title: organoid3

city: Singapore

first: Jinmiao

last: Chen

address: 8a Biomedical Grove

department: SigN

country: Singapore

institute: A*STAR

data_processing:
Illumina BCL files were converted to FASTQ files using the cellranger mkfastq command.
The cell ranger pipeline (version 2.1.1) was used to pre-process the 10X sequencing data generated by the 10X Genomics Chromium Controller.
Each read from the FASTQ files were then aligned to a human reference genome (GRCh38-1.2.0) using the Cellranger count command in order to generate count matrix.
The output (count matrix) was used as the main input file for all downstream analysis.
Assembly: GRCh38-1.2.0
Supplementary files format and content: text files containing the count data

source_name: Human iPSC-derived cells

extract_protocol:
Organoids (cultured in the absence or presence of iMac for 18 days) were digested into single cells and washed once in 0.04% BSAsupplemented PBS. iMac cultured in the absence of organoids for 18 days were also subjectedto the same digestion and washing processes. The cells were then resuspended to a final cellconcentration of 530-1000 cells/μL in PBS/0.04% BSA. Using the 10X Genomics ChromiumController, about 8,700 cells were encapsulated in droplets at a targeted cell recovery of 5000cells, resulting in estimated multiplet rates of 3.9%.
Single cell RNA-seq libraries were prepared using the 10X Genomics Chromium Single Cell 5′ v1 Library & Gel Bead Kit and i7 Multiplex Kit according to the manufacturer’s protocol. The libraries were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 (Illumina, San Diego, CA, USA) at a sequencing depth of 50,000 reads/cell.

value: Brain

value: cerebral organoids


title: iMac1

status: Public on Sep 16 2023

type: SRA

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

value: iPSC-dreived macrophages (iMac) on day 18 of mono-culture


title: iMac2


title: AhRΔIECDSS+I3C2

type: RNA

city: Columbia

first: Philip

middle: Brandon

last: Busbee

state: SC

address: 6439 Garners Ferry Road

department: Pathology, Microbiology, and Immunology

country: USA

institute: University of South Carolina School of Medicine

description: Gene expression data from colon of AhR knockout mice treated with DSS and I3C

hyb_protocol: single-strand cDNA was fragmented, labeled, and hybrized to a  Affymetrix Clariom D array mouse chip in in Hybridization Oven 645 following instructions from manufacturer (Thermo Fisher Scientific)  195 (Thermo Fisher Scientific)

scan_protocol: Hybrized GeneChips were scanned using GeneChip Fludics Station 450 Scanner (Thermo Fisher Scientific)

data_processing: Transcriptome analysis console (TAC, Thermo Fisher Scientific)

label: Uracil-DNA glycosylase

organism: Mus musculus

source_name: Colonic epithelial cells

label_protocol: DNA was labelled using Uracil-DNA glycosylase (GeneChip WT Pico Reagent Kit)

extract_protocol: Total RNA was extracted from whole mouse colon tissue using Qiagen RNA Micro kit according to the manufacturer's instruction .

treatment_protocol: Colitis was induced in WT and conditional AhR knockout (AhRΔIEC) C56BL/6 male using dextran sodium sulfate (DSS). For disease induction, mice were given 3% DSS ab libitum for  7 days, followed by regular drinking water. For treatment (indole-3-carbinol, I3C), mice were given intraperitoneal injections of I3C (40mg/kg) every other day until end of experiment, starting at Day 0.

tag: genotype

value: AhR Flox vs Vil Cre

value: Colonic epithelial cells

tag: treatment

value: treated with DSS and I3C


title: WT DSS+I3C2

description: Gene expression data from colon of mice with DSS induced colitis treated with I3C

value: Wildtype

value: DSS induced colitis treated with I3C


title: AhRΔIECDSS2

description: Gene expression data from colon of AhR knockout mice treated with DSS

value: treated with DSS


title: AhRΔIECDSS1


title: WT DSS2

description: Gene expression data from colon of mice with DSS induced colitis

value: DSS induced colitis


title: WT DSS+I3C1


title: organoid1


title: Patient 14658, Lung tumor, Never-smoker, smoL19, MeDIP

city: St. Louis

first: Ting

last: Wang

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis

description:
smoL19_mCRF.bedGraph.gz
smoL19_mCRF.bedGraph.gz.tbi

library_source: genomic

data_processing:
Adapter trimming, read alignment to the hg19 genome with BWA, and methylQA post-processing were also performed as described the paper: "Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72(C):29–40".
methylCRF was performed on the 28 primary tumor and normal lung samples to estimate the methylation level at each CpG using MRE-seq and MeDIP-seq data. The methylCRF package was downloaded and installed from http://methylcrf.wustl.edu/. methylCRF was run using perl 5.14.4, R 3.3.0, and samtools 1.3.1.
M&M (R package methylMnM) was used to identify DMRs between samples using MRE-seq and MeDIP-seq data. First, the functions countcpgbin and countMREcpgbin were used to count the number of CpGs and restriction enzyme cut sites in 500bp bins across the genome (chromosomes 1-22, X, Y, and M; n=6,166,049 bins). Cut sites for the 4 enzymes used in MRE-seq were considered, and a blacklist file was provided (hg19 DAC Blacklisted Regions, e.g., wgEncodeDacMapabilityConsensusExcludable from the UCSC Genome Browser). Then, 500bp DMRs were identified using the read alignment bed files output by methylQA for MRE-seq and MeDIP-seq from two samples. The functions countMeDIPbin and countMREbin were used to produce normalized read counts per bin for each sample. Default values were used for MnM.test, MnM.qvalue, and MnM.selectDMR, and no PCR threshold was set. DMRs were identified between patient-matched normal lung and tumors from the same patient (n=11), between all pairs of normal samples (n=55), and between all normal-tumor sample pairs from different patients (n=176).
Assembly: hg19
Supplementary files format and content: mCRF bed files and index files were created and are available for each sample, dictating CpG methylation at individual loci.
Supplementary files format and content: DMR bed files and index files were created and are available for each patient where normal and primary data were collected and indicate regions showing differential methylation between the paired normal and primary.

molecule: genomic DNA

source_name: NSCLC tumor

growth_protocol: Snap-frozen primary NSCLC tumor specimens were  collected from surgical remnants with patient consent under an IRB-approved protocol.

extract_protocol:
Genomic DNA was isolated using the Qiagen kit (56304).
MeDIP-seq and MRE-seq were generated using the protocol in the paper: "Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72(C):29–40". MRE-seq was performed with four enzymes: HpaII, SsiI, Hin6I, HpyCH4IV and a base offset of 3 was used during sequencing.

value: NSCLC tumor

value: Never-smoker


title: organoid2


title: Patient 11732, Lung tumor, Unconfirmed smoking status, smoL22, MRE

description:
smoL22_mCRF.bedGraph.gz
smoL22_mCRF.bedGraph.gz.tbi

value: Unconfirmed smoking status


title: TNBS+I3C

source_name: epithelial cells enriched from colon

treatment_protocol: TNBS colitis was induced in mice by single intrarectal injection (1mg; 50 microliters) of TNBS in 60% ethanol vehicle. For treatment with I3C, mice were given i.p. injections of 40mg/kg (100 microliters) I3C in appropriate vehicle (DMSO/corn oil) everyday, up to day 5. Control groups were given appropriate vehicles without either TNBS or I3C.

value: female

value: balb/cJ

tag: age

value: 8-10 weeks old

value: epithelial cells enriched from colon

value: Mice given TNBS injection and I3C treatment


title: AhRΔIECDSS+I3C1


title: coculture1

value: Brain

value: co-cultured cerebral organoids on day 18 of co-culture


title: WT DSS1


title: TNBS+Vehicle

value: Mice given TNBS injections and vehicle (100 microliters of DMSO/corn oil i.p.)


title: coculture3


title: Patient 11584, Lung tumor, Smoker, smoL10, MRE

description:
smoL10_mCRF.bedGraph.gz
smoL10_mCRF.bedGraph.gz.tbi

value: Smoker


title: Patient 11584, Lung tumor, Smoker, smoL10, MeDIP


title: coculture2


title: Patient 11266, Lung tumor, Smoker, smoL8, MRE

description:
smoL8_mCRF.bedGraph.gz
smoL8_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_11266.bedGraph.gz
DMRs_qv_Patient_11266.bedGraph.gz.tbi


title: Patient 11266, Lung tumor, Smoker, smoL8, MeDIP


title: Patient 11266, Normal lung, Smoker, smoL28, MRE

description:
smoL28_mCRF.bedGraph.gz
smoL28_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_11266.bedGraph.gz
DMRs_qv_Patient_11266.bedGraph.gz.tbi

source_name: Normal lung

value: Normal lung


title: Patient 9890, Normal lung, Smoker, smoL14, MRE

description:
smoL14_mCRF.bedGraph.gz
smoL14_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_9890.bedGraph.gz
DMRs_qv_Patient_9890.bedGraph.gz.tbi


title: Patient 9890, Normal lung, Smoker, smoL14, MeDIP


title: Patient 9890, Lung tumor, Smoker, smoL4, MeDIP

description:
smoL4_mCRF.bedGraph.gz
smoL4_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_9890.bedGraph.gz
DMRs_qv_Patient_9890.bedGraph.gz.tbi


title: Vehicle

value: Mice given vehicles (50 microliters 60% ethanol i.r.;100 microliters of DMSO/corn oil i.p.)


title: Patient 9890, Lung tumor, Smoker, smoL4, MRE


title: Patient 8951, Lung tumor, Never-smoker, smoL12, MeDIP

description:
smoL12_mCRF.bedGraph.gz
smoL12_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_8951.bedGraph.gz
DMRs_qv_Patient_8951.bedGraph.gz.tbi


title: Patient 8951, Normal lung, Never-smoker, smoL23, MeDIP

description:
smoL23_mCRF.bedGraph.gz
smoL23_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_8951.bedGraph.gz
DMRs_qv_Patient_8951.bedGraph.gz.tbi


title: Patient 8951, Lung tumor, Never-smoker, smoL12, MRE


title: Patient 11732, Lung tumor, Unconfirmed smoking status, smoL22, MeDIP


title: I3C

value: Mice given I3C and vehicle (50 microliters 60% ethanol i.r.)


