title: CD8_WT_4

city: Grand Rapids

first: Brandon

last: Oswald

address: 333 Bostwick Ave NE

department: Metabolism

institute: Van Andel Institute

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0).
Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8).
Counts were then normalized and differential expression was calculated using DESeq2.
Gene-set enrichment analysis (GSEA) on RNA-seq data was conducted using the gage function and non-parametric Kolmogorov–Smirnov test from the GAGE (version 2.22.0) R Bioconductor package(Luo et al., 2009).
Assembly: mm10
Supplementary files format and content: 20220203 ACLY in vivo RNAseq.xlsx is an excel file containing differential gene expression, pathway and geneset enrichment analysis.
Supplementary files format and content: Normalized_cpm.txt contains normalized counts per million transcripts for each sample.
Supplementary files format and content: raw_counts_7samples_filtered.txt contains raw non-normalized counts of transcripts for each sample.

source_name: CD8 T cells

extract_protocol:
Total RNA was isolated from murine T cells via RNeasy Kit (Qiagen) with DNase digestion (Qiagen) following manufacturer’s instructions.
Total RNA was reverse transcribed using a High-Capacity cDNA Reverse Transcriptase kit (Life Technologies). RNA preparation and library construction for RNA sequencing was conducted by the VAI Genomics Core as previously described(Roy et al., 2020).

value: CD8 T cells

value: CD8 T cell

value: WT


title: CD8_ACLYKO_3

status: Public on Jul 04 2024

type: SRA

state: MI

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: ACLY KO

tag: strain


title: CD8_WT_3


title: CD8_ACLYKO_2


title: CD8_WT_2


title: RAW264.7, SB+LPS1

city: Guangdong Guangzhou, China

first: chen

last: xi

address: 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou City, Guangdong Province,

country: China

institute: Guangzhou medical university

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: ensembl_94_mus_musculus_grcm38_primary
Supplementary files format and content: tab-delimited text files include FPKM values  for each Sample

source_name: connective tissue

extract_protocol:
Total RNA was extracted with AG RNAex Pro Reagent (AG21102, Accurate Biology, Hunan, China) as the manufacture’s instruction.  RNA purity and concentration were measured using Nanophotometer Pearl (IMPLEN, CA, USA).
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China).

value: connective tissue

tag: cell line

value: macrophage

tag: treatment

value: SB+LPS

value: macrophage M1 polarization


title: CD8_WT_1


title: P4_Opn4KO_sample3

city: Cincinnati

first: Shane

middle: Peter

last: D'Souza

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital

data_processing:
Adapters and low-quality reads were trimmed/filtered using Trimmomatic v0.39
Reads were pseudoaligned to the mouse reference genome (GRCm38) and counts were quantified using Kallisto v0.46.1
Differential gene expression analysis was performed using Sleuth v0.30.8
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts for each sample
Supplementary files format and content: comma-delimited text file includes DEGs from Sleuth
Supplementary files format and content: comma-delimited text file includes TPMs from Kallisto

molecule: polyA RNA

source_name: Neural retina

extract_protocol: Library preparation was performed at Azenta (Formerly Genewiz).

value: Neural retina

value: standard lighting


title: P4_Opn4KO_sample2


title: P4_Opn4KO_sample1


title: CD8_ACLYKO_1


title: Cx-3A9-3

city: Shanghai

first: Yangye

last: Lian

address: Xuhui No.180, Fenglin Road

institute: Zhongshan Hospital affiliated to Fudan University

data_processing:
Sequencing data quality was assessed by FastQC software(v0.10.1), and raw reads were filtered by Cutadapt (version 1.9.1). Reads were mapped to the Mus musculus reference genome (GRCm39). The expression level was estimated by FPKM.
Assembly: mm10
Supplementary files format and content: table includes FPKM values for each Sample

source_name: cortex

extract_protocol:
The total RNA was extracted using Trizol (Invitrogen).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: cortex


title: Cx-3A9-2


title: Cx-3A9-1


title: Cx-3A8-4


title: Cx-3A8-1


title: Cx-3A7-4


title: Cx-3A8-2


title: Cx-3A7-3


title: Cx-3A7-2


title: Cx-3A6-4


title: Cx-3A6-1


title: Cx-3A7-2

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters.
Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCh38 (hg38) {GRCm38 (mm10)} transcriptome using STAR(v2.6.1b).
Uniquely mapped reads were then assigned to genes with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrix files

molecule: nuclear RNA

extract_protocol:
The mouse cerebral cortices were dissected quickly, washed with PBS, and quickly frozen in liquid nitrogen. Cell nucleus were released by nuclei lysis buffer and then diluted to 2-2.5×10^5 cells/mL by PBS. 100 μL of resuspended nucleus, 60 μL of resuspended barcoding beads and 100 μL lysis buffer were loaded into the microfluidic chip (Singleron GEXSCOPETM Single Cell RNA-seq Kit). The captured mRNA was used for reverse transcription, cDNA amplification and library preparation.
RNA librabies were prepared with Singleron GEXSCOPETM Single Cell RNA-seq Kit according to the manufacture's protocol


title: Cx-3A6-2


title: Cx-3A7-1


title: Cx-3A6-3


title: Cx-3A6-2


title: Cx-3A6-1


title: Cx-3A9-4


title: WT_WD12_5

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

data_processing:
cDNA libraries were sequenced by NovaSeq 6000 (Illumina) in a paired-end fashion to reach more than 1.5M reads. Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to the mouse genome mm10 using STAR (v2.5, mismatch=2) and quantified using HTSeq (v0.6.1, -m union).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including read counts of genes for each sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from kidneys using Maxwell® RSC simplyRNA Tissue Kits (Cat # AS1340; Promega) in accordance with the manufacturer’s protocol.
cDNA library was generated from total mRNA (1 µg) using NEBNext UltraTM RNA Library Prep Kits for Illumina (New England BioLabs).

treatment_protocol: Kidney samples were harvested from PTC LRP2-SM22 +/+ and -/- mice fed western diet for 2 or 12 weeks.

value: Kidney


title: WT_WD12_6


title: KO_WD12_5

value: KO


title: WT_WD12_3


title: WT_WD12_4


title: WT_WD12_2


title: KO_WD12_3


title: KO_WD12_2


title: KO_WD12_4


title: Cx-3A8-3


title: KO_WD12_1


title: Cx-3A7-1


title: WT_WD12_1


title: KO_WD2_6


title: WT_WD2_6


title: WT_WD2_5


title: KO_WD2_5


title: KO_WD2_3


title: KO_WD2_4


title: Cx-3A7-3


title: WT_WD2_4


title: Lung of Donor 3, MHC2 enriched, EVLP + virus

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description: 10x Genomics 3'

data_processing:
The reads were aligned with Cell Ranger v3.1.0 on the human genome using the GRCh38 assembly and the GTF file downloaded from Ensembl release 101, and on the viral sequence. The 14 samples’ sequencing results were pre-processed and normalized using Seurat v4.3.0. Cells expressing less than 1,000 genes were removed. Dead or lysed cells were excluded by removing cells with a percentage of mitochondrial genes above a threshold calculated using the Scater package (median percentage of mitochondrial genes across all individual cells + 3 median absolute deviations). Filtration of the data also included the removal of doublets using Scrublet (expected doublet rate set to 0.08)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: lung biopsies

extract_protocol:
Lung biopsies (2 g each) were taken from similar lung zones from the upper lobes (wedges) before EVLP (0 h), and after 10 h EVLP, cut in 4 pieces, placed in 10 ml HypoThermosol® (STEMCELL Technologies, Vancouver, Canada) and kept on ice for 10 to max 24 h. This process was shown to maintain lung tissue stability up to 72 h for scRNA-seq. For the EVLP part of the study, the lung tissue from biopsies kept in HypoThermosol was minced finely with scissors, placed in Multi Tissue Dissociation Kit 1 solution as recommended by the manufacturer (Miltenyi Biotec, Bergisch Gladbach, Germany), and incubated at 37°C for 45 min in gentle agitation. The minced preparation was crushed on nylon mesh (1 mm) and filtered through successive nylon filters (500 µm, 100 µm, 40 µm). The cell suspension (referred as total cells) was washed in PBS (470 g, 15 min), processed to erythrocyte lysis, resuspended in RPMI + 2 % FCS, filtered twice on 40 µm and counted by 3 independent measurements with a counting chamber. For donors 2 and 3, both at 0 h and 10 h, MHC class 2 positive cells (referred as MHC class 2pos) were enriched using the anti-human HLA-DR bead kit from Miltenyi Biotech (ref 130-046-101) and MS separation columns (ref 130-042-201), following the manufacturer recommendations. Briefly, 10x106 purified lung cells were incubated with 20 µl beads + 80 µl PBS-EDTA-BSA buffer for 15min, filtered on 40 µm, and loaded on MS column for positive selection. The total cells and HLA-DR-positively-selected cells were counted using a counting chamber and checked for viability using trypan blue, and showed over 90% viability.
Single-cell suspensions were generated from each sample. For each sample, 2 x 10^4 cells were loaded onto the 10x Chromium to produce sequencing libraries, which were processed according to methods provided by 10x Genomics (v3 Chemistry). Cell cDNA was sequenced using the Truseq Illumina Stranded protocol and the Illumina NextSeq 550 sequencing machine.

treatment_protocol: Donor lung retrieval was carried out according to current clinical practice using Perfadex (Vitrolife, Göteborg, Sweden) flush preservation. After transportation at 4°C, lungs were processed to EVLP that was conducted according to the Toronto protocol for 10 h in the BSL3 facilities of the Molecular Virology and Immunology laboratory in Jouy en Josas in the case of the SARS-CoV-2 infection in EVLP, and at the Foch Hospital, Suresnes, in the case of the control EVLP. For SARS-CoV-2 infection in EVLP (3 donor lungs, donors 1, 2, 3), the right lung was connected to the circuit that was filled with 1.5 L of Steen solution supplemented with 1000 mg methylprednisolone, 1500 mg cefuroxime, and 7500 UI heparin. A flow rate at 24% of the theoretical cardiac output was applied at normothermia. The lung was ventilated with a standard ICU-type ventilator equipped with a connected nebulizer with vibrating meshes (Aerogen®), for the delivery of SARS-CoV-2 (see Viruses section). The Steen perfusate (100 ml) was replaced with fresh one every 2 h. The left lung was placed at 4°C and used for sampling before EVLP, designated as 0 h (see sampling section). For control EVLP experiments (2 donor lungs, donors 4 and 5), the whole lung was connected to the circuit that was filled with 1.5 L of Steen solution supplemented with 1000 mg methylprednisolone, 1500 mg cefuroxime, and 7500 UI heparin. A flow rate at 40% of the theoretical cardiac output was applied at normothermia. The Steen perfusate (100 ml) was replaced with fresh one every 2 h.

