title: INMPP1

city: Baltimore

first: Aaron

last: James

address: 720 Rutland Avenue, Ross Bldg., Room 529

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream analysis steps were performed using Seurat. Cells were first filtered to have >500 and <8,000 detected genes, as well as less than 20%  mitochondrial transcripts. SCTransform, including regression for cell cycle scores derived using the CellCycleScoring function, and dimensional reductions using uniform manifold approximation and projection (UMAP) was performed using Seurat. Pathway activation or module scores were generated using the AddModuleScore function of Seurat using validated gene lists from KEGG pathways.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Injured tendon area

extract_protocol:
Tissues were digested in a pre-warmed dissociation solution (3 mg ml−1 collagenase I (Worthington) and 4 mg ml−1 dispase II (Roche) in PBS) in conical tubes positioned horizontally in a shaking water bath for 1.5 h min at 180 r.p.m. at 37 °C. Samples were then lightly triturated with sterilized Pasteur pipettes (VWR) until the tendon fragments broke up, run through a 40 μm filter (VWR) and rinsed with 3 ml TSPC medium (αMEM (Gibco) supplemented with 20% FBS, 1%PS) to inactivate the enzymes. Cells were centrifuged at 300g for 30 min at 4 °C. The cell pellet was washed twice with 1 ml PBS and spun for 10 min at 300g at 4 °C.  Cells were then resuspended in HBSS at a concentration of ~1,000 cells/μl.  Cell viability was assessed with Trypan blue exclusion on a Countess II (ThermoFisher Scientific) automated counter and showed a >85% viability.
Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting Post GEM-RT product was cleaned up using DynaBeads MyOne Silane beads. The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA) cleaned and quantified then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup was performed after end repair and A-tailing. Another single-sided cleanup was done after adapter ligation. Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by Kapa qPCR for Illumina Adapters (Roche) and size was determined by Agilent Bioanalyzer 2100. Read 1 primer, read 2 primer, P5, P7, and sample indices were incorporated per standard GEM generation and library construction via end repair, A-tailing, adaptor ligation and PCR. Libraries were generated with unique sample indices (SI) for each sample. Libraries were sequenced on an Illumina NovaSeq SP 100 cycle (San Diego, CA). CellRanger was used to perform sample de-multiplexing, barcode processing, and single-cell gene counting (Alignment, Barcoding, and UMI Count) at the JHMI Transcriptomics and Deep Sequencing Core

value: Injured tendon area

value: TrkA F592A

value: Tenocytes + injured area

value: 12 weeks old


title: iWAT cont_4

status: Public on Nov 27 2023

type: RNA

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

description: Gene expression profiles of iWAT obtained from control mouse

hyb_protocol: Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent. Then, it was hybridized on microarrays for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: The array was scanned using a SureScan Microarray Scanner (Agilent).

data_processing: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software (version 11.5.1) (Agilent). The log2-intensities of the probes from the arrays were normalized using the quantile normalization method.

molecule: total RNA

organism: Mus musculus

source_name: inguinal white adipose tissue

label_protocol: Cy3 labeled cRNA was prepared from 0.5 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).

growth_protocol: All animals were housed at 22-24°C, with a 12:12-h light-dark cycle and ad libitum access to diet and water.

extract_protocol: Total RNAs were isolated using TRIzol (Invitrogen, MA, USA) according to the manufacturer’s instruction.

treatment_protocol: Eight week-old mice were fed a high-fat diet, (HFD; 58 kcal% fat w/sucrose, D12331; Research Diets, New Brunswick, NJ, USA) for 12 weeks.

tag: tissue

value: inguinal white adipose tissue

tag: strain


title: P8_S12

type: SRA

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

library_source: genomic

data_processing:
Read trimming and filtering were performed with Trimmomatic (version 0.39).
Fastq file was converted to fasta file.
Reads were mapped to the sequence of three genotypes of HIV-1 (CH185 wild-type, the CH185_dPTAP1 mutant, and the CH185_dPTAP2) using BLASTn (version 2.6.0).
Reads were assigned to the top hit genotype. If tie, the read was discarded.
Reads assigned to each genotype were counted.
Genome_build: CH185_WT; AGGGAAAATCTGGCCTTCCAACaaggggaggccagggaatttccttCAGAACAGAGCAGAGCCAACAGCCCCACCAGCAGAGAGCTTCCCTCAGAGCAGACCAGAGCCAACAGCTCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Genome_build: CH185_dPTAP1; AGGGAAAATCTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCCTCAGAGCAGACCAGAGCCAACAGCTCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Genome_build: CH185_dPTAP2; AGGGAAAATCTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGAGCAGAGCCAACAGCCCCACCAGCAGAGAGCTTCGCTCCGAAGCAGGAGCCGAGAGAGAGGGAACCTTTAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAAaagtagggggccaggtaaaggaggctctcttagacacaggagcagatgatacagtattagaagaaataaatttGCCAGGAAAATGGAAACC
Supplementary_files_format_and_content: blast output

molecule: genomic DNA

organism: Human immunodeficiency virus 1

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 353M2

growth_protocol: Three different HIV-1, CH185 wild-type, the CH185 deltaP1 mutant, and the CH185 deltaP2 mutant were co-inoculated into nine humanized mice.

extract_protocol:
for plasma samples, QIAamp viral RNA mini kit (Qiagen); for speen samples, QIAamp RNA blood mini kit (Qiagen)
DNA library preparation kit (NEB)
OTHER: RT-PCR amplicon sequencing

tag: model

value: HIV1-infected humanized mouse


title: SASD,48h

city: Beijing

first: Erquan

last: Zhang

address: 7 Science Park Road, ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

library_source: transcriptomic

data_processing:
adaptor and low-quality sequencing data were removed by trimmomatic(v0.39)
each sample were mapped to the mouse genome (mm10) via STAR (v2.7.9a)
Uniquely mapped reads were assigned to genes based on the annotation file using FeatureCounts (v2.0.3) from Subread package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include feature count values for each Sample

source_name: Blood

extract_protocol:
For blood sampling, each mouse was anesthetized with pentobarbital (i.p. 80 mg/kg) and taken 500 μL blood retro-orbitally which was collected in an EDTA anticoagulant tube (BD Biosciences). Total RNA was extracted from the blood samples of 3 mice in the same group with QIAamp RNA Blood Mini Kit (52304, Qiagen) following the manufacturer’s instructions.
The sequencing libraries were prepared with Illumina Truseq Library Prep Kits v2 (Illumina) according to the manufacturer’s instructions. All libraries were guaranteed quality with quality check

value: Blood

tag: cell type

value: Leukocyte

tag: time


title: iWAT cont_2


title: Bisulfite-seq_fresh_ductal_methyl_2

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

department: Cell Systems & Anatomy

country: USA

institute: University of Texas Health San Antonio

data_processing:
Genomic alignment and CpG calling was performed with Bismark 0.19.1.
Detected sites among all samples were collated, and only those withat least 10 read coverage (methylated + unmethylated) for all samples were retained for analysis.
Assembly: hg38
Supplementary files format and content: bismark.cov are tab delimited tables of all detected DNA methylation sites with beta value, methylated reads, and unmethylated reads for each site
Supplementary files format and content: DNA_methylation_beta_tab.txt.gz is a tab delimited table with beta value for all samples for all retained DNA methylation sites (2349323 sites)

organism: Homo sapiens

source_name: exocrine pancreas

extract_protocol:
Genomic DNA was extracted  with Zymo Quick-DNA miniprep kit.
Reduced-representation bisulfite converted DNA methylation libraries were contructed from genomic DNA with Illumina Truseq methyl capture kit, as per manufacturer instruction.

treatment_protocol: "KPTS" genotype cells have enforced expression of oncogenic KRAS-G12V and CRISPR/Cas9 knockout of P16, P53, and SMAD4 .

value: exocrine pancreas

value: ductal

tag: genotype

value: WT

tag: condition

value: freshly sorted


title: iWAT aKO_2

description: Gene expression profiles of iWAT obtained from Senp2-aKO mouse

value: Senp2flox/flox ; Adipoq Cre


title: P7_S11

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 352M6


title: Bisulfite-seq_fresh_acinar_methyl_2

value: acinar


title: Bisulfite-seq_fresh_acinar_methyl_1


title: Control

state: Maryland

department: Pathology

description: 10x Genomics

library_source: transcriptomic single cell

tag: cell line

value: TrkA WT

tag: age


title: acinar_KPTS_organoid_RNAseq_3

data_processing:
Alignment was performed using TopHat 2.1.1 and gene expression was quantified using HTSeq 0.11.1.
Assembly: hg38
Supplementary files format and content: read_table.txt.gz is tab delimited table of read counts per gene for all samples.
Supplementary files format and content: TPM_table.txt.gz is tab delimited table of transcripts per million per gene for all samples

extract_protocol:
Total RNA was extracted using Zymo Direct-zol RNA Miniprep Kit as per manufacturer instructions.
RNAseq libraries prepared using Illumina Stranded mRNA Prep Ligation kit as per manufacturer instructions.

treatment_protocol: "K" genotype cells have enforced expression of oncogenic KRAS-G12V and "KPTS" genotype cells have KRAS-G12V and CRISPR/Cas9 knockout of P16, P53, and SMAD4 .

value: KPTS

value: organoid culture


title: PT7d.LEV.CX.R

city: Sanuki

first: Rie

last: Komori

department: Kagawa School of Pharmaceutical Sciences

institute: Tokushima Bunri University

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina).
Obtained reads (CAGE tags) were mapped to the mouse GRCm38 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5).
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2020 vertebrates were evaluated by Tomtom.
The list of differentially expressed genes detected by RECLU with false discovery rate (FDR) ≤ 0.05 were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from the whole mouse cerebral cortex using the Maxwell 16 LEV simpleyRNA Tissue Kit (Promega).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping).

value: cerebral cortex

value: Photothrombosis (PT) model of cerebral ischemia

tag: treatment

value: 7 d after PT+LEV (non-infarcted side)


title: SD,24h


title: iWAT cont_1


title: PT7d.LEV.CX.L

value: 7 d after PT+LEV (infarcted side)


title: S1_S14

source_name: Mononuclear cells from the spleen of HIV1-infected humanized mouse, 344M3


title: SD,12h


title: P5_S9

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 352F1


title: SD,6h


title: Con


title: acinar_KPTS_organoid_RNAseq_2


title: P6_S10

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 352M4


title: PT7d.CX.R

value: 7 d after PT (non-infarcted side)


title: i3-4: iWAT_aKO_siC/EBPb_3

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the cutadapt software (version 2.7), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: SVF-derived adipocyte

growth_protocol: Stromal vascular fraction (SVF) cells were isolated from the iWAT or eWAT. SVF cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco Life Technologies) supplemented with 10 % FBS, and seeded in 12-well plates. Adipocyte differentiation of confluent SVF cells was induced by treatment with DMI (1 mol/l dexamethasone, 0.5 mmol/l isobutylmethyxanthine and 0.1 mg/ml insulin) in DMEM supplemented with 10 % FBS. Two days after the treatment, cells were maintained in DMEM supplemented with 10 % FBS and 1 μg/ml insulin for additional 5 days.

