaction zone which was then sampled along with surrounding hyphae for protein and RNA, as described below.

extract_protocol:
Total fungal RNA was extracted from fresh wood sections with TRIzol (Life Technologies) and cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc.) prior to RNA sequencing or quantitative RT-PCR (qRT-PCR), a method validated in Zhang et al. (2016).
For RNA sequencing, TruSeq RNA v2 libraries were prepared and sequenced on a HiSeq 2500 System (Illumina Inc., San Diego, CA) by using the standard protocols from Illumina.

treatment_protocol: not applicable

value: Interaction Zone


title: Mock hepatocytes rep3

city: London

first: Efstathios

last: Giotis

address: Norfolk Place

department: Infectious Diseases

country: United Kingdom

institute: Imperial College London

description: ChimericMiceAnalysis.txt

data_processing:
SOAPnuke (v1.5.2) software was used to filter out non-human sequencing reads
Sequencing data (Fastq raw files) were imported into Partek Flow (version 8.0, build 8.0.19.1125; Partek Inc., St. Louis, MO, USA), quality-controlled, and thereafter processed.
Paired-end reads were trimmed based on the Phred quality score threshold of >20 and aligned to the human genome (hg38) with the STAR - 2.6.1d aligner.
Quantification was done using the transcript model Ensembl Transcripts release 91.
Differential expression analysis was performed using the package DESeq2 (DESeq2 - 3.5).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include output of DESeq2 analysis of the HBV-infected versus mock samples comparison (total counts per gene, FDR, fold change of gene expression).

organism:
Homo sapiens
Mus musculus

source_name: Liver

growth_protocol: Female FNRG mice (Wilson, E. M. et al. Extensive double humanization of both liver and hematopoiesis in FNRG mice. Stem Cell Res 13, 404-412 (2014)) between 8-12 weeks old of age were transplanted with 0.5 × 106 of cryopreserved adult human hepatocytes (Donor 28 from QPS, USA and Hu1583 and Hu8181 from Life Technologies, USA). Hepatocytes were provided by intrasplenic injection. To make possible the engraftment of adult human hepatocytes, mice were cycled off and on with the drug nitisinone (Yecuris, USA) according to weight loss and health state.

extract_protocol:
RNA from four HBV-infected and three uninfected liver chimeric mice were collected using standard procedures and the RNeasy Qiagen kit for library production and strand-specific RNA-sequencing at the Beijing Genomics Institute (BGI, Hong Kong). RNA purity was assessed with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and RNA integrity was determined with a 2100 Bioanalyzer Instrument (Agilent Technologies).
Poly (A) mRNA was purified from total RNA using magnetic beads with oligo (dT) (New England BioLabs, Hitchin, UK). The mRNA was then broken into short fragments using divalent cations at an elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH (New England BioLabs, Hitchin, UK). These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are purified and enriched with PCR amplification. The library is then circularized as previously described (Drmanac, R et al. 2010). From single stranded circles, DNA nanoballs are made and loaded onto patterned nanoarrays (Drmanac, R et al. 2010). The nanoarrays are then subjected to combinatorial probe-anchor synthesis (cPAS) based sequencing on the BGISEQ-500 (Fehlmann, T. et al, 2016; Huang, J. et al, 2017; Mak, S. S. T. et al, 2017), employing the PE100 mode to produce raw paired‐end reads of 100 bp.

treatment_protocol: FNRG mice engrafted with human adult hepatocytes according to serum human albumin secretion (at least 0.1mg human albumin per mL in peripheral blood) were infected with 0.5 million GE per mouse using infectious recombinant HBV produced from the tetracycline-inducible HepDE19 cells as previously described (Ortega-Prieto et al, Nature Communications 2018). Mice were sacrificed and livers were harvested for analysis once stable viremia was established and mice were highly infected (minimum 5 x 107 GE/mL of serum).

tag: infection

value: Uninfected

tag: donor

tag: weeks post transplantation


title: Vero m6A-IP viral genome RNA1

description:
m6A enriched mRNA
PEDV_readCount.txt


title: Mock hepatocytes rep2

description: ChimericMiceAnalysis.txt


title: IZ_rep1


title: iMG [ACTCGCTA]

description:
FACS sorted tdTomato+
sikRun/bamFiles/236_ACTCGCTA_sorted_umi_mdups.bam

value: iMG


title: iMG_ReN [ATCTCAGG]

description:
FACS sorted tdTomato+
sikRun/bamFiles/235_ATCTCAGG_sorted_umi_mdups.bam

value: ReN cells + iMG


title: BS_HNS_BAL_903

value: HNS

value: NS


title: 3347CA1

value: 12 months


title: HBV infected hepatocytes rep4

description: ChimericMiceAnalysis.txt

value: Infected with Hepatitis B virus


title: METTL3 KO U2OS m6A-IP viral genome RNA2

description:
m6A enriched mRNA
PEDV_readCount.txt


title: Mock hepatocytes rep1

description: ChimericMiceAnalysis.txt


title: BS_HS_BAL_910

value: F

value: H

value: HS

value: S


title: iMG_ReN [GGACTCCT]

description:
FACS sorted tdTomato+
sikRun/bamFiles/244_GGACTCCT_sorted_umi_mdups.bam


title: BS_MSS_BAL_854

value: MS

value: MSS

value: IFNb

value: Avonex

value: remission

value: RRMS


title: iMG_ReN [GTAGAGGA]

description:
FACS sorted tdTomato+
sikRun/bamFiles/141_GTAGAGGA_sorted_umi_mdups.bam


title: BS_MSNS_BAL_878

value: MSNS

value: SPMS


title: iMG [GCTCATGA]

description:
FACS sorted tdTomato+
sikRun/bamFiles/142_GCTCATGA_sorted_umi_mdups.bam

value: iMG


title: HBV infected hepatocytes rep3

description: ChimericMiceAnalysis.txt


title: Ctrl_NCD_52wks_3

type: RNA

city: Vancouver

first: Dan

last: Wu

address: 950 West 28th Avenue

description: Control (Foxp3-cre) mice were aged on chow diet for 52 weeks to reach ageing-associated hyperinsulinemia. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.

hyb_protocol: Input total lysate was hybridized to target sequence-specific capture probes and fluorescent-labelled reporter probes for 15-19 hours at 65°C as according to the manufacturer's protocol. https://www.nanostring.com/download_file/view/863/3778

scan_protocol: The hybridized codesets were read by a nCounter® SPRINT Profiler at the BC Children's Hospital Research Institute, Vancouver, Canada.

data_processing: Reporter probe counts for samples were subjected to quality control (QC) metrics using the NSolver software v4.0 (NanoString Technologies). Samples were then normalised, log tranformed and analyzed using Microsoft Excel.

label: Nanostring mRNA probe

organism: Mus musculus

source_name: VAT Treg

label_protocol: A minimum of 4 ul of total Treg lysate was used to measure the expression of 96 genes using the nCounter® SPRINT Profiler (NanoString Technologies) according to the manufacturer's protocol.

growth_protocol: Foxp3-YFP-Cre mice (Jackson Laboratory, 016959) and Insr-fl/fl mice (Jackson Laboratory, 006955) both on a C57/Bl6 background were crossed to generate Foxp3-YFP-Cre;Insr-wt/wt mice (control) and Foxp3-YFP-cre;Insr-fl/fl mice (Treg-specific insulin receptor knockout). Recently, we and others reported that the widely-used Foxp3-YFP-Cre mice displayed ectopic Cre recombination outside of the Treg population (PMID 31713233). In order to generate a sufficient number of animals while maintaining a matched genetic background, we used F4-generation mice obtained by breeding F3 littermates to each other, as described in Figure 6 of Wu et al (PMID 31713233).

extract_protocol: Visceral adipose tissue (VAT) were harvested as described (PMID 25549006). VAT from each animal were minced and digested in 0.5 mg/mL collagenase II (Worthington Biochemical, LS004176) at 37°C for 45 min, passed through a 100 μm cell strainer, and centrifuged to obtain Stromal Vascular Fraction (SVF) cells. SVF cells were resuspended in 1 mL red blood cell lysis buffer (0.8% NH4Cl, STEMCELL Technologies, 07800), incubated for 5 min at room temperature, washed with FACS Buffer (PBS, 0.5% BSA, 2 mM EDTA), and stained for flow cytometry. To isolate Tregs, flow cytometric sorting was performed on a FACSAria II (BD Biosciences). Tregs were sorted as CD45+CD4+Foxp3(YFP)+ cells and immediately lysed to store at -80C until time for Nanostring gene expression assay.

treatment_protocol: For high-fat diet studies, 3-week-old male mice were fed a high-fat-high-sucrose diet (HFD, 58 kcal% fat and sucrose, Research Diet, D12331) or a normal-chow diet (NCD, Lab Diet, 5P76) for 13 weeks. For aging studies, male mice were aged to 52 weeks old on NCD.