value: lung biopsies

value: 10h EVLP + virus

tag: gender

value: Female

tag: age

value: 66 yr

tag: cold ischemia_time

tag: intensive care

value: 8 days


title: WT_WD2_3


title: Lung of Donor 3, MHC2 enriched

description: 10x Genomics 3'

value: no treatment


title: Lung of Donor 3, EVLP + virus

description: 10x Genomics 3'


title: KO_WD2_2


title: Lung of Donor 2, MHC2 enriched, EVLP + virus

description: 10x Genomics 3'

value: 41 yr

value: 2 days


title: KO_WD12_6


title: Lung of Donor 2

description: 10x Genomics 3'


title: Lung of Donor 2, MHC2 enriched

description: 10x Genomics 3'


title: WT_WD2_2

value: WT


title: Lung of Donor 2, EVLP + virus

description: 10x Genomics 3'


title: KO_WD2_1


title: WT_WD2_1


title: RS4;11 VEN ins 5

city: Ulm

first: Alexandra

last: Niedermayer

address: Eythstraße 24

country: Germany

institute: Ulm University Medical Center

data_processing:
FASTQ were generated using Illumina bcl2fastq v2.20.0.422.
For alignment Bowtie 2 version 2.3.5.1 was used with human reference genome hg19/GRCh37 using standard settings.
The resulting SAM were sorted into BAM by samtools 1.9.
Raw read counts for hg19/GRCh37 were generated via htseq 0.9.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: RS4;11 were maintained in RPMI-1640 medium (20% fetal bovine serum, 1%L-Glutamine, 1%Penicillin/Streptomycin) in humidified air at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from RS4;11 cells (Quick-RNA Miniprep Kit, Zymo Research, Freiburg, Germany)  200ng of total RNA (measured by Qubit® analysis) was applied as input material for library construction.
RNA libraries were repared using TruSeq RNA Sample Preparation Kit v2 (Illumina, San Diego, California, USA) according to manufacturers protocol.

treatment_protocol: Starting from the BCP-ALL cell line RS4;11, five VEN resistant lines were generated in parallel by exposure to increasing concentrations of Venetoclax or solvent (DMSO).

value: acute lymphoblastic leukemia

value: VEN treated


title: CD8 T cells, Day 8 Armstrong

description: 10X Genomics

data_processing:
Mapping and quantification of expression profiles was conducted using salmon (v1.8.0) and GRCm39 (GENCODE rel M29). Salmon used the –alevin parameter with library orientation to ISF. Transcript level counts were imported using the tximeta (v1.14.0) in R (v4.2) and creation of a SingleCellExperiment object.
Quality control (QC) and normalization was completed by using scran (v1.24.0) and scater (v1.24.0). Briefly, cells with greater than 25% mitochondrial reads were removed and low quality cells as assessed by perCellQCMetrics in the scater package were removed using default guidelines. Normalization was first conducted using logNormCounts from the scuttle package (v1.6.2). Further normalization was implemented using the scater package. Doublet removal was conducted using computeDoubletDensity, a function in the scDblFinder package (v. 1.10.0).
After normalization and filtering of low quality cells, the top 10% of highly variable genes (HVGs) were used to run a PCA analysis using denoisePCA, a scran function, setting ncomponents equal to 2. Clustering analysis was achieved by using principle components and using buildSNNGraph function in scater to identify and build shared nearest neighbors, where k = 10 in that function. Cluster_walktrap function in igraph (v.1.3.2) was used for identifying clusters.
Assembly: mm10
Supplementary files format and content: quants_mat.gz, Data that contains the compressed count matrix
Supplementary files format and content: clustername_Seurat_filtered_SCE_Mito_out_no_doublets.rds, this the the SCE with all of the post QC methods used for the paper.

source_name: Spleen

extract_protocol:
C57BL/6 mice (3 biological replicates) were infected with LCMV-Arm. At 8 dpi, mice were sacrificed, and single cell suspensions generated from spleens followed by filtration through a 70 mM filter. Spleen samples were split into two halves: the first half was subjected to CD45+ cell isolation (Miltenyi Biotec #130-052-301) and the second half used for CD8+ T cell isolation (negative selection kit, STEMCELL Technologies #19853).
Single cell libraries were prepared using the 10X Genomics 5’ v2 single-cell RNA-seq kit following manufacturer instructions (10X Genomics). Sequencing was performed on an Illumina NovaSeq 6000 S2 flow cell (Illumina Inc., San Diego CA, USA) using 125 cycles - 26 bp for read 1 containing the cell barcode (16bp) and UMI (10bp) and 91 bp for read 2, containing the biological read.

value: Spleen

value: LCMV-Armstrong


title: RS4;11 VEN ins 4


title: RS4;11 VEN ins 2


title: EPA02_P4_MOC2_ATRi_RT_NKG2A_PDL1_4

city: London

first: Anton

last: Patrikeev

state: London

address: Chester Beatty Laboratories, 237 Fulham Rd.

department: Targeted Therapy

country: United Kingdom

institute: The Institute of Cancer Research

data_processing:
Low quality bases and adaptor sequences were removed using Trimmomatic.
Reads were mapped to the M. musculus GRCm38 reference genome using HISAT2 and StringTie was used for gene count matrix generation.
Assembly: M. musculus GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: tumour

growth_protocol: MOC1, MOC2 and mEER tumours were harvested 10 days after the last radiation dose

extract_protocol:
RNA from tumours was extracted and purified from tumours using Qiagen RNA extraction kit
Library preparation and sequencing were performed by Genewiz (Leipzig, Germany). Library prep was strand-specific, used PolyA selection, with 2x150bp sequencing at 10 million pairs performed on an Illumina NovaSeq

treatment_protocol: In vivo treatments were initiated when tumours reached an average of 20-100 mm3. The ATR inhibitor AZD6738 was provided by AstraZeneca and solubilised in 10% DMSO, 40% propylene glycol, 50% water, orally administrated 2 hours before irradiation for 4 consecutive days at 75 mg/kg/dose as indicated. Animal tumours were irradiated under anaesthesia with ketamine/xylazine injected intraperitoneally. Irradiation was initiated one day after ATR inhibitor dosing and was performed using an AGO 250kV X-ray machine at a dose rate of 1.62 Gy/minute (AGO). Animals were irradiated in the prone position positioned underlead shielding with a 16-mm diameter aperture aligned over the Tumour. A total of 9 Gy radiation dose in three fractions were given. Radiation dose was measured using a Farmer Chamberand Unidos-E Dosemeter (both PTW). Three days after the last dose of radiotherapy, mice were treated with anti-NKG2A (200 μg/mouse i.v., every 4/5 days for two weeks for a total of three injections) and/or anti-PD-L1 antibodies (200 μg/mouse i.p., every ¾ days for two weeks for a total of 4 injections) provided by AstraZeneca.

value: tumour


title: RS4;11 VEN ins 3


title: Lung of Donor 1

description: 10x Genomics 3'

value: Male

value: 52 yr


title: EPA02_P2_MOC2_ATRi_RT_NKG2A_PDL1_2


title: RS4;11 VEN sens 5

value: DMSO treated


title: RS4;11 VEN sens 2


title: RS4;11 VEN sens 3


title: RS4;11 VEN sens 4


title: EPA02_O4_MOC2_ATRi_RT_4

value: ATRi/Radiotherapy


title: RS4;11 VEN ins 1


title: EPA02_P3_MOC2_ATRi_RT_NKG2A_PDL1_3


title: RS4;11 VEN sens 1


title: Lung of Donor 3

description: 10x Genomics 3'

value: lung biopsies


title: EPA02_O3_MOC2_ATRi_RT_3


title: Lung of Donor 1, EVLP + virus

description: 10x Genomics 3'

value: 10h EVLP + virus


title: pupae rep 1

city: wenzhou

first: zhu

last: yu

address: ouhai district, liuhongqiao road

institute: Wenzhou Vocational College of Science and Technology

data_processing:
Using the FASTX-Toolkit software to converts data from Solexa format to FASTA format
Assembly: Cnaphalocrocis medinalis NCBI genome
Supplementary files format and content: fasta

organism: Cnaphalocrocis medinalis

source_name: whole body

extract_protocol:
Two fifth instar larvae and two pupae of the rice leaf folder were placed in separate centrifuge tubes containing TRIzol reagent, with each treatment performed in three biological replicates.
The experiment utilized the Illumina TruSeq Small RNA reagent kit to construct the library.

value: whole body

value: pupae


title: pupae rep 2


title: EPA02_O1_MOC2_ATRi_RT_1


title: fifth instar larvae rep 3

value: fifth instar larvae


title: fifth instar larvae rep 2


title: fifth instar larvae rep 1


title: Moderate-plane of nutrition, 3622

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS-UCD1.2) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Anterior pituitary

growth_protocol: Angus X Holstein-Friesian heifer calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-21 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.2 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from anterior pituitary samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks.

tag: diet

value: Moderate

value: Anterior pituitary

tag: breed

value: Holstein-Friesian X Angus


title: EPA02_O2_MOC2_ATRi_RT_2

value: WT


title: High-plane of nutrition, 3620

value: High


title: High-plane of nutrition, 2570


title: Moderate-plane of nutrition, 2551


title: EPA02_N4_MOC2_NKG2A_PDL1_4

value: anti-NKG2A/anti-PD-L1 antibodies


title: Moderate-plane of nutrition, 2537


title: EPA02_P1_MOC2_ATRi_RT_NKG2A_PDL1_1


title: High-plane of nutrition, 2535


title: EPA02_N3_MOC2_NKG2A_PDL1_3


title: Moderate-plane of nutrition, 2532


title: EPA02_N2_MOC2_NKG2A_PDL1_2


title: Moderate-plane of nutrition, 2346


title: High-plane of nutrition, 2528


title: EPA02_N1_MOC2_NKG2A_PDL1_1


title: EPA02_M4_MOC2_control_4

value: Vehicle


title: pupae rep 3


title: EPA02_M3_MOC2_control_3

value: tumour


title: Moderate-plane of nutrition, 1689


title: Moderate-plane of nutrition, 1395


title: High-plane of nutrition, 1707


title: EPA02_M2_MOC2_control_2


title: Moderate-plane of nutrition, 1392


title: Moderate-plane of nutrition, 1082


title: High-plane of nutrition, 1360


title: EPA02_M1_MOC2_control_1


title: High-plane of nutrition, 1089


title: EPA02_H4_mEER_ATRi_RT_NKG2A_PDL1_4

value: mEER


title: Moderate-plane of nutrition, 1057


title: High-plane of nutrition, 1388


title: High-plane of nutrition, 986


title: EPA02_H1_mEER_ATRi_RT_NKG2A_PDL1_1


title: Moderate-plane of nutrition, 981


title: Moderate-plane of nutrition, 975


title: High-plane of nutrition, 1050


title: EPA02_G4_mEER_ATRi_RT_4


title: EPA02_H2_mEER_ATRi_RT_NKG2A_PDL1_2


title: High-plane of nutrition, 2120


title: Moderate-plane of nutrition, 1690


title: High-plane of nutrition, 1531


title: EPA02_G2_mEER_ATRi_RT_2


title: EPA02_G1_mEER_ATRi_RT_1


title: EPA02_F4_mEER_NKG2A_PDL1_4


title: EPA02_F3_mEER_NKG2A_PDL1_3


title: EPA02_H3_mEER_ATRi_RT_NKG2A_PDL1_3


title: Moderate-plane of nutrition, 991


title: High-plane of nutrition, 553


title: Moderate-plane of nutrition, 911


title: EPA02_F2_mEER_NKG2A_PDL1_2


title: EPA02_E4_mEER_control_4


title: EPA02_G3_mEER_ATRi_RT_3


title: EPA02_F1_mEER_NKG2A_PDL1_1


title: SCWAT - ChREBPbeta_WT - Rep6

type: RNA

city: Toulouse Cedex 4

first: Dominique

last: Langin

address: 1 avenue du Professeur Jean Poulhès

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 21 out of 26 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 42868 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 40168 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Subcutaneous White Adipose Tissue

