title: Epithelium rep 4 [2676 - Ep4]

description: replicate 4


title: Fetal LATE gestation exposure replicate 2

status: Public on Jun 03 2022

type: SRA

city: Clemson

first: Susan

middle: K

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

country: USA

institute: Clemson University

library_source: transcriptomic

data_processing:
Novogene's custom perl and python scripts were used to clean and filter the raw data.
Bowtie 0.12.9 without mismatch for alignment.
miRBase 20.0
mirdeep2 0.0.5
srna-tools-cli
RepeatMasker 4.0.3
miREvo v1.1
miRanda v3.3
DeSeq 1.12.0
GOSeq 2.12
KOBAS v 2.0
Genome_build: Ovis aries (TEXEL) Ensembl release 96
Supplementary_files_format_and_content: Raw_read_counts_miRNA.txt: Tab-delimited text file of raw read counts for all miRNA features for all samples.

molecule: total RNA

organism: Ovis aries

source_name: Longissimus

extract_protocol:
Total RNA was extracted with Trizol according to manufacturer's specifications. Quantification and qualification were checked by 1% agarose gel, NanoPhotometer spectrophotometer, and Agilent Bioanalyzer 2100 system.
The NEBNext Multiplex Small RNA Library Prep Set for Illumina following manufacturer's recommendation and index codes were used to prepare the sequencing library.

tag: breed

value: Suffolk

tag: age

value: d 133 of gestation

tag: treatment

value: LATE gestation in utero exposure to endophyte-infected tall fescue seed

tag: tissue

value: Longissimus muscle

tag: replicate

value: replicate 2


title: Superficial Cortex rep 4 [2679 - SCx4]

type: RNA

city: Newark

first: Melinda

last: Duncan

state: DE

address: 105 The Green

department: Biological Sciences

institute: University of Delaware

description: replicate 4

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: The data was processed using the lumi package in R. The data was read into lumi using the lumiR function. The data was transformed using the default lumiT function. The data was normalized using quantile normalization with the lumiN function.

label: biotin

organism: Mus musculus

source_name: Mouse ocular lens

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy Micro Kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Enucleated globes were embedded in optimal cutting temperature medium and frozen in 2-methylbutane over dry ice. Sections were cut on a cryostat and mounted on glass RNase-free PEN-Membrane Slides. Sections were washed in Rnase-free water for 30 seconds and fixed in ethanol for 1 minute, and air dried for 10 minutes. Sections were laser-microdissected to obtain superficial and deep cortical samples and collected directly into lysis buffer supplied with the RNeasy Micro Kit.

value: 1 month

value: Lens Superficial Cortex


title: Fetal LATE gestation exposure replicate 1

value: replicate 1


title: Superficial Cortex rep 2 [2677 - SCx2]

description: replicate 2


title: CTRL rep2 [OE]

city: Ghent

first: Wouter

last: Van Loocke

state: East Flanders

address: C. Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Ghent University

data_processing:
Fastq files were aligned to human reference genome GRCh38 using STARv2.42 and gencode v25 as guide gtf
Counts were generated on the fly by STAR
QC of fastq files was done with FastQC
Genome_build: GRCh38
Supplementary_files_format_and_content: a tab separated raw count matrix file

organism: Homo sapiens

source_name: Natural Killer Cell

growth_protocol: HPC were obtained by isolating peripheral blood monocytes from umbilical cord blood by density gradient centrifugation and by subsequently enriching CD34+ HPC using magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours. Successfully transduced HPC were sorted and co-cultured with mitomycin-inactivated EL08.1D2 cells in Dulbecco’s modified Eagle medium plus Ham’s F-12 medium (2:1 ratio), supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM glutamine, 10 mM sodium pyruvate (all from Life Technologies), 20% of heat-inactivated human AB serum (Biowest, Nuaillé, France), 24 μM β-mercaptoethanol, 20 μg/mL ascorbic acid and 50 ng/mL sodium selenite (all from Sigma-Aldrich). The following cytokines were added: IL-3 (5 ng/mL, first week only, R&D systems), IL-7 (20 ng/mL), IL-15 (10 ng/mL) (all from Miltenyi Biotec), SCF (20 ng/mL; Peprotech, London, UK.), and Flt3-L (10 ng/mL; R&D Systems, Minneapolis, MN, U.S.A.) . Culture medium was refreshed on day 7 by addition of the same volume of fresh medium with cytokines except for IL-3.

extract_protocol:
Total mRNA was extracted using the RNeasy micro kit (Qiagen). The concentration and quality of the total extracted RNA was checked using the Quant-it ribogreen RNA assay (Life Technologies) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, U.S.A), respectively.
Illumina sequencing library preparation was performed using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR.
RNA seq, Lexogen Quantseq FWD

treatment_protocol: CD34+ HPC underwent retroviral transduction with the RUNX2-I isoform overexpression vector or the control vector. After 48 hours, eGFP+CD34+ Lin- HPC were sorted by FACS cell sorting.

tag: day of culture

tag: donor

value: Donor 2

tag: transduction

value: CTRL

value: Retroviral transduction


title: Hospitalized_COVID-19 [COV173]

type: genomic

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

department: Center of Biotechnology

country: United Arab Emirates

institute: Khalifa University

hyb_protocol: Genotyping was performed using the Infinium Global Screening Array-24 v3.0 BeadChip (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s protocol, which contained 654,027 genetic markers and developed by Avera Institute for Huma Genetics (South Dakota, USA). The Infinium Global Screening Array-24 v3.0 BeadChip would be best suited for this ethnically diverse cohort because it features a broad spectrum of diverse exonic content, including both cross population and population specific markers (EUR: 52,980 markers; EAS: 31,375 markers; AMR: 45,977 markers; AFR: 43,122 markers; SAS: 40,298 markers).

scan_protocol: PLINK (version 1·9), R (version 3·4), SPSS (version 16·0), Haploview Software (version 4.2).

data_processing:
The matrix processed and matrix signal intensity files form Genome studio are uploaded.
The statistical analysis was conducted as a case-control panel, with controls characterized as non-hospitalized symptoms and cases characterized as hospitalized symptoms. Case-control association tests of the genotyped and imputed SNPs in the cohort were performed using PLINK (logistic regression). Two different analysis including covariates from the PCA without 1000 Genomes reference samples were run to control for potential population stratification (analysis I), as well as population stratification, age, and gender effects (analysis II).

molecule: genomic DNA

source_name: Hospitalized for COVID-19

label_protocol: DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).

tag: gender

value: male


title: Hospitalized_COVID-19 [COV174]

extract_protocol: DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).


title: Hospitalized_COVID-19 [COV171]


title: Fetal LATE gestation exposure replicate 3

value: replicate 3


title: Fetal MID gestation exposure replicate 1

value: MID gestation in utero exposure to endophyte-infected tall fescue seed


title: Wether MID gestation exposure replicate 1

value: d 250 postnatal


title: LPS, 1000 ng/ml; SAMPLE 72

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

description: Test

hyb_protocol: SYBR Green qPCR reaction mixtures contained 5 ng of total RNA-derived cDNAs, forward primer, reverse primer and 1X iQ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA). The thermal cycle conditions were as follows: 3 min at 95°C, followed by 40 cycles at 95°C for 10 s, 65°C for 30 s and 72°C for 30 s. The qPCR reactions were performed in 96-well clear plates sealed by adhesives with a CFX96 real-time system-C1000 Thermal Cycler (Bio-Rad Laboratories).

data_processing:
Rpl32 mRNA was selected as the internal reference for qPCR analysis for this cell type (HKG).
1% DMSO treatment was used as sample control
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
"LPS normalized to Rpl32 worksheet" reports normalized signal (against housekeeping genes), where deltaCt = (Ct_Target − Ct_Rpl32)
"LPS normalized to Rpl32 and DMSO worksheet" reports normalized signal (against housekeeping genes and smaple control), where deltadeltaCt = delta(Ct_Target )− delta(Ct_DMSO)
"LPS fold Change worksheet" reports test/control (i.e., test/DMSO control) ratios. The 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

label: SYBR Green

source_name: RAW264.7 cells

label_protocol: The cDNAs were synthesized from total RNA using SuperScript II reverse transcriptase (Life Technologies). The cDNA synthesis mixture (20 μl) contained 2.5 μg total RNA, 2.4 μg oligo(dT)12-18 primer, 0.1 μg random primers, 500 μM dNTPs, 10 mM DTT, 40 units RNaseOUT and 200 units SuperScript II reverse transcriptase in 1X first-strand synthesis buffer (Life Technologies). The cDNA synthesis reactions were incubated at 42°C for 50 min. The cDNA samples were stored in -80°C freezer and diluted with water to 1 ng/µl before qPCR analyses.

extract_protocol: Total RNA was extracted frommouse macrophages with Trozol reagent followed by DNase I treatment.

tag: cell type

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

tag: activation agent

value: LPS, 1000 ng/ml

tag: time


title: Fetal MID gestation exposure replicate 3

value: Suffolk


title: shRNA rep5

growth_protocol: HPC were obtained by isolating peripheral blood monocytes from human umbilical cord blood by density gradient centrifugation and by subsequently enriching CD34+ HPC using magnetic activated cell sorting (MACS). Isolated cord blood-derived CD34+ HPC were cultured in complete IMDM containing 10% FCS and supplemented with thrombopoietin (TPO) (20 ng/ml), stem cell factor (SCF) (100 ng/ml) (all from Peprotech, London, UK.) and FMS-like tyrosine kinase 3 ligand (FLT3-L) (100 ng/ml, R&D Systems, Minneapolis, MN, U.S.A.) for 48 hours. Successfully transduced HPC were sorted and co-cultured with mitomycin-inactivated EL08.1D2 cells in Dulbecco’s modified Eagle medium plus Ham’s F-12 medium (2:1 ratio), supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM glutamine, 10 mM sodium pyruvate (all from Life Technologies), 20% of heat-inactivated human AB serum (Biowest, Nuaillé, France), 24 μM β-mercaptoethanol, 20 μg/mL ascorbic acid and 50 ng/mL sodium selenite (all from Sigma-Aldrich). The following cytokines were added: IL-3 (5 ng/mL, first week only, R&D systems), IL-7 (20 ng/mL), IL-15 (10 ng/mL) (all from Miltenyi Biotec), SCF (20 ng/mL; Peprotech, London, UK.), and Flt3-L (10 ng/mL; R&D Systems, Minneapolis, MN, U.S.A.) . Culture medium was refreshed on day 7 by addition of the same volume of fresh medium with cytokines except for IL-3. At day 14 the non-adherent cells were harvested and transferred to new mitomycin-treated EL08.1D2 feeder cells.

extract_protocol:
Total mRNA was extracted using the RNeasy micro kit (Qiagen). The concentration and quality of the total extracted RNA was checked by using the Quant-it ribogreen RNA assay (Life Technologies) and the RNA 6000 nano chip (Agilent Technologies, Santa Clara, CA, U.S.A), respectively.
Illumina sequencing library preparation was performed using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen, Vienna, Austria) according to manufacturer's protocol. Libraries were quantified by qPCR.
RNA seq, Lexogen Quantseq FWD

treatment_protocol: CD34+ HPC underwent lentiviral transduction with a RUNX2-specific shRNA containing vector or the control vector. After 48 hours, eGFP+CD34+ CD45RA- Lin- HPC were sorted by FACS cell sorting.

