title: HepG2-control

first: Qianqian

last: Liu

state: State...

address: Guangzhou City, Guangdong Provinc

institute: Sun Yat-Sen university

data_processing:
Libraries were validated with an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an MGISEQ. A 2000 SE50 sequencer at BGI Tech. TopHat2 and HTSeq were used for RNA-seq data analysis with GRCh38/hg19 as the reference genome.
Assembly: UCSC hg19

source_name: Liver tumor

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
DNase I was used for column digestion to ensure RNA quality. RNA library preparation was performed using the MGISEQ. A 2000 SE50 sequencer at BGI Tech. RNA libraries were prepared for paired-end sequencing using standard BGI protocols.

value: Liver tumor

tag: cell line

value: Human liver cancer cell

value: Control


title: HepG2-GSK805

status: Public on Jan 24 2024

type: SRA

city: Guangzhou

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment


title: IP_Yeast_YPS138mu_REP3

city: Rehovot

first: Ran

last: Shachar

address: 234 Herzl St.

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Synaptic Systems (Cat# 202003; RRID: AB_2279214)  + Cell Signaling D9D9W

data_processing:
alignment using STAR (V. 2.5.3a)
Read coverages were obtained using the R package txtools (https://github.com/AngelCampos/txtools)
Assembly: SK1-YPS138, hg19-mm9, CAST-HOUS
Supplementary files format and content: rds

molecule: polyA RNA

organism: Saccharomyces paradoxus

source_name: Saccharomyces paradoxus YPS138

growth_protocol: All yeast strains used in this work were grown in YPD (2% dextrose) at 30C. To induce synchronous sporulation, cells were grown for 24 h in 1% yeast extract, 2% peptone, 4% dextrose at 30C, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 mM potassium phthalate) to OD600 = 0.2 and grown for another 16 h at 30C, 250 rpm. Cells were then washed two times with water and re-suspended in Sporulation medium (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30C at 190 rpm. Human monochromosome hybrid cells JCRB2201, JCRB2202 and JCRB2203 were purchased from the Japanese Collection of Research Bioresources (JCRB), and cultured in DMEM (GIBCO) supplemented with 10% fetal bovine serum (FBS) and 0.8mg/ml G418(Gibco,79N9555) 37. mESCs, BJ, and NIH 3T3 cells were cultured in DMEM (GIBCO) supplemented with 10% FBS and 1% Penicillin and Streptomycin.

extract_protocol:
Yeast total RNA samples were prepared by adjusting previously published protocols. After fast freezing the yeast cells in liquid nitrogen, yeast cells were resuspended in equal amounts of phenol:Chloroform:Isoamyl alcohol (Sigma Aldrich), buffer AE (50mM sodium acetate, 10mM EDTA 1% SDS), and glass beads in Eppendorf tube. The tube was vortexed for 15 minutes in a bullet blender, heated to 65 °C for 30 minutes, followed by another round of 5 minutes vortex and 30 minutes heating to 65 °C. Samples were placed on ice for 5 minutes and centrifuged for 10 minutes (12000g, 4 °C). The supernatant was isolated, re-extracted with phenol:Chloroform:Isoamyl alcohol, and precipitated with sodium acetate and isopropanol. For all types of mammalian cell lines, total RNA was extracted with BIO TRI RNA reagent (Bio-lab). Enrichment for mRNA was done by two rounds of poly-A selection using Oligo(dT) beads (Dynabeads mRNA DIRECT) in both total RNAs from yeast and mammals.
m6A-seq2: Fragmentation, 3' adapter ligation, pooled(m6A-IP, cDNA synthesis, second adapter ligation and enrichment)
m6A-seq2

tag: strain

value: yeast cell

tag: fraction

value: IP


title: HPAF-II_HA-hSPDEF_GATA6_REP2

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Sequencing reads were mapped to the mouse or human genome (mm10/hg19) using Bowtie2 (2.4.4)
Duplicate read removal and sorting was performed using SAMtools (1.14)
Peaks were called using MACS2 (2.2.7.1) with 5% FDR cut off and broad peak option for histone- or narrow peak option for TF- datasets
Big wig files were generated using deeptools
Assembly: mm10/hg19
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: HPAF-II human PDA cell line

growth_protocol: Human pancreatic cancer cells HPAF-II were cultured in RPMI supplemented with 10% fetal bovine serum (FBS). KPC 2D FC1245 cells were cultured in DMEM with 5% FBS. Penicillin/streptomycin were added to all cell cultures.

extract_protocol:
CUT&RUN was performed according to manufacturer’s instructions (CUTANA ChIC/CUT&RUN Kit, EpiCypher 14-1048).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina according to manufacturer’s instructions.

value: HPAF-II human PDA cell line

value: pancreatic ductal adenocarcinoma (PDA) cell

tag: antibody

value: GATA6, R&D AF1700


title: HPAF-II_HA-hSPDEF_GATA6_REP1


title: control rep2

first: Dongxing

last: Zhu

state: Guangdong

address: Xinzao, Panyu District

department: School of Basic Medical Sciences

institute: Guangzhou Medical University

description: Sample 1-2

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).  Sequence quality was examined using the FastQC [1] software.
The trimmed reads (trimmed 5', 3'-adaptor  bases using cutadapt [2] ) were aligned to reference genome using Hisat2 software
The transcript abundances  for each sample was estimated with StringTie [4] , and the FPKM [8] value for gene and transcript level were  calculated with R package Ballgown
The differentially expressed genes and transcripts were filtered using  R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to  the reference annotation using StringTie and Ballgown, then use CPAT [10] to assess the coding potential of  those sequences. Then use rMATS [11] to detecting alternative splicing events and plots.
Principle Component  Analysis (PCA) and correlation analysis were based on gene expression level, Hierarchical Clustering, Gene  Ontology, Pathway analysis, Gene Ontology, Pathway analysis, scatter plots and volcano plots were performed  with the differentially expressed genes in R, Python or shell environment for statistical computing and graphics
Genome_build: GRCm38
Supplementary_files_format_and_content: The xlsx format file contains the FPKM value of gene in every sample

organism: Mus musculus

source_name: Aortae

extract_protocol:
Mouse aortae were carefully dissected, and fat tissue were removed. Then mouse aortae were flash frozen in liquid nitrogen and strored at -80oC, and RNA was harvested using Trizol reagent.
Total RNA from each sample was quantified using a NanoDrop ND-1000 instrument. 1- 2 ug total RNA  was used to prepare the sequencing library in the following steps: 1. Total RNA is enriched by oligo (dT)  magnetic beads (rRNA removed); 2. RNA-seq library preparation using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library  strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method. To sequence the libraries on the Illumina NovaSeq 6000 instrument, the barcoded  libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified  in situ, and subsequently sequenced for 150 cycles for both ends on Illumina NovaSeq 6000 instrument.

value: aortae

tag: age

value: 7-weeks old

value: control


title: IP_Yeast_YPS138mu_REP2


title: IP_Yeast_YPS138mu_REP1


title: control rep1

description: Sample 1-1


title: HPAF-II_HA-hSPDEF_HA_REP3

value: HA tag, EpiCypher 13-2010


title: Y814-OSM-3

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Reads were aligned to mouse GRCm38 (mm10) genome using Gencode Release M25 reference using STAR aligner. Normalization was done using counts per million (CPM) method. Transcript levels were quantified to the reference using Partek E/M with default parameters. Genes were considered to be differentially expressed based on fold change>2 and p-value<0.05. Functional enrichment analysis for the differentially expressed genes was performed using Ingenuity Pathway analysis (IPA, Qiagen). Pathway schematics were generated using Path designer application of IPA. MA-plots for the differentially expressed genes were generated in R using ggmaplot function of ggpubr (v0.4.0) package.
Genome_build: mouse GRCm38 (mm10) genome- Gencode Release M25
Supplementary_files_format_and_content: Normalized CPM counts

source_name: mouse periarticular stromal cells

extract_protocol:
Total RNA was isolated using QIAGEN RNeasy Mini kit and quantified using Qubit fluorometer (Thermo Fisher Scientific). Quality of the isolated RNA was checked using Agilent Bioanalyzer 2100. Universal Plus mRNA-Seq Library with NuQuant (TECAN) was used to generate stranded RNA-seq libraries. Briefly, poly(A) RNA was selected followed by RNA fragmentation. Double stranded cDNA was generated thereafter using a mixture of random and oilgo(dT) priming. The library was then constructed by end repairing the cDNA to generate blunt ends, ligation of Unique Dual Index (UDI) adaptors, strand selection and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Novaseq SP with paired end 50 base pair reads. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina CASAVA 1.8.2.
Universal Plus mRNA-Seq Library with NuQuant (TECAN)

tag: genotype/variation

value: stimulated with oncostatin M(OSM)


title: IP_Yeast_YPS138_REP3


title: IP_Yeast_YPS138_REP2


title: Y814-OSM-1


title: IP_Yeast_YPS138_REP1


title: Tumor, FLASH-RT hyperoxia, 24 hr, biol rep 1

city: Epalinges

first: Marie-Catherine

last: Vozenin

address: Rue de la Corniche, 9A

department: Radiation Oncologie

country: Switzerland

institute: CHUV

data_processing:
Alignment - RNA-STAR version 2.7.8a, standard parameters with NM-tag added
Merging of BAMs - Samtools merge version 1.13, standard parameters
Filtering of Mouse Reads - XenofilteR version 1.6, MM-threshold = 8
Counting of annotated genes - featureCounts version 2.0.1, standard parameters, reverse stranded, hg38 built-in
Assembly: hg38
Supplementary files format and content: txt - gene counts matrix by ENTREZ ID

source_name: Tumor

growth_protocol: U-87 MG cells were grown and expanded in high-glucose DMEM with 10% FBS at 37°C and 5% CO2. Once sufficient cells were available, 10 million were injected subcutaneously into the right flank of female Swiss nude mice.

extract_protocol:
Tumors were sampled 24h after radiotherapy and were disrupted in cold RLT lysis buffer with automated homogenizer (TissueLyser II, Qiagen) and total RNA extracted using the RNEasy mini kit (Qiagen) according to manufacturer instructions.
RNA quality (RQN > 6.8) was assessed on a Fragment Analyzer (Agilent Technologies). RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified by a fluorimetric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 SR Cluster Kit reagents and sequenced on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents for 150 cycles (single end).

treatment_protocol: Tumors were grown subcutaneously and once the volume measured 50 - 90 mm3, they were treated with 20 Gy electrons at CONV (~0.1 Gy/s) or FLASH (>100 Gy/s) dose rates using the Oriatron eRT6 (PMB-Alcen, FR) at CHUV. No-RT controls were left untreated.