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Mice were fed a regular diet and housed in regular condition of temperature and dark-ligt cycles.

extract_protocol: Tissues were homogenized in Qiazol buffer (Qiagen 79306) using Precellys tissue homogenizer. Total RNA from tissues was extracted using RNeasy kit (Qiagen 75162).

treatment_protocol: All animal were submitted to a 24h fasting period followed by 18h refeeding with food and 20% glucose-supplemented water to favor ChREBP activation.

value: ChREBPbeta

tag: washbatch


title: SCWAT - ChREBPtotal_KO - Rep7

value: ChREBPtotal


title: SCWAT - ChREBPtotal_WT - Rep7


title: SCWAT - ChREBPbeta_KO - Rep5


title: SCWAT - ChREBPtotal_WT - Rep8


title: EPA02_E3_mEER_control_3


title: SCWAT - ChREBPtotal_KO - Rep5


title: SCWAT - ChREBPbeta_WT - Rep8


title: EPA02_E2_mEER_control_2


title: SCWAT - ChREBPbeta_WT - Rep7


title: EPA02_E1_mEER_control_1


title: SCWAT - ChREBPtotal_KO - Rep4


title: SCWAT - ChREBPbeta_KO - Rep4


title: SCWAT - ChREBPtotal_WT - Rep6


title: iOL_Dor

city: Chengdu

first: XueLian

last: He

state: Sichuan

address: Renmin Road

institute: Sichuan University

library_source: genomic

data_processing:
Reads processing. Raw reads of were firstly processed through in-house perl scripts. In this step, clean reads were obtained by removing reads containing adapter, reads containing too many N (>= 10%) and reads with low-quality (>= 50% of bases with Q <= 5).
Clean reads were mapped to reference genome of rat (UCSC, rn5) using bowtie2 (v2.4.4), and low-quality mapped reads were removed and uniquely mapped reads were kept through sambamba (v0.8.1).
To facilitate visualization, BIGWIG files were generated from BAM files via deepTools (v3.5.1).
Peak-calling and data analysis. Primary peaks were identified by using MACS2 (v2.2.7.1) with ‘-p 1e-5 -f BAMPE’, followed by peaks filtering with P-value < 1e-9.
Assembly: rn5
Supplementary files format and content: bigWig, narrowPeak files contain signals density and peaks of CUT&Tag, respectively.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Inmature oligodendrocyte (iOL)

growth_protocol: Primary rat OPCs were isolated as described(Chen et al., 2007). Briefly, mixed glial cells were initially cultured in DMEM-F12 medium plus 15% fetal bovine serum and then changed to B104 conditioned medium for 2 d before isolating OPCs by mechanical detachment in an orbital shaker.

extract_protocol:
Cut&Tag libraries preparing and sequencing. To prepare sequencing libraries of Cut&Tag, fresh specimens from rat were processed following the protocol of Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit for Illumina® (Yeasen Biotech Co., Ltd.).
Library concentration was measured using Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), and library fragment analysis was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Qualified libraries were sequenced on Novaseq 6000 sequencer (Illumina) with 150 bp paired-end reads.

treatment_protocol: Isolated rat OPCs were grown in Sato growth medium supplemented with PDGF-AA (10 ng/ml) and bFGF (20 ng/ml) and differentiated in Sato medium supplemented with T3 (15 nM) and CNTF (10 ng/ml).

value: Inmature oligodendrocyte (iOL)

tag: chip antibody

value: Dor (rabbit, InvitrogenPA538729)


title: EPA02_D4_MOC1_ATRi_RT_NKG2A_PDL1_4


title: OPC_Dor

source_name: Oligodendrocyte procurcer cell (OPC)

value: Oligodendrocyte procurcer cell (OPC)


title: SCWAT - ChREBPbeta_KO - Rep6


title: D3

city: Wuhan

first: Junlin

last: Chen

address: No.1, Shizishan Street

institute: Huazhong Agricultural University

organism: Brassica napus

source_name: flower bud

growth_protocol: experimental field

extract_protocol:
Toal RNA was extracted by using Eastep® Super Total RNA Extraction Kit (Promega) from cotyledon with three replications
mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads, and mRNAs were obtained by removing ribosomal RNAs from the total RNAs.

treatment_protocol: At the bud stage, the apical meristem together with little buds (< 1mm) of each plant

value: flower bud

value: mutant

value: flower buds grow in an experimental field


title: SCWAT - ChREBPbeta_WT - Rep1


title: SCWAT - ChREBPbeta_WT - Rep3


title: SCWAT - ChREBPtotal_WT - Rep5


title: SCWAT - ChREBPbeta_WT - Rep2


title: SCWAT - ChREBPtotal_WT - Rep3


title: SCWAT - ChREBPtotal_KO - Rep8


title: mOL_Dor

source_name: Mature oligodendrocyte (mOL)

value: Mature oligodendrocyte (mOL)


title: SCWAT - ChREBPtotal_KO - Rep2


title: EPA02_D3_MOC1_ATRi_RT_NKG2A_PDL1_3


title: D2


title: RA-LW303

city: Zhanjiang

first: Han

last: Wu

state: Guangdong

address: No.12 Minyou Road, xiashan district, Zhanjiang City

institute: The second Affiliated Hospital of Guangdong Medical University

data_processing:
These high-quality reads were compared to the reference genome/transcriptome using bowtie2 software (v2.2.4), and circ RNA detection and characterization was performed using find_circ software (v1.2). The identified circular RNAs were annotated using the circBase database, circ2Trait disease database. The raw splice reads (junction reads) of each sample were normalized using the total number of reads and log2 transformed. Differential cyclic RNAs were identified using ttest for two groups of samples and fold change for differential cyclic RNAs between two samples. GO and KEGG analyses were performed on the genes of origin of differential cyclic RNAs using the popular GO and KEGG analysis of genes of origin of differential cyclic RNAs was performed, and prediction of cyclic RNA-miRNA interactions was performed using popular miRNA target gene prediction software.
High-quality de-junction reads were aligned to the human reference genome (hg19) using hisat2 software (v2.04) guided by the gtf gene annotation file. Then, FPKM[9] (Fragments per kilobase of exon per million fragments mapped) values for transcript-level LncRNAs and gene-level mRNAs were obtained using the cuffdiff software (part of the cufflinks software suite, v2.2.1) as the The expression profiles of LncRNAs and mRNAs were calculated, and the fold change and p-value between two/group samples were calculated to screen for differentially expressed LncRNAs and mRNAs. Based on the proximity relationship, the target genes of LncRNAs were predicted, and GO and KEGG pathway analyses of the target genes were performed. GO and KEGG pathway analysis of differential mRNAs was also performed.
The circular RNAs are categorized into exonic circular RNAs, intronic circular RNAs, or intergenic circular RNAs based on the location of the ends of the circular RNAs. The newly identified cyclic RNAs were then linked to the circBase database and circ2Trait cyclic RNA-disease database according to the genomic location of the cyclic RNAs.Newly identified cyclic RNAs are labeled with novel.
Assembly: hg19
Supplementary files format and content: LncRNA Expression Profiling.xlsx
Supplementary files format and content: mRNA Expression Profiling.xlsx

source_name: Peripheral blood serum exosomes

extract_protocol:
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accessionnumber(s) can be found in the article/supplementary material.
Double-ended reads were harvested after sequencing on an Illumina HiSeq 4000 sequencer and quality control was performed using Q30. Then, cutadapt (v1.9.2) software was used to remove splices and low-quality reads. based on the high-quality reads obtained, Cloud Sequencing Bio analyzed the circRNAs, LncRNAs, and mRNAs using different methods.

tag: disease

value: RA

value: Peripheral blood serum exosomes


title: EPA02_D2_MOC1_ATRi_RT_NKG2A_PDL1_2

value: WT


title: RA-LW302


title: D1


title: SCWAT - ChREBPtotal_KO - Rep3


title: EPA02_D1_MOC1_ATRi_RT_NKG2A_PDL1_1


title: RA-LW301


title: SCWAT - ChREBPtotal_WT - Rep1


title: S3


title: RA-L205


title: EPA02_C4_MOC1_ATRi_RT_4

value: ATRi/Radiotherapy


title: SCWAT - ChREBPtotal_WT - Rep4


title: SCWAT - ChREBPbeta_KO - Rep1


title: S2


title: EPA02_C3_MOC1_ATRi_RT_3


title: SCWAT - ChREBPtotal_KO - Rep1


title: RA-L204


title: S1


title: RA-L203


title: EPA02_C2_MOC1_ATRi_RT_2


title: Newly diagnosed multiple myeloma _4

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description: 10x Genomics

data_processing:
Raw scRNA-seq data were preprocessed using the Cell Ranger analysis pipelines (10x Genomics) version 6 with reference genome of human genome (GRCh38) to demultiplex for cell and transcript and generate count table.
The count table was loaded into R through Seurat version 4 package for further analysis. Cells that have gene numbers lesser than 200, greater than 7,000, and more than 10% of unique molecular identifiers stemming from mitochondrial genes were discarded from the analysis.
For individual sample, a principal component analysis (PCA) was performed on significantly variable genes for remained high-quality cells. Results of individual samples were used for data integration across samples using reciprocal PCA method to minimize technical differences between samples.
The integration results were employed as input for clustering using Louvain algorithm with multilevel refinement and the Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow aspirate

extract_protocol:
Cryopreserved BM mononuclear cells were rapidly thawed, washed twice with PBS, stained with cell viability dyes and counted using a fluorescence microscope. Samples with viability higher than 95% were processed for 10x genomics scRNA-seq. Approximately 10,000 cells were targeted, and single-cell emulsions were generated with the Chromium Controller (10x Genomics, Pleasanton, CA, USA) using the Chromium Next GEM Chip G (Part Number 1000120, 10x Genomics) with the Chromium NextGEM Single Cell 3’ v3.1 kit (Part Number 1000121, 10x Genomics) following the standard protocol.
Libraries were assessed for mass concentration using the Qubit 1X dsDNA HS Assay Kit (catalog # Q33231; Invitrogen, Waltham MA, USA) and the Qubit 4 fluorometer (catalog # Q33238; Invitrogen, Waltham MA, USA). Library fragment size was assessed with the High Sensitivity NGS Fragment Analysis Kit (catalog # DNF-474-0500; Agilent, Santa Clara CA, USA) on the Fragment Analyzer System (catalog # M5310AA; Agilent, Santa Clara CA, USA). Libraries were functionally validated with the KAPA Universal Library Quantification Kit (catalog # 07960140001; Roche, Basel CH). Initial low-pass “surveillance” sequencing was performed on an Illumina NovaSeq SP 100-cycle flow cell and data were assessed using the Cell Ranger Count output.

