title: M5: Male adult Rep 3

data_processing:
Reads were mapped to mm9 whole genome using tophat2 (2.0.11) with argument  “--library-type fr-firststrand"
Gene annotations were obtained from iGenome Ensembl NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: bone endothelial cells

extract_protocol:
Bone endothelial cells were purified using endomucin expression  and sorted directly into lysis buffer of the RNeasy Plus Micro Kit (QIAGEN). Total RNA was isolated as per the manufacturer’s guidelines.
RNA quality was checked using a 2100 BioAnalyzer (Agilent), and libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit (Illumina) following the manufacturer’s guidelines. Sequencing of libraries was carried out at the LMS Genomics Facility on an Illumina Nextseq500 platform with 40-nucleotide-length paired-end reads.

value: freshly isolated from tibia

value: 12 weeks

tag: Sex

value: M


title: Cap-seq_Human_siCtrl_rep1

status: Public on Aug 29 2022

type: SRA

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description: Mitochondrial RNA

library_source: transcriptomic

data_processing:
Adapter trimming was performed by cutadapt 1.18
Cappable-seq reads were aligned to human or mouse genome using bowtie2
5'-end coordinates were extracted using samtools and bedtools
TSS (transcription start sites) counts were normalized to total mitochondrial reads
Relative Log2 fold changes across a 25 bp window were calculated using normalized TSS from biological repeats plus a pseudocount of one in HeLa cells (siSSBP1 vs siCtrl) or in mouse heart( L/L, cre vs L/L)  with bigwigCompare v3.1.3
Genome_build: GRCm38 or GRCh38
Supplementary_files_format_and_content: Normalized TSS bedgraph file

molecule: total RNA

organism: Homo sapiens

source_name: Hela cell

growth_protocol: All mice maintaining an inbred C57BL/6N nuclear background were housed in a 12-hour light/dark cycle at 21°C and fed ad libitum on a standard mouse food (ssniff RM-H Low-Phytoestrogen). The health status of the animals is specific pathogen free according to the Federation of the European Laboratory Animal Science Association (FELASA) recommendations.

extract_protocol:
Mitochondria isolation from mouse heart was performed as described previously (PMID: 31588022). For Hela cells, cells at about 80% confluence were harvested, and spin down at 500g for 3min at 4°C, washed once with cold PBS. Cell pellet was resuspended in 1 ml of lysis buffer (20mM Tris-Cl pH7.6, 220mM mannitol, 70mM sucrose, 1mM EDTA, 1xprotease inhibitor, 1mg/ml BSA) and incubated on ice for 15 min, then transferred to glass Dounce homogenizer (1 ml), the cells were broken by 20-25 strokes, followed by centrifugation at 1200g for 3 min at 4°C. The supernatant was transferred to a new Eppendorf tube and spin at 14,000g for 3 min at 4°C to pellet the crude mitochondria. Mitochondrial RNA was prepared from crude mitochondria by Trizol extraction following manufacture’s instructions, after ethanol precipitation, the RNA was dissolved in nuclease-free water and treated with RNase-free Dnase I (Thermol) at 37°C for 20 min, followed by purification with Quick RNA Micro prep column (Zymo Research).
Library construction was performed by Vertis Biotechnologie (Freising, Germany)
Cappable-seq

treatment_protocol: HeLa cells were grown at 37°C, 5% CO2 in DMEM GlutaMAX™supplemented with 10% fetal bovine serum (FBS). For siRNA transfections, HeLa cells were reverse transfected with 10 nM of indicated siRNA using Lipofectamine RNAiMAX. Experiments were performed at 72 hours after transfection.

value: 3 days

tag: cell line

value: HeLa


title: CR18 6h BS1

city: Liège

first: Christelle

last: Sanchez

address: Quai G. Kurth 45

country: Belgium

institute: ULiege

data_processing:
Raw data were demultiplexed into individual libraries. After filtering out reads mapping to rRNA, tRNA, mitochondrial RNA, and other contaminants (e.g., adapters, etc.) using bowtie2
Assembly: GRCh38
Supplementary files format and content: reads were aligned onto the human reference genome (GRCh38 and Ensembl 105 annotation) and quantified with Star to give the Counts file.

source_name: Chondrocytes

growth_protocol: Primary OA chondrocytes were isolated from cartilage after enzymatic digestion and growth in alginate beads in high glucose DMEM containing 1% FBS, 2mM glutamine, 50 µg/ml ascorbic acid and 20 µg/ml proline during 3 days

extract_protocol:
18 beads were pooled, degelified in 0,1M cold citrate and cells were homogenized in 600 µl RTL lysis buffer (Qiagen) then extract using Rneasy mini kit from Qiagen according to the manufacturer's instructions. Dnase step were performed during extraction. Samples were eluted in 30 µl RNase free H2O
0,1 µg of RNA from each culture condition was used for this analysis. Libraries were prepared with the Illumina Truseq stranded mRNA sample prep kit according to the manufacturer's instructions

treatment_protocol: Chondrocytes are cultured in 1% FBS, glutamine, ascorbic acid and proline with or without CL and BS for 6h or 24h

tag: cell type

value: Chondrocytes

tag: patient

tag: time

tag: cl treatment

tag: bs treatment


title: VAT_WT_young_1

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
DESeq2_norm_old_young_VAT.txt
B27

data_processing:
Illumina Casava1.82 software used for basecalling and demultiplexing.
After demultiplexing, raw reads were pseudoaligned to the murine transcriptome (mm10, GENCODE general assembly release vM16) using Kallisto with default settings
Based on the pseudoalignment estimated by Kallisto, transcript levels were quantified and counts were imported into R using tximport. Transcript information was summarized on gene-level. We imported the resulting dataset and performed the downstream analysis using the DESeq2 pipeline.
Genome_build: mm10
Genome_build: transcriptome build: mm10, GENCODE general assembly release vM16
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

organism: Mus musculus

source_name: visceral adipose

extract_protocol:
Batch1 :  Cells were stored in Trizol and extracted using Qiagen mini kit according to recommendations from manufacture;    Batch2:  Cells were sorted into RLT buffer and extracted using Qiagen mini kit according to recommendations from manufacture
mRNA is purified from approximately 500pg-1ng of total RNA using the Clontech SMARTer Ultra Low V4 RNA Kit.  The kit utilizes an oligo(dT) primer, which primes the first-strand synthesis reaction.  SPRI beads are used to selectively bind first-strand cDNA.   ss cDNA is then amplified by LD PCR to make ds cDNA and is again purified using SPRI beads.  During amplification the poly A sequence serves as the universal priming site for end-to-end cDNA amplification.  Thus, cDNA without these sequences, such as prematurely terminated cDNAs, containing genomic DNA, or cDNA transcribed from Poly A minus RNA, are not exponentially amplified.  The beads are then washed with 80% ethanol and eluted in purification buffer.  The full-length cDNAs are then sheared using the Covaris, which results in 200-500bp DNA fragments.  The fragmented cDNA library is then end-repaired, A-tailed, and adapters are ligated. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

tag: age

value: young

tag: tissue

value: visceral adipose

value: B cells

tag: genotype

value: WT

tag: cohort


title: Patient10_CD4_RNA

city: Manchester

first: chenfu

last: shi

address: AV Hill Building, Upper Brook Street, room 1.023

country: United Kingdom

institute: the university of manchester

description: RNA-seq library generated using Quant-seq

data_processing:
pCHiC sequencing data was filtered and the adapters were removed using fastp v0.19.4
pCHiC mapping was performed using HICUP 0.7.4 on hg38 genome. CHICAGO 1.13.1 was used to identify significant interactions
RNA-seq sequencing data was filtered and the adapters were removed using fastp v0.19.4
RNA-seq reads were mapped using STAR v2.7.3a on hg38 gencode v32 annotation
RNA-seq counts were generated using Htseq
Assembly: hg38
Supplementary files format and content: .RDs files contain chicago classes containing data for the specified samples
Supplementary files format and content: washU_track.txt.gz files contain the longrage interaction files for washu browser
Supplementary files format and content: csv.gz files contain the data from the differential interaction analysis from chicdiff
Supplementary files format and content: .count file contain the counts from the RNA-seq

source_name: Primary CD4 T cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from blood using Ficoll density gradient centrifugation. EasySep Human CD14+ Positive selection kit (StemCell Technologies, ref:17858) was used to isolate CD14+ cells from PBMCs and, subsequently, Easysep CD4+ T cell isolation kit (StemCell Technologies, ref:17952) was used to isolate CD4+ T cells from the remaining PBMCs, according to the manufacturer’s instructions.
pCHiC: 5-10 million isolated CD4+ T cells and CD14+ monocytes were crosslinked for 10 min in 1% formaldehyde and agitated at room temperature, the reaction was then quenched with ice cold 0.125 M glycine for 5 min. Crosslinked cells were washed in ice-cold PBS, and the supernatant was discarded, the pellets were then stored at -80ºC.  Each Hi-C library was prepared from fixed cells following the Arima HiC kit (Arima Genomics) and the KAPA HyperPrep kit (KAPA Biosystems) following the manufacturer’s protocol. Briefly, crosslinked cells were lysed, and DNA was digested by two different restriction enzymes, and ligated.  The ligated DNA was reverse-crosslinked and fragmented by sonication (Covaris S220), followed by DNA size selection, biotin enrichment, adaptor ligation, and final library amplification. A quality control step to determine the number of PCR cycles needed for library amplification was performed for each library using the NEBNext Library Quant kit (NEBNext, ref: E7630). Final quality and quantity were assessed by Bioanalyzer 2100 (Agilent) and Qubit (Thermo Fisher).  Hi-C samples were then hybridized with the SureSelect custom capture library by following Agilent SureSelectXT HS reagents (ref: G9702A, G9496A) and protocols (ref: G9702-9000). Briefly, target regions are hybridized with designed probes, followed by capture enrichment of these regions through streptavidin pulldown using Dynabeads MyOne Streptavidin T1 (ThermoFisher, ref: 65601). Post-capture amplification was carried out using nine PCR cycles. Final quality and quantity were assessed by Bioanalyzer 2100 (Agilent) and Qubit (Thermo Fisher).   RNA: A total of 0.5 million purified cells was resuspended in 700 uL Qiazol lysis reagent (QIAGEN, ref: 79306) to isolate RNA, then 140 uL of chloroform was added. After centrifugation at 12000 x g for 15 min, approximately 350 uL of the upper layer containing the RNA was transferred and mixed with 525 uL of 100% ethanol. RNA isolation was continued from this point using the RNeasy microkit (QIAGEN, ref: 74004) reagents and protocol. Final quantity was assessed by Qubit (Thermo Fisher). Libraries for RNA-seq were prepared using Illumina Truseq Stranded Total RNA reagents and protocol, except for Control 1 CD4+ and CD14+ samples, for which library preparation failed. Library quality and quantity was assessed by Bioanalyzer. The 28 libraries generated were sequenced using three lanes on Illumina HiSeq4000, generating 75 bp paired-end reads, and leading to an average of 30 million reads per sample (Genomics Facility, University of Manchester).

