title: Rhabdo3, mRNA-derived cDNA

city: TOULOUSE

first: JULIE

last: BELLIERE

state: OCCITANIE

address: 1 avenue Pr Jean Poulhès, CHU TOULOUSE

institute: INSERM U1297

description: 10X Genomics

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline with default settings (v4.0.0) and aligning to the mm10 genome build and Ensembl 98 annotations.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Kidney

extract_protocol:
The kidneys were decapsulated and digested with HBSS, collagenase and DNase. The red blood cells were removed with a red blood cell lysis buffer. Cells were passed through a 40 µM filter. The filters were rinsed with PBS and thr flow through was pelleted. The cells were resuspended in PBS with viability dye (Viobility 405/452 Fixable Dye, Miltenyi Biotec, Bergisch Gladbach, Germany). 20 minutes after incubation in the dark, PBS is added to the mixture and resuspended. The cells were pelleted by centrifugation at 300g for 10 minutes. Cells were resuspended in ice cold fluorescence-activated sorting (FACS) buffer. The single cell suspension was incubated with Fc Block (Miltenyi Biotec, Bergisch Gladbach, Germany) and then incubated with antibodies.  Countbright beads (Molecular Probes; Invitrogen, Waltham, United States) was added. Flow cytometry acquisition was performed on BD-LSR Fortessa cytometer (Becton Dickinson, Franklin Lakes, NJ, United States of America).  The cells were stained with anti-CD45 – PE-Vio770 (Miltenyi Biotec, Bergisch Gladbach, Germany). The cells were then washed with PBS and sorted using the BD Influx Cell Sorter (Becton Dickinson, Franklin Lakes, NJ, United States of America) (BD Biosciences, Sortware software) (pressure 20 psi, nozzle 100µm). The single cell suspensions were prepared by following the recommendations of the Single Cell 3’ Reagent Kit User Guide (10X Genomics, Pleasanton, California, United States of America).
The single cell suspension underwent barcoding and cDNA library preparation through 10X Chromium Controller Instrument (10X Genomics, Pleasanton, California, United States of America) according to the manufacturer’s instructions (CG000206 protocol). The Next Gel Bead-In-Emulsion (GEMs) technology (10x Genomics, Pleasanton, California, United States of America) provides a reagent delivery system where cells are individualized into nanoliter scale droplets with one bead, after which preparation of sequencing libraries is performed such that all the cDNA generated from one cell share a common 10X barcode. GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (BioRad) programed at 53°C for 45 min, 85°C for 5 min, and held at 4°C. Unique Molecular Identifiers (UMIs) are added at the same step to allow the discrimination of the PCR duplicates. After reverse transcription, single-cell droplets were broken, and cDNA was isolated and cleaned with Cleanup Mix containing DynaBeads (Thermo Fisher Scientific). cDNA was then amplified with a C1000 Touch Thermal Cycler programed at 98°C for 3 min, 12 cycles of (98°C for 15 s, 63°C for 20 s, 72°C for 1 min), 72°C for 1 min, and held at 4°C. Subsequently, to construct the Gene Expression library, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated, and cleaned with cleanup mix containing SPRIselect Reagent Kit (Beckman Coulter) in between steps. Post-ligation product was amplified and indexed with a C1000 Touch Thermal Cycler programed at 98°C for 45 s, 15 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and held at 4°C. Besides, the amplified cDNA derived from the barcodes attached to the antibodies is used to construct the Cell Surface Protein library, after addition by PCR of the indexed adapters, with a C1000 Touch Thermal Cycler programed at 98°C for 45 s, 15 cycles of (98°C for 20 s, 54°C for 30 s, 72°C for 20 s), 72°C for 1 min, and held at 4°C.  All the libraries were finally cleaned up with SPRIselect beads and controlled on a Fragment Analyzer HS-NGS run (Agilent). 17     All 10x libraries were pooled and charged with 1% PhiX on one SP lane of the NovaSeq 6000 instrument (Illumina) using the NovaSeq 6000 SP Reagent Kit v1.5 (200 cycles), and the following sequencing parameters: 28 bp read 1 – 8 bp index 1 (i7) – 150 bp read 2. The SP lane generated the following mean reads per cell: 3766, 3301, 3299 and 1865, 2585 and 4547 cells for 3 Control and 3 RM-AKI mice, respectively.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: CD45 Positive Cells

value: Kidney

tag: strain

value: 8 weeks

value: mRNA

tag: antibodies/tags


title: Rhabdo2, ADT-derived cDNA

status: Public on Mar 03 2025

type: SRA

country: France

description: 10X Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: cell type

tag: tissue

tag: age

tag: library type

value: ADT

value: TotalSeq-A 0001  anti-mouse CD4; TotalSeq-A 0002 anti-mouse CD8a; TotalSeq-A 0093  anti-mouse CD19; TotalSeq-A  0114 anti-mouse F4/80; TotalSeq-A  0182 anti-mouse CD3; TotalSeq-A 0824 anti-mouse P2X7R


title: Pulmosphere,control,24hrs,rep2

city: Hyderabad

first: Bappaditya

last: Dey

state: Telangana

address: Survey No. 37, Extended Q City Road, Gachibowli

country: India

institute: National Institute of Animal Biotechnology

library_source: transcriptomic

data_processing:
The raw fastq reads were preprocessed using Fastp v.0.20.1 (parameters: --trim_front1 9 --trim_front2 9 --length_required 50 --correction--trim_poly_g --qualified_quality_phred 30)
The processed reads were aligned to the STAR indexed Bos taurus ARS-UCD1.2 genome using STAR aligner v 2.7.9a (parameters:’--outSAMtype’ BAM SortedByCoordinate, ‘--outSAMunmapped’ Within, ‘--quantMode’, TranscriptomeSAM, '--outSAMattributes' Standard)
The alignment file (sorted BAM) from individual samples were quantified using featureCounts v. 0.46.1 based on the rRNA filtered GTF file to obtain gene counts
Gene counts were used as inputs to DESeq2  for differential expression estimation (parameters: threshold of statistical significance --alpha 0.05; p-value adjustment method: BH). The DESeq2 result files were filtered based on adjusted p-value <= 0.05 and Log2FoldChange ∓ 1.
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Bos taurus

source_name: Lung

extract_protocol:
RNA was isolated from pulmospheres using the RNeasy Plus Mini Kit (QIAGEN) in accordance with the manufacturer’s instructions.
The library preparation was carried out using TrueSeq stranded Total RNA kit following manufacturing protocol.

value: Lung

tag: cell line

value: Primary cell

value: Lung mixed cells

tag: treatment

value: Non-stimulated


title: Rhabdo3, ADT-derived cDNA

description: 10X Genomics


title: Pulmosphere,control,24hrs,rep3


title: H3K27ac-re_stimu_2

city: shenzhen

first: zhiguang

last: chang

address: No. 1068, Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

department: Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology

country: China

institute: Chinese Academy of Sciences

description:
Library name: H3K27ac-re_stimu_2
replicable biosample 2

library_source: genomic

data_processing:
Raw fastq files were processed with fastp (version 0.23.2) to remove adapter sequences and low-quality reads. The quality, adapter content, and duplication rates were assessed using FastQC (version 0.11.9). Cleaned reads were aligned to the mouse reference genome (NCBI build 37, mm9) using Bowtie2 (version 2.4.4), and duplicate alignments were removed using the MarkDuplicates tool in Picard (version 2.25.0). Genome-wide coverage files for H3K27ac, STAT3, H3K4me3, and immunoglobulin G (IgG) were generated using the bamCoverage tool from deepTools (version 3.5.0) (Ramírez et al., 2014). Peaks were called using MACS2 and annotated with the annotatePeaks.pl script from the Homer software suite. Genome region visualizations were created using the Integrative Genomics Viewer (IGV).
Supplementary files format and content: tab-delimited text file includes the PEAK information for each sample
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

source_name: Jurkat

extract_protocol:
Processed samples were incubated with 10 μl of Concanavalin A-coated magnetic beads (NovoNGS® Concanavalin A-coated Magnetic Beads, N251). Bead-bound cells were suspended in Dig Wash Buffer and incubated with antibodies targeting STAT3 (Proteintech, 10253-2-ap), H3K27ac (Abcam, ab4729), or H3K4me3 (Abcam, ab8580) at 4 °C overnight. Subsequently, cells were incubated with secondary antibodies for 60 minutes, followed by incubation with pA-Tn5 adapter complexes for 1 hour.
The samples were then resuspended in fragmentation buffer and incubated at 37 °C for 1 hour. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. The sequencing was performed on the Illumina Novaseq6000 platform using 150 bp paired-end reads.

value: Jurkat

tag: genotype

value: WT

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: Gene expression of the 182 Danish ash accessions [ERR977698]

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

data_processing:
Trimmomatic
Salmon 0.8
tximport in R
Assembly: Fraxinus excelsior 2451S ONT; PRJNA865134
Supplementary files format and content: tximport_182.txt

organism: Fraxinus excelsior

source_name: Leaves

extract_protocol:
Harper et al., 2016, https://doi.org/10.1038/srep19335
100 bp Illumina HiSeq reads

value: Leaves

tag: accession


title: H3K27ac-interval_2

description:
Library name: H3K27ac-interval_2
replicable biosample 2

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: H3K27ac-re_stimu_1

description:
Library name: H3K27ac-re_stimu_1
replicable biosample 1


title: w118 IP Run2 3

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics

description: Library name: w118_IP_3_Run2

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Reads were aligned with STAR 2.6.1b (Settings: --sjdbOverhang 74 --alignIntronMax 30000, otherwise default)
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: all the counts files for 3'Ends for the input and IP datasets were pasted to each other

organism: Drosophila melanogaster

source_name: Adult fly head powder

growth_protocol: Flies were grown in 25C on standard apple juice based food

extract_protocol:
RNA was purified with TRIzol LS Reagent (Ambion 10296028) according to the manufacturer’s instructions.
Libraries were prepared with 10 ng of total RNA using QuantSeq 3’ mRNA-Seq Library Prep Kit REV (Lexogen) according to manufacturer’s instructions.