value: Donor 5

tag: shRNA

value: RUNX2 shRNA

value: Lentiviral transduction


title: LPS, 1000 ng/ml; SAMPLE 71

description: Test


title: Hospitalized_COVID-19 [COV172]


title: Fetal MID gestation exposure replicate 2

value: d 133 of gestation

value: Longissimus muscle

value: replicate 2


title: shRNA rep4

value: Donor 4


title: CTRL rep5


title: LPS, 500 ng/ml; SAMPLE 68

description: Test

value: LPS, 500 ng/ml


title: Non-Hospitalized_COVID-19 [COV137]

source_name: Not Hospitalized for COVID-19


title: LPS, 500 ng/ml; SAMPLE 67

description: Test


title: LPS, 100 ng/ml; SAMPLE 66

description: Test

value: LPS, 100 ng/ml


title: LPS, 500 ng/ml; SAMPLE 69

description: Test


title: shRNA rep3

value: Donor 3


title: Non-Hospitalized_COVID-19 [COV131]

value: male


title: Non-Hospitalized_COVID-19 [COV145]


title: LPS, 1000 ng/ml; SAMPLE 70

description: Test


title: LPS, 50 ng/ml; SAMPLE 63

description: Test

value: LPS, 50 ng/ml


title: shRNA rep2

value: Donor 2


title: CTRL rep4


title: Hospitalized_COVID-19 [COV128]


title: LPS, 50 ng/ml; SAMPLE 61

description: Test


title: LPS, 20 ng/ml; SAMPLE 60

description: Test

value: LPS, 20 ng/ml


title: CTRL rep2


title: CTRL rep3


title: Hospitalized_COVID-19 [COV129]


title: LPS, 50 ng/ml; SAMPLE 62

description: Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.


title: LPS, 10 ng/ml; SAMPLE 57

description: Test

value: LPS, 10 ng/ml


title: Hospitalized_COVID-19 [COV125]


title: LPS, 100 ng/ml; SAMPLE 64

description: Test


title: LPS, 5 ng/ml; SAMPLE 53

description: Test

value: LPS, 5 ng/ml


title: Hospitalized_COVID-19 [COV126]


title: LPS, 100 ng/ml; SAMPLE 65

description: Test


title: human PB NK cells RUNX2 Input

library_source: genomic

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied
reads were aligned to hg38 reference genome with STAR_2.4.2a with parameters --outFilterMultimapNmax 1 and --alignIntronMax 1
MACS2 v2.1.1.20160309 was used for peak calling using input DNA as control
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak bed files with chip locations

extract_protocol:
Sorted human peripheral blood NK cells were fixed in 1% formaldehyde and quenched with 0.125M glycine. DNA was sheared by sonicating the lysates with a microtip sonicator. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 35.5 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4°C. Protein A agarose beads were added and incubation at 4°C for an additional 3 h. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition and adaptor ligation. After a final PCR amplification step, the resulting DNA library was quantified.

treatment_protocol: NK cells (CD3- CD19- CD56+) were isolated from peripheral blood by consecutively Lymphoprep density gradient centrifugation, magnetic activated cell sorting (MACS) using the NK cell isolation kit (Miltenyi Biotec) and flow cytometry assisted cell sorting (FACS) using the BD FACSAria III cell sorter (BD Biosciences). Isolated NK cells were snap frozen in liquid nitrogen and stored at -80°C until fixation and ChIP assay.

value: Peripheral blood NK cell

tag: gating

tag: chip antibody

value: input


title: Hospitalized_COVID-19 [COV127]

value: female


title: LPS, 20 ng/ml; SAMPLE 58

description: Test


title: DMSO, 1%; SAMPLE 51

description: Control

value: DMSO, 1%


title: LPS, 5 ng/ml; SAMPLE 52

description: Test


title: LPS, 20 ng/ml; SAMPLE 59

description: Test


title: Hospitalized_COVID-19 [COV122]


title: CTRL rep1

value: Donor 1

value: Lentiviral transduction


title: DMSO, 1%; SAMPLE 50

description: Control


title: P5D_neg

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

data_processing:
Bulk RNAseq: data processing was performed with the Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform (1.10.18). Deduplicated BAM files were used as input for ht-seq count where reads mapping to the entire gene (-t gene) were counted.
snRNAseq: data processing was performed with Cell ranger v3.0.0 with the pre-mRNA reference from 10X Genomics.
Genome_build: Homo Sapiens GRCh38.86
Supplementary_files_format_and_content: Bulk RNAseq: countfile where each column is a sample and each row is a gene. snRNAseq: one countfile per sample, where columns are barcodes and rows are genes

source_name: Temporal Cortex_NEUNnegOLIG2neg nuclei

extract_protocol:
Nuclei were isolated from fresh frozen human brain tissue using a sucrose gradient ultracentrifugation protocol. Nuclei were separated into 3 populations using FANS: 1) NEUNpos neurons used for bulk RNAseq, 2) OLIG2pos oligodendrocytes and OPCs used for bulk RNAseq, 3) NEUNnegOLIG2neg nuclei used for single-nucleus RNAseq. For bulk RNAseq RNA was isolated with the Arcturus™ PicoPure™ RNA Isolation Kit from Thermo Fisher Scientific
Bulk: Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD with UMI) from Illumina. snRNAseq: Chromium Single Cell 3’ Reagents Kit v3 from 10X Genomics

tag: Sex

value: F

tag: brain region

value: Temporal Cortex

tag: nuclei population

value: NEUNnegOLIG2neg nuclei

tag: rin tissue block


title: LPS, 10 ng/ml; SAMPLE 56

description: Test


title: LPS, 10 ng/ml; SAMPLE 55

description: Test


title: LPS, 5 ng/ml; SAMPLE 54

description: Test


title: Hospitalized_COVID-19 [COV124]

tag: age


title: Hospitalized_COVID-19 [COV123]


title: human PB NK cells RUNX2 ChIP

value: Anti-human RUNX2

tag: chip antibody vendor

value: Cell Signalling Technologies

tag: chip antibody cat. #

tag: chip antibody lot#


title: shRNA rep1

tag: day of culture

tag: donor

value: RUNX2 shRNA

tag: treatment


title: DMSO, 1%; SAMPLE 49

description: Control

tag: cell type


title: Hospitalized_COVID-19 [COV120]

tag: gender

value: male


title: LPS, 1000 ng/ml; SAMPLE 46

description: Test

tag: activation agent

value: LPS, 1000 ng/ml

tag: time

value: 8 h


title: Hospitalized_COVID-19 [COV121]


title: LPS, 1000 ng/ml; SAMPLE 48

description: Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.


title: LPS, 500 ng/ml; SAMPLE 45

description: Test

value: LPS, 500 ng/ml


title: P4D_neg


title: P5B_neg

source_name: Occipital Cortex_NEUNnegOLIG2neg nuclei

value: Occipital Cortex


title: LPS, 500 ng/ml; SAMPLE 44

description: Test


title: LPS, 500 ng/ml; SAMPLE 43

description: Test


title: Hospitalized_COVID-19 [COV118]


title: Hospitalized_COVID-19 [COV119]


title: LPS, 100 ng/ml; SAMPLE 41

description: Test

value: LPS, 100 ng/ml


title: Hospitalized_COVID-19 [COV115]

value: female


title: LPS, 100 ng/ml; SAMPLE 40

description: Test


title: P5A_neg

source_name: Frontal Cortex_NEUNnegOLIG2neg nuclei

value: Frontal Cortex


title: Hospitalized_COVID-19 [COV114]


title: P4B_neg


title: LPS, 100 ng/ml; SAMPLE 42

description: Test


title: P4A_neg


title: Hospitalized_COVID-19 [COV116]


title: LPS, 1000 ng/ml; SAMPLE 47

description: Test


title: LPS, 50 ng/ml; SAMPLE 39

description: Test

value: LPS, 50 ng/ml


title: LPS, 50 ng/ml; SAMPLE 38

description: Test


title: P3D_neg

value: M


title: P3A_neg


title: P2D_neg


title: LPS, 50 ng/ml; SAMPLE 37

description: Test


title: LPS, 20 ng/ml; SAMPLE 35

description: Test

value: LPS, 20 ng/ml


title: LPS, 20 ng/ml; SAMPLE 36

description: Test


title: Hospitalized_COVID-19 [COV113]


title: P2B_neg


title: LPS, 10 ng/ml; SAMPLE 32

description: Test

value: LPS, 10 ng/ml


title: LPS, 5 ng/ml; SAMPLE 29

description: Test

value: LPS, 5 ng/ml


title: P1D_neg

value: F

value: Temporal Cortex

value: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV109]

value: male


title: LPS, 10 ng/ml; SAMPLE 33

description: Test


title: Conchiformibius steedae in BSTSY+FBS medium stationary [Cs_st]

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads were mapped against the reference genomes using bowtie2 v2.4.4, and index-sorted using samtools v1.9. Reads were counted using the bamCoverage program of deeptools v3.5.1 (Ramírez et al. 2016) in non-overlapping 1kb windows and the resulting bigwig file converted to human-readable format using the bigWigToWig of UCSC v391.
Assembly: GCF_023547005.1
Supplementary files format and content: Read counts in 1kb non-overlapping windows; read counts with starting position 1 (read count of 7774) to [length of genome], binned at 1 kb.

organism: Conchiformibius steedae DSM 2580

source_name: bacterial cells

growth_protocol: Cells grown in BSTSY+FBS 37°C 350 rpm

extract_protocol:
Cells were lysed using lysozyme and Proteinase K, DNA extracted using Phenol-Chloform and precipitated using ammonium acetate (2.5M final concentration), 2X 100% ice-cold Ethanol, and 5 ug/ml glycogen. RNA was degraded by incubation with 10 mg/ml RNase A for 30 min at 37°C, and DNA cleaned up using DNA Clean & Concentrator-5 (Zymo).
Enzymatic shearing; NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina, 150 bp PE sequenced on NovaSeq 6000 S4

tag: growth stage

value: stationary growth (OD600 = 1)


title: Hospitalized_COVID-19 [COV112]


title: Conchiformibius steedae in BSTSY+FBS medium late exponential [CS_le]

value: late exponential (OD600 = 0.6)


title: LPS, 20 ng/ml; SAMPLE 34

description: Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

value: 8 h


title: Dox, replicate 2 (n=4), scRNAseq

city: Boston

first: Volkan

last: Ergin

state: MA

address: 243 Charles St.

department: Otolaryngology, Harvard Medical School

institute: Massachusetts Eye and Ear

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Transcriptome sequencing analysis and read mapping were performed using CellRanger pipeline (v5.0; 10X Genomics) according to the manufacturer’s guidelines. Raw sequencing reads processed by CellRanger were demultiplexed and mapped to the mouse reference genome (mm10, GRCm38) using STAR. CellRanger-generated count matrices were loaded into Seurat v3.2.2 for downstream analysis.
Assembly: mm10, GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cochlear explant

growth_protocol: The bulla was first removed from the skull and dipped in 75% ethanol for 3 mins before being placed in HBSS. Under a dissecting microscope, the vestibular region, the middle ear, vessels, and the debris were removed from the bulla. The bone covering the apical turn was removed, and round window and oval window membranes were opened to allow media exchange with the cochlear fluids. The ligament portion and Reissner’s membrane at each end of the cochlea were also removed to facilitate the access of the medium to the sensory epithelial region. The cochlea explants were maintained in DMEM/F12 medium supplemented with N2 and B27 over the course of the experiment.