value: male

tag: genotype

tag: diet

value: chow diet

value: 52 weeks


title: HBV infected hepatocytes rep2

description: ChimericMiceAnalysis.txt

value: Infected with Hepatitis B virus


title: WT U2OS m6A-IP viral genome RNA2

description:
m6A enriched mRNA
PEDV_readCount.txt

value: viral genome

value: WT


title: Ctrl_NCD_52wks_2

institute: BC Children's Hospital Research Institute

tag: strain


title: CD44_ReN [CGAGGCTG]

description:
FACS sorted CD44+
sikRun/bamFiles/137_CGAGGCTG_sorted_umi_mdups.bam

source_name: CD44+ cells

value: ReN cells


title: WT U2OS m6A-IP viral genome RNA1

description:
m6A enriched mRNA
PEDV_readCount.txt


title: Ctrl_NCD_52wks_1


title: Gt_0-5_rep3 (Gloeophyllum trabeum 0-5 mm_rep3)

organism: Gloeophyllum trabeum

tag: tissue

value: Gloeophyllum trabeum colonized wood


title: KO_NCD_52wks_6

description: Knockout (Foxp3-cre;Insr-fl/fl) mice were aged on chow diet for 52 weeks to reach ageing-associated hyperinsulinemia. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.


title: IPEC METTL-KD m6A-IP viral genome RNA2

description:
m6A enriched mRNA
PEDV_readCount.txt

source_name: IPEC

value: IPEC


title: Pooled RNA from brain, liver, kidney, spleen, muscle and ovary of female Etroplus Suratensis

city: Kochi

first: Rejish Kumar

state: Kerala

address: Assistant Professor Dept. of Aquaculture School of Aquaculture and Biotechnology

department: Aquaculture

country: India

institute: Kerala University of Fisheries and Ocean Studies

data_processing:
Cutadapt 1.8 was used for processing adapter sequences
Sickle used for Trimming paired end reads
Trinity (trinity rnaseq 2.2.0) was used for Denovo assembly of sequences
Bowtie 2.2.6 was used for alignment of sequences
DEseq 1.16.0 was used for differential expression analysis
Supplementary_files_format_and_content: csv. files for gene expression contain read count and FPKM values for each gene

organism: Etroplus suratensis

extract_protocol:
Organs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: female


title: CD44_iMGpReN [CTCTCTAC]

description:
FACS sorted CD44+
sikRun/bamFiles/136_CTCTCTAC_sorted_umi_mdups.bam

tag: treatment

value: ReN cells + iMG


title: IPEC METTL-KD m6A-IP viral genome RNA1

description:
m6A enriched mRNA
PEDV_readCount.txt


title: Gt_0-5_rep2 (Gloeophyllum trabeum 0-5 mm_rep2)


title: KO_NCD_52wks_5


title: Pooled RNA from brain, liver, kidney, spleen, muscle and testis of male Etroplus Suratensis


title: BS_MSS_BAL_873

value: F

value: MS

value: MSS

value: S

value: Other

value: Gilenya


title: KO_NCD_52wks_4

value: male


title: Gt_0-5_rep1 (Gloeophyllum trabeum 0-5 mm_rep1)


title: IPEC Control m6A-IP viral genome RNA2

description:
m6A enriched RNA
PEDV_readCount.txt


title: Bagasse_in_natura_rep3

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.32
the evaluation and filtration of the rRNAs were performed using SortmeRNA
The filtered data were mapped into the L. sulphureus ATCC 52600 reference genome sequenced in this work using Tophat2 algorithm
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparisons against the control condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the non-induced condition (T0) were determined by applying p ≤ 0.05 as the threshold.
Genome_build: L. sulphureus ATCC 52600 reference genome sequenced in this work
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results

organism: Laetiporus sulphureus

growth_protocol: Pre-inoculum, consisting of 15 discs (8 mm diameter) of L. sulphureus ATCC 52600 pre-cultivated on agar plates, was inoculated into 100 mL of liquid medium and incubated under 180 rpm for 7 days at 30 °C.  Mycelium from pre-inoculum was used as a reference before induction (T0)

extract_protocol:
The mycelium was ground with liquid nitrogen, and total RNA extraction was performed with mirVana™ Total Isolation Kit (Thermo Fisher), according to the manufacturer's instructions. The resulting solution was treated with DNAse (DNA-Free RNA Kit, Zymo Research), purified with RNeasy Kit (Qiagen) and quality was verified using RNAnano Bioanalyzer 2100 chip (Agilent).
Libraries were prepared using Illumina TruSeq mRNA kit according to the manufacturer's instructions and sequenced on the Illumina HiSeq 2500 platform.

treatment_protocol: Mycelia were then filtered and washed with water and then transferred to liquid medium containing 1.0 g of in natura sugarcane bagasse and 100 mL of medium pH 7.0 composed of 6 g/L (NH4)2SO4, 1 g/L KH2PO4, 1 g/L KCl and 1 g/L MgSO4. Cultivation was performed under 180 rpm for 24 h at 30 °C. Mycelia and substrate mixtures were collected by filtration, washed with sterile water, manually dried in filter paper, and stored at -80 °C before RNA extraction.


title: IZ-5Gt_rep2


title: KO_NCD_52wks_3

value: chow diet


title: IPEC Control m6A-IP viral genome RNA1

description:
m6A enriched RNA
PEDV_readCount.txt


title: METTL3 KO U2OS m6A-IP viral genome RNA1

description:
m6A enriched mRNA
PEDV_readCount.txt


title: HBV infected hepatocytes rep1

description: ChimericMiceAnalysis.txt


title: IZ-5Gt_rep1


title: Bagasse_in_natura_rep1


title: Vero Input viral genome RNA2

description:
Input RNA
PEDV_readCount.txt

value: Vero


title: KO_NCD_52wks_2

value: 52 weeks


title: BS_HNS_BAL_722

value: H

value: HNS

value: NS


title: BS_MSS_BAL_821

value: Untreated

value: remission

value: RRMS


title: Bagasse_in_natura_rep2


title: iMG_ReN [AAGAGGCA]

description:
FACS sorted tdTomato+
sikRun/bamFiles/140_AAGAGGCA_sorted_umi_mdups.bam

value: ReN cells + iMG


title: Time_0_rep3


title: METTL3 KO U2OS Input viral genome RNA2

description:
Input RNA
PEDV_readCount.txt

value: viral genome


title: BS_HS_BAL_828

value: F

value: HS


title: Vero Input viral genome RNA1

description:
Input RNA
PEDV_readCount.txt


title: Time_0_rep2


title: DEKRIP_IP_rep2

city: Hong Kong

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

data_processing:
RIP-seq data were aligned using Hisat2 (version 2.1.0).
Then, flagstat (Samtools version 1.9) was to quantify total aligned reads and featureCounts (Subread version 1.6.4) was to quantify aligned reads according to the reference’s annotations.
Relative gene expression level was calculated by FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: Table of genes by samples of FPKM values.  File format is xlsx file.

source_name: PolyA+ RNA pulled down by Dek protein from freshly-isolated quiescent muscle stem cell

extract_protocol:
RNA was isolated using Nucleospin XS RNA isolation kit (Macherey-Nagel).
cDNA was generated following the protocol of the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). The RNA-Seq libraries were fragmented using Tn5 transposases with adaptors and amplified using PCR. The library was sequencing using an BGISEQ-500RS (2 x 100).

value: Skeletal muscle

tag: cell type

value: Muscle stem cells


title: DEKRIP_IP_rep1


title: KO_NCD_13wks_3

description: Treg-specific insulin receptor deletion (Foxp3-cre;Insr-fl/fl) mice were fed a normal chow diet (NCD) for 13 weeks, starting at 3 weeks old. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.

tag: age

value: 16 weeks


title: KO_NCD_13wks_2

value: male


title: DEKRIP_Input_rep2

source_name: PolyA+ RNA from freshly-isolated quiescent muscle stem cell as input control


title: METTL3 KO U2OS Input viral genome RNA1

description:
Input RNA
PEDV_readCount.txt


title: KO_NCD_52wks_1

value: chow diet


title: BS_HNS_BAL_707


title: Time_0_rep1


title: BS_MSS_BAL_872

value: MS

value: MSS

value: S

value: IFNb

value: Avonex

value: relapse


title: KO_NCD_13wks_1


title: Bd+DSF_3

city: CLEVELAND

first: MOHAMMED

last: DWIDAR

state: OHIO

address: 2111 E96th street

department: Center for Microbiome and Human Health

institute: Cleveland Clinic Lerner Research Institute

description: processed data file: Raw_counts_and_TPM_matrix.xlsx

data_processing:
RNA Seq data was quality trimmed using Nesoni pipeline (https://github.com/Victorian-Bioinformatics-Consortium/nesoni).
Quality trimmed reads were mapped on the reference genome using the Salmon pipeline.
The relative abundances for each transcript, in units of Transcripts Per Million (TPM), were used for the downstream analysis.
Pairwise two group comparisons were performed using Welch’s t-test with Benjamini-Hochberg False Discovery Rate (FDR) correction.
Genome_build: Bdellovibrio bacteriovorus 109J genome downloaded from NCBI (NZ_CP007656.1).
Supplementary_files_format_and_content: Raw_counts_and_TPM_matrix.xlsx: Matrix of raw_counts and TPM data for all samples.