value: Adult fly head powder


title: Gene expression of the 182 Danish ash accessions [ERR977697]


title: Gene expression of the 182 Danish ash accessions [ERR977696]


title: w118 IP Run2 2

description: Library name: w118_IP_2_Run2


title: Rhabdo2, mRNA-derived cDNA

description: 10X Genomics


title: Rhabdo1, ADT-derived cDNA

description: 10X Genomics


title: Gene expression of the 182 Danish ash accessions [ERR977694]


title: H3K27ac-stimu_1

description:
Library name: H3K27ac-stimu_1
replicable biosample 1

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: Pulmosphere,control,24hrs,rep1


title: H3K27ac-interval_1

description:
Library name: H3K27ac-interval_1
replicable biosample 1


title: Gene expression of the 182 Danish ash accessions [ERR977693]


title: Control3, mRNA-derived cDNA

description: 10X Genomics

value: CD45 Positive Cells


title: Gene expression of the 182 Danish ash accessions [ERR977692]


title: w118 IP Run2 1

description: Library name: w118_IP_1_Run2


title: w118 input Run2 3

description: Library name: w118_input_3_Run2


title: Control2, ADT-derived cDNA

description: 10X Genomics

value: Kidney


title: Gene expression of the 182 Danish ash accessions [ERR977695]


title: w118 input Run2 2

description: Library name: w118_input_2_Run2


title: Control3, ADT-derived cDNA

description: 10X Genomics

value: 8 weeks


title: pum IP Run2 3

description: Library name: pum_IP_3_Run2


title: Gene expression of the 182 Danish ash accessions [ERR977690]


title: H3K4me3-control-1

description:
Library name: H3K4me3-control-1
replicable biosample 1

value: Pre-exposure (direct sample collection)


title: Rhabdo1, mRNA-derived cDNA

description: 10X Genomics

value: mRNA


title: H3K4me3-control-2

description:
Library name: H3K4me3-control-2
replicable biosample 2


title: Control2, mRNA-derived cDNA

description: 10X Genomics


title: H3K27ac-stimu_2

description:
Library name: H3K27ac-stimu_2
replicable biosample 2


title: H3K4me3-re_stimu_1

description:
Library name: H3K4me3-re_stimu_1
replicable biosample 1


title: Gene expression of the 182 Danish ash accessions [ERR977689]


title: pum IP Run2 2

description: Library name: pum_IP_2_Run2


title: Gene expression of the 182 Danish ash accessions [ERR977691]


title: w118 input Run2 1

description: Library name: w118_input_1_Run2


title: pum IP Run2 1

description: Library name: pum_IP_1_Run2


title: RPE-1_dH2O_3day_5

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

country: USA

institute: Regeneron Pharmaceuticals

description: Library name: X1707887

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels. For reference, we used b37 genome reference.
Assembly: B37.3
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: RPE-1 hTERT

extract_protocol:
RNA was extracted from cell pallets preserved in TRIzol reagent (Thermo Fisher) using MagMax-96 total RNA isolation kit (Thermo Fisher). RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen).

value: RPE-1 hTERT

value: retinal pigment epithelial cell

value: ctrl


title: Control1, ADT-derived cDNA

description: 10X Genomics

value: ADT

value: TotalSeq-A 0001  anti-mouse CD4; TotalSeq-A 0002 anti-mouse CD8a; TotalSeq-A 0093  anti-mouse CD19; TotalSeq-A  0114 anti-mouse F4/80; TotalSeq-A  0182 anti-mouse CD3; TotalSeq-A 0824 anti-mouse P2X7R


title: RPE-1_dH2O_3day_1

description: Library name: X1707883


title: RPE-1_dH2O_3day_2

description: Library name: X1707884


title: RPE-1_dH2O_3day_3

description: Library name: X1707885


title: RPE-1_100ng/ml IL6/sIL6R_3day_3

description: Library name: X1707895


title: RPE-1_100ng/ml IL6/sIL6R_3day_1

description: Library name: X1707893


title: RPE-1_100ng/ml IL6/sIL6R_3day_2

description: Library name: X1707894


title: RPE-1_dH2O_3day_4

description: Library name: X1707886


title: H3K4me3-interval_2

description:
Library name: H3K4me3-interval_2
replicable biosample 2

value: Jurkat


title: pum input Run2 3

description: Library name: pum_input_3_Run2


title: H3K4me3-re_stimu_2

description:
Library name: H3K4me3-re_stimu_2
replicable biosample 2

value: WT


title: H3K4me3-interval_1

description:
Library name: H3K4me3-interval_1
replicable biosample 1


title: Control1, mRNA-derived cDNA

description: 10X Genomics


title: pum input Run2 1

description: Library name: pum_input_1_Run2


title: In vitro_Alveolar macrophage_Wild type_4h S. pneumoniae_#6

city: Chapel Hill

first: Matthew

last: McPeek

state: NC

address: 125 Mason Farm Rd. CB:7248

institute: University of North Carolina

data_processing:
Paired-end sequencing output were processed by Illumina bcl2fastq used for basecalling.
Sequence reads in FASTQ files were mapped to GRCm38 reference genome with GENCODE vM25 gene annotation by STAR, to generate BAM files.
Gene expression estimates were made as counts, and TPMs, by StringTie from BAM files and GENCODE vM25 annotation.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with gene information, counts, and columns as samples
Supplementary files format and content: tab-delimited text file with gene information, TPMs, and columns as samples

source_name: Alveolar macrophage

extract_protocol: Quick-RNA Microprep Kit (Zymo Research)

treatment_protocol: Naïve mice were euthanized by isoflurane overdose immediently prior to macrophage isolation procedure. Alveolar macrophages were isolated via bilateral, whole lung bronchoalveolar lavage (BAL) using room temperature phosphate buffered saline containing 2mM EDTA (BAL cells consisted of greater than 98% macrophages as determined by differerential cell counts from cytospins). BAL cells were washed 2X in 5mL room temperature PBS containing no EDTA. Cells were resuspended in RPMI medium containing 10% FBS (medium) at 37°C. Cells were plated in duplicate using Nunc Lab-Tek II Chamber Slides (2.2x10^5 cells/well; ThermoFisher, cat# 154534) and incubated at 37°C with 5% CO2. Non-adherent cells were removed by gentle washing 3 hours after plating, and cultures were incubated overnight (24 hours total). S. pneumoniae was collected from agar plates as described above and suspended in RPMI medium (OD: 600nm ~0.175 AU). Cells were stimulated with 200µL medium (unstimulated) or medium containing S. pneumoniae, MOI = 30.5 ± 1.7 (mean ± SEM) viable S. pneumoniae per macrophage, and incubated for 4 hours at 37°C with 5% CO2. At 4 hours post-stimulation, the supernatant was removed and RNA was immediently collected.

value: Alveolar macrophage

value: Wild type

tag: Sex

value: Male

value: In vitro -4 hour S. pneumoniae stimulated


title: In vitro_Alveolar macrophage_Wild type_4h Unstimulated_#6

value: In vitro - Unstimulated


title: H3K4me3-stimu_2

description:
Library name: H3K4me3-stimu_2
replicable biosample 2

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: primary D. melanogaster neuron culture 7

description: Library name: control_primary_cell_culture_7

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: tsv file format, with the gene counts for all the included samples of the primary neuron dataset

source_name: primary D. melanogaster neuron culture

extract_protocol:
RNA was purified with TRIzol LS Reagent (Ambion 10296028) according to the manufacturer’s instructions.
Illumina Stranded total RNA-Seq w/ Ribo-Zero plus, 2x100 bp reads

value: primary D. melanogaster neuron culture

value: primary neurons


title: In vitro_Alveolar macrophage_Mertk-/-_4h Unstimulated_#6

value: Mertk -/-


title: Gene expression of the 182 Danish ash accessions [ERR977686]

value: Leaves


title: ATAC-control-2

description:
Library name: ATAC-control-2
replicable biosample 2

data_processing:
Raw fastq files were processed using fastp (version 0.23.2)  (Chen et al., 2018) to remove adapter sequences and low-quality reads. Quality, adapter content, and duplication rates were evaluated using FastQC (version 0.11.9). Cleaned reads were aligned to the mouse reference genome (NCBI build 37, mm9) using Bowtie2 (version 2.4.4) (Langmead et al., 2009), and duplicate alignments were removed using the MarkDuplicates tool in Picard (version 2.25.0). Accessible chromatin regions were identified by peak calling with MACS2 (Model-based analysis of ChIP-seq) (version 2.2.7.1)(Zhang et al., 2008). Differential accessibility analysis was performed using the DiffBind package (version 3.6.2). Peaks with log2(fold change) > 0.5 and FDR < 0.05 were considered significantly differentially accessible. Peak annotation was conducted using the annotatePeaks.pl script from the Homer suite. ATAC signal tracks were visualized using the Integrative Genomics Viewer(Robinson et al., 2011).
Supplementary files format and content: tab-delimited text file includes the PEAK information for each sample

extract_protocol:
Processed primary cells were subjected to transposition reactions using the TruePrep DNA Library Prep Kit V2 for Illumina (TD501) and TruePrep Index Kit V2 for Illumina (TD202) according to the manufacturer’s instructions.
Nuclei from 5 × 10⁴ cells were pelleted and incubated with Tn5 transposase at 37 °C for 30 minutes. The resulting transposed DNA fragments were purified using the MolPure® PCR Purification Kit. Purified DNA fragments were amplified using 1× NEBNext High-Fidelity PCR Master Mix (New England Biolabs). The resulting library was further purified with the MolPure® PCR Purification Kit, quantified using a Qubit Fluorometer, and analyzed on an Agilent 2100 Bioanalyzer. Sequencing was performed on the Illumina Novaseq6000 platform using a paired-end 150 bp (PE150) strategy.

value: Pre-exposure (direct sample collection)


title: Gene expression of the 182 Danish ash accessions [ERR977685]


title: In vitro_Alveolar macrophage_Mertk-/-_4h S. pneumoniae_#6


title: pum input Run2 2

description: Library name: pum_input_2_Run2

value: Adult fly head powder


title: primary D. melanogaster neuron culture 6

description: Library name: control_primary_cell_culture_6


title: In vitro_Alveolar macrophage_Wild type_4h Unstimulated_#5


title: H3K4me3-stimu_1

description:
Library name: H3K4me3-stimu_1
replicable biosample 1


title: Gene expression of the 182 Danish ash accessions [ERR977687]


title: ATAC-control-1

description:
Library name: ATAC-control-1
replicable biosample 1


title: Gene expression of the 182 Danish ash accessions [ERR977682]


title: Gene expression of the 182 Danish ash accessions [ERR977684]


title: primary D. melanogaster neuron culture 5

description: Library name: control_primary_cell_culture_5


title: ATAC-re_stimu_2

description:
Library name: ATAC-re_stimu_2
replicable biosample 2

value: Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)


title: Gene expression of the 182 Danish ash accessions [ERR977688]


title: ATAC-re_stimu_1

description:
Library name: ATAC-re_stimu_1
replicable biosample 1


title: In vitro_Alveolar macrophage_Wild type_4h S. pneumoniae_#5


title: Gene expression of the 182 Danish ash accessions [ERR977683]


title: Gene expression of the 182 Danish ash accessions [ERR977681]


title: primary D. melanogaster neuron culture 3

description: Library name: control_primary_cell_culture_3


title: ATAC-interval_2

description:
Library name: ATAC-interval_2
replicable biosample 2

value: Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h)


title: primary D. melanogaster neuron culture 2

description: Library name: control_primary_cell_culture_2


title: Gene expression of the 182 Danish ash accessions [ERR977680]


title: primary D. melanogaster neuron culture 4

description: Library name: control_primary_cell_culture_4


title: ATAC-interval_1

description:
Library name: ATAC-interval_1
replicable biosample 1


title: In vitro_Alveolar macrophage_Mertk-/-_4h S. pneumoniae_#5


title: primary D. melanogaster neuron culture 1

description: Library name: control_primary_cell_culture_1


title: Gene expression of the 182 Danish ash accessions [ERR977679]


title: In vitro_Alveolar macrophage_Wild type_4h Unstimulated_#4


title: H_4

description: 3'end mRNA sequencing was carried out on all replicates

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Reads were aligned with STAR 2.6.1b (Settings: --sjdbOverhang 74 --alignIntronMax 30000, otherwise default)
3'seq data was filtered and clusters were identified with a custom 3'seq cluster identification process
3'seq clusters were further validated using a set of long-read validated 3'ends, in addition to high confided ensembl 3'ends
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 93
Supplementary files format and content: Raw count tables of both genewide and cluster specific counts per replicate are linked, cluster and gene specific DESeq results tables are provided for both synaptosome samples (F34 samples) vs Input (H) sampels. A bed file containing long read and high confidence ensembl 3'ends is also included.

