title: TR2, After treatment [miRNA-seq]

description:
Library name: Sample TR2_miRNA
Peripheral blood 5ml
miRNA_Expression(TD-TR).xlsx


title: R3, On admission [miRNA-seq]

status: Public on Sep 17 2025

type: SRA

city: Nanning

first: Pingping

last: Zeng

state: Guangxi

address: Guangxi Medical University, No. 8, Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region, China.

country: China

institute: Guangxi Medical University

description:
Library name: Sample R3_miRNA
Peripheral blood 5ml
miRNA_Expression(D-R).xlsx

library_source: transcriptomic

data_processing:
Downtime data quality control
Match the genome
Modification site recognition (RNA quantification)
Differential site identification (differential RNA identification)
Functional enrichment analysis
Assembly: HG38
Supplementary files format and content: xlsx files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Nasopharyngeal cancer

extract_protocol:
Using the PAXgene Blood RNA Kit (BD, USA), the total RNAs were extracted from samples of the rise distress group (Class 4) and decline distress group (Class 1) divided by LCGM following the manufacturer’s instructions. A Nanodrop ND-1000 (Thermo Fisher, USA) was applied to measure the concentration and quality of total RNAs.
The sequencing library was built using around 1–2 μg of total RNAs per sample. RNA sequencing services were provided by CloudSeq Inc. (Shanghai, China). Trizol (Invitrogen, USA) was utilized to extract Total RNA, and rRNA was removed via the GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China). Directional RNA libraries were built via the GenSeq® Directional RNA Library Prep Kit. RNA was fragmented to ~300 nt in length. Reverse transcriptase and random hexamers were utilized to synthesize the first-strand cDNA. Moreover, the dUTP Mix was applied to synthesize the second-strand cDNA. The double-stranded cDNA fragments underwent end repair, adapter ligation, and dA-tailing. The cDNA, ligated with adapters, was PCR-amplified and purified to generate the final sequencing libraries. Furthermore, the libraries were sequenced in paired-end 150 bp mode.

tag: tissue

value: Nasopharyngeal cancer

tag: Sex

value: male

tag: subject group

value: decline distress upon admission group

tag: treatment

value: Radiotherapy

tag: time point

value: On admission


title: R2, On admission [miRNA-seq]

description:
Library name: Sample R2_miRNA
Peripheral blood 5ml
miRNA_Expression(D-R).xlsx


city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: Tetragonula_carbonaria_ovaries_sRNA_rep2
Small RNA sequencing from Tetragonula carbonaria ovaries replicate 2

library_source: other

data_processing:
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting. The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses. Trimmed reads were first mapped to infrastructural RNAs including ribosomal RNA, small nuclear RNA, small nucleolar RNA, microRNA, and transfer RNA, which are annotated in their respetive genomes or genomes from closely related species using bowtie v1.2.3 allowing up to one mismatch. Reads that did not map to these infrastructural RNAs were subsequently mapped to the corresponding species' genomes. The sam file was further processed to the bam file, then to the bed file using samtools/1.19 and bedtools/2.28.0. The coverage of uniquely mappable reads on 0.5kb genomic tiles was measured using bedtools intersect.
Assembly: GCA_905231855.2_idEriTena2.2 for Eristalis tenax GCF_016617805.1_CSIRO_BtryS06_freeze2 for Bactrocera tryoni GCF_002204515.2_AaegL5.0 for Aedes aegypti GCF_013141755.1_UCI_ANSTEP_V1.0 for Anopheles stephensi GCA_032399595.1_TetCarb_2.0 for Tetragonula carbonaria GCA_031308135.1_ado_dt_MfTpo_fix for Acheta domesticus GCA_964035755.1_iqTelOcea1 for Teleogryllus oceanicus
Supplementary files format and content: *_genomic-tile-coverage.txt: coverage of uniquely mappable piRNA (>22nt) reads on individual 0.5kb genomic tiles <tile position with genomic coodinate and strand> <coverage per 1 million piRNA reads>

molecule: other

organism: Tetragonula carbonaria

source_name: ovaries

growth_protocol: Insects were kept at standard conditions at room temperature.

extract_protocol:
Small RNA sequencing was performed on ovaries and eggs collected from a variety of insects. About 10 pairs of ovaries from 1 week to up to 3 months old females and eggs within up to 8 hours of egg laying have been collected per replicate. Total RNA was extracted by TRIZOL (Thermo Fisher) and the genomic DNA was removed by DNase I (Thermo Fisher).
Small RNAs were first size-selected from the total RNA by 12% w/v UREA-PAGE using radio-labelled 19mer (5′-CGUACGCGGGUUUAAACGA) and 35mer (5'-CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU) spikes, and oxidised using sodium periodate. The oxidised small RNAs were further size-selected by PAGE. The size-selected oxidised small RNAs were ligated to the 3' adapter 5rApp/NNNNAGATCGGAAGAGCACACGTCT/3ddC, and then to the 5' adapter ACACUCUUUCCCUACACGACGCUCUUCCGAUCUNNNN where Ns are randomised. The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the RT primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT. The library was amplified using KAPA LongRange DNA polymerase (Sigma) with a universal TruSeq forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcode-containing TruSeq reverse primer (e.g. CAAGCAGAAGACGGCATACGAGATxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where xxxxxx were the barcode).

value: ovaries

value: female

tag: strain

value: wild type

value: oxidized

tag: age

value: 5 - 7 days old


title: patient TH120 cells, normal fibroblast from lung (non-tumor)

city: Seoul

first: Sang-Won

last: Um

address: 81 Irwon-ro

department: Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center

country: South Korea

institute: Sungkyunkwan University School of Medicine

description: Library name: TH120_NF

data_processing:
After trimming poor quality bases from the FASTQ files, reads were aligned to the human reference genome (hg19) with STAR v2.5.2b (https://github.com/alexdobin/STAR) and estimated gene expression was calculated in terms of estimated expected counts using RSEM v1.3 (https://github.com/deweylab/RSEM).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw count values for for every gene and every sample

source_name: lung

extract_protocol:
The total RNA from cultured cell pellets of CAFs or NFs was extracted with an RNeasy Mini Kit (Qiagen). Nucleic acid extraction was performed according to the manufacturer’s instructions.
Sequencing libraries were prepared with or TruSeq RNA Sample Preparation Kit v2, set A and B (Illumina, Inc., Cat# RS-122-2001 and RS-122-2002) following manufacturer’s protocols.

value: lung

tag: cell line

tag: cell type

value: ADC


title: TR1, After treatment [miRNA-seq]

description:
Library name: Sample TR1_miRNA
Peripheral blood 5ml
miRNA_Expression(TD-TR).xlsx

value: After treatment


title: HiC,NCM,Des+/+

city: Alexandroupolis

first: Panagiotis

last: Liakopoulos

address: Dragana

department: Molecular Biology and Genetics

country: Greece

institute: Democritus University of Thrace

library_source: genomic

data_processing:
Hi-C data were analyzed using FAN-C version 0.9.26. Raw reads for each pair were aligned to the mm10 mouse genome version and the generated sam files were sorted and used to generate filtered pair files, which were used to create Knight–Ruiz (KR) normalized multybinned HiC matrices (5mb, 2mb, 1mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, 5kb) using FAN-C – auto with default parameters.   TAD boundaries were called using the insulation score method from FAN-C. Insulation scores were calculated for 10-kb binned HiC matrices at multiple window sizes (10kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 1.5Mb, 2Mb, 2.5Mb, 3Mb, 3.5Mb, 4Mb). Domain boundaries were calculated from the insulation scores. Genome contact matrices were produced using 10kb binned HiC matrices with color scale of 0.1 for iCM, 0.03 for NCM and 0.01 for ACM and ACM swim. A/B compartment heatmaps were produced using fanc compartments with eigenvector binning at 10 20 30 40 50 60 70 80 90 100 using normalized 1mb binned HiC matrices.
Assembly: mm10
Supplementary files format and content: filtered for coverage (bins with less reads than 10% of the median bin coverage) and corrected using Knight-Ruiz matrix balancing binned Hic files at 5mb, 2mb, 1mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb resolution
Supplementary files format and content: unfiltered and unbalanced fragment-level Hic files

molecule: genomic DNA

organism: Mus musculus

source_name: heart

growth_protocol: For induced Cardiomyocytes (iCM) samples: fibroblasts were isolated by enzymatic digestion with 1mg/ml Trypsin (Gibco) and 1mg/ml Collagenase type2 (worthington) from  hearts of 1-3 day old mouse pups as descibed in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)." Then, they transduced with the viral coctail Gat4+Mef2C+Tbx5 as described in "Qian, L., Berry, E.C., Fu, J.D., Ieda, M. & Srivastava, D. Reprogramming of mouse fibroblasts into cardiomyocyte-like cells in vitro. Nature protocols 8, 1204-1215 (2013)."  These iCMs were grown in DME/M199 edis+10%FBS for 7 days and then underwent FACS sorting analysis. For Neonatal cardiomyocytes (NCM) samples: NCM were isolated by enzymatic digestion using 1mg/ml Trypsin (Gibco) and 1mg/ml Collagenase type2 (worthington) from hearts of 1-3 day old mouse pups as descibed in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)." Then cultured for 3-4 days in  DMEM 7%FBS (with 1% pen/strep and 1.5mM vitamin B12). The adult cardiomyocytes (ACM) were isolated with enzymatic perfutsion using  an enzymatic cocktail of Trypsin (Gibco) and CollagenaseD (ROCHE) as described in "Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)". ACM were isolated form 3 month old mice that have or not undergone swimming excersise as described in ""Diokmetzidou, A., et al. Strategies to Study Desmin in Cardiac Muscle and Culture Systems. Methods in enzymology 568, 427-459 (2016)" and "Diokmetzidou, A., et al. Desmin and alphaB-crystallin interplay in the maintenance of mitochondrial homeostasis and cardiomyocyte survival. Journal of cell science 129, 3705-3720 (2016)". The ACM harvested immediately after isolation.

extract_protocol:
DNA was extracted with phenol-chloroform-isoamyl alcohol mixture and ethanol percipitated
Libraries were built using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: For induced Cardiomyocytes (iCM) samples: fibroblasts  were tranduced with a retroviral cocktail for 24 hrs

value: heart

value: Primary Neonatal cardiomyocytes isolated from 1-3 day old pups of Des+/+ mice

tag: genotype

value: Des+/+

value: WT


title: patient TH128 cells, cancer-associated fibroblast from lymph node

description: Library name: TH128_CAF

source_name: lymph node

value: lymph node


title: patient TH131 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH131_CAF

value: SqCC


description:
Library name: Tetragonula_carbonaria_ovaries_sRNA_rep1
Small RNA sequencing from Tetragonula carbonaria ovaries replicate 1


title: R1, On admission [miRNA-seq]

description:
Library name: Sample R1_miRNA
Peripheral blood 5ml
miRNA_Expression(D-R).xlsx

value: Nasopharyngeal cancer

value: male

value: decline distress upon admission group


title: patient TH114 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH114_CAF


title: Anopheles_stephensi_eggs_sRNA_rep2

description:
Library name: Anopheles_stephensi_eggs_sRNA_rep2
Small RNA sequencing from Anopheles stephensi eggs replicate 2

organism: Anopheles stephensi

source_name: eggs

value: eggs

value: mixed

value: 0 - 4 hour old


title: patient TH131 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH131_NF


title: TD3, After treatment [miRNA-seq]

description:
Library name: Sample TD3_miRNA
Peripheral blood 5ml
miRNA_Expression(TD-TR).xlsx

value: rise psychological distress group

value: Radiotherapy


title: HiC,ACM,Des-/-,Swim

value: Primary cardiomyocytes isolated from 3month old  Des-/- mice

value: Des-/-


title: HiC,ACM,Des+/+,Swim

value: Primary cardiomyocytes isolated from 3month old Des+/+ mice


title: Anopheles_stephensi_eggs_sRNA_rep1

description:
Library name: Anopheles_stephensi_eggs_sRNA_rep1
Small RNA sequencing from Anopheles stephensi eggs replicate 1

value: wild type

value: oxidized


title: D3, On admission [miRNA-seq]