organism: Bdellovibrio bacteriovorus

source_name: Bacterial culture

growth_protocol: Independent 150 ml overnight cultures of B. bacteriovorus were filtered (0.45 μm) to remove the remaining prey cells, centrifuged (16,000xg, 10 min) and concentrated 10-fold. For the attack-phase (AP) tests, portions of these cultures were incubated at 30ºC with or without 50 μM DSF for 30 min before the RNA was extracted. For the intraperiplasmic exposure tests, E. coli MG1655 cells from an overnight LB cultures were centrifuged (16,000xg, 5 min), resuspended in HEPES buffer to an OD of 4.3±0.2 and incubated at 30ºC for 1 h. The concentrated B. bacteriovorus cultures were then mixed 1:1 (v:v) with the E. coli prey so that the MOI (multiplicity of infection) was approximately five. After incubating the mixed cultures for 2 h at 30ºC, either DSF (50 μm) or sterile HEPES buffer was added and they were incubated 30 minutes longer, after which the bdelloplasts were pelleted (16,000xg, 2 minutes) and the RNA extracted.

extract_protocol: RNA was extracted using TRIZOL method then further purified using Qiagen RNA extraction kit.

treatment_protocol: Treatment was done using 50 μM DSF for 30 min before the RNA was extracted.

tag: growth phase

value: 2h Intraperiplasmic growth phase

value: DSF


title: DEKRIP_Input_rep1


title: Bd+DSF_2


title: BS_HNS_BAL_694

value: H

value: HNS

value: NS


title: WT U2OS Input viral genome RNA1

description:
Input RNA
PEDV_readCount.txt

value: viral genome

value: WT


title: IPEC METTL-KD Input viral genome RNA2

description:
Input RNA
PEDV_readCount.txt

value: IPEC


title: Patient_5

city: Shanghai

first: Jinchao

last: Jia

address: No. 197 Ruijin Second Road

country: China

institute: New Markers for Adult-Onset Still's Disease

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Differentially expressed genes (DEGs) with a fold change >2 and p value< 0.05 were determined using DEGseq analysis package
Genome_build: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary_files_format_and_content: text file includes read count values for each Sample

source_name: peripheral neutrophils

growth_protocol: freshly isolated peripheral neutrophils

extract_protocol:
Neutrophils were isolated by density gradient centrifugation on Polymorphprep (Axis-Shield, Dundee, UK) according to the manufacturer’s instructions.
Oligo(dT)-attached magnetic beads-purified mRNA was fragmented into pieces at appropriate temperature. cDNA was generated by random hexamer-primed reverse transcription. Afterwards, RNA Index Adapters and A-Tailing Mix were added to end repair. The cDNA fragments were amplified by polymerase chain reaction (PCR), and products were purified using Ampure XP Beads. The products were qualified on Agilent Technologies 2100 bioanalyzer. The double-strand PCR products were denatured and circularized by the splint oligo sequence to construct the final library. Then the single-strand circle DNA was formatted as the final library. The final library was amplified by phi29 to produce DNA nanoball (DNB) with more than 300 copies of one molecule. DNBs were loaded into patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: disease state

value: Adult-onset Still’s disease (AOSD)

value: Neutrophils


title: Patient_6


title: Ctrl_NCD_13wks_3

description: Control (Foxp3-cre) were fed a normal chow diet (NCD) for 13 weeks, starting at 3 weeks old. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.

tag: Sex

value: male

value: chow diet

value: 16 weeks


title: Patient_4


title: IPEC METTL-KD Input viral genome RNA1

description:
Input RNA
PEDV_readCount.txt


title: BS_HNS_BAL_703

value: F

tag: diagnosis


title: IPEC Control Input viral genome RNA2

description:
Input RNA
PEDV_readCount.txt

tag: group


title: BS_HNS_BAL_719

tag: fvc


title: Bd_2

value: Untreated


title: KO_HFD_13wks_5

description: Treg-specific insulin receptor deletion (Foxp3-cre;Insr-fl/fl) mice were fed  a high-fat diet (HFD) for 13 weeks, starting at 3 weeks old, to reach obesity and hyperinsulinemia. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.

value: high-fat diet


title: Bd_3


title: Patient_3


title: BS_HS_BAL_698

value: HS

value: S


title: Patient_2


title: IPEC Control Input viral genome RNA1

description:
Input RNA
PEDV_readCount.txt

tag: host cell line


title: Ctrl_NCD_13wks_2


title: WT U2OS Input viral genome RNA2

description:
Input RNA
PEDV_readCount.txt


title: Infected_4hpi_Infected_24hpi_Infected_UVvirus_4hpi_Infected_UVvirus_6hpi

city: Taipei

first: Chuan

last: Ku

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Read_1 files were mapped onto the reference sequences of the virus and the host using bowtie 2 (v2.2.4) (-p 10)
Demultiplexing and UMI counting (unique molecular identifiers (UMI) and cell barcodes are in read 2; pool barcodes are in read 1) was performed using the pipeline described in Keren-Shaul et al. 2019 (https://doi.org/10.1038/s41596-019-0164-4)
Each pool is marked by a unique pool barcode. Each plate corresponds to either one (RT1 primers gr1, gr2, gr3, and gr4) or two pools. In the latter case, each pool is a half plate (RT1 primers gr3 and gr4) where columns 1-12 are the processed data file A.txt and columns 13-24 B.txt.
Genome_build: EhV201 (virus) genome: JF974311; Emiliania (host) transcriptome reference (both forward and reverse complement (_rev) sequences): Schatz et al. 2017 Nature Microbiol. (https://doi.org/10.1038/s41564-017-0024-3); ERCC RNA Spike-In Mix
Supplementary_files_format_and_content: Tab-delimited table of UMIs (genes/transcripts by wells)

organism:
Emiliania huxleyi
Coccolithovirus

source_name: Cell culture

growth_protocol: 16/8 h light/dark cycle; K/2 medium; 18 °C; light: 100 μmol photons m-2s-1

extract_protocol:
RNA capture: Plates were forzen at -80C and thawed. Lysis solution (ddH2O, 0.1%triton, RNase inhibitors) was evaporated and reverse transcription was performed directly in the wells.
MARSseq library prepartion was performed as described in Keren-Shaul et al. 2019 (https://doi.org/10.1038/s41596-019-0164-4). Briefly, cDNA from different cells (barcoded in the reverse transcripiton step) was pooled and amplified by in vitro transcription. Amplified RNA was then fragmented, reverse transcribed, and Illumina adaptors were added by PCR.

treatment_protocol: Single cells were separated using fluorescence-activated cell sorting (FACS) directly into a lysis solution in 384-well plates.

tag: host strain

tag: virus strain

tag: well prefix

tag: pool barcode


title: Bd+DSF_1

value: 2h Intraperiplasmic growth phase

value: DSF


title: KO_HFD_13wks_4

tag: genotype

tag: diet


title: Patient_1


title: Bd_1

tag: strain


title: Ctrl_NCD_13wks_1


title: KO_HFD_13wks_2


title: Infected_6hpi_cycloheximide_Infected_8hpi


title: AP+DSF_3

value: Attack phase cells

tag: treatment


title: KO_HFD_13wks_3


title: HC_6

value: control

tag: cell type


title: AP+DSF_1


title: HC_5


title: Infected_0hpi


title: AP_3


title: HC_4


title: HC_3


title: Ctrl_HFD_13wks_4

description: Control (Foxp3-cre) mice were fed a high-fat diet (HFD) for 13 weeks, starting at 3 weeks old, to reach obesity and hyperinsulinemia. VAT Tregs were then isolated by fluorescence-activated cell sorting, and analyzed by a custom Nanostring mRNA panel.

tag: age


title: KO_HFD_13wks_1


title: Infected_6hpi


title: Infected_9.5hpi_Control_10hpi


title: Ctrl_HFD_13wks_2


title: HC_2


title: Ctrl_HFD_13wks_3


title: Infected_4.5hpi


title: AP_2

tag: growth phase


title: AP_1


title: HC_1

tag: disease state


title: Ctrl_HFD_13wks_1

tag: Sex


title: BS_HNS_BAL_641

tag: diagnosis

value: H

value: HNS

value: NS


title: NH_8120

status: Public on May 21 2020

city: Cheonan

first: Jihwan

last: Lee

address: Sinbang 1Gil 114, NIAS

country: South Korea

institute: National Institute of Animal Science

description: microRNA

data_processing:
Illumina bcl2fastq v2.20.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and for low-complexity or low-quality sequence with Cutadapt (v1.16).
In order to eliminate the effect of large amounts of rRNA from this study, the read was aligned to the rRNA sequence and have them removed.
To estimate expression levels, the rRNA filtered miRNA-Seq reads were mapped to the precursor and mature miRNA sequence of Homo sapiens (hg19) using miRDeep2 (2.0.0.8).
Genome_build: Btau_5.0.1
Supplementary_files_format_and_content: Matrix table with raw gene counts and normalized count (RPM) for every mature miRNA and every sample.

organism: Bos taurus

source_name: Blood (jugular vein)

extract_protocol:
MicroRNAs were isolated from whole blood using the PAXgene Blood MicroRNA Kit (Qiagen, 763134) according to the manufacturer’s instructions.
miRNA libraries were prepared for sequencing using Truseq Small RNA Library Prep Kit (Illumina).