source_name: adult fly head homogenate

growth_protocol: Flies were grown in 25C on standard apple juice based food. Adult flies were snap freezed, decapitated and head powder was prepared as described in Carrasco et al., 2020. (for details of sample preparation protocol see methods of this paper)

value: adult fly head homogenate

value: wt

value: none (Input to fraction)


title: In vitro_Alveolar macrophage_Wild type_4h S. pneumoniae_#4

value: Alveolar macrophage


title: Gene expression of the 182 Danish ash accessions [ERR977678]


title: In vitro_Alveolar macrophage_Wild type_4h Unstimulated_#3

value: Wild type


title: ATAC-stimu_1

description:
Library name: ATAC-stimu_1
replicable biosample 1

value: Jurkat

value: WT


title: In vitro_Alveolar macrophage_Mertk-/-_4h Unstimulated_#5

value: Male

value: In vitro - Unstimulated


title: RNAMT

city: shanghai

first: Dengfeng

last: Huang

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People's Hospital

data_processing:
The RNA-seq count data is converted by dividing the counts per kilobase by the total read counts (in millions).The Ribo-seq count data is calculated using TPM = counts per kilobase divided by total read counts (in millions)
Assembly: hg18
Supplementary files format and content: FPKM matrix

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen) following the manufacturer's instructions. In the processing of Ribo-seq, to block translational elongation, 100 µg/ml of cycloheximide was added to the cell culture medium, and the cell extracts were collected after treatment. Subsequently, ribosome-protected fragments (RFs) were generated by adding RNase I and DNase I, and rRNA was removed using an RNA purification kit and antisense DNA probes, ultimately constructing the Ribo-seq library.
Ribo-seq library was created using the NEBNext® Small RNA Library Prep Set for Illumina, RNA-seq cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina

value: ccRCC

value: overexpressing PHYHD1 (MT)


title: H_2


title: In vitro_Alveolar macrophage_Mertk-/-_4h Unstimulated_#3

value: Mertk -/-


title: Gene expression of the 182 Danish ash accessions [ERR977676]

value: Leaves


title: In vitro_Alveolar macrophage_Mertk-/-_4h S. pneumoniae_#3

value: In vitro -4 hour S. pneumoniae stimulated


title: In vitro_Alveolar macrophage_Mertk-/-_4h Unstimulated_#4


title: Gene expression of the 182 Danish ash accessions [ERR977674]


title: F34_3

source_name: synaptic fraction of adult fly head homogenate

value: column fraction


title: H_1


title: F34_4

value: synaptic fraction of adult fly head homogenate


title: Gene expression of the 182 Danish ash accessions [ERR977673]


title: In vitro_Alveolar macrophage_Wild type_4h Unstimulated_#2


title: RNAEV

value: empty vector


title: Gene expression of the 182 Danish ash accessions [ERR977675]


title: F34_2


title: Gene expression of the 182 Danish ash accessions [ERR977677]


title: Huh7 cells,shRBM39_input

city: Chengdu

first: Bo

last: Zhang

state: Sichuan

institute: West China Hospital,SCU

data_processing:
To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the hg38 genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Huh7 cell line was grown in their respective media supplemented with 10% fetal bovine serum, 1000 U/ml penicillin and 100 μg/ml streptomycin, in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA from tissues and cells was extracted with Magna RIP Kit (Merck Millipore, Darmstadt, Germany).
RIP was processed according to the Magna RIP Kit (Merck Millipore, Darmstadt, Germany) protocol with RBM39 antibody.

treatment_protocol: Huh7 cell line was transfection with shRBM39 plasmid to decrease the expression of RMB39.

value: hepatocellular carcinoma


title: RNAWT


title: H_3

value: adult fly head homogenate

value: wt


title: Gene expression of the 182 Danish ash accessions [ERR977672]


title: Huh7 cells,shRBM39_ip


title: Huh7 cells,shControl_ip

value: shControl


title: Gene expression of the 182 Danish ash accessions [ERR977671]


title: In vitro_Alveolar macrophage_Mertk-/-_4h Unstimulated_#2

value: Alveolar macrophage


title: F34_1


title: In vitro_Alveolar macrophage_Wild type_4h Unstimulated_#1

value: Wild type


title: w118_input

data_processing:
Bases were called on an Illumina NovaSeq 6000 platform
Reads were aligned with STAR 2.6.1b (Settings: --sjdbOverhang 74 --alignIntronMax 30000, otherwise default)
3'seq data was filtered and clusters were identified with a custom 3'seq cluster identification process
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 93
Supplementary files format and content: Raw count tables of both genewide and cluster specific counts per replicate were obtained, cluster and gene specific DESeq results tables were obtained for both Pum IP vs Input, and w118 vs input.

source_name: adult fly heads

treatment_protocol: Head powder was UV-crosslinked and homogenized in the lysis buffer. FLAG-tagged Pumilio protein complexes were capture on anti-FLAG magentic beads.

value: adult fly heads

value: adult


title: mixed_genotype_2_input_Run1


title: Gene expression of the 182 Danish ash accessions [ERR977669]


title: NT5

description:
raw_counts2.txt
NT5

source_name: liver

extract_protocol:
Total RNA from tissues and cells was extracted with Trizol reagent.
Total RNA quantity and purity were analyzed using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit.

value: liver

tag: group

value: adjacent tissue


title: mixed_genotype_1_input_Run1


title: w118_IP4

value: w118 RIP


title: pum_input


title: NT2

description:
raw_counts2.txt
NT2


title: Alveolar macrophage_Wild type_Male_9

description: Batch 2

treatment_protocol: Naïve mice were euthanized by isoflurane overdose immediently prior to macrophage isolation procedure. Alveolar macrophages were isolated via bilateral, whole lung bronchoalveolar lavage (BAL) using ice-cold phosphate buffered saline containing 2mM EDTA (BAL cells consisted of greater than 98% macrophages as determined by differerential cell counts from cytospins). BAL pellet was flash frozen in liquid nitrogen and stored at -80 centigrade prior to RNA isolation.

value: Male

value: Naïve


title: In vitro_Alveolar macrophage_Wild type_4h S. pneumoniae_#2

value: In vitro -4 hour S. pneumoniae stimulated


title: NT4

description:
raw_counts2.txt
NT4


title: Gene expression of the 182 Danish ash accessions [ERR977667]

value: Leaves


title: NT1

description:
raw_counts2.txt
NT1


title: w118_IP3


title: ATAC-stimu_2

description:
Library name: ATAC-stimu_2
replicable biosample 2

value: Jurkat

value: WT

value: Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h)


title: Alveolar macrophage_Wild type_Male_8

description: Batch 2


title: Huh7 cells,shControl_input

value: hepatocellular carcinoma


title: Gene expression of the 182 Danish ash accessions [ERR977665]


title: Gene expression of the 182 Danish ash accessions [ERR977670]


title: T5

description:
raw_counts2.txt
T5

value: tumor


title: NT3

description:
raw_counts2.txt
NT3


title: In vitro_Alveolar macrophage_Wild type_4h S. pneumoniae_#1


title: In vitro_Alveolar macrophage_Mertk-/-_4h S. pneumoniae_#1

value: Mertk -/-


title: Gene expression of the 182 Danish ash accessions [ERR977668]


title: Gene expression of the 182 Danish ash accessions [ERR977664]


title: Gene expression of the 182 Danish ash accessions [ERR977666]


title: In vitro_Alveolar macrophage_Mertk-/-_4h Unstimulated_#1

value: Alveolar macrophage

value: In vitro - Unstimulated


title: w118_IP2

value: adult fly heads

value: wt


title: T4

description:
raw_counts2.txt
T4

value: liver


title: pum_IP4

value: adult

value: Pum RIP


title: Gene expression of the 182 Danish ash accessions [ERR977663]


title: Alveolar macrophage_Wild type_Male_11

description: Batch 2

value: Wild type

value: Male


title: Alveolar macrophage_Wild type_Male_6

description: Batch 2

value: Naïve


title: T3

description:
raw_counts2.txt
T3


title: Gene expression of the 182 Danish ash accessions [ERR977662]

value: Leaves


title: T2

description:
raw_counts2.txt
T2


title: pum_IP3


title: Alveolar macrophage_Wild type_Male_10

description: Batch 2


title: Alveolar macrophage_Wild type_Female_9

description: Batch 2

value: Female


title: T1

description:
raw_counts2.txt
T1


title: Gene expression of the 182 Danish ash accessions [ERR977661]


title: Huh7 cells,shRBM39_3

description:
raw_counts1.txt
H7CON_3


title: pum_IP2


title: Gene expression of the 182 Danish ash accessions [ERR977660]


title: FACS_RNAseq salm[340]_rep2

city: SAINT LOUIS

first: Dongkook

last: Park

state: Missouri

address: 660 S. Euclid Avenue Campus Box 8103

department: Developmental Biology

institute: Washington University in St.Louis

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (v2.4)
Trimmed reads were aligned using STAR (v2.5.4b) to the Drosophila reference genome BDGP6 with Ensemble Gene Annotation (v95)
Variants for each line were called using aligned reads with the bcftools (v1.9) mpileup function followed by the bcftools call function
Low quality variants were filtered using bcftools filter. Variants not found in both replicates from a line were discarded. Variants present in any complementary lines were discarded.
Remaining variants were mapped to genes and prioritized using VEP (ensembl.org /Tools/VEP)
Assembly: Drosophila reference genome BDGP6

source_name: Embryonic myoblast_FACS_RNA

growth_protocol: Adult flies were allowed to lay on grape agar plates for 3hr at 25C. The plates were then changed and aged for 7hr to stage the embryos. Embryos were dechorionated and placed on ice.

extract_protocol:
Total RNA was extracted from FACS sorted GFP-positive cells using the Qiagen RNeasy kit.
cDNA libraries were constructed by Novogene

treatment_protocol: Homozygous embryos were identified and collected by hand using GFP expression under a fluorescent dissecting microscope. The collected embryos were dissociated by the homogenizer, following the elastase treatment. The dissoicated cells were sorted by the GFP fluorescency.