title: Patient 8951, Normal lung, Never-smoker, smoL23, MRE


title: Patient 8666, Normal lung, Never-smoker, smoL16, MRE

description:
smoL16_mCRF.bedGraph.gz
smoL16_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_8666.bedGraph.gz
DMRs_qv_Patient_8666.bedGraph.gz.tbi


title: Patient 8868, Lung tumor, Smoker, smoL9, MeDIP

description:
smoL9_mCRF.bedGraph.gz
smoL9_mCRF.bedGraph.gz.tbi


title: Patient 8666, Lung tumor, Never-smoker, smoL11, MRE

description:
smoL11_mCRF.bedGraph.gz
smoL11_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_8666.bedGraph.gz
DMRs_qv_Patient_8666.bedGraph.gz.tbi


title: Patient 8666, Normal lung, Never-smoker, smoL16, MeDIP


title: Patient 6503, Lung tumor, Smoker, smoL24, MeDIP

description:
smoL24_mCRF.bedGraph.gz
smoL24_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_6503.bedGraph.gz
DMRs_qv_Patient_6503.bedGraph.gz.tbi


title: Patient 6356, Lung tumor, Unconfirmed smoking status, smoL21, MRE

description:
smoL21_mCRF.bedGraph.gz
smoL21_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_6356.bedGraph.gz
DMRs_qv_Patient_6356.bedGraph.gz.tbi


title: Patient 11266, Normal lung, Smoker, smoL28, MeDIP


title: Patient 6356, Normal lung, Unconfirmed smoking status, smoL18, MRE

description:
smoL18_mCRF.bedGraph.gz
smoL18_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_6356.bedGraph.gz
DMRs_qv_Patient_6356.bedGraph.gz.tbi


title: Patient 6503, Normal lung, Smoker, smoL27, MeDIP

description:
smoL27_mCRF.bedGraph.gz
smoL27_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_6503.bedGraph.gz
DMRs_qv_Patient_6503.bedGraph.gz.tbi


title: Patient 6339, Lung tumor, Unconfirmed smoking status, smoL6, MRE

description:
smoL6_mCRF.bedGraph.gz
smoL6_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_6339.bedGraph.gz
DMRs_qv_Patient_6339.bedGraph.gz.tbi


title: Patient 6356, Normal lung, Unconfirmed smoking status, smoL18, MeDIP


title: Patient 6339, Lung tumor, Unconfirmed smoking status, smoL6, MeDIP


title: Patient 6339, Normal lung, Unconfirmed smoking status, smoL25, MRE

description:
smoL25_mCRF.bedGraph.gz
smoL25_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_6339.bedGraph.gz
DMRs_qv_Patient_6339.bedGraph.gz.tbi


title: Patient 6130, Lung tumor, Smoker, smoL5, MRE

description:
smoL5_mCRF.bedGraph.gz
smoL5_mCRF.bedGraph.gz.tbi


title: Patient 6130, Lung tumor, Smoker, smoL5, MeDIP


title: Patient 8868, Lung tumor, Smoker, smoL9, MRE


title: DE27NGSUKBR111916: THP-1 dual ELAVL1-KO rep2

city: Bonn

first: Thais

middle: Marina

last: Schlee-Guimarães

address: Venusberg-Campus 1

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital, University of Bonn

library_source: transcriptomic

data_processing:
The quality of fastq files was assessed using FastQC(Andrews, S. et al.,2010)
Reads were  mapped to GRCh38 with STAR(Dobin et al., 2013).
Raw counts were computed using HTSeq(Anders S. et. Al., 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts csv files

source_name: THP-1 dual cells

growth_protocol: THP-1 dual cells were cultured in RPMI 1640 (10 % FCS, 100 U/ml penicillin, 100 mg/ml streptomycin) at 37 °C.

extract_protocol:
For isolation of total RNA, cells were resuspended in 350 µl RLT buffer (Qiagen) and then 350 µl 70 % (v/v) ethanol was added to the mixture. The samples were loaded onto Zymo Spin IIICG columns (Zymo Research) and washed sequentially with 350 µl buffer RW1 (Qiagen) and 350 µl Zymo RNA Wash buffer (Zymo Research). The RNA was eluted in RNase-free H2O.
Total RNA was used to generate RNA sequencing libraries using the QuantSeq 3' mRNA-seq library prep kit FWD (Lexogen).

treatment_protocol: THP-1 dual cells were treated with 1000 U/ml IFNα for 6 h.

value: Monocyte

value: treated with 1000 U/ml IFNα for 6 h

tag: source

value: Invivogen (Cat#thpd-nfis)


title: HiC_Brucella_deltamucR_rep2

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads were mapped to the combined B. abortus 2308 (NCBI Reference Sequence GCA_000054005.1) by the hiclib pipline.
Assembly: B. abortus 2308 (NCBI Reference Sequence GCA_000054005.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Brucella abortus 2308

source_name: Bacterial

extract_protocol:
Wild type and mutant cells of Brucella abortus 2308 growing in LB were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.

value: Bacterial

value: mucR deletion

value: Cells were growing in LB, fixed by 3% formaldehyde for 30min at room temperature


title: DE54NGSUKBR111915: THP-1 dual ELAVL1-KO rep1


title: HiC_Brucella_deltamucR_rep1


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_MORC-antibody_IAA24h

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

country: France

institute: INSERM

description: IAA treated for 24h

data_processing:
Data Analysis: After receiving demultiplexed fastq files from the sequencing service provider (ArrayStar), reads were aligned to Toxoplasma gondii reference genome (TGME49) using BOWTIE2. Aligned reads were used for peak calling of the ChIP regions using MACS2. Statistically significant ChIP-enriched regions (peaks) were identified individually using a p-value threshold of 10-4. BigWig datasets were generated using  bedGraphToBigWig to convert the bedgraph file generated by MACS2
Data visualization: The mapped 100 bp reads represent enriched DNA fragments by ChIP experiment. Any region of interest in the raw ChIP-seq signal profile can be directly visualized in genome browser. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).
Assembly: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" to upload at ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary files format and content: Statistically significant ChIP-enriched regions (peaks) were identified individually, using a p-value threshold of 10-4. Te BigWig format file containing the ChIP-enriched regions and was generated for each sample. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).

organism: Toxoplasma gondii

source_name: intracellular parasites

growth_protocol: Toxoplasma gondii RHKU80 strains were maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Crosslinked chromatin was lysed in ice-cold lysis buffer (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5%NP-40, 0.125% triton X-100, protease inhibitor cocktail) and sheared in shearing buffer (1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris pH8.0, protease inhibitor cocktail) by sonication using a Diagenode Biorupter. Samples were sonicated, for 16 cycles (30 seconds ON and 30 seconds OFF), to 200-500 base-pair average size. Immunoprecipitation was carried out using sheared chromatin, 5% BSA, protease inhibitor cocktail, 10% triton X-100, 10% deoxycholate, DiaMag Protein A-coated magnetic beads (Diagenode) and antibodies (H4K5acK8acK12acK16ac, H4K31me1, HDAC3, and HA). A rabbit IgG antiserum was used as a control mock. After overnight incubation at 4°C on rotating wheel, chromatin-antibody complexes were washed and eluted from beads by using iDeal ChIP-seq kit for Histones (Diagenode) according to the manufacturer’s protocol. Samples were decrosslinked by heating for 4 hours at 65°C. DNA was purified by using IPure kit (Diagenode) and quantified by using Qubit Assays (Thermo Fisher Scientific) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used to prepare libraries and then sequenced by Arraystar (USA, http://www.arraystar.com/).
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. Library Preparation: 10 ng DNA of each sample was converted to phosphorylated blunt-ended with T4 DNA polymerase, Klenow polymerase and T4 polymerase (NEB); An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow (exo minus) polymerase (NEB); Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments using Phusion High Fidelity PCR Master Mix with HF Buffer (Finnzymes Oy). The enriched product of ~200-700 bp was cut out from gel and purified. Sequencing:  The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 4000 according to the manufacturer’s instructions.

treatment_protocol: HFF cells were grown to confluence and infected with RHKU80 single AP2XII-1, AP2XI-2 mAiD or the double AP2-XII-1/AP2XI-2 mAiD strains. Genome-wide Chip sequencing was performed to detect AP2-XII-1 and/or AP2-XI-2, HDAC3, MORC in two conditions; left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours. Harvested intracellular parasites were crosslinked with formaldehyde (final concentration 1%) for 8 mins at room temperature and the crosslinking was stopped by addition of glycine (final concentration 0.125M) for 5 min at room temperature.

tag: strain

tag: chip antibody

value: MORC – Home made antibody (P2)

tag: dev. stage

value: tachyzoites


title: Patient 4999, Lung tumor, Smoker, smoL3, MeDIP

description:
smoL3_mCRF.bedGraph.gz
smoL3_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_4999.bedGraph.gz
DMRs_qv_Patient_4999.bedGraph.gz.tbi

value: NSCLC tumor


title: Patient 6503, Normal lung, Smoker, smoL27, MRE


title: DE33NGSUKBR111905: THP-1 dual WT rep3

value: WT


title: Patient 6503, Lung tumor, Smoker, smoL24, MRE


title: DE60NGSUKBR111904: THP-1 dual WT rep2


title: Patient 6356, Lung tumor, Unconfirmed smoking status, smoL21, MeDIP

value: Unconfirmed smoking status


title: HiC_Brucella_2308_WT_rep2

value: wild type


title: HiC_Brucella_2308_WT_rep1


title: Patient 4999, Normal lung, Smoker, smoL17, MeDIP

description:
smoL17_mCRF.bedGraph.gz
smoL17_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_4999.bedGraph.gz
DMRs_qv_Patient_4999.bedGraph.gz.tbi


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_HDAC3-antibody_IAA24h

description: IAA treated for 24h

value: HDAC3 - Home made antibody (Farhat et al., 2020)


title: Patient 4999, Normal lung, Smoker, smoL17, MRE

value: Smoker


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_MORC-antibody_UT

description: untreated sample


title: DE87NGSUKBR111903: THP-1 dual WT rep1


title: Patient 4796, Lung tumor, Unconfirmed smoking status, smoL7, MRE

description:
smoL7_mCRF.bedGraph.gz
smoL7_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_4796.bedGraph.gz
DMRs_qv_Patient_4796.bedGraph.gz.tbi


title: Patient 6339, Normal lung, Unconfirmed smoking status, smoL25, MeDIP

value: Normal lung


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_Myc-antibody_IAA24h

description: IAA treated for 24h

value: MYC antibody (Cell Signalling)


title: 0% serum HUVEC vPK biol re 2

city: Chapel Hill

first: Xinjun

last: Wu

address: 450 West Drive

institute: UNC-Chapel Hill

data_processing: counts

source_name: Cell line

growth_protocol: 10%, 2% or 0% serum medium culture cells for 24h

extract_protocol: Qiagen Rneasy mini kit

value: Cell line

value: HUVEC

value: hTERT-HUVEC

value: vPK

value: 0% serum 24h


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_HDAC3-antibody_UT

description: untreated sample


title: WGS_Ba2308_WT_rep2

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads were mapped to the combined B. abortus 2308 (NCBI Reference Sequence GCA_000054005.1) by the hiclib pipline.
Assembly: B. abortus 2308 (NCBI Reference Sequence GCA_000054005.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.
Library strategy: WGS

value: Bacterial


title: WGS_Ba2308_WT_rep1

value: Cells were growing in LB, fixed by 3% formaldehyde for 30min at room temperature


title: Patient 4796, Lung tumor, Unconfirmed smoking status, smoL7, MeDIP


title: 0% serum HUVEC vPK biol re 1


title: Patient 4999, Lung tumor, Smoker, smoL3, MRE


title: Patient 8666, Lung tumor, Never-smoker, smoL11, MeDIP

value: Never-smoker


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_Myc-antibody_UT

description: untreated sample

value: tachyzoites


title: ChIP_Anti_MucR_Ba2308_WT_rep2

tag: antibody

value: ChIP using anti-MucR antibodies


title: 0% serum HUVEC EV biol rep 2

value: EV


title: Patient 4796, Normal lung, Unconfirmed smoking status, smoL15, MRE

description:
smoL15_mCRF.bedGraph.gz
smoL15_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_4796.bedGraph.gz
DMRs_qv_Patient_4796.bedGraph.gz.tbi

value: Unconfirmed smoking status


title: ChIP_Anti_MucR_Ba2308_WT_rep1

value: wild type


title: DE97NGSUKBR111917: THP-1 dual ELAVL1-KO rep3

value: Monocyte

value: treated with 1000 U/ml IFNα for 6 h

value: Invivogen (Cat#thpd-nfis)