tag: tissue

value: Blood (jugular vein)

tag: environment state

value: non-heat stress

tag: birth date

tag: condition

value: pregnant

tag: parity


title: NH_13079

description: microRNA

value: not pregnant


title: NH_15044

description: microRNA


title: NH_13003

description: microRNA


title: NH_14088

description: microRNA


title: NH_14054

description: microRNA


title: NH_14087

description: microRNA


title: NH_14045

description: microRNA


title: HS_14106

description: microRNA

value: heat stress


title: HS_14088

description: microRNA


title: HS_15044

description: microRNA


title: HS_14087

description: microRNA


title: HS_14054

description: microRNA


title: HS_13003

description: microRNA


title: AP+DSF_2


title: HS_13079

description: microRNA


title: NH_14106

description: microRNA


title: HS_14045

description: microRNA


title: ApoB_neg_Treg_8wks_Apoe-/-_2

city: La Jolla

first: Klaus

last: Ley

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC mm10 reference genome using TopHat (v 1.4.1)11. DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files. The alignment results were parsed via the SAMtools to generate SAM files. The sequencing performance was assessed by calculating mapping statistics based on the total number of mapped reads, total number of uniquely mapped reads, and read distribution over known gene models was computed by gene body coverage in RSeQC14. Read counts of each genomic feature were obtained with the htseq-count program (v 0.6.0) 70 using the ‘union’ option.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited Raw Expression counts file obtained through HTSeq. Samples as Columns, genes as rows

source_name: Pooled peripheral lymph node CD4 T cells

extract_protocol:
Pooled peripheral lymph nodes from indicated strains, genotypes, and ages were mechanically disrupted. CD4+ T cells were enriched with a magnetic bead negative separation protocol with antibodies against different leukocyte lineages (CD11b, CD11c, Nk1.1, F4/80, Ter-119, CD8, CD19). Enriched CD4+ T cells were then incubated for 50min with an ApoB-MHC-II tetramer in two colors (APC, PE). Leukocytes were then stained with an antibody-cocktail for flow cytometry. CD4+ TCR-alpha/beta+ CD45+, viability dye-negative, Lineage- (CD11b, CD11c, Nk1.1, F4/80, Ter-119, CD8, CD19) negative cells were sorted on an Aria-II flow cytometer. Cells binding the MHC-II tetramer (ApoB+) were separated from ApoB-negative CD4+ T cells and directly sorted into Trizol LS. As applicable, CD4+ T-regulatory cells were additionally identified as FR4+ and CD25+ T cells and sorted within the ApoB-negative population. RNA was extracted using a RNeasy Mini Kit (Qiagen) following the standard protocol.
RNA integrity of total RNA was verified on a pico chip (Agilent Bioanalyzer). Library preparation was done with a SMART-Seq v4 Ultra Low Input RNA Kit by Clontech and the Nextera XT Kit (Illumina) with an input of 0.5 ng RNA. The resulting average concentration was 6.5 ng / μl of DNA library. DNA Library was additionally checked for integrity on an Agilent Tapestation using the High Sensitivity D1000 tapes.

value: Apoe-/-

tag: antigen-specificity

tag: age (weeks)


title: ApoB_neg_3

description: Control ApoB-negative CD4+ T cells_3

data_processing:
FASTQ files were processed with the Cellranger count pipeline (10x Genomics), which uses STAR to align the reads to mm10 mouse reference transcriptome. Default settings were used throughout all samples. A single cell gene expression matrix was obtained as output and further used in down-stream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output of filtered gene matrix with barcodes & features files

source_name: Pooled peripheral lymph nodes

extract_protocol:
Pooled peripheral lymph nodes were mechanically disrupted. CD4+ T cells were enriched with a magnetic bead negative separation protocol with antibodies against different leukocyte lineages (CD11b, CD11c, Nk1.1, F4/80, Ter-119, CD8, CD19). Enriched CD4+ T cells were incubated for 50min with an ApoB-MHC-II tetramer in two colors (APC, PE). Leukocytes were then stained with an antibody-cocktail for flow cytometry. CD4+ TCR-alpha/beta+ CD45+ and viability dye-negative and Lineage-negative (CD11b, CD11c, Nk1.1, F4/80, Ter-119, CD8, CD19) cells binding the MHC-II tetramer in APC and PE (ApoB+) were separated by flow sorting from those not binding the ApoB-MHC-II tetramer negative CD4+ T cells (ApoB-neg). After sorting, cells were washed, resuspended, and up to 10,000 sorted CD4+ T cells (ApoB-negative or ApoB+) were loaded and partitioned into Gel Bead In-Emulsions (GEM) according to the protocol by 10x Genomics. For the ApoB-neg samples, T cells from 10 mice each were pooled for one GEM preparation, 3 GEM pools were prepared in total. For the ApoB+ T cells, T cells from 30 mice were pooled in one sample/GEM preparation.
ScRNAseq libraries were prepared using the Single Cell 3’ Solution v2 Reagent Kit (10xGenomics). GEM reverse transcription was performed by the SimpliAmp thermal cycler (Thermo Fisher Scientific) running the following program: 53° C for 45 minutes and 85° C for 5 minutes; held at 4° C. Following reverse transcription, GEMs were broken, and single-strand cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was amplified with the SimpliAmp thermal cycler: 98° C for 3 minutes, 12 cycles of 98° C for 15 seconds, 67° C for 20 seconds, 72° C 60 seconds; 72° C for 1 minute, and held at 4° C. Subsequently, cDNA was cleaned up using the SPRIselect reagent kit (Beckman Coulter), quantified, and quality controlled with the Agilent Bioanalyzer High Sensitivity Kit. Indexed sequencing libraries were prepared by Single Cell 3’ Solution v2 Reagent Kit’s components: (1) enzymatic fragmentation, (2) end repair, (3) A-tailing, (4) adaptor ligation, (5) post ligation cleanup with the SRPIselect reagent kit, and (6) sample index PCR using the SimpliAmp thermal cycler at 98° C for 45 seconds, 10 cycles of 98° C for 20 seconds, 54° C for 30 seconds, 72° C for 20 seconds; 72° C for 1 minute, and held at 4° C. The SPRIselect reagent kit was used for post sample index double-sided size selection, and the library was quality controlled post construction using the Agilent Bioanalyzer High Sensitivity Kit and Agilent Bioanalyzer high sensitivity chip. The library was quantified post construction by quantitative PCR (Kapa DNA Quantification Kit for Illumina platforms). The constructed libraries were loaded at 13 pM on a HiSeq2500 Rapid Run using a HiSeq Rapid Cluster Kit V2- Paired End (PE), and a HiSeq Rapid SBS Kit V2. A 26-base-pair Read 1 was used to sequence the cell barcode and UMI, an 8 bp i7 index read was used to sequence the sample index, and a 98 bp Read 2 was used to sequence the transcript on an Illumina HiSeq4000 using paired-end sequencing with dual indexing.

tag: genotype

value: ApoE-/-

value: Pooled peripheral lymph nodes

value: Control ApoB-negative CD4+ T cells


title: ApoB_neg_Treg_8wks_Apoe-/-_3

value: Pooled peripheral lymph node CD4 T cells


title: ApoB_neg_1

description: Control ApoB-negative CD4+ T cells_1


title: ApoB_pos_8wks_Apoe-/-_3


title: ApoB_pos_4wks_Apoe-/-_2


title: ApoB_pos_4wks_Apoe-/-_1


title: ApoB_pos_8wks_Apoe-/-_2


title: ApoB_neg_2

description: Control ApoB-negative CD4+ T cells_2


title: ApoB_pos

description: ApoB-reactive CD4+ T cells

value: ApoB-reactive CD4+ T cells


title: ApoB_neg_8wks_Apoe-/-_3


title: ApoB_neg_8wks_Apoe-/-_2


title: ApoB_neg_Treg_8wks_Apoe-/-_1


title: ApoB_neg_8wks_Apoe-/-_1


title: ApoB_pos_8wks_WT_2

value: WT


title: ApoB_pos_20wks_Apoe-/-_3


title: ApoB_pos_20wks_Apoe-/-_1


title: ApoB_pos_20wks_Apoe-/-_2


title: ApoB_pos_8wks_Apoe-/-_1


title: ApoB_pos_8wks_WT_1


title: WT2

city: Hengyang

first: Qingtuan

last: Meng

state: Hunan

address: 69 Chuanshan Road

institute: The First Affiliated Hospital of University of South China

data_processing:
RNA-seq reads were filtered to get clean reads using SOAPnuke (v1.5.6) (https://github.com/BGIflexlab/SOAPnuke).
Reads mapping was done using STAR (2.4.2a)
Transcript Per Million was calculated by RSEM (1.3.0)
Differential gene expression analysis was done using DEseq2 (v1.14.1)
P value was adjusted using the Benjamini–Hochberg method
Genome_build: hg19

source_name: human neural progenitor cells

growth_protocol: Human neural progenitor cells were maintained in Neural Progenitor Medium (STEMCELL Technologies, #05833)

extract_protocol:
Qiagen miRNeasy Mini Kit was used to extract total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA (final concentration is 20 nM) was transfected into human neural progenitor cells using Lipofectamine RNAiMAX. 48 hours post transfection, total RNA was extracted.