tag: developmental stage

value: Stage 11

value: embryo muscle

value: salm[340] mutant


title: Gene expression of the 182 Danish ash accessions [ERR977659]


title: Huh7 cells,shRBM39_2

description:
raw_counts1.txt
H7CON_2

value: hepatocellular carcinoma


title: Gene expression of the 182 Danish ash accessions [ERR977658]


title: pum_IP1


title: Alveolar macrophage_Wild type_Female_6

description: Batch 2


title: Alveolar macrophage_Wild type_Female_7

description: Batch 2


title: Huh7 cells,shControl_3

description:
raw_counts1.txt
H7S39_3

value: shControl


title: Alveolar macrophage_Wild type_Female_8

description: Batch 2

value: Alveolar macrophage


title: w118_IP1

value: w118 RIP


title: Alveolar macrophage_Wild type_Male_7

description: Batch 2


title: FACS_RNAseq WT_rep2

value: WT


title: Gene expression of the 182 Danish ash accessions [ERR977657]


title: FACS_RNAseq salm[340]_rep1


title: Alveolar macrophage_Wild type_Female_11

description: Batch 2


title: Gene expression of the 182 Danish ash accessions [ERR977656]


title: FACS_RNAseq WT_rep1


title: Huh7 cells,shRBM39_1

description:
raw_counts1.txt
H7CON_1


title: Alveolar macrophage_Wild type_Female_10

description: Batch 2


title: Huh7 cells,shControl_2

description:
raw_counts1.txt
H7S39_2


title: Gene expression of the 182 Danish ash accessions [ERR977655]


title: Alveolar macrophage_Mertk-/-_Male_9

description: Batch 2

value: Mertk -/-


title: CD4+ T cell, Combination 3

city: Birmingham

first: David

last: Bending

address: IBR

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

data_processing:
Libraries were sequenced using the NextSeq 500 using a High 75 cycle flow cell. Cluster generation and sequencing was then performed and FASTQ files generated. FASTQ files were then processed by Lexogen as follows: Trimming was performed using Cutadapt version 1.18, followed by mapping using STAR version 2.6.1a to the GRCm38 genome. Reads counting as performed using FeatureCounts version 1.6.4. Uniquely mapped read counts conts in the .txt format were used for further analysis using DESeq2 in R version 4.0.
Assembly: mus_musculus_GRCm38_ensembl_release_1 07_ERCC_SIRV
Supplementary files format and content: csv file includes regularised Log2 normalised expression values for each sample.
Supplementary files format and content: .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.
5ng of RNA was used for generation of sequencing libraries using the Quantseq 3' mRNA-seq Library Preparation kit (Lexogen). Briefly, library generation was commenced with oligodT priming containing the Illumina-specific Read 2 linker sequence. After first strand synthesis, RNA was degraded. Second strand synthesis was initiated by random priming and a DNA polymerase. Random primers contained the illumina-specific Read 1 linker sequence. Double stranded DNAwas purified from the reaction using magnetic beads and libraries amplified (18 cycles) and sequences required for cluster generation and sample indexes were introduced. Libraries were normalized and pooled at a concentration of 4nM for sequencing.

value: Spleen

value: CD4+ T cell

value: Tg4 Nr4a3-Tocky IL-10 GFP mice


title: LCMB-hipp-PRO

city: Chicago

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

library_source: other

data_processing:
FASTQs were processed using 10X SpaceRanger v2.1.1 and saved as Seurat objects for analysis
ST spots with more than 20% of reads attributed to mitochondrial genes in the mRNA assay were removed for FCX, TCX and PCX, and ST spots with more than 30% of reads attributed to mitochondrial genes in the mRNA assay were removed for HIPP.
ST spots with extreme low and high UMI counts in the mRNA assay were omitted on a per-sample basis
ST spots with extreme low mRNA Feature counts were removed on a per-sample basis
ST spots with zero cumulative protein expression were removed from both assays
The outermost edge ST spots of each slide were removed
ST spots not located on cortical or hippocampal tissue were removed from both assays
Raw mRNA counts were lognormalized using Seurat's NormalizeData()
Raw mRNA counts were transformed using SCTransform
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data files are Seurat objects containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are the SpaceRanger output files for each sample: aligned fiducials, scale factors, hires image, lowres image, detected tissue image, tissue positions list, and barcode fluorescence intensity from the spatial output folder, and the barcode, features, and matrix matrices from the filtered_feature_bc_matrix output folder

molecule: protein

source_name: Posterior Hippocampus

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene and Protein Expression for FFPE – Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging (CG000659, Rev B, 10x Genomics) protocol
Libraries were constructed according to the user guide for Visium CytAssist Spatial Gene and Protein Expression Reagent Kits (CG000494; Rev B; 10x Genomics).

value: Posterior Hippocampus

value: lecanemab Immunized AD (iAD)


title: Huh7 cells,shControl_1

description:
raw_counts1.txt
H7S39_1


title: CD4+ T cell, Combination 2


title: Gene expression of the 182 Danish ash accessions [ERR977654]


title: Alveolar macrophage_Mertk-/-_Male_8

description: Batch 2

value: Male

value: Naïve


title: Gene expression of the 182 Danish ash accessions [ERR977653]

value: Leaves


title: LCMB-pcx-PRO

source_name: Left Inferior Parietal Lobule

value: Left Inferior Parietal Lobule


title: Gene expression of the 182 Danish ash accessions [ERR977652]


title: Gene expression of the 182 Danish ash accessions [ERR977651]


title: Alveolar macrophage_Mertk-/-_Male_6

description: Batch 2


title: Alveolar macrophage_Mertk-/-_Male_7

description: Batch 2


title: CD4+ T cell, anti-Lag3 2


title: LCMB-tcx-PRO

source_name: Left Superior Temporal Gyrus

value: Left Superior Temporal Gyrus


title: CD4+ T cell, Combination 1


title: LCMB-fcx-PRO

source_name: Left Middle Frontal Gyrus

value: Left Middle Frontal Gyrus


title: nAD3-hipp-PRO

value: Non-Immunized AD (nAD)


title: Alveolar macrophage_Mertk-/-_Male_11

description: Batch 2


title: Gene expression of the 182 Danish ash accessions [ERR977650]


title: Gene expression of the 182 Danish ash accessions [ERR977649]


title: Gene expression of the 182 Danish ash accessions [ERR977647]


title: Gene expression of the 182 Danish ash accessions [ERR977648]


title: CD4+ T cell, anti-PD-L1 2


title: Alveolar macrophage_Mertk-/-_Female_9

description: Batch 2

value: Female


title: nAD3-pcx-PRO


title: Alveolar macrophage_Mertk-/-_Female_8

description: Batch 2

value: Alveolar macrophage


title: CD4+ T cell, anti-PD-L1 3


title: CD4+ T cell, anti-PD-L1 1


title: nAD3-tcx-PRO


title: nAD3-fcx-PRO


title: CD4+ T cell, anti-Lag3 1


title: CD4+ T cell, IgG Control 3

value: Isotype control


title: CD4+ T cell, anti-Lag3 3


title: Alveolar macrophage_Mertk-/-_Male_10

description: Batch 2


title: Gene expression of the 182 Danish ash accessions [ERR977646]


title: LCMB-tcx-mRNA


title: Alveolar macrophage_Mertk-/-_Female_6

description: Batch 2


title: Gene expression of the 182 Danish ash accessions [ERR977645]


title: Alveolar macrophage_Mertk-/-_Female_11

description: Batch 2


title: CD4+ T cell, IgG Control 1


title: CD4+ T cell, IgG Control 2


title: Gene expression of the 182 Danish ash accessions [ERR977644]


title: LCMB-fcx-mRNA


title: Gene expression of the 182 Danish ash accessions [ERR977643]


title: Alveolar macrophage_Mertk-/-_Female_10

description: Batch 2


title: Gene expression of the 182 Danish ash accessions [ERR977642]


title: Alveolar macrophage_Wild type_Male_5

description: Batch 1

value: Wild type


title: Alveolar macrophage_Mertk-/-_Female_7

description: Batch 2

value: Mertk -/-


title: F14

city: Charlestown

first: Neal

middle: Patrick

last: Smith

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

description: 10X genomics

data_processing:
Raw sequencing data was pre-processed with CellRanger (v3.0.2, 10X Genomics) to demultiplex FASTQ reads, align reads to a modified version of the mouse reference genome (mm10) that included tdTomato, and count unique molecular identifiers (UMI) to produce a cell x gene count matrix
Assembly: mm10 with tdTomato sequence added
Supplementary files format and content: raw_feature_bc_matrix.h5 files includes the UMI counts for all droplets for each sample in .h5 format

source_name: tibia

extract_protocol:
Isolated hindlimbs were mechanically crushed into 2mL of Hank’s Balanced Salt Solution (Sigma Aldrich, H6648). Supernatant was filtered through a 70µm filter (Corning, 352350) into a 50mL Falcon tube. The remaining tissue was further incubated with 2 Wunsch units of LiberaseTM (Sigma Aldrich, 5401127001) and 0.25% Trypsin-EDTA (Fisher Scientific, 15400054) at 37°C for 30 min with agitation. The supernatant was again filtered through a 70µm filter into a 50mL Falcon tube. Cells were then stained with CD45-APC (ThermoFisher, MCD4505), Ter119-APC (ThermoFisher, 17-5921-82) and DAPI (Invitrogen, D1306) for 30min on ice. Cells were washed with FACS Buffer (Phosphate Buffered Solution plus 2% fetal bovine serum). Flow cytometry and sorting was performed with a 4-laser BD LSR II and FACSDivia. TdTomato+/DAPI-/APC- cells were sorted into FACS Buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tibia

value: female

tag: day


title: Alveolar macrophage_Wild type_Male_4

description: Batch 1


title: F35

description: 10X genomics


title: NND-3

data_processing:
FASTQs were processed using 10X SpaceRanger v2.0.0 and saved as Seurat objects for analysis
ST spots with more than 20% of reads attributed to mitochondrial genes were removed
ST spots with extreme low and high UMI counts were omitted
ST spots with extreme low  Feature counts were removed on a per-sample basis
The outermost edge ST spots of each slide were removed
ST spots not located on tissue were removed
Raw counts were lognormalized using Seurat's NormalizeData()
Raw counts were transformed using SCTransform
Assembly: GrCh38-2020-A
Supplementary files format and content: The .rds processed data file is a Seurat object containing count matrices, transformed data matrices, and metadata
Supplementary files format and content: Also included are SpaceRanger output files for each sample: barcode fluorescence intensity (Extended amyloid-ß niche) for applicable  samples, aligned fiducials, scale factors, hires image, lowres image, detected tissue image, tissue positions list from the spatial output folder, and the barcode, features, and matrix matrices from the filtered_feature_bc_matrix output folder

source_name: Frontal Cortex

extract_protocol:
Formalin-fixed, paraffin-embedded samples were processed according to the Visium CytAssist Spatial Gene Expression for FFPE – Deparaffinization, H&E Staining, Imaging & Decrosslinking protocol (CG000520 Rev B, 10x Genomics)
Libraries were constructed according to the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495, Rev E, 10x Genomics)

value: Frontal Cortex

value: Non-Neurological Disease (NND)


title: nAD3-fcx-mRNA


title: Gene expression of the 182 Danish ash accessions [ERR977641]

source_name: Leaves


title: F7

description: 10X genomics


title: NND-2


title: Gene expression of the 182 Danish ash accessions [ERR977640]


title: F2

description: 10X genomics


title: Alveolar macrophage_Wild type_Male_2

description: Batch 1


title: M35

description: 10X genomics

value: male


title: nAD-6


title: NND-1


title: Gene expression of the 182 Danish ash accessions [ERR977639]


title: M14

description: 10X genomics


title: Alveolar macrophage_Wild type_Male_1

description: Batch 1

value: Male


title: nAD3-tcx-mRNA


title: Gene expression of the 182 Danish ash accessions [ERR977636]


title: Gene expression of the 182 Danish ash accessions [ERR977638]