value: Tumor

value: U-87 MG

value: glioblastoma

value: radiotherapy - 20 Gy electrons

value: FLASH-RT hyperoxia, 24 hr


title: HPAF-II_HA-hSPDEF_HA_REP2


title: Y814-3


title: Input_Yeast_YPS138mu_REP3

tag: genotype

value: input


title: HPAF-II_HA-hSPDEF_H3K4me3

value: H3K4me3, EpiCypher 13-0041


title: Input_Yeast_YPS138mu_REP2

value: yeast cell


title: U-251 MG, M2, replicate 3 [20684-005]

city: Kraków

first: Mateusz

last: Wawro

address: Gronostajowa 7

department: Cell Biochemistry

country: Poland

institute: Jagiellonian University

data_processing:
CLC Genomics Workbench (version 12.0.2) and CLC Genomics Server (version 11.0.2)
Assembly: hg38
Supplementary files format and content: Gene Name, Gene Identifier, M2 vs. Control - Max group means, M2 vs. Control - Fold change, M2 vs. Control - Log fold change, M2 vs. Control - P-value, M2 vs. Control - FDR p-value, M2 vs. Control - Bonferroni, Control - 20684-003 - TPM, Control - 20684-004 - TPM, Control - 20684-006 - TPM, Control - Mean, M2 - 20684-001 - TPM, M2 - 20684-002 - TPM, M2 - 20684-005 - TPM, M2 - Mean

growth_protocol: U-251 MG cells were grown in DMEM with 4.5 g/l glucose and 10% tetracycline-free fetal bovine serum in humidified atmosphere with 5% CO2. The cells were transfected with doxycycline-inducible plasmids based on the Sleeping Beauty transposon system (vector backbone - pSBtet-GP, Adggene plasmid # 60495) containing human Regnase-2 N-terminally tagged with a FLAG tag or empty control vector together with Sleeping Beauty expression vector (pCMV(CAT)T7-SB100; Addgene plasmid #34879). After transfection the cells with integrated transposons were selected for one week with 1ug/ml puromycin.

extract_protocol:
Total RNA was isolated using modified Chomczynski's protocol.
Library was constructed using rRNA-depleted total RNA (outsourced to QIAGEN Genomic Services, Germany).

treatment_protocol: After selection, the cells were seeded at 80% confluency, and induced with 1 ug/ml doxycycline for 24 hours for induction of transgene expression.

value: Human glioblastoma astrocytoma

value: Regnase-2 overexpression


title: U-251 MG, M2, replicate 2 [20684-002]


title: U-251 MG, M2, replicate 1 [20684-001]


title: Input_Yeast_YPS138mu_REP1


title: Y814-2


title: Y814-1


title: Input_Yeast_YPS138_REP3


title: WT-OSM-3

value: WT


title: U-251 MG, Control, replicate 3 [20684-004]

value: mock-transfected


title: U-251 MG, Control, replicate 2 [20684-006]


title: WT-OSM-2


title: Input_Yeast_YPS138_REP1


title: Input_Yeast_YPS138_REP2


title: scRNA seq of PBMC from Patient 3 & 4 [TCR]

city: Darlinghurst

first: Peter

last: Croucher

state: New South Wales

address: 384 Victoria St

department: Bone

country: Australia

institute: Garvan Insititute of Medical Research

description:
Multiplexed_fastq
Proliferative_RBD-specific_CD4pos_T_cells_correlate_with_neutralizing_antibody_levels_after_natural_SARS-CoV-2_infection_and_are_induced_following_vaccination_Seuobj.RData

data_processing:
Single-cell sequencing data was demultiplexed, aligned and quantified using Cell Ranger (10x Genomics) against the human reference genome (10x Genomics, July 7, 2020 release) with default parameters.
Raw hashtag data was processed using CITE-Seq count algorithm (Stoeckius et al., 2017). Cell conditions were demultiplexed using ‘HTODemux’ function implemented in Seurat (Stoeckius et al., 2018).
Filtering and quality control was performed using Seurat (Stuart et al., 2019) on data containing 15,276 cells where 14,053 cells were retained satisfying thresholds of both <10% mitochondria content and number of genes between 300 and 5000. ‘SCTransform’ was used for normalization (Hafemeister and Satija, 2019). Genes encoding BCR and TCR were removed to improve cell clustering. Principal Component Analysis (PCA) dimensional reduction was performed on variable genes identified by ‘VariableFeatures’ function and cell clusters were visualised using Uniform Manifold Approximation and Projection (UMAP) clustering implemented in Seurat (Stuart et al., 2019).
Assembly: Human GRCh38 (July 7 2020 release)
Supplementary files format and content: Demultiplexed hashtagged CITE_Seq_count output; Seurat object saved as Rdata format

source_name: PBMC

extract_protocol:
Single cell transcriptomic libraries were generated using the 5’v2 Gene expression and immune profiling kit (10x Genomics). Viable PBMCs were sorted into 2% FBS/PBS and cell counts were performed using a haemocytometer. Up to 40,000 cells were loaded into each lane of Chromium Next GEM Chip K Single Cell Kit (10x Genomics) to achieve a recovery cell number of approximately 20,000 cells.
cDNA and TCR libraries were generated according to manufacturer’s instructions (10x Genomics).
Generated libraries were sequenced on the NovaSeq S4 flow cell (Illumina) at Read 1 = 28, i7 index = 10, i5 index = 10 and Read 2: 90 cycles according to manufacturer’s instructions.

treatment_protocol: PBMC from 4 donors were cultured for 48 hr with SARS-CoV-2 Nucleocapsid protein, spike and RBD peptide pools, respectively. Antigen specific CD4+ T cells were FACS sorted on AriaIII (BD Biosciences) at 48hrs, based on combined expression of CD25 and CD134 (OX40).  Unstimulated purified CD45RO+ ex vivo memory CD4+ T cells were used as a comparator subset. Purified cells from 4 conditions of 2 patients were then pooled (~20,000cells) and 10X single cell Transcriptomics was performed (2 lanes, 4 pooled patients).

tag: subject status

value: convalescent donor at 3 months post SARS-CoV-2 infection

value: PBMC

tag: data type

value: TCR


title: Y814-OSM-2


title: U-251 MG, Control, replicate 1 [20684-003]


title: WT-3


title: WT-2


title: WT-OSM-1


title: scRNA seq of PBMC from Patient 1 & 2 [TCR]


title: Hyperplastic AT, snRNA seq

city: Sherbrooke

first: Run Zhou

last: Ye

state: QC

address: 3001 12e Avenue Nord

department: Medicine

country: Canada

institute: Université de Sherbrooke

description: 10x Genomics

library_source: transcriptomic single cell

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)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Biopsy

extract_protocol:
Frozen biopsy samples were transferred into 1.5 mL microcentrifuge tubes on ice to which 50 μL of nuclei extraction buffer (NEB) (10 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 250 mM sucrose, 0.1% NP-40, and 0.2 U/μL RNase inhibitor [Sigma, 3335399001]) were added. Sterile 0.5 mL microcentrifuge tubes were fitted into the 1.5 mL microcentrifuge tubes, allowing samples to be homogenized with 12 strokes with rotation, while maintaining the samples on ice. After addition of 3 mL of NEB, samples were incubated on ice for 1 min with gentle mixing followed by centrifugation at 1000 x g for 10 min at 4°C. With the supernatant removed, the nuclei pellet was resuspended in 500 μL of nuclei resuspension buffer (NRB) (0.5% BSA, 0.2 U/μL RNase inhibitor [Sigma, 3335399001], and 20 μg/mL DAPI [Fisher, 62248] in PBS). The nuclei suspension was then filtered through a 55 μm nylon mesh and observed under a fluorescence microscope for nuclei integrity and absence of clumps. The filtered suspension was then purified using FACS sorting (BD FACS Aria III, BD, Franklin Lakes) for DAPI+ nuclei. All plasticware had been coated with 4% BSA in PBS overnight at 4°C.
Single nuclei were captured using Chromium Next GEM Single Cell 5' v2 according to the manufacturer’s instructions (10X Genomics, Pleasanton). Around 10000 nuclei were loaded into the reaction chip. Sequencing was done with NextSeq 500/550 High Output Kit v2 aiming at a target depth of 20000 reads/nucleus, with read lengths of 26 cycles (read 1), 10 cycles (i7 index), 10 cycles (i5 index), and 120 cycles (read 2).

value: Adipose tissue

value: Hyperplastic


title: scRNA seq of PBMC from Patient 1 & 2 [GEX]


title: control

type: RNA

city: Durham

first: Adrian

middle: A

last: Epstein

state: NC

address: 300 N Duke

department: Pediatrics, Neonatology

institute: Duke University

description:
FFPE coronal sections
10x Genomics Xenium in situ

hyb_protocol: Data processed through on board analysis software - Xenium Analyzer

scan_protocol: Image pre-processing, puncta detection, transcript decoding and quality score assignment was perofrmed via on-board analysis software Xenium Analyzer.

data_processing:
Xenium analyzer performed read quantification and generated cell by gene count matrix.
mm10-2020-A
read counts in gene-barcode matrix

label: Xenium Mouse Probe Set

source_name: control

label_protocol: Xenium In Situ Analyzer

growth_protocol: Standard mouse breeding

extract_protocol: 5um FFPE tissue sections are placed on a 10x Genomics Xenium slide and dried at room temperature. Once dried, tissue slides are incubated at 60C for 2 hours and then deparaffinized and decrosslinked. Briefly, sections are deparaffinized via xylene immersion to solubilize the paraffin, ethanol to remove the solubilized paraffin and slowly hydrate the tissue, and then immersed in water to remove residual ethanol. Once hydrated, tissues slides are decrosslinked. Briefly, tissue slides are inserted into 10x Genomics Xenium slide cassettes. Decrosslinking buffer is then added to the well created by the cassette and incubated. After incubation, buffer is removed and the sample is washed. Tissue is then processed through Hybridization, Ligation & Amplification protocols. Briefly, pre-designed probe panels, with optional custom probe content, are added to the tissue. Each circularizable DNA probe contains two regions that hybridize to target RNA and a third region that encodes a gene-specific barcode. The two ends of the probes bind the target RNA and are ligated to generate a circular DNA probe. Following ligation, the circularized probe is amplified, producing multiple copies of the gene-specific barcode for each target. Prepared tissue slides are then loaded for imaging on the Xenium Analyzer for in situ analysis. Fluorescently-labeled oligos bind to the amplified DNA probes. Cyclical rounds of fluorescent probe hybridization, imaging, and removal generate optical patterns specific for each barcode, which are converted into a gene identity. Identified transcripts are then visualized using Xenium Explorer software.

treatment_protocol: Brain was removed and formalin fixed, paraffin embedded and sliced in coronal plane.

value: whole brain

value: control


title: MIP

source_name: MIP

value: peritonitis


title: WT-1


title: Human blood, CONTROL 32

status: Public on Jan 23 2024

type: genomic

city: Ancona

first: Tiziana

last: Casoli

address: Via Birarelli 8

department: Scientific Technological Area

country: Italy

institute: INRCA

description: Selective amplification of mtDNA

hyb_protocol: The chips were hybridized for 16 h at 49°C, then washed and stained in Fluidics Station 450 according to the suggested protocol.

scan_protocol: Chips were scanned in Affymetrix GeneChip Scanner 3000 7G and data acquisition was performed using the Affymetrix Genechip Command Console (AGCC) software.

data_processing:
Data analysis was carried out with GSEQ 4.1 with “model type” set at diploid to enable the detection of heteroplasmy and “quality score threshold” set at 3 to provide the best base calling accuracy and rate. The other parameters used by the algorithm were No Signal Threshold= 2, Weak Signal Fold Threshold= 20, Large SNR Threshold= 20, Min Fraction of Calls of Samples = 0.5, Trace Threshold = 1, Sequence Profile Threshold = -0.175.
Homoplasmic and heteroplasmic variants were defined by the software through comparison with the revised Cambridge Reference Sequence (rCRS). Probe Intensity File values were used to calculate the Ratio of Expected Allele (REA).