tag: genotype/variation

value: wild type

tag: sample type


title: WT3


title: WT1


title: Dam, ES cell clone ED.B3 DamID-seq

city: Durham

first: Eda

last: Yildirim

state: NC

address: DUMC Box 3709

department: Cell Biology

institute: Duke University School of Medicine

library_source: genomic

data_processing:
Library strategy: DamID-Seq
Reads were mapped with bowtie2 (2.2.5, with parameters --very-sensitive) to mouse genome (UCSC mm10).
DamID-Seq data was filtered by GATC in 5’ ends. The peaks were called by MACS2 (v 2.1.0, with -q 0.05). The read coverages were quantified by the signal in reads per million per base pair deepTools:bamCoverage with parameters -m 500 -r -d.
ChIP-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2 (2.2.5, with parameters --very-sensitive) to mouse genome (UCSC mm10). The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and duplicated reads were removed by picard (v 1.91).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

source_name: Undifferentiated mouse embryonic stem cell line EL 16.7

growth_protocol: Cells were cultured in complete ES cell medium (1% Pen/Strep, 1% L-glutamine, high-glucose DMEM) with 20% FBS and LIF.

extract_protocol:
DamID was performed as described in Vogel at al. Nat Protoc. 2007; 2(6):1467-78. ChIP-Seq was performed as described in Kadota and Nagata Nucleic Acids Res. 2014; 42(12):7642-53.
For DamID-Seq, purified methyl PCR products were digested with Dpn II to remove adapter sequences from the fragment ends and 30 ng of PCR products were treated as DNA templates to prepare paired-end Solexa libraries as previously described Yildirim et al. Nat Struct Mol Bio 2011; 19(1):56-61.

treatment_protocol: Undifferentiated EL 16.7 ES cells were cultured in the presence of LIF under adherent conditions. Briefly, ES cells were cultured on γ-irradiated mouse embryonic fibroblasts (MEFs) that were isolated from Tg(DR4)1Jae/J mice (The Jackson Laboratory). To transduce ES cells, control (scramble) or mouse NUP153 specific shRNA lentivirus particles (~10e7-10e8 TU/ml) were added into 0.5 ml of complete ES cell medium containing dissociated ES cells (5x10e5), LIF (ESGRO, Sigma-Aldrich) and Polybrene (4 μg/ml) (Sigma-Aldrich) and incubated overnight at 37°C. Next day, ES cells were plated onto a 60-mm tissue culture dish (BD) containing γ-irradiated DR4 MEFs (1x10e6), cultured for 24 hr in regular ES cell media followed by 2 days of selection using 2 μg/ml puromycin (Puro) (Sigma-Aldrich) and collected for subsequent analyses.

tag: strain/background

value: F2:129S1/CastEiJx 129S1

value: Undifferentiated embryonic stem cells

value: Female


title: Dam-NUP153, ES cell clone NP.D2 DamID-seq

tag: cell type


title: KD 1-3

value: GNL3-knock down


title: KD 2-3


title: KD 2-2


title: KD 2-1


title: KD 1-2


title: NPC-GNL3-KD group1-1


title: DIEC_DSS 1

first: Shujuan

last: Chen

address: 9500 Gilman Drive

department: Pharmacology

institute: University of California, San Diego

description: ExpressionTable.xlsx

data_processing:
Base calling was performed using bcl2fastq (Illumina, v2.17.1.14).
RNA-seq reads were aligned to the mouse (mm10) genome with STAR (v2.2.0c) with default parameters
Only uniquely alignable reads were used for downstream analysis.
Gene expression values were calculated using HOMER (v4.9, http://homer.ucsd.edu/homer/) by quantifying strand-specific reads across annotated gene exons (RefSeq) and reported as FPKM (fragments per kilobase of exon per million mapped reads FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: microsoft excel

source_name: Colon

extract_protocol:
Colons were dissected and cleaned, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing by using Illumina protocols

tag: strain

tag: age

value: 8 weeks

value: ko

tag: treatment


title: DIEC_DSS 2

description: ExpressionTable.xlsx


title: DIEC_DSS 4

description: ExpressionTable.xlsx


title: DIEC_DSS 3

description: ExpressionTable.xlsx


title: DIEC_naΪve 4

description: ExpressionTable.xlsx

value: water


title: HS_8120

description: microRNA

value: Blood (jugular vein)

value: pregnant


title: DIEC_naΪve 3

description: ExpressionTable.xlsx


title: DIEC_naΪve 2

description: ExpressionTable.xlsx


title: DIEC_naΪve 1

description: ExpressionTable.xlsx


title: F/F_DSS 4

description: ExpressionTable.xlsx


title: pscra_rep1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

description: RNA from pulldown with scrambled oligo (control)

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: embryonic lung

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: MLE12 cells were grown under standard conditions

extract_protocol: RNA was extracted using QIAgen RNeasy kits.

tag: assay

value: scrambled (random) sequence (pscra)


title: overExpr_rep3

description: mice overexressing miR-154

growth_protocol: Mice were grown under standard conditions.

treatment_protocol: Mice were administrated doxycycline food from E7.5 - E18.5 and embryonic lung were harvested at E18.5.

value: Black/6:Rosa26rtTA/rtTA; Tg(miR-154/+)


title: overExpr_rep1

description: mice overexressing miR-154


title: F/F_DSS 3

description: ExpressionTable.xlsx


title: F/F_DSS 2

description: ExpressionTable.xlsx


title: control_rep2

description: wild-type mice, normal miR-154 expression


title: control_rep1


title: MCF7 breast cancer cell line

city: Ourimbah

first: Judith

last: Weidenhofer

state: NSW

address: 10 Chittaway Rd

department: School of Biomedical Sciences & Pharmacy

institute: University of Newcastle

hyb_protocol: As per affymetrix protocol

scan_protocol: As per affymetrix protocol using Affymetrix GeneChip Scanner 3000 7G

data_processing: Signals were normalized across all microarray chips using Robust Multi-array Analysis (RMA) designed and recommended by Affymetrix using GeneSpring GX software.

label: biotin

source_name: human commercial cell line, RNA extracted at 75% confluency

label_protocol: As per affymetrix protocol for preparation of biotinoylated cRNA using the FlashTag Biotin HSR RNA labelling kit. Input was 1μg of total RNA

growth_protocol: Cells were grown in culture using media as described in the repository from where each cell line was obtained. All cells were maintained at 37C in 5% CO2. All cells were either purchased within 4 years of use or validated to be the correct line using the Promega GenePrint 10 kit.

extract_protocol: Cells were washed with PBS and then Trizol-LS added directly to the cells, the manufacturers protocol was followed with the addition of glycogen during precipitation which was carried out overnight at -20C

treatment_protocol: No treatment, cells were grown to 85% confluency prior to RNA extraction

tag: cell line

tag: tumourigenic status

value: tumourigenic


title: SKBR3 breast cancer cell line


title: pmiR_rep1

description: RNA from pulldown with mirR-154 sequence

value: mir-154 (pmiR)


title: control_rep3


title: F/F_DSS 1

description: ExpressionTable.xlsx


title: F/F_naΪve 4

description: ExpressionTable.xlsx


title: 184A1 breast cell line

value: not tumourigenic


title: F/F_naΪve 3

description: ExpressionTable.xlsx


title: F/F_naΪve 2

description: ExpressionTable.xlsx


title: overExpr_rep2

description: mice overexressing miR-154


title: MDA-MB-231 breast cancer cell line


title: 10_BRCA1-CL_2306: RNA immunoprecipitated with BRCA1 antibody without crosslinking (replicat 3)

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

country: France

institute: university Lyon1

description: gene expression data from RIP experiment

hyb_protocol: After final purification, hybridization was performed following Affymetrix protocols (http://www.affymetrix.com). Microarray analysis was performed using a high-density oligonucleotide array (Human Transcriptome Array GeneChip HG-ST 2.0, Affymetrix, Santa Clara, CA, USA)

scan_protocol: The arrays were read with a confocal laser (GeneChip Scanner 3000 7G, Affymetrix).

data_processing: Then CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0.The obtained data were normalized with Affymetrix Expression Console software using the RMA statistical algorithm.

label_protocol: RNA (900 pg) was reverse-transcribed and pre-amplified with the Ovation WTA System (Nugen). cDNA quantification was performed with a nanodrop and quality checked with the Agilent 2100 Bioanalyzer (Agilent technologies, Inc, Palto Alto, CA, USA). Fragmentation and labeling of cDNA (3.6 µg) using Encore Biotin Module kit (Nugen) were performed. Before amplification, spikes of synthetic mRNA at different concentrations were added to all samples;

extract_protocol: The RNA associated with each type of beads, and the total RNA (input) were then eluted with elution buffer (50 mM Tris-HCl at pH 7.4, 5 mM EDTA, 10 mM DTT, 1 % SDS, 200 U/ml RNase Out) and digested with proteinase K. RNA was finally extracted using the RNeasy micro kit (Qiagen).

treatment_protocol: For RIP experiment, Cells (MCF-7) were washed with ice-cold PBS and lysed in RIP buffer (25 mM Tris-HCl at pH 7.4, 150 mM KCl, 2 mM EDTA, 0.5 % NP40, 0.5 mM DTT, 200 U/ml RNaseOut, protease inhibitors). Where indicated, a small fraction of the lysate (5 %) was used to prepare total RNA extracts and this was considered the input. The remaining lysates were then split into equal parts: half was incubated with anti-BRCA1 antibody (BRCA1) coupled to Dynabeads (Life Technologies) and half was incubated with non-relevant isotype-matched IgG (NR) used as control and coupled to Dynabeads. Immunoprecipitates were washed seven times with RIPA buffer (50 mM Tris-HCl at pH 7.4, 150 mM KCl, 0.5 % NP40).