extract_protocol:
Sensory epithelium from cochlear explants was dissociated to single cells using 0.25% trypsin-EDTA for 15 min incubation at 37C. Tissues were gently singularized by P1000 pipette in a complete medium (DMEM/F12 medium containing 10% FBS). Cells were strained twice through 40 mm mesh into 5 ml medium, spun down for 5 min at 300 g to pellet, and resuspended in 50 ml of complete medium. Roughly 1600 cells were loaded onto a 10X Chip-G for a target recovery of 1000 cells. Single cells from cochlear cultures of control (n=4) and Dox-treated (n=8) groups were captured separately to prepare libraries for 1 x control, and 2 x Dox samples.
Single-cell suspensions were immediately transferred to individual channels of the chip (Chromium Next GEM Chip G) to generate gel beads in emulsion together with reverse transcription master mix on the droplet-based high-throughput Chromium Controller (10X Genomics) allowing cell lysis, individual cell barcoding, and reverse transcription by Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, PN-1000128). Briefly, single-cell library preparation was carried out by emulsion breakage, PCR amplification, cDNA fragmentation, oligo adapter, and Illumina sample index addition following the manufacturer's protocol. The single-cell derived cDNA libraries were then assessed with a bioanalyzer (High Sensitivity DNA Kit, Agilent 2100 Bioanalyzer) for quality control. Following library preparation, next-generation sequencing was performed with paired-end sequencing of 150 bp each end using Illumina HiSeqXTen (Novogene Inc.).

treatment_protocol: In the rtTA/tet-Myc/tet-NICD mouse model, cochlea explants were treated with Dox (2 μg/ml final concentration) in complete medium.

value: Sensory epithelium

tag: tissue

value: Cochlear explant

tag: strain

value: rtTA/tet-on-Myc/tet-on-NICD

value: 4-6 weeks old


title: C5C_neg

tag: Sex

tag: brain region


title: P2A_neg

tag: nuclei population

tag: rin tissue block


title: Hospitalized_COVID-19 [COV107]

tag: age


title: DMSO, 1%; SAMPLE 26

description: Control

value: DMSO, 1%


title: Hospitalized_COVID-19 [COV106]


title: Hospitalized_COVID-19 [COV111]

value: female


title: LPS, 5 ng/ml; SAMPLE 30

description: Test


title: NU24B

city: Houston

first: David

middle: Earl

last: Cogdell

state: Tx

address: 1515 Holcombe

department: Pathology

institute: UT MD Anderson Cancer Center

description:
8959312014_R05C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

hyb_protocol: As per Illumina EPICv1.0 protocol.

scan_protocol: Standard Illumina protocol.

label: Cy3, Cy5

source_name: human ureter

label_protocol: As per Illumina EPICv1.0 protocol.

extract_protocol: Extraction of genomic DNA from fresh bladder tissue was performed using proteinase K and Qiagen kit.

value: Ureter

tag: diagnosis

value: control


title: LPS, 10 ng/ml; SAMPLE 31

description: Test

value: LPS, 10 ng/ml


title: Hospitalized_COVID-19 [COV105]


title: Hospitalized_COVID-19 [COV110]


title: LPS, 1000 ng/ml; SAMPLE 24

description: Test

value: LPS, 1000 ng/ml

value: 2 h


title: P1A_neg

value: F

value: Frontal Cortex

value: NEUNnegOLIG2neg nuclei


title: Hospitalized_COVID-19 [COV108]

value: male


title: P1B_neg

value: Occipital Cortex


title: LPS, 5 ng/ml; SAMPLE 28

description: Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

value: LPS, 5 ng/ml

value: 8 h


title: LPS, 1000 ng/ml; SAMPLE 22

description: Test


title: DMSO, 1%; SAMPLE 27

description: Control


title: LPS, 500 ng/ml; SAMPLE 21

description: Test

value: LPS, 500 ng/ml


title: DMSO, 1%; SAMPLE 25

description: Control


title: Control (n=4), scRNAseq

description: 10x Genomics

value: Sensory epithelium

value: Cochlear explant

value: rtTA/tet-on-Myc/tet-on-NICD

value: 4-6 weeks old


title: C2C_neg

value: Temporal Cortex


title: Dox, replicate 1 (n=4), scRNAseq

description: 10x Genomics


title: C5A_neg

value: M


title: NU10-2

description:
6229033126_R04C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Ureter

value: control


title: C5B_neg


title: C3C_neg

value: F


title: LPS, 500 ng/ml; SAMPLE 19

description: Test

value: 2 h


title: NU11-2

description:
8959312014_R04C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: C2B_neg

value: NEUNnegOLIG2neg nuclei


title: LPS, 500 ng/ml; SAMPLE 20

description: Test


title: Hospitalized_COVID-19 [COV104]

value: female


title: Hospitalized_COVID-19 [COV099]

value: male


title: C3A_neg

value: Frontal Cortex


title: MAP24-T (G9-2)

description:
8942351009_R06C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

source_name: human bladder

value: Bladder

value: Urothelial carcinoma (UC) Grade 3


title: NU08

description:
6229033126_R06C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV103]


title: NU07-2

description:
6229033126_R05C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV102]


title: MAP24-D7

description:
8959312014_R04C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Low-grade intraurothelial neoplasia (LGIN)


title: Hospitalized_COVID-19 [COV098]


title: Hospitalized_COVID-19 [COV101]


title: NU30

description:
6229033126_R03C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: LPS, 1000 ng/ml; SAMPLE 23

description: Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.

value: LPS, 1000 ng/ml


title: MAP24-H10

description:
8959312014_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: C2A_neg


title: LPS, 100 ng/ml; SAMPLE 16

description: Test

value: LPS, 100 ng/ml


title: Hospitalized_COVID-19 [COV096]


title: C3B_neg

value: Occipital Cortex


title: LPS, 100 ng/ml; SAMPLE 18

description: Test


title: MAP24-G7

description:
8959312014_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: High-grade intraurothelial neoplasia (HGIN)


title: Hospitalized_COVID-19 [COV095]


title: LPS, 50 ng/ml; SAMPLE 15

description: Test

value: LPS, 50 ng/ml


title: P5D_olig

description:
P5D_olig_S54
processed data file: countmtx_olig.csv

source_name: Temporal Cortex_OLIG2pos nuclei

value: Temporal Cortex

value: OLIG2pos nuclei


title: LPS, 100 ng/ml; SAMPLE 17

description: Test


title: MAP19-T (H8-2)

description:
6229033068_R05C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV100]


title: P4B_olig

description:
P4B_olig_S47
processed data file: countmtx_olig.csv

source_name: Occipital Cortex_OLIG2pos nuclei

value: F


title: MAP19-F6

description:
6229033126_R03C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: Hospitalized_COVID-19 [COV097]


title: MAP24-F9

description:
8959312014_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: LPS, 20 ng/ml; SAMPLE 12

description: Test

value: LPS, 20 ng/ml

value: 2 h


title: Hospitalized_COVID-19 [COV093]


title: P5B_olig

description:
P5B_olig_S52
processed data file: countmtx_olig.csv


title: P5A_olig

description:
P5A_olig_S53
processed data file: countmtx_olig.csv

source_name: Frontal Cortex_OLIG2pos nuclei


title: P4D_olig

description:
P4C_olig_S48
processed data file: countmtx_olig.csv


title: LPS, 50 ng/ml; SAMPLE 14

description: Test


title: LPS, 50 ng/ml; SAMPLE 13

description: Test


title: Hospitalized_COVID-19 [COV091]


title: P4A_olig

description:
P4A_olig_S46
processed data file: countmtx_olig.csv


title: Hospitalized_COVID-19 [COV094]


title: P3B_olig

description:
P3B_olig_S41
processed data file: countmtx_olig.csv

value: M


title: MAP19-E8-1

description:
6229033068_R06C02
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: LPS, 10 ng/ml; SAMPLE 9

description: Test

value: LPS, 10 ng/ml


title: Hospitalized_COVID-19 [COV090]

value: female


title: LPS, 20 ng/ml; SAMPLE 11

description: Test


title: MAP19-D10

description:
6229033126_R01C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.

value: Bladder


title: P3D_olig

description:
P3D_olig_S42
processed data file: countmtx_olig.csv


title: Hospitalized_COVID-19 [COV092]


title: MAP19-E10

description:
6229033126_R02C01
Genomic DNA extracted from bladder sample was genotyped using Illumina EPIC v1.0 Beadchip.


title: LPS, 10 ng/ml; SAMPLE 8

description: Test


title: Hospitalized_COVID-19 [COV088]

value: male


title: P3A_olig

description:
P3A_olig_S40
processed data file: countmtx_olig.csv

value: Frontal Cortex


title: SR_3420_3 + Dox

city: Odense M

first: Lasse Kruse

last: Markussen

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequencing reads were mapped to the mouse genome mm9 or hg19 using STAR (v2.4.2a), tag counts were summarized at the gene level using HOMER, allowing only one read per position per length. Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v1.1) specifying the -count gene option. Data analysis was performed in R studio (v2022.2.0)
Codes and scripts used to process and analyze data have been deposited to GitHub: https://github.com/LasseKMarkussen/Lipolysis-regulates-major-transcriptional-programs-in-brown-adipocytes
Assembly: mm9
Supplementary files format and content: Counts_Dox_exp.txt contains counts for the entire dataset

source_name: Brown adipocyte cell line

growth_protocol: Lentiviral shRNA to Abhd5 was created from a plasmid purchased from Sigma-Aldrich (TRCN0000032737 NM_026179.1-1063s1c1) and used to stably transduce mouse brown adipocytes. To create an inducible rescue cell line, we mutated the DNA sequence targeted by the shRNA while maintaining the wild-type amino acid sequence of ABHD5, and we tagged the construct with mCherry. Doxycycline-inducible expression was achieved by transferring the shRNA-resistant construct into pINDUCER20 and the resulting lentivirus was used to infect the brown adipocytes in which endogenous ABHD5 was stably knocked down. Propagation and differentiation of brown adipocytes with stable knockdown of ABHD5 were done similar to BAT-LgT but supplemented with 0.125 mM indomethacin from day 0-2. Re-established expression of ABHD5 was achieved by treating cells with 1µg/ml doxycycline for 24-48 hrs.

extract_protocol:
total RNA was harvested using TRIzol reagent and isolated using the chloroform-isopropanol method. cDNA was transcribed using the QuantiTect Reverse Transcription Kit (Qiagen, #205311).
RNA-seq was performed according to the instructions by the manufacturer (TruSeq2, Illumina) using 500ng of total RNA for preparation of cDNA libraries.

treatment_protocol: Brown adipocytes with stable knockdown of ABHD5 stimulated with ISO ( 10 nm) or SR-3420 (20 uM) for 3hrs.

value: Brown adipocyte cell line

tag: cell line

value: Brown preadipocyte cell line

value: Brown adipocyte

tag: genotype

value: WT


title: SR_3420_2 + Dox


title: Hospitalized_COVID-19 [COV087]


title: LPS, 10 ng/ml; SAMPLE 7

description: Test

value: RAW 264.7 is a macrophage cell line that was established from a tumor in a male mouse induced with the Abelson murine leukemia virus.


