title: SN_SNCA_noDBS_r14

city: Wuerzburg

first: Rhonda

last: McFleder

address: Josef-schneider-strasse 11

institute: Neurologische Klinik und Poliklinik des Universitaetsklinikum Wuerzburg

data_processing:
Reads were quality- and adapter trimmed with Cutadapt version 2.5 using a cutoff Phred score of 20 in NextSeq mode, the minimum overlap was set to 6 from 3 (default), and reads without any remaining bases were discarded; Parameters: --nextseq-trim=20 -m 1 -a NNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -O 6
The sequence of hαSynA53T gene was inserted at the end of the rat reference genome (RefSeq GCF_000001895.5)
Processed reads were mapped to the rat Rattus norvegicus Rnor_6.0 reference genome (RefSeq GCF_000001895.5) with splice junction-sensitive read mapper STAR version 2.7.2b using default parameters
Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature; Parameters: -s 2 -t exon -M -O --fraction
Differential expression analysis was carried out employing DESeq2 (version 1.24.0)
Assembly: reference genome: NCBI RefSeq Rattus norvegicus Genome Rnor_6.0 (RefSeq GCF_000001895.5), (https://www.ncbi.nlm.nih.gov/genome/?term=txid10116)
Supplementary files format and content: tab-delimited file with raw counts and rlog transformed counts for each sample

organism: Rattus norvegicus

source_name: Substantia Nigra

growth_protocol: Only male Sprague-Dawley rats were used maintained in a specific pathogen-free environment under standard conditions of the animal facility of the University Hospital of Würzburg

extract_protocol:
After the animals were sacrificed the SN was microdissected and RNA isolated using the RNeasy micro kit (Qiagen #74004) according to manufacturer’s instructions.
Library preparation was performed by using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio, Kusatsu)
Single-end sequencing with a read length of 75nt in was performed on an Illumina NextSeq 500 system (Illumina, San Diego, CA, USA)

treatment_protocol: rats with an average weight of 280 g were stereotactically injected unilaterally in the SN with either 2uL of empty AAV1/2 (EV) or an AAV1/2-expressing the human mutated A53T-aSyn (haSyn) at a concentration of 2.55 x 1012 genomic particles/mL. Three weeks after AAV injection, microelectrode-guided implantation of monopolar Platinum/iridium DBS electrodes (UE-PSEGSECN1M; FHC Inc., Bowdoin, ME) with an impedance between 0.8 and 1.0 Mohm into the ipsilateral STN was performed. All animals were implanted with the electrode however only (DBS) animals received twenty-one days of HFS.

value: Substantia Nigra

value: haSyn

value: no DBS


title: KYSE-150 cells,Control2

status: Public on Dec 09 2024

type: SRA

city: Haikou

first: Yue

last: Zeng

address: Longhua District Yehai Avenue

country: China

institute: The Second Affiliated Hospital of Hainan Medical University

description: Library name: WT_2

library_source: transcriptomic

data_processing:
The original image Data files Sequenced by high-throughput sequencing (such as illumina HiSeqTM2500 and other sequencing platforms) are converted into Sequenced Reads by Base Calling analysis, which are called Raw Data or Raw Reads. The results were stored in FASTQ (fq) file format, which contained sequence information of sequencing sequences (reads) and their corresponding sequencing quality information.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: The human esophageal carcinoma cell line KYSE-150 was cultured in RPMI-1640 medium with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin with 5% CO2 at 37℃.

extract_protocol:
After the sample is qualified, eukaryotic mRNA is enriched with magnetic beads with Oligo (dT) (in the case of prokaryotes, mRNA is enriched by removing rRNA by the kit). Then mRNA was fragmented into short fragments by fragmentation buffer. A cDNA strand was synthesized using the mRNA template with six-base random hexamers, and then a two-strand cDNA was synthesized by buffer solution, dNTPs and DNA polymerase I. AMPure XP beads were then used to purify double-stranded cDNA. The purified double-stranded cDNA was then end-repaired, A tail was added and sequencing joints were connected. Then AMPure XP beads were used for fragment size selection, and finally PCR enrichment was performed to obtain the final cDNA library.
After the completion of the library construction, Qubit2.0 was used for preliminary quantification, and the library was diluted to 1ng/ul. Then Agilent 2100 was used to detect the insert size of the library. After the insert size met the expectation, Q-PCR method was used to quantify the effective concentration of the library accurately (effective concentration of the library > 2nM) to ensure the quality of the library.

tag: cell line

tag: cell type

value: Human esophageal squamous cells

tag: genotype

value: WT


title: Rat mTAL replicate 1

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

country: USA

institute: Versiti Blood Research Institte

description:
RmTAL3
ATAC_RmTAL_consensus_peaks_signaldata.bigwig

library_source: genomic

data_processing:
ATAC-seq reads were aligned to the hg38 (human derived sample) and rn7 (rat derived data) genome assembly using bowtie2 and after removing the mitochondrial read and duplicate reads, all replicates from each sample were merged
MACS2 was used to call peak from these merged bam files as well as each replicate bam files using this criteria  -nomodel-extsize200 -shift 100 -q0.01
The alignmed reads was also used to perform motif enrichment by HOMER
Assembly: hg38 and rn7
Supplementary files format and content: NarrowPeak
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: Kidney

growth_protocol: Kidney segments were dissected from human Patients and salt-sensitive rats (SS/JrHsdMcwi; RRID: RGD 61499) are used for this study

extract_protocol:
Small pieces of kidney segments from both human and rat were subjected to multiple rounds of collagenase digestion to isolate mTAL and PT segments
Nuclei were isolated from the PT and mTAL segments and subjected to the transposition reaction with Illlumina transposase in the appropriate buffer. Library fragments were amplified with indexing primers

tag: tissue

value: Kidney

value: medullary Thick Ascending Limb

value: Control


title: E13.5 Brain

city: Pittsburgh

first: Hisato

last: Yagi

state: PA

address: 530 45th street, Rangos Res Center 8162

institute: University of Pittsburgh

description: Library name: E13.5 Brain

data_processing:
Reads were mapped to the mouse reference genome (GRCm38 from Illumina iGenomes website) using Bowtie1 (Version: 1.1.2) with the commandline options: bowtie -v 2 -t -k 2 -m 1 Peaks were called using MACS2 (Model-based Analysis for ChIP-Seq, version: MACS-2.1.0.20140616) with the command-line options: macs2 callpeak -t sap130File -c ctrlFile -f BOWTIE -g mm -B -q 0.01. (FDR cutoff of 0.01).
Assembly: GRCm38/mm10
Supplementary files format and content: CHiPseqResults; peaks found by comparing Sap130 to Input.

organism: Mus musculus

source_name: Brain

extract_protocol:
Chromatin immunoprecipitation of Sap130 was performed with rabbit anti-Sap130 antibody (A302-491A: Bethyl laboratories, 2ug) and iDeal ChIP-seq Kit for Transcription Factors (Diagenode) following the manufacturer’s protocol
ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

value: Brain

value: B6 wildtype

tag: Stage

tag: antibody

value: rabbit anti-Sap130 antibody (A302-491A:Bethyl laboratories, 2ug)


title: Sample 176_Healthy control_37

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

country: Spain

institute: GENVIP research group

data_processing:
Quality control of raw data was carried out using fastq.gzC.
Alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts.
Assembly: Ensembl GCh38 genome
Supplementary files format and content: Coma-delimited excell file with raw counts (Counts_raw_data.csv)
Supplementary files format and content: Coma-delimited excell file with normalized counts (Normalized_data.csv)

source_name: Whole blood

extract_protocol:
RNA was extracted using PAXgene Blood RNA Kit (IVD) and Tempus™ Spin RNA Isolation Kit
The Illumina’s TruSeq RNA Sample Preparation Kit was used for library preparation, and ribosomal and globin RNA depletion was performed using the Illumina® Ribo-Zero Gold kit

value: Whole blood

tag: Sex

value: M

tag: etiology

value: C

tag: collection tube

value: tempus

tag: batch

value: B

tag: condition


title: Sample 175_Healthy control_36

value: F


title: Sample 173_Healthy control_34


title: Sample 171_Healthy control_32


title: Sample 172_Healthy control_33


title: Sample 170_Healthy control_31


title: Sample 168_Healthy control_29


title: Sample 164_Paediatric pneumonia_138

value: DV

value: PAXgene

value: Pneumonia


title: SN_SNCA_noDBS_r1

country: Germany

molecule: polyA RNA

value: Substantia Nigra

value: haSyn

tag: treatment

value: no DBS


title: ctrl5_untx_ctrl

city: London

first: Oliver

last: Ziff

address: Institute of Neurology, Queen Square

country: United Kingdom

institute: University College London

description: Library name: CLA5407A14

data_processing:
Reads were processed using the nfcore/rna-seq v3.6 pipeline.  Detailed quality control of aligned reads was assessed utilising FastQC, RSeQC, Qualimap, dupRadar, Preseq and MultiQC tools.
Raw reads underwent adaptor trimming with Trim Galore, removal of ribosomal RNA with SortMeRNA, alignment to Ensembl GRCh38.99 human reference genome using splice-aware aligner, STAR v2.7.1 and BAM-level quantification with Salmon.
Assembly: Ensembl GRCh38.99
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: hiPSC derived microglia were maintained in Advanced DMEM/F12 (Invitrogen) with 100 ng/mL IL-34, 10 ng/mL GM-CSF, 1% N2 (Invitrogen), 2 mM Glutamax, penicillin/streptomycin and 0.055 mM β-mercaptoethanol for 14 days, with half media changes twice a week. Motor neurons and astrocytes were treated with microglia conditioned media at a ratio of 50:50 with fresh N2B27 (containing 0.1 μM compound E for motor neuron culture) for 72 hours.

extract_protocol:
The Promega Maxwell RSC simplyRNA cells kit including DNase treatment was used for RNA extractions using the Maxwell RSC instrument. A nanodrop was used to assess RNA concentration and the 260/280 ratio. RNA integrity was assessed using the Agilent TapeStation.
Poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from 4 control and 3 VCP lines using the KAPA mRNA HyperPrep Library kit for Illumina®, with 50 ng of total RNA as input. Libraries were sequenced on the NovaSeq 6000

treatment_protocol: Microglia were transfected using RNAiMAX (Thermo Fisher) to deliver 8.3 nM siRNAs targeting GPNMB (Horizon, ON-TARGETplus; L-011741-01) or a scrambled control siRNA (Horizon, ON-TARGETplus; D-001810-10) in Optimem overnight followed by a media change and then harvested or assayed 48 hours later.

value: ctrl

tag: lps treatment

value: untx

tag: microglia media

tag: sirna treatment

tag: strandedness

value: reverse

tag: library type

value: NEBNext Ultra II Directional PolyA mRNA


title: Sample 160_Paediatric pneumonia_134

value: DB


title: Rat mTAL replicate 2

description:
RmTAL5
ATAC_RmTAL_consensus_peaks_signaldata.bigwig

value: Kidney

value: medullary Thick Ascending Limb

value: Control


title: SN_SNCA_noDBS_r13


title: Sample 166_Healthy control_27

value: Whole blood

value: M

value: C

value: tempus


title: Sample 157_Paediatric pneumonia_131

value: U

value: PAXgene

value: B


title: SN_SNCA_noDBS_r3

value: Substantia Nigra

value: haSyn


title: Sample 165_Paediatric pneumonia_139

value: F

value: DV

value: Pneumonia


title: Sample 169_Healthy control_30


title: SN_SNCA_noDBS_r12

value: no DBS


title: Sample 156_Paediatric pneumonia_130

value: PB


title: SN_SNCA_DBS_r20

value: DBS


title: Sample 161_Paediatric pneumonia_135

value: DB


title: SN_SNCA_noDBS_r18


title: Sample 162_Paediatric pneumonia_136


title: SN_SNCA_DBS_r21


title: SN_SNCA_DBS_r24


title: SN_SNCA_noDBS_r17


title: SN_SNCA_DBS_r23


title: oGCSFR + MSA-oIL2-3

city: Stanford

first: Yang

last: Zhao

state: CA

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

description: Library name: F3

data_processing:
Reads were aligned to the mouse reference genome (mm10) with Rsubread. Gene expression was quantified with featureCounts.
Assembly: mm10
Supplementary files format and content: Gene expression was quantified with featureCounts.