tag: tissue

value: breast carcinoma


title: 06_BRCA1-CL_1006: RNA immunoprecipitated with BRCA1 antibody without crosslinking (replicat 2)


title: 09_NR-CL_2306: RNA immunoprecipitated with non specific antibody without crosslinking (replicat 3)


title: T47D breast cancer cell line


title: F/F_naΪve 1

description: ExpressionTable.xlsx


title: 05_NR-CL_1006: RNA immunoprecipitated with non specific antibody without crosslinking (replicat 2)


title: 02_BRCA1-CL_2005: RNA immunoprecipitated with BRCA1 antibody without crosslinking (replicat 1)


title: HMEC breast cell line

value: HMEC


title: RNA-IWR-3

city: Research Triangle Park

first: Carmen

middle: J

last: Williams

address: 111 TW Alexander Dr.

department: Reproductive & Developmental Biology Laboratory

institute: NIH/NIEHS

data_processing:
Base calling and generation of FASTQ files performed using RTA and bcl2fastq2.
Adapter and low-qualitty tails removed  from RNA-Seq data using Cutadapt v1.11, and from ATAC-Seq data using Trim Galore.
RNA-Seq paired-end reads aligned to mm10 reference using STAR v2.5.1b with default parameters; ATAC-Seq paired-end reads aligned to mm10 using Bowtie2 v2.2.6 with the parameters "--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant".
ATAC-Seq reads mapping to mitochondria were removed.
RNA abundance quantified with featureCounts v1.5.0-p1. ATAC-seq peaks were called with MACS2 'callpeak' (--B –nomodel –nolambda --shift -100 --extsize 200 --SPMR).
ATAC-Seq peaks merged into union set by replicate.
Differential expression and sample normalization factors for RNA-Seq and differential peak calls for ATAC-Seq were determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for each file, XLSX files with peak positions and DESeq2 output with raw count and FPKM for RNA-seq.

source_name: 2-cell embryos

growth_protocol: Pronuclear stage embryos were recovered from superovulated, plug-positive NSA(CF-1) female mice bred to B6SJLF1/J males at 16-20 hours following injection of human chorionic gonadotropin (hCG).

extract_protocol:
For RNA-seq analysis, four independent collections of ten 2-cell embryos were placed in 1 uL of PBS in a 1.5 ml tube and frozen at -80°C until library preparation. For ATAC-seq analysis, two independent collections of 100 late 2-cell embryos/group were performed. Zona pellucidae were removed using acid Tyrode’s solution followed by mechanical removal of polar bodies by pipetting embryos up and down in Ca2+/Mg2+-free CZB. Embryos were placed in a 1.5-ml tube containing 4 ul of ice-cold 1x lysis buffer (10mM Tris-HCl, pH 7.4; 3 mM MgCl2, 0.1% IGEPAL CA630 for 15 min, followed by addition of 6 uL of 2x Tris-DMF-tagmentation buffer (20 mM Tris-HCl, pH 8.0; 10 mM MgCl2; 20% dimethylformamide). Transposase reaction was started by the addition of 2 uL of Nextera Tn5 transposase (Illumina) and incubation at 37C for 30 min. To stop the reaction, 0.5 μL of 10% SDS was added. DNA was then purified using the Qiagen MinElute PCR purification Kit, and eluted in 22 uL of elution buffer.
mRNA libraries were constructed using the SMART-Seq® v4 Ultra® Low Input RNA Kit (TaKaRa) following the manufacturer’s instructions. For ATAC-seq libraries, samples were amplified by 15 cycles of PCR using Phusion High-Fidelity PCR Master Mix with HF Buffer and Nextera universal primer and bar code primers. To deplete mitochondrial fragments from the ATAC-seq libraries, we used the CRISPR/Cas9-assisted removal of mitochondrial DNA (CARM) procedure from (Wu et al., Nature 534, 652-657, 2016).

treatment_protocol: Embryos were cultured in a humidified atmosphere of 5% CO2, 5% O2 and 90% N2 in 4-well dishes containing 500 ml of KSOM with 50 uM of the tankyrase inhibitor IWR1-endo (IWR1) or the respective v/v% of vehicle (DMSO) for the control group. Embryos were collected at 46 hours after hCG injection.

value: NSA(CF-1) x B6SJLF1/J

value: 2-cell embryos


title: CTCF ChIP-seq NUP153 shRNA-1

data_processing:
Reads were mapped with bowtie2 (2.2.5, with parameters --very-sensitive) to mouse genome (UCSC mm10).
DamID-Seq data was filtered by GATC in 5’ ends. The peaks were called by MACS2 (v 2.1.0, with -q 0.05). The read coverages were quantified by the signal in reads per million per base pair deepTools:bamCoverage with parameters -m 500 -r -d.
ChIP-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2 (2.2.5, with parameters --very-sensitive) to mouse genome (UCSC mm10). The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and duplicated reads were removed by picard (v 1.91).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

value: F2:129S1/CastEiJx 129S1

value: NUP153 knockdown

value: Undifferentiated embryonic stem cells

tag: Sex

tag: chip antibody

value: CTCF (Cell Signaling, 2899S)


title: RNA-IWR-2


title: RNA-DMSO-4

value: DMSO


title: CTCF ChIP-seq NUP153 shRNA-2

value: Female


title: CTCF ChIP-seq control shRNA

value: Wild type


title: RNA-IWR-4


title: RNA-IWR-1


title: SMC3 ChIP-seq NUP153 shRNA-2

value: SMC3 (Abcam, ab9263)


title: SMC3 ChIP-seq NUP153 shRNA-1


title: RNA-DMSO-1


title: RNA-DMSO-2


title: SMC3 ChIP-seq control shRNA


title: Input DNA shRNA-2


title: ATAC-DMSO-D


title: Input DNA control shRNA


title: RNA-seq shRNA-2

data_processing:
Reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC mm10 known gene annotation).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: txt files contain the reads counts from htseq-count.

extract_protocol:
Total RNA was isolated from undifferentiated control and two NUP153 knockdown mouse ES cells using Trizol reagent. RNA samples (RNI >8) were depleted of ribosomal RNA using the Illumina Ribo-zero Gold kit and converted into RNA-seq libraries using the Illumina Total RNA-seq kit.
RNA libraries were indexed using a dual indexing approach allowing for multiple libraries to be pooled and sequenced on the same sequencing flow cell of an Illumina HiSeq 4000 sequencing platform.


title: RNA-DMSO-3


title: Control_epiCS

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

institute: Hannover Medical School

data_processing:
Sequencing was performed at the Genomics service (ISCIII) on a NextSeq 500 sequencer using 75 base read lengths in paired-end mode.
First quality control analysis was based on fastQC v0.11.3 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and any adapter sequences and low quality 3′ ends were removed using Trimmomatic v0.36.
High-quality reads were mapped against Hg38 human genome using STAR v2.4.0.1 and mapping quality control was performed using RseQC v2.6.4.
Transcriptome prediction and gene/isoform quantification was calculated using HT-seq v0.11.1 based on Hg38 RefSeq reference genes
The differential expression (DE) was subsequently quantified using generalized fold change (GFOLD) scores with GFOLD v1.1.4
Genome_build: Hg38
Supplementary_files_format_and_content: DE table generated by GFOLD , raw counts data

source_name: 3D human epiCS

growth_protocol: epiCS®, three dimentional (3D), fully differentiated human epidermis equivalent, reconstructed from normal human epidermal keratinocytes were purchased from CellSystems® (Troisdorf, Germany). The cellular structure of reconstructed human epidermis closely resembles the human epidermis including proliferating keratinocytes and a stratum corneum with intact barrier function. Each epiCS batch was tested for contaminants from primary cells (HIV, HBV, and HCV), sterility (bacteria, yeast, and mycoplasma) and histologically. EpiCS were cultured in a special culture medium (Cat. Nr. CS-3051, CellSystems®).

extract_protocol:
The total RNA from epiCS was isolated, and quality was assessed using 1% agarose gels as well as by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit
Libraries were prepared in duplicates by using 200 ng RNA of each insert. TruSeq Stranded mRNA Kit (Illumina Inc., USA) was used for library preparation according to the manufacturer protocol as described in our previous work.  The products were purified with Ampure XP Beads (Beckman Coulter, CA, USA) and enriched with 15 cycles of PCR to create the cDNA library.
Pair-ended RNA-Seq

treatment_protocol: epiCS were treated with various concentrations of AAT added topically or into the culture medium (basolaterally) for different time points up to 48 h. The control epiCS we treated by adding the same volume of Hank`s balance salt solution (HBSS cat nr. 14025092, ThermoFisher Scientific, Germany) as for the AAT treatments. Additionally, epiCS were cultured for 18 h in the medium containing 100µg/ml of combined bacterial lipopolysaccharide (LPS, Sigma-Aldrich, Darmstadt, Germany) and peptidoglycan (PGN, stock solution prepared in 0.1 mg/ml in sterile water and few seconds sonicated; Sigma-Aldrich) mixture with and without topical application of 0.2 mg of native or recombinant AAT. At the end of experiment, we collected culture supernatants and cells for further studies.