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_HA-antibody_UT

description: untreated sample

value: HA antibody (Cell Signaling)


title: WGS_Ba2308_deltamucR_rep2

value: mucR deletion


title: Patient 2422, Lung tumor, Former smoker, smoL2, MRE

description:
smoL2_mCRF.bedGraph.gz
smoL2_mCRF.bedGraph.gz.tbi

value: NSCLC tumor

value: Former smoker


title: AP2-XI-2-KD-HA_MORC-antibody_IAA24h

description: IAA treated for 24h

value: MORC – Home made antibody (P2)


title: 2% serum HUVEC vPK biol re 2

value: Cell line

value: HUVEC

value: hTERT-HUVEC

value: vPK

value: 2% serum 24h


title: Patient 2422, Lung tumor, Former smoker, smoL2, MeDIP


title: AP2-XI-2-KD-HA_MORC-antibody_UT

description: untreated sample

value: tachyzoites


title: ChIP_Anti_MucR_Ba2308_deltamucR_rep2

value: Bacterial

value: Cells were growing in LB, fixed by 3% formaldehyde for 30min at room temperature

value: ChIP using anti-MucR antibodies


title: WGS_Ba2308_deltamucR_rep1


title: Patient 2385, Lung tumor, Unconfirmed smoking status, smoL26, MRE

description:
smoL26_mCRF.bedGraph.gz
smoL26_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_2385.bedGraph.gz
DMRs_qv_Patient_2385.bedGraph.gz.tbi

value: Unconfirmed smoking status


title: 2% serum HUVEC EV biol rep 2

value: EV


title: AP2-XI-2-KD-HA_HDAC3-antibody_IAA24h

description: IAA treated for 24h

value: HDAC3 - Home made antibody (Farhat et al., 2020)


title: Patient 2385, Lung tumor, Unconfirmed smoking status, smoL26, MeDIP


title: ChIP_Anti_MucR_Ba2308_deltamucR_rep1


title: Patient 2385, Normal lung, Unconfirmed smoking status, smoL1, MRE

description:
smoL1_mCRF.bedGraph.gz
smoL1_mCRF.bedGraph.gz.tbi
DMRs_qv_Patient_2385.bedGraph.gz
DMRs_qv_Patient_2385.bedGraph.gz.tbi

value: Normal lung


title: AP2-XI-2-KD-HA_HA-antibody_IAA24h

description: IAA treated for 24h

value: HA antibody (Cell Signaling)


title: AP2-XI-2-KD-HA_HDAC3-antibody_UT

description: untreated sample


title: AP2-XII-1-KD-HA_AP2-XI-2-KD-Myc_HA-antibody_IAA24h

description: IAA treated for 24h


title: 2% serum HUVEC EV biol rep 1


title: Lactation_MG

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

country: China

institute: Zhejiang University

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: Bos_taurus ensemblV99
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Bos taurus

source_name: Mammary gland

extract_protocol:
Animals were euthanized by cervical dislocation using a sharp knife in previously numbed individuals within a surgery room to obtain a ~10 g MG sample. Samples then were rinsed in DBPS and quickly transferred into MACS Tissue Storage Solution (NO. 130-100-008, Miltenyi Biotec, Germany) which was stored in a 37°C vacuum container and was quickly taken to the lab. The dissociation of MG was done according to published studies with some modifications described here. In brief, the MG tissue samples were placed in a sterile RNA-free cell culture dish with 1 × PBS (with 5% FBS) and were cut into 5mm pieces. The tissues were then washed using 1 × PBS (with 5% FBS) after removing non-targeted tissues such as white adipose tissue. Subsequently, samples were gently placed in 20mM EDTA (with 5% FBS) which had been incubated at 37°C at 100rpm for 20min. After that, samples were digested with 25U/ml hyaluronidase, 0.5mg/mL CollagenaseⅡ, 0.5 mg/mL Collagenase IV, 25 U/ml DNAse I and 5% FBS in HBSS for 30 min at 37 °C. The mixture was strained through a 70-30 μm cell strainer and transferred into a new EP tube, centrifuged at around 25°C, 300 × g for 5 mins. After removing the supernatant, the cells were washed with 3 mL HBSS (with 5% FBS) and centrifuged at around 25°C at 300 g for 5 mins. The Countess II Automated Cell Counter (AMQAX1000, ThermoFisher, USA) was applied to measure cell number and viability. The requirement for cell viability is greater than 90%. If the viability for isolated cells was lower than the threshold, we used MACS Dead Cell Remove Kit (NO. 130-090-101, Miltenyi biotec, Germany) to remove dead cells by following the manufacturer’s recommendations.
Single-cell RNA-Seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3' Gel Bead and Library V3 Kit."
Single-Cell RNA-Seq

tag: breed

value: Holstein dairy cow

value: mammary gland

tag: developmental stage

value: adult


title: 10% serum HUVEC vPK biol re 2

value: Cell line

value: 10% serum 24h


title: 0% serum HUVEC EV biol rep 1

value: HUVEC

value: hTERT-HUVEC

value: 0% serum 24h


title: AP2-XI-2-KD-HA_HA-antibody_UT

description: untreated sample

value: tachyzoites


title: 10% serum HUVEC vPK biol re 1

value: vPK


title: 2% serum HUVEC vPK biol re 1

value: 2% serum 24h


title: AP2-XII-1-KD-HA_MORC-antibody_IAA24h

description: IAA treated for 24h

value: MORC – Home made antibody (P2)


title: 10% serum HUVEC EV biol rep 2


title: 10% serum HUVEC EV biol rep 1


title: AP2-XII-1-KD-HA_MORC-antibody_UT

description: untreated sample


title: FoxP3-LAP+ cells

city: Indianapolis

first: Moanaro

last: Biswas

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University

description: 10X Genomics

data_processing:
CellRanger 5.0.1 (http://support.10xgenomics.com/) was implemented to demultiplex raw base sequence files into sample specific FASTQ files, which were then aligned to the mouse reference genome mm10 using RNAseq aligner STAR. Aligned reads were traced to individual cells and gene expression levels were quantified based on the number of UMIs detected. The filtered barcode matrices were used for further analysis. SoupX 1.5.2 was used to remove ambient RNA42. Low quality cells were excluded based on the following criteria: unique features/gene counts >2500<500, >10% reads mapped to the mitochondrial genome.
Assembly: mm10
Supplementary files format and content: HDF5 file of filtered gene-barcode matrices

source_name: Spleen

extract_protocol:
Spleens were harvested and CD4+ T cells magnetically isolated. Cells were stained with CD25 (FoxP3) and LAP antibodies and sorted into FoxP3-LAP+ or FoxP3+ populations using FACS Aria II.
Approximately 10,000 targeted cell recovery per sample was applied to a single cell master mix with lysis buffer and reverse transcription reagents, following the Chromium NextGEM Single Cell 3’ Reagent Kits User Guide, CG000204 Rev D (10X Genomics, Inc, Pleasanton, CA). Along with the single cell gel beads and partitioning oil, the single cell master mixture containing the single cell suspension was dispensed onto a Single Cell Chip G in separate wells, and the chip loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer and Qubit. The resulting barcoded libraries were pooled in equal molarity and sequenced in a custom program for 28bp plus 91bp paired-end sequencing on Illumina NovaSeq 6000 (Illumina, Inc). Approximately 50K reads per cell were generated.

treatment_protocol: Oral gavage factor VIII expressing lettuce and intravenous injections with factor VIII

value: Spleen

value: Primary cells

value: CD4+ T cells

value: BALB/c F8e16-/-


title: FoxP3 cells, split into FoxP3+LAP- and FoxP3+LAP+

description: 10X Genomics

value: Oral gavage factor VIII expressing lettuce and intravenous injections with factor VIII


title: ciji_3: Osteoclast precursor cells 2 treated with DKK1

city: Shanghai

first: Xin

last: Niu

address: 500 Dongchuan Road

institute: East China Normal University

data_processing:
Adaptor sequence and low quality reads were trimmed by fastp and then  clean reads were mapped to reference (mm10) using Hisat2.
Read counts were normalized using TMM normalization and CPM (count per million mapped reads) were calculated to create a matrix of normalized expression values.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Gene.diffexp_res table include differentially-expressed genes analysis results such as FPKM values for every gene and every sample.

source_name: Osteoclast precursor cells

extract_protocol:
Total RNA was harvested using Trizol reagent, and Nanodrop 2000 was used to detect the concentration and purity of the extracted RNA, agarose gel electrophoresis to detect RNA integrity, and Agilent 2100 to determine the RIN value. A single library building requires that the total amount of RNA is not less than 5μg, the concentration is ≥ 200ng/μL, and the OD260/280 is between 1.8~2.2
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteoclast precursor cells from two wild type mice (C57BL/6) treated with or without DKK1 (200 ng/ml) for 3 hours.

value: DKK1 (200 ng/ml) for 3 hours

value: wild type

value: Osteoclast precursor cells


title: AP2-XII-1-KD-HA_HDAC3-antibody_IAA24h

description: IAA treated for 24h

value: HDAC3 - Home made antibody (Farhat et al., 2020)


title: Momet2_2

city: Nanjing

first: Huimin

last: Li

state: Jiangsu

address: No. 1, Weigang,Xiaolingwei Street, Xuanwu District

department: Department of Plant Pathology

institute: College of Plant Protection, Nanjing Agricultural University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: http://ftp.ensemblgenomes.org/pub/fungi/current/fasta/magnaporthe_oryzae/,http://ftp.ensemblgenomes.org/pub/fungi/current/gtf/magnaporthe_oryzae/
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Pyricularia oryzae

source_name: mycelium

extract_protocol:
Grind with a sterile mortar
Total RNA was isolated using DP441 (QIAGEN) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: mycelium

value: Momet2 knockout


title: Momet2_1


title: control_3: Osteoclast precursor cells 2 treated with PBS

value: PBS for 3 hours


title: Patient 4796, Normal lung, Unconfirmed smoking status, smoL15, MeDIP

value: Normal lung

value: Unconfirmed smoking status


title: Newborn_MG

value: Holstein dairy cow

value: mammary gland

value: newborn


title: Foxp2_mPFC_KASH_Saline_control_2

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
The raw sequencing reads were processed by Trim Galore with parameter: --nextera -q 20 --length 30 –paired, to trim the adaptors and remove low quality reads. Then the clean reads were mapped to mouse reference genome (mm10) by hisat2 (Version 2.2.1) with the default parameters. After converting aligned SAM to BAM files using Samtools (Version 1.13), featureCounts (Version 2.0.1) was used to generate the read counts matrix. Then, the matrix was input to edgeR (Version 3.32.1). Then the library size was normalized by TMM (calcNormFactors). Next, exactTest was used to compute genewise exact tests for expression differences between the two groups. Finally, the genes with fold change > 1.2 and p value < 0.05 were defined as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Gene expression matrix

molecule: polyA RNA

source_name: Brain

extract_protocol:
RNA from 10,000 sorted nuclei was extracted from TRIzol with the Direct-zol RNA Microprep Kit (Zymo), and the RNA from each sample was eluted in 10 μl of RNase-free water. The Smart-seq V4 Kit (Takara) was then used for RNA-seq library preparation.
The RNA was then used for cDNA generation with nine PCR cycles to amplify the cDNA. After measuring the cDNA concentration (Qubit dsDNA HS Assay Kit, Thermo Gisher Scientific) and quantifying control with Bioanalyzer 2100 (Bioanalyzer High Sensitivity DNA Analysis, Agilent), 300 ng of cDNA was used for library preparation with the Nextera XT DNA library preparation Kit (Illumina).