source_name: spleen

extract_protocol:
Total RNA was extracted using the Quick-RNA 96 Kit (Zymo Research).
mRNA was isolated using poly-T magnetic beads, fragmented, and converted into cDNA using random hexamer primers. After second-strand synthesis, libraries were prepared through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: spleen

tag: cell line

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

value: Same batch


title: Sample 151_Paediatric pneumonia_125

value: Whole blood

value: M

value: PAXgene


title: Sample 150_Paediatric pneumonia_124

value: B


title: Sample 155_Paediatric pneumonia_129


title: Sample 149_Paediatric pneumonia_123


title: SN_SNCA_DBS_r8

value: Substantia Nigra

value: haSyn


title: Sample 158_Paediatric pneumonia_132

value: Pneumonia


title: Sample 163_Paediatric pneumonia_137

value: F

value: DV


title: Sample 159_Paediatric pneumonia_133

value: U


title: oGCSFR + MSA-oIL2-1

description: Library name: F1

tag: cell type


title: SN_noSNCA_noDBS_r11

tag: genotype

value: EV

value: no DBS


title: oEPOR + MSA-oIL2-3

description: Library name: E12

tag: tissue

value: spleen

value: primary mouse T cells


title: Sample 145_Paediatric pneumonia_119

value: DB


title: SH-SY5Y

type: RNA

city: Boston

first: Pablo

last: Argueso

address: 150 Harrison Avenue

institute: Tufts Medicine

description: rhGal-3 vs BSA

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/us/analyze
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix normalized worksheet reports normalized signal (against housekeeping genes).

label: SYBR Green

source_name: SH-SY5Y human neuroblastoma cell line

label_protocol: PCR assays were performed using the Human Neurotrophin and Receptors PCR Array (Qiagen) following the manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (Qiagen). Quantitative real-time PCR were performed (CFX, Bio-Rad) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Micro Kit with on-column DNA digestion.

treatment_protocol: Cells were treated with 3 µM recombinant human galectin-3 or bovine serum albumin for 48 hours in an incubator set to 37 degrees celcius.

value: Bone marrow


title: phLEC

description: rhGal-3 vs BSA

source_name: Primary human limbal epithelial cells

value: Corneal


title: SN_noSNCA_noDBS_r9


title: phCF

description: rhGal-3 vs BSA

source_name: Primary human corneal fibroblasts


title: oGCSFR + MSA-oIL2-2

description: Library name: F2

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

value: Same batch


title: oEPOR + MSA-oIL2-2

description: Library name: E11


title: Sample 144_Paediatric pneumonia_118

value: Whole blood

value: PAXgene

value: B


title: Sample 143_Paediatric pneumonia_117

value: M

value: Pneumonia


title: SN_SNCA_DBS_r16

value: Substantia Nigra

value: haSyn

value: DBS


title: oIFNLR1 + MSA-oIL2-3

description: Library name: E9

value: spleen


title: Sample 154_Paediatric pneumonia_128

value: F

value: U


title: SN_noSNCA_noDBS_r2

value: EV

value: no DBS


title: SN_SNCA_DBS_r10


title: Sample 152_Paediatric pneumonia_126


title: Sample 137_Paediatric pneumonia_111

value: DB


title: Sample 136_Paediatric pneumonia_110

value: PB


title: oIFNLR1 + MSA-oIL2-1

description: Library name: E7

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2


title: Sample 153_Paediatric pneumonia_127

value: Whole blood

value: PAXgene

value: B


title: SN_noSNCA_noDBS_r19

value: Substantia Nigra


title: Sample 148_Paediatric pneumonia_122

value: M

value: Pneumonia


title: Sample 133_Paediatric pneumonia_107


title: Sample 147_Paediatric pneumonia_121


title: Sample 146_Paediatric pneumonia_120


title: SN_noSNCA_DBS_r5

value: DBS


title: Sample 132_Paediatric pneumonia_106


title: SN_noSNCA_DBS_r4


title: oIFNAR2 + IFN-𝛼-2

description: Library name: D11

value: spleen

value: IFN-𝛼

value: Same batch


title: Sample 142_Paediatric pneumonia_116

value: F


title: SN_noSNCA_noDBS_r7

value: EV

value: no DBS


title: oEPOR + MSA-oIL2-1

description: Library name: E10

value: primary mouse T cells


title: Sample 130_Paediatric pneumonia_104

value: DB


title: Sample 141_Paediatric pneumonia_115

value: U


title: Sample 140_Paediatric pneumonia_114


title: SN_noSNCA_DBS_r26


title: SPF-552-6

description:
Library name: SPF-552-6
Emx-cre_Cont_SPF_552_6

data_processing:
Reads were aligned using TopHat2 (v2.0.9) with the following options: --segment-length 25 --segment-mismatches 2 --no-novel-juncs --min-achor=8 --splice-mismatches 0 --max-intron-length 500000 --microexon-search --no-mixed --no-coverage-search and values for the inner mate distance estimated using RSeQC (v2.3.6).
Gene-level counts were calculated by HTSeq-count (v0.5.4p5) using "union" mode and Ensembl GTF file as retrieved from iGenomes (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt; Ensembl release 66) for mm10.
Differential expression analyses were performed using the R package edgeR (v3.4.2). Genes with low expression (counts-per-million < 1 in all samples) were discarded. Dispersion parameters were estimated accounting for  stage (E13.5, E14.5), disease (Brain defect and control), and their pairwise interactions. For each gene, the maximum of common, trended and tag-wise dispersion estimate was used for subsequent analyses. Linear contrasts were used to compare Mutant to control, using likelihood ratio tests. Genes with an FDR <=0.05 and a fold-change >= 1.5 were considered significantly differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: EMX-cre RNAseq.xlsx

source_name: Forebrain

extract_protocol:
Total RNA was isolated from mouse embryonic brain using the RNeasy plus mini Kit (QIAGEN) with on-column DNase I digestion method (QIAGEN).
Libraries were constructed using TruSeq RNA Sample Preparation Kit v2 (Illumina)

value: Forebrain

tag: genotype (sap130)

tag: genotype (emx1-cre)

tag: Stage


title: Sample 139_Paediatric pneumonia_113

value: Whole blood

tag: Sex

tag: etiology


title: N2_de_RNAseq

city: Shanghai

first: Jinkui

last: Zhu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

data_processing:
After trimming, clean reads were aligned to the reference genome (GRCh38) using STAR (v2.7.10a) and salmon (v 1.10.1) was used for quantifying the expression of genes
Assembly: GRCh38
Supplementary files format and content: gene count matrix in csv format

source_name: organoids

extract_protocol:
total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit according to the manufacturer's protocol
The libraries were constructed using TruseqTM RNA sample prep Kit

value: organoids

value: human embryonic stem cells

value: WT

value: Differentiation according to protocol


title: oIFNLR1 + MSA-oIL2-2

description: Library name: E8

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

tag: batch


title: N1_de_RNAseq


title: Sample 125_Paediatric pneumonia_99

value: M

value: DV

tag: collection tube

value: PAXgene

value: B

tag: condition

value: Pneumonia


title: Sample 135_Paediatric pneumonia_109


title: SPF-539-6

description:
Library name: SPF-539-6
Emx-cre_Cont_SPF_539_6


title: N2_ctrl_RNAseq

tag: treatment


title: SN_noSNCA_DBS_r6

value: Substantia Nigra

value: EV

value: DBS


title: Sample 134_Paediatric pneumonia_108

value: F

value: U


title: Sample 124_Paediatric pneumonia_98

value: Whole blood

value: DB


title: SPF-539-4

description:
Library name: SPF-539-4
Emx-cre_Mut_SPF_539_4

value: Forebrain


title: oIFNAR2 + IFN-𝛼-3

description: Library name: D12

value: spleen

value: primary mouse T cells

value: IFN-𝛼

value: Same batch


title: Sample 123_Paediatric pneumonia_97

value: PB


title: Sample 131_Paediatric pneumonia_105


title: Sample 138_Paediatric pneumonia_112


title: Control 635-303-3

description: Library name: Control 635-303-3

data_processing:
Reads were aligned using TopHat2 (v2.0.9) with the following options: --segment-length 25 --segment-mismatches 2 --no-novel-juncs --min-achor=8 --splice-mismatches 0 --max-intron-length 500000 --microexon-search --no-mixed --no-coverage-search and values for the inner mate distance estimated using RSeQC (v2.3.6).
Gene-level counts were calculated by HTSeq-count (v0.5.4p5) using "union" mode and Ensembl GTF file as retrieved from iGenomes (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt; Ensembl release 66) for mm10.
Differential expression analyses were performed using the R package edgeR (v3.4.2). Genes with low expression (counts-per-million < 1 in all samples) were discarded. Dispersion parameters were estimated accounting for  stage (E13.5, E14.5), disease (Brain defect and control), and their pairwise interactions. For each gene, the maximum of common, trended and tag-wise dispersion estimate was used for subsequent analyses. Linear contrasts were used to compare Mutant to control, using likelihood ratio tests. Genes with an FDR <=0.05 and a fold-change >= 1.5 were considered significantly differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-deliminated text file

value: Brain

tag: genotype (pcdha9)