tag: disease

value: Systemic sclerosis

value: Primary CD4 T cells


title: Patient9_CD14_RNA

source_name: Primary CD14 Monocytes

value: Primary CD14 Monocytes


title: CR18 6h CL1


title: CR18 6h CL2


title: CR18 6h CTRL


title: M3: Male adult Rep 1

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

molecule: polyA RNA

tag: strain


title: TAM1

city: Xi'an

first: Zhiqiang

last: Fang

state: Shaanxi

address: No.169,Changle West Road

country: China

institute: Xijing Hospital

data_processing:
fastp v 0.18.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v 0.18.0
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release100
Supplementary files format and content: excel files include FPKM values for each Sample

source_name: Hepatocytes, tamoxifen

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB
#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were
subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: primary hepatocytes

value: parenchymal cells

tag: treatment

value: tamoxifen

value: Day 5


title: F5: Female adult Rep 3

value: freshly isolated from tibia

value: F


title: Patient9_CD4_RNA


title: CR18 6h BS2


title: Veh1

source_name: Hepatocytes, vehicle

value: vehicle


title: Patient8_CD14_RNA


title: CR16 24h CB1


title: Patient8_CD4_RNA


title: Patient7_CD14_RNA


title: Veh2


title: CR16 24h CB2


title: F1: Female adult Rep 1

value: 12 weeks


title: Cap-seq_Mouse_KO_rep3

description: Mitochondrial RNA

source_name: Heart

value: heart

value: 4-5 weeks


title: Gut IELs isolated from anti-CD3-treated mouse and PBS, 4

city: Toronto

first: Chi Kin

last: Wong

address: 600 University Avenue

country: Canada

institute: LTRI

data_processing:
Sequence alignment was performed in STAR-2.7.9a with default parameters
A count table was compiled and subject to differential analysis in DESeq2
Assembly: mm10
Supplementary files format and content: A count table stored in count_table.csv

source_name: Gut IELs

extract_protocol:
RNA was prepared by lyzing cells in TRIzol followed by standard ethanol precipitation.
Sequencing libraries were constructed using TruSeq stranded mRNA library preparation kit per manufacturer's instructions.
Strand-specific RNA libraries

treatment_protocol: Mice were intraperitoneally injected with anti-CD3 (35 µg) and with or without exendin-4 (10 nmol/kg). Three hours later the mice were euthanized and gut IELs were isolated by Percoll separation and FACS by CD45.

value: Anti-CD3 + PBS

value: gut

value: IEL


title: Gut IELs isolated from anti-CD3-treated mouse and Ex4, 4

value: Anti-CD3 + Ex4


title: F2: Female adult Rep 2


title: CR16 24h BS2

value: Chondrocytes


title: CR16 24h BS1


title: Patient7_CD4_RNA

value: Systemic sclerosis

value: Primary CD4 T cells


title: TAM2

value: primary hepatocytes

value: WT


title: M4: Male adult Rep 2

value: M


title: Cap-seq_Mouse_KO_rep2

description: Mitochondrial RNA


title: Gut IELs isolated from anti-CD3-treated mouse and PBS, 3


title: Patient6_CD14_RNA

value: Primary CD14 Monocytes


title: CR16 24h CL2


title: Cap-seq_Mouse_KO_rep1

description: Mitochondrial RNA


title: Patient6_CD4_RNA


title: Cap-seq_Mouse_WT_rep3

description: Mitochondrial RNA


title: Gut IELs isolated from anti-CD3-treated mouse and Ex4, 2


title: CR16 24h CTRL


title: CR16 24h CL1


title: Gut IELs isolated from anti-CD3-treated mouse and Ex4, 3


title: CR16 6h CB2


title: Patient5_CD4_RNA


title: Patient4_CD14_RNA


title: Cap-seq_Mouse_WT_rep2

description: Mitochondrial RNA


title: Patient5_CD14_RNA


title: Gut IELs isolated from anti-CD3-treated mouse and PBS, 2


title: Gut IELs isolated from anti-CD3-treated mouse and PBS, 1


title: Cap-seq_Mouse_WT_rep1

description: Mitochondrial RNA


title: CR16 6h CB1


title: CR16 6h BS2


title: 45dpi_Rep1_scRNA

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

institute: University of Manchester

description: single cell RNA

library_source: transcriptomic single cell

data_processing:
For FASTQ generation and alignments, illumina basecall files (*.bcl) were converted to FASTQs using bcl2fastq
Gene counts were generated using CellRanger for single cell RNAseq (v.6.0.0) or SpaceRanger for spatial transcriptomics (v.1.2.2)
Mapping strategy was conducted on CellRanger or SpaceRanger against a combined Mus musculus (mm10) and Trypanosoma brucei (TREU927) transcriptome reference
After alignment, reads were grouped based on barcode sequences and demultiplexed using the Unique Molecular Identifiers (UMIs)
Assembly: mm10 + TREU927
Supplementary files format and content: .h5 files were generated as outputs from CellRanger or SpaceRanger. The filter matrices can be used for downstream analysis using the scripts available on https://zenodo.org/record/6387555#.Yksy3y8w1nk

source_name: Brain

growth_protocol: 6-8 weeks old mice were infected (i.p.) with 2,000 Trypanosoma brucei brucei strain Antat 1.1E. Mouse hypothalami from naïve and infected mice were harvested for scRNAseq analysis. Coronal brain sections were flash-frozen in OCT for spatial transcriptomics analysis

extract_protocol:
Single cell suspensions were obtained from murine hypothalami using enzymatic dissociation, followed by library preparation using the 10X Chromium platform. Coronal brain sections were flash-frozen in OCT, and cryo-sections (5 um) were used for tissue analysis using the 10X Visium platform.
Illumina compatible, RNA libraries were prepared with the 10X Chromium technolgy

treatment_protocol: Two biological replicates per time point (naïve, 25- and 45 days post-infection) for single cell transcriptomics. One biological replicate for spatial transcriptomics

value: Female

value: 6-8 weeks old

value: Brain (hypothalamus)

value: 45 days post-infection


title: Patient3_CD14_RNA


title: Gut IELs isolated from anti-CD3-treated mouse and Ex4, 1


title: 45dpi_Rep2_scRNA

description: single cell RNA


title: CR16 6h BS1


title: Patient4_CD4_RNA


title: S.048.J124_S48

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

country: USA

institute: Texas A&M University

data_processing:
FastQC v0.11.9 was used for read quality assessment.
Trimmomatic v0.39 was used for read pair trimming and adaptor removal (parameters- SLIDINGWINDOW:4:20 MINLEN:28 LEADING:3 TRAILING:3 ILLUMINACLIP:adaptor.fa:2:30:20:2:TRUE).
Trimmed reads were mapped to the ARS-UCD1.2 bovine genome assembly with HISAT2 v2.2.1 (parameters- -hSbo).
Gene-level transcriptome assembly was performed with StringTie v2.1.7 (parameters-e -G ARSUCD1.2.gff)
Raw gene counts were generated by the Python3 program prepDE.py, provided by the authors of StringTie (parameters- -l 150).
Assembly: ARS-UCD1.2
Supplementary files format and content: Comma-delimited text file of annotated raw gene counts of all samples.

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated from Tempus RNA blood tubes with Tempus Spin RNA Isolation Kit (Applied Biosystems), based on manufacturer’s instruction.
Sequencing libraries were constructed with the TruSeq Stranded mRNA Library Prep Kit (Illumina), following manufacturer’s instruction.

value: Whole blood

tag: timepoint

tag: pasture location

tag: age at_sampling

tag: vaccination

value: N


title: S.047.J113_S47

value: Y


title: S.046.J109_S46


title: Patient2_CD14_RNA


title: CR16 6h CL1


title: S.045.J053_S45


title: Patient2_CD4_RNA


title: Patient3_CD4_RNA


title: S.044.J040_S44


title: 25dpi_Rep1_scRNA

description: single cell RNA

tag: Sex

value: 25 days post-infection


title: SK-N-BE2 MZ1 750nM_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample.

source_name: SK-N-BE2 MZ1 750nM

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Neuroblastoma cells

tag: cell line

value: 750nM MZ1


title: 25dpi_Rep2_scRNA

description: single cell RNA


title: S.043.J038_S43


title: S.042.J032_S42


title: Naïve_Rep1_scRNA

description: single cell RNA

value: Naive


title: CR16 6h CL2

value: Chondrocytes

tag: patient

tag: time


title: SK-N-BE2 MZ1 750nM_rep1


title: Patient1_CD14_RNA

value: Systemic sclerosis


title: Patient1_CD4_RNA

value: Primary CD4 T cells


title: control5_CD14_RNA

value: healthy


title: SK-N-BE2 MZ1 0nM_rep2

source_name: SK-N-BE2 MZ1 0nM

value: DMSO


title: control5_CD4_RNA


title: S.041.J027_S41


title: S.039.J022_S39


title: SK-N-BE2 MZ1 0nM_rep1


title: S.040.J023_S40


title: CR16 6h CTRL

tag: cl treatment

tag: bs treatment


title: control4_CD14_RNA

value: Primary CD14 Monocytes


title: control4_CD4_RNA


title: WT CD45– cells IL-13

city: San Francisco

first: Roberto

last: Ricardo-Gonzalez

state: CA

address: 513 Parnassus Ave, HSE-1001

institute: University of California San Francisco

data_processing:
Sequencing and base-calling by Illumina NovaSeq 6000
Raw data was processed with 10X Cellranger and analysis was done using Seurat v3.
Sequence data from WT Control,  WT Demodex+, WT IL-4, and WT IL-13 were merged.
Assembly: GRCm38 (mm10)
Supplementary files format and content: The processed data files .h5 files generated from cellranger

source_name: WT CD45– cells (IL-13 treated)

extract_protocol:
C57/BL6 female mice were obtained from Jackson Laboratory at 3 weeks of age and allowed to age concurrently. At 7 weeks of age, mice were divided into the following: WT IL-4 (n = 3), and WT IL-13 (n = 3). Mice were treated with intraperitoneal IL-4 complex (3 μg IL-4 (Peprotech) complexed with 15 μg anti-IL4 antibody (BioXCell, clone 11B11)  in PBS) or  IL-13 (3 μg (Peprotech) in PBS) on days -5, -3, and -1 before analyses. These mice groups were harvested, processed, and batched concurrently as  WT control (n = 3), and WT co-housed with Demodex-infested IL-4Ra–/– mice for 1 month (n = 3) (GSE197982). Single cell suspensions from full thickness skin were stained with antibody to CD45 (to isolate the CD45+ fraction) and integrin alpha 6 to generate a 50:50 representation of CD45–alpha6+ and CD45–alpha6– cells in the CD45– fraction. Cell suspensions were stained with DAPI and live cells (DAPI–) were isolated by FACS using a MoFlo XDP (Beckman Coulter). The concentration of sorted cells was determined using CountBright beads on an LSRFortessa. Replicate samples for each genotype were pooled together. Single-cell libraries from 25,000 cells per sample were prepared with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10 x Genomics PN-1000121) following the manufacturer’s protocol. The libraries were sequenced on the NovaSeq 6000 at the UCSF Institute for Human Genetics with the following number of cycles for each read: Read 1, 28 cycles; i7 Index, 8 cycles; i5 Index, 0 cycles; Read 2, 91 cycles.
10X Chromium Single Cell 3′ Reagent Kit (v3 Chemistry)
single-cell RNA-seq

value: WT

value: CD45- cells

tag: tissue

value: Back skin

tag: age

value: 2 months


title: WT CD45– cells IL-4

source_name: WT CD45– cells (IL-4 treated)

tag: genotype


title: WT CD45+ cells IL-4

source_name: WT CD45+ cells (IL-4 treated)

value: CD45+ cells


title: S.038.J015_S38

value: Whole blood


title: Naïve_Rep2_scRNA

description: single cell RNA

value: Female

value: 6-8 weeks old

value: Brain (hypothalamus)