value: Brain

tag: brain region

value: mPFC

value: Foxp2 positive neurons

value: Saline


title: Foxp2_mPFC_KASH_Saline_control_3


title: Foxp2_mPFC_KASH_CFA_treatment_3

value: CFA


title: AP2-XII-1-KD-HA_HDAC3-antibody_UT

description: untreated sample

value: tachyzoites


title: ciji_2: Osteoclast precursor cells 1 treated with DKK1

value: DKK1 (200 ng/ml) for 3 hours

value: wild type


title: Patient 2385, Normal lung, Unconfirmed smoking status, smoL1, MeDIP


title: Foxp2_mPFC_KASH_CFA_treatment_2


title: AP2-XII-1-KD-HA_HA-antibody_IAA24h

description: IAA treated for 24h

value: HA antibody (Cell Signaling)


title: Guy11_1

value: mycelium

value: WT


title: control_2: Osteoclast precursor cells 1 treated with PBS

value: PBS for 3 hours

value: Osteoclast precursor cells


title: Foxp2_mPFC_KASH_CFA_treatment_1


title: AP2-XII-1-KD-HA_HA-antibody_UT

description: untreated sample


title: Foxp2_mPFC_KASH_Saline_control_1


title: Guy11_2


title: LQ22

status: Public on Sep 15 2023

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

source_name: FFPE tumor sample

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: gender

value: female

value: primary luminal breast cancer

tag: loco-regional recurrence

value: EARLY

tag: disease state

value: luminal breast cancer


title: LQ18

tag: tissue

value: INTERMEDIATE


title: LQ24


title: LQ25


title: LQ17


title: LQ16


title: LP93

value: LATE


title: LQ14


title: LQ13


title: LP94


title: LQ11


title: LQ20


title: LQ10


title: LQ12


title: LQ15


title: LP96


title: LQ21


title: LP97


title: LQ06


title: LQ19


title: LP95


title: LQ05


title: LQ01


title: LQ09


title: LQ08


title: LQ04


title: LQ02


title: LP98


title: LP92


title: LQ03


title: LP90


title: LP89


title: LP87


title: LP86


title: LP84


title: LP79


title: LP82


title: LP80


title: LP69


title: LP78


title: LP76


title: LP77


title: LP66


title: LP73


title: LP74


title: LP71


title: LP70


title: LP68


title: KE81


title: LP72


title: KE74


title: KE80


title: KE79


title: LP67


title: KE73


title: KE78


title: KE76


title: KE75


title: bovine, Mtb, scRNAseq

city: Gliwice

first: Anna

last: Papiez

address: Akademicka 16

department: Department of Data Science and Engineering

country: Poland

institute: Silesian University of Technology

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38; bt12
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
PBMCs sample from cattle and human were isolated using pancoll (Pan-Biotech) gradient density centrifugation following the manufacturer’s protocol. Purified PBMCs were counted using a Neubauer chamber and resuspended in RPMI-1640 + 10% FCS at a concentration of 1 - 5x10^6 PBMCs / ml medium for downstream applications.  Cells were rested overnight at 37°C and 5% CO2 before stimulation with 10 µg/ml Mtb H37Rv whole cell lysate (BEI Resources Repository NIAID) for 3h at 37°C and 5 %CO2. Control samples were left untreated. For qPCR CD14+ monocytes were isolated using an anti-human CD14 antibody (Biolegend, Clone: M5E2) or an anti-bovine CD14 antibody (Kingfisher Biotech, Clone: CAM66A) using magnetic-based enrichment.
Library quality and concentration was assessed by Bioanalyzer (Agilent Technology) and the KAPPA library quantification kit (Roche) following the manufacturer’s instructions. Libraries were pooled and sequenced using a on an Illumina HiSeq1500 instrument using paired-end sequencing (26 bp Read 1 and 98 bp Read 2) with a single sample index (8bp i7 index) and using a HiSeq Rapid SBS Kit V2 (Illumina).

value: PBMC

value: blood

value: Mycobacterium tuberculosis


title: KE71


title: KE69


title: KE72


title: KE77


title: KE66


title: KE68


title: KE62


title: KE61


title: KE63


title: KE64


title: KE67


title: human, Mtb, scRNAseq

description: 10x Genomics


title: KE60


title: KE65


title: KE58


title: KE70


title: 41I

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

institute: National Research Institute of Animal Produstion

data_processing:
Quality control (fastQC)
Filtration of low quality reads (phred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
Mapping with default options (Tophat)
Counting reads to Ensembl GTF version 95 intervals (htseq-count) and differential expresion calculated with the use of Deseq2
Assembly: Sscrofa11.1
Supplementary files format and content: DATE-DESeq2-results-with-normalized_ano.xlsx

organism: Sus scrofa domesticus

source_name: Lung

extract_protocol:
Collected tissues were stored at -80°C. RNA was isolated from 10 lung samples (5 samples from group 1 and 5 samples from group 2, only female) using PureLink™ RNA Mini Kit (Invitrogen, USA).
QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) with 100ng/ul total RNA was used to construct sequencing libraries.

value: Lung

tag: Sex

value: Standard cholecalciferol


title: 59II

value: Increased cholecalciferol


title: 51II


title: 9I


title: 3II


title: 33I


title: 3201_Col1a2-HET

city: Cincinnati

first: Jeffery

middle: D

last: Molkentin

state: Ohio

address: 240 Albert Sabin Way MLC 7020

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from control Col1a2+/- (heterozygous) heart

hyb_protocol: 3.0 ug of fragmented cDNA were hybridized to Clariom S Arrays, Mouse (Applied Biosystems). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Applied Biosystems and contained in the Genechip Hybridization Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create .sst-rma-gene-full.chp files.

label: biotin

source_name: Whole heart harvested from euthanized mouse

label_protocol: The GeneChip 3’ IVT Pico Reagent Kit is used to create biotin – labeled double -strand cDNA targets for hybridization to the Clariom S Arrays, Mouse.

extract_protocol:
cell isolation protocol: Whole hearts were harvested from euthanized mice and flash-frozen
Trizol-based extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain background

value: Col1a2 +/- (heterozygous)

value: Heart


title: 27II


title: 3294_Col1a2-HET

tag: genotype


title: 19II

tag: treatment


title: 2767_Col1a2-KO

description: Gene expression data from experimental Col1a2-/- (homozygous knockout) heart

value: Col1a2 -/- (homozygous knockout)


title: 3200_Col1a2-KO


title: LP81


title: KE56


title: KE54


title: KE49


title: 2770_Col1a2-KO


title: KE55


title: 2769_Col1a2-HET


title: KE51


title: KE50


title: KE52


title: KE59


title: 17I


title: KE48


title: KE47


title: KE57


title: APP-NLGF/RAG2 KO_(18M)_replicate-3

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

data_processing:
Reads were aligned to a combined human GRCh38 and mouse mm10 reference (build 102) using STAR, and counted using SubRead
We filtered out genes with a mean read count < 5
Raw counts were normalized using edgeR v3.34, specifically a weighted trimmed mean of M values (TMM)
Genome_build: GRCh38 + mm10
Supplementary_files_format_and_content: xNeurons_human_rawCounts.tsv
Supplementary_files_format_and_content: xNeurons_mouse_rawCounts.tsv

organism:
Homo sapiens
Mus musculus

source_name: H9-stem cell derived neurons (grafted)

growth_protocol: H9 sem cells were grown in E8-flex media (Thermo). H9 stem cells were differentiated into neuronal progenitors using the shi et al., 2012 protocol (PMID: 22976355).

extract_protocol:
Total RNA was isolated using RNeasy.
Libraries were prepared by BGI TECH SOLUTIONS (HONGKONG) CO., LIMITED and sequenced on DNBSEQ plattform.

treatment_protocol: No treatments were performed. Grafts from control and amyloid mice were dissected at indicated time points. Mice were euthanized using cervical dislocation. Brain samples were dissected and sliced into 1 mm thick sections using a brain matrix. Brian sections were transferred to an ice-cold PBS with RNAase inhibitors. GFP positive regions were dissected out under a fluorescent dissection microscope and snap-frozen in liquid nitrogen.

tag: ID

tag: age

value: M


title: KE46


title: KE45


title: KE44


title: APP-NLGF/RAG2 KO_(18M)_replicate-1


title: RAG2 KO_(18M)_replicae-4


title: RAG2 KO_(18M)_replicae-3


title: APP-NLGF/RAG2 KO_(18M)_replicate-4


title: APP-NLGF/RAG2 KO_(18M)_replicate-2


title: RAG2 KO_(18M)_replicae-1


title: APP NLGF/RAG2 KO_(2M)_replicate-7

value: F


title: RAG2 KO_(18M)_replicae-2


title: APP NLGF/RAG2 KO_(2M)_replicate-6


title: KE53

value: female


title: APP NLGF/RAG2 KO_(2M)_replicate-4


title: APP NLGF/RAG2 KO_(2M)_replicate-3


title: KE43

value: primary luminal breast cancer


title: APP NLGF/RAG2 KO_(2M)_replicate-2


title: KE35

value: EARLY


title: APP NLGF/RAG2 KO_(2M)_replicate-1


title: KE40

value: luminal breast cancer


title: RAG2 KO_(2M)_replicate-5


title: KE41


title: KE38


title: KE37

value: INTERMEDIATE


title: KE34


title: KE33

value: LATE


title: RAG2 KO_(2M)_replicate-4


title: KE39


title: KE32


title: RAG2 KO_(2M)_replicate-3


title: KE42


title: KE36


title: APP NLGF/RAG2 KO_(2M)_replicate-5


title: RAG2 KO_(2M)_replicate-2


title: KE30


title: KE29


title: KE28


title: KE31


title: RAG2 KO_(6M)_replicate-5


title: KE27


title: Morex, irrigated, mock, 96hpi, rep2

city: Freising

first: Ralph

last: Hückelhoven

address: Emil-Ramann-Str. 2

department: Chair of Phytopathology

institute: Technische Universität München

data_processing:
Data processing steps for the CPM_Horvu_Morex_V2
The quality of the raw RNAseq data was analyzed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The trimming step was done with Trimmomatic using the parameters ILLUMINACLIP:Illumina-SE.fasta:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40.
We used Hisat2 with  parameters -U --rna-strandness FR to map the trimmed data to the Morex v2 assembly. In order to add an artificial 3’UTR because of the 3’-RNAseq reads, we used a custom script to elongate the last exon either by 3 kb or until the next gene in the gff file of Morex v2.
The counts of the generated bam files were assigned to genes using featureCounts with the parameters -t gene -s 1 -M -O.
CPM values were calculated using edgeR with "calcNormFactors" and "cpm( log = FALSE, normalized.lib.sizes = TRUE)"

Data processing steps for the CPM_Horvu_Morex_V3 and CPM_Fusarium_culmorum_UK99
The RNAseq data was analyzed using the nf-core/rnaseq pipeline version 3.9 with default settings. An artificially merged genome was used for mapping consisting of MorexV3 and Fc-UK99
The gene counts were split again into the two species and CPM values were calculated separately for each species using edgeR with "calcNormFactors" and "cpm( log = FALSE, normalized.lib.sizes = TRUE)"

Assembly: MorexV2 (Mascher et al., 2019), MorexV3 (Mascher et al., 2020), Fc UK99 (Urban et al., 2016)

Supplementary files format and content: CPM_Horvu_Morex_V2.csv is a comma-separated file containing the counts per million values for all samples, mapped against MorexV2
Supplementary files format and content: CPM_Horvu_Morex_V3.csv is a comma-separated file containing the counts per million values for all samples, mapped against MorexV3
Supplementary files format and content: CPM_Fusarium_culmorum_UK99.csv is a comma-separated file containing the counts per million values for all samples, mapped against Fusarium culmorum UK99

organism: Hordeum vulgare

source_name: spike

growth_protocol: The pots were placed on flooding tables for daily automatic watering and with additional lightning for 16 h per day. Plants were held upright with support devices and were randomized twice a week to assure uniform growth. Temperature was set to 18 °C (day) and 16 °C (night) with a relative air humidity of 60 %. Drought conditions were set on by a stop of automatic watering on separate flooding tables. To prevent plants from early and premature plant death due to fast desiccation of the substrate, each pot received little amounts of water (50 - 100 ml) in the first three days after stopping daily irrigation.

extract_protocol:
Each individual spike sample of each biological triplicate per treatment variation was divided into two pieces using one part for individual RNA extraction. After separation, the spike samples were immediately ground in liquid nitrogen and stored at minus 70 °C. RNA extraction was performed with Direct-zol RNA Miniprep Plus Kit (ZymoResearch, USA) according to manufacturer’s protocol.
Preparation of libraries for 3’mRNA sequencing was carried out with Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit (FWD) (Lexogen, Austria) for Illumina sequencing according to manufacturer’s protocol. Quantification of input RNA was conducted with Qubit Fluorometer 2.0 (Invitrogen, USA) and Qubit RNA BR (broad range) Assay Kit (Invitrogen, USA) according to manufacturer’s protocol in a range of 10 to 1200 ng total RNA. Quantification of library size was performed with Qubit Fluorometer 2.0 und Qubit DNA High Sensitivity Assay Kit (Invitrogen, USA). A check for distribution of mRNA fragment size of each library was performed with am Agilent 2100 Electrophoresis Bioanalyzer (Agilent Technologies, USA). Final quantification of each library was determined according to Illumina qPCR guide with a KAPA SYBR Fast Mastermix Low ROX (Peqlab, Germany) in a QuantStudio 5 real-time PCR system (Applied Biosystems, USA). Final libraries were normalized with elution buffer (Qiagen, Germany) to a final concentration to 2 nM and pooled with an equal amount of each sample library. Denaturation and dilution of libraries for HiSeq Clustering was performed according to protocol A of user guide (Illumina) with a concentration for clustering of 10 pM.