extract_protocol:
Total RNAs were isolated using TRIzol (Invitrogen, MA, USA) according to the manufacturer’s instruction.
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA Seq Kit (NEW  ENGLAND BioLabs, Inc., UK).

treatment_protocol: SVF from control and Senp2-aKO mice was treated with C/EBPβ-specific siRNA.

value: SVF-derived adipocyte

value: inguinal white adipose tissue

value: siC/EBPbeta


title: PT2M.LEVW2W.CX.L

value: 2 m after PT+LEV withdrawal 2 w (infarcted side)


title: acinar_K_organoid_RNAseq_4

value: exocrine pancreas

value: K


title: i1-4: iWAT_aKO_siC/EBPb_1


title: acinar_K_organoid_RNAseq_5


title: i2-4: iWAT_aKO_siC/EBPb_2


title: acinar_KPTS_organoid_RNAseq_1


title: P4_S8

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 353F3

value: HIV1-infected humanized mouse


title: P2_S6

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 344F2


title: acinar_K_organoid_RNAseq_3


title: PT7d.CX.L

value: 7 d after PT (infarcted side)


title: P3_S7

source_name: Mononuclear cells from the plasma of HIV1-infected humanized mouse, 353F1


title: i3-3: iWAT_aKO_siNS_3

value: Senp2flox/flox ; Adipoq Cre

value: siNS


title: acinar_K_organoid_RNAseq_2

value: acinar


title: PT1M.LEV.CX.R

value: 1 m after PT+LEV (non-infarcted side)


title: PT1M.LEV.CX.L

value: cerebral cortex

value: 1 m after PT+LEV (infarcted side)


title: acinar_K_organoid_RNAseq_1

value: organoid culture


title: i2-3: iWAT_aKO_siNS_2


title: acinar_organoid_RNAseq_6

value: WT


title: i1-3: iWAT_aKO_siNS_1


title: PT1M.CX.L

value: Photothrombosis (PT) model of cerebral ischemia

value: 1 m after PT (infarcted side)


title: PT1M.CX.R

value: 1 m after PT (non-infarcted side)


title: i3-2: iWAT_Cont_siC/EBPb_3

value: SVF-derived adipocyte

value: inguinal white adipose tissue

value: siC/EBPbeta


title: PT2M.LEVW2W.CX.R

value: 2 m after PT+LEV withdrawal 2 w (non-infarcted side)


title: acinar_organoid_RNAseq_5

value: exocrine pancreas


title: naive.CX

value: control

value: untreated


title: Intracrnaial tumor treated with NK cells #1

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

institute: Nara Medical University

description: intracrnaial tumor in orthotopic xenograft murine model injected with U87MG, which is treated with NK cells

hyb_protocol: Following labeling, 5.2 ug of cDNA were hybridized for 16 hr at 45 degree C on Clariom S Human Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G system.

data_processing: The data analysis were used Transcriptome Analysis Console Ver.4.0.  Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA),  Expression Analysis was perfoermed using ebayes ANOVA.

label: biotin

label_protocol: The fragmented 5.2 μg of single-stranded cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent that is covalently linked to biotin. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

growth_protocol: The in vivo xenograft assay was performed as below. Briefly, anesthetized NOG mice were secured on a rodent stereotactic frame (SR-6M-HT, Tokyo, Ja-pan). A small drill hole was made at 2 mm right and 1 mm anterior from the bregma, and then 2 µL native Hank’s balanced salt solution containing 105 U87MG cells was infused into the right thalamus at a depth of 3 mm via the drill hole using a Hamilton syringe (33 S-gauge needle) mounted on an infusion syringe pump (Harvard Apparatus, Holliston, MA, USA). The injection was performed over 5 min, left in place for 3 min, and removed over 5 min.

extract_protocol: Intracranial tumors were harvested from dead GBM-injected mice. Total RNA from in-tracranial tumors in the orthotopic GBM xenograft model was extracted using NucleoSpin RNA (Takara Bio, Shiga, Japan).

treatment_protocol: Six mice were randomly assigned to the negative background (PBS/IL-2 10,000 IU/mL), six to the intracranial once infusion (106 NKCs and 10,000 IU/mL IL-2 once), and six to the in-tracranial twice infusion (106 NKCs and 10,000 IU/mL IL-2 twice) groups. NKCs were in-jected into the retro-orbital sinus using a 29G needle under isoflurane anesthesia. The administration schedule was as follows: on day 0, stereotactic GBM in-jection was performed. In the negative background group, IL-2 was infused on days 1 and 7. In the intracranial once infusion group, NKCs were infused on day 1 and IL-2 was infused on day 7. The intracranial twice infusion group was treated on days 1 and 7.


title: Intracrnaial tumor treated with NK cells #2 (external layer)

description: external layer of intracrnaial tumor in orthotopic xenograft murine model injected with U87MG, which is treated with NK cells


title: Intracrnaial tumor treated with NK cells #2 (internal layer)

description: internal layer of intracrnaial tumor in orthotopic xenograft murine model injected with U87MG, which is treated with NK cells


title: i2-2: iWAT_Cont_siC/EBPb_2


title: acinar_organoid_RNAseq_4


title: acinar_organoid_RNAseq_3


title: i1-2: iWAT_Cont_siC/EBPb_1


title: PT7d.LEV.HP.R

data_processing:
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina).
Obtained reads (CAGE tags) were mapped to the mouse GRCm38 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5).
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2020 vertebrates were evaluated by Tomtom.
The list of differentially expressed genes detected by RECLU with false discovery rate (FDR) ≤ 0.05 were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes CPM values for each sample.

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the whole mouse hippocampus using the Maxwell 16 LEV simpleyRNA Tissue Kit (Promega).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.

value: hippocampus

value: 7 d after PT+LEV (non-infarcted side)


title: latTII, rep2

city: Princeton

first: Martin

middle: H

last: Wühr

state: NJ

address: 246 Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton Univeristy

data_processing:
Quality assessment of the raw reads was performed using FastQC. The reads were then trimmed with Trimgalore to remove adapter contamination and poor-quality base calls. After trimming, the reads were mapped to the KY21 transcriptome using Salmon. Subsequent downstream analyses were conducted in either R or Python.
Assembly: KY21
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes TPM for each sample
Supplementary files format and content: tab-delimited file includes DESeq2 normalised counts for each sample

organism: Ciona robusta

source_name: whole embryo

extract_protocol: Approximately 150 embryos were collected at each time point in TRIZOL. RNA was precipitated using the phenol-chloroform method, followed by RNA Clean & Concentrator kit (Zymo) as per the manufacturer's instructions, including a 10-minute DNase treatment on the column. Stranded RNA libraries were constructed on an Apollo324 automated workstation using the PrepX PolyA mRNA isolation kit (Takara) following the manufacturer's protocol. Paired-end sequencing was performed on Illumina Novaseq platform (61bp).

value: whole embryo

tag: developmental stage

tag: developmental time

value: late tailbud II


title: larva, rep2

value: larva


title: i3-1: iWAT_Cont_siNS_3

value: siNS


title: PT7d.HP.R

value: 7 d after PT (non-infarcted side)


title: midTII, rep2

value: WT

value: mid tailbud II


title: acinar_organoid_RNAseq_2

value: acinar

value: organoid culture


title: acinar_organoid_RNAseq_1


title: latN, rep2

value: 7.4 hpf

value: late neurula


title: i2-1: iWAT_Cont_siNS_2

value: SVF-derived adipocyte

value: inguinal white adipose tissue


title: PT7d.HP.L

value: Photothrombosis (PT) model of cerebral ischemia

value: 7 d after PT (infarcted side)


title: iniG, rep2

value: 4.5 hpf

value: initial gastrula


title: fresh_ductal_RNAseq_5

value: exocrine pancreas

value: ductal

value: freshly sorted


title: PT2M.LEVW2W.HP.R

value: hippocampus

value: 2 m after PT+LEV withdrawal 2 w (non-infarcted side)


title: e3-4: eWAT_aKO_siC/EBPb_3

value: epididymal white adipose tissue

value: Senp2flox/flox ; Adipoq Cre

value: siC/EBPbeta


title: fresh_ductal_RNAseq_4

value: WT


title: cell16, rep2

value: whole embryo


title: PT2M.LEVW2W.HP.L

value: 2 m after PT+LEV withdrawal 2 w (infarcted side)


title: i1-1: iWAT_Cont_siNS_1

value: SVF-derived adipocyte

value: siNS


title: e2-4: eWAT_aKO_siC/EBPb_2


title: PT7d.LEV.HP.L

value: Photothrombosis (PT) model of cerebral ischemia

value: 7 d after PT+LEV (infarcted side)


title: PT1M.LEV.HP.R

value: 1 m after PT+LEV (non-infarcted side)


title: fresh_ductal_RNAseq_3


title: e1-4: eWAT_aKO_siC/EBPb_1


title: PT1M.LEV.HP.L

value: 1 m after PT+LEV (infarcted side)


title: unfE, rep2

value: 0 hpf

value: unfertilised egg


title: Intracrnaial tumor #1

description: intracrnaial tumor in orthotopic xenograft murine model injected with U87MG, which is not treated with NK cells


title: fresh_ductal_RNAseq_2

value: exocrine pancreas

value: ductal

value: freshly sorted


title: fertE, rep2

value: 0.4 hpf

value: fertilised egg


title: e3-3: eWAT_aKO_siNS_3

value: epididymal white adipose tissue

value: Senp2flox/flox ; Adipoq Cre


title: PT1M.HP.R

value: hippocampus

value: 1 m after PT (non-infarcted side)


title: e2-3: eWAT_aKO_siNS_2

value: SVF-derived adipocyte


title: latTII, rep1

value: WT

value: whole embryo

value: late tailbud II


title: fresh_acinar_RNAseq_5

value: acinar


title: larva, rep1

value: larva


title: fresh_ductal_RNAseq_1


title: Intracrnaial tumor #2

source_name: intracrnaial tumor in orthotopic xenograft murine model injected with U87MG


title: e1-3: eWAT_aKO_siNS_1

value: siNS


title: naive.HP

value: control

value: untreated


title: fresh_acinar_RNAseq_4

value: exocrine pancreas


title: e3-2: eWAT_Cont_siC/EBPb_3

value: siC/EBPbeta


title: fresh_acinar_RNAseq_3

value: freshly sorted


title: midTII, rep1

value: mid tailbud II


title: e2-2: eWAT_Cont_siC/EBPb_2

value: epididymal white adipose tissue


title: 116_shELK4_3

city: Shanghai

first: Zhehui

last: Zhu

state: Shanghai

address: Kongjiang Road 1665, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

description: ELK4 knockdown

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic ( 0.36 ), then mapped to GR38p7 whole genome using Hisat2 ( 2.0.5 ) with parameters ( --rna-strandness RF --fr  )
FPKM value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count (  0.9.1 )
Genome_build: GR38p7

source_name: HCT116 CELL LINE

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ELK4 knockdown


title: latN, rep1

value: 7.4 hpf


title: iniG, rep1

value: 4.5 hpf

value: initial gastrula


title: fresh_acinar_RNAseq_2

value: WT


title: 116_shELK4_2

description: ELK4 knockdown


title: fresh_acinar_RNAseq_1


title: cell16, rep1

value: whole embryo


title: e1-2: eWAT_Cont_siC/EBPb_1

value: SVF-derived adipocyte


title: fertE, rep1

value: 0.4 hpf

value: fertilised egg


title: Intestinal progenitor cell sample (Human_scRNA-seq)

city: San Francisco

first: Rachel

middle: Klapper

last: Zwick

address: 513 Parnassus Ave.