title: M3_de_RNAseq

value: organoids

value: human embryonic stem cells

value: WT

value: Differentiation according to protocol


title: o20R + MSA-oIL2-3

description: Library name: D3

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2


title: Sample 122_Paediatric pneumonia_96

value: F

value: PAXgene

value: B

value: Pneumonia


title: oIFNAR2 + IFN-𝛼-1

description: Library name: D10

value: spleen


title: SN_noSNCA_DBS_r15

value: Substantia Nigra

value: EV

value: DBS


title: Mutant 635-303-2

description: Library name: Mutant 635-303-2

value: m/m


title: SPF-552-7

description:
Library name: SPF-552-7
Emx-cre_Mut_SPF_552_7

value: Forebrain


title: Sample 129_Paediatric pneumonia_103

value: Whole blood

value: M

value: PB


title: N3_de_RNAseq

value: organoids

value: human embryonic stem cells

value: WT

value: Differentiation according to protocol


title: M2_de_RNAseq


title: o22R + MSA-oIL2-1

description: Library name: D4

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

value: Same batch


title: Sample 121_Paediatric pneumonia_95

value: PAXgene

value: B

value: Pneumonia


title: o20R + MSA-oIL2-2

description: Library name: D2

value: spleen


title: Control 635-195-6

description: Library name: Control 635-195-6

value: Brain


title: oIFNAR2 + MSA-oIL2-3

description: Library name: D9


title: oIFNAR2 + MSA-oIL2-2

description: Library name: D8


title: SPF-552-5

description:
Library name: SPF-552-5
Emx-cre_Cont_SPF_552_5

value: Forebrain


title: Sample 127_Paediatric pneumonia_101

value: Whole blood

value: F


title: oIFNAR2 + MSA-oIL2-1

description: Library name: D7


title: Mutant 635-195-3

description: Library name: Mutant 635-195-3

value: m/m


title: Sample 126_Paediatric pneumonia_100

value: PB


title: SPF-552-4

description:
Library name: SPF-552-4
Emx-cre_Mut_SPF_552_4


title: o10R + IL-10-3

description: Library name: C12


title: M2_ctrl_RNAseq

value: organoids

value: human embryonic stem cells

value: WT


title: N3_ctrl_RNAseq

value: Differentiation according to protocol


title: o22R + MSA-oIL2-3

description: Library name: D6

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression


title: Control 635-260-3

description: Library name: Control 635-260-3


title: M1_ctrl_RNAseq


title: Sample 117_Paediatric pneumonia_91

value: DB

value: PAXgene


title: Control 635-260-2

description: Library name: Control 635-260-2


title: Sample 128_Paediatric pneumonia_102

value: B

value: Pneumonia


title: N1_ctrl_RNAseq


title: o22R + MSA-oIL2-2

description: Library name: D5

value: spleen

value: MSA-orthogonal IL-2

value: Same batch


title: o10R + MSA-oIL2-3

description: Library name: C9


title: Sample 116_Paediatric pneumonia_90

value: Whole blood

value: F


title: M1_de_RNAseq


title: o20R + MSA-oIL2-1

description: Library name: D1


title: Sample 120_Paediatric pneumonia_94

value: PB


title: Female, Nanoparticle Hydrogel, UTY-KD, rep2

city: La Jolla

first: Rayyan

middle: Mohammed

last: Gorashi

address: 9500 Gilman Dr

department: Bioengineering

institute: UC San Diego

description: FNUB

data_processing:
Quality control using fastqc v0.12.1.
Confirmed adaptor sequence content with fastqc, all samples contained <5% adaptor content.
Alignment using HISAT2-2.2.1 and created a custom reference genome for our porcine using Ensembl Sscrofa 11.1 assembly.
Gene counts quantified using featureCounts from subread-2.0.6 using the Sus_scrofa.Sscrofa11.1.111.gtf annotation file.
Assembly: Sus scrofa 11.1 (Ensembl) Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa.gz
Supplementary files format and content: Tab delimited text includes raw counts for each Sample

organism: Sus scrofa

source_name: Porcine aortic valve

growth_protocol: On day 0, aortic valvular interstitial cells (aVICs) were seeded on hydrogels and cultured in Media 199 (1% fetal bovine serum) without antibiotic supplements for 1 day.

extract_protocol:
Total RNA was isolated using Qiagen Rneasy Micro kit, following manufacturer protocol. 200 ng of RNA per sample was used for library preparation.
RNA library for RNA-seq was prepared using Illumina's stranded mRNA kit.

treatment_protocol: On day 1, aVICs were treated with either silencer negative control siRNA or UTY siRNA (diluted in Optimem media) for 48 hours added directly to the culture media. On day 3, aVICs were lysed and total RNA was collected.

value: Porcine aortic valve

value: Female

value: Aortic valvular interstitial cell

tag: biomaterial substrate

value: Nanoparticle hydrogel

value: UTY siRNA vector


title: Control 635-195-2

description: Library name: Control 635-195-2

value: Brain


title: o10R + IL-10-2

description: Library name: C11

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression


title: Sample 118_Paediatric pneumonia_92

value: DB

value: PAXgene

value: B


title: M3_ctrl_RNAseq

value: organoids

value: human embryonic stem cells

value: WT

value: Differentiation according to protocol


title: Female, Nanoparticle Hydrogel, UTY-KD, rep1

description: FNUA


title: DmeaB 45 mM NaNO2 treated 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A. fumigatus Af293 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: https://fungidb.org/common/downloads/release-65/AfumigatusAf293/fasta/data/FungiDB-65_AfumigatusAf293_Genome.fasta; https://fungidb.org/common/downloads/release-65/AfumigatusAf293/gff/data/FungiDB-65_AfumigatusAf293.gff.
Supplementary files format and content: Excel file includes count and RPKM values for each Sample

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: Barratt’s minimal broth supplemented with 5 g/L yeast extract (100 ml aliquots in 500 ml Erlenmeyer flasks) were inoculated with 5 × 107 conidia. Cultures were incubated at 37 °C and 220 rpm for 17 h. Mycelia from these exponentially growing cultures were transferred into fresh minimal broth containing 11.8 g/L Na-glutamate, 10 g/L glucose, 1.52 g/L KH2PO4, 0.52 g/L MgSO4 4 H2O and 0.52 g/L KCl (pH 6.5). After a 4 h long incubation at 37 °C and 220 rpm, cultures were treated or were kept untreated.

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.
RNA-seq (single read, 75 bp)

treatment_protocol: After a 4 h long incubation at 37 °C and 220 rpm, cultures were treated with 45, 90 or 135 mmol/L NaNO2 or were kept untreated and samples were taken for RNA isolation 0.5 h after treatment.

value: mycelium

value: DmeaB mutant

value: 45 mM NaNO2


title: o21R + IL-21-3

description: Library name: C6

value: spleen

value: Same batch


title: Sample 119_Paediatric pneumonia_93

value: Whole blood

value: F

value: PB

value: Pneumonia


title: DmeaB 45 mM NaNO2 treated 1


title: DmeaB 45 mM NaNO2 treated 2


title: o10R + IL-10-1

description: Library name: C10

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression


title: o10R + MSA-oIL2-2

description: Library name: C8

value: MSA-orthogonal IL-2


title: Mutant 635-260-1

description: Library name: Mutant 635-260-1

value: Brain

value: m/m


title: Sample 115_Paediatric pneumonia_89

value: U

value: PAXgene

value: B


title: Sample 114_Paediatric pneumonia_88


title: o10R + MSA-oIL2-1

description: Library name: C7


title: Female, Nanoparticle Hydrogel, Silencer, rep2

description: FNSB

value: Porcine aortic valve

value: Female

value: Aortic valvular interstitial cell

value: Nanoparticle hydrogel

value: Silencer negative control siRNA vector


title: DmeaB 90 mM NaNO2 treated 2

value: mycelium

value: DmeaB mutant

value: 90 mM NaNO2


title: Sample 112_Healthy Control_26

value: Whole blood

value: F

value: C

value: tempus

value: A

value: Control


title: Female, Soft Hydrogel, UTY-KD, rep2

description: FSUB

value: Soft hydrogel

value: UTY siRNA vector


title: o21R + IL-21-2

description: Library name: C5

value: spleen

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: Same batch


title: DmeaB 90 mM NaNO2 treated 3


title: Sample 113_Paediatric pneumonia_87

value: PB

value: PAXgene

value: B

value: Pneumonia


title: Sample 110_Healthy Control_24

value: Whole blood

value: M


title: DmeaB untreated 2

value: mycelium

value: DmeaB mutant

value: untreated


title: Female, Nanoparticle Hydrogel, Silencer, rep1

description: FNSA

value: Porcine aortic valve

value: Female

value: Aortic valvular interstitial cell

value: Nanoparticle hydrogel

value: Silencer negative control siRNA vector


title: o21R + MSA-oIL2-3

description: Library name: C3

value: spleen

value: primary mouse T cells

value: T cells

value: MSA-orthogonal IL-2


title: Female, Soft Hydrogel, Silencer, rep2

description: FSSB

value: Soft hydrogel


title: DmeaB untreated 1


title: DmeaB 90 mM NaNO2 treated 1

value: 90 mM NaNO2


title: Sample 108_Healthy Control_22

value: C

value: tempus

value: A

value: Control


title: o21R + IL-21-1

description: Library name: C4

value: Orthogonal cytokine receptors expression

value: Same batch


title: DmeaB untreated 3

value: mycelium

value: DmeaB mutant

value: untreated


title: Sample 107_Healthy Control_21

value: Whole blood

value: M


title: o21R + MSA-oIL2-1

description: Library name: C1

value: spleen


title: Female, Soft Hydrogel, UTY-KD, rep1

description: FSUA

value: Porcine aortic valve

value: Female

value: Aortic valvular interstitial cell

value: UTY siRNA vector


title: Sample 109_Healthy Control_23


title: Female, Soft Hydrogel, Silencer, rep1

description: FSSA

value: Soft hydrogel

value: Silencer negative control siRNA vector


title: o21R + MSA-oIL2-2

description: Library name: C2

value: primary mouse T cells

value: T cells

value: MSA-orthogonal IL-2


title: Af293 135 mM NaNO2 treated 3

value: 135 mM NaNO2


title: Sample 111_Healthy Control_25

value: F

value: C

value: tempus

value: A

value: Control


title: o9R + MSA-oIL2-3

description: Library name: B12

value: Orthogonal cytokine receptors expression

value: Same batch


title: o9R + MSA-oIL2-2

description: Library name: B11

value: spleen


title: Af293 135 mM NaNO2 treated 2

value: mycelium


title: Sample 106_Healthy Control_20

value: Whole blood

value: M


title: Male, Nanoparticle Hydrogel, UTY-KD, rep2

description: MNUB

value: Porcine aortic valve

value: Male

value: Aortic valvular interstitial cell

value: Nanoparticle hydrogel

value: UTY siRNA vector


title: o9R + MSA-oIL2-1

description: Library name: B10

value: primary mouse T cells

value: T cells

value: MSA-orthogonal IL-2


title: Af293 90 mM NaNO2 treated 3

value: 90 mM NaNO2


title: o7R + IL-7-3

description: Library name: B9


title: Male, Nanoparticle Hydrogel, UTY-KD, rep1

description: MNUA


title: Af293 135 mM NaNO2 treated 1

value: 135 mM NaNO2


title: Male, Nanoparticle Hydrogel, Silencer, rep2

description: MNSB

value: Silencer negative control siRNA vector


title: Sample 105_Healthy Control_19

value: C

value: tempus

value: A

value: Control


title: o7R + IL-7-2

description: Library name: B8

value: spleen

value: Orthogonal cytokine receptors expression

value: Same batch


title: Sample 103_Healthy Control_17

value: Whole blood

value: M


title: Male, Nanoparticle Hydrogel, Silencer, rep1

description: MNSA

value: Porcine aortic valve

value: Male

value: Aortic valvular interstitial cell

value: Nanoparticle hydrogel


title: Male, Soft Hydrogel, UTY-KD, rep2

description: MSUB

value: Soft hydrogel

value: UTY siRNA vector


title: Af293 90 mM NaNO2 treated 1

value: mycelium

value: 90 mM NaNO2


title: o7R + IL-7-1

description: Library name: B7

value: primary mouse T cells

value: T cells


title: Sample 102_Healthy Control_16

value: F

value: C

value: tempus

value: A


title: Male, Soft Hydrogel, Silencer, rep2

description: MSSB

value: Silencer negative control siRNA vector


title: Af293 untreated 3

value: untreated


title: Sample 101_Healthy Control_15

value: Whole blood

value: M

value: Control


title: Sample 100_Healthy Control_14


title: o7R + MSA-oIL2-1

description: Library name: B4

value: spleen

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

value: Same batch


title: o7R + MSA-oIL2-3

description: Library name: B6


title: Af293 untreated 2

value: mycelium


title: o7R + MSA-oIL2-2

description: Library name: B5


title: Sample 104_Healthy Control_18


title: Af293 90 mM NaNO2 treated 2

value: 90 mM NaNO2


title: Primary meningioma, male 5

city: Oklahoma City

first: Anthony

middle: C

last: Johnson

state: OK

address: 1122 NE 13th St, O'Donoghue Research Building 332

department: Neurosurgey

institute: University of Oklahoma Health Sciences

description: Library name: PM5

data_processing:
Standard bioinformatics analyses were conducted by Novogene Co., LTD (Beijing, China).
Assembly: hg38
Supplementary files format and content: matrix table containg gene ID, sample ID, gene name, chromosome, gene start, gene end, strand, gene length, gene biotype, gene description, transcription factor family

source_name: meningioma tumor

extract_protocol:
Total RNA was extracted from tumors saved in RNAlater® Solution (Fisher Scientific, AM7023) with the RNeasy Plus mini kit (QIAGEN, 74136) with QIAshredder (QIAGEN, 79656).
Preparation of cDNA libraries and sequencing was conducted by Novogene Co., LTD (Beijing, China).