treatment_protocol: Fugal inoculum was cultured and propagated according to Linkmeyer et al. (2013). Therefore, three isolates of F. culmorum (Fc002, Fc03, Fc06 – culture collection, Chair of Phytopathology, Technical University of Munich) and three isolates of F. avenaceum (Fa002, Fa02, Fa04 – culture collection, Chair of Phytopathology, Technical University of Munich) known to strongly infect barley spikes and to produce DON (Linkmeyer et al., 2013; Hofer et. al., 2016, Hoheneder et al., 2022) were used in equal amounts. Spore solution was adjusted to 50.000 conidia per ml tap water and contained 1 ml/L Tween 80 to improve wetting of the spike tissue. The respective mock solution contained the same amount of Tween 80. The spikes of the plants were sprayed with handheld spray flasks till run-off either with F. culmorum spore solution or mock solution. To maintain optimal moist conditions for infection (99 % relative air humidity), spikes were covered and sealed with transparent polythene bags for two days. Respective mock sprayed plants were similarly treated. 48h and 96h after inoculation, individual spikes were cut from each pot and flash frozen in liquid nitrogen.

tag: cultivar

value: Morex

value: spike

tag: abiotic stress

value: irrigated

tag: inoculation

value: Mock

tag: harvest time point [hpi]


title: RAG2 KO_(6M)_replicate-2


title: RAG2 KO_(6M)_replicate-1


title: RAG2 KO_(2M)_replicate-1


title: Morex, irrigated, F.avenaceum, 96hpi, rep3

value: Fusarium avenaceum


title: Morex, irrigated, mock, 96hpi, rep1


title: RAG2 KO_(6M)_replicate-4


title: RAG2 KO_(6M)_replicate-3


title: Morex, irrigated, mock, 96hpi, rep3


title: KE24


title: Morex, irrigated, F.avenaceum, 96hpi, rep2


title: Morex, irrigated, F.avenaceum, 96hpi, rep1


title: APP NLGF/RAG2 KO_(6M)_replicate-4


title: APP NLGF/RAG2 KO_(6M)_replicate-5


title: KE26


title: KE25


title: Morex, irrigated, F.culmorum, 96hpi, rep2

value: Fusarium culmorum


title: Morex, irrigated, F.culmorum, 96hpi, rep1


title: KE23


title: Morex, drought, mock, 96hpi, rep3

value: drought


title: APP NLGF/RAG2 KO_(6M)_replicate-1


title: KE22


title: INPUT_MA_1617

city: Barcelona

first: Adria

last: Caballe

address: C/ Baldiri Reixac 10

department: biostatistics

country: Spain

institute: IRB

description: Input in MAF over-expressing MCF7 cells

data_processing:
Sequence reads of human with fly spike-in samples were mapped to the human + fruit fly genome (hg19+dm3) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak detection was performed with MACS (PubMed ID 18798982)
Assembly: hg19/dm3
Supplementary files format and content: Tab delimeted files with macs peaks

source_name: MCF7-MAF OE

growth_protocol: Four 15 cm plates of control and MAF-overexpressing MCF7 cells per condition were prepared at 70-80% confluency. Cells were cultured in hormone-deprived medium [phenol-red free DMEM (Gibco) supplemented with 5% charcoal-stripped FBS (Capricorn Scientific), glutamine 0.29 mg/mL, penicillin 100 units/mL and streptomycin 0.1 mg/mL for 72 h before E2 (10 nM, Sigma-Aldrich) or ethanol (vehicle) addition.

extract_protocol:
Cells were crosslinked in 1% formaldehyde in DMEM for 10 min at RT. Next, glycine was added to a final concentration of 0.125 M and cells were incubated for 5 min at RT to stop the fixation. After two washes with ice-cold PBS, cells were harvested by gently scrapping on ice and centrifuged at 3,000 x g for 5 min. Pellets were stored at 80ºC until use.  Chromatin preparation: cells were lysed in hypotonic lysis buffer (5mM Pipes pH 8; 85mM KCl; 0.5% NP40; plus protease inhibitors). Nuclei were recovered by centrifugation, lysed in nuclear lysis buffer (50mM Tris HCl pH 8; 1% SDS; 10mM EDTA plus protease inhibitors) and sonicated with a Bioruptor Pico, Diagenode (20 cycles 30” ON, 30” OFF) to yield chromatin fragments of 150-300 bp.   For ChIP experiments, chromatin (25 µg DNA) was diluted 1/10 in ChIP Buffer (16.7mM Tris HCl pH 8; 167mM NaCl; 1.2mM EDTA; 1.1% Triton x100 plus protease inhibitors) and mix with 2% Drosophila Spike-in chromatin. Aliquots were removed as input material (1%). ChIP samples were incubated with the specific antibody (5 µg) plus Spike-in antibody (1µg) overnight 4ºC, and immunoprecipitated with Protein A agarose beads (Diagenode) during 2 h at 4°C. Beads were washed 3 times with low-salt buffer (20mM Tris HCl pH8; 150 mM NaCl; 2mM EDTA; 0.1% SDS; 1% Triton X-100) and once with high-salt buffer (20mM Tris HCl pH8; 400 mM NaCl; 2mM EDTA; 1% Triton X-100; 0.1% SDS). ChIPed material was eluted from the beads in Elution buffer (1% SDS, 100 mM NaHCO3) at 65°C in a shaker (1000 rpm) for 1 h. Eluted material and inputs were de-crosslinked overnight at 65°C, treated with Proteinase K and the DNA purified using the QIAquick PCR purification kit (Qiagen).   The following antibodies were used in the ChIP experiments: H3K4me3 (Diagenode, C15410003); H3K27Ac (Millipore, #07–360); Drosophila H2Av (Active Motif #61686).
Libraries were prepared according to Illumina instructions.

treatment_protocol: E2 (10 nM, Sigma-Aldrich) or ethanol (vehicle) was added 1h prior to fixation

tag: cell line

value: MCF7-MAF OE

tag: cell type

value: MCF7 Breast cancer

tag: chip antibody

tag: agent

value: MAF


title: INPUT_MAE_1618

description: Input in E2 stimulated and MAF over-expressing MCF7 cells


title: Morex, drought, mock, 96hpi, rep2


title: Morex, drought, mock, 96hpi, rep1


title: APP NLGF/RAG2 KO_(6M)_replicate-3

value: F


title: Morex, irrigated, F.culmorum, 96hpi, rep3


title: INPUT_CTE_1616

description: Input in E2 stimulated MCF7 cells


title: INPUT_CT_1615

description: Input in control MCF7 cells

value: CT


title: APP NLGF/RAG2 KO_(6M)_replicate-2


title: Morex, drought, F.culmorum, 96hpi, rep3


title: H3K4me3_MA_1613

description: H3K4me3 sites in MAF over-expressing MCF7 cells

value: Anti-H3K4me3 Diagenode #C15410003 + Anti-H2Av, Active Motif #61686


title: Morex, drought, F.avenaceum, 96hpi, rep1


title: H3K4me3_CT_1611

description: H3K4me3 sites in control MCF7 cells


title: H3K4me3_MAE_1614

description: H3K4me3 sites in E2 stimulated and MAF over-expressing MCF7 cells


title: H3K4me3_CTE_1612

description: H3K4me3 sites in E2 stimulated MCF7 cells


title: Morex, drought, F.avenaceum, 96hpi, rep2


title: Morex, drought, F.culmorum, 96hpi, rep1


title: H3K27ac_CTE_1608

description: H3K27ac sites in E2 stimulated MCF7 cells

value: Anti-H3K27ac, Millipore #07-360 + Anti-H2Av, Active Motif #61686


title: H3K27ac_MAE_1610

description: H3K27ac sites in E2 stimulated and MAF over-expressing MCF7 cells


title: Morex, irrigated, mock, 48hpi, rep3


title: Morex, irrigated, mock, 48hpi, rep2


title: H3K27ac_MA_1609

description: H3K27ac sites in MAF over-expressing MCF7 cells


title: H3K27ac_CT_1607

description: H3K27ac sites in control MCF7 cells

value: Control


title: Morex, irrigated, mock, 48hpi, rep1


title: Morex, irrigated, F.avenaceum, 48hpi, rep3


title: Morex, irrigated, F.avenaceum, 48hpi, rep2


title: Morex, drought, F.avenaceum, 96hpi, rep3


title: Morex, irrigated, F.avenaceum, 48hpi, rep1


title: LPM-Lean-4

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

data_processing:
Sequenced libraries were processed with deepTools, using STAR , for trimming and mapping, and featureCounts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2.
Assembly: mm10
Supplementary files format and content: matrix of raw gene counts per sample

source_name: Lamina Propria

extract_protocol:
RNA was extracted using a RNAqueous-Micro Total RNA Isolation kit (Thermo Fisher Scientific) and quantified using Qubit 2.0 (Thermo Fisher Scientific) following manufacturer instructions.
Libraries were prepared using illumina kits and sequenced with a HiSeq 3000 instrument.

tag: diet

value: Chow

value: Lamina Propria

tag: sorted cell

value: CX3CR1hi MHCII+ CD45+ CD11b+ CD64+

tag: time point

value: 12 weeks


title: LPM-Lean-3

tag: tissue


title: Morex, drought, F.culmorum, 96hpi, rep2

value: Morex

value: spike


title: Morex, irrigated, F.culmorum, 48hpi, rep3

value: irrigated


title: LPM-Lean-2


title: LPM-Lean-1


title: Morex, irrigated, F.culmorum, 48hpi, rep2

value: Fusarium culmorum


title: LPM-HFD-4

value: High fat diet


title: LPM-HFD-3


title: Morex, irrigated, F.culmorum, 48hpi, rep1


title: Morex, drought, mock, 48hpi, rep3

value: drought

value: Mock


title: Morex, drought, mock, 48hpi, rep2


title: Morex, drought, mock, 48hpi, rep1


title: LPM-HFD-1


title: SD_P_20_39_3

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description:
porcine myoblasts
The isolation of satellite cells from the M. rhomboideus of ten female five- and twenty days old piglets and the establishment and validation of two muscle cell pools (pool 5 (P5) or pool 20 (P20))
For proliferation experiments cells from both pools stored in liquid nitrogen were defrosted and permanently cultured at 35°, 37° (control), 39° or 41°C over a period of 72 h in growth medium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: muscle

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: pool

tag: temperature


title: SD_P_20_41_1


title: SD_P_20_41_3


title: SD_P_20_37_2


title: SD_P_20_37_3


title: Morex, drought, F.avenaceum, 48hpi, rep3

value: Fusarium avenaceum


title: SD_P_20_39_1


title: SD_P_20_37_1


title: Neurons-Diff16-MEG3_replicate_3

data_processing:
Reads were aligned to the human GRCh38 reference (build 102) using STAR, and counted using SubRead
We filtered out genes with a mean read count < 5
Raw counts were normalized using edgeR v3.34, specifically a weighted trimmed mean of M values (TMM)
Genome_build: GRCh38
Supplementary_files_format_and_content: meg3_inVitro_rawCounts.tsv

source_name: H9-stem cell derived neurons

growth_protocol: H9 stem cell-derived neurons were generated using the shi et al, 2012 protocol (PMID: 22976355).