value: Bone marrow aspirate

tag: disease state

value: NDMM


title: RA-L201


title: SCWAT - ChREBPbeta_WT - Rep4


title: EPA02_C1_MOC1_ATRi_RT_1

value: tumour


title: Newly diagnosed multiple myeloma _3

description: 10x Genomics


title: EPA02_B3_MOC1_NKG2A_PDL1_3

value: anti-NKG2A/anti-PD-L1 antibodies


title: Newly diagnosed multiple myeloma _2

description: 10x Genomics


title: SCWAT - ChREBPbeta_KO - Rep2

value: ChREBPbeta


title: Newly diagnosed multiple myeloma _1

description: 10x Genomics


title: RA-HW104


title: RA-HW105


title: EPA02_B2_MOC1_NKG2A_PDL1_2


title: SMM_4

description: 10x Genomics

value: SMM


title: PG - ChREBPbeta_KO - Rep8

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 25 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 43259 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 40561 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Perigonadal White Adipose Tissue


title: RA-HW103


title: PG - ChREBPbeta_WT - Rep8


title: PG - ChREBPbeta_WT - Rep6


title: PG - ChREBPtotal_WT - Rep8

value: ChREBPtotal


title: SMM_3

description: 10x Genomics


title: PG - ChREBPtotal_KO - Rep1


title: RA-L202


title: EPA02_A4_MOC1_control_4

value: Vehicle


title: RA-HW102


title: SMM_2

description: 10x Genomics


title: EPA02_A3_MOC1_control_3


title: EPA02_B4_MOC1_NKG2A_PDL1_4


title: EPA02_A2_MOC1_control_2


title: SMM_1

description: 10x Genomics


title: Normal-5

value: Normal


title: MGUS_6

description: 10x Genomics

value: MGUS


title: EPA02_A1_MOC1_control_1


title: EPA02_B1_MOC1_NKG2A_PDL1_1


title: Normal-4


title: MGUS_5

description: 10x Genomics


title: Normal-3


title: Dor iKO

data_processing:
Raw reads were firstly filtered by Trimmomatic (v0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean reads were mapped to the reference genome of mouse (GENCODE, vM25) using STAR (v2.7.9a).
Reads count of genes were counted by GenomicAlignments (v1.28.0), and normalized gene expression (Transcripts per million, TPM) were calculated by RSEM (v1.3.1).
Assembly: GRCm38
Supplementary files format and content: *gene.results files contain quantification (TPM/FPKM/count) derived from RSEM.

source_name: cortices

extract_protocol:
RNA were extracted using TRIzol (Life Technologies). RNA quality was determined by examining A260/A280 with NanodropTM OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit   3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched and quantified, and finally sequenced on Novaseq 6000 sequencer (Illumina) with 150 bp paired-end reads.

treatment_protocol: O4+ OLs isolated from cortices of control and Dor iKO mice treated with TAM from P5 to P9

value: cortices


title: Dor Ctrl

value: Ctrl


title: MGUS_4

description: 10x Genomics


title: PG - ChREBPtotal_KO - Rep7


title: Normal-2


title: PG - ChREBPtotal_WT - Rep6


title: PG - ChREBPtotal_WT - Rep2


title: Dor cKO 2

source_name: Optic nerves

extract_protocol:
RNA from the optic nerves of controls, and Dor mutants were extracted using TRIzol (Life Technologies). RNA quality was determined by examining A260/A280 with NanodropTM OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit® 3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched and quantified, and finally sequenced on Novaseq 6000 sequencer (Illumina) with 150 bp paired-end reads.

value: Optic nerves

value: Dor cKO


title: PG - ChREBPbeta_WT - Rep1


title: MGUS_3

description: 10x Genomics


title: Normal-1

value: Peripheral blood serum exosomes


title: PG - ChREBPbeta_KO - Rep5


title: MGUS_2

description: 10x Genomics


title: MGUS_1

description: 10x Genomics


title: Dor cKO 1


title: U2OS_siNAT10_BHB_HiC_rep1

city: Beijing

first: wenhui

last: Zhao

address: 5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
The BWA package was used to map the  sequences against the human reference genome with the parameter -n 0. Mapped  reads with MAPQ quality scores ≥20 were chosen for further analysis.
We applied the ICE  method to normalize the interaction matrix for different resolutions
If a region between two adjacent boundaries was less than 400 kb, the region was  marked as a TAD boundary
The Juicer pipeline’s HiCCUPS was applied for discovery of locally enriched  peaks
Genome_build: hg19
Supplementary_files_format_and_content: all the locally  enriched peaks were determined by HiCCUPS

source_name: U2OS cells

extract_protocol:
The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes
Hi-C libraries were prepared for sequencing using standard Illumina protocols

value: U2OS cells

value: NAT10 knockdown

value: β-hydroxybutyrate treated


title: U2OS_siNAT10_BHB_HiC_rep2


title: Dor WT 2

value: Dor WT


title: Healthy donor_5

description: 10x Genomics

value: Bone marrow aspirate

value: Healthy


title: RA-HW101

value: RA


title: PG - ChREBPbeta_KO - Rep6

value: ChREBPbeta


title: U2OS_siNAT10_HiC_rep2

value: untreated


title: Healthy donor_4

description: 10x Genomics


title: PG - ChREBPbeta_WT - Rep7


title: PG - ChREBPtotal_WT - Rep7

value: ChREBPtotal


title: Dor WT 1


title: PG - ChREBPbeta_WT - Rep2


title: Tgfb1_WT_2

city: San Francisco

first: Jeremy

middle: Michael

last: Shea

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: University of California, San Francisco

data_processing:
cellranger count (version 5.0.1) mapped fastq files to the mm10 transcriptome and created gene expression matrices.
Assembly: mm10
Supplementary files format and content: Sparse expression matrix

source_name: Hippocampal Cd11b+ cells

growth_protocol: 6-7 month old mice were injected with tamoxifen for 5 days.

extract_protocol:
Cd11b+ cells were isolated from hippocampi following enzymatic dissociation. Transcription and translation inhibitors were included in isolation buffers to prevent ex vivo changes.
Libraries were generated with 10x Gene Expression 3' v3.1 dual index kits

treatment_protocol: Mice were maintained for 60 days after injection and then euthanized for cell isolation

value: Cx3cr1-CreERT::Tgfb1 wt/wt

value: Microglia

value: 6-7 month old

value: WT


title: U2OS_siNAT10_HiC_rep1


title: PG - ChREBPtotal_WT - Rep3


title: Tgfb1_WT_1


title: U2OS_siCtrl_BHB_HiC_rep1

value: control


title: Tgfb1_Het_2

value: Cx3cr1-CreERT::Tgfb1 fl/wt

value: Het


title: U2OS_siCtrl_BHB_HiC_rep2

value: U2OS cells


title: Healthy donor_1

description: 10x Genomics


title: Healthy donor_2

description: 10x Genomics


title: Healthy donor_3

description: 10x Genomics


title: U2OS_siCtrl_HiC_rep2


title: PG - ChREBPtotal_KO - Rep3


title: U937 cells, Control, Rep 3

city: Wenzhou, CHINA

first: Xiaofang

last: Wang

state: Zhejiang

address: Shangcai Village, Nanbaixiang, Ouhai District

department: Department of Hematology

institute: The First Affiliated Hospital of Wenzhou Medical University

description: FPKM_ Control-3

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), DEGs with | log2FC | > 1 and Padj < 0.05 were considered to be significantly different expressed genes.
Assembly: Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
Supplementary files format and content: Allgene_info.xls

growth_protocol: U937 acute myeloid leukemia cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the XXX (tissue or cell) using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.

treatment_protocol: U937 cells were treated with 50μM luteoloside or 0.1%  Dimethyl sulfoxide (DMSO) for 72 h.

value: acute myeloid leukemia cells

value: 0.1% DMSO


title: U2OS_siCtrl_HiC_rep1


title: Tgfb1_KO_2

value: Cx3cr1-CreERT::Tgfb1 fl/fl

value: cKO


title: PG - ChREBPtotal_WT - Rep5


title: U937 cells, Control, Rep 2

description: FPKM_ Control-2


title: U937 cells, Control, Rep 1

description: FPKM_ Control-1


title: 11671

data_processing:
FASTQ reads were pseudo aligned to the mouse transcriptome (GRCm39 cDNA from Ensembl) using kallisto with default parameters.
Differential expression analysis was performed using DeSeq2 using the Wald significance test.
Genome_build: mm10 (GRCm39)
Supplementary_files_format_and_content: Kallisto abundance estimates. Differential expression results and abundance estimates from DeSEQ. Both files types are .csv.

source_name: Hippocampal microglia

growth_protocol: 4-5 month old Cx3cr1-CreERT::Tgfb1 fl/fl or Cx3cr1-CreERT::Tgfb1 fl/wt mice

extract_protocol:
Microglia were isolated by FACS 60 days after tamoxifen treatment. Trizol isolation of RNA was performed.
5ng of total RNA was reverse transcribed with SuperScript II (Thermo Fisher) using an oligo-dT RT primer with a PCR binding site and a template switching oligonucleotide with a homotypic PCR binding site. Betaine and MgCl2 were added to enhance the reaction. After reverse transcription, whole transcriptome amplification by PCR was performed for 12 cycles using HiFi HotStart ReadyMix (KAPA) with a PCR primer. The PCR reaction was cleaned up with Ampure XP beads. The amplified DNA was diluted to a concentration of 0.5ng/ul, and subjected to tagmentation with the Illumina Nextera XT kit. Each sample was PCR amplified with a unique set of Nextera indices.

treatment_protocol: Tamoxifen was injected for five days to induce Cre-mediated recombination

tag: sample name

value: Cx3cr1 +/wt ::Tgfb1 fl/wt


title: PG - ChREBPtotal_KO - Rep2


title: PG - ChREBPbeta_WT - Rep4


title: Tgfb1_KO_1


title: U937 cells, Lue, Rep 3

description: FPKM_ Lue-50uM-3

value: 50uM Luteoloside


title: 11670

value: Cx3cr1 +/wt ::Tgfb1 fl/fl


title: Mut_Inf_6 [210019_23_Mut_Inf_40_s23_S234]

city: Tampere

first: Reetta

last: Nätkin

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology, Prostate Cancer Research Center

country: Finland

institute: Tampere University and Tays Cancer Center

data_processing:
Automatic adapter trimming, Base calling bcl2fastq2 conversion software (NovaSeq 6000)
Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11
Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104
Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0
Genome_build: GRCz11
Supplementary_files_format_and_content: Genewise read counts for each sample (featureCounts, .txt) and protein coding gene filtered DESeq2 normalized count matrix (.xlsx)

organism: Danio rerio

growth_protocol: The zebrafish were maintained according to the standard protocols.