institute: University of California, San Francisco

description: 10x Chromium single cell data

data_processing:
Kallisto-bustools v.0.46.2 was used to produce the raw gene count matrix files from the "GEX" fastq files
Kallisto-bustools v.0.46.2 with the kite script was used to produce the raw MULTIseq barcode count matrix files from the "ADT" fastq files
DropletUtils v1.12.3 was used to filter gene count matrixess
DropletUtils v1.12.3 was used to demultiplex datasets
Assembly: Human GRCh38.95
Supplementary files format and content: Matrix, barcodes, and features tables with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
The intestine was washed, cut into 30 pieces of equal length, and incubated with media supplemented with 5mM EDTA and 10mM DTT at 37°C with 5% CO2. Cells were triturated, strained, washed, and labelled with barcodes unique to each segment using the MULTIseq method. The target population was FACS sorted.
10x libraries were prepared for sequencing using standard 10x genomics protocols adapted for MULTIseq as described in McGinnis et al. Nat Methods 2019.
Chromium Single Cell 3'

value: FACS sorted intestinal epithelial progenitor cells (CD45-, EpCAM+, CD44+)

value: small intestine

tag: Sex

value: female

value: adult, homeostasis


title: 116_shELK4_1

description: ELK4 knockdown


title: unfE, rep1

value: 0 hpf

value: unfertilised egg


title: 116_pLKO_2

description: control

value: pLKO


title: e3-1: eWAT_Cont_siNS_3

value: epididymal white adipose tissue

value: siNS


title: e2-1: eWAT_Cont_siNS_2


title: 116_pLKO_1

description: control


title: Total intestinal epithelial cell sample (Human_scRNA-seq)

description: 10x Chromium single cell data

value: FACS sorted intestinal epitheilal cells (CD45-, EpCAM+)


title: PT1M.HP.L

value: hippocampus

value: Photothrombosis (PT) model of cerebral ischemia

value: 1 m after PT (infarcted side)


title: e1-1: eWAT_Cont_siNS_1


title: ARY_PolII_H1085Q_bioRep_3_TSSseq_batch_1

status: Public on Nov 26 2023

city: Pittsburgh

first: Yunye

state: PA

address: 4249 Fifth Avenue

department: Department of Biological Sciences

institute: University of Pittsburgh

data_processing:
Library strategy: TSS-seq
We considered only those reads that contained a perfect match to a 27 nt sequence region downstream of the barcode, as well as expected length of 5’-end: 5’-[15 nt 5’-UMI]-[>1 nt upstream of barcode region, designated as “RNA 5’-end”]-[24 nt barcode]-[the first 27 nt of GFP ORF, ATGTCTAAAGGTGAAGAATTATTCACT]-3’. Next, 15 nt 5’-UMIs, “RNA 5’-end” with varying length, and 24 nt barcode were extracted and individually corrected by UMI-tools (1.0.0). Deduplication was performed based on 5’-UMIs, meaning reads contained a shared UMI-“RNA 5’-end”-barcode linkage were counted as one deduplicated read for further analysis.
Next, the identity of the 24 nt barcode was used to determine the template sequences of randomized TSS region. Then, reads with “RNA 5’-end” sequence perfectly matched to corresponding template sequence were kept and used for downstream analysis. A TSS-seq count table containing TSS usage distribution of each TSS promoter variant was generated. In the count table, each row represents one TSS variant, and each column represents one position between positions -68 to +25 relative to “designed” +1 TSS. The number in each cell represents TSS-seq reads generated from a particular position, with perfectly match to DNA template.
After investigating reproducibility, count tables generated from two batches of TSS-seq and three biological replicates were merged into one by aggregating read counts at each position. TSS variants with >= 5 TSS-seq reads in each replicate and whose Coefficient of Variation (CV) of TSS-seq reads is less than 0.5 were kept.
Each TSS-seq sample links to four processed data files. One tab-delimited file contains “RNA 5’-end”-Barcode linkages and coresponding deduplicated TSS-seq read counts for this particular sample. Three count tables contain TSS usage distributions of each TSS promoter variant, related to this particular TSS-seq sample: one for this partcular TSS-seq sample itself, one after aggregating batches of TSS-seq, one after aggregating three biological replicates.

organism: Saccharomyces cerevisiae

source_name: Laboratory yeast strain

growth_protocol: Plasmid library pools were transformed into yeast strains with wildtype and mutated Pol II using chemical transformation and electroporation, respectively. Transformants were grown on selective SC-His plates with 2% glucose as carbon source at high density. Colonies collected from plates were inoculated into fresh SC-His medium with 2% raffinose (Amresco, J392) at 0.25 x 10^7 cells/ml and grown until 0.5-0.8 x 10^7 cells/ml, as determined by cell counting. Subsequently, galactose (Amresco, 0637) was added for three hours (4% final concentration) to induce library expression. 50 ml and 5 ml culture, for RNA and DNA extraction respectively, were harvested and then cell pellets were stored at -80 C for further processes.

extract_protocol:
Total RNA was extracted by a phenol-chloroform method (Schmitt, Brown, & Trumpower, 1990), followed by RNA purification (RNeasy Mini kit, QIAGEN, 74104) with on-column DNase digestion (RNase-Free DNase Set, QIAGEN, 79254) to remove DNA.
TSS-seq was done using procedures described in (Vvedenskaya, Goldman, & Nickels, 2015). To prepare RNAs for the cDNA library construction, samples were sequentially treated with Terminator 5‘-Phosphate-Dependent Exonuclease, calf-intestine alkaline phosphatase and Cap-Clip Acid Pyrophosphatase to remove 5' monophosphate RNA and convert 5' triphosphate or capped RNAs to 5' monophosphate RNAs. Next, RNA prepared with enzymatic treatments was ligated to the 5'-adapter (s1206-N15, 5'-GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNNNNNNNNN-3') that contains Illumina adapter sequence and a 15 nt randomized 3'-end to reduce ligation bias and serve as a Unique Molecular Identifier (UMI). Next, cDNA was constructed by reverse transcription using RT primer CKO2191-s128A (5'-CCTTGGCACCCGAGAATTCCAAGTGAATAATTCTTCACCTTTA-3') followed by PCR amplification using Illumina PCR primers (RP1 and RPI3-30). Final DNA was gel size selected for 180-250 bp lengths.

value: CKY956 (Pol II H1085Q)

tag: library

value: ARY

tag: replicate

value: biological replicate 3


title: BYR_PolII_H1085Q_bioRep_3_TSSseq_batch_1

value: BYR


title: ARY_PolII_H1085Q_bioRep_1_TSSseq_batch_1

value: biological replicate 1


title: ARY_PolII_H1085Q_bioRep_2_TSSseq_batch_1

value: biological replicate 2


title: AYR_PolII_H1085Q_bioRep_3_TSSseq_batch_1

value: AYR


title: BYR_PolII_H1085Q_bioRep_1_TSSseq_batch_1


title: AYR_PolII_H1085Q_bioRep_1_TSSseq_batch_1


title: AYR_PolII_H1085Q_bioRep_2_TSSseq_batch_1


title: Tcm CTCF KO invitro stim 24h CD8 RNAseq rep2

city: washington dc

first: Shaoqi

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using hisat2 (v2.2.1). UCSC genes for mouse mm9 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by htseq-count (v1.99.2) to estimate expression levels of all genes and identify differentially expressed genes (Fold change = 2, FDR = 0.05). The expression level of a gene is expressed as a gene-level Transcripts per Million mapped reads (TPM) value.
Assembly: mm9

source_name: CD8 T cells

extract_protocol:
WT or CTCF-floxed Tcm cells were sort-purified from the recipient spleens, unstimulated or stimulated with GP33 peptide for 24 hrs ex vivo, and total RNA was extracted using standard Qiagen RNease columns.
RNA-seq libraries were prepared for sequencing using stardard Illumina protocol. The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: CTCF-/-

value: splenocytes

tag: cell phenotype


title: ARY_PolII_G1097D_bioRep_3_TSSseq_batch_1

value: CKY962 (Pol II G1097D)


title: ARY_PolII_G1097D_bioRep_5_TSSseq_batch_1

value: biological replicate 5


title: BYR_PolII_G1097D_bioRep_5_TSSseq_batch_1


title: BYR_PolII_G1097D_bioRep_4_TSSseq_batch_1

value: biological replicate 4


title: Tcm CTCF KO invitro stim 24h CD8 RNAseq rep1


title: Tcm WT invitro stim 24h CD8 RNAseq rep3

value: wild type


title: AYR_PolII_G1097D_bioRep_3_TSSseq_batch_1


title: Tcm resting CD8 RNAseq rep3


title: BYR_PolII_G1097D_bioRep_2_TSSseq_batch_1


title: Tcm WT invitro stim 24h CD8 RNAseq rep2


title: Tcm WT invitro stim 24h CD8 RNAseq rep1


title: AYR_PolII_G1097D_bioRep_2_TSSseq_batch_1


title: AYR_PolII_G1097D_bioRep_1_TSSseq_batch_1


title: ARY_PolII_F1086S_bioRep_3_TSSseq_batch_1

value: CKY960 (Pol II F1086S)