extract_protocol:
Total RNA extracted using Rneasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Mature cortical neurons derived from the H9 stem cells were transduced with lentiviral vectors at DIV68. Seven days post-transduction total RNA was extracted using Rneaasy kit (Qiagen)

value: H9-stem cell derived neurons

tag: meg3 expression

value: yes

tag: differentiation round


title: SD_P_20_35_1


title: SD_P_20_35_2


title: SD_P_5_41_1

value: P 5


title: SD_P_20_35_3


title: SD_P_20_39_2


title: SD_P_5_41_3


title: Morex, drought, F.avenaceum, 48hpi, rep2


title: SD_P_20_41_2


title: SD_P_5_39_2


title: Neurons-Diff16-MEG3_replicate_2

tag: ID


title: LPM-HFD-2


title: SD_P_5_39_3


title: Morex, drought, F.avenaceum, 48hpi, rep1

tag: cultivar


title: Neurons-Diff16-MEG3_replicate_1


title: Neurons-Diff16-control_replicate_3

value: no


title: TET_3

city: Bloomington

first: Richard

last: Hardy

address: 212 S Hawthorne Dr

data_processing:
NextSeq reads were trimmed using fastp (version 0.20.1) with parameters “-l 17 --detect_adapter_for_pe -g -p”
The resulting reads were mapped against GRCh38 using HISAT2 (version 2.2.1) with parameters “--rna-strandness F“
Read counts for each gene were created using featureCounts from the Subread package (version 2.0.2) with the parameters “-O -M --primary -p --largestOverlap -s 0 -B” and Gencode v40 as the annotation
Differential expression analysis was performed using the DESeq2 package (version 1.36.0) in R/Bioconductor (R version 4.2.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample

growth_protocol: C7/10 Aedes albopictus cells were grown at 28 ˚C under 5 % ambient CO2 in 1 X Minimal Essential Media (Corning) supplemented with 10 % heat-inactivated fetal bovine serum (Corning), 1 % L-glutamine (Corning), 1 % non-essential amino acids (Corning), and 1 % antibiotic-antimycotic solution (Corning). Vertebrate baby hamster kidney fibroblast or BHK-21 cells as well as human embryonic kidney epithelial or HEK-293 cells were grown at 37 ˚C under 5 % ambient CO2 in the same 1 X Minimal Essential Media (Corning) as the C7/10 cells. BHK-21 derived viruses were obtained by In Vitro Transcription of pToto1101 SINV full length plasmid using SP6 RNA polymerase (NEB). IVTs were then transfected into confluent BHK cells using LTX transfection mix (Invitrogen), following the manufacturer’s protocol, in a T25 flask (CellStar) with serum free-virus production media (SF-VPM) (Gibco). Four hours post transfection, the SF-VPM was removed and replaced with fresh 1 X MEM supplemented with 10 % FBS. 24 hours post transfection the viral supernatant was harvested and purified by centrifugation at 43,000 x g for 2.5 hours over a 27 % w/v sucrose cushion in HNE buffer (150 mM NaCL, 20 mM HEPES, 0.1 mM EDTA). The media was discarded, and the viral pellet was resuspended in 500 µl of HNE buffer. Plaque assays on BHK-21 cells were then performed to determine viral titer.    C7/10 derived virus was obtained by infecting confluent C7/10 cells in a 150 mm dish (CellStar) with P0 BHK derived virus at an MOI of 0.1 PFU/cell. The inoculum was left on for 3 hours after which the media was replaced, cells washed with 1 X PBS (Phosphate Buffered Saline), and fresh 1 X MEM was added. 48 hours post infection the viral su-pernatant was harvested, purified and plaque assayed as previously described. All vi-ruses were titered on BHK-21 cells and that titer was used for assay on HEK-293 cells

extract_protocol:
RNA was isolated using the BioRad Aurum Total RNA mini kit according to manufacturers protocol
Libraries were prepared by Illumina TruSeq Stranded mRNA LT Sample Prep Kit following the standard manufacturing protocol.  The libraries were analyzed by Agilent 4200 TapeStation, and pooled.  The pooled libraries were loaded on a NextSeq 500/550 High Output v2.5 run with a 75-cycle sequencing module to generate paired-end reads.  The demultiplexing of the reads was performed with bcl2fastq.

treatment_protocol: HEK-293 cells were infected in a 24-well plate with SINV (Toto1101) at an MOI of 5 PFU/cell. Cells were harvested at 8 hours post infection and RNA was isolated using the BioRad Aurum Total RNA mini kit.

tag: treatment

value: infection with viruses of mosquito cells (Tet C7/10)


title: Morex, drought, F.culmorum, 48hpi, rep2

tag: abiotic stress

tag: inoculation


title: TET_1

tag: cell line


title: SD_P_5_39_1


title: TET_2


title: Morex, drought, F.culmorum, 48hpi, rep1

tag: harvest time point [hpi]


title: Neurons-Diff16-control_replicate_1


title: Mock_1

value: Mock infected


title: SD_P_5_41_2


title: Morex, drought, F.culmorum, 48hpi, rep3


title: SD_P_5_37_3


title: SD_P_5_35_3


title: Neurons-Diff15-MEG3_replicate_3


title: Neurons-Diff15-MEG3_replicate_2


title: BHK_2

value: infection with viruses of mammalian cells (BHK)


title: BHK_3


title: Palmella_Blue, irrigated, mock, 96hpi, rep2


title: SD_P_5_37_1


title: Mock_2


title: SD_P_5_37_2


title: Neurons-Diff15-MEG3_replicate_1


title: Palmella_Blue, irrigated, mock, 96hpi, rep3


title: SD_P_5_35_2


title: BHK_1


title: Palmella_Blue, irrigated, mock, 96hpi, rep1


title: Palmella_Blue, irrigated, F.avenaceum, 96hpi, rep3


title: 20230208_MHRNA054_PC9OROTCmp14_Rep1

city: Boston

first: Cigall

last: Kadoch

state: MA

address: 44 Binney St

institute: Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For Cut & Run libraries, the CutRunTools pipeline was used to perform read trimming, quality filtering, alignment, and peak calling using default parameters.
For Cut&Run and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 50 --smoothLength 600 --ignoreDuplicates --samFlagInclude 64). For RNAseq data, tracks were generated using deepTools bamCoverage (--normalizeUsingRPKM).
Assembly: hg19
Supplementary files format and content: Cut&Run and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes. RNAseq bigWig files give the give the normalized coverage of DNA fragments across the genome in RPKM.

source_name: cancer cell line

growth_protocol: PC-9, PC-9_OR, HCC4006, HCC4006_OR, HCC827, and HCC827GR6 were maintained in RMPI-1640 (Gibco) supplemented with 10% fetal bovine serum (GeminiBio) and 1% penicillin-streptomycin (Gibco). PC-9_OR and HCC4006_OR cell lines were generated by continuously culturing the respective parental cell lines in 100 nM osimertinib for at least 2 months before being characterized. Unless stated otherwise, OR lines were maintained in 100 nM osimertinib and the drug was removed for 1 week before use in Cmp14 experiments.

extract_protocol:
ATAC-Seq: The Omni-ATAC protocol (Corces et al., 2017) was used with slight modifications as follows. 100,000 cells per condition were used and washed with PBS before lysis. Cell pellets were lysed in 50μl of cold ATAC-seq resuspension buffer containing 10mM Tris–HCl pH 7.4, 10mM NaCl and 3mM MgCl2, supplemented with fresh NP-40 (final 0.1% v/v), Tween-20 (final 0.1% v/v) and digitonin (final 0.01% v/v) for 3–5min on ice. Next cells were washed with 1ml of resuspension buffer supplemented with Tween-20 (final 0.1% v/v) and pelleted at 500g for 10min at 4 °C. Cell pellets were resuspended in 50μl of transposition reaction mix containing 25μl of 2× TD buffer, 2.5μl of transposase, 16.5μl of 1× PBS, 0.5μl of 1% digitonin (final 0.01% v/v), 0.5μl of 10% Tween-20 (final 0.1% v/v) and 5μl of nuclease-free water. The transposition reaction was incubated at 37 °C for 30min with constant shaking on a thermomixer. The Qiagen MinElute Reaction Cleanup Kit was used for DNA purification. A standard ATAC-seq amplification protocol with 5-7 cycles of amplification was used to amplify the tagmented library (Buenrostro et al., 2015).
RNA-Seq: One million cells were harvested from from PC9*, HCC4006 and HCC827* parental and osi- or gefitinib- resistant cell line pairs and washed with cold PBS to remove trypsin and stored in RLT buffer (Qiagen) until further processing. RNA was purified using the Qiagen RNeasy kit, and further processed using the Illumina NEBNext Ultra II Directional RNA Library Prep Kit.
CUT&RUN: 500,000 cells per sample were harvested from PC9*, HCC4006 and HCC827* parental and osi- or gefitinib- resistant cell line pairs. CUT&RUN was performed following EpiCypher’s protocol within their CUTANA ChIC/CUT&RUN kit with slight modifications to day 1. Prior to wash steps, cells were lysed using a nuclear extraction buffer 20mM HEPES–KOH, pH 7.9, 10mM KCl, 0.1% Triton X-100 and 20% glycerol, supplemented with fresh 0.5mM spermidine, and cOmplete Mini, EDTA-free protease inhibitor. Next, cells were pelleted at 500g for 3 mins. Cell pellets were then washed using protocol’s permeabilization buffer and subsequently incubated with activated Concanavalin A beads at room temperature for 15 mins. Next, beads were mixed in Antibody Buffer and incubated with appropriate primary antibodies overnight (antibodies in key resource table).
CUT&RUN libraries were prepared with Epicypher's CUTANA ChIC/CUT&RUN Library Prep Kit and sequenced on Illumina Next-seq 500 using 37 bp paired-end sequencing parameters.     ATAC-seq samples were sequenced on Illumina NovaSeq 6000 Next Gen Sequencing using 37 bp paired-end sequencing parameters.    RNA-seq libraries were prepared using NEBnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on Illumina Next-seq 500 using 75 bp single-end sequencing parameters.

treatment_protocol: PC9* and PC9-OR* cells were treated with DMSO, 1uM Compound 14 (Cmp14), 100nM Osimertinib (Osi) and 100nM Osimertinib + 30nM Trametinib (OT) for 24hrs before harvesting for ATAC-seq and RNA-seq. The PC9-OR* cells were washed to remove continuous Osimertinib growth media for 7 days prior to experimental setup and then re-challenged with Osi or OT as appropriate.