title: WT CD45- cells Demodex

data_processing:
Sequencing and base-calling by Illumina NovaSeq 6000
Raw data was processed with 10X Cellranger and analysis was done using Seurat v3.
Sequence data from WT Control and WT Demodex+ were merged.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: a .h5 file containing cellranger filtered cell barcodes and gene expression counts

source_name: WT CD45- cells (Demodex+)

extract_protocol:
C57/BL6 female mice were obtained from Jackson Laboratory at 3 weeks of age and divided into the following groups 1 weeks later:  WT control (n = 3), and WT co-housed with Demodex-infested IL-4Ra-/- mice for 1 month (n = 3). Single cell suspensions from full thickness skin were stained with antibody to CD45 (to isolate the CD45+ fraction) and integrin alpha 6 to generate a 50:50 representation of CD45-alpha6+ and CD45-alpha6- cells in the CD45- fraction. Cell suspensions were stained with DAPI and live cells (DAPI-) were isolated by FACS using a MoFlo XDP (Beckman Coulter). The concentration of sorted cells was determined using CountBright beads on an LSRFortessa. Replicate samples for each genotype were pooled together. Single-cell libraries from 25,000 cells per sample were prepared with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10 x Genomics PN-1000121) following the manufacturer’s protocol. The libraries were sequenced on the NovaSeq 6000 at the UCSF Institute for Human Genetics with the following number of cycles for each read: Read 1, 28 cycles; i7 Index, 8 cycles; i5 Index, 0 cycles; Read 2, 91 cycles.
10X Chromium Single Cell 3′ Reagent Kit (v3 Chemistry)
single-cell RNA-seq

tag: infection

value: Demodex+


title: WT CD45+ cells IL-13

source_name: WT CD45+ cells (IL-13 treated)

tag: strain


title: SK-N-BE(2) cells, shPHOX2B_rep2

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample …

source_name: Neuroblastoma cells

value: Neuroblastoma cells

tag: transfection

value: PHOX2B knockdown


title: SK-N-BE(2) cells, shPHOX2B_rep1


title: control3_CD14_RNA

tag: disease


title: SK-N-BE(2) cells, shScb_rep2

value: shScb

value: control


title: WT CD45+ cells Demodex

source_name: WT CD45+ cells (Demodex+)


title: S.035.J113_S35

tag: timepoint

tag: pasture location

value: Y


title: control2_CD14_RNA

value: healthy


title: SK-N-BE(2) cells, shScb_rep1


title: S.036.J124_S36

tag: age at_sampling

tag: vaccination

value: N


title: SK-N-BE2 cells, shTTC8_rep2

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes readcount values for each Sample

tag: cell type


title: control2_CD4_RNA

source_name: Primary CD4 T cells

value: Primary CD4 T cells


title: S.033.J053_S33


title: SK-N-BE2 cells, shScb_rep2

tag: cell line


title: control3_CD4_RNA


title: SK-N-BE2 cells, shTTC8_rep1


title: SK-N-BE2 cells, shScb_rep1


title: S.034.J109_S34


title: S.032.J040_S32


title: IL4/IL13DKO CD45+ cells

data_processing:
10x data for scRNA-seq samples are run through cellranger software to produce the fastqfiles.
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: a .h5 file containing cellranger filtered cell barcodes and gene expression counts

source_name: IL4/IL13DKO CD45+ cells (Demodex+)

extract_protocol:
WT (uninfected, n = 3) or Demodex infected IL-4Ra-/- (n = 3) and IL-4/IL-13-/- (n = 3) were used for analyses. Single cell suspensions from full thickness skin were stained with antibody to CD45 (to isolate the CD45+ fraction) and integrin alpha 6 to generate a 50:50 representation of CD45-alpha6+ and CD45-alpha6- cells in the CD45- fraction. Cell suspensions were stained with DAPI and live cells (DAPI-) were isolated by FACS using a MoFlo XDP (Beckman Coulter). The concentration of sorted cells was determined using CountBright beads on an LSRFortessa. Replicate samples for each genotype were pooled together. Single-cell libraries from 25,000 cells per sample were prepared with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10 x Genomics PN-1000121) following the manufacturer’s protocol. The libraries were sequenced on the NovaSeq 6000 at the UCSF Institute for Human Genetics with the following number of cycles for each read: Read 1, 28 cycles; i7 Index, 8 cycles; i5 Index, 0 cycles; Read 2, 91 cycles.
RNA libraries were prepared for sequencing using standard 10X genomics protocols
single-cell RNA-seq


title: IL4RaKO CD45+ cells

source_name: IL4RaKO CD45+ cells (Demodex+)


title: S.037.J009_S37


title: Epidermis_scRNAseq_1

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

institute: DKFZ

description: single cell RNA

data_processing:
Alignment of the raw fastq-data with CellRanger v.2.1.0 to reference genome.
QC and data filtereing with CellRanger v.2.1.0.
Sample combination with CellRanger v.2.1.0.
QC and sample integration with Seurat v.3.1.1.
Clustering and visualization with Seurat v.3.1.1.
Assembly: hg19
Supplementary files format and content: Seurat object containing the resulting count matrix after QC with CellRanger and Seurat.

source_name: Healthy epidermis

extract_protocol:
A healthy whole skin biopsy was obtained from a 30 y/o male donor of fair-skin type and preserved in MACS Tissue Storage Solution (Miltenyi Biotec). The skin sample was subsequently cut into small pieces that were further processed using the human Epidermis Dissociation Kit (Miltenyi Biotec) and the Gentle MACS Dissociator (Miltenyi Biotec), following the manufacturer’s instructions. The resulting cell suspension was then filtered through a 70-µm cell strainer (Falcon) and depleted of apoptotic and dead cells with the Dead Cell Removal Kit (Miltenyi Biotec).
We used the 10X Genomics platform to generate a sequencing library with the Chromium Single Cell 3’ Reagent Kit, v2 chemistry (10X Genomics), as described by the manufacturer. Approximately 20,000 cells were loaded into a Chromium Single Cell Controller (10X Genomics) as initial input.

value: Healthy epidermis


title: shFOXA1+kc7f2-2 mr217

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, RPKM/FPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of RPKM/FPKM values for each Sample

source_name: Human prostate cancer cells

growth_protocol: LNCaP cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA was isolated from cells using the nucleospin RNA kit (Takara) according to the manufacturer's recommended protocol.
RNA-seq libraries were prepared from 0.5 μg high-quality DNA-free total RNA by using NEBNext® Ultra RNA Library Prep Kit, according to the manufacturer’s instructions. The libraries passing quality control (equal size distribution between 250-400 bp, no adapter contamination peaks, no degradation peaks) were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603) using the Illumina provided protocol.

treatment_protocol: LNCaP cells were infected with control shRNA (pGIPZ), shRNA targeting FOXA1 (shFOXA1), shRNA targeting HIF1A (shHIF1A), or combination of shFOXA1 + shHIF1A  lentiviruses for 5 days. pGIPZ and shFOXA1 lentiviral transduced cells were treated with or without 40µM HIF1A inhibitor KC7F2 for 24h before harvesting. All samples were also treated with 100µM CoCl2 24h before harvesting cells to mimic tumor hypoxia.

value: LNCaP

value: prostate

tag: treatment/infection

value: WT


title: WT CD45+ cells Control

source_name: WT CD45+ cells (uninfected)

value: uninfected

value: CD45+ cells

value: Back skin

value: 2 months


title: shFOXA1+kc7f2-3 mr218


title: A29_DMSO_E2_3

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

data_processing:
Standard Illumina software was used for base calling
Reads were aligned to the human genome (UCSC version hg38AnalysisSet) with STAR.The output was sorted and indexed with samtools.
Stand-specific coverage tracks per sample were generated by tiling the genome in 20bp windows and counting 5'end of reads per window using the function bamCount from the bioconductor package bamsignals.
These window counts were exported in bigWig format using the bioconductor package rtracklayer.The rsubread::featureCounts function was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (gene annotation: ensembldb_Homo_sapiens_GRCh38_ensembl_96.sqlite).
Differential gene expression analysis was performed using limma-voom framework.
Genome_build: Homo_sapiens_GRCh38

source_name: breast cancer cell line

growth_protocol: SUM149PT cells were cultured in phenol red free Ham's F12 (Caisson Labs, cat# HFL05) supplemented with charcoal-stripped 2% FCS (Gibco, cat# A3382101), 5 μg/mL human recombinant insulin (Sigma, cat# 91077C), 1 μg/mL hydrocortisone (Sigma, cat# H0888), 1× penicillin/streptomycin (Sigma, cat# P4333).

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, cat# 74134) according to the manufacturer’s protocol.
Library preparation was performed, starting from 200ng total RNA, using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA). 15 cycles of PCR were performed.

treatment_protocol: SUM149PT cells were treated for 3 days in vitro with 100 nM rigosertib. Depending on the condition, 10 nM estradiol (E2) or ethanol (EtOH) were added in addition.

tag: breast cancer model

value: SUM149PT A29 ESR1 KO clone


title: A29_Rigo_E2_3


title: S.029.J027_S29

source_name: Whole blood

value: Whole blood


title: PGIPZ+kc7f2-3 mr215


title: S.030.J032_S30


title: S.031.J038_S31


title: WT CD45- cells Control

source_name: WT CD45- cells (uninfected)

value: CD45- cells


title: IL4/IL13DKO CD45- cells

source_name: IL4/IL13DKO CD45- cells (Demodex+)

value: Demodex+


title: WT CD45- cells


title: S.028.J023_S28


title: shFOXA1+kc7f2-1 mr216


title: IL4RaKO CD45- cells

source_name: IL4RaKO CD45- cells (Demodex+)


title: A11_Rigo_E2_3

value: SUM149PT A11 ESR1 KO clone


title: WT CD45+ cells


title: S.027.J022_S27

value: Y


title: Par_Rigo_E2_3

value: SUM149PT parental cell line


title: PGIPZ+kc7f2-1 mr213


title: Par_DMSO_E2_3


title: S.026.J015_S26


title: S.025.J009_S25


title: A11_DMSO_E2_3


title: shFOXA1shhi1a-1 mr210


title: S.024.J124_S24

value: N


title: JV_H2AK119Ub

city: Tianjin

first: Zhijian

last: Xiao

address: 288 Nanjing Road

department: MDS and MPN center

institute: State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, CAMS & PUMC

library_source: genomic

data_processing:
For RNAseq, sequence reads were aligned to the reference genome using Hisat2 v.2.0.5
For RNAseq, featureCounts v.1.5.0-p3 was used to count the reads numbers mapped to each gene.
For RNAseq, differential expression analysis of the two groups was conducted using the DESeq2 R package (1.16.1)
For ATAC-seq analysis and ChIPseq, paired sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie 2 version 2.2.9
For ChIPseq, peak calling and annotation were conducted using MACS version 1.4.253 and ChIP-seeker package
For ATAC-seq and ChIPseq analysis,  bigwig files, Heatmaps, and average profiles were generated using the computeMatrix and plotHeatmap utilities from deepTools
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Bigwig files for every sample

molecule: genomic DNA

source_name: bone marrow

extract_protocol:
Murine BM nucleated cells (BMNCs) were isolated by flushing the femur and tibia into PBS with 2% Fetal bovine serum (FBS, Gibco) and 2 mM EDTA (Invitrogen), lysed with red blood cell (RBC) lysis buffer (Solarbio) for 15 min, and then centrifuged at 4°C. BMNCs was enriched for c-kit using CD117 MicroBeads (Miltenyi, 130-091-224) and separated using an AutoMACS Pro separator (Miltenyi) according to the manufacturer’s specifications.
Libraries were prepared for sequencing using standard Illumina protocols