value: epiCS


title: LPS_PGN_exposed_epiCS


title: AAT_exposed_epiCS


title: Hif1a-KO Tumor NK

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

description: 10x Genomics Chromium single cell 3 ́ library

data_processing:
RTA 2.7.7 software used for basecalling
Cell Ranger version 2.0.2 used for read aligment and UMI counting
Seurat R package used for filtering of low-quality cells and doublets
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text files include UMI counts for each Sample.

source_name: tumor-infiltrating NK cells

growth_protocol: WT or NK-Hif1a-/- mice were injected s.c. with RMA-S cells two weeks before mouse sacrifice

extract_protocol:
tumor- infiltrating CD3ε-NK1.1+ NK cells were sorted by flow cytometry
10x Genomics Chromium single cell 3' library

value: Hif1a KO in NK cells


title: UWB+BR

city: Newcastle upon Tyne

first: Sweta

last: Sharma Saha

address: Framlington Place

department: Translational and Clinical Research Institute

institute: Newcastle University

description:
1178-A017396
Raw_read_count_matrix.txt

data_processing:
The sequencing data on mRNA expression of target genes were imported into HTG EdgeSeq Parser software.
The HTG QC App was used to post-sequencing QC and data normalization
A simple normalization procedure, log2(CPM), was used that transformed counts and adjusted for total reads within a sample
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

source_name: Cultured cells

growth_protocol: Cells cultured in recommended culture medium for at least two passages before thawing them

extract_protocol:
40,000 cells/sample were collected and cryopreserved at a concentration of 4,000 cells/μl in HTG Lysis Buffer for shipment to HTG Molecular Diagnostics Inc. All samples were prepared in accordance with OP-00036, HTG EdgeSeq Sample Preparation.
The library was prepared in accordance with OP-00035, HTG EdgeSeq PCR Processing. The sequencing was performed on the Illumina NextSeq platform in accordance with OP-00093, HTG EdgeSeq Illumina NextSeq Sequencing.

tag: cancer type

value: Ovarian cancer cell line

value: UWB+BR

value: Untreated


title: RNA-seq control shRNA


title: CP70 B1 10/12/18

description:
1178-A017395
Raw_read_count_matrix.txt

value: CP70 B1


title: WT Tumor NK

value: wildtype


title: COV362 10/12/18

description:
1178-A017391
Raw_read_count_matrix.txt


title: ATAC-IWR-C

value: NSA(CF-1) x B6SJLF1/J


title: cfDNA1

city: Nagoya

first: Keiko

last: Shinjo

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Cancer Biology

country: Japan

institute: Nagoya Univ. Graduate School of Medicine

data_processing:
The reads were aligned to hg19/GRCh37 with BWA.
Duplicate reads and longer fragments (longer than 150bp) were removed.
Methylation peaks were determined with HOMER software (v4.10, 5-16-2018; style histone, size 150, minDist 370)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include location of peak and annotation

source_name: blood

extract_protocol:
cfDNA was extracted from 1 mL of serum with a QIAamp Circulating Nucleic Acid kit (Qiagen)
The aforementioned methylated DNA enriched by MBD1 protein was used to generate indexed libraries with an NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: cfDNA


title: cfDNA73


title: UWB-BR

description:
1178-A017397
Raw_read_count_matrix.txt

value: UWB-BR


title: N11


title: CP70 A2 10/12/18

description:
1178-A017394
Raw_read_count_matrix.txt

value: CP70 A2


title: FNA1

source_name: Pancreatic cancer

value: tumor


title: N12


title: 01_NR-CL_2005: RNA immunoprecipitated with non specific antibody without crosslinking (replicat 1)

value: breast carcinoma


title: FNA73


title: LPS_PGN_AAT_exposed_epiCS


title: LS600 B

city: Bronx

first: Hequn

last: Liu

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads were aligned to the human reference genome (hg19) by the software HISAT2 version 2.0.4
HTseq version 0.11.0 and StringTie version 1.2.2 were used to determine the read counts and FPKMs (fragments per kilobase of exon per million fragments mapped) of each gene annotated in the GENCODE database (v29) respectively
Differential expression analysis was carried out by DESeq2
Genome_build: hg19

source_name: Neural progenitor cells

growth_protocol: Neural progentior cells were derived by growing iPS in a monlayer culture using STEM Cell Technologies STEMdiff SMADi Neural Induction Kit, according to manufacturer's instructions. Briefly, iPS were detached and plated at a cell density of 1.0 x 106 cells/ml. Two mls of cell suspension was plated into one well of a 6-well precoated matrigel plate containg neural induction medium plus 10uM Y-27632. Cells were fed daily, without Y-27632, and grown for a full 6 days reaching ≥ 90% confluency (passage 0). All passages hereafter are detached similarly, with the exception of plating cells on a precoated PORN/Laminin plate with a cell density of 1.5 x 106 cells/well. Dowstream applications performed at passage 3.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit from Qiagen, according to manufacturer's instructions. An additional treatment with DNase I was included to remove genomic DNA.

value: iPS-derived neural progenitor cells

tag: passage

value: sibling control 3


title: A2780 10/12/18

description:
1178-A017393
Raw_read_count_matrix.txt


title: NUCOLL43 10/12/18

description:
1178-A017392
Raw_read_count_matrix.txt


title: Input DNA shRNA-1

value: F2:129S1/CastEiJx 129S1

value: NUP153 knockdown

value: Undifferentiated embryonic stem cells

value: Female


title: ES-2 10/12/18

description:
1178-A017390
Raw_read_count_matrix.txt

value: Ovarian cancer cell line


title: CAOV3 10/12/18

description:
1178-A017389
Raw_read_count_matrix.txt


title: RNA-seq shRNA-1


title: ATAC-IWR-D

value: 2-cell embryos


title: LS600 A


title: COV318 10/12/18

description:
1178-A017388
Raw_read_count_matrix.txt

value: Untreated


title: LS500 B

value: LS patient 3


title: OAW42 11/12/18

description:
1178-A017387
Raw_read_count_matrix.txt


title: LS500 A


title: ATAC-DMSO-C

value: DMSO


title: LS300 B

value: LS patient 2


title: LS300 A


title: LS200 B

value: sibling control 1


title: LS400 A

value: sibling control 2


title: LS200 A


title: LS100 B

value: LS patient 1


title: NAD 200 uM treated LS 174T_3

city: seoul

first: seongho

last: ma

address: Anamro 145

institute: Korea university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: LS 174T goblet cell

growth_protocol: LS 174T goblet cells were seeded at the concentration of 2.5 × 10^5 cells/ml on 6-well plate and incubated in RPMI 1640 media containing 10% fetal bovine serum and 1% penicillin and streptomycin at 37 ℃ with the atmosphere of 5% CO2 for overnight.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: NAD+ was treated at the final concentration of 200 uM for 48 h.

value: LS 174T

value: colorectal adenocarcinoma

tag: passages


title: hCo alone (experiment 1)

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Libraries were sequenced on Illumina NextSeq500 with 150 cycle kit using the following read length: 26bp Read1 for cell barcode and UMI, 8bp I7 index for sample index and 132bp Read2 for transcript. Cell Ranger 2.2.0 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output. First, “cellranger mkfastq” demultiplexed the sequencing samples based on the 8bp sample index read to generate fastq files for the Read1 and Read2, followed by extraction of 16bp cell barcode and 10bp UMI. Second, “cellranger count” aligned the Read2 to the human reference genome (GRCh38) using STAR45. Then, aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (Ensembl GRCh38) without PCR duplicates. Valid cell barcodes were defined based on UMI distribution.
All single cell analyses were performed using the Seurat package in R (version 2.3.4). Once the gene-cell data matrix was generated, poor quality cells were excluded, including cells with more than 6,000 unique expressed genes (as they are potentially cell doublets). Only genes expressed in 3 or more cells in a sample were used for further analysis. Cells were also discarded if their mitochondrial gene percentages were over 10% or if they expressed less than 600 unique genes, resulting in 20,778 genes across 24,478 cells and median UMI count for each cell across the entire dataset being 7,845 and the median number of unique genes per cell being 2,397..   Following best practices in the package suggestions UMI counts were log-normalized and after the most highly variable genes selected the data matrices were scaled using a linear model with variation arising from UMI counts and mitochondrial gene expression mitigated for.  Principal component analysis was subsequently performed on this matrix and after reviewing principal component heatmaps and jackstraw plots Uniform Manifold Approximation and Projection (UMAP) visualization were performed on the top 29 components and clustering resolution was set at 1.0 for visualizations.  Differential gene expression for gene marker discovery across the clusters were performed using the Wilcoxon rank sum test as used in the Seurat package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample

source_name: Human Epithelial cells from colon

extract_protocol:
The following two experiments were performed for single cell library preparation to establish adaptation of R-VECs upon co-culture with normal or malignant organoids:  Experiment 1: R-VECs were co-cultured alone or together with Normal Colon Organoids for 7 days in complete organoid growth media with FGF2 (Promocell) and Heparin. Normal Colon Organoids were also cultured alone in complete organoid growth media with FGF and Heparin for 7 days. After 7 days, all three conditions (R-VEC alone, R-VEC + Normal Colon Organoids, or Normal Colon Organoids alone) were dissociated with dispase and TryplE (Thermofisher) as described above and submitted for 10x Chromium single cell analysis. All three samples were processed and run at the same time.  Experiment 2: R-VECs were co-cultured alone or together with Colon Tumor Organoids for 7 days in complete organoid growth media with FGF2 and Heparin. Tumor Colon Organoids were also cultured alone in complete organoid growth media with FGF and Heparin for 7 days. After 7 days, all three conditions (R-VEC alone, R-VEC + Colon Tumor Organoids, or Tumor Colon Organoids alone) were dissociated with collagenase, dispase and TryplE (as described above) and submitted for 10x Chromium single cell analysis. All three samples were processed and run at the same time.
The single cell suspension was loaded onto a well on a 10x Chromium Single Cell instrument (10x Genomics). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions. Briefly, the 10x™ GemCode™ Technology partitions thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all the cDNA generated from an individual cell share a common 10x Barcode. In order to identify the PCR duplicates, Unique Molecular Identifier (UMI) was also added. The GEMs were incubated with enzymes to produce full length cDNA, which was then amplified by PCR to generate enough quantity for library construction. Qualitative analysis was performed using the Agilent Bioanalyzer High Sensitivity assay.  The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol. Briefly, after the cDNA amplification, enzymatic fragmentation and size selection were performed using SPRI select reagent (Beckman Coulter, Cat# B23317) to optimize the cDNA size. P5, P7, a sample index and read 2 (R2) primer sequence were added by end repair, A-tailing, adaptor ligation and sample-index PCR. The final single cell 3’ library contains a standard Illumina paired-end constructs (P5 and P7), Read 1 (R1) primer sequence, 16 bp 10x barcode, 10 bp randomer, 98 bp cDNA fragments, R2 primer sequence and 8 bp sample index. For post library construction QC, 1ul of sample was diluted 1:10 and ran on the Agilent Bioanalyzer High Sensitivity chip for qualitative analysis. For quantification, Illumina Library Quantification Kit (KAPA Biosystems, Cat# KK4824) was used.

tag: co-culture protocol

value: R-VEC and hCOs were co-cultured  in LEC for 7 days. Standard hCO media was used + FGF2 (10 ng/ml) and heparin (100 ug/ml) Media was refreshed every other day.


title: R-VEC co-cultured with hCO fraction 1 (experiment 1)

source_name: HUVEC / Human Epithelial cells from colon


title: R-VEC alone (experiment 1)

source_name: HUVEC


title: hCRCO alone (experiment 2)

source_name: Cells from human colorectal cancer

value: R-VEC and hCRCOs were co-cultured  in LEC for 7 days. Standard hCRCO media was used + FGF2 (10 ng/ml) and heparin (100 ug/ml) Media was refreshed every other day.


title: R-VEC co-cultured with hCO fraction 2 (experiment 1)

source_name: HUVEC /Human Epithelial cells from colon


title: R-VEC co-cultured with hCRCO fraction 2 (experiment 2)

source_name: HUVEC /Cells from human colorectal cancer


title: R-VEC co-cultured with hCRCO fraction 1 (experiment 2)


title: NIH-OVCAR3 10/12/18

description:
1178-A017386
Raw_read_count_matrix.txt


title: NAD 200 uM treated LS 174T_2


title: sKelm7L1

city: Madison

first: Cynthia

middle: A

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, contamination and low-quality reads were removed. Reads were mapped to the annotated rat (Rattus Norvegicus) genome in Ensembl.
Technical quality was determined using several parameters. Briefly, trimming software skewer was used to preprocess raw fastq files. Combined cycle base quality, per cycle base frequencies and average base quality, relative 3-Kmer diversity, Phred quality distribution, mean quality distribution, average read length and read occurrence distribution were used as additional quality control measures on the read data. Additionally, the biological coefficient of variation was estimated to be approximately 0.12.
Gene analysis was performed with the glm using the EdgeR Bioconductor Package, v. 3.9. The p-value cutoff was set to 0.05 for significance. A Benjamini-Hochberg correction was applied to control the False Discovery Rate (FDR).
RSEM approach for normalizing RNA seq data was used
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample as well as WGCNA data.

source_name: Periaqueductal gray, brainstem

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using the Bio-Rad Aurum Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad, Hercules, CA, USA) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Long Evans

value: Periaqueductal gray, brainstem

value: 8 months

tag: genotype

value: Male


title: sKelm5L1


title: sKelm9L1


title: sKelm8L1

value: WT


title: sKelm6L1


title: NC_2


title: R-VEC alone (experiment 2)


title: IGROV1 11/12/18

description:
1178-A017385
Raw_read_count_matrix.txt

value: Ovarian cancer cell line


title: LS400 B

value: iPS-derived neural progenitor cells


title: LS100 A


title: sKelm4L1


title: NAD 200 uM treated LS 174T_1


title: NC_3


title: sKelm2L1


title: NC_1


title: sKelm20L1


title: S6F

value: Female


title: CD

description: Aortic leukocytes from Chow-diet-fed mice

data_processing:
FASTQ files were processed with the Cellranger count pipeline (10x Genomics), which uses STAR to align the reads to mm10 mouse reference transcriptome. Default settings were used throughout all samples. A single cell gene expression matrix was obtained as output and further used in down-stream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output of filtered gene matrix with barcodes and features files

source_name: Aorta

extract_protocol:
Leukocytes from atherosclerotic aortas were extracted by enzymatic digestion and stained with an antibody-cocktail for flow cytometry. Viable leukocytes were identified as CD45+ viability-dye-negative cells and sorted into PBS. After sorting, cells were washed, resuspended, and up to 10,000 sorted leukocytes were loaded and partitioned into Gel Bead In-Emulsions (GEM) according to the protocol by 10x Genomics. For each condition (CD and WD), cells from 10 individual aortas were pooled for one GEM preparation.
ScRNAseq libraries were prepared using the Single Cell 3’ Solution v2 Reagent Kit (10xGenomics). GEM reverse transcription was performed by the SimpliAmp thermal cycler (Thermo Fisher Scientific) running the following program: 53° C for 45 minutes and 85° C for 5 minutes; held at 4° C. Following reverse transcription, GEMs were broken, and single-strand cDNA was purified with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific). cDNA was amplified with the SimpliAmp thermal cycler: 98° C for 3 minutes, 12 cycles of 98° C for 15 seconds, 67° C for 20 seconds, 72° C 60 seconds; 72° C for 1 minute, and held at 4° C. Subsequently, cDNA was cleaned up using the SPRIselect reagent kit (Beckman Coulter), quantified, and quality controlled with the Agilent Bioanalyzer High Sensitivity Kit. Indexed sequencing libraries were prepared by Single Cell 3’ Solution v2 Reagent Kit’s components: (1) enzymatic fragmentation, (2) end repair, (3) A-tailing, (4) adaptor ligation, (5) post ligation cleanup with the SRPIselect reagent kit, and (6) sample index PCR using the SimpliAmp thermal cycler at 98° C for 45 seconds, 10 cycles of 98° C for 20 seconds, 54° C for 30 seconds, 72° C for 20 seconds; 72° C for 1 minute, and held at 4° C. The SPRIselect reagent kit was used for post sample index double-sided size selection, and the library was quality controlled post construction using the Agilent Bioanalyzer High Sensitivity Kit and Agilent Bioanalyzer high sensitivity chip. The library was quantified post construction by quantitative PCR (Kapa DNA Quantification Kit for Illumina platforms). The constructed libraries were loaded at 13 pM on a HiSeq2500 Rapid Run using a HiSeq Rapid Cluster Kit V2- Paired End (PE), and a HiSeq Rapid SBS Kit V2. A 26-base-pair Read 1 was used to sequence the cell barcode and UMI, an 8 bp i7 index read was used to sequence the sample index, and a 98 bp Read 2 was used to sequence the transcript on an Illumina HiSeq4000 using paired-end sequencing with dual indexing.

value: ApoE-/-

tag: diet

value: Chow-diet-fed mice

value: Aorta

value: Aortic leukocytes


title: S1F


title: S14F


title: S12F


title: Nrf1-KO carfilzomib 6 hour rep1

city: Richmond

first: Senthil

last: Radhakrishnan

state: VA

address: 1101 E Marshall St

institute: Virginia Commonwealth University

description:
Immortalized
SR13

data_processing:
RNA Express workflow from Illumina Basespace website was used
The steps consist of: Alignment of reads with STAR aligner, assignment of aligned reads to genes, and differential gene expression with DESeq2
Supplementary_files_format_and_content: DeSeq2 results in csv format

source_name: NIH-3T3 cell line

growth_protocol: Cells were grown in DMEM medium supplemented with 10% FBS at 37 degree C in a humidified CO2 incubator

extract_protocol:
Qiagen RNAeasy kit was used for extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO (vehicle) or 200 nM carfilzomib

value: Fibroblasts

tag: agent

value: 200 nM carfilzomib

tag: time point

value: 6 hour


title: Nrf1-KO control rep3

description:
Immortalized
SR12

tag: cell type

value: DMSO


title: Nrf1-KO carfilzomib 6 hour rep2

description:
Immortalized
SR14


title: Nrf1-KO carfilzomib 24 hour rep1

description:
Immortalized
SR16

value: 24 hour


title: S16F

tag: strain

value: Long Evans

tag: age


title: S13F

value: Periaqueductal gray, brainstem


title: Nrf1-KO carfilzomib 24 hour rep2

description:
Immortalized
SR17


title: Nrf1-KO carfilzomib 24 hour rep3

description:
Immortalized
SR18