title: normal tissue-associated fibroblasts_donor4

value: Liver tumor

value: female


title: spinal cord,Gpr37l1-/-,spared nerve injury -1 day

status: Public on Feb 14 2025

type: SRA

city: DURHAM

first: Jing

last: Xu

state: NC

address: 816 Louise Circle

country: USA

institute: Duke university

description:
Library name: KO_SNI
10x 3' gene expression protocol

library_source: transcriptomic single cell

data_processing:
snRNA-seq reads were processed with Cell-Ranger v4.0.0, and aligned to the GRCm38 mouse reference genome with default parameters. Datasets were analyzed with Seurat R package v4.3.0. using R v4.3.0. Cells that expressed less than 500 genes or with more than 10% mitochondrial reads were removed. Gene expression was normalized and scaled using NormalizeData and ScaleData functions respectively, with default parameters. Following the principal component analysis (PCA), downstream analysis was performed with the top 30 PCs. Datasets were integrated, re-normalized and scaled, and batch-corrected using Harmony v0.1.1. Unsupervised clustering was done using the FindClusters function from Seurat with a resolution of 0.8. Uniform Manifold Approximation and Projection (UMAP) was calculated for data visualization embedded in two dimensional space. Cell type of each cluster was annotated based on the expression pattern of known marker genes as well as genes that are differentially expressed in each cluster. Differentially expressed genes were identified using FindAllMarkers in Seurat by filtering the genes with an average log2 fold change of ± 0.25 and a min.pct above 0.25, regardless of the p values. Gene set enrichment analysis was performed on the identified differentially expressed genes with a p value < 0.05 using clusterProfiler in R.
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: spinal cord

extract_protocol:
Fresh SDH tissues from Gpr37l1+/+ and Gpr37l1-/- mice (naive and 1 day after SNI) were microdissected for nuclei isolation according to the previous report. Microdissected SDHs were homogenized in 0.2 ml RNAase-free lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 10 mM Tris-HCl, 1 mM DTT and 0.1% Triton X-100 in diethylpyrocarbonate (DEPC)-treated water) using homogenizer from 10X Genomics nuclei isolation kit (PN-1000493) on ice. The homogenate was loaded into a 3.5-ml polycarbonate ultracentrifuge tube (349622, Beckman-Coulter), and 1.8 ml of sucrose solution (1.8 M sucrose, 3 mM MgAc2, 1 mM DTT, and 10 mM Tris-HCl in DEPC-treated water) was added to the bottom of the tube with the homogenate, and the tube was centrifuged at 24400 RPM for 2.5 h at 4 °C. After removing the supernatants, pellets containing the nuclei were incubated in 100 μl of DEPC-treated water-based PBS for 20 min on ice before resuspending the pellets using the same solution.
Nuclei were counted using a hemocytometer and single-nucleus capture was performed using the 10X Genomics Single-Cell 3′ system (v3.1). Single-nucleus libraries from individual samples were pulled and sequenced on the MGISEQ-2000 machine. RNA integrity analysis was performed using the Agilent 2100 Bioanalyzer.

tag: tissue

value: spinal cord

tag: genotype

value: Gpr37l1 KO

tag: treatment

value: spared nerve injury -1 day


title: MNase-seq of yeast + P. vitis YAC strain, 20min

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
Bowtie2 was used to align paired-end MNase-seq data on the appropriate genome reference. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded.
PCR duplicates were removed using samtools and fragments smaller than 130 or longer than 200 bp were manually removed.
Fragment coverage was normalized by library depth (CPM) and converted into stranded or unstranded genomic tracks (bigwig) using deepTools.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for Mnase-seq coverage (fragments ranging from 130 to 200bp) are provided.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Five 1.5ml Tubes were prepared with 1.5 x 10^8 asynchronous yeast cells: cells were centrifuged, pelleted, washed in 1x PBS and frozen at -80C.

extract_protocol:
Cell pellets were thawed on ice and resuspended in 1mL 1xPBS supplemented with 27ul 37% formaldehyde. Cells were fixed for 20min at room temperature on rotation. 200ul of 2.5M Glycine was added for a further 5 min incubation. Cells were centrifuged at 2500g, 4C for 5 min. Pellets were gently washed with cold 1xPBS before resuspension in 500ul of lysis solution (Sorbitol 1M, EDTA 10mM, Zymo100T 250ug) and incubation at 37C with gently shaking for 30min/45min or until complete spheroplasting.
Cells were gently washed with cold 1xPBS and resuspended in 50ul 1X Nuclease Digest buffer plus an increasing amount of Mnase (NEB, M0247S) enzyme starting with 0.2ul. Digestion was performed at 22C in a shaker set at 1250rpm for 15min. 5ul of 0.5M EGTA and 3ul of 20% SDS were added for incubation at 22C in a shaker set at 1250rpm for 5 min. 65ul of TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) was added and samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified using Zymo Research DNA Clean and Concentrator™-5 Kit. Mnase digestion was verified on a Bioanalyzer System using HS DNA kit. DNA was purified using 1.2x volume of AmpureXP beads and librairies prepared with Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.

tag: background

tag: cell line

tag: Stage

value: Asy

tag: hash


title: C exposed to Clas-positive psyllids_time10_ replicate 6

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

description:
C.Las.10.6
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

library_source: transcriptomic

data_processing:
Adapter removal and quality trimming of raw reads was done with cutadapt.
Clean reads were analysed using FastQC.
Clean read pairs longer than 20 nt were mapped to the reference genomes (for Citrus and Bergera) or de novo transcriptome (for Bergera) using STAR.
Differential expression analysis was performed with DESeq2.
Assembly: Citrus sinensis SWO.v3.0 genome + Liberibacter_asiaticus NZ_CP019958 genome, Murraya paniculata genome + Liberibacter_asiaticus NZ_CP019958 genome (Murraya_paniculata_final.chr.fasta), and Bergera transcriptome + Liberibacter_asiaticus NZ_CP019958 genome (Bergera_ST_Streptophyta.fasta) combined genomes.
Supplementary files format and content: Tab-delimited text files including count of reads for each gene in each sample.

organism: Citrus sinensis

source_name: young flush

growth_protocol: C. × sinensis ‘Valencia’ plants, and M. paniculata and B. koenigii seedlings were pruned at 15-25 cm to promote new flushes. A V2 flush was selected, and the remaining ones were eliminated.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Two µg of total RNA per sample were used for library generation using the TruSeq stranded total RNA Library Kit plus Ribo-Zero and NEBNext kits for ribosomal RNA depletion.
The Illumina NovaSeq6000 was used on a paired-end sequencing of 150pb. All procedures were performed according to Illumina’s protocols.

treatment_protocol: Five 15-20 days-old CLas-positive or negative adult psyllids were confined to a single flush per plant for 48 h.

tag: cultivar

value: Valencia

value: young flush

value: Clas-positive psyllid

tag: time point


title: cancer-associated fibroblasts _donor4

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trimmomatic
Alignment: Star-aligner
Read counting: Salmon -quant mode
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

organism: Homo sapiens

source_name: Liver tumor

growth_protocol: Tissue biopsies from liver tumors and adjacent healthy tissues were received from the Clinic for General, Visceral, and Transplantation Surgery at RWTH Aachen after written consent and following the guidelines of the Ethic Committee for the Use of Human Subjects at the University of Aachen (Permit number: EK 206/09). HCC = hepatocellular carcinoma , CRLM = colorectal carcinoma liver metastasis, ALM = anal cancer liver metastasis.

extract_protocol:
Tissue pieces were minced into small pieces, washed with PBS and incubated at 37°C in collagenase IV (1 mg/ml) containing medium (KnockOut DMEM from Gibco) overnight. After filtering through a strainer, the cells were cultured in DMEM medium containing 10% human platelet lysate, Penicillin-Streptomycin (100 U/ml), and L-Glutamine (2 mM). Cells were expanded at 37°C and 5% CO2 for 2-3 passages upon reaching confluence. CAFs and NAFs were successfully isolated from patients.
Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel). For library preparation the TruSeq Stranded mRNA kit (Illumina) was selected and sequenced on a NextSeq 500 (Illumina) using the NextSeq 500/550 High Output Kit v2.5 (150 cycles). Sequencing was performed at IZKF-associated Genomics Facility of the RWTH University.

tag: individual

tag: cell type

value: CAF

tag: cancer type

value: CRLM

tag: initial sample_id

tag: gender


title: C exposed to Clas-negative psyllids_time20_ replicate 1

description:
C.h.20.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-negative psyllid


title: normal tissue-associated fibroblasts_donor3

value: NAF

value: male


title: spinal cord,Gpr37l1+/+,Naïve

description:
Library name: WT_Naive
10x 3' gene expression protocol

molecule: polyA RNA

value: wild-type

value: Naïve


title: MNase-seq of yeast + P. vitis YAC strain, 10min


title: C exposed to Clas-negative psyllids_time20_ replicate 3

description:
C.h.20.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: spinal cord,Gpr37l1+/+,spared nerve injury -1 day

description:
Library name: WT_SNI
10x 3' gene expression protocol


title: C exposed to Clas-negative psyllids_time30_ replicate 3

description:
C.h.30.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: RNA-seq of Mpneumo strain (upf1-/-, rrp6-/-), rep2

data_processing:
Bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded.
PCR duplicates were removed using samtools.
Fragment coverage was normalized by library depth (CPM) and converted into stranded or unstranded genomic tracks (bigwig) using deepTools.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for forward-strand, reverse-strand and unstranded coverage are provided.

extract_protocol:
RNA was extracted using MN Nucleospin RNA kit and following manufacturer instructions.
Directional mRNA library (rRNA removal) was prepared by the Biomics platform of Institut Pasteur, Paris and Paired-end sequencing (PE150) was performed by Novogene.