value: c-kit+ cells

tag: chip antibody

value: H2AK119Ub(Cell signaling technology, 8240s)


title: JV_H3K4me1

value: H3K4me1(Cell signaling technology, 5326s)


title: shFOXA1shhi1a-3 mr212

value: LNCaP

value: prostate


title: Par_Rigo_EtOH_3


title: shFOXA1shhi1a-2 mr211

value: WT


title: S.023.J113_S23


title: shFOXA1-3 mr209


title: PGIPZ+kc7f2-2 mr214


title: Par_DMSO_EtOH_3


title: shFOXA1-2 mr208


title: AJV_H3K27ac

value: H3K27ac(Cell signaling technology, 8173s)


title: JV_H3K27ac


title: A29_DMSO_E2_2


title: A29_Rigo_E2_2


title: JV_H3K27me3

value: H3K27me3(Cell signaling technology, 9733s)


title: AJV_H2AK119Ub


title: A11_Rigo_E2_2


title: S.021.J053_S21


title: shFOXA1-1 mr207


title: shhif1a-3 mr206


title: AJV_H3K4me1


title: S.020.J040_S20


title: AJV_H3K27me3


title: Par_Rigo_E2_2


title: Par_DMSO_E2_2


title: S.019.J038_S19


title: S.018.J032_S18


title: A11_DMSO_E2_2


title: S.022.J109_S22


title: shhif1a-1 mr204


title: WT_3_RNAseq


title: S.017.J027_S17


title: AJV_ATAC


title: PGIPZ-3 mr203

value: PGIPZ


title: S.016.J023_S16


title: Par_Rigo_EtOH_2


title: shhif1a-2 mr205


title: WT_2_RNAseq


title: Par_DMSO_EtOH_2


title: WT_1_RNAseq


title: S.015.J022_S15


title: PGIPZ-2 mr202


title: AV_2_RNAseq


title: A29_Rigo_E2_1

value: SUM149PT A29 ESR1 KO clone


title: S.014.J015_S14

value: Whole blood


title: S.013.J009_S13


title: AV_1_RNAseq


title: A29_DMSO_E2_1


title: JV_ATAC


title: A11_Rigo_E2_1


title: A11_DMSO_E2_1


title: PGIPZ-1 mr201


title: JV_3_RNAseq


title: JV_2_RNAseq


title: S.012.J124_S12


title: JV_1_RNAseq


title: Par_DMSO_E2_1


title: Par_Rigo_E2_1


title: Par_Rigo_EtOH_1


title: AJV_2_RNAseq


title: S.010.J109_S10


title: S.007.J038_S7


title: S.008.J040_S8


title: S.009.J053_S9


title: Par_DMSO_EtOH_1


title: AJV_1_RNAseq


title: S.011.J113_S11


title: S.006.J032_S6


title: MTC-Q1 mir-21 KO

city: Taipei City

first: han-ying

last: cheng

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of clincal medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Sequence reads from wt and mir21-KO samples were independently de-multiplexed, mapped and count using the Cell Ranger software (10x Genomics, version 3.1.0).
Then, two profiles were merged by the Cell Ranger.
Genome_build: The mouse genome (build mm10)
Supplementary_files_format_and_content: Cell Ranger output files: count matrix, barcode table, feature table.  In barcodes.tsv.gz, BC-1 represents Ctrl, BC-2 represents mir21KO.

source_name: tumor

growth_protocol: 1x10e6 of MTC-Q1 WT or MTC-Q1 miR-21 KO cells were subcutaneous injection in C57BL/6 mice.

extract_protocol:
Tumor tissues were dissociated by tumor dissociation kit (MACS) and remove dead cells by dead cell removal kit (MACS). CD45+ immune cell isolation were isolated by CD45+ microbeads. 10x Genomics Chromium Single Cell 3' Reagent Kit were used to dropped single cells and CDNA libary construction.
CDNA library construction were using 10x Genomics Chromium Single Cell 3' Reagent Kit

treatment_protocol: After 2 weeks of tumor growth, cisplatin (5mg/kg) were inected. Cells were isolated after 72 hr of cisplatin given.

tag: treatment

value: cisplatin

value: MTC-Q1 miR-21 KO tumor tissue

value: CD45+ cells


title: P210325T6

city: Taipei

first: Chih-Hung

last: Chung

address: No.155, Sec.2, Linong Street, Taipei, 112 Taiwan (ROC)

department: Institute of Clinical Medicine

data_processing:
For Visium, libraries were sequenced on Illumina NovaSeq 6000, with 150 bases from read 1 and read 2, and at a depth of 100-209 million reads per sample.
The data was processed with the spaceranger pipeline (version 1.2.1, 10X Genomics) and mapped to the GRCH38 v98 genome assembly.
Genome_build: GRCh38 v98
Supplementary_files_format_and_content: Tab-delimited text files containing genes by barcode counts matrices,PNG images for all sample, barcode file and Visium tissue position lists containing spot barcode position information per sample. Summary data shows number of spots under tissue, mean reads per spot and median genes per spot. Sample information including ID, mapping rate and squencing info.

source_name: HNSCC Patient

extract_protocol:
Patient tumors were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation. Libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
10X Visium platform

treatment_protocol: We collected HNSCC primary tumor from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH), according to the current TVGH-IACUC regulations. IRB approval number : 2017-05-013AC.

tag: tumor site

value: Primary Tumor (Inner site)

tag: unique patient number (upn)

value: head and neck squamous carcinoma


title: C2_c

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: 8*15K Agilent-019118 Human miRNA Microarrays were scanned on an Agilent G2505C scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: not transfected 647-V

label_protocol: manufacturer's instructions

growth_protocol: RPMI 10% FCS, L-Gln 2 mM, Peni/strepto.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Comparisons of miRNA in 647-V bladder cancer cell line following stable MUC4 knocked down by ShRNA transfection (2 assays, KD1 and KD2) and MOCK corresponding control cells.

value: not transfected

value: 647-V cells

value: bladder cancer


title: C2_a


title: AJV_3_RNAseq

value: c-kit+ cells

tag: genotype


title: C2_b


title: S.005.J027_S5

tag: tissue

value: N


title: 421_d


title: P210325T5


title: P210325T3

value: Primary Tumor (Invasive front)


title: 421_a


title: C2_d


title: 4210_d


title: S.004.J023_S4

value: Y


title: Spleen_WT_5

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
190307_9

data_processing:
Illumina Casava1.82 software used for basecalling and demultiplexing.
After demultiplexing, raw reads were pseudoaligned to the murine transcriptome (mm10, GENCODE general assembly release vM16) using Kallisto with default settings
Based on the pseudoalignment estimated by Kallisto, transcript levels were quantified and counts were imported into R using tximport. Transcript information was summarized on gene-level. We imported the resulting dataset and performed the downstream analysis using the DESeq2 pipeline.
Genome_build: mm10
Genome_build: transcriptome build: mm10, GENCODE general assembly release vM16
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the mm10 reference transcriptome

source_name: spleen

extract_protocol:
Batch1 :  Cells were stored in Trizol and extracted using Qiagen mini kit according to recommendations from manufacture;    Batch2:  Cells were sorted into RLT buffer and extracted using Qiagen mini kit according to recommendations from manufacture
mRNA is purified from approximately 500pg-1ng of total RNA using the Clontech SMARTer Ultra Low V4 RNA Kit.  The kit utilizes an oligo(dT) primer, which primes the first-strand synthesis reaction.  SPRI beads are used to selectively bind first-strand cDNA.   ss cDNA is then amplified by LD PCR to make ds cDNA and is again purified using SPRI beads.  During amplification the poly A sequence serves as the universal priming site for end-to-end cDNA amplification.  Thus, cDNA without these sequences, such as prematurely terminated cDNAs, containing genomic DNA, or cDNA transcribed from Poly A minus RNA, are not exponentially amplified.  The beads are then washed with 80% ethanol and eluted in purification buffer.  The full-length cDNAs are then sheared using the Covaris, which results in 200-500bp DNA fragments.  The fragmented cDNA library is then end-repaired, A-tailed, and adapters are ligated. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: spleen

value: B cells

value: WT

tag: cohort


title: S.003.J022_S3


title: Spleen_WT_4

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
190307_7


title: 421_b

tag: transfection


title: P210325T1

tag: disease


title: 421_c


title: 4210_c


title: VAT_Nlrp3_4

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
190307_5

source_name: visceral adipose

value: visceral adipose


title: HNSCC201125T10


title: 4210_b


title: MTC-Q1 wt

description: Ctrl

value: MTC-Q1 WT tumor tissue


title: 4210_a


title: 02_d

source_name: MOCK 647-V

value: mock


title: VAT_WT_5

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
190307_3


title: S.002.J015_S2

value: Whole blood

tag: timepoint


title: HNSCC201125T07


title: Spleen_Nlrp3_4

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
190307_11


title: Wa_20180918_AGATCGCA_S2_L002

city: Hefei

first: yang

last: xia

state: Anhui

address: Sanlian

institute: Anhui medical university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: DMEM medium mixed with 10% fetal bovine serum

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using TRIzol reagent

value: CRC

value: untreated


title: Sa_20180918_ATCCTGTA_S5_L002


title: HNSCC201125T05

value: head and neck squamous carcinoma


title: HNSCC201125T04


title: Spleen_WT_3

first: Joachim

last: Schultze

address: Carl-Troll-Strasse 31

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_9


title: A375_DAB200 3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of A375 treated with DABRAFENIB (200nM), biological rep3

data_processing:
the reads were trimmed toremove adapter sequences and low-quality ends and reads mapping to contaminating  sequences (e.g., ribosomal RNA, phIX control) were filtered-out.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Melanoma cell line A375

growth_protocol: RPMI 10%FBS, splitting every 48-72h at confluency

extract_protocol:
RNA was quantified and mixed at 10ng/µl
For RNA-seq analysis, libraries were prepared according to manufacturer's instructions (QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen GmbH) starting from 250ng of total RNA.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq6000 (Illumina) with a read length of 100 bp

treatment_protocol: cells has been treated with dabrafenib at concetration of 200nM for 48h and with DMSO (0.1%)

value: DAB


title: VAT_WT_4

city: Bonn

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
190307_1


title: WT Biorep3

city: Seattle

first: Alison

last: Paquette

state: Washington

address: 1900 Ninth Ave.

department: Center for Developmental Biology and Regenerative Medicine

institute: Seattle Childrens

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Plasmodium falciparum reference genome using the STAR aligner v.2.5.2b. BAM files were generated because of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 with R v3.4.1 was used when executing DEseq2 analysis for DEGs identification and graphic tools. THe deXseq package  (R v3.2.5) was used to identify splicing variants.  Bioinformatic analyses were performed using default parameters by GENEWIZ (South Plainfield, NJ).
Assembly: Plasmodium falciparum 3D7
Supplementary files format and content: comma-delimited text file include raw gene counts values for each sample
Supplementary files format and content: comma-delimited text file include normalized gene counts values for each sample (DESeq2 median of ratios method)
Supplementary files format and content: comma-delimited text file include rlog gene counts values for each sample (DESeq2 regularized log transformation)
Supplementary files format and content: tab-delimited text file include exon counts values for each sample (deXseq)

organism: Plasmodium falciparum

source_name: stage V gametocytes

extract_protocol:
On day 15 of gametocyte development, stage V gametocytes were harvested using saponin lysis. Total RNA from saponin-lysed parasites was extracted using Trizol (Invitrogen) and QIAGEN RNA-extraction kit. Following RNA isolation, total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA concentrations were measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA).
Libraries were constructed using Illumina Ribo Zero Gold for human/mouse/rat kit. The libraries were multiplexed and clustered on one lane of a flowcell and loaded on an Illumina HiSeq platform paired-end 150bp reads. Sequencing of libraries was conducted by GENEWIZ (South Plainfield, NJ).