extract_protocol:
Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit (ID: 74136) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 9 to 10 months old zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish, treated with identical protocol, were used as controls.

value: M. marinum infection

value: pycard -/- mutant

value: low dose, 4 wpi

tag: tissue

value: Zebrafish kidney


title: Mut_Inf_5 [210019_22_Mut_Inf_39_s22_S233]


title: PG - ChREBPbeta_KO - Rep3

value: ChREBPbeta


title: U937 cells, Lue, Rep 2

description: FPKM_ Lue-50uM-2

tag: cell type

value: WT


title: 11668

value: Microglia

tag: genotype


title: PG - ChREBPtotal_KO - Rep4

tag: strain

value: ChREBPtotal


title: PG - ChREBPbeta_KO - Rep4


title: Mut_Inf_4 [210019_21_Mut_Inf_38_s21_S232]


title: Tgfb1_Het_1

value: Cx3cr1-CreERT::Tgfb1 fl/wt

value: 6-7 month old

value: Het


title: PG - ChREBPbeta_WT - Rep3


title: U937 cells, Lue, Rep 1

description: FPKM_ Lue-50uM-1

tag: cell line

value: acute myeloid leukemia cells


title: PG - ChREBPtotal_WT - Rep4


title: 11578


title: Mut_Inf_3 [210019_20_Mut_Inf_36_s20_S231]

tag: treatment


title: skin construct, inflamed, 48 hours, AC100_3

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

country: Italy

institute: PICB

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: HFF-1, HaCaT

growth_protocol: Fibroblasts and keratinocytes were cocultured in a collagen matrix for 14 days, until the fibroblasts were embedded in the collagen matrix, and the keratinocytes over them

extract_protocol:
RNA was extracted using Quick-DNA/RNA™ Microprep Plus Kit from Zymo Research and store at -80°C
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After 14 days, half of the constructs were perfused with TNF-α to mimic an inflammatory state. Electrostimulation is tested on normal and inflamed samples, to have unstimulated and stimulated samples, at 1 and 5V in direct current (DC), and in alternate current, at 10 and 100 Hz. Each condition was tested in three replicates, and sampling was done at three timepoints (baseline, 1 h and 48 h) following stimulation.

value: HFF-1, HaCaT

value: immortalized human fibroblasts, immortalized human keratinocytes

tag: group

value: inflamed

tag: time point

value: 48 hours


title: Mut_Inf_7 [210019_24_Mut_Inf_42_s24_S235]


title: Mut_Inf_2 [210019_19_Mut_Inf_35_s19_S229]


title: 11576

value: Cx3cr1 +/wt ::Tgfb1 fl/wt


title: Liver - ChREBPtotal_WT - Rep5

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 25 out of 31 microarrays or with a minimal weight of 6 per group from at least one experimental group. At this step, 38719 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36057 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver


title: skin construct, inflamed, 48 hours, AC100_2


title: WT_Inf_9 [210019_17_WT_Inf_33_s17_S227]

value: M. marinum infection

value: wild type


title: Mut_Inf_1 [210019_18_Mut_Inf_34_s18_S228]

value: pycard -/- mutant

value: low dose, 4 wpi


title: skin construct, inflamed, 48 hours, AC100_1


title: 11543


title: PG - ChREBPbeta_KO - Rep2

value: ChREBPbeta


title: Liver - ChREBPbeta_WT - Rep7


title: skin construct, inflamed, 1 hour, AC100_2

value: 1 hour


title: 11542

value: Microglia

value: Cx3cr1 +/wt ::Tgfb1 fl/fl


title: WT_Inf_8 [210019_16_WT_Inf_32_s16_S226]

value: Zebrafish kidney


title: Liver - ChREBPbeta_WT - Rep1


title: skin construct, inflamed, 1 hour, AC100_1


title: WT_Inf_7 [210019_15_WT_Inf_31_s15_S225]


title: MG824TGFBCTL

description: mginvitrosamples.csv

source_name: Primary microglia

growth_protocol: Mixed glial cultures were generated from p1 male pups. Cortices and hippocampi were isolated from the pups, and meninges were removed. The tissue was broken up by repeatedly pipetting up and down, followed by dissociation with Trypsin. Single cell suspensions were plated on poly-L-lysine coated flasks in DMEM supplemented with 10% FBS and antibiotic mix (Penicillin/Streptomycin/Amphotericin B) and incubated at 37C in 5% CO2. Media was changed after 4 days to remove debris. Microglia were isolated after 14 days by agitating the plates to dislodge microglia, then transferring the supernatant of each sample evenly amongst 4 wells of a 24 well plate. Microglia were incubated for 16 hours followed by replacement with serum free macrophage media supplemented with M-CSF (10ng/mL)(Peprotech, 315-02) and antibiotic mix.

extract_protocol:
Tri Reagent was added to the culture plate, and the plates were shaken for 5 minutes. RNA was isolated according to manufacturer’s instructions.
5ng of total RNA was reverse transcribed with SuperScript II (Thermo Fisher) using an oligo-dT RT primer with a PCR binding site and a template switching oligonucleotide with a homotypic PCR binding site. Betaine and MgCl2 were added to enhance the reaction. After reverse transcription, whole transcriptome amplification by PCR was performed for 12 cycles using HiFi HotStart ReadyMix (KAPA) with a PCR primer. The PCR reaction was cleaned up with Ampure XP beads. The amplified DNA was diluted to a concentration of 0.5ng/ul, and subjected to tagmentation with the Illumina Nextera XT kit. Each sample was PCR amplified with a unique set of Nextera indices.

treatment_protocol: Microglia were treated with carbonyl cyanide 3-chlorophenylhydrazone (CCCP, 20uM)(Sigma-Aldrich, C2759), RNA polymerase I Inhibitor 2, CX-5461 (100nM)(EMD Millipore, 509265), or human TGFb1 recombinant protein (10ng/mL)(ThermoFisher Scientific, PHG9204) for 24 hours followed by addition of lipopolysaccharides (LPS, 200nM) from E. coli (Sigma-Aldrich, L2018) for 8 hours and ATP (10nM) for 30 minutes.

value: microglia

tag: primary treatment

value: TGFB

tag: secondary treatment

value: CTL


title: WT_Inf_6 [210019_14_WT_Inf_30_s14_S224]


title: skin construct, inflamed, 48 hours, AC10_2

value: HFF-1, HaCaT


title: 11577


title: skin construct, inflamed, 48 hours, AC10_1

value: immortalized human fibroblasts, immortalized human keratinocytes


title: Liver - ChREBPbeta_KO - Rep6


title: Liver - ChREBPtotal_KO - Rep6

value: ChREBPtotal


title: MG624CCCPCTL

description: mginvitrosamples.csv

value: CCCP


title: WT_Inf_5 [210019_13_WT_Inf_29_s13_S223]


title: Liver - ChREBPbeta_KO - Rep8


title: MG724CCCPCTL

description: mginvitrosamples.csv


title: skin construct, inflamed, 1 hour, AC10_3

value: inflamed


title: MG524CCCPCTL

description: mginvitrosamples.csv


title: Liver - ChREBPbeta_KO - Rep1


title: WT_Inf_4 [210019_12_WT_Inf_28_s12_S222]

value: M. marinum infection


title: Liver - ChREBPtotal_WT - Rep7


title: skin construct, inflamed, 1 hour, AC10_2


title: WT_Inf_3 [210019_11_WT_Inf_27_s11_S221]

value: wild type


title: skin construct, inflamed, 1 hour, AC10_1


title: MG516CXCTL

description: mginvitrosamples.csv


title: MG424CCCPCTL

description: mginvitrosamples.csv


title: skin construct, inflamed, 48 hours, DC5_2

value: 48 hours


title: WT_Inf_2 [210019_10_WT_Inf_25_s10_S220]

value: low dose, 4 wpi


title: MG324CCCPCTL

description: mginvitrosamples.csv


title: MG2016TGFBCTL

description: mginvitrosamples.csv


title: WT_Inf_1 [210019_9_WT_Inf_21_s9_S242]


title: skin construct, inflamed, 48 hours, DC5_1


title: Liver - ChREBPbeta_KO - Rep7

value: ChREBPbeta


title: Mut_PBS_5 [210019_8_Mut_PBS_18_s8_S241]

value: PBS injection

value: pycard -/- mutant


title: skin construct, inflamed, 1 hour, DC5_2

value: 1 hour


title: MG1616TGFBCTL

description: mginvitrosamples.csv


title: Liver - ChREBPtotal_WT - Rep8


title: Liver - ChREBPbeta_WT - Rep8


title: Liver - ChREBPtotal_KO - Rep7


title: skin construct, inflamed, 1 hour, DC5_1


title: Mut_PBS_4 [210019_7_Mut_PBS_15_s7_S240]

value: Zebrafish kidney


title: Mut_PBS_3 [210019_6_Mut_PBS_13_s6_S239]


title: Liver - ChREBPbeta_WT - Rep6


title: MG1224TGFBCTL

description: mginvitrosamples.csv

value: microglia


title: MG1416TGFBCTL

description: mginvitrosamples.csv

value: TGFB


title: skin construct, inflamed, 1 hour, DC1_3


title: skin construct, inflamed, 48 hours, DC1_1


title: skin construct, inflamed, 1 hour, DC1_2


title: Mut_PBS_2 [210019_5_Mut_PBS_12_s5_S238]


title: MG124CXCTL

description: mginvitrosamples.csv

value: CTL


title: Liver - ChREBPbeta_KO - Rep5


title: Mut_PBS_1 [210019_4_Mut_PBS_11_s4_S237]


title: MG516CXLPS

description:
mginvitrosamples.csv
CX5461LPS_vs_DMSOLPS-ExpDiff.csv

value: LPS


title: Liver - ChREBPtotal_WT - Rep6


title: Liver - ChREBPtotal_KO - Rep8


title: WT_PBS_3 [210019_3_WT_PBS_s3_S236]


title: WT_PBS_2 [210019_2_WT_PBS_s2_S230]


title: MG124CXLPS


title: Liver - ChREBPtotal_KO - Rep2


title: MG116CXLPS


title: skin construct, inflamed, 48 hours, NO_3

value: HFF-1, HaCaT

value: immortalized human fibroblasts, immortalized human keratinocytes

value: NO treatment


title: skin construct, inflamed, 48 hours, NO_2

value: inflamed


title: skin construct, inflamed, 48 hours, NO_1


title: Liver - ChREBPbeta_WT - Rep2


title: B6_scRNASeq_2

city: Baltimore

first: Taibo

last: Li

state: MD

address: 1830 E Monument Street, Suite 2-300

institute: Johns Hopkins School of Medicine

data_processing:
Demultiplexing, barcode processing, gene counting and merging was performed using CellRanger
Assembly: mm10
Supplementary files format and content: tab-delimited count files with attribute matrices as separate files