title: Hospitalized_COVID-19 [COV089]


title: SR-3420_1 + Dox


title: LPS, 5 ng/ml; SAMPLE 6

description: Test

value: LPS, 5 ng/ml


title: P2A_olig

description:
P2A_olig_S36
processed data file: countmtx_olig.csv

tag: donor

value: Temporal Cortex


title: P2B_olig

description:
P2B_olig_S34
processed data file: countmtx_olig.csv

value: OLIG2pos nuclei


title: LPS, 20 ng/ml; SAMPLE 10

description: Test


title: Hospitalized_COVID-19 [COV086]


title: P1D_olig

description:
P1D_olig_S30
processed data file: countmtx_olig.csv

value: F


title: LPS, 5 ng/ml; SAMPLE 5

description: Test


title: P2D_olig

description:
P2D_olig_S35
processed data file: countmtx_olig.csv

value: Occipital Cortex


title: P1B_olig

description:
P1B_olig_S29
processed data file: countmtx_olig.csv


title: P1A_olig

description:
P1A_olig_S28
processed data file: countmtx_olig.csv


title: LPS, 5 ng/ml; SAMPLE 4

description: Test

value: 2 h


title: Hospitalized_COVID-19 [COV085]


title: ISO_2 + Dox

tag: treatment

value: ISO (10nM)


title: Hospitalized_COVID-19 [COV084]


title: C5C_olig

description:
C5C_olig_S51
processed data file: countmtx_olig.csv

value: M


title: DMSO, 1%; SAMPLE 3

description: Control

tag: cell type

value: DMSO, 1%


title: DMSO_2 + Dox

value: DMSO


title: DMSO_3 + Dox


title: DMSO, 1%; SAMPLE 2

description: Control


title: C5B_olig

description:
C5B_olig_S50
processed data file: countmtx_olig.csv


title: ISO_3 + Dox


title: Hospitalized_COVID-19 [COV082]

tag: gender

value: female


title: Hospitalized_COVID-19 [COV083]


title: DMSO_1 + Dox


title: DMSO, 1%; SAMPLE 1

description: Control

tag: activation agent


title: C5A_olig

description:
C5A_olig_S49
processed data file: countmtx_olig.csv

value: Frontal Cortex


title: SR_3420_3

value: Brown adipocyte cell line

value: ABHD5 KD


title: SR_3420_1

value: Brown preadipocyte cell line

value: Brown adipocyte


title: Hospitalized_COVID-19 [COV080]

value: male


title: Hospitalized_COVID-19 [COV079]


title: SR_3420_2


title: C4C_olig

description:
C4C_olig_S45
processed data file: countmtx_olig.csv


title: C4A_olig

description:
C4A_olig_S43
processed data file: countmtx_olig.csv


title: Hospitalized_COVID-19 [COV078]


title: C3C_olig

description:
C3C_olig_S39
processed data file: countmtx_olig.csv


title: ISO_1 + Dox

value: WT


title: ISO_3


title: ISO_2


title: Hospitalized_COVID-19 [COV076]


title: Hospitalized_COVID-19 [COV077]


title: C3A_olig

description:
C3A_olig_S37
processed data file: countmtx_olig.csv


title: C2C_olig

description:
C2C_olig_S33
processed data file: countmtx_olig.csv

value: Temporal Cortex


title: Hospitalized_COVID-19 [COV081]


title: C4-2B-siNRP2-2-1

city: Omaha

first: Samikshan

last: Dutta

state: NE

address: 42 and Emile

institute: univ of nebraska medical center

data_processing:
Sequencing was performed on a Illumina NovaSeq 6000 instrument producing 50 bp pairedend reads running Control Software 1.7.0
The sequenced reads were controlled for quality of sequencing with FastQC and trimmed using Trim_Galore.
Trimmed reads were aligned to the reference genome using the STAR aligner version 2.7.0f
RNA abundance was estimated with featureCounts from the Subread package version 1.6.3
Normalization of counts and differential expression analysis were performed with the DESEQ2 R package version 1.26.0
Assembly: GRCh38/hg38
Supplementary files format and content: DESeq2 normalized matrix of counts

source_name: Human prostate cancer cell line

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Library preparation has been done with 770 ng of input RNA using: NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310)) followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® Index Primers Set 1 (NEB# E6440)

value: Human prostate cancer cell line

value: Neuroendocrine like

value: Wild type


title: C4-2B-siNRP2-2-3


title: C4-2B-siNRP2-2-2


title: ISO_1


title: C4B_olig

description:
C4B_olig_S44
processed data file: countmtx_olig.csv

value: F

value: Occipital Cortex

value: OLIG2pos nuclei


title: C4-2B-siNRP2-1-3


title: Hospitalized_COVID-19 [COV074]


title: C3B_olig

description:
C3B_olig_S38
processed data file: countmtx_olig.csv


title: DMSO_3


title: C2A_olig

description:
C2A_olig_S31
processed data file: countmtx_olig.csv


title: DMSO_2


title: C4-2B-siNRP2-1-2


title: DMSO_1


title: C4-2B-siNRP2-1-1


title: Hospitalized_COVID-19 [COV071]


title: Hospitalized_COVID-19 [COV072]


title: P5D_neun

description:
P5D_neun_S27
processed data file: countmtx_neun.csv

source_name: Temporal Cortex_NEUNpos nuclei

value: NEUNpos nuclei


title: Hospitalized_COVID-19 [COV075]


title: C4-2B-Scr-2

value: Non silencing siRNA


title: Hospitalized_COVID-19 [COV070]


title: P5B_neun

description:
P5B_neun_S26
processed data file: countmtx_neun.csv

source_name: Occipital Cortex_NEUNpos nuclei


title: P5A_neun

description:
P5A_neun_S25
processed data file: countmtx_neun.csv

source_name: Frontal Cortex_NEUNpos nuclei


title: C2B_olig

description:
C2B_olig_S32
processed data file: countmtx_olig.csv


title: Hospitalized_COVID-19 [COV073]

source_name: Hospitalized for COVID-19


title: P4B_neun

description:
P4B_neun_S20
processed data file: countmtx_neun.csv


title: Hospitalized_COVID-19 [COV067]


title: C4-2B_AR_3

value: siAR


title: P4D_neun

description:
P4D_neun_S21
processed data file: countmtx_neun.csv


title: Hospitalized_COVID-19 [COV068]


title: C4-2B_AR_2


title: Hospitalized_COVID-19 [COV069]


title: Hospitalized_COVID-19 [COV066]


title: P4A_neun

description:
P4A_neun_S19
processed data file: countmtx_neun.csv

value: Frontal Cortex


title: YTHDF2-iCLIP2

city: Planegg-Martinsried

first: Taku

last: Kureha

address: Grosshaderner Str. 9

department: Institute for Immunology

country: Germany

institute: Ludwig-Maximilians-Universität

data_processing:
Reads were de-multiplexed based on the experimental barcode and adapter sequences were removed from the read ends (Flexbar v3.5.0). UMIs were trimmed and added to the read names. Individual samples were mapped to the respective genome (assembly version GRCm38.p6 for all mouse samples) and its annotation (GENCODE release M25 for all mouse samples) using STAR (v2.7.6a). Reads were de-duplicated if they had identical UMIs. For both m6A-CLIP and Ythdf2-iCLIP significant crosslink sites at single-nucleotide resolution were called using PureCLIP (v1.3.1) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated usingbed GraphToBigWig.

source_name: wild-type_CD4+ cells

growth_protocol: CD4+ T cells were cultured in DMEM (Invitrogen) cell culture medium supplemented with 10% FCS (Gibco), 100U Pen-Strep (Thermo Fisher), 10 mM HEPES-Buffer (Invitrogen), 1% non-essential amino acids (NEAA; Invitrogen) and 50 µM b-mercaptoethanol (Invitrogen) at 37 ºC, 10% CO2

extract_protocol: Cells were washed once with PBS and cross-linked twice with 200 mJ/cm2 UV light (254 nm) in a Stratalinker. After cross-linking, cells were lysed and partial RNA digestion was perfomed by using optimized RNase I dilution (Ambion) together with Turbo DNase (Ambion). After centrifugation, cell lysates were loaded onto a Proteus Clarification Mini Spin Column (Generon) and spun. Protein lysates were incubated with the antibody-coupled beads. Following process and library preparation were perfomed as m6A-CLIP.

treatment_protocol: For activation and differentiation, T cells were stimulated with anti-CD3 (1 µg/mL; cl. 145-2C11, in house production), anti-CD28 (2.5 µg/mL; cl. 37.5N, in house production) under Th1 conditions, 10 μg/mL α-IL-4 (cl. 11B11, in house production) and 10 ng/mL IL-12 (BD Pharmingen) and cultured on six-well plates pre-coated with goat anti-hamster IgG (50 μg/mL, MP Biochemicals) for 40-48h. Following stimulation cells were resuspended in T cell medium supplemented with 200 IU/mL recombinant hIL-2 (Novartis) and expanded in an incubator with 10% CO2. Cells were harvested on day 4 after stimulation.

value: CD4+ cells

tag: antibody

value: rabbit anti-YTHDF2 antibody (Proteintech, Cat. 24744-1-AP)


title: YTHDF2-iCLIP SM-Input2


title: YTHDF2-iCLIP1


title: P3B_neun

description:
P3B_neun_S14
processed data file: countmtx_neun.csv

value: M


title: C4-2B_AR_1


title: Hospitalized_COVID-19 [COV064]


title: P3D_neun

description:
P3D_neun_S15
processed data file: countmtx_neun.csv


title: YTHDF2-iCLIP SM-Input1


title: C4-2B-Scr-3


title: C4-2B_Scr_2

value: Adenocarcinoma


title: P2D_neun

description:
P2D_neun_S8
processed data file: countmtx_neun.csv


title: iKO3

data_processing:
Trimmed RNA-seq reads were pseudoaligned to the ENSEMBL GRCm38 Mus musculus release 99 transcriptome using kallisto, version 0.44.0. Transcript abundances were quantified using default k-mer length 31. Genes differentially expressed between the two conditions were identified using the R statistical package DESeq2, which uses linear modeling to test for each gene the null hypothesis that the log2-fold change between the two conditions is 0.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Wtap KO_CD4+ cells

extract_protocol: RNA-Seq: Total RNA was isolated with the NucleoSpin RNA kit (Macherey-Nagel). Library preparation was performed using SENSE mRNA-Seq Library Prep Kit V2 (LEXOGEN). Libraries were profiled and quantified using the Agilent 2100 Bioanalyzer System (Agilent technologies).The libraries were sequenced with a length of 50 bp, paired-end on an Illumina HiSeq1500 sequencer.

treatment_protocol:
For Wtap depletion, T cells were treated with 1 µM 4’ OH-tamoxifen (Sigma) for 24 h prior to the activation.
For activation and differentiation, T cells were stimulated with anti-CD3 (1 µg/mL; cl. 145-2C11, in house production), anti-CD28 (2.5 µg/mL; cl. 37.5N, in house production) under Th1 conditions, 10 μg/mL α-IL-4 (cl. 11B11, in house production) and 10 ng/mL IL-12 (BD Pharmingen) and cultured on six-well plates pre-coated with goat anti-hamster IgG (50 μg/mL, MP Biochemicals) for 40-48h. Following stimulation cells were resuspended in T cell medium supplemented with 200 IU/mL recombinant hIL-2 (Novartis) and expanded in an incubator with 10% CO2. Cells were harvested on day 4 after stimulation.