value: stage V gametocytes

value: Control; WT


title: A375_DAB200 2

description: Transcriptome profile of A375 treated with DABRAFENIB (200nM), biological rep2


title: Ja_20180918_CAACCACA_S7_L002


title: 02_c

value: 647-V cells

value: bladder cancer


title: 02_b


title: Spleen_WT_2

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_8


title: Fa_20181011_GCCACATA_S66_L003


title: WT Biorep2


title: S.001.J009_S1

data_processing:
FastQC v0.11.9 was used for read quality assessment.
Trimmomatic v0.39 was used for read pair trimming and adaptor removal (parameters- SLIDINGWINDOW:4:20 MINLEN:28 LEADING:3 TRAILING:3 ILLUMINACLIP:adaptor.fa:2:30:20:2:TRUE).
Trimmed reads were mapped to the ARS-UCD1.2 bovine genome assembly with HISAT2 v2.2.1 (parameters- -hSbo).
Gene-level transcriptome assembly was performed with StringTie v2.1.7 (parameters-e -G ARSUCD1.2.gff)
Raw gene counts were generated by the Python3 program prepDE.py, provided by the authors of StringTie (parameters- -l 150).
Assembly: ARS-UCD1.2
Supplementary files format and content: Comma-delimited text file of annotated raw gene counts of all samples.

tag: pasture location


title: VAT_Nlrp3_3

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_7


title: Wp_20180918_AGCAGGAA_S3_L002

source_name: normal


title: Sp_20180918_ATTGAGGA_S6_L002


title: VAT_Nlrp3_2

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_6


title: KO Biorep3


title: Jp_20180918_GACTAGTA_S8_L002


title: VAT_Nlrp3_1

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_5


title: KO Biorep2


title: A375_DMSO _Ctr_2

description: Transcriptome profile of A375 treated with DMSO (0.1%), biological rep2

value: DMSO


title: Fp_20180918_AGAGTCAA_S1_L002


title: A375_DMSO _Ctr_1

description: Transcriptome profile of A375 treated with DMSO (0.1%), biological rep1


title: A375_BIR_DAB200 3

description: Transcriptome profile of A375-BIR treated with DABRAFENIB (200nM), biological rep3

source_name: Melanoma cell line A375-BRAF INHIBITOR RESISTANT (BIR)


title: 02_a


title: S2-3

city: Guiyang

first: jie

last: yu

address: 116 Baoshan North Road

institute: Guizhou Normal Universuty

data_processing:
Illumina software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SCHZ genome using HISAT2
The FPKM (Fragments per Kilobase of transcript per Million mapped reads) was calculated
The GO annotations for the DEGs in leaf were determined by using Blast2GO
Assembly: GCA_018703725.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Brassica juncea

source_name: flowers

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

value: flowers

value: Brassica juncea "YLC"

value: Formation of apetalous mechanism


title: A375_BIR_DAB200 2

description: Transcriptome profile of A375-BIR treated with DABRAFENIB (200nM), biological rep2


title: VAT_WT_2

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_2

value: B cells

value: WT


title: A375_DAB200 1

description: Transcriptome profile of A375 treated with DABRAFENIB (200nM), biological rep1


title: HGTEPP-2

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

data_processing:
Quality control of raw data was done based on three criteria: the contaminated reads for adapters (> 5 bp adapter sequences), low quality reads (Phred quality value ≤ 19 more than 15%) and reads with Ns (Ns > 5%). The filtered clean reads were then aligned to the human reference genome GRCh38.p13 (Genome Reference Consortium Human Build 38) using HISAT2 software (version 2.1.0). Afterwards, the fragments per kilobase million mapped reads (FPKM) (Supplementary file 1) were calculated based on the read counts derived for each gene using HTSeq software (version 0.6.0).
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: Human renal proximal tubular epithelial cell line

growth_protocol: The cultured HK-2 cells were obtained from Beijing Beina Chuanglian Biotechnology Research Institute, where they were cultured in Dulbecco’s modified eagle medium (DMEM) with the low glucose (Sigma-Aldrich Inc, St. Louis, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, USA), 10 units/ml penicillin and 10 mg/ml streptomycin, and maintained in the continuous culture at 37°C in a humidified atmosphere (5% CO2) in an incubator. Growth medium was shifted every 2 or 3 day and cells were sub-cultured until further measurements at 80% colony confluency.

extract_protocol:
2 μg RNA per cell replicate sample were extracted for RNA sample preparation
Libraries were prepared according to Illumina's instructions

treatment_protocol: Three replicates of cells exposed to HG were treated with (case group) or without (control group) 10-μM TEPP-46 for 1 day, separately.

value: Kidney

value: Case group (TEPP-46)

value: HK-2 cells


title: Spleen_Nlrp3_3

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_14

value: spleen


title: S2-2


title: A375_BIR_DAB200 1

description: Transcriptome profile of A375-BIR treated with DABRAFENIB (200nM), biological rep1


title: S2-1


title: Spleen_Nlrp3_2

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_13


title: Spleen_Nlrp3_1

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_12


title: HGTEPP-1


title: A375_DMSO _Ctr_3

description: Transcriptome profile of A375 treated with DMSO (0.1%), biological rep3


title: WT Biorep1


title: HG-3.

value: Control group


title: A375-BIR_DMSO _Ctr_3

description: Transcriptome profile of A375-BIR treated with DMSO (0.1%), biological rep3


title: VAT_WT_3

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_4

value: visceral adipose


title: A375-BIR_DMSO _Ctr_2

description: Transcriptome profile of A375-BIR treated with DMSO (0.1%), biological rep2


title: HGTEPP-3


title: HG-1.


title: KO Biorep1


title: HG-2.


title: Spleen_WT_1

description:
DESeq2_norm_anno_Spleen_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_11


title: S1-2

value: Apetalous Nullisomic Brassica juncea "AN"


title: VAT_WT_1

description:
DESeq2_norm_anno_VAT_only.txt
DESeq2_norm_anno_spleen_vs_vat.txt
181025_1


title: A375-BIR_DMSO _Ctr_1

description: Transcriptome profile of A375-BIR treated with DMSO (0.1%), biological rep1


title: S1-1


title: RAW01, RAW264.7, rep2

status: Public on Aug 28 2022

first: lu

address: No. 28, Guiyi street, Yunyan District, Guiyang City, Guizhou Province

institute: Guizhou medical university

data_processing:
After raw data filtering, sequencing error rate checking, and GC content distribution checking, clean reads for subsequent analysis were obtained
The quality-controlled clean reads were aligned to the reference genome. Use HISAT2 software to quickly and accurately align Clean Reads with the reference genome to obtain the positioning information of Reads on the reference genome
After the gene expression quantification is completed, it is necessary to perform statistical analysis on the expression data, and screen the genes with significantly different expression levels under different states.
ClusterProfiler software was used to perform GO functional enrichment analysis on differential gene sets, and KEGG pathway enrichment analysis
Assembly: mm10
Supplementary files format and content: counts, FPKM

growth_protocol: RAW264.7 macrophages were cultured in DMEM medium containing 5% FBS under 5% CO2 at 37°C

extract_protocol:
Cells were collected by standard methods to extract RNA, and the quality control method was mainly through Agilent 2100 bioanalyzer.
The library construction kit is NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

treatment_protocol: Transfection of RAW264.7 macrophages with ERMAP-shRNA lentivirus

value: celll line


title: ERMAP_shRNA01,RAW264.7,shRNA,rep3

value: ERMAP Knockdown

value: shRNA


title: ERMAP_shRNA01,RAW264.7,shRNA,rep2


title: RAW01, RAW264.7, rep3


title: ERMAP_shRNA01,RAW264.7,shRNA,rep1


title: H9_H

city: Cambridge

first: Thomas

middle: James

last: LaSalle

state: MA

address: 415 Main Street

institute: Broad Institute

description:
Neutrophil_RNAseq_Count_Matrix.txt.gz
Neutrophil_RNAseq_TPM_Matrix.txt.gz

data_processing:
A custom FASTA was generated from the Homo sapiens (human) genome assembly GRCh38 (hg38) following exclusion of ALT, HLA, and Decoy contigs according to documentation in the Broad Institute GTEx-TOPMed RNA-seq pipeline (https://github.com/broadinstitute/gtex-pipeline/), with an appended SARS-CoV2 genome. GENCODE v35 with the appended SARS-CoV2 GTF was used for annotation. Raw FASTQ files were aligned to the custom genome FASTA in the Terra platform with the Broad Institute GTEx pipeline using STAR v2.5.3a, and expression quantification based on a collapsed annotation was performed using RSEM v1.3.0.
RNA-SeQC 2 (https://github.com/getzlab/rnaseqc) was used to calculate quality control metrics for each sample.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) following exclusion of ALT, HLA, and Decoy contigs with an appended SARS-CoV2 genome
Supplementary files format and content: Neutrophil_RNAseq_Count_Matrix.txt.gz: RNA-seq count matrix provided as a gzipped .txt file
Supplementary files format and content: Neutrophil_RNAseq_TPM_Matrix.txt.gz: RNA-seq TPM matrix provided as a gzipped .txt file