description:
Library name: Sample D3_miRNA
Peripheral blood 5ml
miRNA_Expression(D-R).xlsx

value: On admission


title: patient TH107 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH107_NF

value: lung

value: ADC


title: HiC,ACM_Des-/-

value: heart


title: TD2, After treatment [miRNA-seq]

description:
Library name: Sample TD2_miRNA
Peripheral blood 5ml
miRNA_Expression(TD-TR).xlsx

value: Nasopharyngeal cancer

value: After treatment


title: patient TH106 cells, cancer-associated fibroblast from lymph node

description: Library name: TH106_CAF

value: lymph node

value: SqCC


title: HiC,ACM,Des+/+

value: Des+/+

value: WT


title: Anopheles_stephensi_ovaries_sRNA_rep1

description:
Library name: Anopheles_stephensi_ovaries_sRNA_rep1
Small RNA sequencing from Anopheles stephensi ovaries replicate 1

value: ovaries

value: female

value: 1 week old


title: patient TH98 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH98_CAF


title: Anopheles_stephensi_ovaries_sRNA_rep2

description:
Library name: Anopheles_stephensi_ovaries_sRNA_rep2
Small RNA sequencing from Anopheles stephensi ovaries replicate 2


title: Nedd8 RFP3, rep 3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the GRCm39 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCm39 version 110
Assembly: GRCm39 version 110
Supplementary files format and content: Tab-delimited gene counts

source_name: brain

growth_protocol: Continental cultures of primary hippocampal neurons were performed as described in PMID: 32233089. Hippocampi were dissected from homozygous NEDD8cKO P0 mice. The tissue was digested in a solution containing 1 mM CaCl2, 0.5 mM EDTA, 1.65 mM l-cysteine in DMEM (Gibco) for 1 h at 37°C under agitation (450 rpm). Digestion was stopped via a 15 min incubation at 37°C in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), 2.5 mg albumin, and 2.5 mg/ml trypsin inhibitor. The tissue was washed twice with NBA medium containing 500 µL Neurobasal A medium (Gibco), 1% B27 (Gibco) and 20 µg/ml Penicillin-Streptomycin (Gibco). Careful trituration was performed in 100 µL of the same medium. Once the tissue was dissociated, the supernatant was plated in NBA medium onto 60 mm Petri dishes (CytoOne) previously coated with Poly-L-Lysine (Sigma). A cell density of approximately 200 000 cells/well (two hippocampi) was used. NBA medium supplemented with B27 and antibiotics was replaced the next day. Cultures were kept at 37°C with 5% CO2.

extract_protocol:
We extracted RNA using the kit from Zymo
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We generated a nedd8 conditional knock-out. We cultured primary hippocampal neurons and infected these neurons with either an RFP-expressing virus (as control) or a CRE-expressing virus to ablate NEDD8 expression. After 12 days in culture, RNA were extracted from these culture and their transcriptome was analyzed.

value: brain

value: hippocampus

value: virus expressing RFP


title: Spun_Zoospores_rep2

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Library name: 6mA_41

data_processing:
All ChIP-seq data was analysed using fastp to trim the reads, and these were mapped to the genomes using bowtie2, allowing a maximum insert size of 2000 base pairs (-I 2000). Duplicate reads were removed using Sambamba. DeepTools2 was used to generate bigwig files and to visualise epigenomic data, as well as Integrative Genome Viewer.
All RNA-seq data was mapped against the reference transcriptome using Kallisto with default quant parameters
Assembly: Creolimax fragrantissima assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Spizellomyces punctatus: GCF_000182565.1, Acanthamoeba castellanii: https://zenodo.org/records/6800059, Naegleria gruberi: https://github.com/AlexdeMendoza/6mA_evolution/blob/main/Genomes/Naegleria_gruberi.medakaRagTag.genome.fasta.gz
Supplementary files format and content: ChIP-seq bigwig files were generated with DeepTools2 using the bamCoverage tool (bamCoverage -bs 10 --normalizeUsing CPM -p $cores -b "$prefix".dedup.bam -o "$prefix".bigwig)
Supplementary files format and content: Processed mRNA-seq data shows TPM and est_counts values obtained from Kallisto Quant function against the reference transcriptomes.

molecule: polyA RNA

organism: Spizellomyces punctatus

source_name: axenic culture

growth_protocol: Creolimax fragrantissima cells were grown axenically in marine broth liquid medium (Difco 2216) at 17°C. Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034. Spizellomyces punctatus cells were grown axenically at 17°C in liquid medium (containing 2.5 g of yeast extract, 0.5 g of K2HPO4, 2.5 ml of ethanol, 15 ml of glycerol and 485 ml of Milli-Q water).

extract_protocol:
Fixed cell pellets are treated with 2 ul of 3%SDS, to achieve a final concentration of 0.5% SDS. Cells are thoroughly re-suspended and lysed on ice for 10 min. Lysates are transferred into 0.1 ml Bioruptor Microtubes (Diagenode C30010015, Liège, Belgium) and the chromatin was sheared using an NGS Bioruptor Sonicator (Diagenode) at High Intensity and cycles of 30'' ON/30'' OFF. RNA extracted with NEB Monarch RNA kit
ChIP-seq / mRNA-seq

treatment_protocol: No treatments were performed.

value: axenic culture

value: DAOM BR117

value: zoospore

value: Filtered zoospores


title: D2, On admission [miRNA-seq]

description:
Library name: Sample D2_miRNA
Peripheral blood 5ml
miRNA_Expression(D-R).xlsx

value: male

value: rise psychological distress group

value: Radiotherapy

value: On admission


title: patient TH98 cells, normal fibroblast from lung (non-tumor)

description: Library name: TH98_NF

value: lung

value: ADC


title: Nedd8 RFP3, rep 4


title: Spun_Zoospores_rep1

description: Library name: 6mA_40


title: Nedd8 RFP3, rep 2


title: HiC,NCM,Des-/-

value: heart

value: Primary Neonatal cardiomyocytes isolated from 1-3 day old pups of Des-/-mice

value: Des-/-


title: D1, On admission [miRNA-seq]

description:
Library name: Sample D1_miRNA
Peripheral blood 5ml
miRNA_Expression(D-R).xlsx

value: Nasopharyngeal cancer


title: TD1, After treatment [miRNA-seq]

description:
Library name: Sample TD1_miRNA
Peripheral blood 5ml
miRNA_Expression(TD-TR).xlsx

value: After treatment


title: patient TH84 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH84_CAF

value: SqCC


title: Nedd8 RFP3, rep 1

value: brain

value: hippocampus

value: virus expressing RFP


title: Spun_Multinucleated_rep2

description: Library name: 6mA_39

value: axenic culture

value: DAOM BR117

value: multinucleate colony

value: Zoospores filtered and let to grow for 24h


title: Spun_Multinucleated_rep1

description: Library name: 6mA_38


title: TR3, After treatment

description:
Library name: Sample TR3
Peripheral blood 5ml
circRNA_Expression_Profiling(TD-TR).xlsx
mRNA_Expression_Profiling(TD-TR).xlsx

value: male

value: decline distress upon admission group

value: Radiotherapy


title: Nedd8 RFP2, rep 4


title: patient TH79 cells, cancer-associated fibroblast from lymph node

description: Library name: TH79_CAF

value: lymph node


title: R3, On admission

description:
Library name: Sample R3
Peripheral blood 5ml
circRNA_Expression_Profiling(D-R).xlsx
mRNA_Expression_Profiling(D-R).xlsx

value: On admission


title: patient TH107 cells, cancer-associated fibroblast from lung (tumor)

description: Library name: TH107_CAF

value: lung

value: ADC


title: Nedd8 RFP2, rep 3


title: Ngru_30C_RNAseq_rep2

description: Library name: 6mA_37

organism: Naegleria gruberi

value: NEG-M

value: amoeba

value: 30C growth 5 days


title: Ngru_30C_RNAseq_rep1

description: Library name: 6mA_36


title: CTL3spliced

city: Rome

first: Anna

last: Scotto d'Abusco

address: P.le Aldo Moro, 5

department: Biochemical Sciences

country: Italy

institute: Sapienza University of Rome

data_processing:
Galaxy version 23.0.1.dev0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic software (Average quality required: 20) Default parameters. (Version 0.38).
Trimmed sequence reads were alligned to GRCh38/hg38 using HISAT2 software. Default parameters. (Version 2.2.1)
Read count extraction and normalization were performed using FeatureCounts tool. Default parameters. (Version 2.0.3)
Differential expression analyses between selected subsets of samples were performed by using Limma software. Default parameters. (Version 3.50.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include the Geneid and counts for each samples (Counts files).
Supplementary files format and content: tab-delimited text files include the abundance measurements with the ENTREZID, ENSEMBL, SYMBOL, GENENAME, logFc, P.Value and adj.P.Val (limma files).

source_name: Cells from Synovial membrane

growth_protocol: Cells were grown to 80% confluence in DMEM (Merck Life Science, Darmstadt, DE) supplemented with L-glutamine, penicillin/streptomycin (Merck Life Science) and 10% Fetal Bovine Serum (FBS) and cultured at 37 °C and 5% CO2

extract_protocol:
Total RNA was extracted with Blood/Tissues Total RNA extraction kit (Fisher Molecular Biology, Trevose, PA, USA)
The RNA concentration was determined by using the Qubit RNA HS Assay Kit on the Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Quality control was assessed by Labchip GX Touch HT instrument on DNA 5K/RNA/CZE Chip (Perkin Elmer) with RNA Pico Sensitivity Assay Reagents (Perkin Elmer, Waltham, MA, USA).  NextFlex PolyA beads 2.0 kit and NextFlex Rapid Directional RNA-seq Kit 2.0  with UDIs (Perkin Elmer)  were used  for mRNA capture and strand-specific library preparation. The library quantities were measured by Quant-iT 1x dsDNA HS Assay kit (Thermo Fisher) with Fluostar Omega (BMG Labtech, Ortenberg, Germany). The fragment size distribution of the libraries were determined by capillary electrophoresis on Labchip GX Touch Nucleic Acid Analyzer on XMark HT chip by using DNA NGS 3k Assay kit (Perkin Elmer). Pooled libraries were sequenced with 20M 150 bp paired-end reads on NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were left untreated (CTL) or treated for 24h with 0.1 mg/mL of Harpagophytum procumbens root extract (HPE) dissolved in DMSO (HPEDMSO).

value: Cells from Synovial membrane

value: Primary cells

value: Synoviocytes type B

value: WT

value: Untreated

tag: time


title: TR2, After treatment

description:
Library name: Sample TR2
Peripheral blood 5ml
circRNA_Expression_Profiling(TD-TR).xlsx
mRNA_Expression_Profiling(TD-TR).xlsx

value: Nasopharyngeal cancer

value: After treatment


title: Nedd8 RFP2, rep 2

value: brain

value: hippocampus

value: virus expressing RFP


title: CTL2spliced


title: Nedd8 RFP2, rep 1


title: R2, On admission

description:
Library name: Sample R2
Peripheral blood 5ml
circRNA_Expression_Profiling(D-R).xlsx
mRNA_Expression_Profiling(D-R).xlsx

value: male

value: decline distress upon admission group

value: Radiotherapy


title: CTL1spliced


title: Nedd8 RFP1, rep 3


title: R1, On admission

description:
Library name: Sample R1
Peripheral blood 5ml
circRNA_Expression_Profiling(D-R).xlsx
mRNA_Expression_Profiling(D-R).xlsx

value: On admission


title: HPE2


title: RNA-Seq of Medicago truncatula (A17): floral_organ_stg8_stamens, 7w (rep. 3)

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

organism: Medicago truncatula

source_name: stamens

growth_protocol: All plants were grown on soil, except those used for the collection of early-stage root samples, which were grown on 0.8% plant agar plates, pH 5.8, containing ½ MS and vitamins (Duchefa M0222).