tag: genotype

value: EGFR E746-A750del

tag: antibody


title: Mock_3


title: 20230208_MHRNA055_PC9OROTCmp14_Rep2


title: 20230208_MHRNA053_PC9OROT_Rep2


title: Neurons-Diff15-control_replicate_3


title: 20230208_MHRNA052_PC9OROT_Rep1


title: Palmella_Blue, irrigated, F.avenaceum, 96hpi, rep2


title: SD_P_5_35_1


title: 20230208_MHRNA051_PC9ORCmp14_Rep2


title: Neurons-Diff16-control_replicate_2


title: Neurons-Diff15-control_replicate_2


title: 20230208_MHRNA050_PC9ORCmp14_Rep1


title: Palmella_Blue, irrigated, F.avenaceum, 96hpi, rep1


title: Neurons-Diff15-control_replicate_1


title: spleen apoptotic iso, rep1 [AI]

city: Chicago

first: Samantha

middle: L

last: Schroth

state: IL

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
spleens were collagenase D and DNAse I digested and subjected to independent CD45+ and pan DC magnetic enrichment and re-pooled at a 1:1 ratio per condition
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, single cells from splenic cell suspenion were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: spleen

tag: strain

value: Apoptotic iso (B6) splenic cell infusion


title: Palmella_Blue, irrigated, F.culmorum, 96hpi, rep3

value: spike


title: spleen, live iso, rep1 [LI]

description: 10x Genomics

value: Live iso (B6) splenic cell infusion


title: 20230208_MHRNA048_PC9ORDMSO_Rep1


title: Palmella_Blue, irrigated, F.culmorum, 96hpi, rep1

value: irrigated

value: Fusarium culmorum


title: Palmella_Blue, irrigated, F.culmorum, 96hpi, rep2


title: 20230208_MHRNA043_PC9Cmp14_Rep2


title: 20230208_MHRNA049_PC9ORDMSO_Rep2


title: 20230208_MHRNA042_PC9Cmp14_Rep1


title: Palmella_Blue, drought, mock, 96hpi, rep3

value: drought


title: Palmella_Blue, drought, mock, 96hpi, rep2

value: Mock


title: spleen, control, rep1 [C]

description: 10x Genomics

value: Saline IV infusion


title: spleen, live allo, rep1 [LA]

description: 10x Genomics

value: Live allo (Balbc) splenic cell infusion


title: 20230208_MHRNA041_PC9DMSO_Rep2


title: 20230208_MHRNA046_PC9OTCmp14_Rep1


title: 20230208_MHRNA040_PC9DMSO_Rep1


title: 20230206_CGATAC170_PC9_OR_OTandCmp14_Rep1


title: 20230206_CGATAC171_PC9_OR_OTandCmp14_Rep2


title: Palmella_Blue, drought, mock, 96hpi, rep1


title: 20230208_MHRNA045_PC9OT_Rep2


title: 20230208_MHRNA047_PC9OTCmp14_Rep2


title: 20230208_MHRNA044_PC9OT_Rep1


title: spleen, apoptotic allo, rep1 [AA]

description: 10x Genomics

value: Apoptotic allo (Balbc) splenic cell infusion


title: 20230206_CGATAC169_PC9_OR_OT_Rep2


title: 20230206_CGATAC168_PC9_OR_OT_Rep1


title: arf1 2

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

institute: UMass Medical School

data_processing:
RNA for deep sequencing was purified by Qiagen RNAeasy. Duplicate samples were sent for library construction and sequencing at BGI (China)
Raw sequencing reads were processed using anin-house RNA-Seq data processing softwareDolphinat University of Massachusetts Medical School
The raw read pairs were firstaligned to C. elegansreference genome with ws245 annotation. The RSEM method was used to quantify the expression levels ofgenes
Deseq was used to produce differentially expressed gene sets with more than a 2-fold difference in gene expression, with replicates being within 0.05 in a Students T test and a False Discovery Rate (FDR) under 0.01.
Statistics were calculated with DeBrowser
Assembly: ce11 with ws254 notations
Supplementary files format and content: abundance measurements

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole worm

value: Wild type

value: RNAi


title: Palmella_Blue, drought, F.avenaceum, 96hpi, rep2

value: Fusarium avenaceum


title: 20230206_CGATAC166_PC9_OR_Cmp14_Rep1


title: 20230206_CGATAC167_PC9_OR_Cmp14_Rep2


title: Empty Vector 2 (Control)

value: Control


title: 20230206_CGATAC163_PC9_OTandCmp14_Rep2

value: EGFR E746-A750del


title: Palmella_Blue, drought, F.avenaceum, 96hpi, rep3


title: Empty Vector 1 (Control)


title: 20230206_CGATAC161_PC9_OT_Rep2


title: 20230206_CGATAC160_PC9_OT_Rep1


title: 20230206_CGATAC164_PC9_OR_DMSO_Rep1


title: Palmella_Blue, drought, F.avenaceum, 96hpi, rep1


title: Palmella_Blue, drought, F.culmorum, 96hpi, rep2


title: arf1 1


title: 20230206_CGATAC162_PC9_OTandCmp14_Rep1


title: Palmella_Blue, drought, F.culmorum, 96hpi, rep3


title: 20230206_CGATAC158_PC9_Cmp14_Rep1


title: Palmella_Blue, irrigated, mock, 48hpi, rep3


title: 20230206_CGATAC156_PC9_DMSO_Rep1


title: Palmella_Blue, drought, F.culmorum, 96hpi, rep1


title: KO2

city: Rochester

first: Harmeet

last: Malhi

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description: Gene expression of IHLs from RAGE-MKO type mouse fed a FFC diet.

hyb_protocol: Hybridization was done according to the manufacturer's instructions.

scan_protocol: Gene expression was quantified on the nCounter Digital Analyzer (NanoString Technologies).

data_processing: Raw data was normalized in the nSolver Analysis Software (NanoString Technologies) by the geometric mean of 10 housekeeping genes and 6 positive controls.

source_name: Intrahepatic leukocytes

label_protocol: 100 ng of each total RNA sample was labeled according to the manufacturer's instructions.

growth_protocol: Ragefl/fl mice were crossed with LyzM-Cre transgenic mice (Jackson Laboratory) in which the Cre recombinase is expressed under the control of an endogenous lysozyme 2 gene (Lyz2) promoter. The LyzM-Cre approach has been used to specifically target myeloid subsets as this leads to deletion of floxed genes in bone marrow derived macrophages but not embryonic liver resident macrophages. RAGE myeloid-specific knockout (Ragefl/fl;LyzM-Cre/0), referred to as RAGE-MKO, and littermate wild type controls (WT, RAGEfl/fl;0/0) were fed either chow or FFC for 6 months to induce NASH.

extract_protocol: Liver tissue was dissociated with the mouse liver dissociation kit (Miltenyi Biotec, Bergisch Gladbach, Germany) and the gentleMACS Dissociator (Miltenyi Biotec) following manufacturer’s protocols. The enzymatically digested liver was passed through a 40 μm filter to remove debris and cell clusters. The filtered dissociate was centrifuged and IHLs were isolated by Percoll-density gradient centrifugation. Isolated RNA quantity and quality were assessed with a NanoDrop ND1000 (ThermoScientific, Waltham, MA).

treatment_protocol: Adult male mice were fed a FFC diet, which provides 40% kcal from fat and is composed of 34% sucrose, 20% milk fat, and 0.21% cholesterol (AIN-76A Western Diet, originally manufactured as D12079B, TestDiet, St. Louis, MO). Mice in the FFC group also received sweetened drinking water (23.1 g/l fructose and 18.9 g/l glucose) ad lib. This murine model results in the development of insulin resistance, adipose tissue inflammation, and NASH with hepatocyte ballooning and fibrosis, displaying high fidelity to human NASH.

tag: Sex

value: Male

tag: cell type

value: Intrahepatic leukocytes

tag: diet

value: FFC

value: RAGE-MKO


title: KO4


title: KO3


title: 20230207_MHRNA039_HCC827GR6_Rep2

value: EGFR E746-A750del; METamp


title: 20230207_MHRNA038_HCC827GR6_Rep1


title: 20230206_CGATAC165_PC9_OR_DMSO_Rep2


title: Palmella_Blue, irrigated, mock, 48hpi, rep2

tag: tissue

value: spike

value: irrigated


title: KO1


title: 20230206_CGATAC159_PC9_Cmp14_Rep2


title: Palmella_Blue, irrigated, F.avenaceum, 48hpi, rep3


title: Palmella_Blue, irrigated, mock, 48hpi, rep1

value: Mock


title: 20230119_MHRNA026_HCC406OR_Rep4


title: 20230119_MHRNA022_HCC406_Rep4


title: 20230119_MHRNA025_HCC406OR_Rep3


title: 20230119_MHRNA021_HCC406_Rep3


title: Palmella_Blue, irrigated, F.avenaceum, 48hpi, rep1


title: 20230206_CGATAC157_PC9_DMSO_Rep2


title: Palmella_Blue, irrigated, F.avenaceum, 48hpi, rep2


title: 20230119_MHRNA023_HCC406OR_Rep1


title: 20230207_MHRNA036_HCC827_Rep1


title: WT5

description: Gene expression of IHLs from wild type mouse fed a FFC diet.


title: WT2


title: WT4


title: Palmella_Blue, irrigated, F.culmorum, 48hpi, rep3

value: Fusarium culmorum


title: 20230207_MHRNA037_HCC827_Rep2


title: 20230119_MHRNA035_PC9OR_Rep4


title: 20230119_MHRNA020_HCC406_Rep2


title: FFC7_D

description: Gene expression of IHLs from FFC fed mouse treated with TTP488.

growth_protocol: Nine-week-old C56BL/6J male mice were purchased from Jackson Laboratory (Bar Harbor, ME) and were acclimated for 3 weeks, during which all mice received standard rodent chow diet. Mice had unrestricted access to food and water and were housed in standard pathogen-free facilities with 12:12-h day-night circadian cycles. Adult male mice were assigned to 2 groups of similar starting weight, to receive chow, or FFC diet, which provides 40% kcal from fat and is composed of 34% sucrose, 20% milk fat, and 0.21% cholesterol (AIN-76A Western Diet, originally manufactured as D12079B, TestDiet, St. Louis, MO). Mice in the FFC group also received sweetened drinking water (23.1 g/l fructose and 18.9 g/l glucose) ad lib. This murine model results in the development of insulin resistance, adipose tissue inflammation, and NASH with hepatocyte ballooning and fibrosis, displaying high fidelity to human NASH.

treatment_protocol: After 20 weeks on diet, by which time liver inflammation is established, mice in each group were randomly split into treatment arms, either with drug (TTP488, Selleckchem, Houston, TX), dissolved as per manufacturer recommendations in 10% DMSO, 40% PEG300, 5% Tween 80, and 45% ddH20, or vehicle alone. Mice received daily intraperitoneal (i.p.) injections of drug (4 mg/Kg) or equivalent volume of vehicle for 30 days, while they continued to be on their respective diets.


title: WT1


title: FFC2_D


title: Palmella_Blue, irrigated, F.culmorum, 48hpi, rep2


title: 20230119_MHRNA033_PC9OR_Rep2


title: 20230119_MHRNA024_HCC406OR_Rep2


title: Palmella_Blue, irrigated, F.culmorum, 48hpi, rep1


title: 20230119_MHRNA032_PC9OR_Rep1


title: 20230119_MHRNA031_PC9_Rep4


title: 20230119_MHRNA019_HCC406_Rep1


title: FFC8_D


title: Palmella_Blue, drought, mock, 48hpi, rep3

value: drought


title: Palmella_Blue, drought, mock, 48hpi, rep2


title: 20230119_MHRNA028_PC9_Rep2


title: 20230119_MHRNA030_PC9_Rep3


title: 20230119_MHRNA027_PC9_Rep1


title: 20230206_CGCR039_HCC827GR6_K27ac

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For Cut & Run libraries, the CutRunTools pipeline was used to perform read trimming, quality filtering, alignment, and peak calling using default parameters.
For Cut&Run and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 50 --smoothLength 600 --ignoreDuplicates --samFlagInclude 64). For RNAseq data, tracks were generated using deepTools bamCoverage (--normalizeUsingRPKM).
Assembly: hg19
Supplementary files format and content: Cut&Run and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes. RNAseq bigWig files give the give the normalized coverage of DNA fragments across the genome in RPKM.
Library strategy: Cut&Run


title: 20230119_MHRNA034_PC9OR_Rep3


title: 20230206_CGCR037_HCC827GR6_Brg1


title: 20230206_CGCR035_HCC827_K27ac


title: 20230206_CGCR038_HCC827GR6_155


title: Palmella_Blue, drought, mock, 48hpi, rep1


title: 20230206_CGCR034_HCC827_155


title: Palmella_Blue, drought, F.avenaceum, 48hpi, rep2


title: 20230206_CGCR033_HCC827_Brg1


title: CD6_V

description: Gene expression of IHLs from chow fed mouse treated with vehicle.

value: Chow

value: Vehicle


title: FFC9_V

description: Gene expression of IHLs from FFC fed mouse treated with vehicle.