value: meningioma tumor

value: male


title: D0

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

department: BBTD

institute: LLNL

description: 10x Genomics, Formalin Fixed & Paraffin Embedded (FFPE) Visium Spatial Gene Expression

data_processing:
Data processing, including demultiplexing, alignment, barcode assignment, and gene expression quantification, was performed using the Space Ranger software pipeline version 2.1.1, mm10 reference transcriptome, and Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv probe set from 10x Genomics (https://www.10xgenomics.com/support/software/space-ranger/latest).
Assembly: mm10
Supplementary files format and content: The dataset includes the Space Ranger generated files necessary for downstream analysis. It contains barcodes.tsv.gz with a list of spatial barcodes and features.tsv.gz with gene IDs. The gene expression count data is stored in matrix.mtx.gz. Tissue-related images are provided, including aligned_fiducials.jpg.gz for aligned fiducials, detected_tissue_image.jpg.gz for the tissue and spots, tissue_hires_image.png.gz for a high-resolution image, and tissue_lowres_image.png.gz for a low-resolution image. Additionally, scalefactors_json.json.gz contains scalefactors in JSON format, and tissue_positions_list.csv.gz lists spatial barcodes and coordinates specifying spots.
Library strategy: Spatial Transcriptomics

extract_protocol: Visium Spatial Gene Expression for FFPE

value: Brain

tag: strain

tag: timepoint

value: Day 0

tag: infection

value: Uninfected controls


title: D6

value: Day 6

value: Infected with VEEV


title: o4R + IL-4-1

description: Library name: B1

tag: cell line

value: primary mouse T cells

tag: cell type

value: T cells


title: Sample 96_Healthy Control_10

tag: tissue

value: Whole blood

value: F

value: C

value: PAXgene

value: A


title: Af293 untreated 1

tag: genotype

value: untreated


title: Male, Soft Hydrogel, Silencer, rep1

description: MSSA

value: Porcine aortic valve

value: Male

value: Aortic valvular interstitial cell

value: Soft hydrogel

value: Silencer negative control siRNA vector


title: Sample 95_Healthy Control_9

value: M

value: Control


title: o4R + MSA-oIL2-3

description: Library name: A12

value: spleen

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

value: Same batch


title: o4R + IL-4-3

description: Library name: B3

value: primary mouse T cells

value: T cells


title: Sample 99_Healthy Control_13

value: Whole blood

value: C

value: tempus


title: Sample 98_Healthy Control_12

value: A


title: Primary meningioma, male 4

description: Library name: PM4

value: meningioma tumor

value: male


title: Primary meningioma, female 7

description: Library name: PF7

value: female


title: Sample 94_Healthy Control_8

value: F

value: PAXgene


title: o4R + IL-4-2

description: Library name: B2


title: Sample 97_Healthy Control_11


title: Primary meningioma, male 3

description: Library name: PM3


title: Primary meningioma, male 2

description: Library name: PM2


title: Primary meningioma, female 5

description: Library name: PF5


title: Male, Soft Hydrogel, UTY-KD, rep1

description: MSUA

value: Porcine aortic valve

value: Male

value: Aortic valvular interstitial cell

value: Soft hydrogel

value: UTY siRNA vector


title: Blood_D0

description: Uninfected

library_source: transcriptomic single cell

data_processing:
The Cell Ranger Single-Cell Software Suite (10x Genomics) was then used to perform sample demultiplexing, barcode processing, and single-cell gene counting. After demultiplexing the sequencing files with “cellranger mkfastq”, “cellranger count” was used to perform alignment to mouse reference transcriptome (mm10), barcode processing and gene counting.
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Blood

extract_protocol:
C3H/HeN mice were infected intranasally with 2e7 PFU of VEEV TC-83 for  2, 4, or 6 days. Uninfected mice were dosed in parallel with PBS. Mice were euthanized by exsanguination via cardiac perfusion of saline and brains were removed. PBMCs were isolated from effluent blood. Brain tissue was enzymatically digested and immune cells were isolated using percoll gradient centrifugation.
Immune (CD45+) cells from uninfected (D0) and infected (D2, D4, D6) brains or uninfected (D0) and infected (D6) blood  were sequenced using Chromium Single-cell 3ʹ GEM, Library & Gel Bead Kit v3 (10x Genomics Cat # 1000075) on a 10× Genomics Chromium Controller following manufacturers’ protocol.

value: Blood

tag: time point

value: PBMCs

value: Wildtype


title: Brain_D0

description: Uninfected

treatment_protocol: C3H/HeN mice were infected intranasally with 2e7 PFU of VEEV TC-83 for  2, 4, or 6 days. Uninfected mice were dosed in parallel with PBS.

value: Brain

value: Immune cells


title: Primary meningioma, female 4

description: Library name: PF4


title: Sample 91_Healthy Control_5

value: Whole blood

value: M

value: C

value: Control


title: o2R + IL-2-1

description: Library name: A7

value: spleen

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: Same batch


title: Sample 90_Healthy Control_4

value: PAXgene

value: A


title: Blood_D6

description: Infected_day 6

value: Infection with VEEV


title: Primary meningioma, male 1

description: Library name: PM1

value: meningioma tumor

value: male


title: Brain_D6

description: Infected_day 6

value: Wildtype


title: o4R + MSA-oIL2-1

description: Library name: A10

value: MSA-orthogonal IL-2


title: Platelet_iPAH7

city: Guangzhou

first: Qianwen

last: Bai

state: GuangDong

address: Dongfeng Road 195

institute: the First Affiliated Hospital of Guangzhou Medical University

description: Library name: Sample12

data_processing:
Paired-end RNA sequencing reads were processed using a suite of open-source tools, including fastq for preprocessing, HISAT2 for alignment, SAMtools for post-alignment processing, and featureCounts for read counting.
Assembly: HISAT2 for alignment
Supplementary files format and content: csv files include counts values for each sample

source_name: blood

extract_protocol:
Total RNA was extracted from platelets of idiopathic pulmonary arterial hypertension (iPAH) patients and healthy controls using Trizol Reagent (15596-026, Invitrogen, USA). Messenger RNA (mRNA) was enriched by depleting ribosomal RNA (rRNA) with the rRNA Depletion Kit (NEBNext, MA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina and assessed with an Agilent 4200 Bioanalyzer

value: blood

value: platelet

tag: diagnosis


title: Primary meningioma, female 6

description: Library name: PF6

tag: Sex

value: female


title: Sample 93_Healthy Control_7

value: Whole blood

value: M

tag: etiology

value: C


title: o2R + IL-2-3

description: Library name: A9

value: spleen

value: primary mouse T cells

tag: batch


title: Brain_D2

description: Infected_day 2

value: Brain

value: Immune cells


title: o2R + MSA-oIL2-2

description: Library name: A5

value: T cells

value: Orthogonal cytokine receptors expression

value: Same batch


title: Brain_D4

description: Infected_day 4

value: Infection with VEEV


title: o2R + IL-2-2

description: Library name: A8


title: Sample 92_Healthy Control_6

value: F

tag: collection tube

value: PAXgene

value: A

value: Control


title: Primary meningioma, female 3

description: Library name: PF3

value: meningioma tumor


title: Sample 87_Healthy Control_1

tag: condition


title: Platelet_iPAH8

description: Library name: Sample13

value: blood

value: platelet

value: idiopathic pulmonary arterial hypertension (iPAH)


title: o4R + MSA-oIL2-2

description: Library name: A11

tag: treatment

value: MSA-orthogonal IL-2


title: o2R + MSA-oIL2-3

description: Library name: A6

value: spleen


title: Platelet_iPAH4

description: Library name: Sample9


title: Recurrent meningioma, male 2

description: Library name: RM2

value: male


title: Sample 86_Paediatric pneumonia_86

value: Whole blood

value: M

value: DV

value: Pneumonia


title: Platelet_iPAH3

description: Library name: Sample8


title: Sample 89_Healthy Control_3

value: C


title: Primary meningioma, female 2

description: Library name: PF2

value: female


title: No-ICD + MSA-oIL2-2

description: Library name: A2

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: Same batch


title: Sample 88_Healthy Control_2

value: PAXgene

value: A

value: Control


title: Platelet_iPAH6

description: Library name: Sample11

value: blood

value: platelet

value: idiopathic pulmonary arterial hypertension (iPAH)


title: Sample 84_Paediatric pneumonia_84

value: PB


title: Platelet_iPAH5

description: Library name: Sample10


title: Primary meningioma, female 1

description: Library name: PF1

value: meningioma tumor

value: male


title: No-ICD + MSA-oIL2-3

description: Library name: A3

value: spleen

value: MSA-orthogonal IL-2


title: Recurrent meningioma, male 4

description: Library name: RM4


title: Sample 85_Paediatric pneumonia_85

value: Whole blood

value: M

value: Pneumonia


title: Platelet_iPAH2

description: Library name: Sample7


title: No-ICD + MSA-oIL2-1

description: Library name: A1

value: primary mouse T cells

value: T cells


title: Platelet_iPAH1

description: Library name: Sample6


title: Recurrent meningioma, female 1

description: Library name: RF1

value: female


title: Platelet_HC4

description: Library name: Sample4

value: healthy control


title: Sample 83_Paediatric pneumonia_83

value: U

value: PAXgene

value: A


title: Platelet_HC5

description: Library name: Sample5

value: blood

value: platelet


title: Sample 80_Paediatric pneumonia_80

value: F

value: PB


title: SAS cells, siIGF2BP1, siRNA knowdown 1

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

description: Library name: NB_73

data_processing:
Raw fastq files were merged by zcat command, if reads R1/R2 consisted of multiple files.
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 2.8) with parameters -j 0 -q 20 -O 7 -m 20 –trim-n.
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --rna-strandness RF --dta -k 5.
Secondary alignments were filtered out using samtools (v 1.10).
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 2 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.110).
Assembly: hg38
Supplementary files format and content: Comma-separated text files including raw counts for each sample.

source_name: SAS

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: SAS

value: squamous cell cancer derived cell line

value: IGF2BP1 knockdown


title: Sample 79_Paediatric pneumonia_79

value: Whole blood


title: SAS cells, siIGF2BP1, siRNA knowdown 2

description: Library name: NB_74


title: Platelet_HC2

description: Library name: Sample2


title: GEX_HeLaSVF

city: Urbana

first: Yujun

last: Feng

state: IL

address: 1304 W Green St.