title: BYR_PolII_H1085Q_bioRep_2_TSSseq_batch_1


title: Tcm resting CD8 RNAseq rep2


title: Tcm resting CD8 RNAseq rep1


title: ARY_PolII_F1086S_bioRep_2_TSSseq_batch_1


title: ARY_PolII_F1086S_bioRep_1_TSSseq_batch_1


title: Tcm CTCF KO invitro stim 24h CD8 RNAseq rep3


title: BYR_PolII_F1086S_bioRep_3_TSSseq_batch_1


title: BYR_PolII_F1086S_bioRep_2_TSSseq_batch_1


title: BYR_PolII_F1086S_bioRep_1_TSSseq_batch_1


title: 59-RT-PO

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
All reads were independently aligned with STAR_2.4.0f1 for sequence alignment against the human genome build hg19, downloaded via the UCSC genome browser, and SAMTOOLS v0.1.19 for sorting and indexing reads.
HTSeq was used to quantity counts.
Cufflinks (2.0.2) was used to get the expression values (FPKMs), and Gencode v19 GTF file for annotation.
Assembly: hg19
Supplementary files format and content: Gene Expression values quantified as FPKMs

source_name: Lung Tissue, Archival FFPE

growth_protocol: Archival FFPE human lung tissue

extract_protocol:
RNA was extracted from FFPE samples with RNeasy FFPE kit from Qiagen, Part# 73504.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760, New England BioLabs, Ipswich, MA) was used for sample library preparation according to the manufacturer’s instruction.  PCR enrichment of adaptor ligated cDNA were pooled and hybridized with probes from Twist Exome Kit #2 (Twist Bioscience, San Francisco, CA). After post capture PCR amplification and purification, the quality of final libraries was checked and loaded to Illumina NovaSeq6000 for sequencing at PE2x100 cycles

treatment_protocol: Not applicable

value: Lung Tissue, Archival FFPE

value: Adenocarcinoma


title: 61-M-PO


title: 57-M-PO


title: 53-M-PO


title: 55-M-PO


title: AYR_PolII_F1086S_bioRep_2_TSSseq_batch_1


title: AYR_PolII_F1086S_bioRep_1_TSSseq_batch_1


title: 52-RT-PO


title: 47-M-PO

value: Squamous


title: 46-RT-PO


title: ARY_PolII_E1103G_bioRep_3_TSSseq_batch_1

value: CKY964 (Pol II E1103G)


title: 45-M-PO


title: 41-M-PO


title: ARY_PolII_E1103G_bioRep_1_TSSseq_batch_1

value: ARY


title: 44-RT-PO


title: BYR_PolII_E1103G_bioRep_3_TSSseq_batch_1

value: biological replicate 3


title: BYR_PolII_E1103G_bioRep_2_TSSseq_batch_1

value: BYR


title: ARY_PolII_E1103G_bioRep_2_TSSseq_batch_1


title: POD32R


title: AYR_PolII_E1103G_bioRep_2_TSSseq_batch_1


title: AYR_PolII_E1103G_bioRep_3_TSSseq_batch_1


title: 38-M-PO


title: AYR_PolII_F1086S_bioRep_3_TSSseq_batch_1


title: AYR_PolII_E1103G_bioRep_1_TSSseq_batch_1

value: biological replicate 1


title: 36-M-PO


title: POD30R


title: BYR_PolII_E1103G_bioRep_1_TSSseq_batch_1


title: POD27R


title: POD23R


title: ARY_PolII_WT_bioRep_1_TSSseq_batch_1

value: CKY954 (WT)


title: ARY_PolII_WT_bioRep_2_TSSseq_batch_1

value: biological replicate 2


title: POD26R

value: Sarcomatoid


title: BYR_PolII_WT_bioRep_3_TSSseq_batch_1


title: POD20R


title: ARY_PolII_WT_bioRep_3_TSSseq_batch_1


title: 40-M-PO

value: NOS


title: BYR_PolII_WT_bioRep_1_TSSseq_batch_1


title: BYR_PolII_WT_bioRep_2_TSSseq_batch_1


title: Skin normal 24

type: genomic

city: Hanoi

first: Tham

last: Hoang

address: Floor 9th, 458 Minh Khai

country: Viet Nam

institute: Vingroup Big Data Institute

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-24
205685220015_R12C02

hyb_protocol: RA1 resuspended DNA was loaded onto Infinium Asian Screening Array-24 v1.0 BeadChip . After incubation 16 - 24 hours at 48˚C, single-base extension and allele-specific staining was performed on a Te-flow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining the Beadchip was coated with XC4, dried for 1 hour and scanned by IScan Software (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using ASA-24 v1.0 Beadchip (Illumina).

label: Cy3, Cy5

source_name: Saliva

label_protocol: 250ng of genomic DNA was whole-genome amplified in an overnight reaction at 37˚C using amplification master mix (MA1, MA2 and MSM). After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from saliva was performed using MagMAX DNA Multi-Sample Ultra 2.0 Kit on KingFisher™ Flex Purification System.

tag: gender

value: F


title: AYR_PolII_WT_bioRep_3_TSSseq_batch_1

value: AYR


title: Skin normal 23

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-23
205685220015_R12C01


title: pod15

tag: tissue


title: pod13


title: AYR_PolII_WT_bioRep_1_TSSseq_batch_1

tag: strain


title: AYR_PolII_WT_bioRep_2_TSSseq_batch_1


title: Skin normal 22

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-22
205685220015_R11C02


title: EoE/AD MPRA Tag library TE-7

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

library_source: other

data_processing:
Oligo-barcode association: Paired-end, 125 bp reads were first quality filtered using Trimmomatic (v0.38)(flags: PE -phred33, LEADING:25, TRAILING:25, MINLEN:80). Read 1 was separated into the 20 bp barcode region and the oligo-matching region. The trimmed oligo-matching regions of Read 1 and Read 2 were mapped back to the synthesized oligo sequences using Bowtie2 (v2.3.4.1)(flags: -X 250, -very-sensitive, -p 16). Barcodes were then associated with the oligo sequences using the read ID. Only uniquely mapped barcodes were used for downstream analysis.
Barcode counting: Single-end 100 bp reads were first quality filtered using Trimmomatic (v0.38) (flags: PE -phred33, LEADING:3, TRAILING:3, MINLEN:70). Each read was then separated into the 20 bp barcode region and the constant region. The trimmed constant regions of the reads were mapped back to the constant region within the eGFP 3′ UTR using Bowtie2 (v2.3.4.1) (flags: -very-sensitive, -p 16). Only reads with Levenshtein distance of 4 or less within the constant region and perfect matches to the two bases directly adjacent to the barcode were kept. Barcodes were then associated with the retained reads using the read ID. All barcodes were summarized at the oligo level.
Assembly: hg19
Supplementary files format and content: for BC-seq libraries: tab-delimited txt file containing oligo summaries for each sample
Supplementary files format and content: tab-delimited txt file containing barcode counts for each sample
Library strategy: Massively Parallel Reporter Assay (MPRA)

molecule: other

growth_protocol: The TE-7 cell line was grown in RPMI medium supplemented with 10% FBS, 100 units/ml of penicillin, and 100 µg/ml of streptomycin. The HaCaT cell line was grown in DMEM medium supplemented with 10% FBS, 100 units/ml of penicillin, and 100 µg/ml of streptomycin. The Jurkat cell line was grown in RPMI medium supplemented with 10% FBS, 100 units/ml of penicillin, and 100 µg/ml of streptomycin.

extract_protocol:
Total RNA was extracted by the RNeasy Midi Kit following the manufacturer’s instruction. Extracted RNA was subjected to DNase treatment. eGFP mRNA enrichment and elution were performed using biotinylated probes as in Lu et al (PMID: 33712590), and the mRNA was reverse transcribed to cDNA using SuperScript™ IV First-Strand Synthesis System with gene specific primer MPRA_v3_Amp2Sc_R, following the manufacturer’s instruction.
We assembled the MPRA libraries as in Lu et al  (PMID: 33712590), with minor modifications. A total of two versions of the library were assembled. The first version was built following the protocol in Lu et al (PMID: 33712590) and used in TE-7 related experiments. For the second version, an additional step was added after the assembled backbone library was transformed into Escherichia coli (E. coli) through electroporation. Electroporated E. coli were immediately split into eight 1 mL aliquots of SOC medium and recovered for 1 hour at 37°C. For each of the aliquots, serial dilutions of recovered SOC medium were plated to estimate the number of colony forming units. Based on the estimation, volumes enough for 50x, 100x and 200x of the allele number in the oligo pool were independently expanded in 100 mL of LB Broth supplemented with 100 μg/mL of carbenicillin at 37 °C for 12–16 h. Plasmids were then extracted using the QIAGEN Plasmid Maxi Kit. The oligo and barcode regions were amplified from three backbone libraries to build sequencing libraries as described in Lu et al  (PMID: 33712590). Samples were purified, molar pooled, and sequenced using 2 × 150 bp on Illumina NovaSeq 6000. After oligo and barcode association analysis,  the backbone library with ~200x coverage was selected for building the transfection library.  This second version was used in HaCaT and Jurkat related experiments.

treatment_protocol: After transfection, cells were recovered in 30 mL pre-warmed DMEM medium supplemented only with 10% FBS for 24 hrs. Cells were then either stimulated with 100 ng/ml IL-13 or water for another 24 hrs. Cells were then collected for preparation of the sequencing library for barcode counting.


title: pod12


title: Skin normal 21

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-21
205685220015_R11C01


title: parotid gland, PB4, rep3

city: Changchun

first: xin

last: guo

state: Jilin

address: College of Veterinary Medi- 7 cine, Jilin University, Changchun 130062, China.