title: nAD-5


title: nAD-2


title: CDX2creER;APC flox mice rectum tissue #2

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: mm10
Supplementary files format and content: TSV text file containing FPKM for all samples and genes

source_name: rectum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and treated with DNase to reduce gDNA contamination
NEBnext Ultra II directional RNA

treatment_protocol: 5 day consecutive ip injection of Tamoxifen(25mg/kg)

value: rectum

value: CDX2creER;APC flox


title: nAD-1


title: AN1792-22

value: AN1792 Immunized AD (iAD)


title: Alveolar macrophage_Wild type_Female_5

description: Batch 1

value: Naïve


title: Gene expression of the 182 Danish ash accessions [ERR977637]

value: Leaves


title: Alveolar macrophage_Wild type_Female_4

description: Batch 1


title: nAD-3

value: Non-Immunized AD (nAD)


title: Alveolar macrophage_Mertk-/-_Male_5

description: Batch 1


title: Gene expression of the 182 Danish ash accessions [ERR977635]


title: Alveolar macrophage_Wild type_Female_3

description: Batch 1

value: Female


title: AN1792-20


title: CDX2creER;APC flox mice rectum tissue #3

value: 5 day consecutive ip injection of Tamoxifen


title: Gene expression of the 182 Danish ash accessions [ERR977634]


title: AN1792-19


title: WT mice rectum tissue #3

value: CDX2creER;APC flox (WT)


title: Alveolar macrophage_Wild type_Female_2

description: Batch 1

value: Alveolar macrophage

value: Wild type


title: Alveolar macrophage_Wild type_Male_3

description: Batch 1


title: Gene expression of the 182 Danish ash accessions [ERR977633]


title: WT mice rectum tissue #2


title: Alveolar macrophage_Wild type_Female_1

description: Batch 1


title: Gene expression of the 182 Danish ash accessions [ERR977630]


title: AN1792-17


title: AN1792-21


title: Alveolar macrophage_Mertk-/-_Male_2

description: Batch 1

value: Mertk -/-


title: CDX2creER;APC flox mice rectum tissue #1


title: M7

description: 10X genomics

value: tibia


title: Gene expression of the 182 Danish ash accessions [ERR977632]


title: Gene expression of the 182 Danish ash accessions [ERR977631]


title: Alveolar macrophage_Mertk-/-_Male_1

description: Batch 1


title: M2

description: 10X genomics


title: Alveolar macrophage_Mertk-/-_Male_3

description: Batch 1


title: Gene expression of the 182 Danish ash accessions [ERR977628]


title: Alveolar macrophage_Mertk-/-_Male_4

description: Batch 1


title: WT mice rectum tissue #1

value: CDX2creER;APC flox(WT)


title: Gene expression of the 182 Danish ash accessions [ERR977629]


title: Lgr5creER;CDX2creER;APC flox mice rectum tissue #1

value: Lgr5creER;CDX2creER;APC flox


title: AN1792-11

value: Frontal Cortex


title: Lgr5creER;CDX2creER;APC flox mice rectum tissue #2


title: Lgr5creER;APC flox mice rectum tissue #3

value: Lgr5creER;APC flox


title: AN1792-16


title: Alveolar macrophage_Mertk-/-_Female_5

description: Batch 1


title: Gene expression of the 182 Danish ash accessions [ERR977627]


title: Lgr5creER;APC flox mice rectum tissue #4

value: rectum


title: AN1792-10


title: Gene expression of the 182 Danish ash accessions [ERR977624]


title: Gene expression of the 182 Danish ash accessions [ERR977626]


title: Alveolar macrophage_Mertk-/-_Female_3

description: Batch 1


title: Alveolar macrophage_Mertk-/-_Female_2

description: Batch 1


title: Lgr5creER;APC flox mice rectum tissue #1


title: Gene expression of the 182 Danish ash accessions [ERR977625]


title: Alveolar macrophage_Mertk-/-_Female_4

description: Batch 1


title: Lgr5creER;APC flox mice rectum tissue #2


title: AN1792-7


title: Gene expression of the 182 Danish ash accessions [ERR977623]


title: AN1792-8


title: Alveolar macrophage_Mertk-/-_Female_1

description: Batch 1


title: AN1792-6


title: Before treatment in hcc case 12

city: changsha

first: Muqi

last: Liu

state: Hunan

address: No.138 Tongzipo Road, Yuelu District, Changsha

department: Institute for Cell Transplantation and Gene Therapy

institute: the 3rd Xiangya Hospital of Central South University

description: Library name: zhlsh0

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Surgical puncture sample

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: hepatocellular carcinoma

value: male


title: D8 Control diet 8

city: Urbana

first: Andrew

middle: J

last: Steelman

address: 1201 West Gregory

institute: University of Illinois

data_processing:
The libraries were pooled; quantitated by qPCR and sequenced on one S4 lane for 151 cycles from both ends of the fragments on a NovaSeq 6000.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors have been trimmed from the 3'-end of the reads using Trimmomatic (v0.39) and reads shorter than 30 bp were discarded as well as that read's pair.
Salmon (v 1.4.0) was used to index the NCBI Mus musculus Annotation Release 109 transcriptome combined with the Influenza A virus (A/Puerto Rico/8/1934(H1N1)) transcriptome using the decoy-aware method with the entire GRCm39 + H1N1 genomes as the decoy sequence. Then quasi-mapping was performed to map reads to the combined transcriptomes with additional arguments --seqBias, --gcBias,  --numBootstraps=30,  --validateMappings and --recoverOrphans to help improve the accuracy of mappings.
Gene-level counts were estimated from transcript-level counts using the “bias corrected counts without an offset” method from the tximport package (v1.20.0) in R (v4.1.0). Genes without at least 0.25 counts per million (cpm) in at least 5 samples were filtered out. TMM normalized log2 count per million values were calculated and tested for differential expression using the limma-trend method in the limma package (v3.48.0) using a final model that included 6 extra factors estimated from RUVSeq analysis of the 5000 least significant genes (first model with no factors) using the “RUVs” method to control for nuisance effects like batch or library preparation. Ten pairwise comparisons were made: cholesterol vs. normal diet within each time point and within each diet, each of the later time points back to Day 0. Multiple test correction was done using the False Discovery Rate (FDR) method across all 10 comparisons together. Additionally, a Weighted Gene Co-expression Network Analysis (WGCNA package v1.70-3) was done on all genes for all samples (using expression values that had the RUVs factor effects removed) using the blockwiseModules() function with default values except maxBlockSize = 22000, corType = “bicor”, power = 4,networkType = “signed hybrid”, and minModuleSize = 20.  Because the D8 time point overwhelmingly dominated the resulting modules of co-expressed genes, two additional WGCNA were performed on just the D0, D4 and D16 samples (power = 7 ) and the D8 samples by themselves (power = 6). For each WGCNA, the eigengene values from each module were tested for differential expression across the 10 pairwise comparisons using regular limma modeling and global FDR correction.
Genome_build: GRCm39 and Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Supplementary_files_format_and_content: "Steelman_raw_gene_counts_2021-05-25.txt" Tab-delimited text file of gene-level counts for all samples
Supplementary_files_format_and_content: "Steelman_results_1way_pairwise_RUV_WGCNA_2021-06-07.xlsx"  Excel spreadsheet of differential expression testing results

source_name: lung

growth_protocol: Six-week-old C57BL/6J mice were obtained from Jackson Laboratories (No. 000664). Animals were tail-marked and housed four per cage under constant 12-h light/dark cycles (10am-10pm) and constant temperature.

extract_protocol:
Following euthanasia, the left lung was collected from mice inoculated with PBS or IAV, immediately flash frozen in liquid nitrogen, and stored at -80 °C until they could be further processed. Frozen lungs were pulverized into a homogenized powder using a mortar and pestle (Cole-Parmer) on dry ice and RNA was extracted by TRIzol (Thermo, #15596026) then column-purified using the GeneJET RNA purification kit (Thermo, #K0732) as per the manufacturer’s instructions. Purified RNA quantity was determined by a NanoDrop ND-1000 spectrophotometer (Thermo) and quality determined by running samples on a 1% agarose gel.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: Mice were fed either a standard rodent chow (Teklad 2016) or a matched diet containing 2% cholesterol (TD.07841) that differed only in cholesterol content. Feeding of each diet began at six weeks of age. At 11 weeks of age, mice were anesthetized with 3% isoflurane and then intranasally inoculated with either sterile phosphate buffered saline (PBS) or 0.7 HAU of mouse-adapted human influenza A virus strain A/Puerto Rico/8/1934 (H1N1) (A/PR8) diluted in PBS.  Mice were maintained on their respective diets for five weeks prior to inoculation and until termination.

value: lung

value: 12 weeks

tag: diet

value: Control

tag: days post-infection


title: High BMI sample 3

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

description: 10x Genomics

data_processing:
The initial demultiplexing of raw sequencing reads involved the utilization of Illumina bcl2fastq software, resulting in the generation of 150-bp paired-end read files in FASTQ format.
Subsequently, alignment of these reads to the GRCh38 human reference genome was executed using the Cell Ranger (v7.2.0) tool provided by 10X Genomics
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Jejunum

extract_protocol:
The fresh biopsy intestinal fragments from 2-3 volunteers were mixed into one tube, incubated with EDTA buffer, suspended and washed in cold PBS to obtain the crypt fractions as described above. Followed by shaking-incubated with digestive solution containing 1TrypLE Express (Gbico, 12604021) and 0.2 mg/ml DNase I (Thermo, EN0523) at 37℃ for 3-6 minutes, the single cells were centrifuged at 4℃ with 350g for 5 minutes. Then the cell pellets were resuspended and filtered through a 40 m cell strainer (BD). After centrifugating and discarding the supernatant, the cell sediments were stained with Zombie Dyes (Biolegend, 423105; 1:100 dilution) in the dark at the room temperature for 10 minutes. Zombie-negative cells were then sorted and collected by FACS analysis (BD, melody)
Single cells were captured in the 10X Genomics Chromium Single Cell 3′ Solution, and RNA-seq libraries were prepared according to the manufacturer’s protocol (10X Genomics). Then the libraries were sequenced on an Illumina Hiseq X Ten PE150 platform.

value: Jejunum


title: D8 Control diet 9


title: Gene expression of the 182 Danish ash accessions [ERR977621]

data_processing:
Trimmomatic
Salmon 0.8
tximport in R
Assembly: Fraxinus excelsior 2451S ONT; PRJNA865134
Supplementary files format and content: tximport_182.txt

extract_protocol:
Harper et al., 2016, https://doi.org/10.1038/srep19335
100 bp Illumina HiSeq reads

value: Leaves


title: Gene expression of the 182 Danish ash accessions [ERR977622]


title: Before treatment in hcc case 10

description: Library name: YSQ


title: AN1792-4

value: AN1792 Immunized AD (iAD)


title: Gene expression of the 182 Danish ash accessions [ERR977620]


title: D8 Control diet 7


title: AN1792-1


title: Before treatment in hcc case 9

description: Library name: WZR


title: D8 Control diet 6


title: Gene expression of the 182 Danish ash accessions [ERR977619]


title: S38, Human, MASH Fibrosis F3

city: New York

first: Atsushi

last: Sugimoto

address: 1130 Saint Nicholas Avenue

institute: Columbia University

data_processing:
Cellranger software (v2.0.0) for human samples and cell ranger (v8.0.1) for mice sample was used to process the data.
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Assembly: GRCh38
Supplementary files format and content: h5 format raw counts

molecule: nuclear RNA

growth_protocol: None (human samples)

extract_protocol:
Nuclear isolation as described (Filliol et, Nature 2022 Oct;610(7931):356-365). In brief, frozen liver tissue was minced with scissors in 1 ml TST buffer in the well of a 6-well plate for 10 min on ice. The homogenised solution was then passed through a 40 μm cell strainer. An additional 1 mL of TST buffer and 3 ml of 1xST buffer were used to wash the well and passed through a 40 μm cell strainer. The resulting 5 ml of nuclei suspension was centrifuged for 5 min at 500 g at 4°C. The supernatant was discarded, and the pellet resuspended in 1 ml of 1xST buffer. The nuclei suspension was then passed through a 35 μm filter.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s instructions, 12 cycles of cDNA amplification and 12 cycles of library amplification were performed, and samples were sequenced on an Illumina NovaSeq 6000 sequencing system instrument at the JP Sulzberger Columbia Genome Center.