source_name: Anterior segment of mouse eye

extract_protocol:
The anterior segment of the eye including the limbus was dissected from 3-month-old Prox1-GFP mice. A strip of limbal tissue 1-2 mm wide consisting of the aqueous humor outflow tissues SC and TM, ciliary body, iris, and cornea was dissected from each anterior segment in ice-cold Dulbecco’s modified Eagle’s medium DMEM. To enrich for aqueous humor outflow tissues, limbal strips from 6 C57Bl/6J eyes (4 females, 2 males) were pooled for a single run of C57BL/6J scRNA-seq. C57BL/6J scRNA-seq was performed on two separate pools of eyes for a total of 12 eyes (8 females, 4 males). For 129/Sj scRNA-seq, 6 eyes (3 females, 3 males) were pooled for a single run.
Single cell dissociation was performed using Papain and Deoxyribonuclease I (Worthington Biochemical Cat. no. LK003153) for 20 min at 37°C and stopped using Earl’s balanced salt solution (EBSS-Thermo Fisher Scientific, Cat no. 24010-043). Cells were triturated using an 18-gauge needle, centrifuged at 300g at 4 °C, washed with cold DMEM, and filtered using a 100 μm cell strainer. Cells were resuspended in cold DMEM and placed on ice immediately. Cells were counted using Countess II automated cell counter and processed for 10x library preparation immediately

value: Anterior segment of mouse eye


title: B6_sNucRNASeq


title: MG124LPS8

value: DMSO


title: skin construct, inflamed, 1 hour, DC1_1


title: skin construct, inflamed, 1 hour, NO_1


title: MG116LPS8


title: B6_scRNASeq_1


title: MG2016TGFBLPS

description:
mginvitrosamples.csv
DMSOLPS_vs_TGFBLPS-ExpDiff.csv


title: Liver - ChREBPtotal_KO - Rep4

value: ChREBPtotal


title: Liver - ChREBPtotal_WT - Rep1


title: Liver - ChREBPbeta_KO - Rep2


title: Liver - ChREBPbeta_WT - Rep3


title: WT_PBS_1 [210019_1_WT_PBS_s1_S219]

value: wild type

value: low dose, 4 wpi


title: 129S_scRNASeq


title: skin construct, inflamed, 0 hours, NO_2

value: 0 hours


title: MG1616TGFBLPS


title: 18mthhip3

source_name: Hippocampus

growth_protocol: Mice were aged followed by RNA extraction

extract_protocol:
Trizol isolation
5ng of total RNA was reverse transcribed with SuperScript II (Thermo Fisher) using an oligo-dT RT primer with a PCR binding site and a template switching oligonucleotide with a homotypic PCR binding site. Betaine and MgCl2 were added to enhance the reaction. After reverse transcription, whole transcriptome amplification by PCR was performed for 12 cycles using HiFi HotStart ReadyMix (KAPA) with a PCR primer. The PCR reaction was cleaned up with Ampure XP beads. The amplified DNA was diluted to a concentration of 0.5ng/ul, and subjected to tagmentation with the Illumina Nextera XT kit. Each sample was PCR amplified with a unique set of Nextera indices.

value: Bulk hippocampus

tag: age

value: 18 months


title: skin construct, physio, 48 hours, AC100_2

value: physio

value: 48 hours


title: Liver - ChREBPbeta_WT - Rep5

value: ChREBPbeta


title: MG516LPS8

value: microglia


title: skin construct, inflamed, 0 hours, NO_1


title: Liver - ChREBPtotal_WT - Rep3


title: 18mthhip2


title: 18mthhip1


title: Liver - ChREBPbeta_KO - Rep4


title: MG1224TGFBLPS

value: TGFB

value: LPS


title: skin construct, inflamed, 1 hour, NO_2

value: HFF-1, HaCaT

value: immortalized human fibroblasts, immortalized human keratinocytes

value: 1 hour


title: Liver - ChREBPtotal_WT - Rep2


title: skin construct, physio, 48 hours, AC100_1


title: MG824TGFBLPS


title: 6mthhip3

value: 6 months


title: Liver - ChREBPtotal_KO - Rep5


title: skin construct, physio, 1 hour, AC100_3


title: Liver - ChREBPbeta_WT - Rep4


title: MG724CCCPLPS

description:
mginvitrosamples.csv
DMSOLPS_vs_CCCPLPS-ExpDiff.csv

value: CCCP


title: MG524CCCPLPS


title: 6mthhip2


title: MG1416TGFBLPS


title: 6mthhip1


title: skin construct, physio, 1 hour, AC100_1


title: MG324CCCPLPS


title: 24m2

description:
AgeMGAbundance.csv
3m_vs_24m-ExpDiff.csv

value: Microglia

value: 24 months


title: MG824DMSOLPS

description:
mginvitrosamples.csv
DMSOLPS_vs_TGFBLPS-ExpDiff.csv
DMSOCTL_vs_DMSOLPS-ExpDiff.csv

value: DMSO


title: MG424CCCPLPS


title: skin construct, physio, 48 hours, AC10_3


title: 24m1


title: skin construct, physio, 48 hours, AC10_2


title: skin construct, physio, 1 hour, AC10_3


title: MG824DMSOCTL

description:
mginvitrosamples.csv
DMSOCTL_vs_DMSOLPS-ExpDiff.csv

value: CTL


title: skin construct, physio, 1 hour, AC100_2


title: 24m3


title: Liver - ChREBPbeta_KO - Rep3


title: Liver - ChREBPtotal_WT - Rep4

value: ChREBPtotal


title: Liver - ChREBPtotal_KO - Rep1


title: BAT - ChREBPbeta_KO - Rep6

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 26 out of 32 microarrays or with a minimal weight of 6 per group from at least one experimental group. At this step, 39983 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 37304 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Brown Adipose Tissue


title: BAT - ChREBPtotal_WT - Rep6


title: 3m2

value: 3 months


title: skin construct, physio, 1 hour, AC10_2

value: physio


title: BAT - ChREBPbeta_WT - Rep6


title: MG724DMSOLPS


title: 3m1


title: MG624DMSOLPS


title: skin construct, physio, 1 hour, AC10_1


title: 4-cell, HT_3

city: Cheongju

first: Chenglin

last: Zhan

state: Chungcheong-buk do

address: Chungdae-ro 1, Seowon-Gu

department: department of animal science

country: South Korea

institute: chungbuk national university

data_processing:
Paired-end sequencing reads were generated using an Illumina NovaSeq sequencing platform.
Trimmomatic v0.38 was used to remove adapter sequences and trim bases of poor base quality.
The cleaned reads were aligned to Sus scrofa (Sscrofa11.1) using HISAT v2.1.0, based on the HISAT and Bowtie2 implementations.
The aligned data (SAM file format) were sorted and indexed using SAM tools v 1.9.
The transcripts were assembled and quantified using StringTie v2.1.3b.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM and TPM value for each sample

organism: Sus scrofa

source_name: 4-cell embryo

growth_protocol: Oocytes were activated with two direct-current pulses of 120 V for 60 µs.  Activated oocytes were thoroughly washed using in vitro culture (IVC) medium (PZM-5 supplemented with 4 mg/mL BSA)

extract_protocol:
mRNA was extracted according to the instructions of the Dynabeads mRNA Direct Purification Kit(61012, Thermo Fisher)
About 300 samples (4C) in the lysis buffer were used to construct sequencing libraries with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Illumina, following the manufacturer's protocol.

treatment_protocol: Each group was cultured in IVC medium covered with mineral oil for 4 days to four cell stage at 38.5°C in a humid environment containing 5% CO2, among which the HT group was cultured at 41.5°C.

value: 4-cell embryo

value: HT

value: cultured at 41.5°C


title: skin construct, physio, 48 hours, AC10_1

value: 48 hours


title: 3m3


title: skin construct, physio, 48 hours, DC5_2


title: MG624DMSOCTL

value: microglia


title: 4-cell, HT_2


title: 4-cell, HT_1


title: skin construct, physio, 48 hours, DC5_1

value: HFF-1, HaCaT


title: MG724DMSOCTL


title: MG524DMSOCTL


title: BAT - ChREBPtotal_KO - Rep7

extract_protocol: Tissues were homogenized in Qiazol buffer (Qiagen 79306) using Precellys tissue homogenizer. Total RNA from tissues was extracted using RNeasy kit (Qiagen 75162).


title: BAT - ChREBPbeta_WT - Rep8

value: ChREBPbeta


title: BAT - ChREBPtotal_WT - Rep8


title: 4-cell, Control_3

value: WT

value: cultured at 38.5°C


title: skin construct, physio, 48 hours, DC5_3

value: immortalized human fibroblasts, immortalized human keratinocytes


title: skin construct, physio, 1 hour, DC5_1

value: 1 hour


title: 4-cell, Control_2


title: MG424DMSOLPS

description:
mginvitrosamples.csv
DMSOLPS_vs_CCCPLPS-ExpDiff.csv
DMSOCTL_vs_DMSOLPS-ExpDiff.csv

value: LPS


title: 4-cell, Control_1


title: MG524DMSOLPS

value: DMSO


title: skin construct, physio, 48 hours, DC1_2


title: BAT - ChREBPbeta_KO - Rep8


title: BAT - ChREBPtotal_KO - Rep1


title: skin construct, physio, 48 hours, DC1_1


title: MG424DMSOCTL

value: CTL


title: Liver, Treated_Standard_diet, 7

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

data_processing:
Adaptor sequence trimming and quality check were done using fastp, and ribosomal RNA was removed using bowtie2 tool (ver 2.4.5) (parameter: -l  50).
Reads were aligned to the reference genome using the STAR tool (ver 2.7.10a) (parameter: --outSAMstrandField intronMotif, --outFilterMismatchNmax 4, --outFilterMultimapNmax 1, --outSAMunmapped Within).
The aligned reads were counted using featureCounts in Subread package (ver. 2.0.3) (parameter: -B).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample.

extract_protocol:
RNA was harvested with QIAzol lysis reagent (QIAGEN) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Set following manufacturer's protocols.

treatment_protocol: Murine hepatic tissue of 2 experimental sets: 1) C57BL/6J inbred male mice (n=20) fed a CDAHF diet for 12 weeks. Then, 2 weeks of HFD and either 4.3 mg/kg Fc  (control n = 10), or 5 mg/kg Fc(mML1)B3 (n = 10) once a week . 2) C57BL/6J inbreed mice (n=16) were fed a CDAHFD for 12 weeks, Then 10 days of  standard diet and either 4.3 mg/kg Fc (control n = 9), or 5 mg/kg of Fc(mML1)B3 (n = 7) at days 1, 4, and 7.