source_name: Enriched neutrophils from whole blood

extract_protocol:
Blood samples were collected in EDTA vacutainer tubes and transported to the laboratory. Neutrophils were isolated from whole blood via negative selection using the EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL Technologies, Cat# 19666). All described procedures in this section were done at room temperature unless otherwise noted. Between 0.25-0.5 mL whole blood was lysed with ACK Lysis Buffer (ThermoFisher Scientific, Cat# A1049201) in a 15 mL conical tube and white blood cells were pelleted at 300 xg for 5 min. Following aspiration of the lysed red blood cells and resuspension of the pellet in 250 µL 1 mM EDTA in PBS, 50 µL each of the RapidSpheres and Isolation Cocktail were added to the cell suspension. Following a 5 min incubation, sample volumes were completed to 4 mL with 1 mM EDTA in PBS, mixed gently, and placed on an EasyEights™ EasySep™ Magnet (STEMCELL Technologies, Cat# 18103) for 5 min. Next, supernatants were transferred to new 15 mL conical tubes, 25 µL RapidSpheres were added, and the samples were gently mixed and incubated for 5 min. Samples were then placed on the magnet, and after 5 min incubation supernatants were transferred to new tubes, and were placed immediately on the magnet for a second incubation before the supernatants containing the enriched neutrophil populations were collected, pelleted, and resuspended in 1 mM EDTA in PBS. Cells were counted on a TC20™ Automated Cell Counter (Bio-Rad Laboratories, Inc., Cat# 1450102) with trypan blue staining for dead cell exclusion. Neutrophils were then lysed in TCL Buffer (QIAGEN, Cat# 1031576) with 1% 2-Mercaptoethanol at a concentration of 1000 cells/µL, flash-frozen on dry ice, and then stored at -80 °C until use. cDNA was prepared from bulk populations of 2x104 neutrophils per sample via the Smart-Seq2 protocol with some modifications to the reverse transcription step. 20 µL (at a concentration of 1000 cells/µL) of neutrophil lysates were thawed on ice and plated into 96-well plates prior to centrifugation at 1500 rpm for 30 s. RNA was purified with Agencourt RNAClean XP SPRI beads (Beckman Coulter, Cat# A63987) and then the samples were resuspended in 4 µL of Mix-1 [Per 1 sample: 1 µl (10 µM) RT primer (DNA oligo) 5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′; 1 µl (10 µM) dNTPs; 1µl (10%, 4 U/µl) recombinant RNase inhibitor; 1 µl nuclease-free water], denatured at 72 °C for 3 min and placed immediately on ice for 1 min before 7 µL of Mix-2 [Per 1 sample: 0.75 µl nuclease-free water; 2 µl 5X RT buffer (Thermo Fisher Scientific, Cat# EP0753); 2 µl (5 M) betaine; 0.9 µl (100 mM) MgCl2; 1 µl (10 µM) TSO primer (RNA oligo with LNA) 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′; 0.25 µl (40 U/µl) recombinant RNase inhibitor; 0.1 µl (200 U/µl) Maxima H Minus Reverse Transcriptase] was added. Reverse transcription reactions were performed at 50 °C for 90 min, followed by 5 min incubation at 85 °C. Then, 14 µL of Mix-3 [Per 1 sample: 1 µl nuclease-free water; 0.5 µl (10 µM) ISPCR primer (DNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGT-3′; 12.5 µl 2X KAPA HiFi HotStart ReadyMix] was added to each well and the whole-transcriptome amplification step was performed at 98 °C for 3 min, followed by 16 cycles of [98 °C for 15 s, 67 °C for 20 s, and 72°C for 6 min], and final extension at 72C for 5 min. cDNA was purified using AgencourtAMPureXP SPRI beads (Beckman Coulter, Cat# A63881) as described97, to remove all primer residue. Quality control was performed on samples prior library construction and included: (1) concentration measurements via the Qubit dsDNA high sensitivity assay kit (Invitrogen, Cat# Q32854) on the Cytation 5 Microplate Reader (BioTek); (2) cDNA size distribution using the High-Sensitivity DNA Bioanalyzer Kit (Agilent, Cat# 5067-4626).
Libraries were generated using the Nextera XT Library Prep kit (Illumina, Cat# FC-131-1024) with custom indexing adapters in a 384-well PCR plate, followed by a cleanup step to remove residual primer dimers.

value: Enriched neutrophils from whole blood

tag: time point

value: H

tag: patient category

value: healthy

tag: covid-19 status


title: RAW01, RAW264.7, rep1

tag: cell line

tag: cell type


title: H6_H


title: 386_D0

value: COVID- symptomatic


title: H8_H


title: H4_H


title: H7_H


title: S1-3

value: flowers

value: Formation of apetalous mechanism


title: 385_D0

value: COVID+


title: 385_D3


title: shLuc vs. shBLCAP cells

first: Ying-Tzu

last: Huang

address: No.1 Jen Ai road section 1

department: College of Medicine

institute: National Taiwan University

hyb_protocol: 0.3 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to a Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h. After hybridization, slides were washed and dried by nitrogen gun blowing.

scan_protocol: Microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images are analyzed by Feature extraction 10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

source_name: shLuc cells, harvested after several passages.

label_protocol: RNA from Luc was labeled by Cy3 and RNA from BC10-5 was labeled by Cy5. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: HEK293 cells were cultured in minimum essential media (MEM) supplemented with 10% FBS, 100 U/ml of penicillin, 0.1 mg/ml streptomycin and 1 mM sodium pyruvate at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: shRNA against firefly Luciferase or human BLCAP gene were transducted into HEK293 cells by lentivirus infection.

value: shLuc cells

source_name: BLCAP knockdown cells, harvested after several passages.