value: XVIfMpneumo


title: MNase-seq of yeast + P. vitis YAC strain, 40min


title: normal tissue-associated fibroblasts_donor2

value: Liver tumor


title: LPC-1

city: Changsha

first: Panpan

last: Liu

state: China

address: Xiangya road

country: China

institute: Xiangya hospital

data_processing:
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2.
The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05.
The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: T cells

extract_protocol:
RNA was extracted from cells using TRIpure Reagent (Bioteke Cat. RP1001) according to manufacturer’s instructions.
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform. High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2. The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05. The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.

treatment_protocol: Mouse naïve CD4+ T cells were activated in vitro for 3 days with CD3/CD28 antibodies under Th1-polarizing conditions in the presence of vehicle control or LPC (20 μM).

tag: strain

value: spleen

tag: age

value: 3 weeks

tag: agent

value: LPC-treated


title: C exposed to Clas-negative psyllids_time20_ replicate 2

description:
C.h.20.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

tag: tissue


title: MNase-seq of yeast + P. vitis YAC strain, 5min


title: fmo-4 OE C. elegans, test, Day 1 adult, bio replicate 3

city: Ann Arbor

first: Angela

last: Tuckowski

state: MI

address: 109 Zina Pitcher Place

department: Molecular and Integrative Physiology

institute: University of Michigan

description:
Library name: MBH26
RNA from C. elegans was isolated using Zymo Research Direct-zol RNA Miniprep kit

data_processing:
Clustering of the index-coded samples was performed according to manufacturer's instructions.Then library preparations were sequenced on an Illumina platform and pair-end reads were generated
Raw reads were processed through fastp. Reads containing adapter and poly-N sequences and reads with low quality were removed to obtain clean data.
Paired-end clean reads were mapped to reference genome using HISAT2 software. Stringtie was used to then assemble the set of transcript isoforms of each bam file obtained in the mapping step. Gffcompare can compare Stringtie assemblies to reference annotation files and sort out new genes from known ones
Featurecounts was used to count the read numbers mapped of each gene. RPKM of each gene was then calculated based on length of the gene and reads count mapped to the gene.
Assembly: Reference genome and gene model annotation files were downloaded from genome webstie browser directly (NCBI/UCSC/ENSEMBL).
Supplementary files format and content: xls files contain the differential expression analysis of each sample
Supplementary files format and content: bam files contain raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: WT and fmo-4 OE worms were grown on NGM plates containing 3x concentrated OP50 E.coli bacteria lawn from egg to day one adulthood. Worms were then washed 3 times with M9 solution and then RNA was extracted using the Zymo Research RNA miniprep kit

extract_protocol:
RNA was extracted using the Zymo Research Direct-zol RNA Miniprep Kit
mRNA was purified from total RNA using poly-T-oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directly library.

treatment_protocol: The worms were not treated.

value: whole body

tag: genotype

value: fmo-4 overexpression


title: C exposed to Clas-positive psyllids_time10_ replicate 5

description:
C.Las.10.5
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Valencia

tag: treatment


title: MNase-seq of yeast + P. falciparum YAC strain, 60min

tag: background

value: Asy


title: cancer-associated fibroblasts _donor2


title: spinal cord,Gpr37l1-/-, Naïve

description:
Library name: KO_Naive
10x 3' gene expression protocol

value: spinal cord

value: Gpr37l1 KO

value: spared nerve injury -1 day


title: C exposed to Clas-positive psyllids_time10_ replicate 4

description:
C.Las.10.4
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: young flush

value: Clas-positive psyllid


title: RNA-seq of Mpneumo strain (upf1-/-, rrp6-/-), rep1

tag: cell line


title: LPC-4-1

data_processing:
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2.
The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05.
The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LPC-4_mouse skin lesions

treatment_protocol: Intradermal administration of 10 μl LPC (10mM) or 10 μl normal saline (Vehicle) once per day for 6 consecutive days during the application of IMQ in mice (BALB/c) ear.

value: BALB/c

value: 8 weeks

value: skin


title: cancer-associated fibroblasts _donor3

value: CAF

value: CRLM

value: male


title: MNase-seq of yeast + P. falciparum YAC strain, 40min

tag: Stage


title: WT C. elegans, control, Day 1 adult, bio replicate 3

description:
Library name: MBH21
RNA from C. elegans was isolated using Zymo Research Direct-zol RNA Miniprep kit

value: WT


title: C exposed to Clas-positive psyllids_time10_ replicate 2

description:
C.Las.10.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: MNase-seq of yeast + P. falciparum YAC strain, 20min

tag: hash


title: H9 DGCR8 heterozygote HET2 clone replicate 3 (miRNA-seq)

city: Castellón de la Plana

first: Guillermo

last: Peris

state: CAstellón

address: Av. Vicent Sos Baynat, s/n

department: Llenguatges i Sistemes Informàtics

institute: Universitat Jaume I

data_processing:
For each sample, identical small RNA-seq reads were collapsed and only reads that were present more than once were included in further analysis. Mature miRNAs were identified and counted using miRDeep2, using the quantification function with human hairpin and mature miRNA sequences files from miRbase (version 22.1) and allowing no mismatches. Raw miRNA counts were normalized per sample by the total tRNAs detected with blastn (version 2.6.0+) using the commands -num_threads 20 -max_target_seqs 1 -max_hsps 1 1 -outfmt '6 std qseq sseq' -task blastn -word_size 6 -dust no, relative to WT sample 1.
Assembly: GRCh38.p13
Supplementary files format and content: tab delimited output from mirDeep2

growth_protocol: All cell lines were grown at 37℃ and 5% CO2 and were maintained on Matrigel (Corning) coated culture plates in mTeSR1 (STEMCELL Technology).

extract_protocol:
RNA  was extracted using mirVana microRNA isolation kit (ThermoFisher).
Small RNA libraries were generated using NEXTFlex Small RNA Library Prep Kit v3 (Cat #NOVA-5132–06). The manufacturer’s instructions where followed through PCR amplification. The optional stop point was used post the 5' 4N Adapter Ligation prior the Reverse Trascription reaction. In regards to PCR amplification the 200 ng samples received 20 cycles. Following PCR amplification, the libraries were run in a 6% TBE-PAGE Gel for 50 min at 140 V. The 140-170 bp band were excised from the gel and purified by beads. Once purified, libraries were multiplexed and concentration and size check of final pool were measured by Qubit dsDNA HS Assay (Life Technologies) and Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies), repectively

value: embryonic stem cells

value: DGCR8 heterozygote


title: cancer-associated fibroblasts _donor1

value: Liver tumor

value: HCC


title: C exposed to Clas-positive psyllids_time10_ replicate 1

description:
C.Las.10.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

tag: cultivar

value: Valencia


title: normal tissue-associated fibroblasts_donor1

value: NAF


title: MNase-seq of yeast + P. falciparum YAC strain, 10min

value: Asy


title: C exposed to Clas-negative psyllids_time10_ replicate 6

description:
C.h.10.6
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-negative psyllid

tag: time point


title: C exposed to Clas-positive psyllids_time10_ replicate 3

description:
C.Las.10.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: young flush


title: H9 DGCR8 heterozygote HET2 clone replicate 2 (miRNA-seq)


title: MNase-seq of XVIfMmycot1 hho1-/- strain, 60min


title: WT C. elegans, control, Day 1 adult, bio replicate 2

description:
Library name: MBH11
RNA from C. elegans was isolated using Zymo Research Direct-zol RNA Miniprep kit

value: whole body


title: MNase-seq of yeast + P. falciparum YAC strain, 5min


title: WT C. elegans, control, Day 1 adult, bio replicate 1

description:
Library name: MBH1
RNA from C. elegans was isolated using Zymo Research Direct-zol RNA Miniprep kit


title: C exposed to Clas-negative psyllids_time10_ replicate 5

description:
C.h.10.5
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: OMA-1 mutant 4-cell, Total RNA-seq, batch12, rep3, read1

city: Austin

first: Can

last: Cenik

state: Texas

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

data_processing:
Ribosome profiling data were processed using RiboFlow. Input data included gzipped fastq files containing ribosome profiling sequencing data, Bowtie2 index files for the transcriptome reference (appris_celegans_v1) and filter reference (rRNA sequences), a bed file defining CDS, UTR5, and UTR3 regions, and a two-column tsv file containing transcript lengths. Unique Molecular Identifiers (UMIs) were extracted from the reads using UMI-tools (Version 1.1.2) with the parameters "-p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex". Reads were processed using default settings . Alignments with a mapping quality greater than two were retained. Deduplication was performed using UMI-tools. Only footprints between 21 and 40 nucleotides in length were considered for the final analysis.  The RiboFlow platform was also used to process the RNA-seq data. Computational processing of RNA-seq data was performed using a custom pipeline based on the provided YAML configuration. The processing steps were as follows: First, quality control and trimming were conducted using cutadapt, where the first and last 25 nucleotides were trimmed from each read with the parameters '-u 25 -u -25 --quality-cutoff=28', also removing bases with a quality score below 28. Next, filtered reads were aligned using Bowtie2 in a two-step process: reads were initially aligned to a reference of rRNAs using the parameters '-L 15 --no-unal', and then unaligned reads were aligned to the transcriptome reference using the same parameters. Finally, in the post-alignment processing step, only alignments with a mapping quality greater than 2 were retained for further analysis.
Assembly: The reference files can be found here: https://github.com/RiboBase/reference_caenorhabditis-elegans
Supplementary files format and content: Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy  for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.

source_name: embryos

growth_protocol: C. elegans strains were maintained on standard NGM plates and fed OP50 E. coli. The N2 (wild type) strains were maintained at 20°C and the TX20 strains were maintained at 15°C.