treatment_protocol: Sample from healthy liver, liver with metabolic dysfunction-associated liver disease (MASLD) and alcohol-associated liver disease (ALD)

value: Liver

value: All cell types

value: 35 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977618]


title: D8 Control diet 5


title: Gene expression of the 182 Danish ash accessions [ERR977777]


title: Before treatment in hcc case 8

description: Library name: WYB


title: High BMI sample 1

description: 10x Genomics


title: Before treatment in hcc case 7

description: Library name: SMY0


title: D8 Control diet 3


title: Before treatment in hcc case 6

description: Library name: NSS0


title: S35, Human, MASH Fibrosis F3

value: 52 year-old

value: female


title: Before treatment in hcc case 5

description: Library name: LZH0


title: Gene expression of the 182 Danish ash accessions [ERR977616]


title: Before treatment in hcc case 11

description: Library name: YHL0


title: D8 Control diet 2


title: Gene expression of the 182 Danish ash accessions [ERR977617]


title: S33, Human, MASH Fibrosis F2-3

value: 58 year-old


title: High BMI sample 2

description: 10x Genomics


title: Before treatment in hcc case 3

description: Library name: HR0


title: D8 Control diet 4


title: Gene expression of the 182 Danish ash accessions [ERR977614]


title: D4 Control diet 6

value: 11.5 weeks


title: Before treatment in hcc case 4

description: Library name: LLG


title: S36, Human, MASH Fibrosis F3

value: 34 year-old


title: Before treatment in hcc case 2

description: Library name: DYM0


title: S27, Human, Healthy Control

value: 23 year-old


title: D4 Control diet 5


title: D8 Control diet 1


title: S21, Human, MASLD F0

value: 26 year-old


title: SET2_14B5_3

city: Memphis

first: Lance

last: Palmer

state: TN - Tennessee

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

data_processing:
Paired end reads were mapped to the GRCh38 reference genome using STAR (v2.7.9a).  Duplicate reads were marked with the MarkDuplicates (v 4.1.2.0) from the PICARD suite of tools.
Read counts per gene were generated by RSEM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimted file of read-pair counts per gene

source_name: hematopoietic

extract_protocol:
RNA was harvested using NucleoSpin RNA Plus. 250ng 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 manufacturer's protocols.

value: hematopoietic

value: Post MPN AML

value: DYRK1A KO

value: No treatment


title: Gene expression of the 182 Danish ash accessions [ERR977611]


title: Gene expression of the 182 Danish ash accessions [ERR977612]


title: Gene expression of the 182 Danish ash accessions [ERR977613]


title: D4 Control diet 2

value: lung

value: male

value: Control


title: SET2_14B5_2


title: D4 Control diet 4


title: D4 Control diet 1


title: S19, Human, MASLD F0

value: Liver

value: 20 year-old


title: SET2_11H1_3


title: S20, Human, MASLD F0

value: All cell types

value: 41 year-old


title: D4 Control diet 3


title: Gene expression of the 182 Danish ash accessions [ERR977615]

value: Leaves


title: S23, Human, Healthy Control

value: 80 year-old

value: female


title: D16 Control diet 5

value: 13 weeks


title: SET2_14B5_1


title: S18, Human, MASH Cirrhosis

value: 65 year-old


title: SET2_11H1_2


title: S17, Human, MASH Cirrhosis

value: 70 year-old


title: S28, Human, Healthy Control

value: 35 year-old


title: D16 Control diet 4


title: S16, Human, MASH Cirrhosis

value: 71 year-old


title: D16 Control diet 3


title: Gene expression of the 182 Danish ash accessions [ERR977610]


title: S14, Human, Healthy Control

value: 29 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977606]


title: Gene expression of the 182 Danish ash accessions [ERR977605]


title: D16 Control diet 6


title: S12, Human, Healthy Control

value: 31 year-old


title: SET2_11H1_1

value: hematopoietic

value: Post MPN AML

value: DYRK1A KO

value: No treatment


title: SET2_WT_1

value: WT


title: Gene expression of the 182 Danish ash accessions [ERR977607]


title: D16 Control diet 2

value: lung

value: male

value: Control


title: Gene expression of the 182 Danish ash accessions [ERR977604]

value: Leaves


title: SET2_WT_2


title: SET2_WT_3


title: S13, Human, Healthy Control

value: Liver

value: All cell types

value: 49 year-old

value: female


title: Gene expression of the 182 Danish ash accessions [ERR977609]


title: S15, Human, MASH Cirrhosis

value: 61 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977603]


title: D16 Control diet 1

value: 13 weeks


title: S9, Human, Alcohol-associated Hepatitis

value: 42 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977608]


title: D0 Control diet 5


title: Gene expression of the 182 Danish ash accessions [ERR977599]


title: S8, Human, Alcohol-associated Hepatitis

value: 34 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977602]


title: D0 Control diet 4


title: D0 Control diet 3


title: Gene expression of the 182 Danish ash accessions [ERR977598]


title: S7, Human, Alcohol-associated Hepatitis

value: 45 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977596]


title: S6, Human, Alcohol-associated Hepatitis

value: 62 year-old


title: Gene expression of the 182 Danish ash accessions [ERR977597]


title: S4, Human, Alcohol-associated Cirrhosis

value: 56 year-old


title: D8 Cholesterol diet 3

value: 12 weeks

value: Cholesterol (2%)


title: D0 Control diet 2

value: lung


title: D0 Control diet 1

value: male


title: S5, Human, Alcohol-associated Hepatitis


title: D8 Cholesterol diet 4


title: Gene expression of the 182 Danish ash accessions [ERR977595]


title: RA005, Mouse, Cre-negative Rspo3 floxed

description: Library name: RA005

source_name: Liver

growth_protocol: None (human and mice samples)

treatment_protocol: Human samples are from healthy liver, liver with metabolic dysfunction-associated liver disease (MASLD) and alcohol-associated liver disease (ALD). Mouse samples are from untreated liver.

value: Cre-negative Rspo3 floxed

value: 7 weeks old


title: S3, Human, Alcohol-associated Cirrhosis

value: Liver

value: 48 year-old


title: RA003, Mouse, LratCre+ Tdtomhomo

description: Library name: RA003

value: All cell types

value: LratCre+ Tdtomhomo

value: 8 weeks old


title: D0 Control diet 6

value: 13 weeks

value: Control


title: S2, Human, Alcohol-associated Cirrhosis


title: D8 Cholesterol diet 2


title: Ca-6-K-1031-S3_002

city: Szeged

first: Krisztián

last: Laczi

address: 52. Közép Fasor

department: Biotechnology and Microbiology

country: Hungary

institute: University of Szeged

description: Library name: Ca-6-K-1031-S3_002

data_processing:
raw reads were quality trimmed, and mapped to the reference genome (Candida albicans SC5314),  with CLC Genomics Workbench 21.0.3. Read counts and differential expression values were also calculated with the CLC Genomics Workbench.
DEG table was extracted in Excel table format (.xlsx) and the table was filtered in Microsoft Excel. Thresholds were set to 1.5 < Log2FoldChange < -1.5 and the p-value <0.05
The GO and pathway enrichment analysis was carried out on the DAVID web server of the NIH using the locus tags of the filtered DEGs
Assembly: Candida albicans SC5314, GeneBank Assembly: GCA_000182965.3
Supplementary files format and content: tab-delimited text format (.txt) containing the raw read counts

organism: Candida albicans

growth_protocol: C. albicans SC5314 cells from an overnight culture (10 ml LCM, 30°C, 160 rpm) were diluted to 2 × 107 cells mL−1 in 40 ml low ionic strength medium (LCM: 0.5% glucose, 0.25% yeast extract, 0.0125% peptone (w/v)) and incubated for 2 h (untreated samples) or  6 h (NFAP2-treated samples) at 30°C under continuous shaking at 160 rpm.

extract_protocol:
RNA was purified using the Quick-RNA Plant Miniprep Kit (Zymo Research, Tustin, CA, USA) according to the manufacturer’s instructions.
RNA-sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads kit (New England Biolabs, Ipswich, MA, USA) with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: C. albicans SC5314 cells ( 2 × 107 cells mL−1 in 40 ml LCM) were treated with 15 µg mL−1 NFAP2 and incubated for 6 h at 30°C under continuous shaking at 160 rpm.

value: WT

tag: batch


title: S1, Human, Alcohol-associated Cirrhosis

value: 37 year-old


title: SHP77 NKX2-1 siRNA 2 rep 2

city: Toronto

first: Housheng

middle: Hansen

last: He

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
Sample 17
siNKX21_2_B
Pair-end 150bp

data_processing:
Adapters were trimmed with cutadapt (v.2.5). Raw reads were mapped to human genome hg38 GENCODE vM25 annotation with STAR (v2.5.2b). Gene counts were performed with STAR.
Assembly: hg38
Supplementary files format and content: SHP77_shRNA_normalized_counts.csv: Comma-separated-value file containing normalized counts of shRNA samples as generated by DESeq2. In brief, raw counts were normalized by a normalization factor for each sample based on sequencing depth and RNA composition. This allows for comparison between samples. It is not normalized for transcript length.
Supplementary files format and content: SHP77_siRNA_normalized_counts.csv: Comma-separated-value file containing normalized counts of siRNA samples as generated by DESeq2. In brief, raw counts were normalized by a normalization factor for each sample based on sequencing depth and RNA composition. This allows for comparison between samples. It is not normalized for transcript length.

growth_protocol: SHP77 cells were transfected with siRNA with RNAiMAX for 72 hours before harvesting.

extract_protocol:
Cells were collected and lysed with Trizol. Total RNA was extracted with RNeasy Mini Kit (QIAGEN, cat. #74106). Genomic DNA was removed with RNase-Free DNase Set (QIAGEN, cat. #79254).
500ng RNA was used for library construction with the TruSeq RNA library prep kit V2 following manufacturer's protocol.

value: Small cell lung cancer cell line

value: NKX2-1 knockdown


title: Ca-6-K-1031-S3_001

description: Library name: Ca-6-K-1031-S3_001


title: Ca-2-K-1031_S2_002

description: Library name: Ca-2-K-1031_S2_002


title: SHP77 NKX2-1 siRNA 2 rep 1

description:
Sample 16
siNKX21_2_A
Pair-end 150bp


title: SHP77 NKX2-1 siRNA 1 rep 2

description:
Sample 15
siNKX21_1_B
Pair-end 150bp


title: D8 Cholesterol diet 8

tag: strain

value: 12 weeks


title: Ca-2-K-1031_S2_001

description: Library name: Ca-2-K-1031_S2_001


title: Before treatment in hcc case 1

description: Library name: CJ1

value: hepatocellular carcinoma


title: D8 Cholesterol diet 1

value: lung

value: Cholesterol (2%)


title: SHP77 NKX2-1 siRNA 1 rep 1

description:
Sample 14
siNKX21_1_A
Pair-end 150bp


title: Ca-1-K-1031_S1_002

description: Library name: Ca-1-K-1031_S1_002


title: Ca-1-K-1031_S1_001

description: Library name: Ca-1-K-1031_S1_001


title: D8 Cholesterol diet 7

value: male


title: SHP77 SOX2 siRNA 2 rep 2

description:
Sample 13
siSOX2_2_B
Pair-end 150bp

value: SOX2 knockdown


title: Sample 37_1d, WT, 162ug

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: Ottawa

address: 251 Sir Frederick Banting Dr.