institute: Jilin university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the whole genome of Mus musculus (Ensembl release 101) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
genome build/assembly: Mus musculus (Ensembl release 101)
processed data files format and content: tab-delimited text files include FPKM values for each Sample

source_name: parotid gland

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: parotid gland

tag: agent

value: inject PB4 strain


title: parotid gland, PB4, rep2


title: parotid gland, PB4, rep1


title: Skin normal 20

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-20
205685220015_R10C02


title: Skin normal 19

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-19
205685220015_R10C01


title: parotid gland, CVS-11, rep3

value: inject CVS-11 strain


title: pod18

value: Lung Tissue, Archival FFPE

tag: cell type


title: pod08

value: Adenocarcinoma


title: parotid gland, Mock, rep3

value: inject DMEM


title: pod07


title: Skin normal 18

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-18
205685220015_R09C02

value: M


title: parotid gland, Mock, rep1


title: parotid gland, Mock, rep2


title: pod04

value: Squamous


title: Skin normal 17

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-17
205685220015_R09C01


title: EoE/AD MPRA BC library HaCaT/Jurkat


title: pod01


title: NYR_PolII_WT_EtOH_bioRep_2

description: NYR_WT_EtOH-pDs_RepsCmb-ct4-pos_cnt_mtx-stat.csv

data_processing:
Library strategy: TSS-seq
we considered only those reads that contained a perfect match to a 27 nt sequence region downstream of the barcode, as well as expected length of 5’-end: 5’-[15 nt 5’-UMI]-[>1 nt upstream of barcode region, designated as “RNA 5’-end”]-[24 nt barcode]-[the first 27 nt of GFP ORF, ATGTCTAAAGGTGAAGAATTATTCACT]-3’. Next, 15 nt 5’-UMIs, “RNA 5’-end” with varying length, and 24 nt barcode were extracted and individually corrected by UMI-tools (1.0.0). Deduplication was performed based on 5’-UMIs, meaning reads containing a shared UMI-“RNA 5’-end”-barcode linkage were counted as one deduplicated read for further analysis.
Next, the identity of the 24 nt barcode was used to determine the template sequences of randomized TSS region. Only reads with “RNA 5’-end” sequence perfectly matched to corresponding template sequence were used for analysis of TSS efficiency, but all deduplicated reads, including reads with mismatch(es), were used for analysis of relative expression.
Next, a TSS-seq count table containing TSS usage distribution of each TSS promoter variant was generated. In the count table, each row represents one TSS promoter variant, and each column represents one position between positions -68 to +25 relative to “designed” +1 TSS. The number in each cell represents TSS-seq reads generated from a particular position, with perfectly match to the DNA template.
After investigating reproducibility, count tables generated from three biological replicates were merged into one by aggregating read counts at each position. Promoter variants with >= 5 TSS-seq reads in each replicate and whose Coefficient of Variation (CV) of TSS-seq reads is <= 0.5 were kept.
Supplementary files format and content: Each TSS-seq sample links to three processed data files. One tab-delimited file contains “RNA 5’-end”-Barcode linkages and coresponding deduplicated TSS-seq read counts for this particular sample. Two count tables contain TSS usage distributions of each TSS promoter variant, related to this particular TSS-seq sample: one for this partcular TSS-seq sample itself, and one after aggregating three biological replicates.

growth_protocol: Plasmid library pools were transformed into yeast strains with wildtype Pol II using chemical transformation. Transformants were grown on selective SC-His plates with 2% glucose as carbon source at high density. Three biological replicates were performed for each library and on average over two million colonies were collected apiece. Transformants scraped from densely plated transformation plates were inoculated into fresh SC-His medium with 2% raffinose (Amresco, J392) at 0.25 x 107 cells/ml and grown until 0.5-0.8 x 107 cells/ml. Subsequently, galactose (Amresco, 0637) was added for three hours (4% final concentration) to induce library expression. For MPA treated WT libraries, MPA (in 100% ethanol; Sigma-Aldrich, M3536) was added for 20 min (20 µg/ml final concentration) prior to the three-hour galactose induction, in parallel with the same volume of 100% ethanol as control. 50 ml and 5 ml culture aliquots, for RNA and DNA extraction, respectively, were harvested and then cell pellets were stored at -80C for further processing as described below.

extract_protocol:
Total RNA was extracted, followed by RNA purification (RNeasy Mini kit, QIAGEN, 74104) with on-column DNase digestion (RNase-Free DNase Set, QIAGEN, 79254) to remove DNA.
TSS-seq was done using procedures described in (Vvedenskaya, Goldman, & Nickels, 2015).

value: NYR

value: WT

value: EtOH


title: pod09


title: NYR_PolII_WT_EtOH_bioRep_1


title: EoE/AD MPRA BC library TE-7


title: NYR_PolII_WT_MPA_bioRep_3

description: NYR_WT_MPA-pDs_RepsCmb-ct4-pos_cnt_mtx-stat.csv

value: MPA


title: IPW2

city: Nanjing

first: Ying

address: Guangzhou Road

institute: NanJing Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: hg38
Supplementary files format and content: TXT files include FPKM values for each Sample

source_name: human retinal pigment epithelial cells

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: human retinal pigment epithelial cells

value: IPW overexpression


title: parotid gland, CVS-11, rep1


title: Skin normal 15

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-15
205685220015_R08C01


title: IPW1


title: parotid gland, CVS-11, rep2


title: Skin normal 14

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-14
205685220015_R07C02


title: NYR_PolII_WT_MPA_bioRep_1


title: Skin normal 13

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-13
205685220015_R07C01


title: NYR_PolII_WT_MPA_bioRep_2


title: NC2


title: BYR_PolII_H1085Q_bioRep_3_TSSseq_batch_2

value: CKY956 (Pol II H1085Q)

value: BYR

value: biological replicate 3


title: BYR_PolII_H1085Q_bioRep_2_TSSseq_batch_2

value: biological replicate 2


title: NC1


title: Skin normal 12

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-12
205685220015_R06C02


title: Skin normal 16

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-16
205685220015_R08C02


title: NYR_PolII_WT_EtOH_bioRep_3


title: ARY_PolII_G1097D_bioRep_5_TSSseq_batch_2

value: CKY962 (Pol II G1097D)

value: ARY

value: biological replicate 5


title: EoE/AD MPRA Jurkat 5

source_name: Jurkat

value: Jurkat

value: unstimulated


title: Skin normal 10

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-10
205685220015_R05C02

value: F


title: Skin normal 11

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-11
205685220015_R06C01

value: M


title: BYR_PolII_G1097D_bioRep_5_TSSseq_batch_2


title: ARY_PolII_G1097D_bioRep_6_TSSseq_batch_2

value: biological replicate 6


title: BYR_PolII_H1085Q_bioRep_1_TSSseq_batch_2

value: biological replicate 1


title: ARY_PolII_G1097D_bioRep_3_TSSseq_batch_2


title: BYR_PolII_G1097D_bioRep_2_TSSseq_batch_2


title: EoE/AD MPRA Jurkat 3


title: Skin normal 9

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-9
205685220015_R05C01


title: BYR_PolII_G1097D_bioRep_4_TSSseq_batch_2

value: biological replicate 4


title: EoE/AD MPRA Jurkat 2


title: AYR_PolII_G1097D_bioRep_3_TSSseq_batch_2

value: AYR


title: Skin normal 8

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-8
205685220015_R04C02


title: AYR_PolII_G1097D_bioRep_1_TSSseq_batch_2


title: Skin normal 6

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-6
205685220015_R03C02


title: EoE/AD MPRA Jurkat 4


title: Skin normal 7

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-7
205685220015_R04C01


title: AYR_PolII_G1097D_bioRep_2_TSSseq_batch_2


title: EoE/AD MPRA Jurkat 1


title: BYR_PolII_F1086S_bioRep_3_TSSseq_batch_2

value: CKY960 (Pol II F1086S)


title: BYR_PolII_F1086S_bioRep_1_TSSseq_batch_2


title: ARY_PolII_E1103G_bioRep_2_TSSseq_batch_2

value: CKY964 (Pol II E1103G)


title: EoE/AD MPRA HaCaT IL-13 5

source_name: HaCaT

value: HaCaT

value: IL-13 stimulated


title: ARY_PolII_E1103G_bioRep_3_TSSseq_batch_2

value: biological replicate 3


title: EoE/AD MPRA HaCaT IL-13 4


title: Skin normal 5

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-5
205685220015_R03C01


title: EoE/AD MPRA HaCaT IL-13 3


title: ARY_PolII_E1103G_bioRep_1_TSSseq_batch_2


title: BYR_PolII_E1103G_bioRep_2_TSSseq_batch_2

value: BYR

value: biological replicate 2


title: Skin normal 4

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-4
205685220015_R02C02


title: BYR_PolII_E1103G_bioRep_1_TSSseq_batch_2


title: BYR_PolII_F1086S_bioRep_2_TSSseq_batch_2


title: AYR_PolII_E1103G_bioRep_3_TSSseq_batch_2


title: Skin normal 2

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-2
205685220015_R01C02


title: AYR_PolII_E1103G_bioRep_2_TSSseq_batch_2


title: EoE/AD MPRA HaCaT unstimulated 5


title: BYR_PolII_WT_bioRep_3_TSSseq_batch_2

value: CKY954 (WT)


title: AYR_PolII_E1103G_bioRep_1_TSSseq_batch_2


title: BYR_PolII_E1103G_bioRep_3_TSSseq_batch_2


title: Skin normal 1

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-1
205685220015_R01C01


title: BYR_PolII_WT_bioRep_2_TSSseq_batch_2


title: Skin normal 3

description:
Genomic DNA extracted from saliva was genotyped using Infinium Asian Screening Array-24 v1.0 BeadChip).
gst-skin-3
205685220015_R02C01


title: EoE/AD MPRA HaCaT unstimulated 4


title: BYR_PolII_WT_bioRep_1_TSSseq_batch_2


title: ARY_PolII_WT_bioRep_3_DNAseq

data_processing:
Library strategy: DNA-seq
Paired-end reads were merged using PEAR (0.9.11) (J. Zhang, Kobert, Flouri, & Stamatakis, 2014). We considered only those reads that contained a perfect match to three sequence regions common to all variants: 27 nt sequence upstream of the TSS region, 24 nt sequence between TSS region and barcode, and 27 nt sequence downstream of barcode (5'-TTCAAATTTTTCTTTTGATTTTTTTTCNNNNNNNNNACATTTTCAAAAGGCTAACATCAGNNNNANNNNCNNNNTNNNNGNNNNATGTCTAAAGGTGAAGAATTATTCACT-3'). From these reads, 9 nt TSS region and 24 nt barcode were extracted, followed by individually error correction using UMI-tools (1.0.0) (Smith, Heger, & Sudbery, 2017). For barcodes linking to multiple TSS variants, only barcodes for which >= 90% of the sequencing reads containing a specified barcode also contained a shared, exact 9 nt TSS region were kept.
To generate a master pool of TSS-barcode linkages for all TSS-seq samples, for each library ("AYR", "BYR", "ARY"), TSS-barcode linkages that exist in at least two out of one E.coli sample plus three WT yeast replicates and also have >= 5 reads in each sample were kept and pooled.
Each DNA-seq sample links to two tab-delimited files. One contains TSS-Barcode linkages and coresponding DNA-seq read counts for this particular sample. Another one is its corresponding master pool of TSS-barcode linkages that were generated based on all E.coli and yeast samples and were used for DNA-seq and TSS-seq merging.