value: Wtap KO


title: Hospitalized_COVID-19 [COV065]

value: male


title: C4-2B_Scr_3


title: iKO2


title: Hospitalized_COVID-19 [COV059]

value: female


title: P3A_neun

description:
P3A_neun_S13
processed data file: countmtx_neun.csv


title: C4-2B-Scr-1

value: Human prostate cancer cell line


title: P1D_neun

description:
P1D_neun_S3
processed data file: countmtx_neun.csv

value: Temporal Cortex


title: Hospitalized_COVID-19 [COV063]


title: K562 cells expressing dcas9_kox1, replicate 3

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

data_processing:
Sequencing reads were aligned strand-specifically to the human genome (GRCh38) and then aggregated by gene using only reads uniquely mapped to the reverse strand using the spliced read aligner STAR (Dobin et al., 2013), version 2.7.9, against an index containing features from Ensembl release 98 / GENCODE v32 (downloaded from 10x Genomics reference 2020-A).
Assembly: GRCh38
Supplementary files format and content: ReadsPerGene.out.tab described in STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

molecule: polyA RNA

growth_protocol: K562 cells were grown in RPMI 1640 medium with 25 mM HEPES, 2 mM l-glutamine, 2 g/L NaHCO3 (Gibco) supplemented with 10% (v/v) standard fetal bovine serum (FBS, VWR), 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mM l-glutamine (Gibco).

extract_protocol:
To generate RNA-seq libraries of cells expressing each construct, 1 × 106 cells were harvested for each sample 6 d after FACS by centrifugation at 300 × g for 5 min and flash frozen in a dry ice and ethanol bath. RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research) and quantified using the Qubit RNA BR Assay Kit (Life Technologies).
RNA-seq libraries were prepared by the Whitehead Genome Technology Core facility using the Roche Diagnostics KAPA mRNA HyperPrep Kit.

treatment_protocol: K562 cell lines stably expressing CRISPRi constructs from an SFFV promoter linked to GFP via P2A were generated by lentiviral transduction and FACS. Each construct was transduced in triplicate in parallel with all other constructs. 100,000 GFP-positive cells per construct were isolated by FACS on a Sony SH800S Cell Sorter 5 d after transduction and allowed to recover.

tag: disease state

value: chronic myeloid leukemia

tag: time

value: Day 6 post FACS enrichment


title: C4-2B_Scr_1

tag: tissue

value: Wild type


title: Hospitalized_COVID-19 [COV062]


title: P2B_neun

description:
P2B_neun_S7
processed data file: countmtx_neun.csv

tag: Sex


title: K562 cells expressing dcas9, replicate 3


title: WT2

tag: strain

value: Wildtype


title: Hospitalized_COVID-19 [COV061]


title: WT1


title: P2A_neun

description:
P2A_neun_S9
processed data file: countmtx_neun.csv

tag: brain region

tag: nuclei population

value: NEUNpos nuclei


title: iKO1


title: Hospitalized_COVID-19 [COV060]

tag: age


title: WT3


title: C5B_neun

description:
C5B_neun_S23
processed data file: countmtx_neun.csv

value: Occipital Cortex

tag: rin tissue block


title: Hospitalized_COVID-19 [COV057]


title: P1B_neun

description:
P1B_neun_S2
processed data file: countmtx_neun.csv

value: F


title: P1A_neun

description:
P1A_neun_S1
processed data file: countmtx_neun.csv

value: Frontal Cortex


title: K562 cells expressing zim3_dcas9, replicate 3

tag: cell line


title: Hospitalized_COVID-19 [COV058]


title: ETO+SR3420_3

data_processing:
Sequencing reads were mapped to the mouse genome mm9 or hg19 using STAR (v2.4.2a), tag counts were summarized at the gene level using HOMER, allowing only one read per position per length. Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v1.1) specifying the -count gene option. Data analysis was performed in R studio (v2022.2.0)
Codes and scripts used to process and analyze data have been deposited to GitHub: https://github.com/LasseKMarkussen/Lipolysis-regulates-major-transcriptional-programs-in-brown-adipocytes
Assembly: mm9
Supplementary files format and content: Triascin.txt contains raw gene counts for the entire dataset.

growth_protocol: Mouse brown preadipocytes immortalized with SV40 large T antigen were propagated in basal Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich, #D6249) with high glucose (4500 mg/L) containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Lonza, #09-757F) at 37°C in a humidified atmosphere with 5% CO2 with exchange of medium every second day. To induce differentiation, cells were cultured to two days post confluence (designated day 0) and then added fresh medium supplemented with 0,5µM dexamethasone, 0,5mM 3-isobutyl-1-methylxanthine, 1nM T3 and 20nM insulin. At day 2 cells were given fresh medium containing 1nM T3 and 20nM insulin, and from day 4 cells were cultured in medium without additional inducers. Cells were considered fully differentiated by day 6-7.

treatment_protocol: Immortalized mouse brown adipocytes (D7) pretreated for 1hr with etiher etomoxir (50uM) or triascin C (5uM) and subsequently stimulated +/-  SR-3420 (10uM) for 3hrs.

value: Brown adipocyte cell line

value: Brown preadipocyte cell line

value: Brown adipocyte

tag: genotype

value: WT

value: Etomoxir (50 uM) + SR-3420 (10 uM)


title: C5A_neun

description:
C5A_neun_S22
processed data file: countmtx_neun.csv

tag: donor

value: M


title: ETO_3

tag: treatment

value: Etomoxir (50 uM)


title: Hospitalized_COVID-19 [COV055]

value: male


title: C4C_neun

description:
C4C_neun_S18
processed data file: countmtx_neun.csv

value: Temporal Cortex


title: C5C_neun

description:
C5C_neun_S24
processed data file: countmtx_neun.csv


title: Hospitalized_COVID-19 [COV053]


title: K562 cells expressing dcas9_kox1_mecp2_church, replicate 3

value: chronic myeloid leukemia


title: K562 cells expressing empty_backbone, replicate 3

value: Day 6 post FACS enrichment


title: K562 cells expressing sid_dcas9_kox1, replicate 3


title: TC+SR-3420_3

tag: cell type

value: SR-3420 (10 uM) + Triascin C (5 uM)


title: K562 cells expressing dcas9_kox1, replicate 2


title: K562 cells expressing gal4_4, replicate 3


title: C4B_neun

description:
C4B_neun_S17
processed data file: countmtx_neun.csv


title: TC_3

value: Triascin C (5 uM)


title: Hospitalized_COVID-19 [COV051]

tag: gender


title: Hospitalized_COVID-19 [COV054]


title: Vehicle_DMSO 3

value: DMSO


title: Hospitalized_COVID-19 [COV050]


title: SR-3420_3 (10 uM)


title: K562 cells expressing dcas9, replicate 2


title: C4A_neun

description:
C4A_neun_S16
processed data file: countmtx_neun.csv

value: NEUNpos nuclei


title: C3C_neun

description:
C3C_neun_S12
processed data file: countmtx_neun.csv

value: F


title: Hospitalized_COVID-19 [COV049]


title: C3B_neun

description:
C3B_neun_S11
processed data file: countmtx_neun.csv

value: Occipital Cortex


title: Hospitalized_COVID-19 [COV048]


title: ETO+SR3420_2

value: Brown adipocyte cell line


title: ETO_2

value: Brown preadipocyte cell line


title: K562 cells expressing zim3_dcas9, replicate 2


title: Hospitalized_COVID-19 [COV052]


title: K562 cells expressing dcas9_kox1_mecp2_church, replicate 2


title: TC+SR-3420_2

value: Brown adipocyte


title: C3A_neun

description:
C3A_neun_S10
processed data file: countmtx_neun.csv

value: Frontal Cortex


title: Hospitalized_COVID-19 [COV046]


title: C2C_neun

description:
C2C_neun_S6
processed data file: countmtx_neun.csv


title: TC_2

value: WT


title: K562 cells expressing empty_backbone, replicate 2


title: Hospitalized_COVID-19 [COV045]


title: C2B_neun

description:
C2B_neun_S5
processed data file: countmtx_neun.csv


title: K562 cells expressing sid_dcas9_kox1, replicate 2


title: C2A_neun

description:
C2A_neun_S4
processed data file: countmtx_neun.csv


title: Hospitalized_COVID-19 [COV044]


title: Vehicle_DMSO 2


title: ETO_1


title: Hospitalized_COVID-19 [COV043]


title: K562 cells expressing dcas9, replicate 1


title: K562 cells expressing dcas9_kox1, replicate 1


title: Hospitalized_COVID-19 [COV042]


title: Hospitalized_COVID-19 [COV047]

value: female


title: TC+SR-3420_1


title: K562 cells expressing zim3_dcas9, replicate 1


title: Hospitalized_COVID-19 [COV041]


title: TC_1


title: SAM17356747

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

institute: Genentech

description: These are biopsy samples derived from the Braf;PTEN melanoma GEMM. An initial biopsy from before treatment with vemurafenib and another biopsy sample after resistance on treatment was collected.

data_processing:
Sequences were trimmed to 75 bp and filtered for sequencing quality and ribosomal RNA. Reads for which 30% or more of the nucleotides had a Phred quality score of 23 or lower were discarded. The remaining reads were aligned to the mouse genome using the Genomic Short-read Nucleotide Alignment Program (GSNAP), with default settings and the following parameters: -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna = 200000 --clip-overlap. Further trimming was not performed. Multimapping reads were discarded. PCR duplications were filtered using PicardTools. We used established gene models from the National Center for Biotechnology Information (NCBI) database and extended those with internal Genomic Mapping and Alignment Program for mRNA and EST sequences (GMAP) alignments for additional genes not in NCBI database.
Assembly: mm9
Supplementary files format and content: Raw counts are provided in a gene x sample format. Entrez gene ids are given.

source_name: skin

extract_protocol:
Total RNA was extracted from cells using the Qiagen All Prep nucleic isolation kit (Qiagen, Inc.; catalog number 80204, Valencia, CA) as per the manufacturer’s protocol, including the on-column DNase digestion. Quality control of samples was done to determine RNA quantity and quality before their processing by RNA sequencing (RNA-seq). The concentration and the integrity of total RNA samples were determined using NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA) and 2200 TapeStation (Agilent Technologies, Santa Clara, CA), respectively.
One microgram of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, CA). Library size was confirmed using the 2200 TapeStation and high-sensitivity D1K screen tape (Agilent Technologies, Santa Clara, CA), and their concentration was determined by quantitative PCR-based method using Library quantification kit (Kapa Biosystems, Wilmington, MA). The libraries were multiplexed and then sequenced on HiSeq2500 (Illumina, San Diego, CA) to generate 30 M of single-end 50 base pair reads.