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.

tag: cultivar

value: Medicago truncatula (A17)

value: stamens


title: TD3, After treatment

description:
Library name: Sample TD3
Peripheral blood 5ml
circRNA_Expression_Profiling(TD-TR).xlsx
mRNA_Expression_Profiling(TD-TR).xlsx

value: rise psychological distress group


title: RNA-Seq of Medicago truncatula (A17): floral_organ_stg8_stamens, 7w (rep. 2)


title: Nedd8 RFP1, rep 1


title: HPE1

value: Cells from Synovial membrane


title: RNA-Seq of Medicago truncatula (A17): floral_organ_stg8_stamens, 7w (rep. 1)


title: RNA-Seq of Medicago truncatula (A17): floral_organ_stg8_carpels, 7w (rep. 3)

source_name: carpels

value: carpels


title: D3, On admission

description:
Library name: Sample D3
Peripheral blood 5ml
circRNA_Expression_Profiling(D-R).xlsx
mRNA_Expression_Profiling(D-R).xlsx


title: TD2, After treatment

description:
Library name: Sample TD2
Peripheral blood 5ml
circRNA_Expression_Profiling(TD-TR).xlsx
mRNA_Expression_Profiling(TD-TR).xlsx


title: CTL3

value: Primary cells

value: Synoviocytes type B


title: Nedd8 Cre3, rep 4

value: virus expressing RFP-CRE


title: Nedd8 Cre3, rep 3


title: D2, On admission

description:
Library name: Sample D2
Peripheral blood 5ml
circRNA_Expression_Profiling(D-R).xlsx
mRNA_Expression_Profiling(D-R).xlsx

value: Nasopharyngeal cancer


title: CTL2

value: WT

value: Untreated


title: RNA-Seq of Medicago truncatula (A17): floral_organ_stg8_carpels, 7w (rep. 2)


title: Ngru_23C_RNAseq_rep2

description: Library name: 6mA_35

value: axenic culture

value: NEG-M

value: amoeba

value: 23C growth 5 days


title: CTL1


title: TR1, After treatment

description:
Library name: Sample TR1
Peripheral blood 5ml
circRNA_Expression_Profiling(TD-TR).xlsx
mRNA_Expression_Profiling(TD-TR).xlsx

value: male

value: decline distress upon admission group

value: Radiotherapy

value: After treatment


title: TD1, After treatment

description:
Library name: Sample TD1
Peripheral blood 5ml
circRNA_Expression_Profiling(TD-TR).xlsx
mRNA_Expression_Profiling(TD-TR).xlsx

value: rise psychological distress group


title: Ngru_23C_RNAseq_rep1

description: Library name: 6mA_34


title: RNA-Seq of Medicago truncatula (A17): floral_organ_stg8_carpels, 7w (rep. 1)

value: Medicago truncatula (A17)


title: Nedd8 Cre3, rep 1

value: brain

value: hippocampus


title: NIND, Patient_12_RSEC_MolsPerCell

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Raw fastq-sequencing reads were loaded into BD Targeted Rhapsody Analysis Pipeline hosted by SevenBridgesGenomics and analyzed using version 1.9 of the pipeline.
Data were filtered as follows using Partek Flow version 10.0.20.1231: cells with more than 2% mitochondrial genes and doublets (outliers in detected genes) were excluded; a noise reduction filter was used to filter out features with an expression value of 0 in 100% of cells;
Data were normalized by calculating counts per million (CPM), adding 1 and log transforming to the base of 2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every cell, gene and sample.  Python script (Index_to_CL.csv) allows conversion of the cell indices back to sequences.

source_name: Cerebrospinal fluid (CSF)

extract_protocol:
Cerebrospinal fluid (Csf) was extracted using lumbar puncture in a diagnostic setting.
Capturing of single cells was performed using the BD Rhapsody system (BD Biosciences). Cells from cerebrospinal fluid (Csf) were loaded on BD Rhapsody cartridge (one cartridge per patient). Capture of single RNA molecules on barcoded magnetic polydT- beads and cDNA synthesis was performed as described in the manual (Single cell capture and cDNA synthesis with the BD Rhapsody single-cell analysis system; Doc ID: 210966 Rev. 1.0). Targeted human immune response panel (BD) together with custom selected primers for the detection of additional genes was used for library preparation. mRNA libraries were prepared following the manual (mRNA targeted and sample tag library preparation with BD single-cell multiplexing kit; Doc ID 214062 Rev. 1.0) using 12 cycles in PCR1, 10 cycles in PCR2 and 6 cycles in PCR3. Upon purifying mRNA targeted library, concentration of libraries was assessed by Qubit 2.0 using the DNA high sensitivity kit and average library size was determined on a bioanalyzer using a high-sensitivity DNA chip. Final sequencing library was prepared by dilution and pooling targeted mRNA library following the recommendations of the sequencing preparation sheet provided by BD. The libraries were sequenced on a HiSeq2500 (Illumina) using a HiSeq PE Rapid Cluster Kit v2 (PE-402-4002) and combining three HiSeq Rapid SBS Kits v2 (50 cycles). For processing of the sequencing raw data BD targeted multiplex Rhapsody analysis pipeline version 1.5 was used. For visualization the software Partek Flow (Partek) has been used.
Targeted single cell Seq

tag: disease state

value: NIND (non-inflammatory neurological disease)

value: untreated

value: Cerebrospinal fluid (CSF)


title: HPE3

value: Cells from Synovial membrane

value: Primary cells

value: Synoviocytes type B

value: WT


title: Nedd8 RFP1, rep 2

value: virus expressing RFP


title: D1, On admission

description:
Library name: Sample D1
Peripheral blood 5ml
circRNA_Expression_Profiling(D-R).xlsx
mRNA_Expression_Profiling(D-R).xlsx

value: Nasopharyngeal cancer

value: On admission


title: RNA-Seq of Medicago truncatula (A17): floral_organ_mature_pollen, 7w (rep. 3)

source_name: pollen

value: pollen


title: NIND, Patient_10_RSEC_MolsPerCell


title: 4sU_RNA_gTOP2

city: Seville

first: Silvia

last: Jimeno-González

address: Avda. Américo Vespucio 24

department: Genética

country: Spain

institute: Universidad de Sevilla

description: Library name: 4sU_RNA_gTOP2

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Libraries were de-multiplexed and trimmed using FASTQ Generation based on “bcl2fastq”. European Galaxy Server and customized scripts were used for subsequent analysis. To discard reads coming from ribosomic DNA (rDNA), reads were mapped against a copy of 45S rDNA using “STAR” 2.7.11b 58 with default parameters but specifying --genomeSAIndexNbases 5. Only unmapped reads were selected for subsequent analysis. Reads were mapped to GRCh38/hg38 and Saccharomyces cerevisiae genome assembly SacCer3 (GCA_000146045.2) using “STAR” 2.7.11b 58 with default parameters for each specie but specifying
BAM files from the two independent replicates were merged with 'Merge BAM Files' (v.1.2.0).
Genome coverage was obtained with “bamCompare” 59 tool, which calculates a ratio between each IP and Input pair, with parameters --skipNAs and --skipZeroOverZero. Reads were scaled using a spike-in factor that was calculated by the number of uniquely mapped reads to S. cerevisiae genome in each sample. Average files from independent replicates were generated with “bigwigCompare” tool 59.
Assembly: hg38
Supplementary files format and content: bedgraph files include IP/Input ratios

source_name: hTert RPE-3

growth_protocol: RPE-1 cells were grown in Dubelcco’s Modified Eagle’s Medium (DMEM) F-12 supplemented with 50 units ml-1 penicillin, 50 units ml-1 streptomycin and 10% Fetal Bovine Serum (FBS). Cells were cultured at 37ºC in 5% CO2 atmosphere.

extract_protocol:
Total RNA (200-300 µg) was used for biotinylation and purification of 4sU-labeled nascent RNAs. 1 µg spike-in from yeast per 100 µg total RNA was added. Total RNA was fragmentated using Bioruptor Pico. The biotynilation reaction consisted of total fragmented RNA and EZLink HPDP-Biotin (Thermo Scientific, 20217) dissolved in dimethylformamide (DMF) and was performed in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) for 2h with rotation at room temperature. Unbound Biotin-HPDP was removed by chloroform extraction. RNA was precipitated with 10th volume of 5M NaCl and 1 volume of isopropanol. Following one wash in 75% ethanol, the RNA pellet was left to dry and resuspended in 100 µl RNase-free water. Biotinylated RNA was purified using µMACs Streptavidin kit (Miltenyi Biotec, 130-074-101). Specifically, 100 µl of beads per 100 µg of RNA was incubated with rotation for 15 min and then washed three times with washing buffer (100 mM Tris pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20) at 65ºC, followed by three washes at room temperature. RNA was eluted twice using 100 mM DTT (Sigma) and recovered using miRNeasy Micro Kit (Qiagen, 217084) according to instructions.
Libraries preparation of chromatin-associated RNA were done using Kapa RNA HyperPrep (Roche)

treatment_protocol: For TTseq, RPE-1 cells were serum starved by 48h incubation in the same medium, but with reduced 0.1% FBS content. Then, cells were treated with 50µM etoposide for 30 minutes and 10 minutes with 4sU. Also, RPE-1 Cas9 cells were transfected with a guide RNA to generate Knock-Out for TOP2B.

value: hTert RPE-3

value: Immortalized retinal pigment epithelial cells

tag: cell cycle

tag: hydroxyurea (hu)_treatment

value: Non treated


title: Nedd8 Cre2, rep 3

value: virus expressing RFP-CRE


title: RNA-Seq of Medicago truncatula (A17): floral_organ_mature_pollen, 7w (rep. 2)

value: Medicago truncatula (A17)


title: 4sU_RNA_gC

description: Library name: 4sU_RNA_gC

source_name: hTert RPE-2

value: hTert RPE-2


title: NIND, Patient_7_RSEC_MolsPerCell

value: NIND (non-inflammatory neurological disease)


title: RNA-Seq of Medicago truncatula (A17): flower_stg8, 7w (rep. 3)

source_name: flowers

value: flowers


title: RRMS, Patient_5_RSEC_MolsPerCell

value: RRMS (relapsing-remitting multiple sclerosis)

value: untreated

value: Cerebrospinal fluid (CSF)


title: Nedd8 Cre2, rep 1

value: brain

value: hippocampus


title: RNA-Seq of Medicago truncatula (A17): flower_stg8, 7w (rep. 2)


title: RRMS, Patient_4_RSEC_MolsPerCell


title: Nedd8 Cre1, rep 4


title: Nedd8 Cre3, rep 2


title: RNA-Seq of Medicago truncatula (A17): flower_stg8, 7w (rep. 1)


title: lymph node metastases 3

city: Xi’an

first: Shuang

last: Xie

address: No. 569, Xinsi Road, Baqiao District, Xi’an, Shaanxi 710038, China

institute: Department of General Surgery, The Second Affiliated Hospital of Air Force Medical University

description:
Library name: LN_P3
GEXSCOPE

library_source: transcriptomic single cell

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17  to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a  to map reads to the reference genome GRCh38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1  software, and used to generate expression matrix files for subsequent analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts values for each Sample …
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: lymph node metastases

extract_protocol:
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters.
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: lymph node metastases

value: male

tag: pathological stage


title: RRMS, Patient_2_RSEC_MolsPerCell


title: tumor deposits 3

description:
Library name: TD_P3
GEXSCOPE

source_name: colon tumor deposits

value: colon tumor deposits


title: HEK293T_Tc1-ITR-HSMAR2

city: Boston

first: Long-Wen

last: Zhao

state: Massachusetts

address: 77 Avenue  Louis Pasteur, NRB Room 266

department: Genetics

country: USA

institute: Harvard Medical School

description:
Library name: S7
cDNA (RT-PCR amplicon)

data_processing:
Reads were mapped using Minimap2 (V 2.22 --r1109dirty), and isoform identification was performed using IsoQuant (V 3.5.0).
Assembly: The reference FASTA files were provided as supplementary files.
Supplementary files format and content: IsoQuant output (.bed.gz, transcript isoforms).

growth_protocol: C. elegans strains were maintained at 20 °C on nematode growth medium (NGM) plates seeded with Escherichia coli (E. coli) OP50. HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, 11995-065) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10437-028). All cells were maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNAs were extracted using RNA Clean & Concentrator-5 (Zymo, R1014), followed by DNase treatment to eliminate genomic DNA contamination.
Total RNA was reverse transcribed using Induro® Reverse Transcriptase (NEB, M0681L) with Random Primer Mix. cDNA was amplified using primers covering the SOS splicing events.