extract_protocol:
Plasmid DNA was isolated from yeast cells pellets using YeaStar Genomic DNA Kit (Zymo Research, D2002) per manufacturer's instructions.
Amplicon pools containing the TSS and barcode regions were generated by Micellula DNA Emulsion & Purification (ePCR) Kit (EURx/CHIMERx, 3600) per manufacturer's instructions. To minimize amplification bias, each sample was amplified in a 15-cycle ePCR reaction, purified and subject to an additional 10-cycle scale-up ePCR reaction. To create the necessary sequence diversity for sequencing, 18-25 bp and 1-7 bp "stuffer" sequences were added to 5'- and 3'-end, respectively, during amplicon preparation.

value: ARY


title: EoE/AD MPRA HaCaT unstimulated 2


title: Muscidifurax zaraptor, 24-hour adult male, on housefly hosts, replicate 2

city: Auburn University

first: Xu

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

data_processing:
The raw RNA-seq data was checked for sequencing quality using FastQC
Adapter sequences and low-quality bases in the paired-end RNA-seq reads were trimmed with Trimmomatic v0.39
RNA-seq reads mapped uniquely to the N. muscidifuracis were used for de novo transcriptome assembly by Trinity v2.4.0
The gene read counts of each sample were quantified and summarized using HTseq version1.0 (Anders et al. 2015)
Assembly: JAIOKI000000000
Supplementary files format and content: tab-delimited text file includes gene read counts for each sample

organism: Muscidifurax zaraptor

source_name: whole body

extract_protocol:
RNA extractions were performed with AllPrep DNA/RNA Mini Kit (Qiagen, MD, USA) following the manufacturer’s protocol.
For RNA-seq library preparation, 1 μg of total RNA was used as input for all samples. To remove the abundant rRNA (ribosomal RNA) in the sample, an rRNA removal protocol was performed using the NEBNext rRNA Depletion Kit (New England Biolabs, MA, USA). The remaining mRNA was used for RNA-seq library construction using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, MA, USA) with the manufacturer-provided protocol. After quality control, the RNA-seq library was sequenced on an Illumina NovaSeq6000 platform.

value: whole body

value: USDA

value: Male

value: adult, 24 hours after eclosion


title: Muscidifurax zaraptor, 24-hour adult male, on housefly hosts, replicate 3


title: ARY_PolII_WT_bioRep_2_DNAseq


title: EoE/AD MPRA HaCaT IL-13 1


title: NCV_0916

first: Haochen

last: Yang

address: 320 Yue-yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
The output gene expression matrices were analyzed by R software (v4.2.0) with the Seurat package (version 4.2.0). All samples were merged into one Seurat object using the merge function in Seurat. Low quality cells with < 200 or >7000 genes detected, < 500 or >100,000 UMI counts detected or > 5% mitochondrial UMI counts detected were removed.
Dimension reduction and unsupervised clustering were performed according to the standard workflow in Seurat. SCTransform function was applied to normalize and find highly variable genes (HVGs) within the single-cell gene expression data. Mitochondrial genes, dissociation-induced genes and HLA genes were removed from HVGs for downstream analyses. Then, the effect of the percentage of mitochondrial gene counts was regressed out by using SCTransform function with parameter “vars.to.regress = ‘percent.mt’ ”.
A principal component analysis (PCA) matrix was calculated to reduce noise by using RunPCA with default parameters. After PCA analysis, we use Findneighbors and FindClusters (by Louvain algorithm) function provided by Seurat. Then UMAP and graph-based clustering were performed on the object for visualization and cell clustering by RunUMAP function. The main immune cell types were annotated based on the expression pattern of DEGs and the well-known cellular markers from the literature.
In the first-round of unsupervised clustering of all cells, we found 5 spread small clusters (less than 10 cells) of WT group which might be caused by sequencing noise. Therefore, we removed these clusters for downstream analysis.
Assembly: Cell Ranger (version 7.0) was applied to filter low quality reads, align reads to mouse reference genome (GRCm38), assign cell barcodes, and generate the UMI matrices.
Supplementary files format and content: The output gene expression matrices were analyzed by R software (v4.2.0) with the Seurat package (version 4.2.0). All samples were merged into one Seurat object using the merge function in Seurat. Low quality cells with < 200 or >7000 genes detected, < 500 or >100,000 UMI counts detected or > 5% mitochondrial UMI counts detected were removed.

source_name: colon tumor

growth_protocol: Cyp51-KO or sg-Ctrl CT26 tumors were harvested at day 26 post orthotopic injection in BALB/c mice. Single cell suspensions of tumor tissues were prepared as described above.

extract_protocol:
For the quality check and counting of single cell suspension, the cell survival rate is generally above 90%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/μl.
Then the cells were loaded ~18,000 cells/chip position using the 10× Chromium Next GEM Single Cell 5’ Kit v2. The system is operated on the machine. GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested.

treatment_protocol: Cells from 9 (Cyp51-KO) and 12 (sg-Ctrl) tumors were stained with antibodies for surface proteins at 4℃ for 30 min and sorted into bulk CD45+ cells, CD45+ CD3+ T cells and CD45- BFP+ tumor cells with MA900 Multi-Application Cell Sorter (SONY). Sorted cell subsets were combined at a ratio of 50 % bulk CD45+ cells, 40 % CD45+ CD3+ T cells and 10 % tumor cells.

value: colon tumor


title: 51V_0927

value: CD45+ cells, CD45+ CD3+ T cells and CD45- BFP+ tumor cells


title: NCV_0927


title: EoE/AD MPRA HaCaT unstimulated 1

value: unstimulated


title: BYR_PolII_WT_bioRep_3_DNAseq


title: Muscidifurax zaraptor, 24-hour adult male, on housefly hosts, replicate 1


title: 51V_0916


title: EoE/AD MPRA TE-7 IL-13 5


title: Muscidifurax zaraptor, 24-hour adult male, on fleshfly hosts, replicate 3

value: AUB


title: BYR_PolII_WT_bioRep_2_DNAseq


title: Liver,  Asgr1 KO, 6 months old, 3

city: xianyang

first: leng

last: xiangkai

state: shanaxi

address: No.22, Xinong Road, Yangling National Agricultural High-tech Industry Demonstration Zone

institute: Northwest A&F University

data_processing:
QuantiFluor® dsDNA System
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SeqPrep （https://github.com/jstjohn/SeqPrep）and Sickle（https://github.com/najoshi/sickle）.The specific steps are as follows:1) Remove the splice sequences in the reads, remove the reads without inserted fragments due to splice self-connection and other reasons.2) Trim off the bases with low quality (quality value less than 20) at the end of the sequence (3' end), if there is still a quality value less than 10 in the remaining sequence then the whole sequence will be removed, otherwise it will be kept.3) Remove the reads with more than 10% of uncertain bases.4) Discard the sequences with length less than 20bp after the adapter and quality trimming.
Trimmed sequence reads were mapped to GrCM38/mm10 using HiSat2(http://ccb.jhu.edu/software/hisat2/index.shtml) and TopHat2 (http://ccb.jhu.edu/software/tophat/index.shtml)
Read count extraction and normalization were performed using RSEM（http://deweylab.github.io/RSEM/）
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count for each Sample

source_name: Liver

growth_protocol: All mice were housed in the Northwest A&F University animal facility under standard conditions with 12 h of light and 12 h dark cycle with free access to food and water.

extract_protocol:
RNA was harvested using  Total RNA was extracted from liver tissue using TRIZOL (Invitrogen, Carlsbad, CA) following the manufacturer's instructions for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing following manufacturer's protocols.

treatment_protocol: Global Asgr1-/- mice were generated on the C57BL/6 background by CRISPR/Cas9-mediated gene targeting. We designed two sgRNAs targeting exons 2 and 9 of the mouse ASGR1 gene using online tools (http:crispr.mit.edu/), respectively. ASGR1 sgRNA and Cas9 protein were microinjected into the zygotes of C57BL/6 mice to generate embryos. The mouse ASGR1 sequence was deleted 3047 bp and inserted 9 bp. The heterozygotes were identified and intercrossed to generate Asgr1-/- mice with heterozygous (Asgr1+/-) and WT littermates. Genomic DNA was extracted from tail biopsies for PCR genotyping and sequencing by using Tiangen Bio-Universal Genomic DNA Extraction kit.

value: Liver

value: Asgr1 knockout

value: male

value: 6 months old


title: EoE/AD MPRA HaCaT unstimulated 3

value: HaCaT


title: Liver,  Asgr1 KO, 6 months old, 2


title: EoE/AD MPRA TE-7 IL-13 4

value: IL-13 stimulated


title: Muscidifurax zaraptor, 24-hour adult male, on fleshfly hosts, replicate 2


title: BYR_PolII_WT_bioRep_1_DNAseq

value: BYR

value: biological replicate 1


title: EoE/AD MPRA TE-7 IL-13 3


title: Muscidifurax zaraptor, 24-hour adult male, on fleshfly hosts, replicate 1


title: ARY_PolII_WT_bioRep_1_DNAseq

value: CKY954 (WT)

value: ARY


title: Muscidifurax zaraptor, 24-hour adult female, on housefly hosts, replicate 3

value: whole body

value: USDA

value: Female


title: Liver,  Asgr1 KO, 6 months old, 1


title: AYR_PolII_WT_bioRep_3_DNAseq

value: AYR

value: biological replicate 3


title: AYR_PolII_WT_bioRep_2_DNAseq

value: biological replicate 2


title: EoE/AD MPRA HaCaT IL-13 2


title: Muscidifurax zaraptor, 24-hour adult female, on housefly hosts, replicate 2

value: adult, 24 hours after eclosion


title: Liver, WT, 6 months old, 2

value: Liver

value: WT


title: Liver, WT, 6 months old, 1

value: male


title: EoE/AD MPRA TE-7 unstimulated 5

value: unstimulated


title: EoE/AD MPRA TE-7 unstimulated 4


title: KO-Ovary4_362_215_S2

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

data_processing:
Partek Flow
RNAseq data were trimmed and aligned to the Anopheles genome, with associated annotation file using STAR (v2.7.3a).
The aligned reads were quantified to Ensembl transcripts using the Partek E/M algorithm and the subsequent steps were performed on gene-level annotation followed by total count normalization.
The counts generated were processed by gene set analysis (GSA).
Assembly: Anopheles gambiae PEST
Supplementary files format and content: tab-delimited text files include baseMean for each gene

organism: Anopheles gambiae

source_name: ovary

extract_protocol:
The whole body, ovaries, and fat bodies were collected from blood-fed mosquitoes 24 h after completion of the meal. Total RNA was extracted from the whole body, ovaries, or fat bodies from mosquitoes. Trizol was added to the tissues and RNA was isolated using a RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mosGILTnull and Wild type (WT,control) mosquitoes were fed on naïve mice

value: ovary

value: mosGILTnull

value: Blood feeding


title: AYR_PolII_WT_bioRep_1_DNAseq

value: biological replicate 1


title: Muscidifurax zaraptor, 24-hour adult female, on fleshfly hosts, replicate 3

value: AUB


title: ARY_Ec_DNAseq

organism: Escherichia coli

source_name: Laboratory E.coli strain

growth_protocol: Ligation products were transformed into Escherichia coli TOP10F' cells (Invitrogen) and grown on LB plates supplemented with carbenicillin (100 µg/ml) at high density.