value: skin

value: Genetically engineered mouse model (GEMM) tumor

tag: background

tag: animal id

tag: biopsy type

value: second

value: vemurafenib


title: SR-3420_1  (10 uM)


title: SAM17356749


title: SAM17356748

value: initial


title: Hospitalized_COVID-19 [COV040]

value: male


title: K562 cells expressing dcas9_kox1_mecp2_church, replicate 1

tag: disease state

value: chronic myeloid leukemia

tag: time

value: Day 6 post FACS enrichment


title: K562 cells expressing gal4_4, replicate 2


title: Hospitalized_COVID-19 [COV039]


title: SAM17356750

tag: tissue


title: Hospitalized_COVID-19 [COV038]


title: ETO+SR3420_1

value: Etomoxir (50 uM) + SR-3420 (10 uM)


title: K562 cells expressing empty_backbone, replicate 1


title: SAM17356751


title: SAM17356746


title: Brown adipocyte Lipase Inh. + SR-3420_3

data_processing:
Sequencing reads were mapped to the mouse genome mm9 or hg19 using STAR (v2.4.2a), tag counts were summarized at the gene level using HOMER, allowing only one read per position per length. Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v1.1) specifying the -count gene option. Data analysis was performed in R studio (v2022.2.0)
Codes and scripts used to process and analyze data have been deposited to GitHub: https://github.com/LasseKMarkussen/Lipolysis-regulates-major-transcriptional-programs-in-brown-adipocytes
Assembly: mm9
Supplementary files format and content: Lipolysis_DK.txt contains raw gene counts for the entire dataset.

source_name: Brown adipocyte

growth_protocol: Mouse brown preadipocytes immortalized with SV40 large T antigen, BAT-LgT, were kindly provided by Patrick Seale. Cells were propagated in basal Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma-Aldrich, #D6249) with high glucose (4500 mg/L) containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Lonza, #09-757F) at 37°C in a humidified atmosphere with 5% CO2 with exchange of medium every second day. To induce differentiation, cells were cultured to two days post confluence (designated day 0) and then added fresh medium supplemented with 0,5µM dexamethasone, 0,5mM 3-isobutyl-1-methylxanthine, 1nM T3 and 20nM insulin. At day 2 cells were given fresh medium containing 1nM T3 and 20nM insulin, and from day 4 cells were cultured in medium without additional inducers. Cells were considered fully differentiated by day 6-7.

treatment_protocol: Mature brown adipocytes at D7 were treated with lipase inhibitors (ATGLi and HSLi) for 1hr and subsequently stimulated with 100nM isoproterenol, 10uM SR-3420 or Vehicle (DMSO) for 3hrs before harvest.

value: BAT-LgT

value: Lipase Inh. + SR-3420


title: Brown adipocyte Lipase Inh. + ISO_3

value: Lipase Inh. + ISO


title: K562 cells expressing gal4_4, replicate 1


title: Brown adipocyte Lipase Inh. + Vehicle_3

value: Lipase Inh. + Vehicle


title: Hospitalized_COVID-19 [COV037]


title: SAM17356752


title: SAM17356753


title: Hospitalized_COVID-19 [COV035]


title: Brown adipocyte SR-3420_3

value: Brown adipocyte


title: Hospitalized_COVID-19 [COV034]


title: Brown adipocyte ISO_3

value: ISO


title: SAM17356754


title: K562 cells expressing sid_dcas9_kox1, replicate 1


title: SAM17356756


title: Hospitalized_COVID-19 [COV033]


title: Brown adipocyte Vehicle_3

value: WT

value: Vehicle


title: Hospitalized_COVID-19 [COV032]


title: SAM17356757

value: skin


title: Brown adipocyte Lipase Inh. + SR-3420_2


title: Brown adipocyte Lipase Inh. + ISO_2


title: Hospitalized_COVID-19 [COV030]


title: Patient B207 10x RNA Replicate 2

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description: 5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
The demultiplexing, barcoded processing, TCR assembly and gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, VDJ_filtered_contig_annotations.csv

source_name: PBMC

extract_protocol:
PBMCs were obtained from HIV-1 infected, aviraemic individuals under ART by leukapheresis and stored on liquid nitrogen. CD4+ CD45RA- cells were isolated by magnetic-activated cell sorting. Cells were subsequently incubated with Fc blocking reagent, and stained with a combination of anti-CD3 and/or anti-CD4, anti-TRBC1, and one or a combination of various anti-TRBV antibodies. Cells were sorted for CD3 and/or CD4, a specific TRBC domain and/or a specific TRBV domain or a subset of various TRBV domains.
Library was performed according to the manufacter’s instructions (single cell 5’ and V(D)J Enrichment v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: individual

value: Patient B207

tag: Sex

value: Male

tag: hiv-1 infected

value: Yes

tag: aviraemic

tag: art

value: PBMC

value: CD4+ T cells

tag: library type

value: mRNA


title: Brown adipocyte Lipase Inh. + Vehicle_2

tag: cell line

tag: genotype


title: Patient B207 10x RNA Replicate 1

tag: age


title: Brown adipocyte SR-3420_2

tag: cell type

tag: treatment


title: Patient 9247 10x RNA Replicate 1

value: Patient 9247


title: Hospitalized_COVID-19 [COV031]

tag: gender

value: male


title: SAM17356755

value: Genetically engineered mouse model (GEMM) tumor

tag: background

tag: animal id

value: second

value: vemurafenib


title: Brown adipocyte ISO_2

value: BAT-LgT


title: Patient 605 10x RNA Replicate 1

value: Patient 605


title: Patient 9247 10x RNA Replicate 2


title: SAM17356758

tag: biopsy type

value: initial


title: Hospitalized_COVID-19 [COV028]


title: Brown adipocyte Vehicle_2

value: Brown adipocyte

value: WT


title: SAM17356760

value: skin


title: Hospitalized_COVID-19 [COV026]


title: Hospitalized_COVID-19 [COV029]


title: SAM17356762


title: Hospitalized_COVID-19 [COV027]


title: SAM17356761


title: Brown adipocyte Lipase Inh. + SR-3420_1

value: Lipase Inh. + SR-3420


title: Hospitalized_COVID-19 [COV025]


title: SAM17356763


title: Patient 5104 10x RNA Replicate 2

value: Patient 5104

value: Male


title: Patient 603 10x RNA Replicate 1

value: Patient 603

value: Yes

value: PBMC


title: Patient 5125 10x RNA Replicate 1

value: Patient 5125

value: CD4+ T cells

value: mRNA


title: SAM17356764

value: Genetically engineered mouse model (GEMM) tumor


title: Brown adipocyte Lipase Inh. + ISO_1

value: Lipase Inh. + ISO


title: Brown adipocyte Lipase Inh. + Vehicle_1

value: BAT-LgT

value: Lipase Inh. + Vehicle


title: Hospitalized_COVID-19 [COV022]

value: male


title: Patient 5104 10x RNA Replicate 1


title: Hospitalized_COVID-19 [COV021]


title: Hospitalized_COVID-19 [COV023]


title: SAM17356766

value: initial


title: SAM17356765

value: second

value: vemurafenib


title: Hospitalized_COVID-19 [COV020]


title: HS2, Mel

city: Guangzhou

first: Yunxian

last: Dong

address: 58 Zhongshan Road II

department: Department of Burn and Plastic Surgery

country: China

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

data_processing:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then   FPKM of each gene was calculated based on the length of the gene and reads count mapped   to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Genome_build: h19
Supplementary_files_format_and_content: all_compare.txt (FPKMs, counts)

source_name: hypertrophic scar fibroblasts

growth_protocol: Individual skin tissues were cut into small pieces (1 mm3) and digested with collagenase type II (S10054, 0.8 mg/ml, Yuanye, China) at 37 C for 8 h. The generated fibroblasts were cultured in 1 DMEM (Gibco, USA) medium supplemented with 10% fetal bovine serum (FBS) at 37 C in 5% CO2. The cells at passage 4 were used for experiments.

extract_protocol:
Total RNA was extracted using the RNA Easy Fast Tissue/Cell kit (TIANGEN, China)
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: Hypertrophic scar fibroblasts (HSFs) were treated with or without vehicle or melatonin at 37°C for 24 h.

value: hypertrophic scar fibroblasts

value: with melatonin

tag: passage

value: primary cell at passage 3


title: HS1, Mel


title: SAM17356768

tag: tissue

value: skin


title: Brown adipocyte SR-3420_1

value: Brown adipocyte

value: WT


title: Brown adipocyte ISO_1

value: ISO


title: HS3, Mel


title: HS3

value: without melatonin


title: SAM17356769


title: Hospitalized_COVID-19 [COV018]


title: Hospitalized_COVID-19 [COV019]


title: BKSWT, scRNAseq

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

description: 10x Genomics

data_processing:
The Cell Ranger software was downloaded from 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). Alignment (mm10 reference for mouse samples), filtering, barcode counting, and UMI counting were performed with cell ranger count module to generate gene-cell matrix (v3.0.1, 10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Both BKSDB (n = 2) and BKSWT (n = 2) mice were euthanized with cervical dislocation at 13 weeks of age. Tape the limbs of the mouse in supine position, spray the skin of the head area with 75% ethanol. Retinas of two eyes were isolated carefully and enzymatically digested to generate single-cell suspensions for scRNA-seq.
The concentration of single cell suspension was determined using the Count Star instrument and adjusted to 1000 cells/ul. Using single cell 3’ Library and Gel Bead Kit v3.1 (10x Genomics, Cat. No. 1000121) and Chromium Next GEM Chip G Single Cell Kit (10x Genomics, Cat. No. 1000120), the cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In brief, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered (about 3000 cells). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed in 200 ul tube (NEST Biotechnology, Cat. No. 401001) on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 minutes, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using the Agilent 4200. The cDNA libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with paired-end 150 bp (PE150) reading strategy.

value: Retina

value: No treatment


title: HS2


title: Brown adipocyte Vehicle_1

value: Vehicle


title: BKSDB, scRNAseq

description: 10x Genomics


title: Differentiated si-Setd2#2-3

city: Chapel Hill

first: Jimena

last: Giudice

state: NC

address: 6340B MBRB, Campus Box 7545

department: Cell Biology and Physiology

institute: UNC - Chapel Hill

data_processing:
Sequenced reads were aligned to the mm10 genome with STARv2.7.6a
Alternative splicing was determined using rMATS
Gene counts were generated using Salmonv1.4.0
Differential gene expression was determined using DESeq2
Assembly: mm10
Supplementary files format and content: TPM and read count

source_name: C2C12 myotubes

extract_protocol:
RNA was extracted immediately after stretching using Qiagen kits
RNA libraries were prepared for sequencing using standard Illumina protocols

value: myotubes

tag: biological replicate


title: Roten4

city: Bethesda

first: Christopher

middle: William

last: Schultz

state: MD

address: 37 Convent Dr, Building 37

institute: NIH

data_processing:
Base calling was done by Novogene Co., Ltd. (CASAVA)
Conversion to FASTQ was done by Novogene Co., Ltd. (bcl2fastq2)
paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCh38.p5
Supplementary_files_format_and_content: tab-delimited text files with FPKM and count files

growth_protocol: Cells were cultured in standard DMEM(+++) with 10% FBS, 1% Pen-Strep, 1%L-glutamine

extract_protocol:
RNA was extracted using Qiagen RNAseEasy Kit as per manufacturer's instructions
Done by Novogene Co., Ltd.

treatment_protocol: Cells were treated with Pyrvinium Pamoate at 0.3µM, Oligomycin at 4µM or rotenone at 0.5 µM for 48 hours and then RNA was collected.