title: RNA-Seq of Medicago truncatula (A17): meristem_inflorescence, 7w (rep. 3)

source_name: inflorescence apex

value: inflorescence apex


title: Nedd8 Cre1, rep 2


title: serosal side 3

description:
Library name: To_P3
GEXSCOPE

source_name: colon tumor

value: colon tumor


title: Nedd8 Cre2, rep 4


title: HEK293T_HSMAR2-ITR-Tc1

description:
Library name: S6
cDNA (RT-PCR amplicon)


title: HEK293T_HSMAR2_GFP_AKAP17AKO

description:
Library name: S21
cDNA (RT-PCR amplicon)


title: mucosal side 3

description:
Library name: Ti_P3
GEXSCOPE


title: RNA-Seq of Medicago truncatula (A17): meristem_inflorescence, 7w (rep. 1)


title: RNA-Seq of Medicago truncatula (A17): floral_organ_mature_pollen, 7w (rep. 1)

value: pollen


title: Nedd8 Cre2, rep 2


title: 4sU_RNA_ETOP

description: Library name: 4sU_RNA_ETOP

source_name: hTert RPE-1

value: hTert RPE-1

value: Immortalized retinal pigment epithelial cells

value: Non treated


title: Sp_9w_RNA_BxC_XX_3

city: Munich

first: Tim

last: Hasenbein

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

data_processing:
Paired-end RNA-seq data of 9-week-old mice were aligned using STAR. Reads characterized by intron sizes exceeding 100000, multimappers, and alignments containing non-canonical junctions were removed prior to subsequent analysis. Uniquely aligned reads were quantified using htseq-count and the –stranded reverse flag.
Assembly: mm10
Supplementary files format and content: Text file including the raw read counts for each sample

source_name: Spleen

extract_protocol:
Samples were harvested for brain, heart, liver, lung, kidney, and spleen from 9-week-old F1 hybrid mice (BL6 x CAST) and snap-frozen in liquid nitrogen. The GentleMACS Dissociator (program RNA_02_01) was used to homogenize tissues in 1 ml TRIzol per 50-100 mg sample. RNA isolation was conducted as described in the manufacturer's instructions (Invitrogen, TRIzol Reagent, Cat. #15596018) using 1 ml of the sample solution.
RNA-seq libraries were constructed with 100 ng of RNA and Illumina's Stranded mRNA Prep Ligation Kit. The Agilent TapeStation System was used to assess the concentration and fragment length of the libraries. Sequencing was performed using a NovaSeq6000 50bp paired-end sequencing.

value: Spleen

value: 9 weeks

value: F


title: HEK293T_HSMAR2_GFP_WT

description:
Library name: S20
cDNA (RT-PCR amplicon)


title: 4sU_RNA_DMSO

description: Library name: 4sU_RNA_DMSO


title: Sp_9w_RNA_BxC_XX_2


title: RNA-Seq of Medicago truncatula (A17): apex_vegetative, 6d (rep. 3)

source_name: vegetative apex

value: Medicago truncatula (A17)

value: vegetative apex


title: HEK293T_Tc1_GFP_AKAP17AKO

description:
Library name: S19
cDNA (RT-PCR amplicon)


title: lymph node metastases 2

description:
Library name: LN_P2
GEXSCOPE

value: female


title: tumor deposits 2

description:
Library name: TD_P2
GEXSCOPE


title: RNA-Seq of Medicago truncatula (A17): apex_vegetative, 6d (rep. 2)


title: HEK293T_Tc1_GFP_WT

description:
Library name: S18
cDNA (RT-PCR amplicon)


title: Nedd8 Cre1, rep 3

source_name: brain

value: brain

value: virus expressing RFP-CRE


title: serosal side 2

description:
Library name: To_P2
GEXSCOPE


title: Lu_9w_RNA_BxC_XX_3

source_name: Lung

value: Lung


title: RNA-Seq of Medicago truncatula (A17): meristem_inflorescence, 7w (rep. 2)


title: mucosal side 2

description:
Library name: Ti_P2
GEXSCOPE


title: RNA-Seq of Medicago truncatula (A17): leaf_2, 7d (rep. 3)

source_name: leaf

value: leaf


title: Nedd8 Cre1, rep 1

value: hippocampus


title: TgSNF2a_TgSNF2b_IAA_ATAC_2

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

description:
Library name: TgSNF2a_TgSNF2b_IAA_ATAC_2
ATAC_SEQ

data_processing:
For CUT&Tag and ATAC-seq analysis, the paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2.  The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
Raw RNA-seq reads were filtered by fastp with parameters: -z 4 -q 20 -u 30. The resulted clean reads were mapped to the T. gondii genome of ME49 strain (ToxoDB release 68) using Hisat2, and the read count for each gene was calculated by featureCounts using the sorted bam files. Differentially expressed genes were calculated by R package DESeq2. Gene expression with a |Log2 fold change| >1 and adjusted p value < 0.01 was considered as significantly differentially expressed.
Assembly: ToxoDB-68_TgondiiME49 genome
Supplementary files format and content: bigwig, narrowPeak

organism: Toxoplasma gondii

source_name: tachyzoites

growth_protocol: Transgenic strains were inoculated in 75 cm2 cell culture flasks and washed after 4 h to remove non-invasive parasites. Transgenic strains (1 x 107) were harvested after 20 h of incubation.

extract_protocol:
The CUT&Tag experiments were performed by using NovoNGS CUT&Tag 4.0 High-Sensitivity Kit for Illumina (Novoprotein, Suzhou, China) as previously described. Briefly, fresh tachyzoites (1 × 107) were purified and were bound to activated concanavalin A beads (10 μL/sample) and incubated for 10 min at room temperature. The mixture was resuspended and incubated with primary antibody (1:50, mouse anti-HA) at 4°C overnight, and followed by secondary antibody (1:100, goat anti-mouse IgG) for 1 h at room temperature. The parasites were then resuspended with pAG-Transposome buffer and incubated for 1 h at room temperature on a rotator. Tagmentation was stopped by MgCl2 treatment and DNA extraction was performed using DNA extract beads (Novoprotein, Suzhou, China). For RNA-SEQ, T. gondii tachyzoites (~5 ×107) of TgSNF2b-mAID, TgSNF2a-mAID and double knockdown strains were treated with either 500 μM IAA or vehicle were purified for total RNA extraction by using Trizol regent (Invitrogen). The quality and integrity of RNA were detected using Qubit Fluorometer (Life Technologies, CA, USA) and Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively. For ATAC-seq, The double knockdown strain TgSNF2a-mAID/TgSNF2b-mAID were treated with either 500 μM IAA or vehicle for 48 hours, and were purified for ATAC-seq analysis by using Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711-02, Vazyme, China). Briefly, fresh tachyzoites were resuspended with 50 μL cold Lysis Buffer (containing 0.1% NP40, 0.1% Tween20, 0.01% Digitonin) and incubated for 5 min on ice. Then, the supernatants were removed by centrifugation and the pellets were resuspended in 50 μL transposition reaction mix buffer (containing 0.1% Tween20, 0.01% Digitonin, 1×TTBL, 0.1% TTE Mix V50) at 37℃ for 30 min with gentle mix. The reactions were terminated by addition of 5 μL STOP buffer, and the released DNA fragments were extracted by ATAC DNA Extract Beads in the kits and eluted with Nuclease-free ddH2O.
For CUT&Tag and ATAC Library construction, . Illumina sequencing libraries were generated by PCR amplification using specific adaptors according to the manufacturer’s recommendations. Sequencing of the CUT&Tag libraries was performed using the Illumina Novaseq 6000 platform (Beijing Novogene Technology Co., Ltd).  For RNA-seq library construction, Illumina sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations. Sequencing was performed using the Illumina Novaseq 6000 platform (Beijing Novogene Technology Co., Ltd) to generate 150 bp paired-end reads.

treatment_protocol: Transgenic parasite strains cultured in Vero cells were treated with either 500 μM IAA or vehicle for indicated hours.

value: tachyzoites

value: co-culture with 500 μM IAA for 48 h


title: lymph node metastases 1

description:
Library name: LN_P1
GEXSCOPE

value: lymph node metastases


title: TgSNF2a_TgSNF2b_IAA_ATAC_1

description:
Library name: TgSNF2a_TgSNF2b_IAA_ATAC_1
ATAC_SEQ


title: Lu_9w_RNA_BxC_XX_2


title: RNA-Seq of Medicago truncatula (A17): leaf_2, 7d (rep. 2)


title: RNA-Seq of Medicago truncatula (A17): leaf_2, 7d (rep. 1)


title: Lu_9w_RNA_BxC_XX_1


title: tumor deposits 1

description:
Library name: TD_P1
GEXSCOPE

value: colon tumor deposits


title: TgSNF2a_TgSNF2b_ATAC_2

description:
Library name: TgSNF2a_TgSNF2b_ATAC_2
ATAC_SEQ

value: Untreated


title: Li_9w_RNA_BxC_XX_3

source_name: Liver

value: Liver


title: TgSNF2a_TgSNF2b_ATAC_1

description:
Library name: TgSNF2a_TgSNF2b_ATAC_1
ATAC_SEQ


title: primary colon tumor1

description:
Library name: T_P1
GEXSCOPE

value: colon tumor


title: RNA-Seq of Medicago truncatula (A17): hypocotyl, 8d (rep. 3)

source_name: hypocotyl

value: hypocotyl


title: ME49_RNASEQ_3

description:
Library name: ME49_RNASEQ_3
RNA_SEQ


title: Li_9w_RNA_BxC_XX_2

value: 9 weeks

value: F


title: RNA-Seq of Medicago truncatula (A17): hypocotyl, 8d (rep. 2)

value: Medicago truncatula (A17)


title: STX4

city: New Haven

first: Suyavaran

last: Arumugam

state: Connecticut

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

description: Library name: STX4

data_processing:
Data cleaning with cutadapt, to remove low quality reads and adapters.
Mapping to genome (bam format) using HISAT2. Mapping the reads of each sample to the reference genome.
StringTie to perfom assembly of the transcripts. Merged all assemblies to create StringTie merged gtf
mRNA expression profiling with StringTie
Differential expression analysis with edgeR
Assembly: GRCh38
Supplementary files format and content: Text files with FPKM files, transcript count matrix and gene count matrix

source_name: LX2 cells

growth_protocol: LX2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), Glutamax and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.5μg of total RNA was used for the construction of sequencing libraries. RNA integrity was checked using Agilent Technologies 2100 Bioanalyzer. (poly (A) tail containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. Following purification, poly (A) RNA was fragmented using divalent cation buffer in elevated temperature.
Poly(a) RNA sequncing library was prepared using Illumina's Truseq-stranded mRNA sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 bioanalyzer high sensitivity DNA chip. Paired-ended sequencing was performed on Illumina's Novaseq 6000 sequencing system.

treatment_protocol:
Post 24 hr of seeding the cells were serum starved for 16 hrs prior to stimulation protocol.
Post 16 hr of serum starvation the cells were either pretreated with 10μM IFM - 004990-7 (STINGX) for 3 hrs or directly subjected to 50mM ethanol for 24hrs.