extract_protocol:
We used a slightly modified version of the previously described Ribo-ITP protocol 3 and a detailed protocol can be obtained from (https://ceniklab.github.io/ribo_itp/) which can be referred to for more details. In brief, the PCR tubes with 9 embryos were centrifuged to collect them at the bottom. We then added 2.5µl of 100µg/ml cycloheximide to the PCR tubes and we lysed the embryo by freeze thawing them in liquid nitrogen. We then added 2.5 µl of 2x lysis buffer (40mM Bistris, 2% Triton-X-100, 10mM MgCl2, 10 mM CaCl2) and mixed well by pipetting. To obtain ribosome protected fragments, we added 1µl of 1:50 diluted MNase and incubated at 37°C for 30 mins. The digestion was then stopped using 1µl EGTA and vortexed for at least 30 seconds and stored on ice. The microfluidics chip for ribosome profiling via isotachophoresis was setup and run as provided in 3. The ribosome protect fragments were collected in Dephosphorylation Buffer from the Diagenode. RNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB #E6420S/L), following the manufacturer's protocol with some modifications. Briefly, embryo samples, each consisting of 9 embryos, were collected in PCR tubes containing 4.5 µl of water. These samples underwent a freeze-thaw cycle using liquid nitrogen to lyse the cells and release the RNA. For library preparation, we employed a
The library preparation was conducted as described in the D-Plex Small RNA-seq Kit ( Diagenode Cat. No C05030001). We made a few modifications to the kit’s protocol, and they were as follows. At the RNA-tailing step we used 0.5µl of Dephosphorylation Reagent along with 0.5µl of T4 Polynucleotide Kinase (New England Biolabs M0201L). Upon adding these two reagents the mixture is incubated for 25 mins at 37°C. Next, during the reverse transcription with template switching, we diluted the STSO by half and used 2µl in the mixture. We used 16 cycles for the final PCR amplification to produce the DNA library. RNA libraries were prepared using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB #E6420S/L), following the manufacturer's protocol with some modifications. Briefly, embryo samples, each consisting of 9 embryos, were collected in PCR tubes containing 4.5 µl of water. These samples underwent a freeze-thaw cycle using liquid nitrogen to lyse the cells and release the RNA. For library preparation, we employed a two-step PCR amplification process. The initial cDNA enrichment PCR was performed for 14 cycles, followed by a final library amplification PCR for 8 cycles.

treatment_protocol: For wild-type strains, embryos were collected as follows: Microscope slides were prepared by placing five Eppendorf tube stickers in a row and applying Sigmacote to the surrounding area. After drying under a fume hood for 5-10 minutes, the slides were washed with water and the stickers removed, creating wells. For embryo collection, approximately 20 worms were placed in 100 µL of egg buffer and dissected. 10 µL of bleach was added, and the solution was pipetted for 10 seconds. Eggs were selected and washed five times through 100 µL of SGM in the wells created on the treated slides (taking ~ 2 mins). After reaching the desired stage, eggs were washed five times in water, then in water with 1x cycloheximide (CHX). During the final wash, embryos were inspected using a microscope, and those not at the correct stage were segregated. The correctly staged embryos were transferred to a PCR tube, flash-frozen in liquid nitrogen, and then kept on a metal rack placed on dry ice. More embryos were added to the same PCR tube on dry ice, with the tube being flash-frozen in liquid nitrogen each time new embryos were added. This process was repeated until 9 embryos were collected in a single PCR tube for each stage. For TX20 C. elegans strains, L4/young adult worms were incubated overnight at 20°C prior to collection. Following this incubation, the same collection process as described for wild-type strains was conducted.

tag: developmental stage

tag: number of_embryos

tag: strain name

tag: lib. prep._method

value: RNA-seq

value: embryos


title: C exposed to Clas-negative psyllids_time10_ replicate 4

description:
C.h.10.4
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: H9 DGCR8 heterozygote HET2 clone replicate 1 (miRNA-seq)

tag: cell type


title: MNase-seq of XVIfMmycot1 hho1-/- strain, 40min


title: scRNAseq GEX 10x Lane 6

city: Bethesda

first: Eduard

last: Ansaldo

state: MD

address: 4 Memorial Drive

department: LHIM

institute: NIH/NIAID

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 6

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger (57) v7.1.0 (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. The TCR data was processed with Cell Ranger v7.1.0 using a VDJ reference based on the IGMT database: The IGMT reference was generated with Cell Ranger v7.1.0 using the 'fetch-imgt' and 'cellranger mkvdjref' functions. Processing of the expression data was performed with the 'cellranger multi' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 114629 estimated number of cells, 21832 mean reads per cell (from eight GEX libraries), 543 Median hashtag UMIs per Cell (across eight HTO libraries), 66544 cells with a productive V-J spanning TRA and TRB pair (from eight VDJ libraries).
In the downstream analysis of the expression data, the Cell Ranger aggregation output (filtered_feature_bc_matrix directory) was loaded into Seurat version 4.4.1 (58) using the CreateSeuratObject function with min.cells=3. For filtering out low-quality cells, we established minimum thresholds for gene (nCount_RNA > 1000) and UMI counts (nFeature_RNA > 300), and a maximum threshold for percentage mitochondrial content (percent.mt < 6) based on visual inspection of the corresponding metric distributions across all cells. Log-normalization (LogNormalize function) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing cells into the individual mice within nulliparous/pregnant/lactation groups and removing any doublets, HTODemux was run with a positive quantile = 0.99. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA  function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 60. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 60 dimensions and a range of resolutions to determine the optimal resolution that captures biological diversity in the dataset, which was determined to be 0.25, resulting in 16 clusters. The clusters identified by the FindClusters function of Seurat (default Louvain clustering setting and 0.25 resolution) were further annotated using cell type-specific markers.
TCR repertoire sequencing data were analyzed with the scRepertoire package v2.0.0 (59) in R v4.4.1. Starting with the filtered contig annotations output table from 'cellranger aggr', the createHTOContigList, combineTCR, and combineExpression functions were used for combining the TCR data from each sample and for integration of the combined TCR data with the Seurat object. We utilized the amino acid sequence of the paired CDR3 regions of the alpha and beta chains as the clonotype definition. T cell repertoire diversity was estimated using the D50 metric, which was calculated in R as the fraction of clonotypes, ordered by abundance, which account for 50 percent of total TCR sequences (defined as paired aminoacid CDR3 sequences). Clonotype size was defined at the level of each biological replicate (Rare: between 0% and 0.01%, Small: between 0.01% and 0.1%, Medium: between 0.1% and 1%, Large: between 1% and 10%, Hyperexpanded: between 10% and 100%). Cells with a putative iNKT TCR were defined as containing a TRAV11-TRAJ18 alpha chain V gene usage, while cells with a putative MAIT TCR were defined as containing a TRAV1-TRAJ33 alpha chain V gene usage. TCR overlap between clusters or between mice was defined at the level of the CDR3 amino acid region for the combined alpha and beta chains, and visualized using the package circlize (PMID: 24930139).
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The filtered_contig_annotations.csv file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The scRNAseq_Tcells.rds file contains the final Seurat object, product of the analysis described in the processing step section.

source_name: Mammary Gland

extract_protocol:
Mammary T cells from nulliparous,  pregnant (G18.5), and lactating (L5) mice were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter.
Sorted cells were pooled and 42000 cells per lane (total of 8 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX),  hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents (100 cycles)).

value: Mammary Gland

value: T cells

tag: strain

value: Pregnancy


title: fmo-4 OE C. elegans, test, Day 1 adult, bio replicate 2

description:
Library name: MBH16
RNA from C. elegans was isolated using Zymo Research Direct-zol RNA Miniprep kit

value: fmo-4 overexpression


title: OMA-1 mutant 4-cell, Total RNA-seq, batch12, rep2, read1

value: NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®


title: MNase-seq of XVIfMmycot1 hho1-/- strain, 20min


title: fmo-4 OE C. elegans, test, Day 1 adult, bio replicate 1

description:
Library name: MBH6
RNA from C. elegans was isolated using Zymo Research Direct-zol RNA Miniprep kit


title: H9 DGCR8 heterozygote HET1 clone replicate 2 (miRNA-seq)

value: embryonic stem cells


title: OMA-1 mutant 4-cell, Total RNA-seq, batch11, rep1, read1


title: MNase-seq of XVIfMmycot1 hho1-/- strain, 10min


title: C exposed to Clas-negative psyllids_time10_ replicate 3

description:
C.h.10.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: H9 DGCR8 heterozygote HET1 clone replicate 1 (miRNA-seq)

value: DGCR8 heterozygote


title: RNA-seq of XVIfMmycot1 strain +DMSO, rep1


title: OMA-1 mutant 2-cell, Total RNA-seq, batch12, rep3, read1


title: C exposed to Clas-negative psyllids_time10_ replicate 2

description:
C.h.10.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: MNase-seq of XVIfMmycot1 hho1-/- strain, 5min


title: OMA-1 mutant 2-cell, Total RNA-seq, batch12, rep2, read1


title: H9 DGCR8 heterozygote HET1 clone replicate 3 (miRNA-seq)


title: C exposed to Clas-negative psyllids_time10_ replicate 1

description:
C.h.10.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: H9 WT replicate 2 (miRNA-seq)

value: wildtype


title: C exposed to Clas-positive psyllids_time0_ replicate 3

description:
C.Las.0.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-positive psyllid


title: MNase-seq of Mpneumo strain, 40min

value: UEVKWW


title: scRNAseq GEX 10x Lane 3

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 3

value: WT


title: LPC-2

value: spleen

tag: age

value: 3 weeks

value: LPC-treated


title: OMA-1 mutant 1-cell, Total RNA-seq, batch12, rep3, read1


title: H9 WT replicate 1  (miRNA-seq)