department: Materials Science and Engineering

institute: University of Illinois, Urbana-Champaign

description: GEX: 3' polyA mRNA read. Read 1 file contains barcode and UMI reads. Read 2 file contains cDNA reads. L1 and L2 are 2 index reads.

data_processing:
CellRanger v7.1.0 count is used for both transcripts and HTO data all three tests and for each test, CellRanger v7.1.0 generated a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz that contains both transcripts and HTO data
Assembly: mm39, hg38
Supplementary files format and content: CellRanger Output files for mouse spleen cells mix test: sp_barcodes.tsv.gz, sp_features.tsv.gz, sp_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for HeLa-SVF mixing test: SVF_barcodes.tsv.gz, SVF_features.tsv.gz, SVF_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for Young and Aged mouse SVF mixing test: SVF_YA_barcodes.tsv.gz, SVF_YA_features.tsv.gz, SVF_YA_matrix.mtx.gz

source_name: mouse adipose

extract_protocol:
Cells are loaded to Gel-bead-in-emulsion (GEM) microfluidic device by Chromium Next GEM Single-Cell 3’ dual-index kit version 3.1 with Feature Barcode technology for Cell Surface Protein (10X Genomics, CA) following the manufacturer’s protocols.
The cell transcripts and HTO barcode libraries are prepared per to the manufacturer's protocol:  https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000317_ChromiumNextGEMSingleCell3-v3.1_CellSurfaceProtein_RevD.pdf

treatment_protocol: For spleen cells and HeLa cells, no sorting or enrichment was implemented, and samples are directly loaded for library preparation after labeling. For SVF cells, live cell enrichment (Miltenyi Biotech) and CD45+ enrichment (Miltenyi Biotech) are implemented after cell labeling, then cells are loaded to single-cell transcript extraction step.

value: mouse adipose

value: HeLa

value: CD45+ stromal vascular fraction cell

tag: library type

value: mRNA

value: mixed sample( HeLa cell, obese mice)


title: GEX_spleen

source_name: mouse spleen

value: mouse spleen

value: spleen cells

value: mixed sample( lean mice, obese mice)


title: Sample 82_Paediatric pneumonia_82

value: M

value: PAXgene

value: A

value: Pneumonia


title: SurfaceP_HeLaSVF

description: HTO: 3' barcode. A read. Read 1 file contains cell barcode and UMI reads. Read 2 file contains barcode reads. L1 and L2 are 2 index reads.

library_source: other

data_processing:
CellRanger v7.1.0 count is used for both transcripts and HTO data all three tests and for each test, CellRanger v7.1.0 generated a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz that contains both transcripts and HTO data
Assembly: mm39, hg38
Supplementary files format and content: CellRanger Output files for mouse spleen cells mix test: sp_barcodes.tsv.gz, sp_features.tsv.gz, sp_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for HeLa-SVF mixing test: SVF_barcodes.tsv.gz, SVF_features.tsv.gz, SVF_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for Young and Aged mouse SVF mixing test: SVF_YA_barcodes.tsv.gz, SVF_YA_features.tsv.gz, SVF_YA_matrix.mtx.gz
Library strategy: CITE-seq

molecule: other

value: HTO

tag: hto

value: developed Nanocoding method and molecules


title: SAS cells, siC, siRNA control 1

description: Library name: NB_70

value: SAS

value: squamous cell cancer derived cell line

value: WT


title: MEFs, C865S, SeV rep 1

city: Hangzhou

first: Bin

last: Wang

state: Zhejiang

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

institute: Zhejiang University

description: Library name: C865S_SeV_rep1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to GRCm38/mm10 using CLC genomic benchwork with the following parameters: mismatch cost of 2, insertion cost of 3, deletion cost of 3, length fraction of 0.8, and similarity fraction of 0.8.
Read count extraction and normalization were also performed using CLC genomic benchwork.
Assembly: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include count values for each sample.

source_name: embryonic fibroblasts

growth_protocol: MEFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Rig-IWT/WT and Rig-IC865S/C865S MEFs were infected with SeV or PBS for 12 hours.

value: embryonic fibroblasts

value: MEFs

value: mouse embryonic fibroblasts

value: Rig C865S knock in

value: SeV, 12 hours


title: SAS cells, siIGF2BP1, siRNA knowdown 3

description: Library name: NB_75

value: IGF2BP1 knockdown


title: o2R + MSA-oIL2-1

description: Library name: A4

value: spleen

value: primary mouse T cells

value: T cells

value: Orthogonal cytokine receptors expression

value: MSA-orthogonal IL-2

value: Same batch


title: Cell_SurfaceP_spleen

value: mouse spleen

value: spleen cells

value: HTO

value: mixed sample( lean mice, obese mice)


title: Sample 81_Paediatric pneumonia_81

data_processing:
Quality control of raw data was carried out using fastq.gzC.
Alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts.
Assembly: Ensembl GCh38 genome
Supplementary files format and content: Coma-delimited excell file with raw counts (Counts_raw_data.csv)
Supplementary files format and content: Coma-delimited excell file with normalized counts (Normalized_data.csv)

value: Whole blood

value: F

value: PB

value: PAXgene

value: A

value: Pneumonia


title: Platelet_HC3

description: Library name: Sample3

value: blood

value: platelet

value: healthy control


title: SAS cells, siC, siRNA control 3

description: Library name: NB_72

value: SAS

value: squamous cell cancer derived cell line

value: WT


title: Recurrent meningioma, male 1

description: Library name: RM1

value: meningioma tumor

value: male


title: MEFs, C865S, SeV rep 2

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

description: Library name: C865S_SeV_rep2

value: embryonic fibroblasts

value: MEFs

value: mouse embryonic fibroblasts

value: Rig C866S knock in

value: SeV, 12 hours


title: SAS cells, siC, siRNA control 2

description: Library name: NB_71


title: Sample 78_Paediatric pneumonia_78

value: Whole blood

value: F

value: U


title: MEFs, WT, SeV rep 2

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

description: Library name: WT_SeV_rep2


title: MEFs, WT, PBS rep 1

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

description: Library name: Control_rep1

value: PBS, 12 hours


title: Sample 74_Paediatric pneumonia_74

value: PAXgene

value: A

value: Pneumonia


title: Sample 77_Paediatric pneumonia_77

value: M

value: PB


title: hRMECs, 1% O2+r-APOC3, 24h

first: guanrong

last: Wu

address: 106 Zhongshan Er Road

institute: Guangdong Provincial People's Hospital

description: Library name: Sample 4

data_processing:
The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy.
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include RPKM values for each Sample

source_name: retina

growth_protocol: hRMECs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and  1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
After pretreating hRMECs under indicated conditions for 24 hours, total RNA was extracted using TRIZOL reagent. Total RNA was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) and library quality was assessed on the Agilent 5400 system (Agilent，USA).

value: retina

value: human retinal microvascular endothelial cells


title: MEFs, WT, SeV rep 1

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

description: Library name: WT_SeV_rep1

value: WT


title: Patient1093, Relapsed-Refractory, scRNAseq

city: Aurora

first: Dan

last: Sherbenou

state: CO

address: 12700 E 19th Ave Box B170

institute: UC Denver Hematology

description: posttx

data_processing:
Cellranger v.3.1.0
Assembly: Human GRCh38
Supplementary files format and content: Feature-barcode matrices

source_name: Bone marrow aspirate

extract_protocol:
Bone marrow aspirates from one patient at three timepoints (diagnosis, first relapse, relapse/refractory) were collected at the University of Colorado Anschutz Medical Campus after informed consent and protocol approval. Mononuclear cells were isolated using SepMate Ficoll tubes (Stemcell Technologies) and cryopreserved in Iscove M odified Dulbecco medium with 45% fetal bovine serum and 10% dimethyl sulfoxide. Bone marrow samples were thawed, resuspended in DNAse and washed in PBS . A sort using a BD FACSAria (BD) was performed to remove dead cells.
Single cells were captured using Chromium X Series (10X G enomics ) and sequen ced on a NovaSeq6000 (Illumina).

value: Bone marrow aspirate

tag: time

value: Relapsed-Refractory


title: MEFs, WT, PBS rep 2

address: 浙江省杭州市浙江大学紫金港校区纳米楼575

description: Library name: Control_rep2

value: embryonic fibroblasts

value: MEFs

value: mouse embryonic fibroblasts


title: Sample 76_Paediatric pneumonia_76

source_name: Whole blood

extract_protocol:
RNA was extracted using PAXgene Blood RNA Kit (IVD) and Tempus™ Spin RNA Isolation Kit
The Illumina’s TruSeq RNA Sample Preparation Kit was used for library preparation, and ribosomal and globin RNA depletion was performed using the Illumina® Ribo-Zero Gold kit

value: Whole blood


title: Sample 75_Paediatric pneumonia_75

value: F


title: Sample 72_Paediatric pneumonia_72

value: U


title: hRMECs, r-APOC3, 24h

description: Library name: Sample 3


title: hRMECs, 1% O2, 24h

description: Library name: Sample 2


title: 9-Sup: Aged kidney tissue replicate 2

city: shenyang

first: xiuli

last: Guo

address: No. 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province

institute: The First Hospital of China Medical University

description: total RNA without m6A

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: scanned using an Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level”, “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities of RNA. Differentially m6A-methylated RNAs or differentially expressed RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

label_protocol: The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Ki

extract_protocol: Trizol extraction total RNA was performed according to the manufacturer's instructions and quantified using the NanoDrop ND-1000.the total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”.

tag: age

value: age 85

value: aged kidney


title: 8-Sup: Aged kidney tissue replicate 3

description: total RNA without m6A

value: age 83


title: Uterus, 3.5dpc, model, PBMC-hCG, rep5

city: Kyoto

first: Yoshimi

last: Kitawaki

state: Kyoto

address: 54 Shogoin-kawahara-cho, Sakyo-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Trimmomatic tool.
Trimmed reads were mapped to the reference genome (mm10) with HISAT2.
Transcript assembly was performed using Stringtie.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes TPM values for each sample

source_name: Uterus

growth_protocol: B6D2F1 female mice (age: 8–12 weeks) in the estrous cycle were mated with males. The morning of the vaginal plug was designated as day 0.5.

extract_protocol:
Total RNA was extracted from the uterine tissues on the evening of day 3.5 (18:00) using Invitrogen PureLink RNA mini kit (Thermo Fisher Scientific)  with on-column DNase I treatment.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: PBMCs after culture with or without hCG were administered intrauterine on day 1.5. RU486 was administered subcutaneously on day3.5 morning to all but the control group.