value: LX2 cells

value: Hepatic stellate cells

value: Wild type

value: 10μM STX

value: 24 hr


title: Sp_9w_RNA_BxC_XX_1

value: Spleen


title: Li_9w_RNA_BxC_XX_1


title: RNA-Seq of Medicago truncatula (A17): apex_vegetative, 6d (rep. 1)

value: vegetative apex


title: STX3

description: Library name: STX3


title: Ki_9w_RNA_BxC_XX_3

source_name: Kidney

value: Kidney


title: ME49_RNASEQ_2

description:
Library name: ME49_RNASEQ_2
RNA_SEQ

value: tachyzoites


title: ME49_RNASEQ_1

description:
Library name: ME49_RNASEQ_1
RNA_SEQ


title: STX1

description: Library name: STX1


title: Ki_9w_RNA_BxC_XX_2


title: RNA-Seq of Medicago truncatula (A17): root_whole_root, 4d (rep. 3)

source_name: root

value: root


title: TgSNF2a_TgSNF2b_24h_RNASEQ_2

description:
Library name: TgSNF2a_TgSNF2b_24h_RNASEQ_2
RNA_SEQ

value: co-culture with 500 μM IAA for 24 h


title: RNA-Seq of Medicago truncatula (A17): hypocotyl, 8d (rep. 1)


title: ETOH_STX4

description: Library name: ETOH_STX4

value: 50mM Ethanol + 10μM STX


title: TgSNF2a_TgSNF2b_24h_RNASEQ_1

description:
Library name: TgSNF2a_TgSNF2b_24h_RNASEQ_1
RNA_SEQ


title: Ki_9w_RNA_BxC_XX_1


title: RNA-Seq of Medicago truncatula (A17): root_whole_root, 4d (rep. 1)


title: STX2

description: Library name: STX2


title: RNA-Seq of Medicago truncatula (A17): root_whole_root, 4d (rep. 2)


title: He_9w_RNA_BxC_XX_3

source_name: Heart

value: Heart


title: TgSNF2b_72h_RNASEQ_2

description:
Library name: TgSNF2b_72h_RNASEQ_2
RNA_SEQ

value: co-culture with 500 μM IAA for 72 h


title: ETOH_STX3

description: Library name: ETOH_STX3


title: He_9w_RNA_BxC_XX_2

value: 9 weeks


title: ETOH_STX2

description: Library name: ETOH_STX2


title: TgSNF2b_72h_RNASEQ_1

description:
Library name: TgSNF2b_72h_RNASEQ_1
RNA_SEQ


title: Aedes_aegypti_eggs_sRNA_rep1

description:
Library name: Aedes_aegypti_eggs_sRNA_rep1
Small RNA sequencing from Aedes aegypti eggs replicate 1

organism: Aedes aegypti

source_name: eggs

value: eggs

value: mixed

value: wild type

value: oxidized

value: 0 - 4 hour old


title: TgSNF2b_24h_RNASEQ_3

description:
Library name: TgSNF2b_24h_RNASEQ_3
RNA_SEQ


title: He_9w_RNA_BxC_XX_1

value: F


title: Aedes_aegypti_ovaries_sRNA_rep2

description:
Library name: Aedes_aegypti_ovaries_sRNA_rep2
Small RNA sequencing from Aedes aegypti ovaries replicate 2

source_name: ovaries

value: ovaries

value: female

value: 1 week old


title: Br_9w_RNA_BxC_XX_3

source_name: Brain

value: Brain


title: ETOH_STX1

description: Library name: ETOH_STX1

value: LX2 cells

value: Hepatic stellate cells

value: Wild type

value: 24 hr


title: TgSNF2b_24h_RNASEQ_2

description:
Library name: TgSNF2b_24h_RNASEQ_2
RNA_SEQ

value: tachyzoites

value: co-culture with 500 μM IAA for 24 h


title: ETOH4

description: Library name: ETOH4

value: ETOH


title: Aedes_aegypti_ovaries_sRNA_rep1

description:
Library name: Aedes_aegypti_ovaries_sRNA_rep1
Small RNA sequencing from Aedes aegypti ovaries replicate 1


title: Br_9w_RNA_BxC_XX_2

value: 9 weeks


title: TgSNF2b_24h_RNASEQ_1

description:
Library name: TgSNF2b_24h_RNASEQ_1
RNA_SEQ


title: ETOH3

description: Library name: ETOH3


title: Br_9w_RNA_BxC_XX_1


title: TgSNF2a_24h_RNASEQ_3

description:
Library name: TgSNF2a_24h_RNASEQ_3
RNA_SEQ


title: TgSNF2a_24h_RNASEQ_2

description:
Library name: TgSNF2a_24h_RNASEQ_2
RNA_SEQ


title: ETOH1

description: Library name: ETOH1


title: ID8 omentum tumor - HSCDA Deficient mouse - ear tag 800

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTQ generated with bcl2fastq (version 2.20.0.422) files were processed using the nf-core/rnaseq pipeline (version 3.12, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCm39, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package (version 1.26.0) under R version 4.2.2.
Assembly: GRCm39
Supplementary files format and content: *_quant.sf.gz: Salmon transcript quantification file (tab-sparated text, https://salmon.readthedocs.io/en/latest/file_formats.html); to be used together with salmon_tx2gene.tsv by software accepting Salmon data

source_name: omentum tumor

growth_protocol: 5 million ID8 cells were implanted into HSCDA Proficient or Deficient mice by intraperitoneal injection. Tumors were allowed to progress for 39 days prior to sacrifice and necropsy.

extract_protocol:
Omentum tumors were homogenized in Qiagen RLT Plus buffer supplemented with 1% 2-mercaptoethanol at 4 °C using a Biospec Products Minibeadbeater. RNA was isolated using Qiagen RNeasy Plus mini kit.
Ribosomal RNA depletion was performed using QIAseq FastSelect -rRNA kit (Qiagen #335376). Step 1 of fragmentation was performed for 7 minutes at 94 °C, followed by FastSelect hybridization. First-strand synthesis, second-strand synthesis, A-tailing, adapter ligation, and library amplification were performed using the KAPA mRNA HyperPrep kit (Roche #08105952001). We used 5 μL of 1.5 μM KAPA single index adapters for Illumina (Roche #0800577001) for adapter ligation. We performed 12 amplification cycles. KAPA Pure magnetic beads (Roche #08105901001) were used for all cleanup steps

value: omentum tumor

value: ovarian cancer


title: Aedes_aegypti_eggs_sRNA_rep2

description:
Library name: Aedes_aegypti_eggs_sRNA_rep2
Small RNA sequencing from Aedes aegypti eggs replicate 2

value: eggs

value: mixed

value: wild type

value: oxidized


title: HFF His-GTG KO, rep1

city: Rehovot

first: Noa

last: Aharon-Hefetz

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample 7
His3_R1_S10

data_processing:
tRNA-seq analysis is described in (DOI: 10.1073/pnas.2106556118)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes read counts of mature tRNA genes for all samples

source_name: HFF

growth_protocol: Human Foreskin Fibroblasts (ATCC) were grown in DMEM high glucose medium (Biological Industries) supplemented with 10% heat-inactivated FBS (Life Technologies), 1% penicillin/ streptomycin (P/S), and 1% L-Glutamine.

extract_protocol:
Samples were harvested with Tri-Reagent (Sigma-Aldrich). Total RNA was extracted according to the manufacturer’s protocol.
tRNA-seq libraries were constructed based on DM-TGIRT-seq protocol (DOI: 10.1038/nmeth.3478) with some modifications, as described in (DOI: 10.1073/pnas.2106556118)

treatment_protocol: HFF (passage 25) were transduced with lentivirus containing the sgRNA-cloned CRISPR-V2 plasmid at a MOI=1. Media containing lentiviruses was supplemented with 8ug/ml of Hexadimethrine Bromide (Sigma Aldrich). 48 hours after transduction, 1.75ug/ml puromycin (Thermo Fisher) was added to select for infected cells. Then, the media was refreshed (without antibiotics), and cells were recovered for 48 hours.

value: HFF

value: His-GTG KO


title: HFF His-GTG KO, rep3

description:
Library name: Sample 9
His3_R3_S12


title: HFF His-GTG KO, rep2

description:
Library name: Sample 8
His3_R2_S11


title: ID8 omentum tumor - HSCDA Deficient mouse - ear tag 721


title: TgSNF2a_24h_RNASEQ_1

description:
Library name: TgSNF2a_24h_RNASEQ_1
RNA_SEQ


title: ME49_CUT&Tag_2

description:
Library name: ME49_CUT_Tag_2
CUT&Tag

data_processing:
For CUT&Tag and ATAC-seq analysis, the paired-end reads were filtered and then aligned to the T. gondii reference genome using Bowtie2.  The resulting sam files were transformed into bam files. PCR duplicates were removed from the sorted bam files using Picard tools. The filtered reads were then employed to identify peaks using MACS2. The overlapped peaks in the two biological replicates were identified by the Irreproducibility Discovery Rate (IDR).
Raw RNA-seq reads were filtered by fastp with parameters: -z 4 -q 20 -u 30. The resulted clean reads were mapped to the T. gondii genome of ME49 strain (ToxoDB release 68) using Hisat2, and the read count for each gene was calculated by featureCounts using the sorted bam files. Differentially expressed genes were calculated by R package DESeq2. Gene expression with a |Log2 fold change| >1 and adjusted p value < 0.01 was considered as significantly differentially expressed.
Assembly: ToxoDB-68_TgondiiME49 genome
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

value: Untreated


title: HFF iMet-CAT KO, rep2

description:
Library name: Sample 5
sg8_R2_S17

value: iMet-CAT KO


title: Control, 16hr, CT3

description: Library name: CT3

value: LX2 cells

value: Hepatic stellate cells


title: HFF iMet-CAT KO, rep3

description:
Library name: Sample 6
sg8_R3_S18


title: Control, 16hr, CT4

description: Library name: CT4

value: Wild type

value: 24 hr


title: ID8 omentum tumor - HSCDA Deficient mouse - ear tag 714


title: ID8 omentum tumor - HSCDA Deficient mouse - ear tag 720


title: Control, 16hr, CT2

description: Library name: CT2


title: HFF iMet-CAT KO, rep1

description:
Library name: Sample 4
sg8_R1_S16


title: ID8 omentum tumor - HSCDA Proficient mouse - ear tag 708


title: Control, 16hr, CT1

description: Library name: CT1


title: HFF non-targeting, rep3

description:
Library name: Sample 3
NT1_R3_S3

value: non-targeting sgRNA


title: ME49_CUT&Tag_1

description:
Library name: ME49_CUT_Tag_1
CUT&Tag

value: tachyzoites


title: ID8 omentum tumor - HSCDA Proficient mouse - ear tag 707


title: TgSNF2b_CUT&Tag_2

description:
Library name: TgSNF2b_CUT_Tag_2
CUT&Tag


title: TgSNF2b_CUT&Tag_1

description:
Library name: TgSNF2b_CUT_Tag_1
CUT&Tag


title: HFF non-targeting, rep2

description:
Library name: Sample 2
NT1_R2_S2


title: ETOH2

description: Library name: ETOH2

value: ETOH


title: C3_R+35_CD8

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

institute: University Stuttgart

description: Library name: C3_R+35_CD8

data_processing:
Sequencing was performed on an Illumina NovaSeq 600 deep sequencer acquiring 2 x 150 bp paired end reads.
Adapter sequences and low quality bases were remode using using Trim Galore!.
Reads were mapped to the human reference genome T2T-CHM13v2.0 (hs1) using Bowtie2.
Peak-calling was performed using SEACR in the “stringent” mode with the “norm” flag set and control type set to “Threshold” with a threshold of 0.03.
Assembly: T2T-CHM13v2.0 (hs1)
Supplementary files format and content: bigWig files and bed files containing called peaks
Library strategy: Cut&Tag

source_name: CD8+ immune cells

extract_protocol:
PBMCs were isolated from whole blood using density gradient centrifugation. PBMC subtypes were isolated from total PBMCs using antibody-coupled magnetic microbeads
Cut&Tag libraries were prepared using the Cell Signaling Technology CUT&Tag Assay Kit and the the CUT&Tag Dual Index Primers and PCR Master Mix for Illumina Systems. Libraries were sequenced at Novogene.