value: Liver

tag: Sex

value: male

value: Standard diet


title: Liver, Treated_Standard_diet, 6


title: MG324DMSOCTL


title: BAT - ChREBPtotal_KO - Rep8

value: ChREBPtotal

tag: washbatch


title: skin construct, physio, 1 hour, DC1_1

value: physio


title: skin construct, physio, 48 hours, DC1_3


title: MG2016DMSOLPS


title: Liver, Treated_Standard_diet, 5


title: skin construct, physio, 48 hours, NO_3

value: NO treatment


title: Liver, Treated_Standard_diet, 4


title: MG516DMSOCTL


title: MG1416DMSOLPS


title: BAT - ChREBPtotal_WT - Rep1


title: skin construct, physio, 48 hours, NO_2

value: 48 hours


title: Liver, Treated_Standard_diet, 2


title: MG1416DMSOCTL

value: microglia


title: MG324DMSOLPS


title: skin construct, physio, 48 hours, NO_1

value: HFF-1, HaCaT


title: skin construct, physio, 1 hour, DC1_2


title: BAT - ChREBPbeta_WT - Rep5

value: ChREBPbeta


title: BAT - ChREBPbeta_WT - Rep7


title: BAT - ChREBPtotal_KO - Rep6


title: MG1224DMSOLPS


title: BAT - ChREBPtotal_WT - Rep7


title: BAT - ChREBPbeta_KO - Rep5


title: BAT - ChREBPbeta_KO - Rep7


title: MG1224DMSOCTL


title: skin construct, physio, 1 hour, NO_2


title: Liver, Treated_Standard_diet, 3


title: MG124DMSOLPS


title: Liver, Control_Standard_diet, 9

value: Fc


title: BAT - ChREBPbeta_WT - Rep3


title: Liver, Control_Standard_diet, 7


title: Liver, Control_Standard_diet, 8


title: skin construct, physio, 0 hours, NO_2

value: 0 hours


title: skin construct, physio, 0 hours, NO_3

value: immortalized human fibroblasts, immortalized human keratinocytes


title: skin construct, physio, 1 hour, NO_1

value: 1 hour


title: BAT - ChREBPtotal_KO - Rep5


title: Liver, Control_Standard_diet, 6


title: Liver, Treated_Standard_diet, 1


title: MG124DMSOCTL


title: BAT - ChREBPtotal_WT - Rep5


title: 24 month hippocampal microglia

data_processing:
cellranger mkfastq (version 2.1.1) generated fastq files
cellranger count (version 2.1.1) mapped fastq files to the mm10 transcriptome and created gene expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Sparse expression matrix

source_name: Cd11b+ cells

extract_protocol:
Hippocampi were dissociated using Miltenyi Neural Tissue Dissociation kit (P) followed by myelin depletion and CD11b cell enrichment using magnetic beads. Gel bead emulsions are generated on the 10x Chromium controller that contain single cells, barcodes, and reverse transcription reagents
10x Single Cell 3' v2
scRNA-Seq

value: hippocampus

value: 24 month


title: BAT - ChREBPbeta_KO - Rep2


title: Liver, Control_Standard_diet, 5


title: 18 month hippocampal microglia

value: 18 month


title: BAT - ChREBPbeta_WT - Rep4


title: Liver, Control_Standard_diet, 4

value: Liver


title: skin construct, physio, 0 hours, NO_1


title: BAT - ChREBPbeta_WT - Rep1


title: 12 month hippocampal microglia

value: 12 month


title: N2ko_UPF1scr,rep3

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
The raw reads were subjected to FastQC (v0.11.9). Low-quality bases and adaptor sequences were removed using Trimmomatic (v0.38) with options (ILLUMINCLIP:Adapter.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW: 4:20 MINLEN:50). Clean reads were mapped to 4S rRNA using bowtie2 (v2.3.5) with parameters (‘-q --sensitive --reorder --no-unal --un-conc-gz’). Unmapped reads were mapped to hg38 genome using HISAT2 (v2.1.0) with parameters (‘--no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k5 --dta’). The mapped reads were processed to featureCounts (v2.0.1) for feature counting.
To quantify RNA, fragment abundance in genes with ≥50 mapped reads were selected and normalized using the size factors estimated by the median of all genes implemented in the DESeq2 (v1.30.1) Bioconductor package. Differential expression analysis was performed by DESeq2. Genes with log2(fold change) ≥ 1.2 and adjusted p-value ≤ 0.05 were regarded as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: HeLa

growth_protocol: HeLa cells (human cervical cancer) were obtained from ATTC and confirmed with CellBank Australia. Cells were grown in DMEM medium (Gibco™) supplemented with 10% FBS and 1% antibiotic-antimycotic solution (Sigma) and passaged when 70–90% confluent.

extract_protocol:
Extraction of total RNA was performed using the Direct-zol RNA Miniprep (Zymo Research) kit according to the manufacturer’s instructions.
RNA enrichment (rRNA depletion); RNA fragmentation (enzymatic digestion); cDNA reverse transcription; RNA library preparation.

treatment_protocol: For knockdown experiments, 200x103  WT or NSUN2 KO HeLa cells were plated in 35mm plates and transfected 6-12hrs later with the siRNA against the target selected (FlexiTube siRNA UPF-1, Cat. No. GS5976; Qiagen) or the negative control (non-silencing siRNA, Cat. No. 1022076; Qiagen) with a final concentration 30nM, using 5μL of Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) and 300μL of Opti-MEM (Thermo Fisher Scientific). The medium was replaced 12hrs later and cells were harvested 48hrs later.

value: HeLa

value: NSUN2 knockout


title: Liver, Control_Standard_diet, 3

value: male

value: Standard diet


title: BAT - ChREBPbeta_KO - Rep3


title: Liver, Control_Standard_diet, 2


title: 6 month hippocampal microglia

value: 6 month


title: N2ko_UPF1si,rep3

value: NSUN2 knockout, UPF1 knockdown


title: N2ko_UPF1si,rep2


title: BAT - ChREBPtotal_WT - Rep2

value: ChREBPtotal


title: uninfected perch spleen 488

city: Stockholm

first: Anti

last: Vasemägi

address: Stångholmsvägen 2

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
The raw sequence files in fastq format returned from Novogene were run through FastQC v0.11.9 both before and after trimming to check the overall quality of the reads. The trimming was performed by fastp v.0.20 . Only reads which were both longer than 50 bp and were of mean quality of 25 were processed further.
The reads which passed the quality control were mapped on the reference genome of Perca fluviatilis using hisat2 v.2.1.1 using default parameters. The produced .sam files were subsequently processed with samtools v.1.10. Lastly, the mapped reads were extracted in bam format for subsequent differential expression analysis.
Analysis for differentially expressed genes (DEGs) was performed in R v.4.2.2 using the DESeq2 v.1.36.0 package. When designing the DESeq dataset object, we considered infection status and population as fixed factors, and the DESeq model internally corrects for potential differences in library sizes. Genes with an adjusted p-value (p-adj) ≤ 0.05 [40] were considered as significantly differentially expressed between infected and uninfected individuals. Human orthologue genes were obtained via Ozerov et al., and DEGs without human orthologues were manually searched using BLAST.
Supplementary files format and content: processed fastq files

organism: Perca fluviatilis

source_name: spleen

extract_protocol:
Tissue samples were crushed with a steel mortar and pestle to produce a homogenized powder, while frozen spleen tissue was mechanically crushed (the tissue consistency of spleen samples was not conducive to mortar and pestle homogenization) using a Retsch Mixer Mill MM 400 (Retsch). Total RNA was extracted using a NucleoSpin RNA extraction kit (MACHEREY-NAGEL, Duren, Germany). RNA sample concentrations were measured with a NanoDrop 2000 (ThermoFisher), and sample quality was evaluated using a TapeStation 2200 (Agilent Technologies)
Sequencing libraries were prepared at the Novogene Cambridge Science Park (Cambridge, United Kingdom) from 300 ng total RNA

value: spleen

value: Male

tag: infection status

value: uninfected


title: infected perch spleen 478

value: infected


title: Liver, Treated_HFD, 10

value: HFD


title: Liver, Control_Standard_diet, 1

value: Fc


title: BAT - ChREBPtotal_KO - Rep4


title: N2ko_UPF1scr,rep2


title: uninfected perch spleen 483


title: uninfected perch liver 489

source_name: liver

value: liver

value: Female


title: N2wt_UPF1si,rep3

value: UPF1 knockdown


title: N2wt_UPF1si,rep2


title: Liver, Treated_HFD, 9

value: Liver


title: N2wt_UPF1scr,rep2

value: HeLa

value: WT


title: Liver, Treated_HFD, 8

value: male


title: BAT - ChREBPbeta_KO - Rep4

value: ChREBPbeta


title: BAT - ChREBPtotal_WT - Rep3


title: uninfected perch liver 479


title: BAT - ChREBPbeta_WT - Rep2


title: Liver, Treated_HFD, 7


title: N2ko_UPF1si,rep1


title: N2wt_UPF1scr,rep3


title: infected perch liver 469


title: infected perch liver 474


title: BAT - ChREBPtotal_WT - Rep4


title: BAT - ChREBPtotal_KO - Rep3


title: N2ko_UPF1scr,rep1

value: NSUN2 knockout


title: BAT - ChREBPtotal_KO - Rep2


title: Normal control3

city: nanjing

first: Qinglin

state: jiangsu

address: Jiangsu Cancer Hospital

institute: Jiangsu Cancer Hospital

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller soft_x0002_ware, v1.8). Sequencing quality are examined by FastQC  and trimmed reads (pass Illumina quality filter, trimmed 5ÿ,3ÿ-adaptor bases by cutadapt ) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
Assembly: hg18
Supplementary files format and content: Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5ÿ,3ÿ-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precur_x0002_sor tRNA sequences with bowtie software. The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2. The abundance of tRF & tiRNA and miRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM). The tRFs & tiRNAs and miRNAs differentially expressed are screened based on the count value with R package edgeR

source_name: Lung

extract_protocol:
Total RNA samples are qualified by agarose gel electrophoresis and quantified using Nanodrop. We use the commercial kit for tRF & tiRNA-seq library preparation, which includes 3ÿ-adapter and 5ÿ-adapter ligation adaptor ligation, cDNA synthesis and library PCR amplification. The prepared tRF & tiRNA-seq libraries are finally quantified using Agilent BioAnalyzer 2100, then sequenced using Illumina NextSeq 500.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100
For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50bp single_x0002_read.