title: MNase-seq of Mpneumo strain, 20min

value: Asy


title: OMA-1 mutant 1-cell, Total RNA-seq, batch12, rep2, read1

value: RNA-seq


title: BHLHE41_DEC2

city: Philadelphia

first: Mai

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample 2

data_processing:
Sequencing reads were mapped to the human mm9 reference genome assembly using bowtie2 (Langmead and Salzberg, 2012) with default parameters. Peak calling was performed using macs14 with --pvalue=1e-9. Filtered BED files are generated excluding peaks that overlapped with the mm9 blacklist. BigWig files are generated using genomeCoverageBed and bedGraphToBigWig
Assembly: mm9
Supplementary files format and content: bigwig, bed

source_name: Beta TC6 cells lines

growth_protocol: Beta-TC6 cells (ATCC; CRL-11506) cultured in DMEM supplemented with 15% FBS, 1% L glutamine, and 1% penicillin/streptomycin

extract_protocol:
FACS-purified fixed cells (typically ~1million) were pelleted and flash-frozen. ChIP-seq was conducted as described in (Gifford et al., 2013) with minor modifications. Briefly, cell pellets were thawed on ice for 30min, incubated in lysis buffer (0.5% NP-40 +85mM KCl +20mM Tris-HCl pH8.0 +protease inhibitor) for 10min on ice, and nuclei were pelleted and incubated in lysis buffer (1% NP-40 +0.5% sodium deoxycholate +0.1% SDS +10mM Tris-HCl pH7.5 +protease inhibitor) for 10min on ice. Chromatin was then sheared with a Branson Sonifier (model S-450D) at 4ºC and incubated with 1µg/million cells H3K27Ac (Active Motif; 39133) or H3K4me1 (Millipore, 17-614) antibody overnight at 4ºC. Next, antibody-protein complexes were isolated by incubation with Protein A/G beads (Life Technologies; 100-02D/100-07D) for 2h at 4ºC. Samples were then sequentially washed twice with low-salt buffer (0.1% SDS +1% Triton X-100 +2mM EDTA +20mM Tris-HCl pH8.1 +150mM NaCl), twice with high-salt buffer (0.1% SDS +1% Triton X-100 +2mM EDTA +20mM Tris), twice with LiCl buffer (0.25M LiCl +1% NP-40 +1% deoxycholate +1mM EDTA +10mM Tris-HCl pH8.1), twice with TE (10mM Tris-HCl pH8.0 +1mM EDTA), and finally eluted in freshly-prepared elution buffer (1% SDS +0.1M NaHCO3) at 65ºC for 30min. Eluates were then treated with reverse crosslinking salt mixture (250mM Tris-HCl pH6.5 +62.5mM EDTA pH8.0 +1.25M NaCl +5mg/ml Proteinase K + 62.5ng/µl RNase A) overnight at 65ºC
DNA was purified using AMPure XP magnetic beads (Beckman Coulter), and sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs; E7103), pooled, and sequenced on a HiSeq 2500 instrument (Illumina).

value: Beta TC6 cells lines


title: MNase-seq of Mpneumo strain, 10min


title: C exposed to Clas-positive psyllids_time0_ replicate 1

description:
C.Las.0.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Valencia

value: young flush


title: OMA-1 mutant 1-cell, Total RNA-seq, batch11, rep1, read1

value: embryos


title: C exposed to Clas-negative psyllids_time0_ replicate 3

description:
C.h.0.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-negative psyllid


title: MNase-seq of Mpneumo strain, 5min

value: PHLPTK


title: Wild-type 8-cell, Total RNA-seq, batch12, rep3, read1

value: NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®


title: OMA-1 mutant 2-cell, Total RNA-seq, batch11, rep1, read1


title: C exposed to Clas-negative psyllids_time0_ replicate 2

description:
C.h.0.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: MNase-seq of Mpneumo strain, 60min


title: CD163_NC

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

description:
Library name: SAMPLES 1
10X Genomics

data_processing:
Single-cell RNA-seq data were pre-processed and qualitied with Seurat (version 4). We removed the cells that had greater than 15% expression originating from mitochondrial genes as well as expressed less than 200 genes or greater than 6,000 genes to filter out low-quality cells and doublets.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separted values files and matrix files

source_name: gut

extract_protocol:
For the collection of the immune cells in colon, mice were sacrificed by CO2 overdose and colon was removed and placed in ice-cold HBSS (GIBCO) with 5% FBS. Isolated cells were resuspended in 10 ml of the 40% fraction of a 40: 80 Percoll gradient and overlaid on 5 ml of the 80% fraction in a 15 ml Falcon tube. Percoll gradient separation was performed by centrifugation for 20 min at 1,800 rpm at room temperature. lymphocytes were collected at the interphase of the Percoll gradient, washed and resuspended in medium, and then stained for sorting and analyzed by flow cytometry. Dead cells were eliminated through 7-AAD staining.
According to the manufacture’s introduction, single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: gut

value: gut lamina propria


title: BHLHE40_DEC1

description: Library name: Sample 1


title: CD163_FL

description:
Library name: SAMPLES 2
10X Genomics


title: MNase-seq of Mmyco strain, 40min


title: C non-inoculated replicate 3

description:
C.h.prior.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: no treatment

value: before exposure


title: Wild-type 8-cell, Total RNA-seq, batch11, rep1, read1


title: MNase-seq of Mmyco strain, 60min


title: C exposed to Clas-positive psyllids_time0_ replicate 2

description:
C.Las.0.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-positive psyllid


title: C exposed to Clas-negative psyllids_time0_ replicate 1

description:
C.h.0.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: Wild-type 4-cell, Total RNA-seq, batch12, rep3, read1


title: mammary_DN_NK11_Tcells_rep2

city: BETHESDA

first: Cihan

last: Oguz

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

description: mammary_Tcells_bulk_RNA_Seq_count_mtx.tsv.gz

data_processing:
Samples were demultiplexed with bcl-convert and mkfastq (Cell Ranger v7.1.0) to generate the fastq files
Cell Ranger (v7.1.0) count and aggr functions were used to generate the filtered_feature_bc_matrix.h5 files that have the integrated RNA-HTO count matrices for each scRNA-Seq sample, whereas Cell Ranger (v7.1.0) vdj function was used to generate the filtered_contig_annotations.csv files
Assembly: mm10
Supplementary files format and content: Cell Ranger scRNA-seq count matrices are in the h5 data format (one h5 file per sample for which the RNA and HTO counts are integrated) and bulk RNA-Seq count matrix with the raw counts of all bulk RNA-Seq samples are in a single txt file that is tab-separated. The processed immune repertoire (VDJ) sequencing data is provided in the filtered_contig_annotations.csv.gz files.

source_name: mammary gland

extract_protocol:
scRNA-Seq: Mammary lymphoid cells (CD45+CD90.2+) from pregnant (G18.5) and lactating (L5) mice were sorted from samples labeled with TotalSeqC hashtag oligos using a Sony MA900 sorter. Likewise, the mammary epithelial cells and myoepithelial cells from samples labeled with TotalSeqC hashtags oligos (Biolegend) with a Sony MA900 sorter. Sorted cells were pooled together and loaded to a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. Bulk RNA-Seq: T cells were sorted with a Sony MA900 sorter from the mammary glands of pregnant (E18.5) mice. The RNA from these sorted T cells were extracted using RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions and libraries were prepared using Tecan’s Solo mouse kit according to manufacturer’s instructions.
scRNA-seq libraries were prepared using 10X scRNAseq 5' v2 with hashtag oligos (HTOs) and VDJ (T cell receptor) sequences, whereas the bulk RNA-Seq libraries prepared using Tecan’s Solo mouse kit. All libraries were prepared according to the manufacturer's instructions.
scRNA-seq on mammary epithelial-myoepithelial and lymphoid cells in mice. Bulk RNA-Seq on CD8 beta+ T-cells and DN (double negative) NK1.1+ lymphocytes in mice. The scRNA-seq libraries were coupled with hashtag oligo (HTO) libraries for labeling the samples in order to demultiplex the pooled RNA libraries into individual mice for downstream analysis, whereas the lymphoid cells were also used for generating T cell receptor (VDJ region) sequencing libraries for characterizing the immune repertoire landscape.

value: mammary gland

value: DN NK1.1+ lymphocytes


title: C non-inoculated replicate 1

description:
C.h.prior.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: Wild-type 4-cell, Total RNA-seq, batch12, rep2, read1


title: Wild-type 8-cell, Total RNA-seq, batch12, rep2, read1


title: MNase-seq of Mmyco strain, 10min


title: mammary_DN_NK11_Tcells_rep3


title: MNase-seq of Mmyco strain, 20min

value: LYVCPG


title: MNase-seq of Mmyco strain, 5min

value: Asy


title: mammary_CD8b_Tcells_rep3

value: CD8 beta+ Tcells


title: mammary_DN_NK11_Tcells_rep1


title: Wild-type 4-cell, Total RNA-seq, batch11, rep1, read1

value: RNA-seq


title: wien_R7

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Preprocessing was done using PRINSEQ-lite (version 0.20.4)
Alignment to the C. suis reference genome (GenBank assembly accession: GCA_002600585.1, Genome assembly: ASM260058v1) using STAR (version 2.7.9a)
Alignment postprocessing was performed using samtools (version 1.4)
featureCounts (version 2.0.3) from the Subread package was employed to quantify reads per gene
Normalization and differential gene expression analysis was then conducted using DESeq2
Assembly: GenBank assembly accession: GCA_002600585.1, Genome assembly: ASM260058v1
Supplementary files format and content: tab-delimited text file includes normalized counts per gene for all samples

organism: Cystoisospora suis

source_name: Wien I

growth_protocol: Intestinal porcine epithelial cells (IPEC-1, ACC 705) were used as host cells in vitro. Cells were grown in in DMEM/Ham’s F-12 medium with 5% foetal calf serum (Gibco) and 100 U/ml penicillin and 0.1 mg/ml streptomycin  at 37 °C in 5% CO2. Confluent IPEC-1 cells were infected with 5 × 103 sporozoites/well released from excysted oocysts and incubated further at 40 °C under 5% CO2.