value: Uterus

value: PBMC-hCG, RU486


title: 4-Sup: Control kidney tissue replicate 3

description: total RNA without m6A

value: age 43

value: control kidney


title: Platelet_HC1

description: Library name: Sample1

value: blood

value: platelet

value: healthy control


title: Patient1093, Diagnosis, scRNAseq

description: dx

value: Bone marrow aspirate

value: Diagnosis


title: Uterus, 3.5dpc, model, PBMC-hCG, rep4

value: WT


title: Sample 73_Paediatric pneumonia_73

first: Alberto

last: Gómez-Carballa

institute: GENVIP research group

value: PB

value: PAXgene

value: A

value: Pneumonia


title: Patient1093, First Relapse, scRNAseq

description: relapse

value: First-Relapse


title: Uterus, 3.5dpc, model, PBMC-hCG, rep3


title: BCM-15006_EGFP-

city: Houston

first: Michael

middle: T

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

description: 10X Genomics

data_processing:
Barcode processing, gene counting, and alignment were performed using the Cell Ranger Single Cell software v.6.1.2 (SUM159) or v7.0.1 (BCM-4272 and BCM-15006) (10X Genomics)
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast

extract_protocol:
Xenograft tumors were harvested and digested using 5mL digestion media (phenol red-free DMEM/F12 [Corning cat. 16-405-CV], 100mg/mL gentamicin [Worthington, cat. LS004176], 250U/mL collagenase II [Worthington cat. LS004174] and 2mg/mL DNase I [Stemcell, cat. 07900]) per 1g tumor at 37oC in a gentleMACS dissociator (Miltenyi). The tumor digestion was passed through a 200mM filter and centrifuged at 300g for 1 minute. Red blood cells were lysed by adding 9mL ddH2O to the cell pellet for 20 seconds and lysis was stopped by the addition of 1mL 10X PBS. To dissociate cell clumps further, the cell suspension was centrifuged at 300 g for 1 minute, then resuspended in TrypLE Express (Gibco, cat. 12605-010) for 5 minutes. To stop the digestion, 9mL of PBS was added, and the cell suspension was passed through a 40mm cell strainer. SUM159, BCM-4272, and BCM-15006 were sorted based on fluorescent reporter activity (SUM159: EGFP+/mNeptune2+, EGFP+/dsRed+, EGFP-/mNeptune2+, EGFP-/dsRed+; BCM-4272 and BCM-15006: EGFP+ or EGFP-).
Single-cell gene expression libraries were prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification.

value: Breast

value: Breast cancer patient-derived xenograft

value: SCID/beige

tag: sorted cells

value: EGFP-


title: hRMECs, 24h

description: Library name: Sample 1

value: retina

value: human retinal microvascular endothelial cells


title: Uterus, 3.5dpc, model, PBMC-hCG, rep2

value: Uterus

value: PBMC-hCG, RU486


title: Uterus, 3.5dpc, model, PBMC-hCG, rep1


title: Sample 69_Paediatric pneumonia_69

city: Santiago de Compostela

address: Choupana sn

value: Whole blood

value: M

value: U


title: BCM-15006_EGFP+

description: 10X Genomics

tag: cell line

value: EGFP+


title: Uterus, 3.5dpc, model, PBMC, rep5

value: WT

value: PBMC, RU486


title: Sample 71_Paediatric pneumonia_71

value: PAXgene

value: A


title: Sample 68_Paediatric pneumonia_68

value: DB

value: Pneumonia


title: BCM-4272_EGFP-

description: 10X Genomics

value: Breast

tag: cell type

value: Breast cancer patient-derived xenograft


title: 1-Sup: Control kidney tissue replicate 1

description: total RNA without m6A

value: age 43

tag: tissue

value: control kidney


title: 5-Sup: Aged kidney tissue replicate 1

description: total RNA without m6A

value: age 72

value: aged kidney


title: BCM-4272_EGFP+

description: 10X Genomics

tag: genotype

value: SCID/beige


title: Sample 67_Paediatric pneumonia_67

value: Whole blood


title: 5-IP: Aged kidney tissue replicate 1

description: total RNA with m6A


title: Sample 66_Paediatric pneumonia_66

value: M


title: 8-IP: Aged kidney tissue replicate 3

description: total RNA with m6A

value: age 83


title: Sample 70_Paediatric pneumonia_70

value: F

value: U


title: SUM159_EGFP-_dsRed+

description: 10X Genomics

value: Breast cancer cell line


title: 9-IP: Aged kidney tissue replicate 2

description: total RNA with m6A

value: age 85


title: Sample 65_Paediatric pneumonia_65

value: PB

value: PAXgene

value: A


title: 11-IP: Control kidney tissue replicate 2

description: total RNA with m6A

value: age 36


title: 1-IP: Control kidney tissue replicate 1

description: total RNA with m6A


title: Uterus, 3.5dpc, model, PBMC, rep2

value: Uterus

value: WT

value: PBMC, RU486


title: Uterus, 3.5dpc, model, PBMC, rep1


title: 4-IP: Control kidney tissue replicate 3

description: total RNA with m6A

value: age 43

value: control kidney


title: Uterus, 3.5dpc, model, PBMC, rep4


title: Sample 64_Paediatric pneumonia_64

value: Pneumonia


title: SUM159_EGFP+_dsRed+

description: 10X Genomics

value: Breast

value: SCID/beige


title: SUM159_EGFP-_Nep+

description: 10X Genomics


title: Uterus, 3.5dpc, model, rep5


title: Sample 63_Paediatric pneumonia_63

value: Whole blood

value: M


title: Uterus, 3.5dpc, model, PBMC, rep3


title: Uterus, 3.5dpc, model, rep4


title: Uterus, 3.5dpc, model, rep3


title: SUM159_EGFP+_Nep+

description: 10X Genomics


title: Jurkat cells shAKR1B1_1_2

city: Harbin

first: Huitao

last: Fan

state: Heilongjiang

address: 23 Youzheng street

department: NHC Key Laboratory of Cell Transplantation

institute: The First Affiliated Hospital of Harbin Medical University

data_processing:
The quality of input data in following process was verified using FastQC (v0.11.9).
We used STAR (v 2.7.0f) to map reads to the reference genome Homo sapiens (GRCh38.p13, v36) and used RseQC (v3.38.4) to verified mapping quality.
The verified alignment data was quantified by STAR (--quantMode GeneCounts) according to genome annotation file (gencode.v36.annotation.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes RPKM value for each sample

source_name: Cell line

growth_protocol: Jurkat cells were cultured in RPMI1640, supplemented with 10% FBS and 1% P/S in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested by TRNA Easypure RNA Kit. 1.3μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactuer's ptotocal.

treatment_protocol: ShRNA targeting human AKR1B1 (shAKR1B1_1) were designed and cloned into pLKO.1-puro lentiviral vector.  Packaging of lentivirus was performed according to standard procedures. In brief, HEK 293T cells were transfected with target plasmid as well as plasmids psPAX2 (Addgene, #12260) and pMD2.G (Addgene, #12259) to make lentivirus particles. Infected leukemia cells were selected with 2 μg/ml puromycin

value: Cell line

value: Jurkat

value: Acute lymphoblastic leukemia (ALL)

value: AKR1B1 knockdown

value: no treatment


title: EO771 tumor, PCSK9 mouse, biol rep6

city: New York

first: Wenbin

last: Mei

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm39) using STAR aligner v2.7.10b at default settings.
Expression of genes was quantified with featureCounts v2.0.6.
Assembly: GRCm39
Supplementary files format and content: Comma separated files including raw counts of each sample

source_name: breast tumor

extract_protocol:
Total RNA from primary tumors from mice was isolated with the Total RNA Purification Kit (Norgen Biotek, 17200) with 5ul/ml of RNasin Plus (Promega, N2615) and 10ul/ml of 2-mercaptoethanol (Sigma-Aldrich, M6250) added to buffer RL.
Libraries were constructed from 1μg of total RNAs using the TruSeq RNA Library Prep Kit (Illumina, RS-122-2001)

value: breast tumor

value: breast cancer cell


title: Jurkat cells shAKR1B1_1_3


title: EO771 tumor, PCSK9 V474I mouse, biol rep7


title: Il10-eGFP-Positive_2

city: Birmingham

first: David

last: Bending

address: IBR

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

description:
Library name: Sample 4
P2

data_processing:
Libraries were sequenced using the NextSeq 500 using a v2.5 150 cycles Mid output (75 single read) flow cell. Cluster generation and sequencing was then performed and sequencing data filtered and trimmed to remove UMIs and FASTQ files generated. FASTQ files were then processed by Lexogen as follows. FASTQC files were generated and Bbduk v35.92 from the bbmap suite was used for trimming of low-quality tails, poly(A)read-through and adaptor contamination. STAR v2.5.2a aligner was used for alignment of reads to the mouse GRCm38 (mm10) genome. HTSeq-count v0.6.0 was used to generate read counts for mRNA species and mapping statistics. Raw read counts in the .txt format were used for further analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: normrlognamed.csv file includes regularised Log2 normalised expression values for each sample.
Supplementary files format and content: raw.txt file with raw  counts for every gene and every sample

source_name: Spleen

extract_protocol:
RNA was extracted from lysates using the PureLink RNA Micro Scale Kit (Invitrogen) according to the manufacturer’s instructions.
Library prep kit: Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina. RNA input for prep: 5ng. The protocol for low input samples was followed, this includes alterations to incubation times. Unique Molecular Identifiers (UMIs) were used for the evaluation of input and PCR duplicates and to eliminate amplification bias. 22 cycles of PCR was performed. 4nM of pooled library was sequenced.

value: Spleen

value: CD4+ T cell

value: Tg4 Nr4a3-Tocky IL-10 GFP mice


title: Sample 60_Paediatric pneumonia_60

value: DB

value: PAXgene

value: A


title: Il10-eGFP-Negative_2

description:
Library name: Sample 2
N2


title: Il10-eGFP-Negative_1

description:
Library name: Sample 1
N1


title: Jurkat cells shAKR1B1_1_1


title: Sample 61_Paediatric pneumonia_61

value: F

value: PB

value: Pneumonia


title: EO771 tumor, PCSK9 mouse, biol rep5


title: Uterus, 3.5dpc, model, rep2

value: Uterus

value: WT


title: Uterus, 3.5dpc, control, rep5


title: EO771 tumor, PCSK9 mouse, biol rep4


title: Jurkat cells shControl_3

value: Cell line

value: Jurkat

value: Control


title: Jurkat cells shControl_2

value: Acute lymphoblastic leukemia (ALL)

value: no treatment


title: EO771 tumor, PCSK9 mouse, biol rep3

value: breast tumor

value: breast cancer cell


title: Uterus, 3.5dpc, control, rep4


title: Jurkat cells shControl_1


title: Sample 57_Paediatric pneumonia_57

value: Whole blood

value: M


title: EO771 tumor, PCSK9 mouse, biol rep2


title: Sample 58_Paediatric pneumonia_58

value: U


title: Sample 62_Paediatric pneumonia_62

value: PAXgene


title: Sample 55_Paediatric pneumonia_55

value: A


title: 11-Sup: Control kidney tissue replicate 2

description: total RNA without m6A

value: age 36

value: control kidney


title: RNAseq Human PT replicate 3

city: Milwaukee

first: Sridhar

last: Rao

address: 8797 Watertown Plank Rd

institute: Versiti Blood Research Institte

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using STAR aligner
Gene expression in terms of count data was determined by featureCounts
DESeq2 package was used to perform differential gene expression analysis
Assembly: hg38
Supplementary files format and content: .csv file for normalized count data and significant differentially expressed genes
Supplementary files format and content: bigwig file for the signal data

source_name: Kidney

growth_protocol: Kidney segments were dissected from human Patients were used for this study

extract_protocol:
Small pieces of kidney segments from both human and rat were subjected to multiple rounds of collagenase digestion to isolate mTAL and PT segments
Nuclei were isolated from the PT and mTAL segments and RNA was isolated and sent them to the Novaseq for library preparation and sequencing

value: Kidney

value: Proximal tubule


title: Uterus, 3.5dpc, control, rep2

value: Uterus

value: WT


title: EO771 tumor, PCSK9 mouse, biol rep1


title: Uterus, 3.5dpc, model, rep1


title: Sample 59_Paediatric pneumonia_59

value: PB

value: Pneumonia


title: RNAseq Human PT replicate 1

value: Control


title: EO771 tumor, PCSK9 V474I mouse, biol rep6


title: Sample 54_Paediatric pneumonia_54

value: F


title: Sample 56_Paediatric pneumonia_56


title: Uterus, 3.5dpc, control, rep1


title: Sample 53_Paediatric pneumonia_53


title: WT_R3_female_HiC

city: Moscow

first: Ekaterina

last: Khrameeva

address: Bolshoy Boulevard 30, bld. 1

department: Center of Life Sciences

country: Russia

institute: Skolkovo institute of science and technology

data_processing:
The resulting Hi-C sequencing reads were processed using the distiller software (https://github.com/open2c/distiller-nf). Reads not corresponding to valid contacts were filtered out. Residual read pairs were assigned to a particular restriction fragment in the genome to produce a raw contact matrix. We downsampled all raw contact maps to the same total number of contacts. An iterative correction was applied to normalize the raw contact matrix. The obtained Hi-C maps binned from 2-kb to 1-Mb resolutions were further used as an input for downstream analyses.
Assembly: GRCm38 (mm10)
Supplementary files format and content: processed data files include files in Hi-C mult-resolution (.mcool) format suitable for analysis with cooler library for Python.