title: 20230206_CGCR050_HCC4006_OR_155


title: FFC6_V


title: CD4_V


title: 20230206_CGCR051_HCC4006-OR_K27ac


title: CD8_V


title: Palmella_Blue, drought, F.avenaceum, 48hpi, rep1


title: Palmella_Blue, drought, F.culmorum, 48hpi, rep3


title: 20230206_CGCR049_HCC4006_OR_Brg1


title: SC_PGCLC_d3_rep2 [SC_rPGCLC_d3_2]

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

country: Japan

institute: Nara Medical University

data_processing:
>Basecalls were performed using NextSeq 500/550 RTA software,v2.11.3.
>FASTQ files were generated using bcl2fastq,v2.17.1.14
>TPM valuses were calculated using RaNA-seq program (https://ranaseq.eu/index.php).
Assembly: rn6
Supplementary files format and content: A single text file that lists coding gene log2(TPM+1) values for each sample

organism: Rattus norvegicus

source_name: Primordial germ cell-like cell

growth_protocol:
rESCs were maintained on mitomycin-C-treated mouse embryonic fibroblasts (MEFs) in rESC medium; N2B27 medium supplemented with 1 µM PD0325901 (Axon, Groeningen, The Netherlands), 3 µM CHIR99021 (Axon), and 1000 U/ml of rat LIF (Millipore, Bedford, MA). For passaging, confluent rESC colonies were dissociated by 0.25% Trypsin-EDTA and re-plated to a well of 12-well plates (IWAKI, Shizuoka, Japan) containing 1 ml of rESC medium per well. The rESCs are routinely passaged every 3 days.
For derivation of rEpiSCs, E7.5-8.5 rat epiblasts were isolated as described previously (Kobayashi et al., 2020). Briefly, the ectoplacental cone and extra-embryonic ectoderm were mechanically dissected out and used for genotyping. The embryonic visceral endoderm surrounding the epiblast was removed by enzyme solution containing 1.0 mg/ml collagenase type IV (Worthington Biochemical Corporation), 1.0 mg/ml dispase (FUJIFILM Wako, Osaka, Japan), and 0.3 mg/ml hyaluronidase (Sigma-Aldrich) for 5 min at 37°C followed by repeated pipetting with a glass capillary. The isolated epiblasts were individually explanted on MEF in rEpiSC medium; N2B27 medium supplemented with 5% KSR, 20 ng/ml Activin-A (Peprotech, Cranbury, NJ), 12 ng/ml bFGF (Peprotech), two Wnt inhibitors (2 µM IWP2 (Tocris Bioscience, Bristol, UK) and 5 µM XAV-939 (Abcam), and 5 µM ROCKi (Tocris Bioscience). After 5 days, the expanded epiblast outgrowth was mechanically dissociated using a glass capillary. From the second passage, rEpiSC colonies were dissociated by Accutase (Innovative Cell Technologies) and re-plated to a well of MEF coated 12-well plates containing 1 ml of rEpiSC medium per well. The rEpiSCs were routinely passaged every 3-4 days.
rEpiLCs and rPGCLCs inductions were performed according to our recent report (Oikawa et al., 2022). Briefly, trypsinized rESCs were seeded in 96-well Nunclon Sphera-Treated U-shaped microplate containing 100 µl of rEpiLC medium (N2B27 medium supplemented with 1% KSR, 20 ng/ml Activin-A, and 12 ng/ml bFGF) at 4x10e3 cells per well. After culture for 48-60 h, rEpiLC-aggregates were transferred into a well of 96-well Nunclon Sphera-Treated U-shaped microplate containing 100 µl of rPGCLC medium [N2B27 medium supplemented with 500 ng/ml BMP4 (Peprotech), 1000 U/ml rLIF, 100 ng/ml SCF (R&D Systems), and 50 ng/ml EGF (R&D Systems)]. After 3 days, rEpiLC-derived rPGCLCs (LC-rPGCLCs) were analyzed by FACS, IF and RT-qPCR. To directly induce rPGCLCs from rEpiSCs, trypsinized rEpiSCs were seeded in 96-well Nunclon Sphera-Treated U-shaped microplate containing 100 µl of rPGCLC medium at 0.5-1.5x10e4 cells per well. After 3 days, rEpiSC-derived rPGCLCs (SC-rPGCLCs) were analyzed.
For the reprogramming of rEpiSCs, the 6 candidate genes (rKlf2, rKlf4, rEsrrb, rTbx3, rTfcp2l1, rNanog) were cloned individually into a PiggyBac transposon vector containing Doxycycline (Dox)-inducible Tet-On system. The plasmids were transfected into rEpiSCs by reverse transfection protocol using lipofectamine 2000 (Kobayashi et al., 2017). Transfected rEpiSCs were harvested on neomycin-resistant feeder (Kitayama labes, Nagano, Japan). Two days after transfection, 400 µg/ml G418 (Sigma-Aldrich) was added in the medium and rEpiSCs were cultured for 3-4 days. After G418 selection, 6 transcription factors-transfected rEpiSCs (6TFs-rEpiSCs) were re-plated at 2~10 x 10e4 cells per well of MEF coated 12-well plates containing 1 ml of rEpiSC medium supplemented with 1 µg/ml Dox (Sigma-Aldrich). On the next day, the medium was replaced by rESC medium supplemented with Dox. The PV(+) dome-shaped colonies were picked manually at day 5-7, and then dissociated by 0.25% Trypsin-EDTA into single cells, and re-plated into a well of 12-well plates containing 1 ml of rESC medium without Dox. PV(+) rESCLCs were routinely passaged every 3 days.

extract_protocol:
Total RNA was extracted using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer’s protocols.
RNA-seq libraries were prepared using the SMART-Seq HT PLUS Kit (Takara Bio).

value: Wild type

value: Primordial germ cell-like cell


title: 20230206_CGCR046_HCC4006_155


title: Palmella_Blue, drought, F.avenaceum, 48hpi, rep3

value: Fusarium avenaceum


title: 20230206_CGCR045_HCC4006_Brg1


title: 20230206_CGCR053_PC9_OR_Brg1


title: LCSC_PGCLC_d3_rep2 [LC_SC_rPGCLC_d3_2]


title: Palmella_Blue, drought, F.culmorum, 48hpi, rep1


title: Grace, irrigated, mock, 96hpi, rep3

value: Grace


title: 20230206_CGCR054_PC9_OR_155

value: EGFR E746-A750del


title: 20230206_CGCR047_HCC4006_K27ac


title: Palmella_Blue, drought, F.culmorum, 48hpi, rep2


title: 20230206_CGCR042_PC9_155


title: 20230206_CGCR041_PC9_Brg1


title: FFC4_V

value: Male


title: LC_PGCLC_d3ag3_rep2 [LC_rPGCLC_d3ag3_2]


title: LC_PGCLC_d3ag3_rep1 [LC_rPGCLC_d3ag3_1]


title: Grace, irrigated, mock, 96hpi, rep2


title: REH DUX4-del50 rep3

first: Davide

last: Gabellini

address: Via Olgettina 60

department: Division of Genetics and Cell Biology

institute: SAN RAFFAELE SCIENTIFIC INSTITUTE

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
The remaining reads were mapped to the reference human genome GRCh38, using STAR aligner (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode release 31).
Assembly: GRCh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: REH

growth_protocol: Inducible REH cells were grown in RPMI-1640 medium (Euroclone) supplemented with 20% FBS and 1% Pen-Strep

extract_protocol:
RNA extraction using PureLink RNA Mini Kit (catalog # 12183025, Life Technologies), following manifacturer's protocol. cDNA synthesis using SuperScript® III First-Strand Syntesis SuperMix for qRT-PCR (cat. #11752-250, Life Technologies)
NGS libraries were generated with the mRNA Stranded TruSeq protocol. Libraries were barcoded, pooled and sequenced on IlluminaNextSeq 500 sequencing system in single-end reads mode, with reads 76nt long.

treatment_protocol: Nearly 3x10^6 inducible REH cells were induced with 1ug/mL of Doxycycline in 2mL of fully-supplemented RPMI with at a density of 1,5x10^6/mL

tag: condition

value: REH

value: B cell precursor ALL

value: + 1ug/mL Doxycycline


title: Grace, irrigated, mock, 96hpi, rep1


title: LCSC_PGCLC_d3_rep1 [LC_SC_rPGCLC_d3_1]


title: REH DUX4-del50 rep4


title: LC_PGCLC_d3_rep2 [LC_rPGCLC_d3_2]


title: 20230206_CGCR055_PC9_OR_K27ac


title: REH DUX4-del50 rep2


title: REH DUX4-IGH rep4


title: LC_PGCLC_d3_rep1 [LC_rPGCLC_d3_1]


title: REH DUX4-IGH rep3


title: Grace, irrigated, F.avenaceum, 96hpi, rep2


title: ESCLC_P6 [rESCLC_P6]

source_name: Embryonic stem cell-like cell

value: Embryonic stem cell-like cell


title: Grace, irrigated, F.avenaceum, 96hpi, rep3

value: spike


title: Grace, irrigated, F.avenaceum, 96hpi, rep1

value: irrigated


title: ESCLC_P5 [rESCLC_P5]


title: 20230206_CGCR043_PC9_K27ac


title: REH DUX4-IGH rep2


title: REH DUX4 rep2


title: REH DUX4 rep4


title: REH DUX4 rep3


title: REH DUX4-IGH rep1


title: ESCLC_P2_rep2 [rESCLC_P2_2]


title: Grace, irrigated, F.culmorum, 96hpi, rep3


title: REH EV rep4

value: EV


title: Grace, irrigated, F.culmorum, 96hpi, rep2

value: Fusarium culmorum


title: REH DUX4-del50 rep1


title: REH EV rep3


title: ESCLC_P2_rep1 [rESCLC_P2_1]


title: EpiSC_N3TAG_rep2 [rEpiSC_N3T/AG_2]

source_name: Epiblast stem cell

value: Epiblast stem cell


title: REH EV rep2


title: Grace, irrigated, F.culmorum, 96hpi, rep1


title: Grace, drought, mock, 96hpi, rep2

value: drought

value: Mock


title: SK-OV-3-EPZ-5676 treated replicate 2

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
The raw fastq sequences were aligned to the human hg38 reference genome (GenBank assembly accession: GCA_000001405.28). The alignments were carried out using STAR (version 2.7.1a) (Dobin et al 2013) with default parameters. Gene expression was quantified as gene level counts using the htseq-count function (version 0.12.3) (Anders et al 2015); the UCSC gene annotations for the human genome were used. The htseq-count default parameters were used, except for the strand parameter which was set to reverse to consider the strandedness of library. Genes for which there are less than 3 samples with normalized counts greater than or equal to 4 were filtered out. Differentially expressed genes were identified using DESeq2 (version 1.28) (Love et al 2014).
Genome_build: human hg38 reference genome (GenBank assembly accession: GCA_000001405.28)
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for each gene in each sample

source_name: SK-OV-3 cell line

growth_protocol: IGROV-1 and SK-OV-3 cells were grown in RPMI medium and DMEM medium respectively with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: IGROV-1 and SK-OV-3 cells were treated with  DOT1L inhibitor (10 micomolar) EPZ-5676 for 48 hours,  were harvested and were used for preparing the total RNA and to perfrom RNA Seq.

tag: agent

value: EPZ-5676 treated, 10 micromolar, 48 hours


title: REH EV rep1


title: Grace, drought, mock, 96hpi, rep3


title: SK-OV-3-EPZ-5676 treated replicate 1


title: EpiSC_N3TAG_rep1 [rEpiSC_N3T/AG_1]

value: Wild type


title: EpiSC_PV_rep2 [rEpiSC_PV_2]


title: SK-OV-3-DMSO treated replicate 3

value: DMSO treated


title: Grace, drought, mock, 96hpi, rep1

value: Grace


title: SK-OV-3-DMSO treated replicate 2


title: REH DUX4 rep1


title: SK-OV-3-DMSO treated replicate 1