extract_protocol:
RNA was isolated using RNeasy® Mini kit (Qiagen, Hilden, Germany) and treated with RNase-free DNase (Qiagen) according to the manufacturer’s instructions to remove any DNA contamination.
RNA samples with an RNA integrity number above 8.0 were used for library preparation, and samples were sent for library preparation using a reverse stranded protocol with poly-A enrichment. Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module® and the NEBNext Ultra® II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols (New England Biolabs, Ipswich, Massachusetts, USA). Libraries were QC-checked on a Bioanalyzer 2100® (Agilent Technologies, Santa Clara, CA, USA) using a High Sensitivity® DNA kit for correct insert size and quantified using Qubit dsDNA HS® assay (Invitrogen, Waltham, Massachusetts, USA).
Pooled libraries were sequenced on a NextSeq2000® instrument (Illumina, San Diego, California, USA) in 2 × 150 bp paired-end sequencing mode.

treatment_protocol: Infected cells with Holland-I were additionally incubated in the presence of 10 μM of toltrazuril dissolved in DMSO from day 6 for 72 h.

value: Wien I

value: untreated


title: Hi-C of yeast + P. vitis YAC strain (G1)

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.


title: mammary_CD8b_Tcells_rep2


title: H9 WT replicate 3 (miRNA-seq)

value: embryonic stem cells

value: wildtype


title: Hi-C of yeast + P. falciparum YAC strain, rep2 (G1)

value: UMNUEC


title: Wild-type 2-cell, Total RNA-seq, batch12, rep2, read1

value: NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

value: embryos


title: mammary_CD8b_Tcells_rep1


title: wien_R5


title: wien_R4


title: Wild-type 2-cell, Total RNA-seq, batch11, rep1, read1


title: HDPS cells [H2]

city: Sharjah

first: Muhammad

middle: Tehsil

last: Gul

address: University street

country: United Arab Emirates

institute: university of sharjah

data_processing:
Illumina Casava, 1.8 version base calling software, Qphred = -10log10€
Sequence reads were trimmed for adaptor sequence/low-quality sequence, Reads containing N>10% are removed, Remove read Qscores of over 50% bases below 5.
Trimmed sequence reads were mapped to hg38 using HISAT2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Dental Pulp

growth_protocol: HDPSC were maintained in alpha MEM supplemented with 20% fetal bovine serum (FBS), 1% L-Glutamine and 1% antibiotics(Pen/Strep) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Neural differentiation was induced by treatment of 1 day post transfection cells with Neurocult basal media media (StemCell Technologies) supplemented with 50 ml Neurocult proliferation supplement (StemCell Technologies), Heparin (StemCell Technologies), 20ng/ul EGF (GIBCO), and 20 ng/ul FGF (GIBCO). Media was changed every 2 days for the nuerospheres generated.

value: Dental Pulp

value: HDPSC

value: Primary culture:Human Dental Pulp stem cells

value: WT

value: No treatment

tag: time

value: Day 0


title: HDPS cells [H1]

tag: tissue


title: Wild-type 1-cell, Total RNA-seq, batch12, rep2, read1

tag: genotype


title: HDPS cells, miR22-3p Inhibitor, Day7 [I3_D7]

tag: treatment

value: Neural differentiation

value: Day 7


title: Hi-C of XVIfMmycot1 strain, hho1-/- (G1)

tag: background


title: Wild-type 1-cell, Total RNA-seq, batch12, rep3, read1


title: Hi-C of XVIfMmycot1 strain, hho1+/+ (G1)

tag: cell line

value: EECNQU


title: Hi-C of XVIfMmycot1 strain (quiescence)

tag: Stage

value: Quiescence


title: wien_R1

value: Wien I


title: Wild-type 1-cell, Total RNA-seq, batch11, rep1, read1

value: RNA-seq


title: Hi-C of XVIfMmycot1 strain +TSA (G1)

tag: hash


title: HOLI_treated_R7

source_name: Holland I

value: Holland I

value: toltrazuril treatment


title: OMA-1 mutant 4-cell,ribosomes profiling, batch9, rep4, read1

data_processing:
Ribosome profiling data were processed using RiboFlow. Input data included gzipped fastq files containing ribosome profiling sequencing data, Bowtie2 index files for the transcriptome reference (appris_celegans_v1) and filter reference (rRNA sequences), a bed file defining CDS, UTR5, and UTR3 regions, and a two-column tsv file containing transcript lengths. Unique Molecular Identifiers (UMIs) were extracted from the reads using UMI-tools (Version 1.1.2) with the parameters "-p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex". Reads were processed using default settings . Alignments with a mapping quality greater than two were retained. Deduplication was performed using UMI-tools. Only footprints between 21 and 40 nucleotides in length were considered for the final analysis.  The RiboFlow platform was also used to process the RNA-seq data. Computational processing of RNA-seq data was performed using a custom pipeline based on the provided YAML configuration. The processing steps were as follows: First, quality control and trimming were conducted using cutadapt, where the first and last 25 nucleotides were trimmed from each read with the parameters '-u 25 -u -25 --quality-cutoff=28', also removing bases with a quality score below 28. Next, filtered reads were aligned using Bowtie2 in a two-step process: reads were initially aligned to a reference of rRNAs using the parameters '-L 15 --no-unal', and then unaligned reads were aligned to the transcriptome reference using the same parameters. Finally, in the post-alignment processing step, only alignments with a mapping quality greater than 2 were retained for further analysis.
Assembly: The reference files can be found here: https://github.com/RiboBase/reference_caenorhabditis-elegans
Supplementary files format and content: Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy  for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Library strategy: RIBO-seq

value: Diagenode D-Plex Small RNA-seq Kit v2 (UDI module)

value: Ribosome Profiling (Mnase)


title: Hi-C of yeast + P. falciparum YAC strain, rep1 (G1)

value: JYMQSN


title: HDPS cells, miR22-3p Inhibitor, Day7 [I2_D7]

value: Dental Pulp


title: Hi-C of XVIfMmycot1 strain +thiolutin, rep2 (G1)


title: Wild-type 2-cell, Total RNA-seq, batch12, rep3, read1

value: NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

value: embryos


title: wien_R6

value: untreated


title: HDPS cells, miR22-3p Inhibitor, Day7 [I1_D7]

value: HDPSC

value: Primary culture:Human Dental Pulp stem cells

value: WT


title: HDPS cells [H3]

value: No treatment

value: Day 0


title: C non-inoculated replicate 2

description:
C.h.prior.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

tag: cultivar

value: Valencia

value: young flush

value: no treatment

value: before exposure


title: HDPS cells, miR22-3p Inhibitor, Day3 [I3_D3]

value: Neural differentiation

value: Day 3


title: wien_R3

value: Wien I


title: wien_R2


title: HOLI_treated_R6

value: Holland I

value: toltrazuril treatment


title: OMA-1 mutant 4-cell,ribosomes profiling, batch5, rep2, read1

value: Diagenode D-Plex Small RNA-seq Kit v2 (UDI module)

value: Ribosome Profiling (Mnase)


title: Hi-C of XVIfMmycot1 strain +thiolutin, rep1 (G1)


title: HOLI_treated_R5


title: HDPS cells, miR22-3p Inhibitor, Day3 [I1_D3]

value: Dental Pulp


title: HDPS cells, miR22-3p Inhibitor, Day3 [I2_D3]

value: HDPSC


title: OMA-1 mutant 2-cell,ribosomes profiling, batch9, rep6, read1

value: embryos


title: Hi-C of XVIfMmycot1 strain +DMSO, rep1 (G1)


title: HOLI_treated_R4


title: Hi-C of XVIfMmycot3 strain (G2/M)


title: OMA-1 mutant 4-cell,ribosomes profiling, batch4, rep1, read1


title: Hi-C of XVIfMmycot3 strain (G1)


title: HOLI_treated_R3


title: HDPS cells, miR22-3p Inhibitor, Day1 [I2_D1]

value: Primary culture:Human Dental Pulp stem cells

value: WT

value: Day 1


title: OMA-1 mutant 2-cell,ribosomes profiling, batch10, rep4, read1


title: HOLI_treated_R2


title: HDPS cells, miR22-3p Inhibitor, Day1 [I3_D1]


title: HOLI_treated_R1


title: OMA-1 mutant 2-cell,ribosomes profiling, batch8, rep5, read1


title: Hi-C of XVIfMmycot2' strain (G2/M)


title: HDPS cells, miR22-3p Inhibitor, Day1 [I1_D1]


title: OMA-1 mutant 2-cell,ribosomes profiling, batch6, rep3, read1


title: HOLI_cont_R7

value: untreated


title: OMA-1 mutant 4-cell,ribosomes profiling, batch6, rep3, read1


title: PolII ChIP-seq of XVIfMmycot1 strain +thiolutin (input), rep2

data_processing:
For standard ChIP-seq, bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. For calibrated Scc1 ChIP-seq, bowtie2 was used in two rounds of alignments, first on C. glabrata (CBS138) and then on the appropriate S. cerevisiae genome reference, allowing the generation of IP and input (WCE) alignments that exclusively mapped on S. cerevisiae (and vice-versa for C. glabrata).
Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded. PCR duplicates were removed using samtools. When available, the input was similarly processed.
Fragment coverage was normalized by library depth (CPM) and converted into a genomic track (bigwig) using deepTools. Input-normalized fragment coverage was also generated, when possible, using bamCompare from deepTools with “--scaleFactorsMethod readCount”.
For calibrated Scc1 ChIP-seq, CPM-normalized fragment coverages were also multiplied by the ORi factor for calibration (WCEglabrata x IPcerevisiae / WCEcerevisiae x IPglabrata, in which WCEglabrata and IPglabrata correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads).
MACS2 2.2.7.1 was used to call peaks using the input alignment files as control.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for ChIP-seq coverage (IP, IP/Input and calibrated) are provided. Peaks are provided as .narrowPeak files.