value: Roten


title: SAM17356759

value: Genetically engineered mouse model (GEMM) tumor


title: Roten3


title: Hospitalized_COVID-19 [COV014]

data_processing:
The matrix processed and matrix signal intensity files form Genome studio are uploaded.
The statistical analysis was conducted as a case-control panel, with controls characterized as non-hospitalized symptoms and cases characterized as hospitalized symptoms. Case-control association tests of the genotyped and imputed SNPs in the cohort were performed using PLINK (logistic regression). Two different analysis including covariates from the PCA without 1000 Genomes reference samples were run to control for potential population stratification (analysis I), as well as population stratification, age, and gender effects (analysis II).

extract_protocol: DNA was extracted using the automated MagPurix 12 system according to the manufacturer’s protocol. DNA was quantified using the DS-11 Series of Spectrophotometer/Fluorometer (DeNovix).

value: male


title: Differentiated si-Setd2#1-2


title: Roten2


title: Hospitalized_COVID-19 [COV013]


title: SAM17356770

value: initial


title: SAM17356775

value: second

value: vemurafenib


title: Differentiated si-Setd2#1-3


title: SAM17356771


title: Differentiated si-Setd2#2-1


title: SAM17356767


title: Differentiated si-Ctrl-3

value: si-Ctrl


title: SAM17356772


title: HS1

value: hypertrophic scar fibroblasts

value: primary cell at passage 3


title: SAM17356773

value: skin


title: Hospitalized_COVID-19 [COV015]


title: Differentiated si-Setd2#2-2


title: Differentiated si-Setd2#1-1


title: Hospitalized_COVID-19 [COV011]


title: Differentiated si-Ctrl-1


title: Hospitalized_COVID-19 [COV017]


title: Differentiated si-Ctrl-2


title: SAM17356778


title: SAM17356774


title: Roten1


title: Hospitalized_COVID-19 [COV010]


title: Oligo4

value: Oligo


title: Undifferentiated si-Setd2#1-3

source_name: C2C12 myoblasts

value: myoblasts


title: Undifferentiated si-Setd2#2-3


title: Hospitalized_COVID-19 [COV005]


title: Hospitalized_COVID-19 [COV016]

value: female


title: PP1

value: PP


title: Hospitalized_COVID-19 [COV008]


title: Undifferentiated si-Setd2#2-2


title: Hospitalized_COVID-19 [COV004]


title: PP3


title: PP2


title: mouse embryonic fibroblasts, co-culture, con 48h

city: Fuzhou

first: Gui

last: Wu

state: Fujian

address: No. 20 Chazhong Road, Taijing District

department: Department of Orthopedics

institute: First Affiliated Hospital of Fujian Medical University

data_processing:
Raw sequences were mapped to mouse genome mm10 by STAR (v2.5.4b_ENREF_32) with key parameters setting of --readMatesLengthsIn Equal --outFilterMultimapNmax 20 --alignEndsType Local --al    ignSJDBoverhangMin 10 --alignMatesGapMax 10000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3.
The expression level FPKM values were obtained from Cuffnorm in Cufflinks package (v2.2.1).
Assembly: mm10
Supplementary files format and content: counts, FPKM  values for each Sample

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse mesenchymal cells (derived form bone  marrow) and mouse embryonic fibroblast cells (derived from embryos at 13.5 day) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA library preparation was performed as described in the QIAseq Stranded RNA Library Kits (QIAGEN). Total RNA was extracted from mice tissuescells. The mRNA was fragmented to an average insert size of 200–400 bp. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase (Thermo Fisher Scientific) and random primers. The first-strand cDNA was converted into double-stranded DNA in the presence of dUTP. These cDNA fragments were subjected to the addition of a single ’A’ base and subsequent ligation of the adapter. The products were purified and enriched via PCR to generate the final library.

treatment_protocol: Fibroblasts were placed on the upper layer of Corning cell culture insert with 0.4μm polyester membrane and were placed below the permeable membrane. NF-KB inhibitor QNZ was used to block the function of fibroblasts. After co-cultured for 48h, fibroblasts were harvested and total RNA was extracted.

value: mouse embryonic fibroblasts

value: WT

value: co-cultured with MSCs

tag: time


title: Oligo1


title: PP4


title: Oligo3


title: SAM17356779


title: Hospitalized_COVID-19 [COV007]

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

institute: Khalifa University


title: SAM17356776


title: Undifferentiated si-Ctrl-2


title: SAM17356777


title: Hospitalized_COVID-19 [COV006]


title: mouse embryonic fibroblasts, con, 48h

description: Con

value: con


title: mouse embryonic fibroblasts, co-culture, QNZ,48h

value: co-cultured with MSCs,QNZ


title: Hospitalized_COVID-19 [COV009]

value: male


title: Oligo2


title: Hospitalized_COVID-19 [COV003]


title: DMSO1

value: DMSO


title: bone_marrow_RNA_wild_type

city: Guadalajara

first: Jennifer

last: Santana Hernández

state: Jalisco

address: Sierra Mojada 950, Independencia Oriente

department: Instituto de Genética Humana

country: Mexico

institute: Universidad de Guadalajara

hyb_protocol: Following fragmentation, 2.3 ug of fragmented and labeled ss-DNA were hybridized with hibridation master mix, incubate with rotation at 60 rpm for 16 hr at 45C on GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 Dx v.2, and Workstation.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000Dx v.2 with AutoLoaderDx, with Affymetrix Molecular Diagnostic Software (AMDS)

data_processing:
All data were captured in an Applied Biosystems Transcriptome Analysis Console (TAC) Software version 4.0.2
According to the analysis, the genes with a Fold Change ±1.5 are considered statistically significant expression differences (p<0.05), however, we selected only those genes with fold change over ±10.0 (a highest selection).

source_name: Expression profile wild type

label_protocol: Total RNA were prepared according to the standard ThermoFisher Scientific protocol from 6 µL total RNA (GeneChip WT PLUS Reagent Kit USER GUIDE. Manual target preparation for GeneChip whole transcript (WT) Expression Arrays, 2020, Thermo Fisher Scientific-Affymetrix).

growth_protocol: bone marrow sample obtained from a female pediatric patient diagnosed with leukemia and a healthy patient

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

treatment_protocol: Isolated lymphocytes of BM keep in solution Phosphate Buffered Saline

tag: disease state

value: healthy

value: bone marrow

value: 10 years


title: DMSO4


title: Undifferentiated si-Ctrl-1

value: si-Ctrl


title: Undifferentiated si-Setd2#1-2


title: bone_marrow_RNA_acute_promyelocytic_leukemia

source_name: Expression profile leukemia PML/RARA

value: acute promyelicytic leukemia

value: 12 years


title: Ncl-CLIP_5-Cys-LNA_2

city: New York

first: Sohail

last: Tavazoie

state: NY

address: 1230 York Ave

data_processing:
Adaptors were removed using cutadapt.
Reads were aligned to mm10 or tRNA space using bwa (HITS-CLIP and sRNA-Seq) or STAR (RNA-Seq and Ribo-Seq).
HITS-CLIP peaks were called using Piranha.
HITS-CLIP and sRNA-Seq reads that were aligned to peaks, tRNA space were counted using featureCounts.
RNA-Seq and Ribo-Seq reads that were aligned to RefSeq transcripts and coding sequence respectively were counted using featureCounts.
Differential expressed transcripts were determined using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables: tsv files.
Supplementary_files_format_and_content: Called peaks: bed files.

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS, sodium pyruvate, L-glutamine, Pen/Strep and Amphotericin.

extract_protocol:
Total RNAs were extracted using TRIzol and RNeasy MINI kit (Qiagen).
RNA-Seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Ribo-Seq libraries were constructed as described previously (McGlincy and Ingolia, 2017). HITS-CLIP libraries were constructed as described previously (Moore et al., 2014). small RNA-Seq libraries were constructed using RealSeq-AC (SomaGenics).

treatment_protocol: Cells were transfected with a scrambled control (Scr-LNA) or  5'-tRFCys antisense LNAs (5'-Cys-LNA1) using Lipofectamine 2000.

value: breast cancer cells

tag: clip antibody

value: Nucleolin

value: transfected with 5-Cys-LNA1

tag: molecule subtype

value: crosslinked RNA


title: Undifferentiated si-Ctrl-3

value: myoblasts


title: Hospitalized_COVID-19 [COV002]

value: female


title: DMSO3


title: Ncl-CLIP_5-Cys-LNA_1


title: Ncl-CLIP_Scr-LNA_1

value: transfected with Scr-LNA


title: BMDM R848 biol rep 2

status: Public on Jun 02 2022

city: Los Angeles

first: Caius

middle: Gabriel

last: Radu

address: 650 Charles E. Young Drive, South

department: Molecular and Medical Pharmacology

institute: UCLA

description: BMDM R848 biol rep 2

data_processing:
Sequencing was performed on Illumina HiSeq 3000 (1x50).
Data quality checking was done on Illumina SAV. Data de-multiplexing was performed with Illumina Bcl2fastq v 2.19.1.403 software.
The reads were mapped by STAR 2.27a and read counts per gene were quantified using the mouse Ensembl Mus_musculus.GRCm38.97 GTF file.
Read counts were normalized by CPM +1.0E-4.
Assembly: GRm39
Supplementary files format and content: CPM +1.0E-4 normalized counts.

source_name: bone marrow derived marophage (BMDM) derived from female C57BL/6 mice.

growth_protocol: Bone marrow derived macrophages were derived from female C57BL/6 mice and  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) supplemented with 50 ng/mL MCSF.

extract_protocol:
Total RNA was isolated from bone marrow derived macrophages (BMDM) treated with TLR7 agonists using the NucleoSpinRNA kit (Macherey-Nagel Catalog#NC0707522).
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming, followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation, and PCR amplification.

treatment_protocol: Bone marrow derived macrophage (BMDM) cells from female C57BL/6 mice were treated with: 1) vehicle control; 2) 5 µg poly-uridine (polyU) ssRNA complexted with DOTAP; 3) 1 µM ulodesine (PNPi) + 5 µM guanosine (rG) + 5 µM  deoxyguanosine (dG); 4) polyU(DOTAP) + PNPi + rG + dG; 5) 1 ng/mL R848.

value: BMDM

value: WT

value: 4 hour 1 ng/mL R848 treatment


title: mouse embryonic fibroblasts, QNZ, 48h

description: QNZ

value: mouse embryonic fibroblasts

value: QNZ


title: Ncl-CLIP_Scr-LNA_2


title: Hospitalized_COVID-19 [COV001]

value: male


title: DMSO2

value: DMSO


title: Undifferentiated si-Setd2#2-1


title: Undifferentiated si-Setd2#1-1


title: BMDM polyU (DOTAP)+PNPi+rG+dG biol rep 1

description: BMDM poly U(DOTAP)+PNPi+dG+rG biol rep 1

value: bone marrow derived marophage (BMDM) derived from female C57BL/6 mice.