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (200ng) were co-hybridized to Agilent Sureprint Whole Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Lung

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Five-to-seven week old female wild type C57BL/6 mice (WT) and C57BL/6 mice deficient in  STAT6 (STAT6 KO) (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and heart were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Wild type (WT) C57BL/6 and STAT6 KO mice were exposed to Mitsui-7 (multiwalled carbon nanotubes (MWCNT)) at a dose of 162 µg/mouse by intratracheal administration in a 50 µl suspension   Tissues were collected 1 and 28 days post-instillation.

tag: gender

value: Female

value: wild type C57BL/6 mice

tag: dose

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines

tag: sample type

value: reference


title: D8 Cholesterol diet 5

tag: tissue

tag: age


title: Sample 35_28d, WT, 162ug

tag: cell type


title: Sample 33_28d, STAT6 KO, Control

value: STAT6 deficient C57BL/6 mice

tag: treatment


title: D8 Cholesterol diet 9


title: Sample 34_1d, STAT6 KO, Control


title: D4 Cholesterol diet 6

value: 11.5 weeks


title: Ca-Klen-3_S6_001

description: Library name: Ca-Klen-3_S6_001

tag: cell line

tag: genotype

value: untreated


title: SHP77 SOX2 siRNA 1 rep 2

description:
Sample 11
siSOX2_1_B
Pair-end 150bp


title: Ca-Klen-2_S5_002

description: Library name: Ca-Klen-2_S5_002

value: WT


title: D4 Cholesterol diet 5

tag: Sex


title: Sample 39_28d, WT, 162ug


title: Sample 29_28d, STAT6 KO, 162ug


title: D8 Cholesterol diet 6


title: Sample 40_1d, WT, Control


title: SHP77 SOX2 siRNA 1 rep 1

description:
Sample 10
siSOX2_1_A
Pair-end 150bp


title: Sample 36_1d, WT, Control


title: SHP77 SOX2 siRNA 2 rep 1

description:
Sample 12
siSOX2_2_A
Pair-end 150bp


title: Sample 31_1d, STAT6 KO, 162ug


title: Ca-Klen-2_S5_001

description: Library name: Ca-Klen-2_S5_001


title: D4 Cholesterol diet 3


title: Ca-Klen-3_S6_002

description: Library name: Ca-Klen-3_S6_002


title: SHP77 si-control rep 3

description:
Sample 9
siC_3
Pair-end 150bp

value: Negative control


title: Ca-Klen-1_S4_002

description: Library name: Ca-Klen-1_S4_002


title: SHP77 si-control rep 2

description:
Sample 8
siC_2
Pair-end 150bp

value: Small cell lung cancer cell line


title: Ca-Klen-1_S4_001

description: Library name: Ca-Klen-1_S4_001


title: Sample 27_ 28d, WT, 162ug


title: Sample 32_1d, WT, 162ug


title: D4 Cholesterol diet 4


title: D4 Cholesterol diet 1


title: Adipose tissue, exercise, 48

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.9a
Alternative splicing analysis via Whippetv1.6.2 and rMATSv4.1.1
Assembly: mm10
Supplementary files format and content: Excel file containing the Alternative splicing events

source_name: White adipose tissue

extract_protocol:
total RNA was extracted using the miRNAeasy Mini Kit (Qiagen, Germany) as per the manufacturer's protocol, with additional DNase treatment
done by BGI (Yantian District, Shenzhen, China)

value: White adipose tissue

value: Male

value: Exercise

tag: intervention group

value: exercise(EX)


title: Sample 38_28d, STAT6 KO, 162ug

value: lung


title: SHP77 si-control rep 1

description:
Sample 7
siC_1
Pair-end 150bp


title: Moc2 cells,HUR KD3

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
Bulk RNA-seq
8457-MR-1_6

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Human hg38
Supplementary files format and content: tab-delimited text file for count data

growth_protocol: MOC2 cells cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug 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 manufacturer's protocols.

treatment_protocol: 25 MOI of lentiviral particles containing the control and HUR Crispr/cas9 were used to treat the cells for 18 hrs. A single clone isolated and cultured for the loss of HuR. Cells were washed after 18 hrs, kept for 72hrs more in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: Knockout

value: HNSCC cell line


title: D16 Cholesterol diet 3

value: male

value: 13 weeks

value: Cholesterol (2%)


title: Adipose tissue, exercise, 47


title: Moc2 cells, HUR KD2

description:
Bulk RNA-seq
8457-MR-1_5


title: D16 Cholesterol diet 2


title: Moc2 cells, HUR KD1

description:
Bulk RNA-seq
8457-MR-1_4


title: Sample 30_ 28d, WT, Control

value: Female

value: wild type C57BL/6 mice

value: 11 mouse cell lines

value: reference


title: Sample 25_ 28d, STAT6 KO, 162ug

value: STAT6 deficient C57BL/6 mice


title: Sample 22_1d, WT, 162ug


title: Adipose tissue, exercise, 45


title: D16 Cholesterol diet 1


title: Sample 23_1d, STAT6 KO, Control


title: D4 Cholesterol diet 2

value: 11.5 weeks


title: Sample 20_1d, STAT6 KO, Control


title: Sample 28_28d, STAT6 KO, Control


title: Sample 21_1d,STAT6 KO, 162ug


title: Moc2 cells, Control 3

description:
Bulk RNA-seq
8457-MR-1_3

value: Control


title: Sample 19_ 28d, WT, Control


title: Adipose tissue, exercise, 44

value: White adipose tissue


title: MOC2 cells, Control 1

description:
Bulk RNA-seq
8457-MR-1_1


title: D16 Cholesterol diet 6


title: MOC2 cells, Control 2

description:
Bulk RNA-seq
8457-MR-1_2


title: Sample 24_ 28d, WT, Control


title: Sample 17_ 28d,STAT6 KO, Control


title: Adipose tissue, exercise, 43

value: Male

value: sedentary(SED)


title: D16 Cholesterol diet 4


title: Adipose tissue, exercise, 46

value: Exercise

value: exercise(EX)


title: D0 Cholesterol diet 6

value: lung


title: Adipose tissue, exercise, 42


title: Sample 26_1d, WT, Control


title: Brain and spinal cord, Stripe adult corn snake, replicate 2

city: Geneva

first: Athanasia

last: Tzika

address: Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

data_processing:
FASTQ files (gene expression and CellPlex) were used as inputs to the 10X Genomics Cell Ranger pipeline (v3.0.2) with pre mRNA transcript detection of the CU corn snake genome.
The generated library was converted to a Seurat object containing the CMO information and processed for quality controls. Only nuclei with more than 500 detected genes and more than 900 detected RNA molecules were retained.
We ran the DoubletFinder package (2.0.3) to exclude doublets.
We then performed: (i) gene count normalization to the total expression and log-transformation, (ii) highly variable genes detection and principal component analysis, (iii) graph-based clustering (30 first PCAs and a clustering resolution of 1.0), and (iv) UMAP calculation.
Assembly: GCF_029531705.1
Supplementary files format and content: Seurat object containing raw and analysed data

organism: Pantherophis guttatus

source_name: Brain and spinal cord

extract_protocol:
A Stripe corn snake was frozen at -20°C after euthanasia. It was then thawed for the dissection of the brain and the spinal cord. The tissues were then flash frozen. Nuclei were isolated using the Nuclei EZ Prep Kit (NUC-101, Sigma). Briefly, frozen tissue was resuspended in 2mL of cold isolation buffer, dounce homogenized with a KIMBLE Dounce tissue grinder (D8938, Sigma) and incubated at 4°C during 5 minutes in the same buffer. The samples were centrifuged, resuspended and incubated in fresh buffer for 5 extra minutes. Nuclei were washed twice using 1% BSA (bovine albumin serum) PBS (phosphate-buffered saline) containing 50 U/ml of SUPERase-In (AM2696, Thermo Fisher) and 50 U/ml of RNasin (N2611Promega). Nuclei were resuspended in the appropriate volume of specific cell multiplexing oligos (CMO – CG000388, 10x Genomics,) and incubated for 5 minutes at room temperature. After adding 1.9mL of 1% BSA-PBS, nuclei were centrifuged for 10 minutes at 4°C and 500g. A second washing step was performed in order to remove the excess of CMOs. Nuclei were finally filtered through a 30μm strainer and stained with Hoechst (Invitrogen H3570, 1:500) for 5 minutes. To remove debris and only retain good quality nuclei, we used fluorescence-activated nuclei sorting (FANS) on a Beckman Coulter MoFloAstrios. CMO-labelled and sorted samples were pooled after sorting.
We used approximatively 10,000 nuclei per sample and 42 μl of nuclei suspension was used for the 10x Genomics snRNA-seq preparation according to the manufacturer’s instructions (10X Genomics Chromium 3′ GeneExpression Kit). The cDNA libraries were quality controlled using a 2100 Bioanalyzer and TapeStation from Agilent and sequenced using a HiSeq 2500 sequencer from the iGE3 platform at the University of Geneva.