growth_protocol: Cells of either S. cerevisiae or Candida glabrata were grown exponentially to OD600 = 0.5. 15 OD600 units of S. cerevisiae cells were mixed with 3 OD600 units of C. glabrata cells to a total volume of 45 mL for Scc1 calibration only.

extract_protocol:
Cells were fixed using 4mL of fixative solution (50 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA; 30% (v/v) formaldehyde) for 30 min at room temperature (RT) with rotation. The fixative was quenched with 2mL of 2.5M glycine (RT, 5 min with rotation). The cells were then harvested by centrifugation at 3,500 rpm for 3 min and washed with ice-cold PBS. The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transferred in 2mL tubes containing glass beads (ozyme, P000913-LYSK0-A.0) before mechanical cells lysis. The soluble fraction was isolated by centrifugation at 2,000 rpm for 3min then transferred to sonication tubes (Covaris milliTUBE 1ml, 520135) and samples were sonicated to produce sheared chromatin with a size range of 200-1,000bp using a Covaris sonicator. After sonication the samples were centrifuged at 13,200 rpm at 4°C for 20min and the supernatant was transferred into 700µL of ChIP lysis buffer. 80µL (27µl of each sample) of the supernatant was removed (termed ‘whole cell extract [WCE] sample’) and store at -80°C. 5ug of antibody was added to the remaining supernatant which is then incubated overnight at 4°C (wheel cold room). 50µL of protein G Dynabeads or protein A Dynabeads was then added and incubated at 4°C for 2h. Beads were washed 2 times with ChIP lysis buffer, 3 times with high salt ChIP lysis buffer (50mMHEPES-KOH, pH 8.0; 500 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate;1 mM PMSF), 2 times with ChIP wash buffer (10 mM Tris-HCl, pH 8.0; 0.25MLiCl; 0.5% NP-40; 0.5% sodium deoxycholate; 1mM EDTA;1 mMPMSF) and 1 time with TE pH7.5. The immunoprecipitated chromatin was then eluted by incubation in 120µL TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) for 15min at 65°C and the supernatant is collected termed ‘IP sample’. The WCE samples were mixed with 40µL of TES3 buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 3% SDS). ALL (IP and WCE) samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified by a phenol/Chloroform extraction.
The triplicate IP samples were mixed in 1 tube and libraries for IP and WCE samples were prepared using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.

value: Asy

tag: antibody

value: PolII

tag: step

value: WCE


title: HDPS cells, miR22-3p Mimic, Day7 [M3_D7]

value: Neural differentiation

value: Day 7


title: HOLI_cont_R6


title: OMA-1 mutant 2-cell,ribosomes profiling, batch4, rep1, read1

tag: developmental stage

tag: number of_embryos


title: OMA-1 mutant 2-cell,ribosomes profiling, batch5, rep2, read1

tag: strain name

tag: lib. prep._method


title: Hi-C of XVIfMmycot2' strain (G1)

value: XQBZUC


title: HOLI_cont_R5

tag: strain

value: Holland I


title: PolII ChIP-seq of XVIfMmycot1 strain +thiolutin (IP), rep2

value: IP


title: HOLI_cont_R4


title: OMA-1 mutant 1-cell,ribosomes profiling, batch10, rep3, read1

value: Diagenode D-Plex Small RNA-seq Kit v2 (UDI module)


title: HDPS cells, miR22-3p Mimic, Day7 [M1_D7]

tag: cell type


title: HDPS cells, miR22-3p Mimic, Day3 [M3_D3]

tag: time

value: Day 3


title: PolII ChIP-seq of XVIfMmycot1 strain +thiolutin (input), rep1


title: OMA-1 mutant 1-cell,ribosomes profiling, batch10, rep2, read1

value: Ribosome Profiling (Mnase)

tag: tissue


title: HDPS cells, miR22-3p Mimic, Day3 [M2_D3]

value: Dental Pulp

value: HDPSC

tag: genotype


title: OMA-1 mutant 1-cell,ribosomes profiling, batch6, rep1, read1

tag: treatment

value: embryos


title: HOLI_cont_R3


title: PolII ChIP-seq of XVIfMmycot1 strain +thiolutin (IP), rep1

tag: background


title: HDPS cells, miR22-3p Mimic, Day3 [M1_D3]

tag: cell line

value: Primary culture:Human Dental Pulp stem cells

value: WT


title: HOLI_cont_R1

value: untreated


title: PolII ChIP-seq of XVIfMmycot1 strain +DMSO (input)

tag: Stage

value: Asy


title: HDPS cells, miR22-3p Mimic, Day1 [M3_D1]

value: Day 1


title: Hi-C of XVIfMmycot1 strain +DMSO, rep2 (G1)

tag: hash


title: Wild-type 8-cell,ribosomes profiling, batch9, rep4, read1


title: HDPS cells, miR22-3p Mimic, Day7 [M2_D7]


title: PolII ChIP-seq of XVIfMmycot1 strain +DMSO (IP)

value: PolII


title: HDPS cells, miR22-3p Mimic, Day1 [M2_D1]

value: Neural differentiation


title: HDPS cells, miR22-3p Mimic, Day1 [M1_D1]


title: H4K16ac ChIP-seq of XVIfMmycot1 strain +TSA (IP)


title: Wild-type 8-cell,ribosomes profiling, batch7, rep2, read1

value: 18(lysate was split - techinally 9 embryos )


title: H4K16ac ChIP-seq of XVIfMmycot1 strain +NAM (input)

value: WCE


title: B exposed to Clas-positive psyllids_tiBe60_ replicate 1

description:
B.Las.60.1
Bergera koenigii

data_processing:
Adapter removal and quality trimming of raw reads was done with cutadapt.
Clean reads were analysed using FastQC.
Clean read pairs longer than 20 nt were mapped to the reference genomes (for Citrus and Bergera) or de novo transcriptome (for Bergera) using STAR.
Differential expression analysis was performed with DESeq2.
Assembly: Citrus sinensis SWO.v3.0 genome + Liberibacter_asiaticus NZ_CP019958 genome, Murraya paniculata genome + Liberibacter_asiaticus NZ_CP019958 genome (Murraya_paniculata_final.chr.fasta), and Bergera transcriptome + Liberibacter_asiaticus NZ_CP019958 genome (Bergera_ST_Streptophyta.fasta) combined genomes.
Supplementary files format and content: Tab-delimited text files including count of reads for each gene in each sample.

organism: Murraya koenigii

value: young flush

value: Clas-positive psyllid

tag: time point


title: B exposed to Clas-positive psyllids_tiBe60_ replicate 3

description:
B.Las.60.3
Bergera koenigii


title: B exposed to Clas-positive psyllids_tiBe60_ replicate 2

description:
B.Las.60.2
Bergera koenigii


title: H4K16ac ChIP-seq of XVIfMmycot1 strain +TSA (input)

tag: antibody


title: HDPS cells, Untransfected Control, Day7 [C2_D7]

value: Day 7


title: Wild-type 8-cell,ribosomes profiling, batch3, rep1, read1

value: Diagenode D-Plex Small RNA-seq Kit v2 (UDI module)


title: B exposed to Clas-negative psyllids_tiBe60_ replicate 3

description:
B.h.60.3
Bergera koenigii

value: Clas-negative psyllid


title: H4K16ac ChIP-seq of XVIfMmycot1 strain +NAM (IP)

tag: step

value: IP


title: HOLI_cont_R2

value: Holland I


title: Wild-type 8-cell,ribosomes profiling, batch10, rep5, read1

tag: developmental stage

value: Ribosome Profiling (Mnase)

value: embryos


title: B exposed to Clas-negative psyllids_tiBe60_ replicate 2

description:
B.h.60.2
Bergera koenigii


title: H4K16ac ChIP-seq of XVIfMmycot1 strain +DMSO (input)


title: Wild-type 4-cell,ribosomes profiling, batch3, rep3, read1

tag: number of_embryos


title: B exposed to Clas-negative psyllids_tiBe60_ replicate 1

description:
B.h.60.1
Bergera koenigii


title: Wild-type 4-cell,ribosomes profiling, batch3, rep2, read1

tag: strain name


title: HDPS cells, Untransfected Control, Day3 [C3_D3]

value: Dental Pulp

value: HDPSC

value: Primary culture:Human Dental Pulp stem cells

value: WT

value: Day 3


title: Wild-type 4-cell,ribosomes profiling, batch7, rep4, read1

tag: lib. prep._method


title: CRAC-seq of Mpneumo strain, rep2

data_processing:
CRAC-seq datasets were processed and aligned on the appropriate genome reference using the pyCRAC script
Only reads longer than 20 nt were mapped on the M. mycoides and M. pneumoniae chimeric genomes and only reads longer than 40 nt were mapped to the S. pombe genome for the spike-in to avoid inter-species mapping. Signals mapping to the chimeric genomes were normalized using the S.pombe spike-in. Homopolymers (fragments with 6+ identical nt) and poly-adenylated reads were discarded.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for CRAC-seq coverage (fwd, rev) are provided.
Library strategy: CRAC-seq

growth_protocol: 2 L of yeast cells containing Rpb1 tagged with a his6-TEV-proteinA (HTP) tag were grown in CSM-Trp medium to an OD600 of 0.6. 5% of S. pombe cells also containing an HTP tagged version of Rpb1 were added to the culture before crosslinking.