label: biotin

source_name: COVID-19 negative subjects_buffy coat

label_protocol: Total DNA was amplified by means of REPLI-g mitochondrial DNA kit (Qiagen) that contains DNA polymerase, buffers, and reagents for the specific amplification of the mitochondrial genome using Multiple Displacement Amplification (MDA). After purification, DNA was quantified  spectrophotometrically  and Genechip Resequencing array kit (Affymetrix) was employed for fragmentation and labeling.

extract_protocol: Total DNA was extracted using a QIAamp DNA blood mini kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: DNA was extracted from buffy coat specimens collected within 48 hours after patient admission at the hospital. Briefly, EDTA blood samples were centrifuged at 2,500 x g at 4°C for 15 minutes, the buffy coat layer was removed and stored at -80°C.

tag: disease state

value: CONTROL

value: Blood

tag: age (y)

tag: Sex

value: male


title: Mat-1_OsEPF1-oe

city: Sheffield

first: Julie

middle: E

last: Gray

state: South Yorkshire

address: University of Sheffield, Firth Court, Western Bank

department: Plants, Photosynthesis and Soil, School of Biosciences

country: United Kingdom

institute: University of Sheffield

data_processing:
Sequencing was conducted by Novogene (China) on an Illumina Nova-seq 6000 PE150 platform, producing a minimum of 30 million paired-end reads.
Reads were subjected to quality trimming and adapter filtering using Trimmomatic 0.38 (Bolger et al., 2014). Adapter sequences were identified in the palindrome mode, searching for seed matches of 16 bases, with a maximum of 2 base mismatches. Extended paired-end seeds of alignment score of 30 or higher, with a minimum adapter length of 8 bases, were clipped and pairs were kept. For quality trimming, any trailing sequence of quality lower than 10 (Phred score) were removed and the first 12 bases of the reads were cropped. Reads were scanned with a 4-base sliding window and were cut if the average quality per base was lower than 15. After these steps, reads with less than 60 bases long or unpaired were discarded.
Processed reads were mapped to the Nipponbare IRGSP 1.0 genome assembly (Kawahara et al., 2013), using the genome annotation available on the Rice Annotation Project Database (RAPDB, https://rapdb.dna.affrc.go.jp) (Sakai et al., 2013)
Mapping of reads was performed with HISAT2 v2.1.0 (Kim et al., 2015) in the default settings of paired-end mode.
Mapped reads were quantified using featureCounts from Subread 2.0.0 (Liao et al., 2014). Quantification was performed at gene level, considering only DNA fragments bookended by a pair of reads that were mapped to exonic regions. FeatureCounts was run at default settings for pair-ended reads, multi-mapping and multi-overlapping reads were not counted
Genome_build: Nipponbare IRGSP 1.0 genome assembly
Supplementary_files_format_and_content: csv file shows raw counts from FeatureCounts for every sample and gene in the Rice Annotation Project Database (RAPDB) at the time.

organism: Oryza sativa

source_name: Florets

growth_protocol: Plants were grown in Conviron growth cabinets under 12 h photoperiod (850 - 1000 µmol m-2 s-1 PAR at canopy level), 30°C day and 24°C night temperature, and 60 % relative humidity, with a constant supply of water to the pot base. From the 4th growth week, plants were fertilized in intervals of two weeks with Chempak High Nitrogen Feed No. 2 (Thompson & Morgan, Ipswich, UK).

extract_protocol:
IR64 and OsEPF1-oeS developing florets were collected ~75-85 days after sowing, and mature florets were collected after panicle heading, but prior to anthesis (~ 95 days after sowing). RNA was extracted from floret samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich), with the On-Column DNase I Digest step, according to the manufacturer’s instructions. RNA samples extracted from developing florets of three individual plants were then mixed, in proportional RNA quantities. Therefore, each biological replicate for developing florets comprised RNA from three different rice plants. Three biological replicates per stage were sequenced.
Enrichment of mRNA was carried out using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Biolabs), and library preparation was performed using the NEBNext Ultra RNA Library Prep Kit (Biolabs).

tag: cultivar

tag: line (genotype)

value: florets

tag: Stage

value: Mature


title: Mat-2_IR64

value: Wild type (IR64-control)

tag: tissue


title: Mat-3_OsEPF1-oe


title: Human blood, CONTROL 33

description: Selective amplification of mtDNA

value: female


title: Human blood, CONTROL 31

description: Selective amplification of mtDNA


title: Human blood, CONTROL 30

description: Selective amplification of mtDNA


title: S5-1_OsEPF1-oe


title: Mat-3_IR64


title: S5-2_OsEPF1-oe


title: scRNA seq of PBMC from Patient 3 & 4 [GEX]


title: Human blood, CONTROL 27

description: Selective amplification of mtDNA


title: S4-2_OsEPF1-oe


title: Human blood, CONTROL 26

description: Selective amplification of mtDNA


title: Mat-2_OsEPF1-oe


title: Human blood, CONTROL 28

description: Selective amplification of mtDNA


title: S4-1_OsEPF1-oe


title: S5-3_OsEPF1-oe


title: Human blood, CONTROL 23

description: Selective amplification of mtDNA


title: Human blood, CONTROL 25

description: Selective amplification of mtDNA


title: S4-3_OsEPF1-oe


title: S3-3_OsEPF1-oe


title: Hypertrophied AT, snRNA seq

description: 10x Genomics

tag: cell type

value: Hypertrophied


title: Human blood, CONTROL 22

description: Selective amplification of mtDNA


title: Human blood, CONTROL 29

description: Selective amplification of mtDNA


title: Mat-1_IR64


title: S3-2_OsEPF1-oe


title: Human blood, CONTROL 21

description: Selective amplification of mtDNA


title: Human blood, CONTROL 20

description: Selective amplification of mtDNA


title: S2-3_OsEPF1-oe


title: S3-1_OsEPF1-oe


title: Human blood, CONTROL 24

description: Selective amplification of mtDNA


title: 1222, MRTX1133 treated, bio rep 1

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
nf-core/rnaseq  version 3.3.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files, contain raw read counts at isoform level.

growth_protocol: Cells were grown in Keratinocyte Serum-Free media (KSF) supplemented with 2% FBS, EGF (0.2 ng/mL) and bovine pituitary extract (30 µg/mL) (Life Technologies, Carlsbad, CA)

extract_protocol:
RNA was extracted using Quiagen Rneasy plus mini Kit.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The cells were treated with 0.1% DMSO and MRTX1133 (500 nM) up to 48 hours

tag: cell line

tag: treatment


title: Human blood, CONTROL 17

description: Selective amplification of mtDNA


title: Human blood, CONTROL 18

description: Selective amplification of mtDNA


title: S2-2_OsEPF1-oe


title: S1-3_OsEPF1-oe


title: S2-1_OsEPF1-oe


title: Human blood, CONTROL 14

description: Selective amplification of mtDNA


title: S1-1_OsEPF1-oe


title: Human blood, CONTROL 19

description: Selective amplification of mtDNA


title: S5-3_IR64


title: Human blood, CONTROL 13

description: Selective amplification of mtDNA


title: Human blood, CONTROL 11

description: Selective amplification of mtDNA


title: Human blood, CONTROL 15

description: Selective amplification of mtDNA


title: Human blood, CONTROL 16

description: Selective amplification of mtDNA


title: Human blood, CONTROL 10

description: Selective amplification of mtDNA


title: S5-2_IR64


title: Human blood, CONTROL 12

description: Selective amplification of mtDNA


title: S1-2_OsEPF1-oe


title: S4-3_IR64


title: Human blood, CONTROL 9

description: Selective amplification of mtDNA


title: S4-2_IR64


title: S4-1_IR64


title: S3-3_IR64


title: Human blood, CONTROL 6

description: Selective amplification of mtDNA


title: S3-2_IR64


title: Human blood, CONTROL 7

description: Selective amplification of mtDNA


title: S3-1_IR64


title: Human blood, CONTROL 4

description: Selective amplification of mtDNA


title: S2-3_IR64


title: Human blood, CONTROL 3

description: Selective amplification of mtDNA


title: S2-1_IR64


title: S1-3_IR64


title: S5-1_IR64


title: Human blood, CONTROL 2

description: Selective amplification of mtDNA


title: S2-2_IR64


title: S1-2_IR64


title: Human blood, COVID 29

description: Selective amplification of mtDNA

source_name: COVID-19 positive patients_buffy coat


title: S1-1_IR64


title: Human blood, COVID 28

description: Selective amplification of mtDNA


title: Human blood, COVID 27

description: Selective amplification of mtDNA


title: Human blood, COVID 26

description: Selective amplification of mtDNA


title: Human blood, CONTROL 8

description: Selective amplification of mtDNA


title: Human blood, COVID 25

description: Selective amplification of mtDNA


title: Human blood, COVID 24

description: Selective amplification of mtDNA


title: Human blood, CONTROL 5

description: Selective amplification of mtDNA


title: Human blood, COVID 23

description: Selective amplification of mtDNA


title: Human blood, COVID 30

description: Selective amplification of mtDNA


title: Human blood, COVID 22

description: Selective amplification of mtDNA


title: Human blood, CONTROL 1

description: Selective amplification of mtDNA


title: Human blood, COVID 21

description: Selective amplification of mtDNA


title: Human blood, COVID 19

description: Selective amplification of mtDNA


title: Human blood, COVID 20

description: Selective amplification of mtDNA


title: HPAF-II_HA-hSPDEF_HA_REP1

value: HPAF-II human PDA cell line

value: pancreatic ductal adenocarcinoma (PDA) cell

value: HA tag, EpiCypher 13-2010


title: Human blood, COVID 17

description: Selective amplification of mtDNA


title: Pc_hypno_Mm_hepatocyte_ATAC-seq_5000

first: Haoyu

last: Wu

address: Kai Yuan Avenue 190

institute: GIBH

data_processing:
For ATAC-seq data analysis, pair-end reads were mapped to a merged genome reference of Mmul_10 and PlasmoDB44 using BWA 0.7.17-r1188 mem with default settings. Next, reads mapped to the PlasmoDB44 genome only were extracted for further analysis. Duplicates and reads with mapping quality lower than 30 were removed using samtools 1.7
Open chromatin profile tracks were generated using deeptools 3.5.0 bamCoverage function with the following setting, --normalizeUsing CPM.
Genome_build: Mmul_10 and PlasmoDB44
Supplementary_files_format_and_content: bigwig files containing genomic signals of each ATAC samples

organism:
Plasmodium cynomolgi
Mus musculus

source_name: hypnozoites

growth_protocol: 3 hypnozoite (GFP+/mCherry-) and 3 liver-schizonts (GFP++/mCherry++) infected hepatocyte populations were collected in two independent experiments

extract_protocol:
Sorting was performed using the AriaIIIu as described previously {Voorberg-van der Wel, Elife 2021}. Parasites were collected into PBS containing 1% BSA, centrifuged (5 min, 500g, 4 °C) and kept on ice until transposase treatment.
Transposase treatment was performed in 10ul volume containing 1xTD buffer (Nextera kit, Illumina), 0.5ul “home-made” Tn5 transposase adapter complex and 0.4mg/ml digitonin (Promega, #G9441) at 30 min at 37 °C. After column purification (MinElute PCR Purification Kit, Qiagen) transposed DNA fragments were PCR amplified (98 °C for 2 min; 13 cycles of 98 °C for 20 sec, 62 °C for 3 min; 62 °C for 5 min) using Nextera i5/i7 indexing primers (Illumina) and 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems). The resulting libraries were subsequently purified with Agencourt AMPure XP bead (Beckman Coulter) first at 1:0.65 ratio to remove large DNA fragments, followed by addition of extra beads to the supernatant to 1:1.8 ratio and removal of adapter dimers.
ATAC-seq libraries were sequenced on the Illumina NextSeq 500 system (Illumina, FC-110-3001) to generate 2x38 bp paired-end reads.