value: Brain and spinal cord


title: Adipose tissue, exercise, 41


title: Sample 18_1d, STAT6 KO, 162ug


title: Brain and spinal cord, Stripe adult corn snake, replicate 1


title: D16 Cholesterol diet 5

value: male


title: D0 Cholesterol diet 5

value: 13 weeks


title: Adipose tissue, exercise, 40


title: Adipose tissue, exercise, 39


title: Sample 16_ 1d, WT, 162ug


title: Rb/p107 DKO

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

description: 10x Genomics

data_processing:
scRNAseq samples were de-multiplexed and aligned to mouse reference genome mm10 before being quantified using CellRanger version 2.2.0
Quality control filtering was applied to retain only genes expressed in greater thhan 3 cells and cells expressing greater than 500 genes and less than 15% mitochondrial reads
non-retinal cells were removed
Assembly: mm10
Supplementary files format and content: The filtered count matrix from cellranger as matrix files with barcodes and genes as tab-separated values files

source_name: Retina

extract_protocol:
P8 eyeballs of α-Cre; Rbf/f; P107-/- (DKO, tumor-prone) and α-Cre; Rbf/f; P107-/-; Skp2+/- (DKO-Skp2+/-, tumor-resistant) mice were enucleated, and peripheral retinas (α-Cre expression areas) were dissected in fresh and cold 1X HBSS. Dissected peripheral retinas were then transferred to 200μl of cold HBSS per retina. An equivalent amount of Papain solution [for 1ml - 700μl reagent grade water, 100μl of freshly prepared 50mM L-Cysteine (Sigma), 100μM 10mM EDTA, 10μM 60mM 2-mercaptoethanol (Sigma), and Papain added to 1mg/ml (Worthington)] was added and incubated at 37°C for 10 min, the tube was inverted gently every 2 min during the incubation. After the incubation steps, the digestion solution was discarded by pipetting without disturbing the retina. Mechanical trituration of the retina was performed in 600μl of Neurobasal media supplemented with 10% FBS by pipetting slowly 10 to 15 times with a P1000 pipette tip. Samples then were subjected to DNAse treatment [5μl DNAseI (RNAse free Recombinant DNAse I; Roche) for every 1ml of dissociation solution] for 5 min at 37°C. Cell suspensions were then centrifuged using a swing-bucket rotor at 200×g for 5 min. Supernatant was carefully aspirated off the cell pellet, followed by resuspension of the pellet in 1-5ml Neurobasal media with 1% FBS. Cellular aggregates were removed by straining cells through a 50μm cell strainer (pluriSelect).
Single cell gene expression libraries were prepared using the Single Cell 3′ Reagent Kit v2 (10x Genomics) according to the manufacturers protocol.
Libraries were sequenced using the HiSeq3000 (Illumina) with the 10x Gene Expression recommended parameters (read-1 28 cycles and read-2 100 cycles).

value: Retina

tag: developmental stage

value: alphaCre, Rbf/f, p107-/-


title: D0 Cholesterol diet 4

value: Cholesterol (2%)


title: Sample 15_1d, WT, Control

value: Female

value: wild type C57BL/6 mice

value: 11 mouse cell lines


title: Rb/p107 DKO; Skp2+/-

description: 10x Genomics

value: alphaCre, Rbf/f, p107-/-, skp2+/-


title: D0 Cholesterol diet 3


title: Sample 13_1d, STAT KO, 162ug

value: STAT6 deficient C57BL/6 mice

value: reference


title: Sample 14_1d, STAT6 KO, Control


title: Adipose tissue, intermittent fasting, 38

value: White adipose tissue

value: NZO/HIBomDife

value: Male

value: Intermittent Fasting

value: caloric restriction(CR)


title: WCS23_S_3

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
The sequenced reads generated from RNA-seq were mapped onto the reference genome (GCA_000184185.1) using bowtie2. The mapped information was converted as bam file format, and the number of mapped reads at each gene was counted using htseq-count pipeline. Differentially expressed genes were calculated with DESeq2. As a normalized count metric, transcripts per million (TPM) was manually calculated.
Assembly: GCA_000184185.1
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Escherichia coli W

source_name: bacterial cell

growth_protocol: For itaconic acid production, strains were grown at a modified M9 acetate medium with 0.5 g/L MgSO4·7H2O, 2 g/L NH4Cl, 1 g/L NaCl, 2 g/L L-glutamic acid, 2 g/L yeast extract, 100 mM potassium phosphate buffer for pH balancing for the value of 7, and 10 g/L of neutralized acetate (adjusted to pH 7 by adding 10 M NaOH)

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer's instructions. RNA concentration was quantified using a NanoDrop OneC spectrophotometer (Thermo Scientific). The quality of the isolated RNA was checked by running 1% agarose gel electrophoresis.
One microgram of the RNA from each sample was used for rRNA depletion with riboPOOL (siTOOLs Biotech) and Dynabeads MyOne Streptavidin C1 (Invitrogen), followed by purification using RNA Clean & Concentrator Kit (Zymo Research) according to the manufacturer's instructions. The suitable RNA samples were then used to construct paired-end, strand-specific RNA-seq libraries using KAPA RNA Hyper Prep kit (Kapa Biosystems) with the modification of shortened fragmentation of 2 minutes at 85℃ to include sRNAs in the library. The concentration of the final library was measured with Qubit 4 fluorometer (Thermo Scientific) and the size distribution was checked with Agilent 2100 Bioanalyzer (Agilent). The library was sequenced on NextSeq 550 (Illumina) platform with NextSeq 500/550 High Output Kit v2.5 (Illumina) in accordance with the manufacturer's instructions. All RNA-seq experiments were performed in biological triplicate.

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: ale

tag: phase

value: stationary phase

value: bacterial cell


title: D0 Cholesterol diet 1

value: lung

value: male

value: 13 weeks

tag: diet


title: Adipose tissue, intermittent fasting, 36


title: WCS23_S_1


title: D0 Cholesterol diet 2

value: Cholesterol (2%)

tag: days post-infection


title: WCS23_T_3

value: transition phase


title: RT4

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

data_processing:
We utilized HiC-Pro to process the raw Hi-C data to generate the iced contact matrices with 20k resolution for all tissue samples. The interacting loci were identified by FitHiC2 with the parameters -r 20000 -L 40000 -x intraOnly -U 1000000. We filtered out the low interacting loci with contact counts under the 0.98 quantile of all interacting loci’s contact counts.
Assembly: hg19
Supplementary files format and content: txt, chromatin interaction locus

source_name: Recurrent breast tumor

extract_protocol:
Approximately 100-200 mg of each tissue was chopped into fine pieces before being fixed. Hi-C was performed using Phase Genomics Proximo Hi-C kits v4.0 (Phase genomics, Seattle, WA) according to the manufacturer’s instructions21. Briefly, the finely chopped tissues were incubated with crosslinking solution for 15 minutes with gentle rotation. Tissue lysis was performed with motor and pestle with liquid nitrogen and grinded to a fine powder, and resuspended in 700 µl of Lysis buffer 1.
The chromatin containing supernatant was pelleted and washed with 500 µl of 1x CRB, resuspended in 100 µl of Lysis Buffer 2. 100 µl of SPRI beads were added, incubated and washed with 200 µl of 1x CRB. SPRI beads containing chromatin were resuspended in 150 µl of fragmentation buffer, 5 µl of restriction enzyme (Sau3AI) and incubated at 37 oC for 1 hour. 2.5 µl of finishing enzyme is added and mixed by vortexing. Ligation was performed by adding 95 µl of Ligation buffer and 5 µl ligation enzyme to the SPRI beads containing chromatin. To revert the crosslinking, 5 µl of RX enzyme was added to the reaction and then incubated overnight at 65 oC with shaking (900 rpm). The pellet was washed, air dried, resuspended in 100 µl of elution buffer and then incubated for 5 minutes at room temperature. The beads were washed and resuspended in 100 µl of bead binding buffer. After the final wash the beads were resuspended in 200 µl of deionized water and measured the concentration of DNA using Qubit dsDNA HS assay kit. About 500 ng of streptavidin beads containing DNA were separated, resuspended in 20 µl of deionized water, and a total of 25 µl of library reagent and an approximate amount of library reagent 1 is added. The reaction was mixed gently and incubated at 55 oC for 10 min. PCR was performed by adding 26 µl of HSR mix (PCR Hotstart Ready mix) and 5 µl of PCR index primer to each reaction. After the amplification, the sample was size selected by adding 25 µl of SPRI beads to the library. The beads were separated and washed twice with 200 µl of 80% ethanol for at least 30 sec each and the pellet was air dried for no longer than 5 min at room temperature. The beads were resuspended and separated and the supernatant containing the final Hi-C library which was quantified using Qubit dsDNA HS assay kit on a Qubit. The library was sequenced on Illumina HiSeq3000.

value: Recurrent breast tumor


title: Adipose tissue, intermittent fasting, 34


title: WCS23_T_2


title: Sample 8_1d, STAT6 KO, 162ug

value: Female

value: 11 mouse cell lines


title: Sample 11_ 28d, WT, Control

value: wild type C57BL/6 mice

value: reference


title: Sample 9_28d, STAT6 KO, Control

value: STAT6 deficient C57BL/6 mice


title: WCS23_S_2


title: Adipose tissue, intermittent fasting, 37

value: White adipose tissue

value: NZO/HIBomDife

value: Male


title: Sample 7_1d, WT, Control


title: Sample 10_28d, STAT6 KO, 162ug


title: Adipose tissue, intermittent fasting, 33

value: Intermittent Fasting

value: intermittent fasting(IF)


title: WCS23_T_1

value: ale

value: bacterial cell


title: RT3


title: Sample 6_ 28d, WT, 162ug

value: lung


title: Adipose tissue, intermittent fasting, 31


title: Sample 12_ 28d, WT, 162ug


title: Adipose tissue, intermittent fasting, 32


title: WCS23_E_3

value: mid-exponential phase


title: Adipose tissue, intermittent fasting, 35

value: caloric restriction(CR)


title: RT1


title: WCS23_E_1


title: Adipose tissue, intermittent fasting, 30


title: PT5

source_name: Primary breast tumor

value: Primary breast tumor


title: RT5

value: Recurrent breast tumor


title: WCS19_S_3

value: stationary phase


title: Sample 5_ 28d, WT, Control

value: Female

value: 11 mouse cell lines


title: Adipose tissue, intermittent fasting, 28

value: Ad libitum(AL)


title: Adipose tissue, intermittent fasting, 29


title: WCS23_E_2


title: Adipose tissue, intermittent fasting, 27


title: Sample 1_ 28d, STAT6 KO, Control

value: STAT6 deficient C57BL/6 mice

value: reference


title: PT1


title: Adipose tissue, intermittent fasting, 26

value: White adipose tissue

value: NZO/HIBomDife


title: WCS19_S_1


title: WCS19_T_3

value: transition phase


title: Sample 2_1d, WT, 162ug,

value: wild type C57BL/6 mice


title: NT2

source_name: Normal breast tumor

value: Normal breast tumor


title: RT2


title: Adipose tissue, intermittent fasting, 25

value: Male

value: Intermittent Fasting


title: PT4


title: NT1


title: WCS19_T_1

value: ale

value: bacterial cell


title: Sample 38_IL1-R1 KO 28d Control

growth_protocol: Five-to-seven week old female wild type C57BL/6 mice (WT) and C57BL/6 mice deficient in IL1-R1 (IL1-R1 KO)  (Jackson Laboratory, Bar Harbor, Maine) were housed in autoclaved cages, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

treatment_protocol: Wild type (WT) C57BL/6 and IL1-R1 KO mice were exposed to Mitsui-7 (multiwalled carbon nanotubes (MWCNT)) at a dose of 162 µg/mouse by intratracheal administration in a 50 µl suspension   Tissues were collected 1 and 28 days post-instillation.

value: lung

value: IL1-R1 deficient C57BL/6 mice


title: PT3

value: Primary breast tumor


title: Sample 37_IL1-R1 KO 1d Control

value: Female


title: PT2


title: Sample 35_WT 1d Control

value: 11 mouse cell lines


title: WCS19_T_2


title: Muscle, exercise, 23

source_name: skeletal muscle

value: skeletal muscle

value: Exercise

value: exercise(EX)