extract_protocol:
Cells were exposed to UV light using a W5 UV crosslinking unit (UVO3 Ltd) for 50 seconds, harvested and resuspended in TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol, 2.4 ml/g of cells) with protease inhibitors. Cells were broken using a Mixer Mill MM 400.
Extracts were treated for one hour at 25°C with DNase I (165 U/g of cells) to solubilize chromatin and then clarified by centrifugation (20 min at 20000g at 4°C). Rpb1-RNA complexes were purified by a two-step procedure using the protein A and the his-6 portion of the tag, with TEV cleavage for eluting complexes at the proteinA-dependent purification step. Adaptors were added during the purification steps. The protein-RNA adduct was further purified by denaturing PAGE and the RNA recovered by proteinase K degradation and phenol extraction. The library was amplified by 10 cycles of PCR after reverse transcription and sequenced using Illumina technology

value: Asy

value: TGC

tag: sequencing

value: single-end


title: HDPS cells, Untransfected Control, Day3 [C2_D3]

tag: cell type

value: Neural differentiation


title: B exposed to Clas-positive psyllids_tiBe30_ replicate 3

description:
B.Las.30.3
Bergera koenigii

value: young flush

value: Clas-positive psyllid


title: Wild-type 8-cell,ribosomes profiling, batch8, rep3, read1

value: Diagenode D-Plex Small RNA-seq Kit v2 (UDI module)


title: B exposed to Clas-positive psyllids_tiBe30_ replicate 2

description:
B.Las.30.2
Bergera koenigii


title: HDPS cells, Untransfected Control, Day7 [C3_D7]

tag: time

value: Day 7


title: HDPS cells, Untransfected Control, Day3 [C1_D3]

tag: tissue


title: Wild-type 2-cell,ribosomes profiling, batch3, rep3, read1

value: 18(lysate was split - techinally 9 embryos )

tag: genotype


title: CRAC-seq of Mmyco strain, rep2

value: ACT


title: Wild-type 2-cell,ribosomes profiling, batch7, rep4, read1

tag: treatment

value: Ribosome Profiling (Mnase)


title: CRAC-seq of Mpneumo strain, rep1

tag: background

value: CTA


title: B exposed to Clas-negative psyllids_tiBe30_ replicate 3

description:
B.h.30.3
Bergera koenigii

value: Clas-negative psyllid


title: HDPS cells, Untransfected Control, Day1 [C2_D1]

value: Dental Pulp

tag: cell line

value: HDPSC

value: Day 1


title: Wild-type 2-cell,ribosomes profiling, batch2, rep2, read1

value: embryos


title: HDPS cells, Untransfected Control, Day7 [C1_D7]

value: Primary culture:Human Dental Pulp stem cells

value: WT


title: HDPS cells, Untransfected Control, Day1 [C1_D1]


title: ATAC of Mpneumo strain (gDNA), rep2

data_processing:
Bowtie2 was used to align paired-end ATAC-seq data on the appropriate genome reference. Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded. PCR duplicates were removed using samtools.
Fragment coverage was normalized by library depth (CPM) and converted into a genomic track (bigwig) using deepTools.
MACS2 2.2.7.1 was used to call peaks using the input alignment files as control.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for ATAC-seq coverage (ATAC, ATAC/gDNA) are provided. Peaks are provided as .narrowPeak files.

growth_protocol: Independent clones for each strain were inoculated into SC–HIS for overnight culture at 30 °C. Saturated overnight cultures were diluted to an OD600 of 0.1 and cultured for 6 h at 30 °C, until OD600 reached ~0.6.

extract_protocol:
Around 1-5 × 106 cells were taken from each culture, pelleted at 3,000g for 5 min, washed twice with spheroplasting buffer (1 M sorbitol, 40 mM HEPES-KOH pH 7.5, 10 mM MgCl2), resuspended in 200 μl spheroplasting buffer with 10 µL of Zymolyase (10 mg/mL), then incubated for 30 min at 37 °C. Spheroplasts were washed twice with 500 μl spheroplasting buffer then resuspended in 50 μl 1× TD buffer with 2.5 µL of TDE1 (Illumina 20034197). Tagmentation was performed for 30 min at 37 °C, 800 rpm with a thermomixer, and DNA was purified using the DNA Clean and Concentrator 5 kit (Zymo Research D4004).
PCR was performed using Phusion Master Mix, 11 total cycles. Paired-end sequencing on an Illumina NextSeq2000 (2 x 50 bp) was performed.

tag: Stage

value: Asy

value: gDNA

value: paired-end


title: H4K16ac ChIP-seq of XVIfMmycot1 strain +DMSO (IP)

value: IP

tag: hash


title: Wild-type 2-cell,ribosomes profiling, batch1, rep1, read1

value: Diagenode D-Plex Small RNA-seq Kit v2 (UDI module)


title: B exposed to Clas-negative psyllids_tiBe30_ replicate 1

description:
B.h.30.1
Bergera koenigii

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Two µg of total RNA per sample were used for library generation using the TruSeq stranded total RNA Library Kit plus Ribo-Zero and NEBNext kits for ribosomal RNA depletion.
The Illumina NovaSeq6000 was used on a paired-end sequencing of 150pb. All procedures were performed according to Illumina’s protocols.

value: young flush

tag: time point


title: NB4.ATO.rep3

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing reads were aligned to hg38 with the HISAT2 (version 2.1.0).
Gene expression and frequencies were calculated from the aligned data by htseq-count.
Differentially expressed genes (DSGs) were identified using DEseq2 with a FDR value < 0.1 and |Log2(Fold change)| <Log2(1.5)
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file containing the FPKM value and DEseq2 statistics per gene

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA). Ribosomal RNAs were depleted according to the manufacturer's protocol (Vazyme, China, N406-01).
RNA-seq libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, E7530S) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were treated with arsenic trioxide for 6 hours.

value: Treated with arsenic trioxide for 6 hours


title: CRAC-seq of Mmyco strain, rep1

value: GAG

value: single-end


title: Wild-type 4-cell,ribosomes profiling, batch2, rep1, read1

value: 18(lysate was split - techinally 9 embryos )

value: Ribosome Profiling (Mnase)


title: Wild-type 1-cell,ribosomes profiling, batch10, rep2, read1


title: B exposed to Clas-positive psyllids_tiBe20_ replicate 3

description:
B.Las.20.3
Bergera koenigii

value: Clas-positive psyllid


title: NB4.ATO.rep2


title: B exposed to Clas-positive psyllids_tiBe30_ replicate 1

description:
B.Las.30.1
Bergera koenigii


title: ATAC of Mpneumo strain (gDNA), rep1


title: HDPS cells, Untransfected Control, Day1 [C3_D1]

value: Dental Pulp

value: HDPSC

value: Neural differentiation


title: ATAC of Mpneumo strain, rep1

value: ATAC


title: ATAC of Mmmyco strain (gDNA), rep2


title: NB4.Ctrl.Rep3

value: control


title: NB4.ATO.rep1


title: B exposed to Clas-negative psyllids_tiBe20_ replicate 3

description:
B.h.20.3
Bergera koenigii

value: Clas-negative psyllid


title: B exposed to Clas-positive psyllids_tiBe20_ replicate 1

description:
B.Las.20.1
Bergera koenigii


title: B exposed to Clas-negative psyllids_tiBe30_ replicate 2

description:
B.h.30.2
Bergera koenigii


title: Wild-type 1-cell,ribosomes profiling, batch7, rep1, read1

value: embryos


title: ATAC of Mmmyco strain, rep2

value: Asy

value: paired-end


title: NB4.Ctrl.Rep2


title: Cultured CDSCs

city: chongqing

first: Debao

last: Li

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

institute: Chongqing International Institute for Immunology

description: Library name: Sample 2

data_processing:
The Cellranger (version 7.0.0) single-cell software suite is used to perform sample demultiplexing, barcoding processing, and single-cell 3' gene counting. Align the cDNA insert with the mm10/GRCm38 reference genome.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Bone  marrow

extract_protocol:
The primary and cultured CDSCs at passaged P2-P3 underwent single cell RNA-seq (scRNA-seq) (MobiDrop, China).
Briefly, the cell viability was determined by staining with Trypan blue (Beyotime, C360I-2) under a microscope. 20000 viable cells were prepared for application to a Chromium Controller (10x Genomics, USA), where the chromium Single Cell 3’ v3.1 kit (1000121, 10x Genomics, USA) was used to generate oligo (dT)-primed cDNA libraries. These libraries were quantified using the Agilent TapeStation High sensitivity D5000 ScreenTape and subsequently analyzed via Next Generation Sequencing (Nova-Seq 6000, Illumine, USA) with a data output of 200G.