value: Lung

tag: disease

value: adjcent tissue

value: Normal control


title: Liver, Treated_HFD, 6


title: Liver, Treated_HFD, 5


title: N2wt_UPF1si,rep1


title: Normal control2


title: infected perch spleen 473

value: spleen


title: uninfected perch liver 59

value: uninfected


title: Liver, Treated_HFD, 4


title: infected perch liver 314

value: infected


title: HaCaT cells expressing Cas9, control gRNA, Low-density

city: Sapporo

first: Yosuke

last: Mai

state: Hokkaido

department: Department of Dermatology

institute: Hokkaido University

data_processing:
Sequence reads were trimmed using Trim Galore (v.0.6.4).
Trimmed sequence reads were then mapped to hg38 using STAR (v.2.7.3).
Gene expression levels were quantified using RSEM (v.1.3.1)
Assembly: hg38
Supplementary files format and content: tab-separated text file includes raw counts for each Sample
Supplementary files format and content: tab-separated text file includes CPM values calculated by edgeR for each Sample

source_name: HaCaT

growth_protocol: HaCaT cells were mainained in DMEM supplemented with 10% fetal bovine serum and antibitics in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was extracted using the FastGene RNA Premium Kit (Nippon genetics) according to the manufacturers’ instructions.
The library preparation and sequencing were performed in Novogene. Briefly, mRNA is enriched using oligo(dT) beads. The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. After a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: HaCaT cells were seeded into 6-cm plastic dishes at the concentration of 2.5 x 105/mL (Low-density) or 7.5 x 105/mL (High-density). After the overnight incubation at 37ºC in humidified 5% CO2, RNA was extracted.

value: HaCaT

value: epidermal keratinocyte

value: High-density


title: Liver, Treated_HFD, 3

value: HFD


title: uninfected perch liver 49

value: liver

value: Male


title: N2wt_UPF1scr,rep1

value: HeLa


title: Liver, Treated_HFD, 2

value: Liver


title: Low-Risk2

value: lung adenocarcinoma

value: Low-Risk


title: Low-Risk3


title: Liver, Treated_HFD, 1

value: male


title: HaCaT cells expressing Cas9, no gRNA, Low-density

value: WT


title: infected perch spleen 48

value: Female


title: HaCaT cells expressing Cas9, control gRNA, High-density


title: Low-Risk1

value: Lung


title: uninfected perch spleen 43

value: spleen


title: Normal control1

value: adjcent tissue

value: Normal control


title: BAT - ChREBPbeta_KO - Rep1

city: Toulouse Cedex 4

first: Dominique

institute: INSERM

value: ChREBPbeta


title: HaCaT cells expressing Cas9, no gRNA, High-density

value: HaCaT

value: epidermal keratinocyte


title: Liver, Control_HFD, 10

value: HFD

value: Fc


title: High-Risk3

value: High-Risk


title: uninfected perch spleen 38

value: Male

value: uninfected


title: Liver, Control_HFD, 9

value: Liver


title: infected perch liver 309K

value: liver

value: infected


title: 9/10/7-U937 Lacz with Ethanol, replicate 1

city: Freiburg im Breisgau

first: Usama Ur

last: Rehman

address: Breisacher Str. 115

department: ZTZ

institute: Uniklinik Freiburg

description:
replicate 1
U397_9107_EtOH1

data_processing:
All steps were performed at Galaxy server Europe. Read quality was assessed by FastQC and MultiQC. Reads were first trimmed to remove adapter sequences and poor-quality reads were removed with Cutadapt Galaxy Version 3.7+galaxy0).
Filtered reads were then aligned to the human genome (hg38) using STAR  (Version 2.7.8a+galaxy0) and read counts per gene were quantified using Featurecounts (Version 2.0.1+galaxy2).
The differential gene expression analysis was performed with the DESeq ( Version 2.11.40.7+galaxy1).  The significance threshold was set to adjusted p-value < 0.05 and fold change > 1.5
Assembly: hg38
Supplementary files format and content: tab-delimited text file of normalized counts

growth_protocol: RPM1 1640 Medium supplemented with 10% fetal bovine serum und 1 % Penicilin/Streptomicin/Glutamine

extract_protocol:
RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions
Truseq stranded mRNA kit (Illumina), Ligation with Ribo-Zero Plus kit.

treatment_protocol: Ponasterone A vs Ethanol

value: histiocytic lymphoma

value: control

value: Ethanol


title: High-Risk2

value: Lung

value: lung adenocarcinoma


title: 9/10/7-U937 Lacz with Ethanol, replicate 2

description:
replicate 2
U397_9107_EtOH2


title: 9/10/7-U937 Lacz with Pon A, replicate 2

description:
replicate 2
U397_9107_PonA2

value: Ponasterone A


title: ZFP740_KO3,replicate3,RNAseq

city: Guiyang

first: Hao

last: Zhang

address: No.9, Beijing Road City:guiyang

institute: College of Clinical Medicine

data_processing:
RNA libraries for RNA- seq were prepared using SMARER mRNA-Seq Library Prep Kit following manufacturers's protocols.
The raw reads obtained from sequencing were filtered to remove splice sequences, redundant sequences and low-quality reads to obtain high-quality sequences (clean reads). Reference genome-based alignment analysis was carried out using HISAT2!2) software. Based on the comparison results of HISAI2, transcripts were reconstructed using Stinatie, and the expression of all genes in each sample was calculated. The information of basal stem gene expression amount was used to carry out the principal component analysis (PCA) using R (htp:/ww.r-proiect.org).The data of gene differential expression analysis were the reads count data obtained from the gene expression level analysis, which was analyzed and screened for differentially expressed genes using the DESeg2 [23] software, and the differential multiplicity screened for FDR<0.05 day 1og, and the genes with FCI>1 as the genes that were differentially expressed. Genes with FCI>1 were significantly differentiated genes
Functional annotation of differentially expressed genes was performed using GO and KEGG databases, and FPKM values were used to reflect the expression of the genes
Assembly: GRCh38-3.0.0
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: ZFP740 knockdown HepG2 cells

growth_protocol: HepG2 hepatocellular carcinoma cells were obtained from the American Model Culture Depository. The cells were cultured in RPMI 1640 medium (HyClone, USA) containing 10% fetal bovine serum (FBS: NQBB, USA) and penicillin/streptomycin double antibody (Shanghai Baili Biological Company) in a humidified incubator at 37°C with 5% CO,.

extract_protocol:
Total RNA was isolated from the HepG2 cells using the RNeasy mini kit (Qiagen GMBH, Hilden, Germany) according to the manufacturer’s instructions, yielding 150 μg of total RNA.
The amount of total RNA was determined using a NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE). The quality of the RNA preparation was evaluated using the Agilent RNA 6000 Nano Kit on an Agilent Bioanalyzer 2100 system (Agilent, Palo Alto, CA). The quality of the preparation was considered to be high based on an RIN value of 8.7.

treatment_protocol: used the hepatocellular carcinoma cell line HepG2, and then divided into two groups, in which the control group was HepG2, and the intervention group was HepG2 with the knockdown of the ZNF740 gene

value: ZFP740 knockdown HepG2 cells

value: HepG2 cell

value: ZFP740 knockdown


title: High-Risk1


title: infected perch spleen 308

value: spleen

value: Female


title: uninfected perch liver 304


title: Liver, Control_HFD, 6

value: male

value: HFD

value: Fc


title: ZFP740_KO2,replicate2,RNAseq


title: 9/10/7-U937 Lacz with Pon A, replicate 1

description:
replicate 1
U397_9107_PonA1


title: 9/14/18-U937 AML1/ETO with Ethanol, replicate 2

description:
replicate 2
U397_91418_EtOH2


title: uninfected perch liver 299S

value: uninfected


title: Liver, Control_HFD, 5

value: Liver


title: Liver, Control_HFD, 4


title: ZFP740_KO1,replicate1,RNAseq


title: uninfected perch spleen 298S

value: Male


title: WT3,replicate3,RNAseq

source_name: HepG2 cell control

value: HepG2 cell control

value: WT


title: Liver, Control_HFD, 3


title: Liver, Control_HFD, 8


title: 9/14/18-U937 AML1/ETO with Pon A, replicate 2

description:
replicate 2
U397_91418_PonA2

value: histiocytic lymphoma


title: Liver, Control_HFD, 7


title: WT2,replicate2,RNAseq


title: infected perch spleen 303

value: infected


title: infected perch liver 294S

value: liver


title: Liver, Control_HFD, 2


title: uninfected perch spleen 293S


title: 40195_SetPoint_TCRgd

status: Public on Jul 03 2024

city: silver spring

first: Dohoon

last: Kim

address: 503 BLDG, Walter Reed Army institute of research

institute: Henry M Jackson Foundation

description: non broad neutralizer

data_processing:
Quality control was performed on raw FASTQ files using FastQC to assess the quality of the sequencing data.
Adapters and low-quality bases were trimmed using Trimmomatic.
Cleaned reads were aligned to the reference genome using STAR aligner(ver. 2.6.1d) with default parameters.
Aligned reads were quantified to gene-level expression using RSEM(ver. 1.3.1).
Raw read counts and TPM (Transcripts Per Million) were generated for each sample.
Differential expression analysis was carried out using edgeR.
Assembly: hg38
Supplementary files format and content: The processed data files are in tab-delimited text format and include gene expression matrices (TPM and raw counts) and differential expression results (gene IDs, log2 fold changes, p-values, and FDR).

source_name: PBMC

growth_protocol: Cryopreserved PBMC were thawed, stained, and sorted directly without any culture

extract_protocol:
200 cells were directly sorted into 1x lysis buffer supplemented with 6U RNase inhibitor (both Takara Bio). Post sort, sample tubes were vortexed, incubated at RT for 2 minutes, and snap frozen on dry ice prior to storage at -80˚ C.
Upon thawing, cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) as per the manufacturer’s instructions. A total of 150-300pg amplified cDNA was used as input for library preparation

treatment_protocol: Cells were not treated other than staining and sorting

value: PBMC

value: gamma delta T cells


title: 9/14/18-U937 AML1/ETO with Ethanol, replicate 1

description:
replicate 1
U397_91418_EtOH1

value: control

value: Ethanol


title: 30156_SetPoint_TCRgd

description: Broad neutralizer


title: 10204_SetPoint_TCRgd

description: Broad neutralizer


title: 10204_Chronic_TCRgd

description: Broad neutralizer


title: 40195_Chronic_TCRgd

description: non broad neutralizer


title: Liver, Control_HFD, 1


title: 9/14/18-U937 AML1/ETO with Pon A, replicate 1

description:
replicate 1
U397_91418_PonA1

value: Ponasterone A


title: 30156_Pre-Infection_TCRgd

description: Broad neutralizer


title: WT1,replicate1,RNAseq

value: HepG2 cell


title: 40511_Chronic_TCRgd

description: non broad neutralizer


title: 10204_Peak_TCRgd

description: Broad neutralizer


title: 40511_Peak_TCRgd

description: non broad neutralizer


title: 40511_Pre-Infection_TCRgd

description: non broad neutralizer


title: 40195_Pre-Infection_TCRgd

description: non broad neutralizer


title: 40265_SetPoint_TCRgd

description: non broad neutralizer


title: 40265_Peak_TCRgd

description: non broad neutralizer


title: 40265_Pre-Infection_TCRgd

description: non broad neutralizer