value: hypnozoites


title: Human blood, COVID 15

description: Selective amplification of mtDNA


title: CD8_HOPX_S26_M42

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 300 ng Cy3-labeled cRNA and 300 ng of a Cy5-labeled universal standard was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v3 8x60K Microarray gene expression microarrays for 17 hours at 65°C 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), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using a dual-intensity Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Peripheral Blood Mononuclear Cells (PBMCs) were freshly isolated from healthy donor blood by Ficoll-Hypaque density gradient centrifugation. Dynabeads T cell isolation kits (pan, CD4+, CD8+) were used to isolate T cells from PBMCs. All procedures followed the manufacturer’s protocol. Isolated cells were counted and used for subsequent analysis. Cells were stained with anti-CD8, anti-CD4, anti-CD62L, and anti-CD45RA, and the MoFlo XDP Sorter (Beckman Coulter) was used to sort CD45RA+ CD62L+ naïve cells (TN), CD45RA-CD62L+ central memory (TCM) cells, and CD45RA- CD62L- effector memory (TEM) cells. All cells were maintained at 37°C and 5% CO2. The human leukemic T-cell line Jurkat, subclone E6 (ATCC), was maintained in standard growth medium (RPMI 1640 medium supplemented with 10% fetal bovine serum). 293T (ATCC) was cultured in DMEM/HG media with 10% FBS. Passages 5-15 were used in this study.

extract_protocol: Microarray analysis of gene expression was performed on total RNA was extracted from tdTomato+CD8+ T cells sorted by BD FACSAria Fusion on Day 3.Total RNA was isolated from tdTomato+CD8+ T cells sorted by BD FACSAria Fusion on Day 3. RNA was isolated with RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions and stored at -80oC. RNA concentration and quality was assayed on an RNA 6000 Bioanalyzer chip (Agilent).

treatment_protocol: HOPX (a,b,c) CDS sequences were synthesized by Genewiz) and inserted into the lentiviral transfer vector pLVX-IRES-tdTomato (Clontech) under the CMV promoter using EcoR1 (5′) and BamH1(3′), with a blank pLVX-IRES-tdTomato transfer vector used for control virus. The overexpression efficiency of each construct was tested in vitro with fluorescence and verified by qPCR.To produce lentiviruses, 293T cells were initially plated into a p10 dish and then transfected around 80% confluent with 1 µg of VSVG (envelop vector), 8 µg of dR8.2 (packaging vector), and 10 µg of the transfer vector in the presence of 50ul FuGENE (Promega). The viral supernatant was collected after 48 hours, cleared by centrifugation with 1500 rpm for 5 min at 4°C, and then passed through a 0.45 μm pore PVDF Millex-HV filter (Millipore). Lentivirus was concentrated using PEG solution (5X) centrifuged at 2800 rpm for 1 hour. The virus pellets were resuspended in 100 μL PBS and stored at -80°C until use. CD8+ T cells were stimulated with anti-CD3/CD28 conjugated microbubbles antibodies one day before transduction. Lentiviral stocks were added to primary T lymphocytes cultured in RPMI 1640 media supplemented with 10% FBS and 5 μg/mL polybrene. After overnight incubation, lentivirus was removed by centrifugation, and fresh media added. Transduced T cells were harvested for examining the expression of tdTomato by flow cytometer at indicated time point. tdTomato+CD8+ T cells (both HOPX and control virus) were sorted by BD FACSAria Fusion on Day 3 and used for gene expression analysis by Microarray (Agilent).

value: CD8+ T lymphocytes

value: M

tag: age (years)


title: CD8_HOPX_S28_F43

value: F


title: Human blood, COVID 14

description: Selective amplification of mtDNA


title: CD8_HOPX_S12_F58


title: CD8_CTR_S27_F43


title: Human blood, COVID 13

description: Selective amplification of mtDNA


title: CD8_CTR_S11_F58


title: miR-126 KD+M.marinum 2

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

institute: Centenary Institute

data_processing:
Raw reads were checked for quality using FASTQC (v 0.11.8).
Low-quality reads and adapter sequences were removed to obtain clean reads using TRIMMOMATIC (v 0.39).
Clean reads were then mapped to Ensembl zebrafish genome (Danio_rerio.GRCz11.108) using STAR aligner.
The aligned bam files were quantified with featureCounts (v 2.0.2) [5] to generate read counts of each gene for all samples.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCz11
Supplementary files format and content: Tab-separated raw count file
Supplementary files format and content: Bigwig files

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Zebrafish embryos raised in E3 + PTU at 28 degrees

extract_protocol:
Trizol, phenol chloroform extraction, Qiagen RNAeasy
mRNA-seq (poly-A enriched); TruSeq RNA Library Prep Kit v2

treatment_protocol: Single cell embryos injected with scrambled or miR-126 antagomir, infected at 2 dpf with M. marinum

value: Whole embryo

value: miR-126 KD+M.marinum

value: miR-126 antagomir injected and M. marinum infected


title: control WT +M.marinum 2

value: Scram antagomir and M. marinum infected


title: control WT +M.marinum 1


title: CD8_HOPX_S14_F56


title: miR-126 KD+M.marinum 1


title: control WT1

value: WT

value: Scram antagomir injected


title: miR-126 KD2

value: miR-126 KD

value: miR-126 antagomir injected


title: miR-126 KD1


title: CD8_CTR_S13_F31


title: Human blood, COVID 12

description: Selective amplification of mtDNA

value: Blood

value: female


title: CD8_CTR_S25_M42


title: 4T1_4

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
quality control by fastqc
adaptor and low quanlity reads were removed by trimmomatic (0.39)
rRNA removed by sortMeRNA(2.1)
reads were aligned to GRCm38.98 (mm10) using Salmon (1.4.0) ans summrized to gene level using tximport (1.15.10)
Assembly: mm10
Supplementary files format and content: tab separated, normalized counts

source_name: Parental 4T1

extract_protocol:
treated or untreated 4T1 cells were lysing in the well directly.
RNA was isolated using RNeasy plus mini (Qiagen) following manufacturer’s instructions. Isolated RNA sample quality was assessed by HS Total RNA 15nt on Fragment Analyzer (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA).
Truseq Stranded RNA

treatment_protocol: Gr1+ cells isolated from tumor or spleen of 4T1 tumor bearing Balb/C mice at day 21 post injection using MACS milteny magnetic column separation. Isolated cells were co-cultured using trasnwell 0.4µM pores with parental 4T1 cells for 48h using DMEM with Glutamax complemented with 10% FBS, 1% NEAA and PS.

value: Parental 4T1

tag: group

tag: replicate


title: 4T1_3


title: Human blood, COVID 18

description: Selective amplification of mtDNA

value: male


title: Human blood, COVID 11

description: Selective amplification of mtDNA


title: Human blood, COVID 10

description: Selective amplification of mtDNA


title: 4T1_2


title: Human blood, COVID 16

description: Selective amplification of mtDNA


title: Human blood, COVID 9

description: Selective amplification of mtDNA


title: 4T1_1


title: 4T1MDSC S4

source_name: Co-cultured 4T1 cells with Spleen Gr1+ cells

value: 48h of co culture with Gr1+ cells using transwell


title: Human blood, COVID 8

description: Selective amplification of mtDNA


title: control WT2


title: 4T1MDSC S3


title: 4T1MDSC S2


title: Human blood, COVID 6

description: Selective amplification of mtDNA


title: Human blood, COVID 4

description: Selective amplification of mtDNA


title: Human blood, COVID 5

description: Selective amplification of mtDNA


title: 4T1MDSC T1

source_name: Co-cultured 4T1 cells with Tumor Gr1+ cells


title: Human blood, COVID 2

description: Selective amplification of mtDNA


title: synovial cells, Decitabine- KBxN, replicate 3

city: SaintLouis

first: Gaurav

last: Swarnkar

state: MO

address: 425 South Euclid Ave BJCIH Room 11406

department: Orthopedic Surgery

institute: Washington University in School of Medicine

description: 10x Genomics

data_processing:
Preprocessing of scRNA-seq data. Paired-end sequencing reads were processed by Cell Ranger (10x Genomics software, version 3.1). Reads were aligned to the GRCh38 (version 90) for genome annotation, demultiplexing, barcode filtering, and gene quantification. Cell Ranger also removes any barcode that has less than 10% of the 99th percentile of total unique molecular identifiers (UMI) counts per barcode as these barcodes are associated with empty droplets. After this quality control, gene barcode matrices for each sample were generated by counting the number of UMIs for a given gene (as row) in individual cell (as column).
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Arthritic paw and ankle

extract_protocol:
For sc-RNA-seq, synovial cells were isolated from paw and ankle joints (n=3 per group). Briefly, at the end of the experiment, animals were sacrificed, and paw and ankle joints were dissected. Skin from the paw and ankle joints was removed, and the tissues were chopped in 50 ml tube containing digestion solution 2mg/ml Collagenase D solution, 2mg/ml Dispase and 1mg/ml DNase I. Tissues were digested for 30 min at 37oC in shaking water bath (250rpm). After 30 minutes, samples were vortexed briefly and supernatant was collected through a 70u strainer. This digestion cycle was repeated thrice. At the end of three times digestion, cells were centrifuged and suspended in appropriate buffer and processed for further analysis.
10X chromium platform scRNA-seq with cell hashing Three samples were collected from each experimental condition (i.e., control, STIA, STIA_DAC and DAC groups). cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration. Gene Expression and Feature libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding Technology for Cell Surface Protein with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), Dual Index Kit TT Set A, 96 rxns (PN-1000215), 3’ Feature Barcode Kit (1000262) and Dual Index Kit NT Set A, 96 rxns (PN-1000242) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library and 5000 reads/cell for each Feature Library.