value: Bone  marrow

value: cultured cells

value: costal-cartilage-derived stem cells (CDSCs)

value: cultured


title: Primary CDSCs

description: Library name: Sample 1

value: primary cells

value: primary


title: K27me3-WT_rep2

city: ChangChun

first: Mingming

last: Liang

address: xi an Road 5333

institute: Jilin university

data_processing:
The paired-end raw reads were trimed for adaptor seqence and low-quality seqences (-q 30) using Trim Galore 0.4.1. The filtered ChIP-seq reads were aligned to the hg19 genome using bowtie2 (Version 2.4.1) with   default parameters. PCR duplicates in bam files were moved by using Picard tool.
MACS2 (Version 2.2.7.1 43) was used to call narrow peaks for H3K4me3 and H3K27ac with the parameters (-q 0.001) or broad peaks for H3K27me3 with the parameters (-q 0.1 --broad). The input sequencing data was set as a control.
The ChIP signal was normalized by using bamCoverage function in deeptools 3.5.0 with the parameters ( --normalizeUsing CPM,  --ignoreDuplicates,  --minMappingQuality 30,  --minFragmentLength 50)
Assembly: GRCm38（mm10）
Supplementary files format and content: bigWig files of the ChIP signal for each sample
Supplementary files format and content: Peak bed files of each sample include the significant enriched regions of the detected hitone modifications

source_name: Tail

growth_protocol: mouse primary MEF cells were cultured in  high-glucose DMEM (Invitrogen) supplemented with 10% FBS (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37 °C, 5% CO2.

extract_protocol:
106 cells were crosslinked in 1% formaldehyde for 10 minutes and quenched using 125mM of Glycine for 5 minutes. The chromosome was fragmented to the fragment range of 200-400 bp in the Bioruptor® Pico via sonicating 5 cycles. The fragmented histone-DNA complexes were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
The VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607)  was used with 5 ng of ChIP DNA of each sample for the construction of sequencing libraries.

value: Tail

value: primary MEF cell line


title: B exposed to Clas-negative psyllids_tiBe20_ replicate 1

description:
B.h.20.1
Bergera koenigii

value: young flush


title: NB4.Ctrl.Rep1


title: B exposed to Clas-negative psyllids_tiBe20_ replicate 2

description:
B.h.20.2
Bergera koenigii


title: K27me3-WT_rep1


title: ATAC of Mmmyco strain (gDNA), rep1

value: gDNA


title: ATAC of Mmmyco strain, rep1


title: bESC_E_BL_p9_MEF

city: Davis

first: Anna

middle: Carolina

last: Denicol

state: CA

address: 450 BIOLETTI WAY, MEYER HALL

department: Animal Science

institute: University of California Davis

description:
Library name: Sample 4
S4 PE150

data_processing:
Trimmomatic was used to trim adaptors with the following settings: SLIDINGWINDOW:4:15 MINLEAN: 36 LEADING:3 TRAILING:3.
Assembly: Alignment was performed using star/2.7.10a (default settings) and Bos taurus reference genome UCD2.0 NCBI.
Supplementary files format and content: Raw counts table was prepared using FeatureCounts (subread/1.6.2), using -p -O -g gene_id arguments. Raw data was processed removing low counts and normalization with edgeR, TMM function.

organism: Bos taurus

source_name: Embryonic stem cell

growth_protocol: Bovine ESCs were derived from early (eBL) or full (BL) blastocyst-staged embryos and maintained in NBFR medium on mouse embryonic fibroblast feeders (Samples 1-4) or feeder-free on vitronectin-N (Samples 6-9). MEF (Sample 5) were grown according to manufacturer protocols (Gibco, A34180).

extract_protocol:
RNA was isolated using the Purelink Mini Kit (12183018A, Invitrogen) with DNAse treatment (12185010, Invitrogen).
Library preparation was performed using 1000 ng input with the KAPA mRNA Hyper Prep kit (Batch 1) or NEBNext Ultra II kit (Batch 2).

value: Embryonic stem cell

value: E

value: Bovine ESC

value: NBFR, p9, MEF

tag: batch


title: B exposed to Clas-positive psyllids_tiBe20_ replicate 2

description:
B.Las.20.2
Bergera koenigii

value: Clas-positive psyllid


title: K27me3-B_rep3


title: M exposed to Clas-positive psyllids_time10_ replicate 6

organism: Murraya paniculata


title: B exposed to Clas-positive psyllids_tiBe10_ replicate 6

description:
B.Las.10.6
Bergera koenigii


title: K27me3-B_rep2


title: B exposed to Clas-positive psyllids_tiBe10_ replicate 5

description:
B.Las.10.5
Bergera koenigii


title: bESC_D_eBL_p9_MEF

description:
Library name: Sample 2
S4 PE150

value: D


title: K27me3-B_rep1


title: B exposed to Clas-positive psyllids_tiBe10_ replicate 4

description:
B.Las.10.4
Bergera koenigii


title: bESC_A_eBL_p9_MEF

description:
Library name: Sample 1
S4 PE150

value: A


title: M exposed to Clas-positive psyllids_time10_ replicate 3


title: B exposed to Clas-positive psyllids_tiBe10_ replicate 3

description:
B.Las.10.3
Bergera koenigii


title: Input-WT_rep2


title: ATAC of Mpneumo strain, rep2

city: Paris

first: Romain

address: 25 Rue du Dr Roux

institute: Institut Pasteur

value: Asy

tag: step

value: ATAC

value: GSUSFD

value: paired-end


title: B exposed to Clas-positive psyllids_tiBe10_ replicate 2

city: Valencia

first: Javier

address: Ingeniero Fausto Elio, s/n

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

description:
B.Las.10.2
Bergera koenigii


title: Input-WT_rep3


title: Cells incubated under normoxic conditions_3

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.20.0.4).
The 3' end of the sequenced read was trimmed by one nucleotide. Reads with more than 2 ambiguous nucleotides and reads with low quality scores were removed using CLC Genomics Workbench software (ver.20.0.4).
Trimmed sequence reads were mapped to Canis lupus familiaris sequence CanFam3.1 release-98 using CLC genomics workbench with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.20.0.4).
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

organism: Canis lupus familiaris

extract_protocol:
Total RNA was isolated from the melanoma cells using the Maxwell RSC simplyRNA Cells Kit (Promega). Polyadenylated mRNA was purified using oligo dT beads included in the NEBNext Poly (A) mRNA Magnet Isolation Module (New England Biolabs, NEB). Purified mRNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences included in NEBNext Multiplex Oligos for Illumina were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Agilent 2100 Bioanalyzer (Agilent). The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NextSeq DNA sequencer with 75 bp paired-end cycle sequencing kit (Illumina).

value: Canine malignant melanoma cell line

value: normoxia


title: Input-WT_rep1

value: Tail


title: Input-B_rep3

value: primary MEF cell line


title: M exposed to Clas-positive psyllids_time10_ replicate 2

value: young flush


title: M exposed to Clas-positive psyllids_time10_ replicate 1


title: Cells incubated under normoxic conditions_1


title: Cells incubated under normoxic conditions_2


title: B exposed to Clas-negative psyllids_tiBe10_ replicate 6

description:
B.h.10.6
Bergera koenigii

value: Clas-negative psyllid


title: M exposed to Clas-negative psyllids_time10_ replicate 6


title: bESC_C_BL_p9_MEF

description:
Library name: Sample 3
S4 PE150

value: Embryonic stem cell

value: C


title: B exposed to Clas-negative psyllids_tiBe10_ replicate 5

description:
B.h.10.5
Bergera koenigii


title: Input-B_rep2


title: M exposed to Clas-positive psyllids_time10_ replicate 5


title: M exposed to Clas-negative psyllids_time10_ replicate 5


title: Cells incubated under hypoxic conditions_2

value: hypoxia


title: Input-B_rep1


title: B exposed to Clas-negative psyllids_tiBe10_ replicate 4

description:
B.h.10.4
Bergera koenigii


title: M exposed to Clas-negative psyllids_time10_ replicate 4


title: Cells incubated under hypoxic conditions_1


title: M exposed to Clas-positive psyllids_time10_ replicate 4


title: H2Aub1-WT_rep3


title: B exposed to Clas-negative psyllids_tiBe10_ replicate 2

description:
B.h.10.2
Bergera koenigii


title: M exposed to Clas-negative psyllids_time10_ replicate 2


title: M exposed to Clas-negative psyllids_time10_ replicate 3


title: B exposed to Clas-negative psyllids_tiBe10_ replicate 3

description:
B.h.10.3
Bergera koenigii


title: B exposed to Clas-positive psyllids_tiBe10_ replicate 1

description:
B.Las.10.1
Bergera koenigii


title: H2Aub1-B_rep3


title: M exposed to Clas-positive psyllids_time0_ replicate 3


title: B exposed to Clas-positive psyllids_tiBe0_ replicate 2

description:
B.Las.0.2
Bergera koenigii


title: Cells incubated under hypoxic conditions_3


title: M exposed to Clas-negative psyllids_time10_ replicate 1


title: B exposed to Clas-negative psyllids_tiBe10_ replicate 1

description:
B.h.10.1
Bergera koenigii


title: H2Aub1-WT_rep1


title: B exposed to Clas-positive psyllids_tiBe0_ replicate 3

description:
B.Las.0.3
Bergera koenigii


title: M exposed to Clas-positive psyllids_time0_ replicate 2


title: H2Aub1-B_rep2


title: H2Aub1-B_rep1


title: M exposed to Clas-positive psyllids_time0_ replicate 1


title: B exposed to Clas-positive psyllids_tiBe0_ replicate 1

description:
B.Las.0.1
Bergera koenigii


title: ATAC-WT_rep3


title: M exposed to Clas-negative psyllids_time0_ replicate 3


title: H2Aub1-WT_rep2


title: B exposed to Clas-negative psyllids_tiBe0_ replicate 3

description:
B.h.0.3
Bergera koenigii


title: ATAC-WT_rep2


title: M exposed to Clas-negative psyllids_time0_ replicate 2


title: B exposed to Clas-negative psyllids_tiBe0_ replicate 2

description:
B.h.0.2
Bergera koenigii


title: ATAC-WT_rep1


title: B exposed to Clas-negative psyllids_tiBe0_ replicate 1

description:
B.h.0.1
Bergera koenigii


title: M exposed to Clas-negative psyllids_time0_ replicate 1