extract_protocol:
Plasmid DNA was isolated from E. coli cell pellets using ZymoPURE II Plasmid Maxiprep Kit (Zymo Research, D4203) per manufacturer's instructions.
Amplicon pools containing the TSS and barcode regions were generated by Micellula DNA Emulsion & Purification (ePCR) Kit (EURx/CHIMERx, 3600) per manufacturer's instructions. To minimize amplification bias, each sample was amplified in a 15-cycle ePCR reaction, purified and subject to an additional 10-cycle scale-up ePCR reaction. To create the necessary sequence diversity for sequencing, 18-25 bp and 1-7 bp "stuffer" sequences were added to 5'- and 3'-end, respectively, during amplicon preparation.

value: ARY

value: not applicable


title: Muscidifurax zaraptor, 24-hour adult female, on fleshfly hosts, replicate 2

value: whole body


title: EoE/AD MPRA TE-7 unstimulated 3


title: KO-2Ovary_085_108_S78


title: KO-1Ovary_014_179_S76


title: BYR_Ec_DNAseq

value: BYR


title: Muscidifurax zaraptor, 24-hour adult female, on fleshfly hosts, replicate 1

value: Female


title: Wt-Ovary5_350_227_S3

value: mosGILT WT


title: AYR_Ec_DNAseq

value: AYR


title: EoE/AD MPRA TE-7 IL-13 1

value: IL-13 stimulated


title: Liver, WT, 6 months old, 3

value: Liver

value: 6 months old


title: Muscidifurax zaraptor, 24-hour adult female, on housefly hosts, replicate 1

value: USDA

value: adult, 24 hours after eclosion


title: EoE/AD MPRA TE-7 unstimulated 1

value: unstimulated


title: Wt-Ovary4_374_203_S1

value: ovary


title: EoE/AD MPRA Tag library HaCaT/Jurkat


title: EoE/AD MPRA TE-7 IL-13 2


title: CTCF CUT&RUN, Day8 Teff cells, rep3

data_processing:
The sequencing quality of CUT&RUN-sequencing libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For CUT&RUN libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9
Supplementary files format and content: narrowPeak
Library strategy: CUT&RUN

extract_protocol:
Teff and Tcm cells (day 8 and ≥day 30 post-infection) were sort purified and used for CTCF CUT&RUN analysis in live cells .
The DNA segments from CTCF CUT&RUN were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: wild type

value: splenocytes

value: CD45.2+  KLRG1+ IL-7Ra– CD8+

tag: chip antibody

value: Anti-CTCF Antibody, Millipore Sigma. Cat. No. 07-729, Lot#:3388643


title: T3_3

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

data_processing:
CLC Gencmics Workbench v 11.0.1
Sequence reads were timmed for adaptor sequence/low-aualty sequence using ClC genomic benchwork (parameler- Quality limit: 0 05)
Trimmed sequence reads were mappedto GrCM38/mm 10 using lC genoric benchaok (parnamelers- mismath cost: 2 insericn cost 3 delesion cost 3 lengh facticn 0.8 similarty faction 0.8)
Read count extraction and normalization were performed using ClC genmic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

organism: Ovis aries

source_name: Longissimus dorsi muscle

extract_protocol: Thirty-six 5-month-old Tan sheep with similar health statuses and weights were selected and randomly divided into four groups, with 9 sheep in each group, and reared in individual pens (4 m × 4 m). The four groups were as follows: control group (basal diet), SUC1 group (basal diet + 0.5% succinate), SUC2 group (basal diet + 1% succinate) and SUC3 group (basal diet + 2% succinate). The diets of each group were formulated according to the "Nutritional Requirements of Sheep" (Ministry of Agriculture of China, 2021) and the actual production of Tan sheep. The pretrial period was 10 days and the formal trial period was 60 days. During the experiment, all experimental sheep had free access to water and were fed twice a day (at 06:30 and 17:30).

value: Longissimus dorsi muscle

tag: group


title: EoE/AD RNA-seq HaCaT IL-13 2

data_processing:
RNA-seq reads were mapped to the human genome (Genome Reference Consortium Human Build 37 (GRCh37)) using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon)
The tximport package was used to prepare Salmon’s transcription abundance estimates (provided in TPM format).
Gene-level differential expression analysis between conditions (unstimulated vs. IL-13 stimulated) was analyzed using DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited txt file containing TPM values for each sample

growth_protocol: The TE-7 cell line was grown in RPMI medium supplemented with 10% FBS, 100 units/ml of penicillin, and 100 µg/ml of streptomycin. The HaCaT cell line was grown in DMEM medium supplemented with 10% FBS, 100 units/ml of penicillin, and 100 µg/ml of streptomycin.

extract_protocol:
Total RNA was extracted using Thermo Fisher's mirVana miRNA isolation kit according to the manufacturer's instructions.
Libraries were prepared with the SMARTer Stranded Total RNA - Hi Mammalian Kit according to the manufacturer's protocol.

treatment_protocol: Cells were either stimulated with 100 ng/ml IL-13 or water for 24 hrs.

value: HaCaT


title: CTCF CUT&RUN, Day8 Teff cells, rep2

tag: genotype


title: Wt-2Ovary_002_191_S77

value: Blood feeding


title: EoE/AD MPRA TE-7 unstimulated 2

tag: cell line


title: T3_1


title: Wt-1Ovary_026_167_S75


title: EoE/AD RNA-seq HaCaT IL-13 1


title: CTCF CUT&RUN, Day8 Teff cells, rep1


title: T2_3


title: ARY_PolII_G1097D_bioRep_6_TSSseq_batch_1

extract_protocol:
Total RNA was extracted by a phenol-chloroform method (Schmitt, Brown, & Trumpower, 1990), followed by RNA purification (RNeasy Mini kit, QIAGEN, 74104) with on-column DNase digestion (RNase-Free DNase Set, QIAGEN, 79254) to remove DNA.
TSS-seq was done using procedures described in (Vvedenskaya, Goldman, & Nickels, 2015). To prepare RNAs for the cDNA library construction, samples were sequentially treated with Terminator 5‘-Phosphate-Dependent Exonuclease, calf-intestine alkaline phosphatase and Cap-Clip Acid Pyrophosphatase to remove 5' monophosphate RNA and convert 5' triphosphate or capped RNAs to 5' monophosphate RNAs. Next, RNA prepared with enzymatic treatments was ligated to the 5'-adapter (s1206-N15, 5'-GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNNNNNNNNN-3') that contains Illumina adapter sequence and a 15 nt randomized 3'-end to reduce ligation bias and serve as a Unique Molecular Identifier (UMI). Next, cDNA was constructed by reverse transcription using RT primer CKO2191-s128A (5'-CCTTGGCACCCGAGAATTCCAAGTGAATAATTCTTCACCTTTA-3') followed by PCR amplification using Illumina PCR primers (RP1 and RPI3-30). Final DNA was gel size selected for 180-250 bp lengths.

value: CKY962 (Pol II G1097D)

value: ARY

value: biological replicate 6


title: KO-FB2_302_275_S7

source_name: fat body

value: fat body

value: mosGILTnull


title: ATAC WT, Tcm cells, rep3

data_processing:
The sequencing quality of CUT&RUN-sequencing libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ATAC-seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit and llocal = 7500 as identified binding sites.
Assembly: mm9
Supplementary files format and content: narrowPeak

growth_protocol: CreER+ WT or CTCF-floxed P14 CD8+ T cells were first transferred into B6.SJL mice followed by LCMV-Arm infection.

extract_protocol:
Sorted Tcm cells at the resting state were treated with TN5 transposase to generate tagged DNA fragments.
TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries

treatment_protocol: After ≥30 days, the immune mice were treated with tamoxifen for two days, and CD62L+ P14+ central memory (Tcm) cells were sorted on the third day.


title: ATAC WT, Tcm cells, rep2


title: T2_2


title: EoE/AD RNA-seq HaCaT unstimulated 2


title: KO-FB1_314_263_S6


title: EoE/AD RNA-seq HaCaT unstimulated 1


title: T3_2


title: T2_1


title: ATAC WT, Tcm cells, rep1


title: Wt-FB2_326_251_S5

value: mosGILT WT


title: EoE/AD RNA-seq TE-7 IL-13 3

value: IL-13 stimulated


title: ATAC CTCFKO 72hr, Tcm cells, rep3

value: CTCF KO


title: T1_3


title: T1_2


title: Wt-FB1_338_239_S4


title: EoE/AD RNA-seq TE-7 IL-13 2


title: EoE/AD RNA-seq TE-7 IL-13 1


title: ATAC CTCFKO 72hr, Tcm cells, rep2


title: KO-6WB_138_055_S6

value: whole body


title: T1_1


title: KO-4WB_186_007_S2


title: ATAC CTCFKO 72hr, Tcm cells, rep1


title: EoE/AD RNA-seq TE-7 unstimulated 3

value: unstimulated


title: C_3

value: control group


title: Wt-6WB_150_043_S5


title: EoE/AD RNA-seq TE-7 unstimulated 2


title: C_2


title: CTCF CUT&RUN, Tcm cells, rep2

data_processing:
library strategy: CUT&RUN
The sequencing quality of CUT&RUN-sequencing libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.2.5, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For CUT&RUN libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9
Supplementary files format and content: narrowPeak

value: wild type

value: splenocytes


title: Wt-5WB_174_019_S3


title: CTCF CUT&RUN, Tcm cells, rep1

value: Anti-CTCF Antibody, Millipore Sigma. Cat. No. 07-729, Lot#:3388643


title: Wt-4WB_103_090_S1


title: C_1

value: Longissimus dorsi muscle


title: Tet2, IL-1β antibody, ZsGreen1-

status: Public on Nov 25 2023

first: Eunyoung

last: Kim

institute: Columbia University

description: 10x Genomics 3' mRNA library

data_processing:
Fastq files were processed by Cell Ranger 6.0.2 for Jak2VF samples and Cell Ranger 5.0.1 for Tet2 samples. Prebuilt reference mm10-2020-A (GENCODE vM23/Ensembl 98) was used for all samples.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Aorta

extract_protocol:
RNA was extracted using 10x Genomics Chromium Single Cell 3' v3 protocol.
Library was constructed using 10x Genomics Chromium Single Cell 3' v3 protocol.