value: CD8+ immune cells

tag: cut&tag antibody

tag: subject

value: Control subject

tag: timepoint


title: ID8 omentum tumor - HSCDA Proficient mouse - ear tag 704

tag: tissue

value: omentum tumor

value: ovarian cancer


title: TgSNF2a_CUT&Tag_2

city: Nanning

description:
Library name: TgSNF2a_CUT_Tag_2
CUT&Tag

tag: treatment


title: HFF non-targeting, rep1

description:
Library name: Sample 1
NT1_R1_S1


title: C3_R+1_CD8

description: Library name: C3_R+1_CD8


title: TgSNF2a_CUT&Tag_1

description:
Library name: TgSNF2a_CUT_Tag_1
CUT&Tag


title: QKI_293T_siQKI3

city: Houston

first: Eric

last: Van Nostrand

state: TX

address: 1 Baylor Plaza Rm T334

department: Therapeutic Innovation Center

institute: Baylor College of Medicine

description:
Library name: QKI_293T_siQKI3
10

data_processing:
Remove 10nt UMI from 5' end of read (293T experiment only): umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
Adapter trimming: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.2 --quality-cutoff 6 -m 18 -a AGATCGGAAGAGCACACGTC -a AAAAAAAAAAAAAAAAAAAA -a GGGGGGGGGGGGGGGGGGGG -A AGATCGGAAGAGCGTCGTGT -A TTTTTTTTTTTTTTTTTTTT -O 5 -o $prefix.fastq.r1.gz -p $prefix.fastq.r2.gz
UMI removal from end of R2 (293T experiment only): cutadapt -j 8 -U -10 -o $fastq1_working_trim2 -p $fastq2_working_trim2 $fastq1_working_trim $fastq2_working_trim
Repeat removal: STAR --runMode alignReads --runThreadN 8 --genomeDir $rep_star_database --readFilesCommand zcat --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFileNamePrefix $output_rep_database --outSAMtype BAM Unsorted --outFilterType BySJout --outBAMcompression 10 --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outStd Log --readFilesIn $fastq1_working_trim2 $fastq2_working_trim2
Sort: fastq-sort --id $prefix.sorted.RepUnmapped.out.mate1 > $prefix.sorted.RepUnmapped.out.mate1.sorted.fq fastq-sort --id $prefix.sorted.RepUnmapped.out.mate2 > $prefix.sorted.RepUnmapped.out.mate2.sorted.fq
Genome mapping: STAR --runMode alignReads --runThreadN 8 --genomeDir /hg19/star_2.4.0j_encode/ --genomeLoad NoSharedMemory --readFilesIn $prefix.RepUnmapped.out.mate1.s.fq $prefix.RepUnmapped.out.mate2.s.fq --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix $prefix.rmRep.genomemap --outSAMattributes All --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outStd Log --alignEndsType EndToEnd --outBAMcompression 10 --outSAMmode Full
Remove PCR duplicates (293T experiment only): umi_tools dedup --random-seed 1 --stdin $output_genome_sorted_bam --method unique --stdout $output_rmDup_bam
Gene-level expression quantification: featureCounts -p -a /path/to/gencode.v19.annotation.gtf -s 2 -o $prefix1.feature.count /path/to/sortedbam1.bam /path/to/sortedbam2.bam /path/to/sortedbam3.bam …
Isolate protein-coding genes only: perl pull_proteincodinggenes.pl $prefix1.feature.count hg19
Gene-level expression analysis: deseq $prefix1.feature.count.proteincodingonly.txt $prefix1.experiment.design.tsv $prefix1.feature.count.tsv.proteincodingonly.deseq.txt
Splicing analysis (rmats v4.3.0): rmats.py --b1 bamfilist.siNC.txt --b2 bamfilist.siQKI.txt --gtf gencode.v19.annotation.gtf -t paired --libType fr-secondstrand --variable-read-length --readLength 150 --nthread 8 --od rmats/ --tmp rmats/tmp/
Assembly: hg19
Supplementary files format and content: Bigwig genome coverage files (.bw), rmats splicing analysis output (.rmats), Gene-level read counts (featureCounts .txt file)

growth_protocol: For D0 (pluripotency), cells were dissociated (Accutase), plated in FTDA growth medium (Rao, et al. Cell Stem Cell 2016 PMID 26748419), and cultured overnight prior to UV crosslinking. Cardiomyocyte differentiation was conducted following a previously established protocol (M. Zhang et al., 2015 PMID 25639979, Rao, et al. Cell Stem Cell 2016 PMID 26748419). In summary, confluent human embryonic stem cells (hESCs) dissociated (Accutase), pelleted, resuspended in ITS buffer supplemented with CHIR and BMP4 based on differentiation efficiency screening (WT: 1.5 uM CHIR, 1.5 ng/mL BMP4 ; QKI KO: 1.25 uM CHIR, 1.5 ng/mL BMP4), and plated. After 24 hours, media was replaced with TS media and cultured for 24 hours, followed by replacement with TS media supplemented with 100nM C59 for 48 hours (D4 (cardiac progenitors) were crosslinked at this stage). Fresh media (TS+100 mM C59) was added, followed by 24 hours, followed by media changes with TS media every 48 hours. D8 (cardiomyocyte) samples were UV crosslinked after confirmation of beating at days 7-8.

extract_protocol:
RNA was extracted by standard Trizol extraction.
For cardiomyocytes, RNA was polyA-enriched, followed by library preparation with Illumina stranded mRNA kits. For 293T experiments, polyA-enriched RNA was isolated with NEBNext® High Input Poly(A) mRNA Isolation kit, followed by library preparation utilizing the same protocol as seCLIP (Blue SM et al, Nature Protocols. 2022 PMID 35322209), based off of a published RNA-seq approach (Shishkin AA, Nature Methods. 2015 PMID 25730492).

treatment_protocol: For 293T QKI siRNA knockdown experiments, non-targeting siRNA (Silencer® select Negative control# 1, Invitrogen) or siRNA against QKI (Silencer® select-ID s18084, Invitrogen) was transfected at a concentration of 10 µM per well using Lipofectamine™ RNAimax (Cat# 13778150, Invitrogen) according to the manufacturer’s guidelines.

value: QKI siRNA


title: plt3_plt7_IM_biorep5

city: Wageningen

first: Merijn

last: Kerstens

address: Droevendaalsesteeg 1

department: Plant Developmental Biology

country: Netherlands

institute: Wageningen University & Research

description: Library name: plt3plt7_IM_5

data_processing:
Raw reads were trimmed with fastp v0.23.4
Counts were generated with kallisto v0.46.1
Assembly: TAIR10.1 cDNA
Supplementary files format and content: TSV format of estimated counts by kallisto

organism: Arabidopsis thaliana

source_name: inflorescence meristem

growth_protocol: Seedlings for SAM harvest where grown on agar plates on top of a nylon mesh for 7 days. Plants for IM harvest were sown directly on soil and harvested at 31-33 dpg. Each sample contains roughly 50 meristems.

extract_protocol:
Tissues were collected in RNAlater on ice. Total RNA was extracted according to the LogSpin protocol (Yaffe et al, 2012) and purified with EtOH precipitation
The NEBNext Ultra II Directional RNA Library Prep Kit was used at GenomeScan BV according to the manufacturers instructions

value: inflorescence meristem

value: plt3 plt7

tag: harvest group


title: C3_PF_CD8

description: Library name: C3_PF_CD8

value: PF


title: QKI_293T_siQKI2

description:
Library name: QKI_293T_siQKI2
10


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_mid_stg12_stamens, 7w/8w/17d (rep. 3)

organism: Eutrema salsugineum

source_name: stamens

value: Eutrema salsugineum (Shandong)

value: stamens


title: QKI_293T_siQKI1

description:
Library name: QKI_293T_siQKI1
10


title: plt3_plt7_IM_biorep4

description: Library name: plt3plt7_IM_4


title: plt3_plt7_IM_biorep3

description: Library name: plt3plt7_IM_3


title: C2_R+1_CD8

description: Library name: C2_R+1_CD8


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_mid_stg12_stamens, 7w/8w/17d (rep. 1)


title: plt3_plt7_IM_biorep2

description: Library name: plt3plt7_IM_2


title: C2_PF_CD8

description: Library name: C2_PF_CD8


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_early_stg12_carpels, 7w/8w/18d (rep. 3)

source_name: carpels

value: carpels


title: QKI_293T_siNC3

description:
Library name: QKI_293T_siNC3
10

value: control siRNA


title: C1_R+35_CD8

description: Library name: C1_R+35_CD8


title: QKI_293T_siNC2

description:
Library name: QKI_293T_siNC2
10


title: plt3_plt7_IM_biorep1

description: Library name: plt3plt7_IM_1


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_early_stg12_carpels, 7w/8w/18d (rep. 2)


title: C1_R+1_CD8

description: Library name: C1_R+1_CD8


title: Col-0_IM_biorep5

description: Library name: WT_IM_5


title: QKI_293T_siNC1

description:
Library name: QKI_293T_siNC1
10


title: ID8 omentum tumor - HSCDA Proficient mouse - ear tag 703


title: QKI_293T_IP2

description:
Library name: QKI_293T_IP2
seCLIP

data_processing:
Steps were performed using an eCLIP processing pipeline, with scripts available at https://github.com/VanNostrandLab/eclip , based off of the published analysis pipeline described in Blue, SM, et al. Nature Protocols (2022), PMID 35322209.
Remove 10nt UMI from 5' end of read: umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin /storage/vannostrand/path/to/clip1.fastq.gz
First adapter trimming. Command: cutadapt -j 8 --match-read-wildcards --times 3 -e 0.1 --quality-cutoff 6 -m 18 -a file:/storage/vannostrand/software/eclip/data/se.2.round.adapters.fasta -O 1 - --report minimal
Second adapter trimming (removes 10nt from 3' end to account for possible UMIs on 3' end of read). Command:  cutadapt -j 8 -u -10 -o clip1.trim.fastq.gz - --report minimal
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping and peak calling, in order to reduce peak artifacts). Command: STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/repbase/species_specific/homo_sapiens_repbase_v2 --genomeLoad LoadAndKeep --outBAMcompression 10 --outFileNamePrefix clip1.repeat.map/ --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesCommand zcat --readFilesIn clip1.trim.fastq.gz
Unique genomic mapping (takes repeat-removed raeds and maps to the reference genome). Command: STAR --runMode alignReads --runThreadN 8 --alignEndsType EndToEnd --genomeDir /storage/vannostrand/genomes/hg19/star_2.4.0j_encode --genomeLoad LoadAndKeep --outBAMcompression 10 --outFileNamePrefix clip1.genome.map/ --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped None --outStd Log --readFilesIn clip1.repeat.unmap.fastq
Sorting (sorts genome mapped output file). Command: samtools sort -@ 8 -m 2G -o clip1.genome.map.bam clip1.genome.map/Aligned.out.bam
Indexing: indexes sorted bam file. Command: samtools index clip1.genome.map.bam
PCR duplicate removal (uses UMI that was appended to read name to remove PCR duplicate reads that map to the same position and have the same UMI). Command: umi_tools dedup --random-seed 1 --stdin clip1.genome.map.bam --method unique --stdout clip1.bam > /dev/null
Index bam file. Command: samtools index input1.bam
Create bigwig from bam file. Command: b2bw --bam clip1.bam --cpus 1
Peak calling (runs CLIPper peak calling algorithm). Command: clipper --species hg19 --processors 8 --bam clip1.bam --outfile clip1.peak.bed
Peak processing (input normalization and identification of reproducible peaks). Command: process_peak --outdir /storage/vannostrand/software/eclip/tests/hg19/--read_type SE --species hg19 --report test.peak.summary.html --ip_bams clip1.bam clip2.bam --input_bams input1.bam input2.bam --peak_beds clip1.peak.bed clip2.peak.bed --ids clip1 clip2
Assembly: hg19
Supplementary files format and content: Bigwig genome coverage files (.bw), narrowPeak format peak bed files (.narrowPeak.bed.gz)

growth_protocol: 293T (Clontech) were cultured in proper medium supplemented with 10% FBS (Cytivia) and antibiotics and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
For each 10cm plate (~15 million cells), cells were washed once with cold phosphate buffered saline, and then UV crosslinked (254 nm, 400 mJ/cm2) on ice. Cells were then spun down, supernatant removed, and washed with cold phosphate buffered saline. Cell pellets were flash frozen on dry ice and stored at -80°C.
eCLIP was performed as described in Blue, SM, et al. Nature Protocols (2022), PMID 35322209. IP fragments were ligated to 3' RNA adapters and RNA was isolated and reverse-transcribed following SDS-PAGE and Western blot. cDNA products were ligated to 5' adapters and PCR-amplified.