source_name: cortex

extract_protocol:
The mice were sacrificed using isoflurane and perfused with cold PBS. The cortices were isolated on ice, and caution was taken to avoid keeping the isolated cortices on ice for more than 10–15 minutes. The cortical tissues were homogenized in 500 μL of ice-cold low sucrose buffer using a Dounce homogenizer on ice. The homogenate volumes were measured, and equal amounts of low sucrose buffer with 2% formaldehyde were added to achieve a final 1% formaldehyde low sucrose buffer. The fixation times were standardized for all samples, and glycine was added to quench the crosslinking reaction. After centrifugation, the pellets were resuspended in 3 mL of low sucrose buffer with PIC and homogenized using a mechanical homogenizer. Iodixanol gradients were prepared to isolate nuclei, and the samples were centrifuged. The nuclei interphase fractions were collected, diluted, and washed before staining with NeuN-PE for sorting. The sorted immunolabeled nuclei were processed and filtered through a 35-μm cell strainer for fluorescence-activated sorting of fixed nuclei. We performed Hi-C in neurons isolated using FACS from the cortex tissue of the aging, adult, and control mice. Hi-C was performed using the DpnII restriction enzyme, according to a previously published protocol at  https://pubmed.ncbi.nlm.nih.gov/34308377/
We performed Hi-C in neurons isolated using FACS from the cortex tissue of the aging, adult, and control mice. Hi-C was performed using the DpnII restriction enzyme, according to a previously published protocol 19. Each Hi-C library was sequenced to 150-350 million paired-end reads. All details regarding library construction protocol can be found at https://pubmed.ncbi.nlm.nih.gov/34308377/

value: cortex

value: Cortex neurons

tag: strain


title: RNAseq Human mTAL replicate 3

value: medullary Thick Ascending Limb


title: RNAseq Human mTAL replicate 2


title: EO771 tumor, PCSK9 V474I mouse, biol rep4

value: breast tumor

value: breast cancer cell


title: EO771 tumor, PCSK9 V474I mouse, biol rep3


title: WT_R2_female_HiC


title: WT_R1_male_HiC


title: Sample 51_Paediatric pneumonia_51

value: Whole blood

value: M

value: PAXgene


title: Uterus, 3.5dpc, control, rep3


title: Sample 52_Paediatric pneumonia_52

value: A


title: RNAseq Human mTAL replicate 1

value: Kidney


title: young_R3_female_HiC


title: EO771 tumor, PCSK9 V474I mouse, biol rep2


title: RNAseq Human PT replicate 2

value: Proximal tubule


title: Sample 50_Paediatric pneumonia_50

value: U


title: EO771 tumor, PCSK9 V474I mouse, biol rep5


title: young_R2_female_HiC


title: Human PT replicate 4

description:
HPT7
ATAC_HPT_consensus_peaks_signaldata.bw

data_processing:
ATAC-seq reads were aligned to the hg38 (human derived sample) and rn7 (rat derived data) genome assembly using bowtie2 and after removing the mitochondrial read and duplicate reads, all replicates from each sample were merged
MACS2 was used to call peak from these merged bam files as well as each replicate bam files using this criteria  -nomodel-extsize200 -shift 100 -q0.01
The alignmed reads was also used to perform motif enrichment by HOMER
Assembly: hg38 and rn7
Supplementary files format and content: NarrowPeak
Supplementary files format and content: bigwig

extract_protocol:
Small pieces of kidney segments from both human and rat were subjected to multiple rounds of collagenase digestion to isolate mTAL and PT segments
Nuclei were isolated from the PT and mTAL segments and subjected to the transposition reaction with Illlumina transposase in the appropriate buffer. Library fragments were amplified with indexing primers


title: Human PT replicate 3

description:
HPT5
ATAC_HPT_consensus_peaks_signaldata.bw


title: Sample 49_Paediatric pneumonia_49

value: DB


title: Il10-eGFP-Positive_1

description:
Library name: Sample 3
P1

value: Spleen

value: CD4+ T cell

value: Tg4 Nr4a3-Tocky IL-10 GFP mice


title: Human PT replicate 2

description:
HPT3
ATAC_HPT_consensus_peaks_signaldata.bw

value: Control


title: Sample 47_Paediatric pneumonia_47

value: F

value: PV

value: Pneumonia


title: young_R1_male_HiC

value: cortex

value: Cortex neurons


title: EO771 tumor, Pcsk9 WT mouse, biol rep8

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm38) using STAR aligner v2.7.10b at default settings.
Expression of genes was quantified with featureCounts v2.0.6.
Assembly: GRCm38
Supplementary files format and content: Comma separated files including raw counts of each sample

value: breast tumor

value: breast cancer cell


title: Human PT replicate 1

description:
HPT1
ATAC_HPT_consensus_peaks_signaldata.bw


title: Sample 46_Paediatric pneumonia_46

value: Whole blood

value: M

value: PB

value: PAXgene


title: EO771 tumor, Pcsk9 WT mouse, biol rep5


title: EO771 tumor, Pcsk9 WT mouse, biol rep7


title: old_R3_female_HiC


title: old_R2_female_HiC


title: EO771 tumor, Pcsk9 WT mouse, biol rep6


title: old_R1_male_HiC


title: EO771 tumor, Pcsk9 KO mouse, biol rep7


title: Human mTAL replicate 2

description:
HMTAL8
ATAC_HmTAL_consensus_peaks_signaldata.bw

value: Kidney

value: medullary Thick Ascending Limb


title: Control Wildtype Neuron 6

city: Madison

first: Rozalyn

last: Anderson

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

description:
Rsubread_edgeRglm_GENE_01_tg_con_vs_wt_con.csv
Rsubread_edgeRglm_GENE_01_tg_con_vs_wt_con.csv

data_processing:
Sequencing reads were trimmed to remove adaptors and low-quality bases
Trimmed reads were aligned to mm10 reference genome using STAR aligner
Differential gene expression analysis was conducted via EdgeR generalized linear model method
Assembly: mm10
Supplementary files format and content: excel file from differential gene expression anaylsis conducted in EdgeR

source_name: neuron

growth_protocol: Upon first change to Neurobasal media, neurons were treated with 1 uM AraC (cytosine arabinoside) to eliminate glial cell populations. Media was changed by ½ volume every 3–4 days until experiments. To induce neurofibrillary tau tangle accumulation in the P301S, transgenic neurons were seeded with 3 g/mL of pre-formed fibrils (PFF) (StressMarq) on day 7 in vitro and then cultured for 18 days before AdipoRon treatment.

extract_protocol:
RNA was collected using Direct-zol RNA kit (Zymo Research).
RNA libraries were generated following the Illumina TruSeq RNA Sample preparation guide. mRNA libraries were generated using NEBNext Poly(A) mRNA Magnetic isolation module and NEBNext Ultara RNA library prep kit.

treatment_protocol: Cells were treated with 10 mM AdipoRon or DMSO (vehicle control) accompanied by a 50% media change for 24 hours prior to RNA extraction.

value: neuron

value: wildtype

value: DMSO


title: Sample 45_Paediatric pneumonia_45

value: U

value: A


title: Sample 43_Paediatric pneumonia_43

value: DB


title: Control Wildtype Neuron 5


title: EO771 tumor, Pcsk9 KO mouse, biol rep6


title: Sample 44_Paediatric pneumonia_44

value: Pneumonia


title: Sample 48_Paediatric pneumonia_48

value: F


title: Control Wildtype Neuron 3


title: hNMSO,day56,neural compartment

city: Shanghai

first: Jinkui

last: Zhu

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

institute: ShanghaiTech University

data_processing:
To obtain count matrices, reads were aligned to human genome GRCh38 (v 3.0.0, provided by 10X genomics) using Cell Ranger (v 6.1.2) pipeline with the default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoids

extract_protocol:
For single-nucleus sequencing, organoids of the same stage were pooled together and were frozen immediately at - 80℃.  The Chromium Nuclei Isolation Kit with RNase Inhibitor was used according to the manufacturer’s instructions to isolate nuclei for subsequent sequencing steps. In short, frozen organoids were homogenized with a pestle in the Lysis Buffer and passed through a column. Next, the debris was removed via centrifugation in the Debris Removal Buffer.
For single-nucleus sequencing, nuclei were used to generate cDNA libraries using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index). Briefly, cell nuclei were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs), and microfluidic cell nuclei were streamed at limiting dilution into a stream of Single Cell 3’ v3.1 Gel Beads, and then a stream of oil. After lysis, an Illumina TruSeq Read 1, a 16 base pair 10x Barcode, a 12 bp unique molecular identifier (UMI), a 30 nt poly(dT) sequence, and a Capture Sequence 1 were released and mixed with the lysate and the Master Mix containing the RT reagents, full-length cDNA from poly-adenylated messenger RNA was generated. After individual droplets were broken down, homogenized, and cleaned from the remaining noncDNA with silane magnetic beads, the libraries were size-selected, followed by the addition of TruSeq Read 2, P5, P7, i7, and i5 sample indexes sequences to each selected cDNA. Finally, each library was sequenced using the Illumina Novaseq6000, read1 28bp, read2 151bp Mode.

value: organoids

value: human embryonic stem cells

value: WT

value: Differentiation according to protocol


title: EO771 tumor, PCSK9 V474I mouse, biol rep1

value: breast tumor

value: breast cancer cell


title: Sample 42_Paediatric pneumonia_42

value: Whole blood

value: PAXgene


title: EO771 tumor, Pcsk9 KO mouse, biol rep5


title: EO771 tumor, Pcsk9 KO mouse, biol rep4


title: Control Wildtype Neuron 2


title: Human mTAL replicate 1

description:
HMTAL3
ATAC_HmTAL_consensus_peaks_signaldata.bw

value: Kidney

value: medullary Thick Ascending Limb

value: Control


title: Sample 40_Paediatric pneumonia_40

value: M

value: DV


title: Sph-SKMEL28, rep1

city: Odense

first: Jakob

middle: Rask

last: Tornby

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned to the human genome assembly (GRCh38, Ensembl release 107) with STAR (v. 2.7.8a).
FeatureCounts (v. 2.0) was used to quantify exon reads.
FastQC (v. 0.11.8) and MultiQC (v. 1.10.1) was used to assess the quality of the raw sequencing data.
Assembly: GRCh38, Ensembl release 107
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy Mini Kit according to the manufacturers protocol.
For construction of libraries, the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, San Diego, CA) was used according to the manufacturer’s protocol.