treatment_protocol: Clean aortas (ascending and arch) from mice were minced and digested. Cells were stained and subject to flow cytometry sorting. Sorted ZsGreen1+ and ZsGreen1- cells were submitted to scRNA-seq sequencing.

value: Aorta

value: Cx3cr1-Tet2(-/-), Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-)

value: 17-week Western diet, IL-1Beta antibody

tag: lineage

value: non-SMC lineage


title: Jak2VF, IL-1β antibody, ZsGreen1-

description: 10x Genomics 3' mRNA library

value: Jak2VF, Myh11(Cre), ROSA(ZsGreen1), Ldlr(-/-)

tag: treatment


title: Jak2VF, IgG, ZsGreen1-

description: 10x Genomics 3' mRNA library

value: 17-week Western diet, IgG


title: WT, IL-1β antibody

description: 10x Genomics 3' mRNA library

value: Wild-Type


title: Jak2VF, IgG, ZsGreen1+

description: 10x Genomics 3' mRNA library

value: SMC lineage


title: Jak2VF, IL-1β antibody, ZsGreen1+

description: 10x Genomics 3' mRNA library


title: WT, IgG

description: 10x Genomics 3' mRNA library


title: Tet2, IL-1β antibody, ZsGreen1+

description: 10x Genomics 3' mRNA library


title: Tet2, IgG, ZsGreen1+

description: 10x Genomics 3' mRNA library


title: Tet2, IgG, ZsGreen1-

description: 10x Genomics 3' mRNA library


title: IgG CUT&RUN, Day8 Teff cells

value: CD45.2+  KLRG1+ IL-7Ra– CD8+

value: Normal Rabbit IgG, Cell Signaling Technologies,Cat No. 2729s, Lot#:9


title: EoE/AD RNA-seq TE-7 unstimulated 1


title: Jak2VF On [mRNA]

description:
TA0043
10x Genomics 3' mRNA library
Cellular Indexing of Transcriptomes and Epitopes by sequencing

data_processing:
Fastq files were processed by Cell Ranger 5.0.1. Prebuilt reference mm10-2020-A (GENCODE vM23/Ensembl 98) was used for RNA expression quantification. Annotation from TotalSeq-B antibodies was used for ADT library quantification. A suffix number was added to duplicate gene symbols.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.
Supplementary files format and content: Tab-delimited text file includes ADTs and barcode sequences.
Library strategy: CITE-seq

treatment_protocol: Clean aortas (ascending and arch) from mice were minced and digested. Cells were incubated with CD45 antibodies and washed. Cells were then stained and subject to flow cytometry sorting for DAPI negative and CD45+ cells. Sorted cells were incubated with CITE-seq antibodies before library preparation.

value: Jak2VF(Dre), Ubc(Cre), Ldlr(-/-)

value: 10-week Western diet

tag: library type

value: mRNA

tag: antibody


title: Jak2VF Off Regression [mRNA]

description:
10x Genomics 3' mRNA library
TA062_CITEseq_barcodes.tsv.gz
TA062_CITEseq_features.tsv.gz
TA062_CITEseq_matrix.mtx.gz

data_processing:
Fastq files were processed by Cell Ranger 5.0.1. Prebuilt reference mm10-2020-A (GENCODE vM23/Ensembl 98) was used for RNA expression quantification. Annotation from TotalSeq-A panel was used for ADT library quantification.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

value: 10-week Western diet, 1-week tamoxifen, AAV-LDLR, 6-week chow diet

tag: antibodies


title: Jak2VF Off [ADT]

description:
TA0042F
10x Genomics feature barcode library
Cellular Indexing of Transcriptomes and Epitopes by sequencing

molecule: protein

value: 10-week Western diet, 1-week tamoxifen

value: ADT

value: CD45.1, CD45.2, Ly-6G, Mac-2, CD68 from TotalSeq-B panel


title: Jak2VF Off [mRNA]

description:
TA0042
10x Genomics 3' mRNA library
Cellular Indexing of Transcriptomes and Epitopes by sequencing

value: Aorta


title: Control [ADT]

description:
TA0041F
10x Genomics feature barcode library
Cellular Indexing of Transcriptomes and Epitopes by sequencing

value: Jak2VF, Ldlr(-/-)


title: Jak2VF On Regression [ADT]

description:
10x Genomics feature barcode library
TA061_CITEseq_barcodes.tsv.gz
TA061_CITEseq_features.tsv.gz
TA061_CITEseq_matrix.mtx.gz

value: Jak2VF(Dre), Ldlr(-/-)

value: TotalSeq-A panel 750002548


title: Jak2VF Off Regression [ADT]

description:
10x Genomics feature barcode library
TA062_CITEseq_barcodes.tsv.gz
TA062_CITEseq_features.tsv.gz
TA062_CITEseq_matrix.mtx.gz


title: Jak2VF On Regression [mRNA]

description:
10x Genomics 3' mRNA library
TA061_CITEseq_barcodes.tsv.gz
TA061_CITEseq_features.tsv.gz
TA061_CITEseq_matrix.mtx.gz


title: Sakuranetin_3

first: Chi

address: Deshengzhong Road No.298

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated.Rawreads of fastqformatwere firstly processed using fastp and the low quality reads were removed to obtainthecleanreads.Then the clean reads for each sample were retained for subsequent analyses. Thecleanreads were mapped to the reference genome using HISAT. FPKM of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 . Qvalue 2 or foldchange < 0.5 was set as the threshold for significantly differential expressiongene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) todemonstratetheexpression pattern of genes in different groups and samples. The radar map of top 30 geneswasdrew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome andWikiPathwaysenrichment analysis of DEGs were performed to screen the significant enriched termusingR(v3.2.0),respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagramandbubblediagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. Theanalysiswas www.oebiotech.com used a predefined gene set, and the genes were ranked according to the degreeof differentialexpression in the two types of samples. Then it is tested whether the predefinedgenesetwasenriched at the top or bottom of the ranking list.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Pyricularia oryzae

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Sakuranetin


title: Sakuranetin_2


title: ABA_3

value: abscisic acid (ABA)


title: Sakuranetin_1


title: ABA_2


title: Control [mRNA]

description:
TA0041
10x Genomics 3' mRNA library
Cellular Indexing of Transcriptomes and Epitopes by sequencing


title: SA_3

value: salicylic acid (SA)


title: Jak2VF On [ADT]

description:
TA0043F
10x Genomics feature barcode library
Cellular Indexing of Transcriptomes and Epitopes by sequencing


title: SA_2


title: Mock_3

value: Mock (DMSO)


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_80_Liver_S20_L001

city: Riverside

first: Brendan

last: Gongol

state: Ca

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Following DNA sequencing and read mapping to the mouse GRCm39 genome, reads aligning to coding regions were retained and the number of read counts per gene were calculated.
Assembly: GRCm39
Supplementary files format and content: Excel files include FPKM or values for each sample.

extract_protocol:
RNA was extracted using QIAzol reagent followed by chloroform extraction followed by an additional purification step using RNeasy mini kit with a DNAse digestion (Qiagen).
For each sample, total RNA was normalized to 100 ng before undergoing library preparation using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit per manufacturer’s instructions. The Agilent Bioanalyzer and Qubit Fluorometer were used to libraries were qualified and quantified using the the Agilent Bioanalyzer and Qubit Fluorometer prior to pooling samples. Samples were sequenced on the Illumina Novaseq 6000 using 2x100 cycles, per manufacturer’s instructions.

tag: Sex

value: Male

tag: age

value: 20 wk

tag: diet

value: CDAA-HFD + BLT1i


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_79_Liver_S19_L002


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_80_Liver_S20_L002


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_79_Liver_S19_L001


title: SA_1

last: Zhang


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_78_Liver_S18_L002


title: Mock_2


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_78_Liver_S18_L001


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_77_Liver_S17_L001


title: ABA_1


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_75_Liver_S15_L002


title: Mock_1


title: EXT1 suspension rep 1

city: Liege

first: Maximilien

last: Lopes

state: Liege

address: Avenue de l'hopital 11

department: Molecular Biology of Disease

country: Belgium

institute: University of Liege

data_processing:
The sequencing reads/raw reads often contain low quality reads or reads with adapters, which will affect the quality of downstream analysis. To avoid this, it is necessary to filter the raw reads and obtain the clean reads. It was done as follows: Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.(Yan et al, 2011)
Mapping was done with HISAT2 with the reference GRCh38
Quantification was done with featureCounts v1.5.0 with default parameters
Assembly: hg38
Supplementary files format and content: gene_count.xls file includes counts for each sample
Supplementary files format and content: gene_FPKM.xls file includes Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced for each sample

source_name: HEK293 kd_EXT1

growth_protocol: Adherent cells were grown in T75 in DMEM+FBS and suspension cells in EX-CELL 293 serum-free media at 120 rpm 37°C and 5% CO2.

extract_protocol:
NucleoSpin RNA Extraction kit from Macherey-Nagel
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: HEK293 kd_EXT1


title: WT suspension rep 3

value: wildtype


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_77_Liver_S17_L002


title: EXT1 suspension rep 2


title: EXT1 suspension rep 3


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_76_Liver_S16_L002


title: WT suspension rep 2


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_75_Liver_S15_L001


title: EXT1 adhesion rep 2


title: WT suspension rep 1


title: EXT1 adhesion rep 3


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_76_Liver_S16_L001


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_74_Liver_S14_L002


title: WT adhesion rep 3


title: EXT1 adhesion rep 1


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_74_Liver_S14_L001


title: WT adhesion rep 2


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_73_Liver_S13_L001


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_72_Liver_S12_L002


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_72_Liver_S12_L001


title: TT04_subj6_V2

city: Hoerholm

first: Niels Peter

last: Hell Knudsen

address: Bøge Alle 3

country: Denmark

institute: ALK-Abello

data_processing:
Cellranger 6.1.2
Seurat v4
Assembly: GRCh38-2020-A
Supplementary files format and content: Cellranger filtered and raw bc matrix counts
Supplementary files format and content: Integrated Seurat object with UMAP

source_name: blood

extract_protocol: Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium 5’ Single Cell Gene Expression assay and Chromium Controller Instrument according to the manufacturer’s published protocol

value: blood

value: PBMCs

value: allergic


title: WT adhesion rep 1


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_71_Liver_S11_L002


title: Gr4_CDAA_HFD_90mpk_L_286_EC014_73_Liver_S13_L002


title: TT04_subj6_V3


title: Gr2_CDAA_HFD_EC014_40_Liver_S10_L001

value: CDAA-HFD


title: Gr2_CDAA_HFD_EC014_39_Liver_S9_L002


title: TT04_subj4_V3


title: TT04_subj5_V2


title: Gr2_CDAA_HFD_EC014_38_Liver_S8_L001