value: BLCAP knockdown


title: 383_DE

value: DE


title: 383_D7


title: 384_D7


title: 384_D0


title: 383_D3


title: 381_D0


title: 382_D3


title: 383_D0


title: 382_D0


title: 382_D7


title: 380_D3


title: 379_D0


title: 380_D0


title: 376_D0


title: 376_D3


title: 375_D3


title: 377_D3


title: 379_D7


title: 379_D3


title: 375_D7


title: 375_D0


title: 369_D7


title: 371_D3


title: 374_D0


title: 373_D0


title: 369_D0


title: 371_D0


title: 377_D0


title: 372_D0


title: 368_D0


title: 369_D3


title: 366_D3


title: 370_D0


title: 378_D3


title: 380_D7


title: 367_D7


title: 374_D3


title: 366_D0


title: 364_D3


title: 364_D0


title: 362_D3


title: 363_D7


title: 363_D3


title: 367_D3


title: 365_D0


title: 358_D0


title: 358_D3


title: 359_D0


title: 367_D0


title: 364_DE


title: 361_D0


title: 378_D0


title: 356_D7


title: 357_D0


title: 356_D0


title: 364_D7


title: 356_D3


title: 363_D0


title: 360_D3


title: 358_D7


title: 360_D0


title: 358_DE


title: 357_D7


title: 355_D3


title: 354_D7


title: 357_D3


title: 354_D3


title: 355_D0


title: 353_D3


title: 353_D7


title: 353_D0


title: 354_D0


title: 362_D0


title: 350_D0


title: 349_D3


title: 349_D7


title: 349_D0


title: 347_D7


title: 348_D0


title: 353_DE


title: 348_DE


title: 351_D0


title: 348_D7


title: 347_D0


title: 346_D0


title: 345_D3


title: 348_D3


title: 345_D0


title: 346_D7


title: 352_D3


title: 346_D3


title: 344_D3


title: 352_D0


title: 342_D7


title: 343_D0


title: 342_D0


title: 344_D0


title: 344_DE


title: 345_D7


title: 340_D7


title: 341_D0


title: 341_D3


title: 340_D0


title: 339_D0


title: 344_D7


title: 337_D0


title: 335_D0


title: 336_D3


title: 334_D7


title: 336_D7


title: 334_DE


title: 340_D3


title: 338_D0


title: 336_D0


title: 333_D7


title: 334_D0


title: 332_D0


title: 334_D3


title: 342_D3


title: 333_D0


title: 331_D0


title: 330_D7


title: 330_D3


title: 333_D3


title: 331_D7


title: 328_D7


title: 330_D0


title: 328_D3


title: 328_D0


title: 327_D0


title: 325_D3


title: 325_D0


title: 324_D3


title: 326_D3


title: 324_D0


title: 322_D0


title: 321_D7A


title: 321_D7B


title: 321_DE


title: 323_D3


title: 323_D0


title: 321_D0


title: 320_D7


title: 329_D0


title: 319_D7


title: 320_D0


title: 319_D3


title: 317_D0


title: 319_D0


title: 318_D0


title: 326_D0


title: 316_D0


title: 316_D3


title: 313_D0


title: 315_D0


title: 313_D3


title: 312_DE


title: 312_D3


title: 320_D3


title: 314_D0


title: 309_D7


title: 310_D0


title: 310_D7


title: 312_D0


title: 311_D7


title: 311_D0


title: 309_D3


title: 312_D7


title: 309_D0


title: 307_D0


title: 308_D0


title: 305_D0


title: 305_D3


title: 302_DEA


title: 302_D7


title: 306_D3


title: 306_D0


title: 304_D0


title: 307_D7


title: 311_D3


title: 303_D0


title: 300_D3


title: 302_DEB


title: 302_D3


title: 300_D7


title: 301_D0


title: 298_D0


title: 307_D3


title: 299_D0


title: 300_D0


title: 297_D3


title: 296_D0


title: 297_D0


title: 299_D3


title: 295_D7


title: 295_D0


title: 295_DE


title: 294_D0


title: 295_D3


title: 293_D0


title: 290_D0


title: 302_D0


title: 292_D0


title: 292_D3


title: 291_D7


title: 291_D3


title: 289_D0


title: 288_D3


title: 289_D3


title: 288_D7


title: 287_D0


title: 292_D7


title: 286_D0


title: 284_D0


title: 285_D3


title: 282_D7


title: 282_D0


title: 283_D3


title: 288_D0


title: 280_D7


title: 280_D0


title: 280_D3


title: 286_D3


title: 281_D0


title: 291_D0


title: 275_D0


title: 274_D3


title: 283_D0


title: 279_D0


title: 285_D7


title: 278_D0


title: 276_D0


title: 277_D0


title: 285_D0


title: 283_D7


title: 273_D0


title: 272_D0


title: 267_DE


title: 267_D7


title: 268_D0


title: 267_D0


title: 267_D3


title: 266_D0


title: 263_D7


title: 263_DE


title: 264_D3


title: 265_D0


title: 264_D7


title: 263_D3


title: 264_D0


title: 274_D0


title: 261_DE


title: 263_D0


title: 271_D0


title: 262_D0


title: 262_D3


title: 261_D7


title: 261_D3


title: 259_DE


title: 260_D0


title: 259_D0


title: 259_D3


title: 259_D7


title: 258_D0


title: 257_D3


title: 256_D0


title: 255_D0


title: 255_D3


title: 254_D7


title: 261_D0


title: 252_D0


title: 251_DE


title: 253_D3


title: 254_D3


title: 250_D7


title: 254_D0


title: 250_D3


title: 251_D3


title: 251_D7


title: 246_D0


title: 248_D0


title: 247_D0


title: 249_D0


title: 250_D0


title: 244_D0


title: 257_D0


title: 245_D0


title: 242_D3


title: 243_D0


title: 244_D3


title: 242_D0


title: 253_D0


title: 241_D7


title: 241_D3


title: 241_D0


title: 249_D3


title: 244_D7


title: 238_D7


title: 239_D7


title: 239_D3


title: 242_D7


title: 238_D0


title: 240_D0


title: 237_D0


title: 236_D7


title: 236_D0


title: 235_D0


title: 233_D0


title: 233_D3


title: 232_D0


title: 231_D0


title: 235_D3


title: 234_D0


title: 229_D0


title: 227_D0


title: 228_D0


title: 230_D3


title: 230_D0


title: 226_D3


title: 239_D0


title: 238_D3


title: 225_D3


title: 225_D0


title: 224_D7


title: 236_D3


title: 224_D3


title: 224_D0


title: 223_D3


title: 222_DE


title: 222_D3


title: 222_D0


title: 226_D0


title: 221_DE


title: 222_D7


title: 217_D7


title: 218_D3


title: 213_D3


title: 216_D0


title: 215_D0


title: 217_D0


title: 217_D3


title: 219_D0


title: 221_D3


title: 221_D0


title: 214_D3


title: 220_D0


title: 214_D0


title: 212_D0


title: 213_D0


title: 211_DE


title: 223_D0


title: 211_D7


title: 211_D3


title: 221_D7


title: 210_D3


title: 211_D0


title: 218_D0


title: 209_D3


title: 210_D0


title: 209_D0


title: 208_D7


title: 208_D0


title: 206_D7


title: 206_D3


title: 208_D3


title: 204_D3


title: 207_D3


title: 205_D0


title: 204_D7


title: 198_D0


title: 203_D3


title: 197_D3


title: 200_D0


title: 201_D0


title: 199_D0


title: 197_D7


title: 204_D0


title: 197_D0


title: 203_D0


title: 196_D3


title: 193_DE


title: 193_D7


title: 194_D3


title: 207_D0


title: 196_D0


title: 195_D0


title: 193_D3


title: 193_D0


title: 192_D3


title: 192_D7


title: 192_D0


title: 194_D0


title: 188_D7


title: 188_D3


title: 189_D0


title: 185_D7


title: 191_D0


title: 188_D0


title: 190_D0


title: 187_D7


title: 187_D3


title: 185_D0


title: 186_D0


title: 187_D0


title: 186_D7


title: 184_D3


title: 184_D7


title: 184_D0


title: 186_D3


title: 182_D3


title: 182_D0


title: 181_D0


title: 180_D0


title: 179_D3


title: 179_D0


title: 178_D7


title: 178_D0


title: 185_D3


title: 177_D3


title: 176_D0


title: 177_D0


title: 172_D7


title: 173_D0


title: 174_D0


title: 172_D0


title: 171_DE


title: 175_D0


title: 171_D7


title: 175_D3


title: 171_D0


title: 169_D0


title: 170_D0


title: 168_D7


title: 168_D0


title: 168_D3


title: 167_D0


title: 169_D3


title: 166_D0


title: 166_D3


title: 165_D7


title: 165_D3


title: 163_D0


title: 164_D0


title: 165_D0


title: 166_D7


title: 171_D3


title: 162_D0


title: 161_D0


title: 160_D0


title: 169_D7


title: 159_D3


title: 158_D0


title: 156_D7


title: 157_D0


title: 158_D3


title: 153_D7


title: 154_D7A


title: 155_D7


title: 154_D3


title: 155_D0


title: 155_D3


title: 159_D0


title: 154_DE


title: 154_D0


title: 158_D7


title: 156_DE


title: 155_DE


title: 156_D0


title: 154_D7B


title: 153_D3


title: 153_D0


title: 152_D7


title: 152_D3


title: 151_D0


title: 150_D3


title: 149_D3


title: 149_D0


title: 150_D0


title: 148_D3


title: 146_DE


title: 147_D0


title: 146_D7


title: 144_D3


title: 143_D7


title: 144_D0


title: 146_D0


title: 139_D7


title: 139_D0


title: 145_D0


title: 137_D3


title: 140_D3


title: 143_DE


title: 143_D3


title: 138_D0


title: 152_D0


title: 136_D3


title: 135_DE


title: 137_D0


title: 140_D0


title: 135_D0


title: 139_D3


title: 136_D0


title: 146_D3


title: 140_D7


title: 133_D0


title: 135_D3


title: 148_D0


title: 134_D0


title: 131_D0


title: 134_D3


title: 126_D0


title: 124_D3


title: 132_D7


title: 127_D0


title: 139_DE


title: 125_D0


title: 129_D0


title: 132_D0


title: 135_D7


title: 130_D3


title: 124_D0


title: 132_DE


title: 120_D0


title: 122_D0


title: 128_D3


title: 123_D0


title: 123_D3


title: 130_D0


title: 121_D7


title: 121_D0


title: 115_D7


title: 121_D3


title: 119_D3


title: 114_D0


title: 113_D0


title: 119_D0


title: 118_D0


title: 132_D3


title: 116_D0


title: 112_D0


title: 115_D0


title: 115_D3


title: 117_D0


title: 110_D0


title: 111_D0


title: 108_D0


title: 107_D0


title: 106_D7


title: 106_D0


title: 105_D0


title: 104_D0


title: 102_DE


title: 102_D7


title: 101_D3


title: 102_D3


title: 102_D0


title: 103_D0


title: 114_D3


title: 101_D7


title: 109_D0


title: 108_D3


title: 100_D0


title: 98_D0


title: 98_D3


title: 99_D0


title: 101_D0


title: 98_D7


title: 97_D0


title: 97_D3


title: 106_D3


title: 99_D3


title: 97_DE


title: 95_D0


title: 94_D0


title: 93_D3


title: 93_D0


title: 96_D0


title: 92_D3


title: 92_D0


title: 91_D7


title: 91_D0


title: 96_D3


title: 90_D7


title: 90_D3


title: 89_D0


title: 89_D3


title: 96_D7


title: 89_D7


title: 88_D0


title: 92_D7


title: 87_D0


title: 87_D3A


title: 87_D3B


title: 85_D0


title: 86_D0


title: 83_D3


title: 84_D3


title: 82_D3


title: 83_D0


title: 82_D0


title: 81_D0


title: 80_D0


title: 79_D3


title: 80_D7


title: 76_D0


title: 75_D0


title: 77_D0


title: 74_D3


title: 84_D0


title: 76_D3


title: 73_D0


title: 80_D3


title: 69_D0


title: 74_D0


title: 72_D0


title: 79_D0


title: 66_DE


title: 68_D0


title: 71_D0


title: 67_D0


title: 77_D3


title: 70_D0


title: 78_D0


title: 79_D7


title: 74_D7


title: 63_D3


title: 63_D0


title: 66_D0


title: 65_D0


title: 66_D3


title: 66_D7


title: 62_D0


title: 61_D3


title: 61_D0


title: 59_D7


title: 64_D0


title: 61_D7


title: 59_D3


title: 60_D0


title: 57_D0


title: 55_D0


title: 57_D3


title: 58_D0


title: 59_D0


title: 56_D0


title: 54_D7


title: 54_D0


title: 53_D7


title: 54_DE


title: 54_D3


title: 53_D3


title: 52_D7


title: 53_D0


title: 52_D3


title: 52_D0


title: 50_D7


title: 49_D7


title: 49_DE


title: 50_D0


title: 49_D0


title: 46_D0


title: 47_D0


title: 45_D3


title: 45_D7


title: 48_D0


title: 45_D0


title: 43_D0


title: cfDNA28

city: Nanjing

first: Shicai

last: Liu

address: Sipailou 2#, Sipailou 2#

institute: Southeast University

data_processing:
The raw reads data were separated according to the barcode using a homemade Perl scripts.
The constant sequence (19 bp) and barcode (6 bp) sequences were removed from the 5ʹ end of the pair-end sequencing reads 2 then mapped to human genome (hg19) using Bowtie2 (version 2.2.6).
Genome_build: hg19
Supplementary_files_format_and_content: bw files

source_name: Cell free DNA

extract_protocol:
The plasma was separated from whole blood, then cell free DNA was isolated with the Plasma Circulating DNA Kit (TIANGEN, DP339).
The denatured cell free DNA was ligated with variant single strand adaptors. Then elongated, purified with Ampure XP beads and ligated with barcoded T overhanging adaptors. After purified with Ampure XP beads, amplification was performed with Illumina compatible primers.

value: blood

tag: condition

value: Esophageal cancer patient pre-operation


title: cfDNA30


title: 51_D0


title: 42_DE


title: cfDNA29


title: 43_D3


title: 43_D7B


title: 43_D7A


title: 49_D3


title: 42_D7


title: cfDNA25


title: 42_D3


title: cfDNA26


title: cfDNA24


title: 48_D3


title: cfDNA23


title: 42_D0


title: cfDNA22


title: 41_D0


title: cfDNA21


title: 40_D3


title: 44_D0


title: 40_D0


title: cfDNA27


title: P30

city: Wuhan

first: Xiangbin

last: You

state: Hubei

address: Huazhong agricultural university, hongshan district, wuhan

institute: Huazhong Agricultural University

description:
PRRSV-uninfected 60h
microRNA

data_processing:
The raw sequence reads were filtered for composition.
The presence of adaptor dimers, length, sequence repetition, and copy numbers using SOAP V2.0.
Determine conserved miRNAs, the filtered sequences were initially used to search the miRBase 18.0 with BLASTN.
MiRNAs were first filtered to retain only those with a mean expression value of at least 28 read counts between the two groups were compared.
A miRNA was labeled as differentially expressed by RNA-seq when fold-change = |log2Treatment/control| ≥1 and P-value ≤0.01.
Genome_build: miRBase 18.0
Supplementary_files_format_and_content: *RPKM.xlsx: Excel files include RPKM values for each Sample.

organism: Sus scrofa

source_name: pig alveolar macrophages

growth_protocol: PAMs were isolated by lung lavage from 5-week-old and specific pathogen-free (SPF) Meishan, Landrace, Pietrain and Qingping pigs.

extract_protocol:
RNA was harvested using Trizol reagent.
Total RNA were prepared for small RNA Sequencing by Synthesis according to the procedure and standards of the Illumina Sample Preparation Protocol.

treatment_protocol: PRRSV-infected and uninfected PAMs at 9 h (early), 36 h (middle) and 60 h (later) were chose to systematically investigate the effect of PRRSV infection on PAMs’ miRNAomes of different pig breeds.

tag: breed

value: Pietrain

tag: age

value: 5 weeks

value: Alveolar macrophages

tag: infection

value: Uninfected

tag: infection/uninfected time point


title: 39_DE


title: Lane2_cfDNA20

value: Health people


title: P31

description:
PRRSV-infected 60h
microRNA

value: PRRSV


title: 39_D7

value: Enriched neutrophils from whole blood


title: 39_D3


title: Lane2_cfDNA18


title: 39_D0


title: 38_D3


title: 38_D0


title: P20

description:
PRRSV-uninfected 36h
microRNA


title: Lane2_cfDNA17


title: Lane2_cfDNA19


title: P21

description:
PRRSV-infected 36h
microRNA


title: Lane2_cfDNA16

value: Esophageal cancer patient post-operation


title: P11

description:
PRRSV-infected 9h
microRNA


title: 37_D7


title: 36_D7


title: CB31

description:
PRRSV-infected 60h
microRNA

value: Landrace


title: 37_D0


title: 35_D0


title: 37_D3


title: P10

description:
PRRSV-uninfected 9h
microRNA


title: 36_D0


title: 36_D3


title: 33_D0


title: 32_D7


title: Lane2_cfDNA15


title: Lane2_cfDNA11


title: CB11

description:
PRRSV-infected 9h
microRNA


title: Lane2_cfDNA10


title: 35_D3


title: 31_D0


title: 30_D0


title: CB10

description:
PRRSV-uninfected 9h
microRNA


title: CB30

description:
PRRSV-uninfected 60h
microRNA


title: 28_D0

value: COVID- symptomatic


title: 32_D3


title: Lane2_cfDNA14


title: 29_D3


title: CB21

description:
PRRSV-infected 36h
microRNA


title: Lane2_cfDNA13


title: Lane2_cfDNA8


title: Lane2_cfDNA9


title: QP30

description:
PRRSV-uninfected 60h
microRNA

value: QingPing


title: 32_D0

value: COVID+


title: 29_D0


title: 26_D0


title: 29_D7


title: QP21

description:
PRRSV-infected 36h
microRNA


title: Lane2_cfDNA12


title: 34_D0


title: QP31

description:
PRRSV-infected 60h
microRNA


title: 25_D0


title: CB20

description:
PRRSV-uninfected 36h
microRNA


title: 27_D0


title: Lane2_cfDNA7


title: 24_D3


title: 24_D0


title: Lane2_cfDNA6


title: QP20

description:
PRRSV-uninfected 36h
microRNA


title: 23_D3


title: 23_D0


title: Lane2_cfDNA5


title: 22_D7


title: QP11

description:
PRRSV-infected 9h
microRNA


title: 22_D3


title: 22_D0


title: Lane2_cfDNA3


title: QP10

description:
PRRSV-uninfected 9h
microRNA


title: 20_D3


title: Lane2_cfDNA4


title: 19_D7


title: MS30

description:
PRRSV-uninfected 60h
microRNA

value: Meishan


title: MS21

description:
PRRSV-infected 36h
microRNA


title: Lane1_cfDNA19


title: MS31

description:
PRRSV-infected 60h
microRNA


title: Lane1_cfDNA20


title: 18_D3


title: MS20

description:
PRRSV-uninfected 36h
microRNA


title: 19_D0


title: Lane2_cfDNA2


title: MS11

description:
PRRSV-infected 9h
microRNA


title: 19_D3


title: 21_D0


title: 16_D0


title: Lane1_cfDNA18


title: 17_D0


title: MS10

description:
PRRSV-uninfected 9h
microRNA


title: 20_D0


title: Lane1_cfDNA17


title: 20_D7


title: 15_D0


title: HUVEC-FUCCI - Late G1 4

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

data_processing:
Sequencing was performed at the Yale Center for Genomic Analysis (Illumina HiSeq4000)
Raw read data was quality controlled with FastQC v0.11.9 (Babraham Bioinformatics)
Raw read data was quality controlled with FastQC v0.11.9 (Babraham Bioinformatics)
Raw read data was filtered and trimmed with Trimmomatic v0.33
Peaks were called with MACS2 v2.2.7.1
Assembly: hg38
Supplementary files format and content: Excel file contains peak calls from combined data
Supplementary files format and content: bam files contain filtered sequences, with location in bai files, to view in a genome browser