title: EO771 tumor, Pcsk9 WT mouse, biol rep3


title: Sph-A375, rep3


title: Human mTAL replicate 3

description:
HMTAL9
ATAC_HmTAL_consensus_peaks_signaldata.bw


title: Sample 39_Paediatric pneumonia_39

value: PB

value: A


title: Sph-SKMEL28, rep2


title: Sph-SKMEL28, rep3


title: Sph-A375, rep2


title: AdipoRon Wildtype Neuron 6

description:
Rsubread_edgeRglm_GENE_01_tg_con_vs_wt_con.csv
Rsubread_edgeRglm_GENE_04_tg_ron_vs_wt_ron.csv

value: neuron

value: wildtype

value: 10uM AdipoRon


title: Control Wildtype Neuron 1

value: DMSO


title: EO771 tumor, Pcsk9 WT mouse, biol rep1


title: AdipoRon Wildtype Neuron 4


title: Sample 38_Paediatric pneumonia_38

value: F

value: Pneumonia


title: EO771 tumor, Pcsk9 WT mouse, biol rep2

value: breast tumor


title: AdipoRon Wildtype Neuron 5


title: Sample 37_Paediatric pneumonia_37


title: Sph-A375, rep1


title: EO771 tumor, Pcsk9 WT mouse, biol rep4

value: breast cancer cell


title: EO771 tumor, Pcsk9 KO mouse, biol rep3


title: AdipoRon Wildtype Neuron 3


title: Sample 36_Paediatric pneumonia_36

value: Whole blood


title: Sample 41_Paediatric pneumonia_41

value: PAXgene


title: FT-SKMEL28-Epi, rep2

source_name: N/TERT-1, HDF, SK-MEL-28

value: N/TERT-1, HDF, SK-MEL-28


title: EO771 tumor, Pcsk9 KO mouse, biol rep2


title: AdipoRon Wildtype Neuron 1


title: EO771 tumor, Pcsk9 KO mouse, biol rep1


title: Sample 35_Paediatric pneumonia_35


title: Sample 34_Paediatric pneumonia_34

value: PV


title: EO771 cells, sgPcsk9, shLrp1-3, biol rep4

source_name: cell line

extract_protocol:
Total RNA from cells cultured in quadruplicate was isolated with the Total RNA Purification Kit (Norgen Biotek, 17200) with 5ul/ml of RNasin Plus (Promega, N2615) and 10ul/ml of 2-mercaptoethanol (Sigma-Aldrich, M6250) added to buffer RL.
Libraries were constructed from 1μg of total RNAs using the TruSeq RNA Library Prep Kit (Illumina, RS-122-2001)

value: cell line


title: FT, rep3

source_name: N/TERT-1, HDF

value: N/TERT-1, HDF


title: Control Tau Neuron 5

description:
Rsubread_edgeRglm_GENE_01_tg_con_vs_wt_con.csv
Rsubread_edgeRglm_GENE_02_tg_ron_vs_tg_con.csv

value: Tg (hTau P301S)


title: FT, rep2


title: Sample 33_Paediatric pneumonia_33

value: PB


title: EO771 cells, sgPcsk9, shLrp1-3, biol rep3


title: Control Tau Neuron 4


title: Control Tau Neuron 3


title: FT, rep1


title: Sample 32_Paediatric pneumonia_32

value: A


title: EO771 cells, sgPcsk9, shLrp1-3, biol rep2


title: Sample 31_Paediatric pneumonia_31

value: M


title: EO771 cells, sgPcsk9, shLrp1-1, biol rep4


title: Sample 30_Paediatric pneumonia_30


title: Sample 29_Paediatric pneumonia_29

value: U


title: EO771 cells, sgPcsk9, shLrp1-3, biol rep1


title: FT-SKMEL18, rep3


title: AdipoRon Wildtype Neuron 2

value: neuron

value: wildtype

value: 10uM AdipoRon


title: EO771 cells, sgPcsk9, shLrp1-1, biol rep3


title: Control Tau Neuron 2

value: DMSO


title: FT-SKMEL18, rep2


title: FT-SKMEL18, rep1


title: Control Tau Neuron 1


title: AdipoRon Tau Neuron 5

description:
Rsubread_edgeRglm_GENE_02_tg_ron_vs_tg_con.csv
Rsubread_edgeRglm_GENE_04_tg_ron_vs_wt_ron.csv


title: FT-SKMEL28-Epi, rep1


title: Sample 28_Paediatric pneumonia_28

value: Pneumonia


title: FT-A375, rep3

source_name: N/TERT-1, HDF, A375

value: N/TERT-1, HDF, A375


title: EO771 cells, sgPcsk9, shLrp1-1, biol rep2

value: breast cancer cell


title: AdipoRon Tau Neuron 4


title: Sample 27_Paediatric pneumonia_27

value: Whole blood

value: PAXgene


title: FT-A375, rep2


title: AdipoRon Tau Neuron 3


title: FT-A375, rep1


title: EO771 cells, sgPcsk9, sh002, biol rep4


title: Sample 26_Paediatric pneumonia_26


title: AdipoRon Tau Neuron 2


title: Sample 25_Paediatric pneumonia_25

value: F


title: EO771 cells, sgPcsk9, sh002, biol rep3

value: cell line


title: Dermis, rep3

source_name: HDF

value: HDF


title: AdipoRon Tau Neuron 1

value: Tg (hTau P301S)


title: Dermis, rep2


title: Sample 22_Paediatric pneumonia_22


title: Phloroglucinol

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

description: single cell transcriptome sequencing

data_processing:
Sequences were aligned to the mm10  reference genome, the counts separated by cell, the data filtered and processed using Cell Ranger version 6.1.2 according to manufacturer recommendations
Each dataset underwent processing with Seurat (v4.3.0), which included quality control, removal of predicted doublets, and cell cycle scoring.
After defining 3,000 anchors, both datasets were integrated, 50 principal components were selected to generate a uniform manifold approximation and projection (UMAP), and clusters were identified using a resolution of 0.7.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

source_name: Bone marrow

extract_protocol:
Bone marrow was isolated from tibias and femurs through flushing with complete DMEM.  Following erythrocyte lysis, lineage negative (Lin–) cells were enriched using magnetically-activated cell separation (MACS) columns following incubation with biotinylated lineage cocktail and anti-biotin magnetic beads.  Enriched Lin– cells were stained with biotinylated lineage cocktail, anti-cKit-PE, anti-biotin-PerCP-Vio700, annexin V-FITC, and DAPI.  Cells from each mouse were sorted as Lin– cKit+ Annexin V– DAPI–, and equal numbers of cells were pooled within each group for analysis by scRNAseq.
single-cell 3' mRNA Transcriptomics; Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127 and “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3’ Reagent Kits v3.1(Dual Index) User Guide” (Document number CG000315).

treatment_protocol: Mice were treated orally with phloroglucinol for two weeks then rested for four weeks before sacrifice.

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: Phloroglucinol


title: Sample 24_Paediatric pneumonia_24

data_processing:
Quality control of raw data was carried out using fastq.gzC.
Alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts.
Assembly: Ensembl GCh38 genome
Supplementary files format and content: Coma-delimited excell file with raw counts (Counts_raw_data.csv)
Supplementary files format and content: Coma-delimited excell file with normalized counts (Normalized_data.csv)

value: M

value: PB

value: A


title: EO771 cells, sgPcsk9, sh002, biol rep1


title: Dermis, rep1


title: EO771 cells, sgPcsk9, sh002, biol rep2


title: EO771 cells, shPcsk9, PCSK9, biol rep 3

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm38) using STAR aligner v2.7.10b at default settings.
Expression of genes was quantified with featureCounts v2.0.6.
Assembly: GRCm38
Supplementary files format and content: a comma separated file including raw counts of each sample

value: 2ug/ml PCSK9


title: EO771 cells, shPcsk9, PCSK9, biol rep 4


title: Epi, rep3


title: Epi, rep2


title: Control

description: single cell transcriptome sequencing

value: Control


title: Sample 23_Paediatric pneumonia_23

value: U

value: Pneumonia


title: Sample 20_Paediatric pneumonia_20


title: Epi, rep1


title: EO771 cells, sgPcsk9, shLrp1-1, biol rep1

value: breast cancer cell


title: Sample 21_Paediatric pneumonia_21

value: Whole blood


title: Sample 19_Paediatric pneumonia_19

value: PAXgene


title: EO771 cells, shPcsk9, PCSK9, biol rep 2


title: EO771 cells, shPcsk9, PCSK9, biol rep 1


title: iNOA, donor 6, scRNAseq

city: Milano

first: Silvia

last: Gregori

state: Italy

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: iNOA, Patient,  CD3+ T cells

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Seurat data analysis workflow
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: Tab-separate files of barcodes, features, and matrix counts for each sample
Supplementary files format and content: .xlsx Single-Cell seurat metadata (Full and subset dataset sheet)

source_name: CD3+ T cells purified from peripheral blood(PBMC)

extract_protocol:
CD3+ T cells were isolated from PBMCs obtained by FER (n=5), OAT (n=4), and iNOA (n=6) subjects by magnetic beads negative selection (Miltenyi Biotech, Germany).  After generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a T100 Thermal Cycler (Bio-Rad, CA, USA) at 53 °C for 45min, followed by 85 °C for 5min, and held at 4 °C. Single-cell droplets were broken, and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing Dynabeads MyOne SILANE (10x Genomics, CA, USA). cDNA was amplified using 13 PCR cycles, and then fragmented, end-repaired, A-tailed and adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter, CA, USA) with cleanup in between steps according to the manufacturers’ instructions.
Single-cell libraries were generated through the Chromium Single-Cell Controller using the Chromium Single Cell 3′ Reagent kit v.3.1 according to the manufacturers’ instructions. (10x Genomics, CA, USA). For each donor, samples were loaded to obtain a target cell recovery of 8000 cells. The concentration of the scRNA-seq libraries was determined using Qubit dsDNA HS Assay kit (Invitrogen, MA, USA) at Qubit 3.0, and size distribution was assessed using an Agilent D1000 TapeStation system (Agilent, CA, USA). Libraries were sequenced on an Illumina NovaSeq6000 instruments with a paired-end 150-bp (performed by GENEWIZ, Germany).

value: iNOA


title: iNOA, donor 5, scRNAseq

description: iNOA, Patient,  CD3+ T cells

value: CD3+ T cells purified from peripheral blood(PBMC)


title: Sample 17_Paediatric pneumonia_17

source_name: Whole blood

value: F


title: EO771 cells, shPcsk9, BSA, biol rep 4

value: cell line

value: BSA


title: EO771 cells, shPcsk9, BSA, biol rep 3


title: iNOA, donor 4, scRNAseq

description: iNOA, Patient,  CD3+ T cells


title: iNOA, donor 3, scRNAseq

description: iNOA, Patient,  CD3+ T cells


title: EO771 cells, shPcsk9, BSA, biol rep 2


title: Sample 16_Paediatric pneumonia_16


title: Sample 15_Paediatric pneumonia_15


title: iNOA, donor 2, scRNAseq

description: iNOA, Patient,  CD3+ T cells


title: Sample 14_Paediatric pneumonia_14


title: EO771 cells, shPcsk9, BSA, biol rep 1


title: iNOA, donor 1, scRNAseq

description: iNOA, Patient,  CD3+ T cells