value: Synovial cells

value: Arthritic paw and ankle

tag: strain

tag: age

value: 8 weeks

value: Decitabine- KBxN


title: Human blood, COVID 3

description: Selective amplification of mtDNA


title: 4T1MDSC T4


title: 4T1MDSC T2


title: 53

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

data_processing:
CAGE sequences were trimmed with fastx_trimmer (FASTX Toolkit 0.0.13.2), adapters removed with Trimmomatic-0.39, RNAdust 1.06 program used to remove ribosomal sequences matched to ribosomal DNA repeating unit U13369.1
Reads were aligned to reference genome assembly with BWA-0.7.10, unmapped reads were realigned by using Hisat2-2.2.1.
CAGE tag start sites (CTSS) for each sample with subsequent peak clustering were performed using the PromoterPipeline aggregation script from the C1 CAGE protocol.
CAGE peaks located within ±1000 bp from start sites of Augustus, Genscan, Gencode v33, RefSeq models were assigned to the corresponding genes (https://github.com/Deviatiiarov/CAGE_peak_annotation) and used as a training set for TSSClassifier (https://sourceforge.net/p/tometools/wiki/TssClassifier).
Bidirectional enhancers were called according to Andersson et al., 2014 (https://github.com/anderssonrobin/enhancers) with masking regions ±1000 bp from gene start and ±200 bp for exons.
Assembly: hg38
Supplementary files format and content: tab-delimited text files with annotation and TPM normalized counts for CAGE promoters and enhancers

source_name: facial mesenchyme

extract_protocol:
Total RNA (2-3 µg) was extracted from facial part of the embryos preserved in RNAlater and stored under -80C.  Total RNA was isolated from frozen tissues using RNeasy Fibrous Tissue Kit (Qiagen, Hilden, Germany), according to the manufacturer’s protocol. The concentration and purity of extracted RNA was measured by the NanoDrop™ 8000 Spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA). The RNA quality was verified by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA ).
Libraries were prepared according to the standard nAnT-iCAGE protocol (non-Amplified non-Tagging Illumina Cap Analysis of Gene Expression)

tag: developmental stage

value: 3-4 weeks

value: facial mesenchyme


title: Human blood, COVID 1

description: Selective amplification of mtDNA


title: synovial cells, KBxN, replicate 3

description: 10x Genomics

value: KBxN


title: 4T1MDSC T3


title: synovial cells, Control, replicate 3

description: 10x Genomics

value: control


title: 50

value: 9-10 weeks


title: 48

value: 5-6 weeks


title: 51

value: 3 weeks


title: synovial cells, Decitabine, replicate 3

description: 10x Genomics

value: Decitabine


title: 47

value: 12 weeks


title: 49


title: 46


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 15 [K4483]

city: New Brunswick

first: Jessie

middle: Yanxiang

last: Guo

state: NJ

address: 195 Little Albany Street, Room 3039, Lab 3029

department: Rutgers Cancer Institute of New Jersey

institute: Rutgers, The State University of New Jersey

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GRCm39/mm39
Read count extraction and nomalization were performed
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung tumor

extract_protocol:
Total RNA was harvasted using RNeasy Min Kit (QIAGEN). Total RNA was used for the construction of sequencing liabries.
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

value: Lung tumor

tag: genotype

tag: time

value: 12 weeks after tumor induction


title: 45

value: 9 weeks


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 14 [K4579]


title: Human blood, COVID 7

description: Selective amplification of mtDNA

tag: disease state

value: Blood

tag: age (y)

value: male


title: 4T1MDSC S1

value: 48h of co culture with Gr1+ cells using transwell


title: E22

value: 7 weeks


title: Sectm1a-KO rep3

city: Cincinnati

first: Guo-Chang

last: Fan

state: ohio

address: 231 Albert Sabin Way

department: Pharmacology & Systems Physiology

institute: University of Cincinnati

data_processing:
Isas (3.19.5.13)
SAMtools (0.1.20)
STAR (Aligner, STAR_2.6.1a)
Salmon Quantificartion (0.11.2)
Illumina Annotation Engine (2.0.10.0)
Assembly: Mus musculus (mm10)
Supplementary files format and content: tab-delimited txt files includes raw counts for each sample

source_name: Primary cells

extract_protocol:
RNA was extracted from mouse macrophages using the RNeasy kit (Qiagen, Cat. 217004). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary cells

value: Macropahges

value: Sectm1a Knockout

value: 10-12 weeks


title: Sectm1a-KO rep1


title: Sectm1a-KO rep2


title: E19

value: 7-8 weeks

value: facial mesenchyme


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 13 [K4577]


title: WT rep3

value: wild type


title: E14

value: 10 weeks


title: E18

value: 11-12 weeks


title: WT rep2


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 11 [K4922]


title: E15

value: 5-6 weeks


title: E9


title: E10


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 9 [K4485]

value: Lung tumor


title: BHLHE40-KO, biological replicate 5

city: New York

first: Anna

last: Podlesny-Drabiniok

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads QC FastQC v0.11.8
Adapter trimming Cutadapt v2.6
Alignment to the human genome STAR v2.5.3a
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: Cell line

growth_protocol: iPSC were differentiated to iPSC-derived microglia (iMGLs) using StemDiff Hematopoietic kit followed by iMGLs media supplemented with IL34, TGFb, MCSF as described by McQuade et al., 2019 protocol

extract_protocol:
RNA was extracted by using Rneasy Mini column (Qiagen) according to the manufacturer's protocol
cDNA was constructed using TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions

treatment_protocol: no treatent has been used

value: Cell line

value: iPSC (WTC11)

value: iPSC-derived microglia

value: no treatment


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 8 [K4482]

value: 12 weeks after tumor induction


title: wild type, biological replicate 5

value: WT


title: BHLHE40-41-DKO, biological replicate 5

value: DKO


title: BHLHE41-KO, biological replicate 4


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 7 [W5109]


title: BHLHE40-41-DKO, biological replicate 4


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD knock-out, 12 weeks, sample 10 [K4486]


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 6 [W5129]


title: WT rep1

value: Primary cells

value: Macropahges


title: wild type, biological replicate 4


title: BHLHE41-KO, biological replicate 5


title: BHLHE40-KO, biological replicate 3


title: BHLHE41-KO, biological replicate 3


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 5 [W5128]


title: wild type, biological replicate 3


title: BHLHE40-41-DKO, biological replicate 3


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 4 [W4540]


title: E12


title: BHLHE40-KO, biological replicate 4


title: RNA-seq_GW4064_5

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
The original FASTQ read files were trimmed and cleaned using fastp/0.23.2, then quality analysis was performed using FastQC/0.11.8.
A custom genome reference index was created by combining human (GRCh38.p13) and mouse (GRCm38.p6) genome sequences for alignment of humanized mouse chimeric liver RNA-seq data as we previous introduced;the primary assemblies were obtained from the GENCODE database (https://www.gencodegenes.org/).
The trimmed reads were aligned with default settings of HISAT2/2.2.1.0 and quantified using featureCounts (subread/2.0) with human annotation GENCODE v33 and mouse GENCODE vm24.
Assembly: GRCh38 and mm10
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: TKNOG

tag: host organism

value: TKNOG Mus musculus

tag: xenograft organism

value: Homo sapiens

value: Liver


title: BHLHE41-KO, biological replicate 2


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 2 [W4273]


title: RNA-seq_GW4064_4


title: BHLHE40-KO, biological replicate 1


title: wild type, biological replicate 2


title: RNA-seq_GW4064_3


title: MR13, sample 3

description: 4T1 cells, selected with 13ug/ml methotrexate

hyb_protocol: Mouse Gene Exon 1.0 ST Array

scan_protocol: Affymetrix protocol

data_processing: Microarray analyses were carried out with R, a free software environment available at http://www.r-project.org/. After quantification of gene expression with robust multi-array normalization using the BioConductor package Affy, (http://www.bioconductor.org/) significance of differential gene expression was determined by computing moderated t-statistics and false discovery rates with the limma package (63). Annotation was based on the genome version NCBI Build 36 (Feb. 2006). The obtained p-values were corrected for multiple testing by calculating estimated false discovery rates (FDR) using the method of Benjamini-Hochberg. The transcriptional factors enrichment analysis were then performed by using MetaCore from Thomson Reuters (version 6.11) by filter with thresholds 1.5 and p-value 0.01. Heatmaps were produced by color-coding gene-wise standardized log gene expression levels (mean zero standard deviation one).

label_protocol: Affymetrix protocol

growth_protocol: 10e6 tumor cells were plated in 10 cm cell cuture dish overnight before treatment.

extract_protocol: Tiplicates wells of 4T1 WTR- and MR13 cells grown in culture were used for RNA extraction using RNeasy kit (QIAGEN, Basel, Switzerland).

treatment_protocol: For MTX selection, cells were treated with 13ug/ml methotrexate in culture medium. The medium with MTX were replaced in 2nd and 3rd day and then every 2-3 days. The treatment was continued for up to 2 weeks until single colonies os surviving cells were visible.

value: treated


title: MR13, sample 2

source_name: 4T1 cells, selected with 13ug/ml methotrexate


title: BHLHE41-KO, biological replicate 1


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 1 [W4272]


title: BHLHE40-41-DKO, biological replicate 1


title: MR13, sample 1


title: WTR-, sample 2

description: 4T1 cells, untreated

source_name: 4T1 cells, untreated

value: untreated


title: WTR-, sample 3

description: 4T1 cells, untreated


title: wild type, biological replicate 1


title: RNA-seq_GW4064_2


title: BHLHE40-KO, biological replicate 2


title: RNA-seq_GW4064_1


title: Lung tumor with KRAS/LKB1 co-Mutation, G6PD wild-type, 12 weeks, sample 3 [W4277]


title: RNA-seq_Rosiglitazone_5

value: Rosiglitazone


title: BHLHE40-41-DKO, biological replicate 2


title: Tconv_TNFR2_Donor5

city: Leiden

first: Mark

last: Mensink

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Center

description: 6377_18_52_Donor5_Tconv_aTNFR2_GTGAAAC_S98

data_processing:
The 65 bp single end reads were mapped to the human reference genome (hg38, genome_snp_tran) using HISAT2 (version 2.1.0). Read counts were generated using Gensum (https://github.com/NKI-GCF/gensum). Ensembl GTF version 102 was used as a reference.
BAM files were imported in Qlucore Omics Explorer software (version 3.8) with GRCh38.104.gtf as reference genome, using trimmed mean of M values (TMM) normalization. !Sample_data_processing = Transcripts with less than 10 reads in at least 80% of the samples were excluded from downstream expression analysis, as well as remaining transcripts with low expression in all samples.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file including data after TMM normalization and log-transformation

source_name: Peripheral blood

growth_protocol: Naïve Tconv and Treg cells were sorted from buffy coats from healthy donors (Sanquin) by flow cytometry. After cell sorting (day 0), naïve Tconv and tTreg cells were cultured for 7 days at 37°C/5% CO2 in 96-well round bottom plates (Corning, Thermo Scientific; 1×10^4 cells per well) in 100 µl IMDM (Capricorn Scientific) with 8% FCS (Serana), penicillin/streptomycin (Gibco) and IL-2 (300 IU/ml, DuPont Medical). Soluble agonistic mAb to CD3 (0.1 µg/ml, clone CLB-T3/4.E, IgE isotype, Sanquin) was used for TCR/CD3 stimulation, and soluble agonistic mAb to either CD28 (0.2 µg/ml, clone CLB-CD28/1, Sanquin) or TNFR2 (2.5 µg/ml, clone MR2-1, Hycult Biotech) for costimulation. On day 4, 100 µl supplemented IMDM including IL-2 (300 IU/ml) was added to the culture. On day 7, cells were collected for transcriptomic analysis.