source_name: Human Umbilical Vein Endothelial Cells

extract_protocol:
Subconfluent, HUVEC-FUCCI were lifted and sorted into early G1 and late G1 cell cycle states, then immediately collected for ATAC-sequencing analysis (n = 4 biological replicates).
Cells were pelleted by 13,000 rpm for 1.5 min in a tabletop centrifuge, cells were resuspended in 50 mL Transposase Reaction Mix (25 mL 2x TD Buffer, 2.5 mL Transposase Enzyme from Illumina Nextera Cat# FC121-1030, 22 mL nuclease-free water, 0.5 mL 0.1% digitonin) and incubated for 30 min at 37 C, then DNA was purified using a QIAGEN MinElute PCR Purification Kit (Cat# 28004) amplified using KAPA HiFi HotStart ReadyMix PCR kit and sequenced tagged primers according to the published protocol, then amplified DNA was purified using AMPure Beads (Beckman Coulter Cat# A63880)

value: Human Umbilical Vein Endothelial Cells

value: Endothelial Cells

tag: genotype

value: FUCCI

tag: treatment


title: 14_D7


title: Lane1_cfDNA16

tag: tissue

value: blood


title: 15_D3


title: 14_D0


title: HUVEC-FUCCI - Late G1 3


title: 13_D3


title: HUVEC-FUCCI - Late G1 2


title: Lane1_cfDNA14


title: 13_D0


title: Lane1_cfDNA15


title: 12_D0


title: 12_D3


title: Lane1_cfDNA13


title: 12_D7


title: Lane1_cfDNA12


title: HUVEC-FUCCI - Early G1 4


title: 10_D0


title: HUVEC-FUCCI - Late G1 1


title: 9_D3


title: Lane1_cfDNA11

value: Esophageal cancer patient pre-operation


title: 11_D0


title: 9_D0


title: HUVEC-FUCCI - Early G1 3


title: 7_D0


title: 12_DE

value: DE


title: 6_D7


title: 8_D0


title: HUVEC-FUCCI - Early G1 2


title: Lane1_cfDNA10


title: HUVEC-FUCCI - Early G1 1


title: 6_D3


title: Lane1_cfDNA9


title: Lane1_cfDNA7


title: covid-19_pt7 [GC1003248]

city: Vienna

first: Laura

middle: de

last: Rooij

address: Lazarettgasse 14

country: Austria

institute: CeMM

description:
GC1003248
bulk RNA-seq

data_processing:
Bulk RNA-seq: Single-end reads of 50 bp length were produced with aminimum of 1 million reads per sample. Quality control of raw reads was performed with FastQC v0.11.7, available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc . Adapters were filtered with ea-utils fastq-mcf v1.05 (https://github.com/ExpressionAnalysis/ea-utils). Splice-aware alignment was performed with HiSAT2 against the human reference genome hg38. Reads mapping to multiple loci in the referencegenome were discarded. Resulting BAM files were handled with Samtoolsv1.5. Quantification of reads per genewas performed with htseq-count v2.7.14.
Genome_build: human reference genome GRCh38
Supplementary_files_format_and_content: raw counts (.csv) and accompanying metadata/cell annotations (.csv).

source_name: lung

extract_protocol: Bulk RNA-seq: For RNA preparation from formalin fixed paraffin embedded (FFPE) material, up to 5 10-um tissue sections were pooled, deparaffinized with Deparaffinization Solution (Qiagen) and RNA was isolated using the miRNEASY FFPE kit (Qiagen) according to the manufacturer’s instructions. Sequencing libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq library prep kit according to the manufacturer’s instructions. Samples were indexed to allow for multiplexing. Library quality and size range was assessed using a Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA). Libraries were diluted to a final concentration of 2nM and subsequently sequenced on an Illumina HiSeq4000 instrument.

value: lung

tag: sample type

value: autopsy


title: Lane1_cfDNA8


title: Lane2_cfDNA1


title: Lane1_cfDNA5


title: covid-19_pt6 [GC1003247]

description:
GC1003247
bulk RNA-seq


title: 1_D0


title: 2_D3


title: 5_D7


title: 5_D3


title: covid-19_pt2 [GC1003243]

description:
GC1003243
bulk RNA-seq


title: 5_D0


title: Lane1_cfDNA2


title: Lane1_cfDNA3


title: covid-19_pt5 [GC1003246]

description:
GC1003246
bulk RNA-seq


title: INFL_pt2 [GC1003241]

description:
GC1003241
bulk RNA-seq


title: H1299 cells, Bro40-3, 24 hours

first: Nai Yang

last: Yeat

address: 128, Academia Road Sec. 2, Nankang

institute: Academia Sinica

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format.
The obtained raw paired-end reads were filtered by Trimmomatic to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software.
Differentially expressed genes (DEGs) analysis of two conditions was performed in R using DEGseq (without biological replicate) and DESeq2 (with biological replicate), which based on negative binomial distribution and Poisson distribution model, respectively. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the FDR. GO and KEGG pathway enrichment analysis of DEGs were conducted using clusterProfiler.
Assembly: GRCh38
Supplementary files format and content: Excel file for each independent sample

growth_protocol: H1299 cells were maintained in M10 medium (DMEM High Glucose:DMEM Low Glucose = 1:1) supplemented with 10% fetal bovine serum (FBS) and antibiotics (Penicillin/Streptomycin) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Thermo Fisher Scientific), followed by chloroform phase separation, isopropanol precipitation and ethanol dehydration. 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: H1299 cells were cultured in 10cm petridish and transfected with 5ug of GFP-Bro40 and GFP-Bro40mut, respectively for 24 hours.

value: Non-small cell lung cancer cells

value: Wild type

value: GFP-Bro40 transfection

tag: time

value: 24 hours


title: 3_D3

value: Enriched neutrophils from whole blood


title: 4_D0


title: Lane1_cfDNA6


title: 3_D0


title: covid-19_pt1 [GC1003242]

description:
GC1003242
bulk RNA-seq


title: H1299 cells, Bro40mut-3, 24 hours

value: GFP-Bro40mut transfection


title: 2_D0


title: H1299 cells, Bro40-1, 24 hours


title: 6_D0


title: covid-19_pt3 [GC1003244]

description:
GC1003244
bulk RNA-seq


title: Lane1_cfDNA4


title: H1299 cells, Bro40-2, 24 hours


title: KO_3_S6

city: Chicago

first: Md Zahid

last: Akhter

state: IL

address: 835 S Wolcott Ave

department: Pharmacology & Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to reference genome mm10 using STAR (Dobin et al., 2013). Ensembl gene expression was quantified using featureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: Control_vs_KO_Differential_Expression.xlsx

source_name: Lung

growth_protocol: FAK floxe and EC-FAK knockout mice were maintained following Institute Animal Care and Use guidelines.

extract_protocol:
Lungs harvested from FAK flox and EC-FAK knockout mice  were subjected to single cell suspension and stained with anti-CD31 and CD45 antibodies. Endothelial cells (CD31+CD45-) were flow sorted and RNA isolation was performed using Trizol. Quality check was done by Bioanalyzer. RNA-seq was performed on samples with RIN 7-10.
Oligo-dT library

value: Lung

value: Flow sorted endothelial cells (CD31+CD45-) from mice lung

value: EC-FAK knockout


title: INFL_pt7 [GC1003239]

description:
GC1003239
bulk RNA-seq


title: 4_D3

value: COVID+


title: covid-19_pt4 [GC1003245]

description:
GC1003245
bulk RNA-seq


title: KO_2_S5


title: 1_D3


title: H1299 cells, Bro40mut-2, 24 hours


title: Lane1_cfDNA1


title: KO_1_S4


title: H1299 cells, Bro40mut-1, 24 hours


title: INFL_pt1 [GC1003240]

description:
GC1003240
bulk RNA-seq


title: INFL_pt6 [GC1003238]

description:
GC1003238
bulk RNA-seq


title: INFL_pt4 [GC1003236]

description:
GC1003236
bulk RNA-seq


title: INFL_pt5 [GC1003237]

description:
GC1003237
bulk RNA-seq


title: 4121 NSTC H3K27ac

city: Beijing

first: Jiayi

last: Chen

address: Taiping Road 27, Haidian district

institute: National Center of Biomedical Analysis, Beijing

data_processing:
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v 2.4.2) and generated SAM files were converted to BAM files using Samtools (v 1.11) using the view function.
Samblaster (v 0.1.26) was used to further sort, index and remove potential PCR duplicates (rmdup) from BAM files which were converted to BigWig files using Deeptools (v 3.5.3; bamCoverage —ignoreDuplicates —skipNonCoveredRegions —normalizeUsing RPKM -p 16 —extendReads —binSize 50).
BigWig files were visualized using the Integrative Genomics Viewer (IGV; Broad Institute).
Assembly: hg38
Supplementary files format and content: bigWig

source_name: 4121 NSTC

growth_protocol: 4121GSC were maintained in the Neurobasal™ Medium supplemented with B-27™ Supplement, sodium pyruvate, L-glutamine, penicillin-streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF) and 10 ng/ml epidermal growth factor (EGF). 4121GSC were cultured in DMEM with 10% FBS for 7 days to differentiate into 4121NSTC.

extract_protocol:
1×106 cells were harvest and following the manufacturer’s protocol of the SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology, Cat# 9003S).
Libraries were prepared according to Illumina's standard protocol.

value: 4121 NSTC

value: Non-stem tumor cell

tag: chip antibody

value: H3K27ac (Millipore, #17-683)


title: 4121 NSTC H3K4me3

value: H3K4me3 (Millipore, #07-473)


title: 4121 GSC H3K27me3

value: glioblstoma stem cell


title: 4121 NSTC H3K27me3


title: Control_1_S1

value: FAK Flox


title: 4121 NSTC H3K4me1

value: H3K4me1 (Millipore, #07-436)


title: INFL_pt3 [GC1003235]

description:
GC1003235
bulk RNA-seq

value: lung

value: autopsy


title: 4121 GSC H3K4me1


title: Control_2_S2