value: 4 hour 5 ug polyU ssRNA (DOTAP) + 1 uM ulodesine + 5 uM dG + 5 uM rG treatment


title: BMDM PNPi+rG+dG biol rep 1

description: BMDM PNPi+dG+rG biol rep 1

value: 4 hour 1 uM ulodesine + 5 uM dG + 5 uM rG treatment


title: BMDM polyU (DOTAP)+PNPi+rG+dG biol rep 2

description: BMDM polyU (DOTAP)+PNPi+dG+rG biol rep 2


title: BMDM vehicle biol rep 1

description: BMDM vehicle biol rep 1

value: 4 hour vehicle treatment


title: BMDM PNPi+rG+dG biol rep 2

description: BMDM PNPi+dG+rG biol rep 2


title: BMDM polyU (DOTAP) biol rep 1

description: BMDM polyU (DOTAP) biol rep 1

value: 4 hour 5 ug polyU ssRNA (DOTAP) treatment


title: D3, Ctrl

city: xiamen

first: Liu

last: Zhixiong

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

data_processing:
At least 20 million clean reads of sequencing depth were obtained for each sample
After getting clean reads, we used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
For samples with good quality and sufficient sequencing data, most of the transcripts will be completely covered, and reads will be evenly distributed in various regions of the transcript.
StringTie was used to estimate the expression level of detected genes
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM and read count values for each Sample

source_name: Brain

growth_protocol: Cortical mouse NPCs were cultured using P0 mouse cortex in laminin and poly-L-ornithine-coated plates and maintained in DMEM/F12 (11320033, Thermo) containing 1% penicillin/streptomycin, 1% l-glutamine, 1% N-2 supplement, 1% B27,1×Glutamax (10565-042, Life technologies)，5 mM Hepes, 0.06% Glucose, 50 μM beta-mercaptoethanol, 20 ng/ml EGFand 20 ng/ml bFGF

extract_protocol:
Total RNA fraction was extracted using RNA isolater Total RNA Extraction Reagent (Vazyme)
RNA libraries for RNA-seq were prepared using BGI RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: withdrawal of EGF and bFGF for neural stem cell differentiation

value: Brain

value: neural stem cell

value: primary neural stem cell

value: Seh1 f/f

value: differentiation medium


title: D3, iKO

value: cmv-cre-ert,seh1 f/f


title: BMDM R848 biol rep 1

description: BMDM R848 biol rep 1

value: BMDM

value: WT


title: BMDM vehicle biol rep 2

description: BMDM vehicle biol rep 2


title: D0, Ctrl

value: growth medium

value: DO


title: BMDM polyU (DOTAP) biol rep 2

description: BMDM polyU (DOTAP) biol rep 2


title: WNV infeccted aSyn KO 2

city: Aurora

first: J.

middle: David

last: Beckham

state: Colorado

address: 12800 East 19th Avenue, RC1N\P18-8404A

department: Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Performed by Novogene
Overall gene expression was analyzed using principal component analysis and DESeq2 R package
ClusterProfiler software was used for enrichment
Supplementary files format and content: Xcel file including FPKM reads

source_name: Whole Brain

extract_protocol:
RNA was extracted using the E.Z.N.A. Total RNA kit II (Omega Bio-Tek).
RNA libraries were prepared for RNA-seq using the Agilent2100 system according to manufacturer protocol

treatment_protocol: Mice were infected via footpad injection with 1000 PFU of West Nile Virus NY99 strain. Brains were harvested 8 days post-infection.

value: Whole Brain

value: SNCA KO

value: WNV infected


title: D0, iKO


title: WNV infected aSYN KO 3


title: WNV infected aSyn KO 1


title: WNV infected WT 3


title: WNV infected WT 2


title: WNV infected WT 1


title: Mock infected WT 3

value: Mock Infected


title: patient 15_002 aortic wall  GCH_15_0028

city: Heidelberg

first: Philipp

last: Erhart

address: Im Neuenheimer Feld 420

department: Vascular and Endovascular Surgery

institute: Heidelberg University Hospital

description: biopsy from region with high wall stress

hyb_protocol: 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12-Microarray according to the Whole-Genome Gene Expression  Direct Hybridization Assay Guide.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  (Whole-Genome Gene Expression  Direct Hybridization Assay Guide)

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: Biotin, Cy3-Streptavidin

source_name: abdominal aortic wall

label_protocol: The Illumina TotalPrep RNA Amplification Kit (life technologies) was used to generate single-stranded cRNA from input amounts of 200ng total RNA.

growth_protocol: no cell cuture used - RNA was extracted directly from aortic wall biopsies, immediately after tissue sampling during open surgical aortic replacement.

extract_protocol: Total RNA was extracted from fresh frozen biopsy material using RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany). A two-step quality and quantity control in terms of spectrophotometric analysis using the NanoDrop 2000c (Thermo Fisher Scientific, Waltham MA, USA was performed

treatment_protocol: no treatment applied

tag: Sex

value: female

value: 48 years

tag: aaa diameter

tag: disease

value: abdominal aortic aneurysm


title: patient 15_017 aortic wall  GCH_15_0173

description: biopsy from region with low wall stress

value: male

tag: age

value: 75 years


title: patient 14_010baortic wall  GCH_14_0105

description: biopsy from region with low wall stress

value: 80 years


title: patient 15_033 aortic wall  GCH_15_0331

description: biopsy from region with low wall stress

value: 77 years


title: WNV infected WT 4

tag: genotype


title: patient 14_007 aortic wall  GCH_14_0072

value: 61 years


title: patient 15_017 aortic wall  GCH_15_0172


title: patient 14_011 aortic wall  GCH_14_0114

description: biopsy from region with low wall stress

value: 72 years


title: patient 14_010 aortic wall  GCH_14_0106


title: patient 14_009 aortic wall  GCH_14_0098

description: biopsy from region with low wall stress

value: 54 years


title: patient 15_007 aortic wall  GCH_15_0070

description: biopsy from region with low wall stress


title: patient 15_002 aortic wall  GCH_15_0029

description: biopsy from region with low wall stress


title: patient 14_009 aortic wall  GCH_14_0099


title: patient 15_033 aortic wall  GCH_15_0332


title: patient 14_004 aortic wall  GCH_14_0046

description: biopsy from region with low wall stress

value: 70 years


title: patient 15_011 aortic wall  GCH_15_0118

description: biopsy from region with low wall stress


title: patient 15_007 aortic wall  GCH_15_0071


title: patient 15_011 aortic wall  GCH_15_0117


title: C. albicans culture, Surfactin 2

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

data_processing:
Quality control of sequencing data was performed using FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
STAR RNA-Seq aligner was used to map the sequenced reads to the reference genome and generate BAM files
DESeq algorithm was used to obtain normalized gene expression values (StrandNGS software)
Gene expression differences between treated and control groups were compared by moderated T-test; Benjamini-Hochberg False Discovery Rate was used for multiple testing correction.
Raw reads were aligned to the reference genome (https://www.ncbi.nlm.nih.gov/genome/?term=Candida+albicans+SC5314) aligned reads varied between 92-95 % in each sample.
Genome_build: ASM18296v3
Supplementary files format and content: Excel file includes p corrected p values, fold change values and raw data.

organism: Candida albicans

source_name: fungal cells

growth_protocol: The strain was maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). The pre-cultures were grown in YPD medium at 37ºC  for 18 hours then diluted to OD640 0.1 value in 20 mL of YPD and incubated at 37ºC with 2.3 Hz shaking frequency.

extract_protocol:
Freeze- lyophilized cells were processed using TRISOL reagent (Invitrogen, Austria) reagent and glass beads. RNA concentration and purity were determined using NanoDrop (ThermoFisher Scientific, Waltham, MA USA) and capillary electrophoresis.
RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs) according to the manufacturer’s protocol. Briefly, poly-A RNAs were captured by oligo-dT conjugated magnetic beads then the eluted mRNAs were fragmented at 94°C. First strand cDNA was generated by random priming reverse transcription; double stranded cDNA was generated in a second strand synthesis step. After repairing ends, A-tailing and adapter ligation steps, adapter-ligated fragments were amplified in enrichment PCR and finally sequencing libraries were generated. Sequencing libraries were normalized to the same molar concentration and pooled together. Library pool was sequenced on NextSeq500 instrument (Illumina, San Diego, CA, USA) generating single read 75bp-long sequencing reads. Fastq files were generated automatically after the sequencing run by Illumina BaseSpace.

treatment_protocol: Following 4 hours incubation time YPD medium was supplemented with a final concentration of 128 mg/L surfactin and fungal cells were collected 1 hour following surfactin exposure by centrifugation (5 min, RCF=4000g, 4°C). The cells were washed three times with phosphate-buffered saline and stored at -70°C until use.

tag: strain

value: wild type

tag: treatment

value: Surfactin


title: patient 14_007 aortic wall  GCH_14_0071

description: biopsy from region with low wall stress


title: patient 14_011 aortic wall  GCH_14_0113


title: C. albicans culture, Surfactin 3


title: C. albicans culture, Surfactin 1


title: Mock infected WT 2

value: Whole Brain

value: WT


title: Mock infected aSyn KO 2

value: SNCA KO


title: BMDM cells, LPS+INFg treatment, replicate 2

city: Solna

first: Heshuang

last: Qu

address: L8:03, visionsgatan 18

country: Sweden

institute: Karolinska Institutet

data_processing:
The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation
The indexed cDNA libraries were normalized and combined and the pools were sequenced on the Illumina Nextseq 2000 for a P2 100 cycle sequencing run, generating paired end reads.
Base calling and demultiplexing was performed using CASAVA software with default settings generating FASTQ files for further downstream mapping and analysis.
Reads were mapped to the GRCm38 reference genome using STAR
Data normalization and analysis of differential gene expression was done using the DESeq2 R-package using a negative binomial test.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw data count for each sample/library

source_name: Bone marrow

growth_protocol: Bone marrow cells from mouse hind limbs were pooled and matured into macrophages in DMEM supplemented with 10% fetal bovine serum (FBS; F7524, Sigma, St. Louis, MO, USA), 2 mM L-glutamine (Sigma), 1 mM sodium pyruvate (Sigma), 22 μM β-mercaptoethanol (Gibco, Paisley, United-Kingdom), 10,000 I.U./mL Penicillin–Streptomycin (PenStrep; Sigma), and 10 ng/mL macrophage colony-stimulating factor (M-CSF; R&D Systems, Minneapolis, MN, USA) for 10 days at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer´s instructions.
To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with 200 ng total RNA as starting concentration. The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries.

treatment_protocol: BMDMs were detached from the flask using Trypsin (Sigma). Cells were washed and re-seeded in 24-well culturing plates (Sarstedt, Nümbrecht, Germany) at a density 0.5 million cells/well in DMEM containing 1% FBS and 10,000 I.U./mL PenStrep and rested overnight. To generate cells with an M1 phenotype, 100 ng/mL LPS-EK (InvivoGen, Toulouse, France) and 20 ng/mL IFN-γ (R&D Systems) were added. FrHMGB1 (in-house production) and dsHMGB1 (a kind gift from Prof. Kevin Tracey’s laboratory, Feinstein Institute, Mannhasset, NY, USA), produced and stored in buffers without DTT, was used in 5 µg/mL concentration. LPS-EK was used in 1 µg/mL concentration. PBS was included in all experiments as an unstimulated control. BMDMs were stimulated 24 hours at 37 °C with 5% CO2 before RNA isolation.

value: Bone marrow

tag: cell type

value: Bone marrow derived macrophage

value: 1ug/mL LPS-EK + 20 ng/mL IFN-gamma


title: Mock infected aSyn KO 1

value: Mock Infected


title: BMDM cells, LPS+INFg treatment, replicate 1


title: BMDM cells, LPS+INFg treatment, replicate 3


title: Mock infected WT 1