extract_protocol:
T cells were washed in cold PBS and resuspended in RLT buffer (Qiagen). Total RNA isolation was performed according to the manufacturer’s protocol using the RNeasy MinElute Cleanup Kit (Qiagen) including an on-column DNAse digestion (Qiagen). Quality and quantity of the total RNA were assessed on a 2100 Bioanalyzer using a Nano chip (Agilent).
Library preparation was performed on RNA samples with a measured RNA Integrity Number (RIN) between 8.0 and 10.0. Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc.) according to manufacturer’s instructions (Illumina, Part # 15031047 Rev. E). RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Peripheral blood

value: Conventional CD4 T cell

value: IL-2 and anti-CD3/TNFR2 agonistic mAbs


title: tTreg_TNFR2_Donor5

description: 6377_20_54_Donor5_tTreg_aTNFR2_GTTTCGG_S100

value: Regulatory CD4 T cell


title: Tconv_CD28_Donor5

description: 6377_17_51_Donor5_Tconv_aCD28_GTCCGCA_S97

value: IL-2 and anti-CD3/CD28 agonistic mAbs


title: tTreg_CD28_Donor5

description: 6377_19_53_Donor5_tTreg_aCD28_GTGGCCT_S99


title: WTR-, sample 1

description: 4T1 cells, untreated


title: RNA-seq_Rosiglitazone_4


title: RNA-seq_Rosiglitazone_3


title: tTreg_CD28_Donor4

description: 6377_15_49_Donor4_tTreg_aCD28_ATGTCAG_S90


title: Sciatic nerve CD45+ cells, spontaneous autoimmune neuropathy, biol rep1, TCR-seq

city: Los Angeles

first: Maureen

last: Su

address: 615 Charles E. Young Dr. S

department: Microbiology, Immunology, and Molecular Genetics

institute: UCLA David Geffen School of Medicine

description:
TCR-seq data from the sciatic nerve-infiltrating CD45+ cells from one neuropathic NOD.AireGW/+ mouse
Mouse1_scTCRseq

data_processing:
*library strategy: TCR-seq
The reads are first assembled into contigs using the 10x Genomics Cell Ranger V(D)J software
Contigs are annotated as V(D)J segments followed by grouping of cells into clonotypes by barcode and V(D)J sequence.
Subsequent analyses using Seurat are described in the full manuscript.
Assembly: mm10
Supplementary files format and content: TCR-seq: Comma-separated values from 10x Genomics Cell Ranger analysis of VDJ sequence files

source_name: Sciatic nerve

extract_protocol:
Chromium Single Cell GEM, Library & Gel Bead Kit
10x Genomics single cell RNA-Seq

treatment_protocol: The sciatic nerve was collected from neuropathic NOD.AireGW/+ mice after cardiac perfusion. Nerves were minced with a razor blade and digested in DPBS containing collagenase IV with 10% FBS. A 20-gauge needle was then used to triturate the nerve fragments to further aid in digestion. The further digested nerves were then filtered through a 40 μm mesh and washed to generate a single-cell suspension for collection of CD45+ cells] by FACS.

value: Sciatic nerve

value: Immune cells (CD45+)

tag: number of_mice


title: Sciatic nerve CD45+ cells, spontaneous autoimmune neuropathy, biol rep2, TCR-seq

description:
TCR-seq data from the sciatic nerve-infiltrating CD45+ cells from one neuropathic NOD.AireGW/+ mouse
Mouse2_scTCRseq

tag: tissue


title: Sciatic nerve CD45+ cells, spontaneous autoimmune neuropathy, biol rep3 (2 mice pooled), TCR-seq

description:
TCR-seq data from the sciatic nerve-infiltrating CD45+ cells from two neuropathic NOD.AireGW/+ mice
PooledMice3-4_scTCRseq

tag: cell type


title: Sciatic nerve CD45+ cells, spontaneous autoimmune neuropathy, biol rep3 (2 mice pooled), scRNAseq

description:
scRNA-seq data from the sciatic nerve-infiltrating CD45+ cells from two neuropathic NOD.AireGW/+ mice
PooledMice3-4_scRNAseq

data_processing:
The reads are first mapped to mm10 (mouse) reference using Cell Ranger software from 10x Genomics
Filtered output matrices that contained only barcodes with unique molecular identifier (UMI) counts that passed the threshold for cell detection were used for downstream analysis with Seurat. These filtered output matrices are provided as processed data files.
Subsequent analyses using Seurat are described in the full manuscript.
Assembly: mm10
Supplementary files format and content: scRNA-seq: Tab-separated values or matrix files from 10x Genomics Cell Ranger analysis of scRNA-seq files

treatment_protocol: The sciatic nerve was collected from neuropathic NOD.AireGW/+ mice after cardiac perfusion. Nerves were minced with a razor blade and digested in DPBS containing collagenase IV with 10% FBS. A 20-gauge needle was then used to triturate the nerve fragments to further aid in digestion. The further digested nerves were then filtered through a 40 μm mesh and washed to generate a single-cell suspension for collection of CD45+ cells by FACS.


title: Tconv_TNFR2_Donor4

description: 6377_14_48_Donor4_Tconv_aTNFR2_AGTTCCG_S95


title: Tconv_CD28_Donor4

description: 6377_13_47_Donor4_Tconv_aCD28_AGTCAAC_S86


title: tTreg_TNFR2_Donor3

description: 6377_12_46_Donor3_tTreg_aTNFR2_CTTGTAA_S83


title: RNA-seq_Rosiglitazone_2


title: tTreg_CD28_Donor3

description: 6377_11_45_Donor3_tTreg_aCD28_GGCTACA_S81


title: RNA-seq_Rosiglitazone_1


title: Sciatic nerve CD45+ cells, spontaneous autoimmune neuropathy, biol rep1, scRNAseq

description:
scRNA-seq data from the sciatic nerve-infiltrating CD45+ cells from one neuropathic NOD.AireGW/+ mouse
Mouse1_scRNAseq


title: Tconv_CD28_Donor3

description: 6377_9_41_Donor3_Tconv_aCD28_GATCAGA_S94


title: tTreg_TNFR2_Donor2

description: 6377_8_40_Donor2_tTreg_aTNFR2_ACTTGAA_S92


title: primary cultured mouse hepatocyte, Input

city: Pars

first: Renaud

last: Dentin

address: 24 rue du Faubourg Saint Jacques

department: Endocrinology, Metabolism and Diabetes

country: France

institute: INSERM U1016

data_processing:
Basecalls were performed using Bcl2fastq V2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score>30, using trimmomatic V0.33 discardy reads left with < 20 pb
ChIP-seq reads were aligned to the UCSC mm9 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To creae ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 pb to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.0 with a significance cul-off q-value <=0.01. bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: primary cultured hepatocytes

growth_protocol: M199, 2 mM glutamine, 1 X penicillin/streptomycin. Cells were cultured at 37°C with 5% CO2

extract_protocol:
Cells were fiwed with 1% formaldehyde for 10 minutes. After quenching and cells lysis,chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and IP samples. Libraried were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp lenght using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Cells were stimulated 24h with M199 supplemented with 2mM glutamine, 25 mM glucose and 100 nM insulin

tag: Sex

value: male

value: primary cultured hepatocytes

value: 25 mM glucose and 100 nM insulin for 24h


title: Tconv_TNFR2_Donor3

description: 6377_10_42_Donor3_Tconv_aTNFR2_TAGCTTA_S91

tag: treatment


title: RNA-seq_Fenofibrate_5

value: TKNOG

value: Fenofibrate


title: primary cultured mouse hepatocyte, H3K4me3,  ChIP


title: Tconv_TNFR2_Donor2

description: 6377_6_36_Donor2_Tconv_aTNFR2_GCCAATA_S87


title: Tconv_CD28_Donor2

description: 6377_5_35_Donor2_Tconv_aCD28_ACAGTGA_S89


title: RNA-seq_Fenofibrate_3

value: TKNOG Mus musculus

value: Homo sapiens


title: tTreg_TNFR2_Donor1

description: 6377_4_34_Donor1_tTreg_aTNFR2_TGACCAA_S88


title: Sciatic nerve CD45+ cells, spontaneous autoimmune neuropathy, biol rep2, scRNAseq

description:
scRNA-seq data from the sciatic nerve-infiltrating CD45+ cells from one neuropathic NOD.AireGW/+ mouse
Mouse2_scRNAseq


title: primary cultured mouse hepatocyte, ChREBP,  ChIP


title: tTreg_TNFR2_Donor4

description: 6377_16_50_Donor4_tTreg_aTNFR2_CCGTCCC_S96


title: tTreg_CD28_Donor1

description: 6377_3_33_Donor1_tTreg_aCD28_TTAGGCA_S84


title: RNA-seq_Fenofibrate_4

value: Liver


title: primary cultured mouse hepatocyte, RNA PolII,  ChIP


title: Tconv_TNFR2_Donor1

description: 6377_2_30_Donor1_Tconv_aTNFR2_CGATGTA_S85


title: RNA-seq_Fenofibrate_2


title: Tconv_CD28_Donor1

description: 6377_1_29_Donor1_Tconv_aCD28_ATCACGA_S82


title: RNA-seq_Fenofibrate_1


title: tTreg_CD28_Donor2

description: 6377_7_39_Donor2_tTreg_aCD28_CAGATCA_S93


title: C2C12 cells, Arrdc2 treatment 5, 48 h

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

data_processing:
Adapters were trimmed during demultiplexing by the core facility and trimmed reads were aligned to the genome using STAR version 2.7.10a for alignment to the mouse genome (GRCm39) and to generate count tables using default settings.
Differential expression analysis of count tables was performed using the default settings of DESeq2 version 1.30.1 (Benjamini-Hochberg FDR correction).
Assembly: NCBI GRCm39
Supplementary files format and content: Microsoft Excel Worksheet (.xlsx). Contains normalized counts generated by DESeq2.

growth_protocol: C2C12 myoblasts were cultured subconfluently at 37°C in 5% CO2 in complete growth media consisting of high glucose DMEM containing 10% FBS and 1% PS. Experiments were conducted in 12-well plates that were pre-coated with a Type I rat tail collagen matrix. Coating consisted of diluting RatCol collagen solution (cat. #5056-20ML; Advanced Biomatrix, Carlsbad, CA) and acetic acid into sterile water to a final concentration of 100 µg/mL for rat collagen and 0.1% acetic acid. Five hundred µL of the final solution was added to each well of the plate and incubated under UV light for 2 h to allow collagen to polymerize. Prior to plating myoblasts, the collagen solution was aspirated, and wells were rinsed twice with sterile phosphate buffered saline (PBS). Myotube differentiation was initiated when cells reached ~95% confluency by changing to differentiation media consisting of high glucose DMEM containing 2% horse serum,  1% PS, and 1 µm insulin. Media changes occurred every 48 h.