treatment_protocol: For myc-tagged QKI experiments, HEK293T cells were transiently transfected with 10 µg of either WT (myc-QKI-5) or mutant (myc-QKI-5(K120A; R124A)) plasmid in 10 cm plates using the Viafect transfection reagent at a ratio of 1:2 (DNA: reagent) according to manufacturer’s guidelines and cultured for 72 hrs prior to crosslinking.

tag: modification

tag: eclip antibody


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_mature_pollen, 7w/8w/17d (rep. 3)

source_name: pollen

value: pollen


title: Col-0_IM_biorep4

description: Library name: WT_IM_4


title: A3_R+35_CD8

description: Library name: A3_R+35_CD8

value: Astronaut


title: C1_PF_CD8

description: Library name: C1_PF_CD8


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_mature_pollen, 7w/8w/17d (rep. 2)


title: C2_R+35_CD8

description: Library name: C2_R+35_CD8


title: Col-0_IM_biorep3

description: Library name: WT_IM_3


title: QKI_293T_input2

description:
Library name: QKI_293T_input2
seCLIP

tag: cell line


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_mid_stg12_stamens, 7w/8w/17d (rep. 2)


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_mature_pollen, 7w/8w/17d (rep. 1)


title: QKI_293T_IP1

description:
Library name: QKI_293T_IP1
seCLIP


title: Col-0_IM_biorep1

description: Library name: WT_IM_1


title: Col-0_IM_biorep2

description: Library name: WT_IM_2


title: A3_R+1_CD8

description: Library name: A3_R+1_CD8

tag: cell type


title: RNA-Seq of Eutrema salsugineum (Shandong): flower_stg12, 7w/8w/15d (rep. 3)

source_name: flowers

value: flowers


title: plt3_plt7_SAM_biorep5

description: Library name: plt3plt7_SAM_5

source_name: shoot apical meristem

value: shoot apical meristem

tag: genotype


title: QKI_293T_input1

description:
Library name: QKI_293T_input1
seCLIP


title: A2_R+35_CD8

description: Library name: A2_R+35_CD8


title: QKI_MYC_MUT_IN2

description:
Library name: QKI_MYC_MUT_IN2
seCLIP

value: Transfection of myc-QKI-5(K120A; R124A) transgene

value: anti-MYC (Santa Cruz sc-40)


title: A2_R+1_CD8

description: Library name: A2_R+1_CD8

value: CD8+ immune cells


title: RNA-Seq of Eutrema salsugineum (Shandong): floral_organ_early_stg12_carpels, 7w/8w/18d (rep. 1)


title: RNA-Seq of Eutrema salsugineum (Shandong): flower_stg12, 7w/8w/15d (rep. 2)


title: RNA-Seq of Eutrema salsugineum (Shandong): flower_stg12, 7w/8w/15d (rep. 1)


title: QKI_MYC_MUT_IP2

description:
Library name: QKI_MYC_MUT_IP2
seCLIP


title: A2_PF_CD8

description: Library name: A2_PF_CD8


title: QKI_MYC_MUT_IN1

description:
Library name: QKI_MYC_MUT_IN1
seCLIP


title: RNA-Seq of Eutrema salsugineum (Shandong): apex_inflorescence, 7w/8w/12d (rep. 3)

source_name: inflorescence apex

value: inflorescence apex


title: plt3_plt7_SAM_biorep3

description: Library name: plt3plt7_SAM_3


title: plt3_plt7_SAM_biorep2

description: Library name: plt3plt7_SAM_2


title: QKI_MYC_MUT_IP1

description:
Library name: QKI_MYC_MUT_IP1
seCLIP


title: RNA-Seq of Eutrema salsugineum (Shandong): apex_inflorescence, 7w/8w/12d (rep. 2)


title: A1_R+35_CD8

description: Library name: A1_R+35_CD8


title: plt3_plt7_SAM_biorep1

description: Library name: plt3plt7_SAM_1


title: RNA-Seq of Eutrema salsugineum (Shandong): apex_inflorescence, 7w/8w/12d (rep. 1)


title: A1_R+1_CD8

description: Library name: A1_R+1_CD8


title: QKI_MYC_WT_IN2

description:
Library name: QKI_MYC_WT_IN2
seCLIP

value: Transfection of myc-QKI-5 transgene


title: A3_PF_CD8

description: Library name: A3_PF_CD8


title: A1_PF_CD8

description: Library name: A1_PF_CD8


title: QKI_MYC_WT_IP2

description:
Library name: QKI_MYC_WT_IP2
seCLIP


title: Col-0_SAM_biorep5

description: Library name: WT_SAM_5


title: Col-0_SAM_biorep4

description: Library name: WT_SAM_4


title: QKI_MYC_WT_IN1

description:
Library name: QKI_MYC_WT_IN1
seCLIP


title: C3_R+35_CD4

description: Library name: C3_R+35_CD4

source_name: CD4+ immune cells

value: CD4+ immune cells

value: Control subject


title: QKI_MYC_WT_IP1

description:
Library name: QKI_MYC_WT_IP1
seCLIP


title: C3_R+1_CD4

description: Library name: C3_R+1_CD4


title: RNA-Seq of Eutrema salsugineum (Shandong): apex_vegetative, 9d (rep. 2)

source_name: vegetative apex

value: vegetative apex


title: C3_PF_CD4

description: Library name: C3_PF_CD4

value: PF


title: plt3_plt7_SAM_biorep4

description: Library name: plt3plt7_SAM_4

value: plt3 plt7


title: Col-0_SAM_biorep2

description: Library name: WT_SAM_2


title: C2_R+35_CD4

description: Library name: C2_R+35_CD4


title: Kidney, ACE-Seq

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

description: Library name: KidneyACE

data_processing:
Raw reads were trimmed for base quality and adaptor sequences using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and reads below a length of 20 bases were discarded.
The trimmed reads were aligned to the reference genomes using Bismark (v0.22.3) with the following parameters -D 15 -R 2 -L 20 -N 0 –score_min L,0,-0.2.
To account for A3A failure due to double-stranded DNA, reads with three or more consecutive non-converted cytosines in the CpH context were removed using the filter_non_conversion script included in the Bismark package.
Assembly: mm10
Supplementary files format and content: Tab-delimited file containing the chromosome, start position, end position, methylation percentage, count methylated, count unmethylated

source_name: Kidney

extract_protocol:
Extraction was carried out using a phenol/chloroform/isoamyl alcohol protocol with minor modifications {Molecular cloning: a laboratory manual. No. Ed. 2. Cold Spring Harbor laboratory press, 1989}. 500 µL of the lysed mouse tissues were transferred to pre-centrifuged (at 20,000g for 1 min) 5PRIME Phase Lock Gel tube (Quanta bio, 10847- 802). In a fume hood, 500 µL of phenol/chloroform/isoamyl alcohol (Sigma-Aldrich, 77617) was added to the phase Lock Gel tube. The aqueous phase was then transferred to a new 1.5 mL tube. 500 µl of 100% isopropanol (MilliporeSigma), 1.7 µl of GlycoBlue (Invitrogen), and 33 µl of 7.5 M ammonium acetate solution (Sigma-Aldrich) were added. The mixture was vortexed and incubated at -20°C for 30 min overnight. The samples were subsequently centrifuged at 16,000g for 30 min at 4°C. Following centrifugation, the samples were washed twice with 1 mL of 70% ethanol (MilliporeSigma). After the final wash and removal of 70% ethanol, the samples were air-dried for 10 min and then resuspended in 46 to 200 µL of Tris buffer pH 8.0 at 55°C for 10 min. If the DNA was not fully dissolved, it was further incubated at 4°C for one to two days. DNA concentration was measured using a Qubit 4.0 Fluorometer (Invitrogen) with the dsDNA HS Assay Kit (Invitrogen).
30 ng of purified mouse gDNA was mixed with 5% of unmethylated λ gDNA spike-in and 5% 5mCpG methylated plasmid spike-in, in a total volume of 50 µL in low TE buffer. This input DNA was then sheared to 350 bp using a Covaris instrument. Each sample was then split three ways to serve as technical replicates, with each treated as a sample starting from a 10 ng input. Libraries were prepared using the NEBNext Enzymatic Methyl-seq kit in accordance with the manufacturer’s instructions, with the noted modifications: 5pyC Y-shaped adaptors were used during ligation rather than the EM-Seq adaptors and only bGT was used rather than TET/bGT as detailed above. 2X KAPA HiFi U+ Polymerase (KAPA) was used to amplify the libraries following conversion and then subjected to a 0.8x left-sided SPRI purification, with elution in nuclease-free water to yield final libraries. Final libraries were quantified with a Qubit HS kit (Invitrogen), assessed for quality using an Agilent TapeStation D1000, and sequenced on an Illumina MiSeq.

value: Kidney


title: RNA-Seq of Eutrema salsugineum (Shandong): leaf_1+2, 9d (rep. 3)

source_name: leaf

value: Eutrema salsugineum (Shandong)

value: leaf


title: RNA-Seq of Eutrema salsugineum (Shandong): apex_vegetative, 9d (rep. 1)


title: Col-0_SAM_biorep1

description: Library name: WT_SAM_1


title: RNA-Seq of Eutrema salsugineum (Shandong): leaf_1+2, 9d (rep. 2)


title: Blood, ACE-Seq

description: Library name: BloodACE

source_name: Blood

value: Blood


title: Heart, ACE-Seq

description: Library name: HeartACE

source_name: Heart

value: Heart


title: C2_R+1_CD4

description: Library name: C2_R+1_CD4


title: RNA-Seq of Eutrema salsugineum (Shandong): leaf_1+2, 9d (rep. 1)


title: C2_PF_CD4

description: Library name: C2_PF_CD4


title: Ngru_H3K4me3_rep3

data_processing:
All ChIP-seq data was analysed using fastp to trim the reads, and these were mapped to the genomes using bowtie2, allowing a maximum insert size of 2000 base pairs (-I 2000). Duplicate reads were removed using Sambamba. DeepTools2 was used to generate bigwig files and to visualise epigenomic data, as well as Integrative Genome Viewer.
Assembly: Creolimax fragrantissima assembly: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_002024145.1/. Spizellomyces punctatus: GCF_000182565.1, Acanthamoeba castellanii: https://zenodo.org/records/6800059, Naegleria gruberi: GCF_000004985.1
Supplementary files format and content: ChIP-seq bigwig files were generated with DeepTools2 using the bamCoverage tool (bamCoverage -bs 10 --normalizeUsing CPM -p $cores -b "$prefix".dedup.bam -o "$prefix".bigwig)

source_name: microorganism

growth_protocol:
Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034.
Creolimax fragrantissima cells were grown axenically in marine broth liquid medium (Difco 2216) at 17°C. Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034. Spizellomyces punctatus cells were grown axenically at 17°C in liquid medium (containing 2.5 g of yeast extract, 0.5 g of K2HPO4, 2.5 ml of ethanol, 15 ml of glycerol and 485 ml of Milli-Q water).

extract_protocol:
Fixed cell pellets are treated with 2 ul of 3%SDS, to achieve a final concentration of 0.5% SDS. Cells are thoroughly re-suspended and lysed on ice for 10 min. Lysates are transferred into 0.1 ml Bioruptor Microtubes (Diagenode C30010015, Liège, Belgium) and the chromatin was sheared using an NGS Bioruptor Sonicator (Diagenode) at High Intensity and cycles of 30'' ON/30'' OFF.
100 ng chromatin per species was pooled per ChIP. Pooled chromatin was incubated at 4°C for 12−14 h with rotation with 2.5 µg anti-H3K27ac (Abcam, ab4729) or  2.5 µg anti-H3K4me3 (Millipore, 07-473). Immunoprecipitated complexes were captured using a mix of Protein A (16-661, Sigma-Aldrich) and Protein G magnetic beads (16-662, Sigma-Aldrich), washed, and reverse crosslinked for 30 min at 55°C followed by an hour at 68°C. Immunoprecipitated DNA was purified using SPRI beads (A63881, Beckman Coulter). The NEBNext Ultra II DNA Library Prep Kit (New England BioLabs) was used to produce the resulting ChIP libraries according to the manufacturer's protocol.

tag: strain

value: NEG-M

value: Axenic culture

tag: library type

value: ChIP-seq with anti-H3K4me3 (Millipore, 07-473)

tag: time

value: 7 days culture

value: microorganism


title: Ngru_H3K4me3_rep2


title: Cerebellum, ACE-Seq

description: Library name: CerebellumACE

source_name: Cerebellum

value: Cerebellum


title: RNA-Seq of Eutrema salsugineum (Shandong): hypocotyl, 12d (rep. 3)

data_processing:
Paired-end sequencing reads, were adapter- and quality trimmed by cutadapt (version 1.10) and sickle (version 1.33) with parameters pe -t sanger -q 20 -l 50
RNA-seq reads were aligned to the respective reference genome using the RNA-Seq aligner STAR (version 2.7.1a) with the parameters --alignIntronMin 20 --alignIntronMax 10000 --bamRemoveDuplicatesType UniqueIdenticalNotMulti --chimSegmentMin 10 --chimOutType Junctions WithinBAM --outFilterMismatchNmax 3 --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD AS nM jM jI XS ch --outSAMprimaryFlag AllBestScore --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Gene expression values were quantified as estimated counts by salmon (0.14.1).
Assembly: Genomic reference sequences and annotations for the genome-guided transcriptome assembly and subsequent annotation procedures were obtained from Ensembl, release 34 (for A. thaliana), Phytozome, version 12 (for A. lyrata, C. rubella, E. salsugineum, M. truncatula, and B. distachyon), and RefSeq (for T. hassleriana).
Supplementary files format and content: gene transfer format files contain updated gene and transcript structure information for each organism
Supplementary files format and content: semicolon-separated text files contain estimated raw counts for each sample

source_name: hypocotyl

tag: cultivar

value: hypocotyl


title: RNA-Seq of Eutrema salsugineum (Shandong): apex_vegetative, 9d (rep. 3)


title: C1_R+35_CD4

description: Library name: C1_R+35_CD4

value: CD4+ immune cells


title: RNA-Seq of Eutrema salsugineum (Shandong): hypocotyl, 12d (rep. 2)


title: Ngru_H3K4me3_rep1


title: C1_R+1_CD4

description: Library name: C1_R+1_CD4

value: Control subject


title: Col-0_SAM_biorep3

description: Library name: WT_SAM_3

value: shoot apical meristem


title: Ngru_H3K27ac_rep2

value: ChIP-seq with anti-H3K27ac (Abcam, ab4729)


title: C1_PF_CD4

description: Library name: C1_PF_CD4

value: PF


title: CD19_C_CART_2_invivo

city: chengdu

first: pei

last: shu

address: guoxue lane

institute: west chia hospital, sichuan university

description:
Library name: CD19_C_CART_2.fq.gz
CXCR4 modified CD19 CAR-T in vivo in another mice

data_processing:
Sequencing by Synthesis
Assembly: HISAT2 v2.0.5
Supplementary files format and content: processed data in vivo.xls

source_name: blood

extract_protocol:
RNA was harvested Rneasy mini plus kit (Qiagen).
RNA libraties for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit (Illumina).

value: blood

value: CAR-T cells

tag: batch

value: same batch


title: CD19_C_CART_1_invivo

description:
Library name: CD19_C_CART_1.fq.gz
CXCR4 modified CD19 CAR-T in vivo

value: CXCR4 modified CD19 CAR-T in vivo


title: Ngru_H3K27ac_rep1

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

institute: Queen Mary University of London


title: RNA-Seq of Eutrema salsugineum (Shandong): root_whole_root, 6d (rep. 3)

source_name: root

extract_protocol:
Dissected organs were homogenised and total RNA was isolated using RNeasy Plant Mini Kit (QIAGEN 74904), following the manufacturer's instructions. RNA integrity was measured using an Agilent 2200 TapeStation.
Strand-specific total RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to the manufacturer’s specifications (Illumina 20020610). ERCC RNA Spike-In Control Mix (Ambion 4456740) was added at the beginning of the library preparation before the ribosomal RNA (rRNA) depletion step to allow sample-specific estimation of the lower detection limit. All RNA-Seq libraries were sequenced as paired-end 75bp reads.

value: Eutrema salsugineum (Shandong)

value: root


title: CD19_CART_1_invivo

description:
Library name: CD19_CART_1.fq.gz
CD19 CAR-T in vivo

value: CD19 CAR-T in vivo


title: A3_R+35_CD4

description: Library name: A3_R+35_CD4

value: Astronaut


title: Acas_H3K4me3_rep3

organism: Acanthamoeba castellanii

growth_protocol:
Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712.
Creolimax fragrantissima cells were grown axenically in marine broth liquid medium (Difco 2216) at 17°C. Acanthamoeba castellaniii cells were grown axenically at 23°C in ATCC medium 712. Naegleria gruberi cells were grown axenically  at 30°C in ATCC medium 1034. Spizellomyces punctatus cells were grown axenically at 17°C in liquid medium (containing 2.5 g of yeast extract, 0.5 g of K2HPO4, 2.5 ml of ethanol, 15 ml of glycerol and 485 ml of Milli-Q water).

value: Neff

value: Axenic culture

value: ChIP-seq with anti-H3K4me3 (Millipore, 07-473)

value: 7 days culture


title: NT_2_invivo

description:
Library name: NT_2.fq.gz
NT in vivo in another mice

value: NT in vivo in another mice


title: A3_R+1_CD4

description: Library name: A3_R+1_CD4

value: CD4+ immune cells


title: Acas_H3K4me3_rep2

value: microorganism


title: RNA-Seq of Eutrema salsugineum (Shandong): root_whole_root, 6d (rep. 2)


title: RNA-Seq of Eutrema salsugineum (Shandong): root_whole_root, 6d (rep. 1)


title: A3_PF_CD4

description: Library name: A3_PF_CD4


title: NT_1_invivo

description:
Library name: NT_1.fq.gz
NT in vivo

value: NT in vivo


title: Acas_H3K4me3_rep1


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_late_stg12_stamens, 8w/10w/21d (rep. 3)

organism: Arabidopsis lyrata

source_name: stamens

value: Arabidopsis lyrata (MN47)

value: stamens


title: Acas_H3K27ac_rep1

value: ChIP-seq with anti-H3K27ac (Abcam, ab4729)


title: A2_R+35_CD4

description: Library name: A2_R+35_CD4


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_late_stg12_stamens, 8w/10w/21d (rep. 2)


title: A2_R+1_CD4

description: Library name: A2_R+1_CD4


title: CD19_C_CART_S_2

description:
Library name: CD19_C_CART_S_2.fq.gz
CXCR4 modified CAR-T in vitro repeated

value: blood

value: T cells

value: CAR-T cells

value: CXCR4 modified CAR-T in vitro repeated

value: same batch


title: RNA-Seq of Eutrema salsugineum (Shandong): hypocotyl, 12d (rep. 1)

value: Eutrema salsugineum (Shandong)

value: hypocotyl


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_late_stg12_stamens, 8w/10w/21d (rep. 1)


title: CD19_C_CART_S_1

description:
Library name: CD19_C_CART_S_1.fq.gz
CXCR4 modified CAR-T in vitro

value: CXCR4 modified CAR-T in vitro


title: CD19_C_CART_RS_2

description:
Library name: CD19_C_CART_RS_2.fq.gz
CXCR4 modified CAR-T pretreated with raji


title: CD19_CART_2_invivo

description:
Library name: CD19_CART_2.fq.gz
CD19 CAR-T in vivo in another mice

value: CD19 CAR-T in vivo in another mice


title: A2_PF_CD4

description: Library name: A2_PF_CD4

value: Astronaut

value: PF


title: Cerv-Moli-5

city: Lyon

first: Pierre-Olivier

last: Vidalain

address: 21 Avenue Tony Garnier

country: France

institute: CIRI

description: Library name: S09

data_processing:
The produced paired-end reads which passed Illumina’s chastity filter were subject to de-multiplexing and trimming of Illumina adaptor residuals using Illumina’s bcl2fastq software version 2.20.0.422 (no further refinement or selection).
Quality of the reads in fastq format was checked with the software FastQC (version 0.11.8; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Raw reads having average Q-values below 24 or incorporating uncalled ‘N’ bases or being smaller than 25 bases after trimming were filtered using the BBTools software suite (version 38.86; https://sourceforge.net/projects/bbmap/). The splice aware RNA mapping software STAR (version 2.7.10a; PMID: 23104886) was used to map the surviving reads to the GCF_017639785.1 reference genome provided by NCBI.
To count the uniquely mapped reads to annotated genes, the software htseq-count (HTSeq version 0.13.5) was used.
Normalization of the raw counts and differential gene expression analysis was carried out with help of the R software package DESeq2 (version 1.26.0).
Assembly: GCF_017639785.1
Supplementary files format and content: Text files (.couts) containing genes counts (raw values)

organism: Mesocricetus auratus

growth_protocol: Hamster cerebellum slices were cultured on inserts at the air-liquid interface (37°C; 5% CO2) with Minimal Essential Medium GlutaMAX (ThermoFisher Scientific) supplemented with 25% heat-inactivated horse serum (Gibco), D-glucose (5 g/L; Sigma-Aldrich) and human recombinant insulin (0.02 mg/mL; Sigma-Aldrich).

extract_protocol:
Hamster cerebellum slices were collected in 350 µL of TRI reagent (Euromedex) with two stainless steel beads and lysed using a TissueLyserII (Qiagen) at Vmax for 10 min. RNA was extracted using Direct-zol RNA Miniprep Kits (Zymo Research).
DNA library construction, sequencing and data analysis described in these sections were performed by Microsynth AG (Balgach, Switzerland). Total RNA was quantified using Quant-iT RiboGreen (Thermofisher) and integrity was checked on Fragment analyzer (Agilent) with a kit suitable for RNA. Library Preparation was done using the Illumina® Stranded mRNA Prep, Ligation and 60 ng total RNA input. Final libraries were quantified using pico488 (Lumiprobe) and library size was checked on Fragment analyzer (Agilent). Samples were pooled equimolar prior to sequencing. Subsequently the Illumina NovaSeq platform and an SP, 300 cycles kit were used to sequence the libraries in paired-end fashion.

treatment_protocol: Cultures were treated with DMSO alone or Molidustat at 25 microM for 24 h.

value: Cerebellum

value: treated for 24h with Molidustat at 25 microM


title: Cerv-Moli-4

description: Library name: S08


title: CD19_CART_S_2

description:
Library name: CD19_CART_S_2.fq.gz
CD19 CAR-T in vitro in SDF-1 repeated

value: CD19 CAR-T in vitro in SDF-1 repeated


title: A1_R+35_CD4

description: Library name: A1_R+35_CD4

value: CD4+ immune cells


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_mid_stg12_stamens, 8w/10w/24d (rep. 2)

city: Würzburg

first: Alexander

last: Gabel

address: Josef-Schneider-Str. 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

value: Arabidopsis lyrata (MN47)

value: stamens


title: Cerv-Moli-3

description: Library name: S07


title: CD19_CART_S_1

description:
Library name: CD19_CART_S_1.fq.gz
CD19 CAR-T in vitro in SDF-1

value: blood

value: CD19 CAR-T in vitro in SDF-1


title: A1_R+1_CD4

description: Library name: A1_R+1_CD4


title: Cerv-Moli-2

description: Library name: S06


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_mid_stg12_stamens, 8w/10w/24d (rep. 1)


title: RNA-Seq of Arabidopsis lyrata (MN47): floral_organ_early_stg12_stamens, 8w/10w/23d (rep. 3)


title: CD19_CART_RS_2

description:
Library name: CD19_CART_RS_2.fq.gz
CD19 CAR-T in vitro pretreated with raji in sdf-1 repeated

value: T cells

value: CAR-T cells


title: A1_PF_CD4

description: Library name: A1_PF_CD4


title: CD19_CART_RS_1

description:
Library name: CD19_CART_RS_1.fq.gz
CD19 CAR-T in vitro pretreated with raji in sdf-1

value: same batch


title: Cerv-DMSO-5

description: Library name: S04

value: treated for 24h with DMSO alone


title: CD19_CART_R_2

description:
Library name: CD19_CART_R_2.fq.gz
CD19 CAR-T in vitro pretreated with raji repeated