extract_protocol:
RNA was isolated using Zymo RNA Miniprep kit with on-column Dnase treatment. 300 micrograms of total RNA was used for construction of sequencing libraries.
A cDNA library was prepared for each sample using the the NEBNext PolyA mRNA and Ultra II Directional RNA library kit for Illumina. Libraries were barcoded for multiplexing with NEBNext Multiplex Oligos for Illumina unique dual index Primer Pairs. The multiplexed sample was quantified with qPCR (Kapa Biosystems) specific for Illumina sequencing primers and the average fragment size was determined with a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). The pooled sample was sequenced, with paired-end, 50 base reads on an Illumina NovaSeq 6000 located in the Translational Science Laboratory at the College of Medicine, Florida State University.  The pooled data were demultiplexed into individual sample data.

treatment_protocol: C2C12 myocytes were differentiated for 3 days. On day 3 post differentiation, C2C12 myotubes were transfected using adenoviruses encoding Arrdc2+Gfp or Gfp only as a control. Virus-containing media was changed 24 h after transfection to fresh differentiation media.

tag: cell line

value: Myoblast

value: WT

value: Arrdc2 transfection


title: C2C12 cells, Arrdc2 treatment 4, 48 h


title: RNA-seq_DMSO_5

value: DMSO


title: RNA-seq_DMSO_4


title: C2C12 cells, Arrdc2 treatment 3, 48 h


title: RNA-seq_DMSO_3


title: G-28

city: Shenbei

first: Weidong

last: Zhao

state: Liaoning

address: 77 Puhe Road, Shenbei New District

department: Department of Developmental Cell Biology

institute: China Medical University

data_processing:
FASTP v 0.18.0
Alignment with rRNA: Bowtie2(version 2.2.8) was used for mapping reads to rRNA database. The rRNA mapped reads then will be removed.
Alignment with Reference Genome: Paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance:The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM value was calculated to quantify its expression abundance and variations, using StringTie software.
Differentially expressed genes (DEGs): RNAs differential expression analysis was performed by DESeq2 software between two different groups.
Assembly: Ensembl release 98 GRCh38.p13
Supplementary files format and content: processed data.txt file includes count and FPKM values of each sample

source_name: blood

growth_protocol: The blood samples from the recruited subjects were collected in anticoagulant tubes.

extract_protocol:
RNA was harvested using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA). 1.0 μg of tatal RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: The erythrocytes were lysed by Red Blood Cell Lysis Solution and the leukocytes were isolated by density gradient centrifugation.  CD14+ monocytes were separately isolated from the leukocytes using magnet‐mediated separation with the specific magnetic beads (Miltenyi Biotech.), respectively.

value: blood

value: Primary monocyte


title: G-8


title: G-30


title: G-29


title: G-4


title: G-27


title: G-5


title: C2C12 cells, Arrdc2 treatment 1, 48 h


title: RNA-seq_DMSO_2


title: C2C12 cells, Arrdc2 treatment 2, 48 h


title: G-23


title: C2C12 cells, GFP control 5, 48 hr

value: GFP transfection


title: G-25


title: G-22


title: RNA-seq_DMSO_1


title: C2C12 cells, GFP control 4, 48 hr


title: G-20


title: G-21


title: G-9


title: G-19


title: C2C12 cells, GFP control 3, 48 hr


title: G-17


title: Fast_donor2

data_processing:
The raw FASTQ reads were processed using the pipeline from Kundaje Laboratory [https://github.com/kundajelab/atac_dnase_pipelines], which included adapter trimming, alignment with genome using Bowtie2, and peak calling using MACS2.
The genome used for Bowtie2 alignment was established using the same method as that used in the analysis of the humanized mouse RNA-Seq data.
A custom genome reference index was created by combining human (GRCh38.p13) and mouse (GRCm38.p6) genome sequences for alignment of humanized mouse chimeric liver ATAC-seq data ; the primary assemblies were obtained from the GENCODE database (https://www.gencodegenes.org/).
Assembly: GRCh38 and mm10
Supplementary files format and content: BED

extract_protocol:
Transposase-accessible chromatin DNA were purified using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer's instructions. The purified DNAs were stored at -80 °C or processed to ATAC-Seq library preparation.
Libraries were constructed according to the Illumina TruSeq  protocol.

value: Fast


title: C2C12 cells, GFP control 2, 48 hr


title: G-15


title: G-16


title: AL_donor2

value: AL


title: G-14


title: C2C12 cells, GFP control 1, 48 hr


title: GW4064


title: AL_donor1


title: HEK293T, Dengue-infected, m6AIP, replicate 1

city: Barcelona

first: Juana

last: Diez

address: Dr. Aiguader, 88

country: Spain

institute: Pompeu Fabra University

data_processing:
Raw reads were adapter trimmed using cutadapt v4.1, which allowed removal of reads with low quality bases (q<20), short lengths after trimming (<25 bp) and orphan read pairs. The resulting fastq files were mapped using STAR v2.7.6a with parameters --outFilterType BySJout against a merger of the hg38 reference genome and the given viral genome, added as an additional contig. m6A peaks were called using m6aViewer v1.6.1 with default parameters and MACS2 using parameters -q 0.01 --nomodel --extsize 100 -B --SPMR --bdg --keep-dup all -f BAMPE. R software was used to filter significant peaks, defined as showing > 2-fold enrichment over input and a false discovery rate (FDR) < 5% across two biological replicates. Conserved viral peaks found by both analyses were considered significant, with the fold-change over input at peak maxima displayed within genome browser visualization using the output from MACS2 bdgcmp –m FE. Motif analysis across conserved m6AViewer-called m6A peaks was performed using HOMER v4.11 with parameters -rna -len 5,6 -size 50, which identified motifs within the flanking 100 bases of sequence surrounding the peak center.
Assembly: hg38, DENV-2-16681(NC_001474.2)
Supplementary files format and content: bigwig, narrowpeak

organism:
Homo sapiens
Dengue virus

growth_protocol: HEK293T cells were cultured at 37 ºC and 5 % CO2 in Dulbecco’s modified Eagle’s medium with glutamine (DMEM) (Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS) (Gibco) and 1% (v/v) non-essential amino acids (Gibco).

extract_protocol:
total RNA was isolated, DNase-treated, ethanol-precipitated and fragmented with RNA fragmentation reagent for 10 min at 70°C. Then, the RNA was ethanol-precipitated followed by a ribodepletion step using the human FFPE/degraded RNA riboPOOL kit (siTOOLs Biotech) according to the supplier’s protocol. 5 μg of fragmented and ribodepleted RNA was used for m6A-IP. 50 μl of slurry of Magna ChIP Protein G magnetic beads (Sigma-Aldrich) were washed twice with IP/wash buffer 20 mM Tris HCl pH 7.4, 150 mM NaCl, and 0.1% NP-40 (v/v). Beads were re-suspended in 100 μl of IP/wash buffer and coated with 5 μg of rabbit anti-m6A antibody (Active motif, 61495) for 45 min at room temperature with rotation. Beads were then washed 3x with IP/wash buffer and m6A-IPs were prepared by mixing the antibody-coated beads with 910 μl of IP/wash buffer, 35 μl of 0.5 M EDTA pH 8.0, 4 μl of murine RNase inhibitor (New England Biolabs), and 40 μg of fragmented total RNA. 1% input samples (10 μl from the total 1 mL m6A-IP mixture) were removed before immunoprecipitation and stored at −80°C. m6A-IPs were incubated overnight at 4°C with rotation. Beads were then washed 3x with IP/wash buffer. IP samples were further incubated with 126 μl of IP/wash buffer, 15 μl of 10% SDS (v/v) and 9 μl of PCR-grade proteinase K (20 mg/mL) (Thermo Fisher) for 30 min at 55°C. After incubation, 150 μl of the supernatant containing the RNA was transferred to a new microcentrifuge tube and 100 μl of IP/wash buffer was added to each sample. RNA was purified with Trizol LS (Thermo Fisher) and ethanol-precipitated together with 1.5 µl of RNA-grade glycogen (Thermo Fisher). Input samples were processed together with m6A-IPs from the proteinase K treatment onwards.
1 to 5 ng of RNA from input and corresponding m6A-IPs were used for NGS library production following the protocol NEBNext Ultra II directional RNA library prep kit for Illumina (New England Biolabs), treating samples as rRNA-depleted and fragmented RNAs.

treatment_protocol: Stocks of Dengue strain DENV-2 strain were generated in BHK-21 cells and titered by standard plaque assay in HEK293T cells. The viral inoculum was incubated for 2 hr. DENV infections of HEK293T cells were carried out at an MOI of 2 for 48 hours.

value: human embryonic kidney

tag: antibody

value: m6A (Active Motif, 61495)

value: 48 hours DENV infection, MOI 2


title: G-11


title: HEK293T, Dengue-infected, m6AIP, replicate 2


title: G-13


title: HEK293T, Dengue-infected, Input, replicate 2

description:
DENV-rep2.narrowPeak
DENV-rep2-FC.bw


title: 873_WT_brain_RNAseq_R1

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq (k=4) v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

source_name: Brain

growth_protocol: Embryonic placenta collections at designated time points

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 (Illumina RS-122-2001)

value: Brain

tag: chip antibody


title: 876_WT_brain_RNAseq_R1


title: DMSO

tag: strain

value: TKNOG


title: Fenofibrate

value: TKNOG Mus musculus

value: Fenofibrate


title: HEK293T, CHIKV-infected, m6A, replicate 2

data_processing:
Raw reads were adapter trimmed using cutadapt v4.1, which allowed removal of reads with low quality bases (q<20), short lengths after trimming (<25 bp) and orphan read pairs. The resulting fastq files were mapped using STAR v2.7.6a with parameters --outFilterType BySJout against a merger of the hg38 reference genome and the given viral genome, added as an additional contig. m6A peaks were called using m6aViewer v1.6.1 with default parameters and MACS2 using parameters -q 0.01 --nomodel --extsize 100 -B --SPMR --bdg --keep-dup all -f BAMPE. R software was used to filter significant peaks, defined as showing > 2-fold enrichment over input and a false discovery rate (FDR) < 5% across two biological replicates. Conserved viral peaks found by both analyses were considered significant, with the fold-change over input at peak maxima displayed within genome browser visualization using the output from MACS2 bdgcmp –m FE. Motif analysis across conserved m6AViewer-called m6A peaks was performed using HOMER v4.11 with parameters -rna -len 5,6 -size 50, which identified motifs within the flanking 100 bases of sequence surrounding the peak center.
Assembly: hg38, LR2006_OPY1
Supplementary files format and content: bigwig, narrowpeak

organism:
Homo sapiens
Chikungunya virus

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher) according to the supplier’s protocol. TURBO DNA-free Kit (Thermo Fisher) was used to remove any contaminating DNA from RNA samples. Isolated RNA was further purified by ethanol precipitation and 30-40 µg of total RNA were subjected to poly(A)-selection with Dynabeads Oligo (dT)25 (Thermo Fisher) according to the manufacturer’s instructions. poly(A)+ RNA from CHIKV-infected HEK293T cells (12 hr p.i. MOI of 4) was fragmented for 10 min at 70°C with RNA fragmentation reagent (Thermo Fisher). After fragmentation, the RNA was cleaned up through an ethanol precipitation step. At this stage, a sample of fragmented poly(A)+ RNA was saved as input RNA for later use in cDNA library construction while 5 μg of fragmented poly(A)+ RNA were used per m6A-IP. For each m6A-immunoprecipitation (m6A-IP), 50 μl of slurry of Magna ChIP Protein G magnetic beads (Sigma-Aldrich) were washed twice with IP/wash buffer 20 mM Tris HCl pH 7.4, 150 mM NaCl, and 0.1% NP-40 (v/v). Beads were re-suspended in 100 μl of IP/wash buffer and coated with 5 μg of rabbit anti-m6A antibody (Active motif, 61495) for 45 min at room temperature with rotation. Beads were then washed 3x with IP/wash buffer and m6A-IPs were prepared by mixing the antibody-coated beads with 910 μl of IP/wash buffer, 35 μl of 0.5 M EDTA pH 8.0, 4 μl of murine RNase inhibitor (New England Biolabs), and 40 μg of fragmented total RNA. 1% input samples (10 μl from the total 1 mL m6A-IP mixture) were removed before immunoprecipitation and stored at −80°C. m6A-IPs were incubated overnight at 4°C with rotation. Beads were then washed 3x with IP/wash buffer. IP samples were further incubated with 126 μl of IP/wash buffer, 15 μl of 10% SDS (v/v) and 9 μl of PCR-grade proteinase K (20 mg/mL) (Thermo Fisher) for 30 min at 55°C. After incubation, 150 μl of the supernatant containing the RNA was transferred to a new microcentrifuge tube and 100 μl of IP/wash buffer was added to each sample. RNA was purified with Trizol LS (Thermo Fisher) and ethanol-precipitated together with 1.5 µl of RNA-grade glycogen (Thermo Fisher). Input samples were processed together with m6A-IPs from the proteinase K treatment onwards.
1 to 5 ng of RNA from input and corresponding m6A-IPs were used for NGS library production following the protocol NEBNext Ultra II directional RNA library prep kit for Illumina (New England Biolabs), treating samples as rRNA-depleted and fragmented RNAs.

treatment_protocol: Stocks of CHIKV strain LR2006-OPY1 were generated in BHK-21 cells and titered by standard plaque assay in HEK293T cells. The viral inoculum was incubated for 1 hr. CHIKV infections of HEK293T cells were carried out at an MOI of 4 for 12 hours.

value: 12 hours CHIKV infection, MOI 4


title: 874_WT_brain_RNAseq_R1


title: Rosiglitazone

value: Homo sapiens

value: Rosiglitazone

value: Liver


title: G-12


title: 866_WT_brain_RNAseq_R1

value: WT


title: 868_WT_brain_RNAseq_R1


title: G-10

value: blood


title: HEK293T, CHIKV-infected, m6A, replicate 1


title: Fast_donor1


title: N-9

value: Primary monocyte

value: control


title: N-7


title: LCL_Ctrl_2_Basal

city: Paris

first: Sylvain

last: Latour

address: 24 bd du Montparnasse

institute: Institut Imagine

data_processing:
RNAseq libraries were sequenced (paired-end reads 100 bases + 100 bases) on Illumina NovaSeq6000.
A total of ~90 million of passing filter paired-end reads was produced per library. Reads were mapped and aligned to the human reference genome and to EBV1 and EBV2 reference genomes using STAR52, and the number of uniquely mapped reads for each gene was counted using HTSeq53. Only genes with an average ≥1 read/sample were used in our analysis.DESeq2 was used for normalization and the negative binomial model was used for differential expression analysis.
Assembly: FASTQ files were mapped to the ENSEMBL Human GRCh38/hg38 reference using Illumina DRAGEN aligner and counted by featureCounts from the Subread R package
Supplementary files format and content: csv file includes raw counts for the different samples

source_name: Lymphoblastoid Cell Lines (LCLs)

extract_protocol:
Total RNA was isolated from LCLs stimulated or not with IL-27 for 6 h hours using the RNeasy Kit (QIAGEN) including DNAse treatment. RNA quality was assessed by capillary electrophoresis by Fragment Analyzer using High Sensitivity RNA reagents (Agilent Technologies) and RNA concentration measured by spectrophotometry withXpose (Trinean) and Fragment Analyzer.
RNAseq libraries were generated from 600 ng of RNA using Universal PlusTM mRNA-Seq with NuQuant® (NuGEN, San Juan, Puerto Rico)

value: Lymphoblastoid Cell Lines (LCLs)

value: complete medium without IL27


title: 790_SertKO_brain_RNAseq_R1

value: SertKO


title: N-5


title: 789_SertKO_brain_RNAseq_R1


title: LCL_Ctrl_2_Stim_IL27

value: complete medium with IL27


title: HEK293T, CHIKV-infected, Input, replicate 2

description:
CHIKV-rep2.narrowPeak
CHIKV-rep2-FC.bw

value: human embryonic kidney


title: HEK293T, CHIKV-infected, Input, replicate 1

description:
CHIKV-rep1.narrowPeak
CHIKV-rep1-FC.bw


title: HEK293T, Dengue-infected, Input, replicate 1

description:
DENV-rep1.narrowPeak
DENV-rep1-FC.bw

value: 48 hours DENV infection, MOI 2


title: LCL_Ctrl_1_Basal


title: N-30


title: LCL_Ctrl_1_Stim_IL27


title: 750_Oct3KO_brain_RNAseq_R1

value: Brain


title: Fast_donor2_3

description:
donor2
fasting3_donor2.fastq
nanopore_human_transcripts_tpm_donor2.txt
nanopore_mouse_transcripts_tpm_donor2.txt

data_processing:
The ONT Guppy workflow (version 2.1.0) was used for basecalling the DRS data with the parameters "--flowcell FLO-MIN106 --kit SQK-RNA002 -x cuda:all --records_per_fastq 0" being employed
The FASTQ files were aligned to the GRCh38 human genome reference and GRCm38 mouse genome reference respectively using minimap2/2.17, with the parameters "-ax splice -uf -k14" being employed.
The FLAIR pipeline (https://github.com/BrooksLabUCSC/flair) with some modifications was employed to identify the isoform from the aligned reads.
The nanopore reads were quantified to DRS annotation using FLAIR quantify by default parameters. Only alignments with quality scores of 1 or greater were counted.
Assembly: GRCh38 and mm10
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample; isoform structure BED files

extract_protocol:
The 75 ug of fresh Trizol isolated RNAs were adjusted to a volume of 100 μL with nuclease-free water. The polyadenylated RNAs were selected using the Dynabeads™ mRNA Purification Kit (Invitrogen, Cat. 61006) following the manufacturer's instructions.
The 500 ng of fresh isolated polyadenylated RNAs were used for nanopore direct RNA sequencing (DRS) generally following the Oxford Nanopore Technologies (ONT) SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. Libraries were loaded onto ONT R9.4 flow cells (Oxford Nanopore Technologies) and were sequenced using the GridION platform, with the standard MinKNOW/19.12.5 protocol script being used.

value: TKNOG

value: TKNOG Mus musculus

value: Fast


title: 788_SertKO_brain_RNAseq_R1


title: LCL_P2_Basal

value: IL27RA mutation


title: Fast_donor2_2

description:
donor2
fasting2_donor2.fastq
nanopore_human_transcripts_tpm_donor2.txt
nanopore_mouse_transcripts_tpm_donor2.txt

value: Homo sapiens


title: 748_Oct3KO_brain_RNAseq_R1


title: LCL_P1_1_Basal


title: AL_donor2_3

description:
donor2
fed4_donor2.fastq
nanopore_human_transcripts_tpm_donor2.txt
nanopore_mouse_transcripts_tpm_donor2.txt

value: AL

value: Liver


title: LCL_P2_Stim_IL27


title: LCL_P1_1_Stim_IL27


title: 718_SertKO_brain_RNAseq_R1


title: 717_SertKO_brain_RNAseq_R1


title: AL_donor2_2

description:
donor2
fed3_donor2.fastq
nanopore_human_transcripts_tpm_donor2.txt
nanopore_mouse_transcripts_tpm_donor2.txt


title: AL_donor2_1

description:
donor2
fed1_donor2.fastq
nanopore_human_transcripts_tpm_donor2.txt
nanopore_mouse_transcripts_tpm_donor2.txt


title: N-26

value: blood


title: N-25

value: Primary monocyte


title: N-24

value: control


title: 716_SertKO_brain_RNAseq_R1


title: PC-9OR, ZNF263, ChIP

city: Shanghai

first: Jiaqi

last: Liang

state: Shanghai

address: 180 Fenglin Road

institute: Zhongshan Hospital Fudan University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Peak extraction was conducted using the MACS2 software (ver.2.1.1) and genomic positions were identified by calculating the peak enrichment and estimating the empirical false discovery rate (FDR) value using the Poisson probabilities. Genomic regions in which FDR value < 0.05 is selected as the ZNF263 binding peaks.
MEME method was used for de novo motif analysis of the genomic DNA sequences flanking ChIP-sequencing peaks.
bigWig files were generated using the genomicRanges R package
Assembly: GRCh38.p13
Supplementary files format and content: bigWig

source_name: Tumor

extract_protocol:
Cells were fixed with 1% fomaldehyde for 10 minutes. After guenching and cellysis, chromatin was digested with micrococcal nuclease into DNA/protein fragments.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material ofr input or library samples.

value: Tumor

value: non-small cell lung carcinoma


title: PC-9OR, IgG, ChIP

value: IgG


title: N-22


title: Fast_donor1_4

description:
donor1
fasting4_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: N-28


title: N-29


title: 700_Oct3KO_brain_RNAseq_R1


title: Fast_donor2_1

description:
donor2
fasting1_donor2.fastq
nanopore_human_transcripts_tpm_donor2.txt
nanopore_mouse_transcripts_tpm_donor2.txt


title: 749_Oct3KO_brain_RNAseq_R1


title: N-20


title: N-27


title: PC-9OR, ZNF263, Input


title: N-19


title: Fast_donor1_3

description:
donor1
fasting3_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: 697_Oct3KO_brain_RNAseq_R1


title: lung adenocarcinoma tissue 4, post osimertinib treatment

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCh38.p13
Supplementary files format and content: FPKM

source_name: lung adenocarcinoma

extract_protocol:
RNA was harvested using TRIZOL
RNA libararies for RNA-seq were prepared using SMARTER mRNA-seq Library Kit

value: lung adenocarcinoma

value: Osimertinib


title: Fast_donor1_1

description:
donor1
fasting1_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: lung adenocarcinoma tissue 3, post osimertinib treatment


title: 683_Tph1KO_brain_RNAseq_R1


title: lung adenocarcinoma tissue 2, post osimertinib treatment


title: N-16


title: 682_Tph1KO_brain_RNAseq_R1


title: 676_Tph1KO_brain_RNAseq_R1


title: AL_donor1_4

description:
donor1
fed4_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: 684_Tph1KO_brain_RNAseq_R1


title: lung adenocarcinoma tissue 1, post osimertinib treatment


title: AL_donor1_3

description:
donor1
fed3_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: AL_donor1_2

description:
donor1
fed2_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: 174_Tph1KO_brain_RNAseq_R1


title: lung adenocarcinoma tissue 4, prior to osimertinib


title: N-14


title: AL_donor1_1

description:
donor1
fed1_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: lung adenocarcinoma tissue 3, prior to osimertinib


title: Fast_donor1_2

description:
donor1
fasting2_donor1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt