title: MCM2-2A ESC MINCE-seq 2h repeat 3

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)
Library strategy: MINCE-seq

value: MCM2-2A ESC


title: H358.siNeg.1

status: Public on May 15 2023

type: SRA

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence  then mapped to hg38 genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf from genecode
Sequences were imported into R , scaled, filter for low counts and  TMM normalized using the edgeR package.
log2 cpm, prior.count=1
Assembly: hg38
Supplementary files format and content: single tab delimited file containing   log2 cpm: genes as rows and one sample per column

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured in RPMI medium with 10% serum and passaged twice per week (1:10 for A549, 1:6 for H358).

extract_protocol:
72h post transfection total RNA was extracted using the AllPrep kit (Qiagen) following manufacturer's instructions.
Libraries  created with TruSeq Stranded mRNA kit (Illumina, RS-122-2101) following manufacturer's instructions and sequenced on an Novaseq

treatment_protocol: Cells were seeded into 6-well plates and 24h later transfected with siRNA (10nM) using Lipofectamine RNAiMAX (following manufacturer's instructions for forward transfection).

tag: sirna

value: siNeg

tag: cell line

tag: lineage

value: Adenocarcinoma

tag: mutation

value: KRAS p.Gly12Cys


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #3 rep#1

city: Bethesda

first: Matthew

last: Chung

state: MD

address: 50 South Dr

institute: NIAID (National Institute of Allergy and Infectious Diseases)

library_source: genomic

data_processing:
Library strategy: amplicon sequencing
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the miRNA-seq dataset, miRNA primary quantification was performed in the GeneGlobe Data Analysis Center (Qiagen) for trimming, mapping, and unique molecular indices (UMI) analysis. Although both miRNAs and piRNAs were detected in the small RNA libraries, only miRNAs were used in the downstream analyses.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment.
Genome_build: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary_files_format_and_content: For the RNA-seq and miRNA-seq datasets, a tab-delimited text file containing the raw gene or miRNA counts for all the samples was provided.

molecule: genomic DNA

organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Whole lungs of DI222-treated IFNAR-/- mouse

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen).
Viral genomic RNA (vRNA) in the lung homogenate was amplified using multi-segment reverse-transcription PCR (M-RT-PCR) and then subject to Illumina library preparation with Nextera XT DNA library prep kit.

treatment_protocol: Mice were intranashally inoculated with 1,000 TCID50 units of PR8 virus and approximately 3,000,000 units of DI222 virus in 50µL PBS.

tag: tissue

value: Lung

tag: mouse strain

value: IFNAR-/-

tag: treatment

value: DI222 co-treatment


title: e4_atac_2

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

data_processing:
scRNA-seq data were processed from FASTQs to gene-cell barcode matrices using 10X CellRanger v4.0 with alignment to the GRCz11 genome.
scATAC-seq data were processed from FASTQs to peak-cell barcode matrices using 10X CellRanger ATAC v1.2 with alignment to the GRCz11 genome
RNA-seq data were processed from FASTQs to normalized abundance using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome.
ATAC-seq data were processed from FASTQs to peak bed files and bigwig files using the ENCODE pipeline for replicated samples with alignment to the GRCh38 genome.
Genome_build: GRCz11, GRCh38
Supplementary_files_format_and_content: scRNAseq:  hdf5 file format containing gene-cell barcode matrices.  scATACseq:  hdf5 file format containing peak-cell barcode matrices.  RNA-seq:  Normalized abundance table from RSEM with TPM, FPKM and other metrics per gene.  ATAC-seq:  bigwig file with genome-weide accessibility tracks and narrowPeak files (standard BED6+4 format).

source_name: HUVEC cells transduced with E4ORF1

growth_protocol: Cells were grown in M200 medium supplemented with large vessel endothelial cell supplement (LVES) at 37C in a 5%CO2 atmosphere.

extract_protocol:
Nuclei were isolated and libraries prepared using the Active Motif ATAC Seq Kit.
Nuclei were isolated and libraries prepared using the Active Motif ATAC Seq Kit.

treatment_protocol: Cells were serum starved in M200 for 8 hours and treated with rhCXCL8 or PBS as a control for 6 hours.

tag: Stage

value: fetal

tag: class

value: control

value: umbilical cord


title: e4_atac_3


title: Glioblastoma shRNA SRPK1 cells, rep2

city: Campinas

first: Pedro

last: Cruz

address: Av Candido Rondon 400

country: Brazil

institute: UNICAMP

data_processing:
Sequence quality was assessed by fastQC software.
Sequenced reads were trimmed for adaptor sequence, exogeneous RNA, rRNA, and masked for low-complexity or low-quality sequence using Trimmomatic and SortmeRNA
Reads were aligned to the hg38 genome assembly using STAR v2.5.3.

growth_protocol: Human glioblastoma (GBM) cells T98G (ATCC, Manassas, VA, USA)  and A178 (shared by Dr. Roger Frigério Castilho, FCM/UNICAMP) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Invitrogen, Carlsbad, CA, USA) at 37°C with 5% CO2 in a humidified incubator. Transient transfection for overexpression and shRNA in GBM cells was performed in 6-well plates using Lipofectamine 2000 (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions.

extract_protocol:
Total RNA for RNA-seq and RT–PCR was extracted using a PureLink RNA Mini Kit (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions.
The quality of the RNA was assessed by a Bioanalyzer (Agilent Technology, Santa Clara, CA, USA). For library preparation, only samples that presented RNA integrity greater than 8 were selected. mRNA was isolated using poly(A) selection. The mRNA-seq library was prepared following the standard protocol by Illumina, and the sequencing was processed as 101 bp paired-end RNA-seq by the LACTAD facility (UNICAMP, Campinas, BR) using the HiSeq 2000 Sequencing System (Illumina, San Diego, CA, USA).
RNA-seq was performed in duplicate. Approximately 26 million reads were obtained for each sample.

treatment_protocol: The shRNA sequences were cloned into a pLKO.1 plasmid (Addgene, Wathertown, MA, USA), The cDNA used for full-length cloning and overexpression of SRPK1, SRPK2, and CLK1 was obtained from GBM T98G and reverse transcribed using Superscript III Reverse Transcriptase (ThermoFisher Scientific, Waltham, MA, USA) with oligodT and was amplified by Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific, Waltham, MA, USA). The full-length sequences corresponding to the kinases were cloned into the pcDNA3.1 plasmid (Addgene, Wathertown, MA, USA).

tag: cell type

value: Glioblastoma multiforme

value: SRPK1 shRNA knockdown

tag: transfection

value: transient


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #4 rep#1


title: LIR2

city: Kamigyo-ku, Kyoto-shi

first: Atsushi

last: Hoshino

state: Kyoto-hu

address: 465, Kajii-chou

country: Japan

institute: Kyoto Prefectural University of Medicine

description: RNA-seq

data_processing: Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19. The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated from the livers using TRIzol (Life Technologies, Inc., Carlsbad, CA) and Direct-zol RNA MiniPrep (Zymo Research Corporation., Irvine, CA) according to the manufacturer's protocol.
The Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer's instructions.
Sequencing was performed on an Illumina HiSeq 2500 platform in a 100 bp paired-end mode.

tag: strain

tag: surgery

value: Lipophagy


title: H358.siKRAS.2

value: siKRAS


title: e4_atac_1


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #1 rep#1


title: Glioblastoma Non-treated cells, rep2

value: non-treated


title: H358.siKRAS.1


title: WT ESC ATAC-seq repeat 2

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

country: China

institute: Shenzhen Institute of Advanced Technology

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)

source_name: WT ESC

growth_protocol: Mouse embryonic stem cell (ESC) E14TG2a (kind gift from Bing Zhu lab, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China) were cultured on gelatin coated dishes in DMEM/F-12 (Gibco) supplemented with 15% (v/v) fetal bovine serum (Gibco), 1% penicillin/streptomycin (Gibco), 1 mM sodium pyruvate (Gibco), 2 mM GlutaMAX (Gibco), 1% MEM nonessential amino acids (Gibco), 55 μM β-mercaptoethanol (Sigma-Aldrich), and 10 ng/ml mouse leukemia inhibitory factor (Millipore) in a 37°C incubator with a humidified, 5% CO2 atmosphere. Cells were passaged using Trypsin-EDTA (Gibco) and routinely tested for mycoplasma contamination. ESCs were differentiated into Neuronal precursor cell (NPC) as previous described with modifications3. Briefly, ESCs were grown on gelatin coated dishes in N2B27 medium that 1:1 mixed of DMEM/F-12 (Gibco) and Neurobasal media (Gibco) and supplemented with 2 mM GlutaMAX (Gibco), 100 μM β-mercaptoethanol (Sigma-Aldrich), 1× N-2 and 0.5× B-27 supplements (Gibco). After 7 days, ESCs were re-plated in suspension using nonadherent plates to promote the formation of cellular aggregates for 3 additional days. Cellular aggregates were harvested and plated on gelatin coated dishes in N2B27 medium supplemented with 10 ng/ml EGF and FGF, respectively. The aggregates will attach and NPCs will grow out of the attached aggregates on differentiation day 11. Medium was changed every 2 days without exposing the NPC culture to air and passaged using Accutase (Sigma-Aldrich).

extract_protocol:
CUT&Tag was performed as previously reported with modifications4,5. Cells (1-2×105) were washed twice in 1 mL Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1×Protease inhibitor cocktail) at room temperature. Concanavalin-coated magnetic beads (Bangs Laboratories) were washed twice in 1 mL Binding Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Cells were resuspended in 1 mL Wash Buffer and incubated with 10 μL pre-washed Concanavalin-coated magnetic beads at room temperature for 15 min. Beads (bound to cells) were incubated in Antibody Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells, 2 mM EDTA, 0.1% BSA, 1:100 dilution of the appropriate primary antibody) on a rotating platform overnight at 4°C. Prepare mixture of 1 μg appropriate secondary antibody (Table S1) and pAG-Tn5 adapter complex (Novoprotein) at 1:2 molar ratio at room temperature for 1 hour. Beads were washed once with 1 mL Dig-wash Buffer (Wash Buffer, 0.08% Digitonin for ESCs/0.05% Digitonin for other cells) and nutated in 100 μL Dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1×Protease inhibitor cocktail, 0.01% Digitonin) added the secondary antibody bound pAG-Tn5 complex at room temperature for 1 hour. Beads were washed 3 times with 1 mL Dig-300 buffer and resuspended in Tagmentation Buffer (Dig-300 buffer, 10 mM MgCl2) at 37°C for 1 hour. Beads were washed once with 1 mL TAPS Wash Buffer (10mM TAPS, pH 7.5, 0.4 mM EDTA) and incubated in 250 µL Dig-300 buffer containing 15 mM EDTA, 0.1% SDS and 100 µg/mL Proteinase K at 37°C for 1 hour with shaking of 900rpm. Then CUT&Tag DNA was extracted by phenol-chloroform-isoamyl alcohol and purified again by DNA Clean & Concentrator-5 Kit (Zymo Research) to 20 µL EB buffer. CUT&Tag DNA was Incubated by RNase A (1/400) at 37°C for 10 min. To amplify libraries, 10 μL CUT&Tag DNA was mixed with 1 μL of a uniquely barcoded i5, 1 μL a uniquely barcoded i7 primer, using a different barcode for each sample, and 12 μL NEBNext 2× PCR mix, and run the following cycling conditions with lid heat on: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 10 s; final extension at 72 °C for 1 min and hold at 10 °C. Post-PCR clean-up was performed by adding 1× volume of Ampure XP beads (24 μL) (Beckman Counter), and libraries were incubated with beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 20 μL EB buffer. The libraries were used for paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq Xten platform by Annoroad Gene Technology Co. Ltd.
RNA-seq library preparation and deep sequencing were performed by Annoroad Gene Technology Co. Ltd.. Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit (10x Genomics).

value: WT ESC

tag: media

tag: chip antibody


title: MCM2-2A ESC MINCE-seq 2h repeat 1

source_name: MCM2-2A ESC

value: MCM2-2A ESC


title: LIR1

description: RNA-seq


title: WT ESC MINCE-seq 2h repeat 2


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #5 rep#1

source_name: Whole lungs of PR8-infected IFNAR-/- mouse

treatment_protocol: Mice were intranashally inoculated with 1,000 TCID50 units of PR8 virus in 50µL PBS.

value: PR8-only infection


title: e4_cxcl8_rep2

extract_protocol:
Total RNA was extracted and libraries prepared using the Zymo-Seq RiboFree Total RNA Library Kit.
Total RNA was extracted and libraries prepared using the Zymo-Seq RiboFree Total RNA Library Kit.


title: Cont3

description: RNA-seq

value: Control


title: Glioblastoma Non-treated cells, rep1


title: WT ESC MINCE-seq 2h repeat 1


title: LIR3

description: RNA-seq


title: e4_cxcl8_rep1


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #4 rep#1


title: Cont2

description: RNA-seq


title: MCM2-2A ESC MINCE-seq 0h repeat 3


title: Viral genome sequencing dataset: DI222-treated IFNAR-/- mouse #2 rep#1


title: MCM2-2A ESC MINCE-seq 2h repeat 2


title: WT ESC MINCE-seq 2h repeat 3


title: e4_control_rep2


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #3 rep#1


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #1 rep#1


title: e4_control_rep1


title: MCM2-2A ESC MINCE-seq 0h repeat 1


title: Cont1

description: RNA-seq


title: WT ESC MINCE-seq 0h repeat 3


title: Donor69, Th17, iPIP5K1a, rep2

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
75bp paired-end reads
Raw RNA-seq data in fastq format were processed using FastQC and trimmed reads were aligned using a pipeline that combines STARv.2.7.3a 50 and RSEM version 1.3.2
DESEQ2 was used for differential expression.
Assembly: Hg19
Supplementary files format and content: rsem.genes.summary.TPM.txt

source_name: Peripheral blood

growth_protocol: Naïve CD4+ T cells were isolated from healthy human donor leukopacs using Miltenyi Biotec naïve cell isolation kit. T cells were stimulated with plate-bound anti-CD3, and IL-23 and IL-1b in complete RPMI media for 5 days

extract_protocol:
Rneasy mini RNA isolation kit
ultra DNA library prep kits

treatment_protocol: vehicle or iPIP5K1a (ISA-2011B) added on day 3 of culture.

tag: individual

value: Peripheral blood

value: Th17 cells


title: Donor69, Th17, Vehicle, Control, rep3

value: vehicle control


title: WT ESC MINCE-seq 0h repeat 2


title: Donor69, Th17, iPIP5K1a, rep1


title: WT ESC MINCE-seq 0h repeat 1


title: Donor69, Th17, Vehicle, Control, rep2


title: MCM2-2A ESC MINCE-seq input repeat 3


title: sample.30832451_EcN_NOTgate_BetI_IPTG = 0.001M, biol rep 4

city: Cambridge

first: Christopher

middle: A

last: Voigt

state: MA

address: 500 Technology Square, NE47-140

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Sequencing reads were trimmed using Trimmomatic (Bolger et al., 2014)
Using theBurrows-Wheeler alignment tool (Li and Durbin, 2009), reference sequences were indexed and all trimmed reads were aligned to the indexed reference
Gene expression tables were constructed from the aligned reads using featureCounts (Liao et al., 2014) and normalized to fragments per kilobase of transcript per million mapped reads (FPKM). Samples with fewer than 5 x 106 mapped reads were excluded
Using custom Python code (see https://github.com/VoigtLab/EcN_analysis),  differentially expressed genes were identified. Mapped reads at each nucleotide position were normalized where tRNA regions were removed before calculating the total number of mapped nucleotides used for normalizing RNA-seq profiles.
Assembly: E. coli Nissle 1917 genome (NCBI CP007799)
Supplementary files format and content: comma-separated values (CSV) file includes FPKM values for all samples

organism: Escherichia coli Nissle 1917

growth_protocol: Cultures were inoculated from glycerol stock and grown overnight for 15 h at 37 °C and 1000 rpm in 1 mL M9 media in a 96-well deep well plate. The following day, cultures were diluted to OD 0.3 in 1 mL fresh M9 media and grown under the same conditions for 3 hours.  For induction, cells were diluted a second time to OD600 = 0.3 in 1 mL fresh M9 media in the presence or absence of 1 mM IPTG in a 96-well deep well plate. Culture flasks were incubated at 37 °C for 5 h.

extract_protocol:
Total RNA extraction was performed according to the manufacturer’s instructions
Cells were collected, lysed, loaded as a multiplexed library on all lanes of a flowcell, and sequenced on an Illumina NovaSeq sequencer

tag: time(h)

tag: passed qc_mapped_reads

value: TRUE


title: sample.30832450_EcN_NOTgate_IcaR_IPTG = 0.001M, biol rep 4


title: sample.30832449_EcN_NOTgate_AmeR_IPTG = 0.001M, biol rep 4


title: sample.30832448_EcN_NOTgate_LitR_IPTG = 0.001M, biol rep 4


title: Donor69, Th17, Vehicle, Control, rep1


title: Viral genome sequencing dataset: PR8-infected IFNAR-/- mouse #2 rep#1

value: Lung

value: IFNAR-/-


title: Donor69, Th17, iPIP5K1a, rep3


title: sample.30832446_EcN_NOTgate_AmtR_IPTG = 0.001M, biol rep 4


title: sample.30832447_EcN_NOTgate_QacR_IPTG = 0.001M, biol rep 4


title: MCM2-2A ESC MINCE-seq 0h repeat 2


title: MCM2-2A ESC MINCE-seq input repeat 2


title: Cystic echinococcosis, Treated, Rep 3

city: Buenos Aires

first: Marcela

middle: Alejandra

last: Cucher

address: Paraguay 2155, Piso 13

country: Argentina

institute: IMPaM, UBA-CONICET

data_processing:
Quality control was performed with FastQC (v0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) before and after pre-processing. Adapter (5´AACTGTAGGCACCATCAAT3´), Illumina sequences (5´AGATCGGAAGAGCACACGTCTGAACTCCAGTCA3´, 5´ AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT3´, 5´ GATCGGAAGAGCACACGTCTGAACTCCAGTCAC3´) and spike-ins (QIAseq™ miRNA Library QC PCR Handbook, 2017) were sequentially removed via cutadapt (version 2.10, --error-rate=0.1 -O = 10) [50]. Reads with low-quality bases and length < 18-bp were discarded using Trimmomatic SE sliding window approach (version 0.39, SLIDINGWINDOW:4:20 MINLEN:18). miRNAs from Homo sapiens, E. multilocularis and E. granulosus s. l. were identified with mirDeep2. For the three species, sequence alignment to the corresponding reference genome was performed with the mapper module using default parameters (-e -j -h -m -p) and dis-carding reads that mapped ≥ five times.   For non-miRNA sequences, processed reads were aligned to the corresponding genome using Botwie version 1.2.2 (-v 0 --sam --best --time --threads 8). For sequence annotation, ad hoc non-coding RNA databases were constructed. For the human database, the following types of sequences were downloaded from the RNAcentral sequence database version 18 18 ( https://rnacentral.org/):  lncRNA, piRNA, snRNA, snoRNA, SRP RNA, rRNA, Y RNA, antisense RNA, vault RNA, RNAse MRP RNA, scRNA, telomerase RNA, RNAse P RNA, transcript and intron (filters “Homo sapiens”, “No QC warnings”, “genomic mapping: available”). Human tRNA sequences were retrieved from GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi38/) and pre-miRNA sequences from the miRBase database. For the Echinococcus spp. database, the following types of sequences were retrieved from RNAcentral: tRNAs, snRNA, snoRNA, rRNA, RNAse P, SRP, misc RNA and mit RNA. Pre-miRNA sequences were downloaded from the miRBase database. Sequence identity analysis was performed with BLAST version 2.9.0 (-task "blastn-short" -max_target_seqs "1" -max_hsps "1" -evalue "0.01") and reads that fulfilled the following criteria were retained: gap = 0, hit start 1 or 2, mismatch = 0, read coverage ≥ 95, read count number ≥ 10 and alignment to forward strand.
Assembly: Reference genomes corresponded to the GenBank Assembly ID GCA_000001405.28 (Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13)) (ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/dna/),  the NCBI EMUL-TI002 genome assembly of E. multlilocularis (https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS14/species/echinococ-cus_multilocularis/PRJEB122/echinococcus_multilocularis.PRJEB122.WBPS14.genomic.fa.gz) and the NCBI assembly EGRAN001 of E. granulosus sensu stricto (https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS14/species/echinococ-cus_granulosus/PRJEB121/echinococcus_granulosus.PRJEB121.WBPS14.genomic.fa.gz).

source_name: Serum

extract_protocol:
miRNeasy Serum/Plasma Kit (Qiagen)
QIAseq® miRNA Library Kit (Qiagen)

value: Serum

value: Cystic echinococcosis albendazole-treated patient

tag: Sex

value: Male


title: Cystic echinococcosis, Treated, Rep 1

value: Female


title: WT ESC MINCE-seq input repeat 2


title: Cystic echinococcosis, Treated, Rep 2


title: Cystic echinococcosis, Positive (CE5), Rep 3

value: Cystic echinococcosis positive patient, cyst stage CE5


title: HIRA-/-; MCM2-2A H3.3 eSPAN

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)
Library strategy: eSPAN

source_name: ESC

value: ESC

value: DMEM


title: sample.30832444_EcN_NOTgate_HlyIIR_IPTG = 0.001M, biol rep 4


title: sample.30832445_EcN_NOTgate_BM3R1_IPTG = 0.001M, biol rep 4


title: sample.30832452_EcN_NOTgate_PhlF_IPTG = 0.001M, biol rep 4


title: Cystic echinococcosis, Positive (CE4), Rep 2

value: Cystic echinococcosis positive patient, cyst stage CE4


title: Cystic echinococcosis, Positive (CE5), Rep 2


title: sample.30832443_EcN_NOTgate_PsrA_IPTG = 0.001M, biol rep 4


title: A909 dCas9_covRPS OD1_2 biol rep2

first: Thomas

middle: Alexander

last: Hooven

address: 4401 Penn Ave., Rangos Research Bldg #8128

description:
A909_dCas9_CovR_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
A909_dCas9_CovR_12_vs_A909_dCas9_Sham_12_unfiltered_degenes.txt

data_processing:
Alignment to the corresponding genome was performed using Bowtie2 in paired end mode with a maximum insert size of 600bp
Raw read counts were estimated for all samples using HTSeq in “union” mode
DESeq2 was used to perform comparisons between read depth-normalized alignments
Assembly: NZ_CP006910
Assembly: NC_007432
Supplementary files format and content: 1084_VST_counts.txt is a matrix of variance stabilizing transformation (VST) transcript counts for each sample
Supplementary files format and content: Remaining processed files are DESeq2 comparison output files across samples following normalization and merging of biological replicates

organism: Streptococcus agalactiae CNCTC 10/84

source_name: Bacterial cell

growth_protocol: Stationary growth at 37°C in ambient atmospheric conditions

extract_protocol:
ThermoFisher MagMAX Viral/Pathogen Ultra Nucleic Acid Isolation reagents (cat. #A42356) on a Hamilton Nimbus/ThermoFisher Kingfisher Presto integrated robotic molecular purification instrument
Strand-specific, dual unique indexed libraries for sequencing on all Illumina platforms were made using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Manufacturer protocol was modified by diluting adapter 1:30 and using 3 μl of this dilution. Size selection of the library was performed with AMPure SPRI-select beads (Beckman Coulter Genomics, Danvers, MA). Glycosylase digestion of adapter and 2nd strand was done in the same reaction as the final amplification to avoid further cleanups. Sample input for this method was ribosomal RNA reduced RNA. Libraries were assessed for concentration and fragment size using the DNA High Sensitivity Assay on the LabChip GX Touch (Perkin Elmer, Waltham, MA). The library concentrations were also assessed by qPCR using the KAPA Library Quantification Kit (Complete, Universal; Kapa Biosystems, Woburn, MA).

treatment_protocol: Once target OD600 was reached, samples were pelleted and mixed with Qiagen RNAProtect Bacteria Reagent and stored at -80°C until RNA extraction

value: Bacterial cell

tag: genotype

value: dCas9 with covR targeting sgRNA plasmid

value: Laboratory outgrowth with erythromycin plasmid selection to OD600 = 1.2 (early-stationary phase)


title: A909 dCas9_covRPS OD1_2 biol rep3

description:
A909_dCas9_CovR_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
A909_dCas9_CovR_12_vs_A909_dCas9_Sham_12_unfiltered_degenes.txt


title: WT H3.3 eSPAN


title: MCM2-2A H3.3 eSPAN


title: WT ESC MINCE-seq input repeat 3

value: WT ESC


title: Cystic echinococcosis, Positive (CE4), Rep 1


title: A909 dCas9_covRPS OD1_2 biol rep1

description:
A909_dCas9_CovR_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
A909_dCas9_CovR_12_vs_A909_dCas9_Sham_12_unfiltered_degenes.txt


title: A909 dCas9_shamPS OD1_2 biol rep3

description:
A909_dCas9_Sham_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
A909_dCas9_CovR_12_vs_A909_dCas9_Sham_12_unfiltered_degenes.txt

value: dCas9 with sham targeting sgRNA plasmid


title: POLE3-/- H3K27me3 eSPAN 8h timelaps


title: sample.30832441_Escherichia_coli_Nissle_WT_IPTG = 0.001M, biol rep 4


title: A909 dCas9_shamPS OD1_2 biol rep2

description:
A909_dCas9_Sham_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
A909_dCas9_CovR_12_vs_A909_dCas9_Sham_12_unfiltered_degenes.txt


title: Cystic echinococcosis, Positive (CE3b), Rep 2

value: Cystic echinococcosis positive patient, cyst stage CE3b


title: sample.30832440_EcN_NOTgate_PhlF_IPTG = 0.001M, biol rep 3

value: TRUE


title: Cystic echinococcosis, Positive (CE3b), Rep 3


title: sample.30832439_EcN_NOTgate_BetI_IPTG = 0.001M, biol rep 3


title: HIRA-/- H3.3 eSPAN


title: sample.30832438_EcN_NOTgate_IcaR_IPTG = 0.001M, biol rep 3


title: POLE3-/- H3K27me3 eSPAN 0h timelaps


title: POLE3-/- H3K27me3 eSPAN 3h timelaps


title: 1084 dCas9_cylPS OD1_2 biol rep3

description:
X1084_dCas9_Sham_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_Cyl_12_vs_1084_dCas9_Sham_12_unfiltered_degenes.txt

value: dCas9 with cyl operon targeting sgRNA plasmid


title: MCM2-2A H3K27me3 eSPAN 3h timelaps


title: sample.30832437_EcN_NOTgate_AmeR_IPTG = 0.001M, biol rep 3


title: Cystic echinococcosis, Positive (CE3a), Rep 3

value: Cystic echinococcosis positive patient, cyst stage CE3a


title: MCM2-2A H3K27me3 eSPAN 8h timelaps


title: sample.30832442_EcN_SensorArrayOnly_IPTG = 0.001M, biol rep 4


title: 1084 dCas9_cylPS OD1_2 biol rep2

description:
X1084_dCas9_Sham_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_Cyl_12_vs_1084_dCas9_Sham_12_unfiltered_degenes.txt


title: Cystic echinococcosis, Positive (CE3a), Rep 1

value: Serum


title: sample.30832436_EcN_NOTgate_LitR_IPTG = 0.001M, biol rep 3


title: 1084 dCas9_cylPS OD1_2 biol rep1

description:
X1084_dCas9_Sham_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_Cyl_12_vs_1084_dCas9_Sham_12_unfiltered_degenes.txt


title: MCM2-2A H3K27me3 eSPAN 0h timelaps


title: sample.30832435_EcN_NOTgate_QacR_IPTG = 0.001M, biol rep 3


title: Cystic echinococcosis, Positive (CE2), Rep 3

value: Cystic echinococcosis positive patient, cyst stage CE2


title: 1084 dCas9_shamPS OD1_2 biol rep3

description:
X1084_dCas9_Cyl_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_Cyl_12_vs_1084_dCas9_Sham_12_unfiltered_degenes.txt


title: sample.30832434_EcN_NOTgate_AmtR_IPTG = 0.001M, biol rep 3


title: A909 dCas9_shamPS OD1_2 biol rep1

description:
A909_dCas9_Sham_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
A909_dCas9_CovR_12_vs_A909_dCas9_Sham_12_unfiltered_degenes.txt


title: 1084 dCas9_shamPS OD1_2 biol rep2

description:
X1084_dCas9_Cyl_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_Cyl_12_vs_1084_dCas9_Sham_12_unfiltered_degenes.txt


title: sample.30832433_EcN_NOTgate_BM3R1_IPTG = 0.001M, biol rep 3


title: Cystic echinococcosis, Positive (CE2), Rep 1

value: Male


title: 1084 dCas9_shamPS OD1_2 biol rep1

description:
X1084_dCas9_Cyl_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_Cyl_12_vs_1084_dCas9_Sham_12_unfiltered_degenes.txt


title: WT H3K27me3 eSPAN 0h timelaps


title: WT H3K27me3 eSPAN 3h timelaps


title: Non-parasitic cyst, Rep 3

value: Patient with non-parasitic cyst

value: Female


title: Non-parasitic cyst, Rep 2


title: Cystic echinococcosis, Positive (CE3b), Rep 1


title: MCM2-2A H3K27me3 D0 ESC scCUT&Tag repeat 4

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
MINCE-seq, Repli-ATAC-seq and CUT&RUN, data processing steps were similar as CUT&Tag data analysis. The signal profile densities were normalized and calculated using a custom Perl (v.5.26.2) script with scan bin size of 50 bp or 100 bp.
Assembly: mm10
Supplementary files format and content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)
Library strategy: CUT&Tag

source_name: D0 ESC

value: D0 ESC

value: Anti-H3K27me3 Antibody (CST_9733)


title: 1084 sCas9 OD1_2 biol rep2

description:
X1084_sCas9_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_sCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_sCas9_12_unfiltered_degenes.txt

value: sCas9 mutant

value: Laboratory outgrowth to OD600 = 1.2 (early-stationary phase)


title: 1084 sCas9 OD1_2 biol rep3

description:
X1084_sCas9_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_sCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_sCas9_12_unfiltered_degenes.txt

value: Bacterial cell


title: WT H3K27me3 eSPAN 8h timelaps

value: ESC

value: DMEM


title: Cystic echinococcosis, Negative, Rep 3

value: Cystic echinococcosis negative patient


title: MCM2-2A H3K27me3 D0 ESC scCUT&Tag repeat 2


title: sample.30832431_EcN_NOTgate_PsrA_IPTG = 0.001M, biol rep 3


title: sample.30832430_EcN_SensorArrayOnly_IPTG = 0.001M, biol rep 3


title: 1084 sCas9 OD1_2 biol rep1

description:
X1084_sCas9_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_sCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_sCas9_12_unfiltered_degenes.txt


title: Cystic echinococcosis, Positive (CE1), Rep 2

value: Cystic echinococcosis positive patient, cyst stage CE1


title: sample.30832429_Escherichia_coli_Nissle_WT_IPTG = 0.001M, biol rep 3

value: TRUE


title: Cystic echinococcosis, Negative, Rep 2


title: WT H3K27me3 D0 ESC scCUT&Tag repeat 2


title: 1084 sCas9 OD0_6 biol rep3

description:
X1084_sCas9_06_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_sCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_sCas9_12_unfiltered_degenes.txt

value: Laboratory outgrowth to OD600 = 0.6 (mid-log phase)


title: Siah1a/2 KO lung Cd45+ scRNA-seq

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

library_source: transcriptomic single cell

data_processing:
Barcoded processing, gene counting and aggregation were made using Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: 10x Genomics Cellranger aggregate output files for WT and Mutant samples (Cell IDs: "-1" = WT, "-2" = Mutant): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: lung

extract_protocol:
Mutant or WT mice were sacrificed 7 weeks after first urethane treatment. Lungs were digested and single cell suspensions were washed with 1XPBS-4%FBS before incubation for 20 min on ice at 5•107 cells/ml with 500 ng/ml Fc block (2.4G2, BD Pharmingen). Cells were then incubated for 1 hour on ice with AF700 conjugated CD45.2 monoclonal antibody (104, Biolegend). For scRNA-seq libraries, DAPI negative (live) CD45+ cells were sorted using a flow cytometer, and sorted cells were resuspended in RPMI for counting.
Libraries were prepared using Single Cell 3’ Reagent Kits v3.1: ChromiumTM Single Cell 3’ Library & Gel Bead Kit v3.1, PN-1000196 and PN-1000129 and following the Single Cell 3’ Reagent Kits v3 (PN-1000269) User Guide (Manual Part # CG000315 Rev C). Libraries were sequenced on NovaSeq S4, using half full lanes for 2 samples, with mean read depth of 87-128 thousand reads per cell.

value: lung

value: Siah1a/2 KO


title: sample.30832428_EcN_NOTgate_PhlF_IPTG = 0.001M, biol rep 2

value: FALSE


title: Cystic echinococcosis, Negative, Rep 1

value: Serum


title: sample.30832432_EcN_NOTgate_HlyIIR_IPTG = 0.001M, biol rep 3


title: MCM2-2A H3K27me3 D0 ESC scCUT&Tag repeat 3


title: Alveolar echinococcosis, Treated, Rep 3

value: Alveolar echinococcosis albendazole-treated patient


title: 1084 sCas9 OD0_6 biol rep2

description:
X1084_sCas9_06_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_sCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_sCas9_12_unfiltered_degenes.txt


title: WT lung Cd45+ scRNA-seq

value: WT


title: sample.30832426_EcN_NOTgate_IcaR_IPTG = 0.001M, biol rep 2


title: Alveolar echinococcosis, Treated, Rep 2

value: Female


title: sample.30832427_EcN_NOTgate_BetI_IPTG = 0.001M, biol rep 2


title: Alveolar echinococcosis, Positive, Rep 2

value: Alveolar echinococcosis positive patient


title: Day6_Ezh2_uKO_H3K27me3_2

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

data_processing:
Basecalls performed using bcl2fastq version 2.20.0
RNA-seq and ChIP-seq reads were aligned to the mm10 (for mice) or hg38 (for humans) genome using Hisat2 version 2.1.0. and bowtie2 version 2.3.3.1.
For RNA-seq analysis, To quantify uniquely aligned reads on respective annotated transcript loci (NCBI RefSeq transcripts), the htseq-count function with  –s reverse option, part of the HTSeq package
For ChIP-seq analysis, Pearson correlation coefficient (R) in 2kb bins between biological replicates were calculated with R. Peak calling for ChIP-seq data were performed by MACS 2.1.1 with default arguments; a cut-off P value of 10-2 was used.  Relative ChIP-seq enrichments in respective peak regions were calculated by dividing input controls.
Assembly: mm10 for mice, hg38 for humans
Supplementary files format and content: bam files were generated from each alignment step

source_name: mouse endometria

growth_protocol: For RNA-seq analysis using mouse uteri, all mice were housed in 12h/12h light cycle. Mice were mated with fertile males to get pregnant. The day vaginal plugs found is considered as day 1 of pregnancy. On day 4 or day 6 morning, uteri were collected.

extract_protocol:
For RNA-seq analysis , total RNA were collected using NucleoSpin RNA (MACHEREY-NAGEL) for mice and the RNeasy Plus Mini Kit (Qiagen) for humans, with genomic DNA elimination. For ChIP-seq analysis, to extract chromatin, isolated day 6 endometrial cells were suspended in 20 µl of Nuclei EZ Lysis Buffer (SIGMA), and extensively digested chromatin with 20 IU/µl Micrococcal Nuclease (MNase, NEB) at 37℃ for 5 min.
RNA-seq library preparation was carried out using TruSeq Stranded mRNA Library Prep kit (Illumina) following manufacturer’s instructions. ChIP-seq library preparation was carried out by NEBNext ChIP-seq for Illumina (NEB) following manufacturer’s instructions.

treatment_protocol: For RNA-seq analysis using human endometria, fertile or RIF patients were treated with P4. Their endometria were collected 7days later.

tag: no. of passages and ages of weeks

value: 7-12 weeks, day 6 of pregnancy

tag: genotype/treatment condition

tag: background strain

value: Anti-H3K27me3 antibody (39156, Active motif)


title: Day6_Ezh2_uKO_H3K27me3_1

value: Anti-H3K27me3 antibody (39155, Active motif)


title: 1084 dCas9 OD1_2 biol rep2

description:
X1084_dCas9_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_dCas9_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_dCas9_12_unfiltered_degenes.txt

value: Bacterial cell

value: dCas9 mutant

tag: treatment

value: Laboratory outgrowth to OD600 = 1.2 (early-stationary phase)


title: Alveolar echinococcosis, Positive, Rep 1

tag: tissue


title: sample.30832425_EcN_NOTgate_AmeR_IPTG = 0.001M, biol rep 2


title: 1084 dCas9 OD1_2 biol rep3

description:
X1084_dCas9_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_dCas9_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_dCas9_12_unfiltered_degenes.txt


title: sample.30832424_EcN_NOTgate_LitR_IPTG = 0.001M, biol rep 2


title: Day6_floxed_control_H3K27me3_2


title: Alveolar echinococcosis, Negative, Rep 3

value: Alveolar echinococcosis negative patient


title: sample.30832423_EcN_NOTgate_QacR_IPTG = 0.001M, biol rep 2

value: TRUE


title: 1084 dCas9 OD1_2 biol rep1

description:
X1084_dCas9_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_dCas9_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_dCas9_12_unfiltered_degenes.txt


title: 1084 dCas9 OD0_6 biol rep3

description:
X1084_dCas9_06_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_dCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_dCas9_12_unfiltered_degenes.txt

value: Laboratory outgrowth to OD600 = 0.6 (mid-log phase)


title: 1084 dCas9 OD0_6 biol rep2

description:
X1084_dCas9_06_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_dCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_dCas9_12_unfiltered_degenes.txt


title: sample.30832422_EcN_NOTgate_AmtR_IPTG = 0.001M, biol rep 2


title: Day6_floxed_control_H3K27me3_1


title: Alveolar echinococcosis, Negative, Rep 1


title: Day6_Ezh2_uKO_input_1

value: Rabbit control IgG


title: Alveolar echinococcosis, Negative, Rep 2


title: sample.30832421_EcN_NOTgate_BM3R1_IPTG = 0.001M, biol rep 2


title: 1084 dCas9 OD0_6 biol rep1

description:
X1084_dCas9_06_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_dCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_dCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_dCas9_12_unfiltered_degenes.txt


title: Day6_floxed_control_input_2


title: 1084 sCas9 OD0_6 biol rep1

description:
X1084_sCas9_06_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_sCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_sCas9_12_unfiltered_degenes.txt

value: sCas9 mutant


title: sample.30832420_EcN_NOTgate_HlyIIR_IPTG = 0.001M, biol rep 2


title: 1084 Cas9_AEKO OD1_2 biol rep3

description:
X1084_AEKO_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_dCas9_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_AEKO_12_unfiltered_degenes.txt

value: cas9 gene allelic exchange knockout


title: Bystander 8

first: Amy

middle: K.

last: Barczak

address: The Ragon Institute, 400 Technology Square

department: Medicine/Infectious Diseases

institute: Massachusetts General Hospital

description: Cuffdiff output sorted infected

data_processing:
Raw reads were aligned to human genome using TopHat
Cufflinks was used to estimate the transcript abundance
Cuffdiff was used to calculate fold difference in expressions and the log2 fold change values

molecule: polyA RNA

source_name: monocyte differentiated to macrophages with PMA

extract_protocol:
Cells were harvested in RLT buffer (Qiagen) and extracted using an Rneasy kit (Qiagen). mRNA was then isolated with an NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina, Index Primers Sets 3 and 4 (New England Biolabs)

tag: cell line

value: Bystander


title: Day6_floxed_control_input_1


title: sample.30832419_EcN_NOTgate_PsrA_IPTG = 0.001M, biol rep 2


title: sample.30832418_EcN_SensorArrayOnly_IPTG = 0.001M, biol rep 2


title: MCM2-2A H3K27me3 eSPAN 24h

data_processing:
Library strategy: eSPAN
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)

source_name: whole cell

tag: cell type

value: ESC

value: DMEM

value: MCM2-2A mutant

value: Anti-H3K27me3 Antibody (CST_9733)


title: 1084 Cas9_AEKO OD1_2 biol rep1

description:
X1084_AEKO_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_dCas9_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_AEKO_12_unfiltered_degenes.txt


title: 1084 Cas9_AEKO OD1_2 biol rep2

description:
X1084_AEKO_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_dCas9_12_unfiltered_degenes.txt
1084_AEKO_12_vs_1084_sCas9_12_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_AEKO_12_unfiltered_degenes.txt


title: Bystander 5

description: Cuffdiff output sorted infected

value: monocyte differentiated to macrophages with PMA


title: Bystander 6

description: Cuffdiff output sorted infected


title: MCM2-2A H3K27me3 eSPAN 8h


title: sample.30832417_Escherichia_coli_Nissle_WT_IPTG = 0.001M, biol rep 2


title: 1084 Cas9_AEKO OD0_6 biol rep3

description:
X1084_AEKO_06_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_dCas9_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_AEKO_12_unfiltered_degenes.txt


title: Day6_Ezh2_uKO_input_2

value: 7-12 weeks, day 6 of pregnancy


title: Bystander 4

description: Cuffdiff output sorted infected


title: 1084 Cas9_AEKO OD0_6 biol rep2

description:
X1084_AEKO_06_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_dCas9_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_AEKO_12_unfiltered_degenes.txt


title: MCM2-2A H3K27me3 eSPAN 0h


title: sample.30832416_EcN_NOTgate_PhlF_IPTG = 0.001M, biol rep 1


title: Bystander 3

description: Cuffdiff output sorted infected


title: sample.30832415_EcN_NOTgate_BetI_IPTG = 0.001M, biol rep 1


title: 1084 Cas9_AEKO OD0_6 biol rep1

description:
X1084_AEKO_06_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_dCas9_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_sCas9_06_unfiltered_degenes.txt
1084_AEKO_06_vs_1084_AEKO_12_unfiltered_degenes.txt


title: WT H3K27me3 eSPAN 24h

value: WT


title: Bystander 2

description: Cuffdiff output sorted infected


title: 1084 WT OD1_2 biol rep3

description:
X1084_WT_12_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_sCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_WT_06_vs_1084_WT_12_unfiltered_degenes.txt

value: Bacterial cell

value: Wild type


title: sample.30832414_EcN_NOTgate_IcaR_IPTG = 0.001M, biol rep 1


title: Bystander 1

description: Cuffdiff output sorted infected


title: Bystander 7

description: Cuffdiff output sorted infected


title: sample.30832413_EcN_NOTgate_AmeR_IPTG = 0.001M, biol rep 1


title: H37Rv-infected 8

description: Cuffdiff output sorted infected

value: Infected


title: WT H3K27me3 eSPAN 0h


title: MCM2-2A H3K27me3 D0 ESC scCUT&Tag

data_processing:
Library strategy: CUT&TAG
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)


title: sample.30832412_EcN_NOTgate_LitR_IPTG = 0.001M, biol rep 1


title: 1084 WT OD1_2 biol rep1

description:
X1084_WT_12_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_sCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_WT_06_vs_1084_WT_12_unfiltered_degenes.txt

value: Laboratory outgrowth to OD600 = 1.2 (early-stationary phase)


title: WT H3K27me3 D0 ESC scCUT&Tag


title: sample.30832411_EcN_NOTgate_QacR_IPTG = 0.001M, biol rep 1

value: TRUE


title: H37Rv-infected 7

description: Cuffdiff output sorted infected


title: H37Rv-infected 6

description: Cuffdiff output sorted infected


title: 1084 WT OD0_6 biol rep3

description:
X1084_WT_06_3 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_WT_06_vs_1084_WT_12_unfiltered_degenes.txt

value: Laboratory outgrowth to OD600 = 0.6 (mid-log phase)


title: H37Rv-infected 5

description: Cuffdiff output sorted infected


title: 1084 WT OD0_6 biol rep2

description:
X1084_WT_06_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_WT_06_vs_1084_WT_12_unfiltered_degenes.txt


title: sample.30832409_EcN_NOTgate_BM3R1_IPTG = 0.001M, biol rep 1


title: WT D7 NPC scRNA-seq

data_processing:
Sequence reads were mapped back to the mouse reference genome (mm10) using Bowtie2 software (version 1.3.0). Only consistent pair-end reads were chosen for further analysis.
Uniquely aligned reads were extracted using SAMtools (Version 1.7). Peaks were called using MACS2 (version 2.2.7.1) and SICER (version 1.0). For each data source, peaks were called using all samples from all replicates combined. For visualization, bigWig files and count matrices in bins around peak summits were produced using deepTools (version 3.5.1).
scCUT&Tag data was analysis by cellranger-atac (version 2.0.0) and custom python scripts. scRNA-seq data was preprocessed by kallisto-bustools (version 0.46.0) workflow, and further analysed by Seurat (version 4.0.3) and monocle (version 2.18.0) R packages.
eSPAN anaylsis was implemented as described in the publication (Zhiming Li et al., 2021), Watson and Crick strands were merged and partition or RFD was calculated using custom R scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated, and gz files are the outputs of cellranger (scCUT&Tag) or kallisto workflow (scRNA-seq)

value: NPC


title: H37Rv-infected 4

description: Cuffdiff output sorted infected


title: 1084 WT OD0_6 biol rep1

description:
X1084_WT_06_1 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_dCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_sCas9_06_vs_1084_WT_06_unfiltered_degenes.txt
1084_WT_06_vs_1084_WT_12_unfiltered_degenes.txt


title: WT H3K27me3 eSPAN 8h


title: sample.30832408_EcN_NOTgate_HlyIIR_IPTG = 0.001M, biol rep 1


title: MCM2-2A D0 ESC scRNA-seq


title: miRNA-seq dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #3

description:
DJA267_DODI3
DIinfKOmice_miRNAseq_counts.txt

data_processing:
For the RNA-seq dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment. featureCounts in the subread package (v.1.5.1) was used for gene counting.
For the miRNA-seq dataset, miRNA primary quantification was performed in the GeneGlobe Data Analysis Center (Qiagen) for trimming, mapping, and unique molecular indices (UMI) analysis. Although both miRNAs and piRNAs were detected in the small RNA libraries, only miRNAs were used in the downstream analyses.
For the viral genome sequencing dataset, reads were trimmed with trimmomatic (v.0.36) to remove the adaptors and low quality bases. STAR (v2.7.3a) was used for the alignment.
Genome_build: GRCm38.99 and influenza A/Puerto Rico/8/34/Mount Sinai (H1N1) were used for RNA-seq
Supplementary_files_format_and_content: For the RNA-seq and miRNA-seq datasets, a tab-delimited text file containing the raw gene or miRNA counts for all the samples was provided.

organism:
Mus musculus
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: Whole lungs of DI222-treated IFNAR-/- IFNLR-/- mouse

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen).
Total RNAs in the lung homogenate were subject to miRNA sequencing library preparation with QIAseq miRNA library kit for Illumina (Qiagen).

value: Lung

tag: mouse strain

value: IFNAR-/- IFNLR-/-

value: DI222 co-treatment


title: H37Rv-infected 3

description: Cuffdiff output sorted infected


title: H37Rv-infected 2

description: Cuffdiff output sorted infected


title: miRNA-seq dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #2

description:
DJA268_DODI2
DIinfKOmice_miRNAseq_counts.txt


title: WT D0 ESC scRNA-seq

value: ESC


title: sample.30832407_EcN_NOTgate_PsrA_IPTG = 0.001M, biol rep 1

tag: strain


title: 1084 WT OD1_2 biol rep2

description:
X1084_WT_12_2 (column name in GBS_FullGEOSet_VST_counts.txt)
1084_AEKO_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_dCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_sCas9_12_vs_1084_WT_12_unfiltered_degenes.txt
1084_WT_06_vs_1084_WT_12_unfiltered_degenes.txt


title: MCM2-2A D16 NPC RNA-seq repeat 2


title: H37Rv-infected 1

description: Cuffdiff output sorted infected


title: sample.30832406_EcN_SensorArrayOnly_IPTG = 0.001M, biol rep 1


title: MCM2-2A D16 NPC RNA-seq repeat 1


title: miRNA-seq dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #1

description:
DJA260_DODI1
DIinfKOmice_miRNAseq_counts.txt


title: miRNA-seq dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #3

description:
DJA263_DOP3
DIinfKOmice_miRNAseq_counts.txt

source_name: Whole lungs of PR8-infected IFNAR-/- IFNLR-/- mouse

value: PR8-only infection


title: sample.30832405_Escherichia_coli_Nissle_WT_IPTG = 0.001M, biol rep 1


title: MCM2-2A D7 NPC scRNA-seq

value: MCM2-2A mutant


title: WT D16 NPC RNA-seq repeat 3


title: miRNA-seq dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #2

description:
DJA247_DOP2
DIinfKOmice_miRNAseq_counts.txt


title: sample.30832404_EcN_NOTgate_PhlF_IPTG = 0M, biol rep 4


title: uninfected 6

description: Cuffdiff output sorted infected

value: Uninfected


title: sample.30832410_EcN_NOTgate_AmtR_IPTG = 0.001M, biol rep 1


title: uninfected 5

description: Cuffdiff output sorted infected

value: monocyte differentiated to macrophages with PMA


title: WT D16 NPC RNA-seq repeat 2


title: sample.30832403_EcN_NOTgate_BetI_IPTG = 0M, biol rep 4


title: miRNA-seq dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #1

description:
DJA258_DOP1
DIinfKOmice_miRNAseq_counts.txt


title: uninfected 4

description: Cuffdiff output sorted infected


title: sample.30832402_EcN_NOTgate_IcaR_IPTG = 0M, biol rep 4


title: WT D16 NPC RNA-seq repeat 1


title: uninfected 3

description: Cuffdiff output sorted infected


title: miRNA-seq dataset: DI222-treated IFNLR-/- mouse #4

description:
FDK263_LDI4
DIinfKOmice_miRNAseq_counts.txt

source_name: Whole lungs of DI222-treated IFNLR-/- mouse

value: IFNLR-/-


title: sample.30832401_EcN_NOTgate_AmeR_IPTG = 0M, biol rep 4


title: miRNA-seq dataset: DI222-treated IFNLR-/- mouse #3

description:
FDK237_LDI3
DIinfKOmice_miRNAseq_counts.txt


title: MCM2-2A D0 ESC RNA-seq repeat 2

value: DMEM/F12 _serum


title: uninfected 2

description: Cuffdiff output sorted infected


title: Uninfected 1

description: Cuffdiff output sorted infected


title: sample.30832400_EcN_NOTgate_LitR_IPTG = 0M, biol rep 4


title: miRNA-seq dataset: DI222-treated IFNLR-/- mouse #2

description:
FDK256_LDI2
DIinfKOmice_miRNAseq_counts.txt


title: MCM2-2A D0 ESC RNA-seq repeat 1


title: WT D0 ESC RNA-seq repeat 2

value: WT


title: miRNA-seq dataset: DI222-treated IFNLR-/- mouse #1

description:
FDK218_LDI1
DIinfKOmice_miRNAseq_counts.txt


title: sample.30832399_EcN_NOTgate_QacR_IPTG = 0M, biol rep 4


title: WT D0 ESC RNA-seq repeat 1


title: sample.30832398_EcN_NOTgate_AmtR_IPTG = 0M, biol rep 4


title: miRNA-seq dataset: PR8-infected IFNLR-/- mouse #6

description:
FDK261_LP6
DIinfKOmice_miRNAseq_counts.txt

source_name: Whole lungs of PR8-infected IFNLR-/- mouse


title: Total cell wall lipid extracts 1

description: DMSO and PAMP treatments

value: total cell wall lipid extracts from H37Rv


title: manLAM 2

description: DMSO and PAMP treatments

value: manLAM


title: sample.30832397_EcN_NOTgate_BM3R1_IPTG = 0M, biol rep 4

value: FALSE


title: sample.30832396_EcN_NOTgate_HlyIIR_IPTG = 0M, biol rep 4

value: TRUE


title: miRNA-seq dataset: PR8-infected IFNLR-/- mouse #4

description:
FDK239_LP4
DIinfKOmice_miRNAseq_counts.txt


title: MCM2-2A H3K4me3 D0 ESC CUT&Tag repeat 2

value: Anti-H3K4me3 Antibody (Active Motif_39159)


title: MCM2-2A H3K4me3 D0 ESC CUT&Tag repeat 1


title: sample.30832395_EcN_NOTgate_PsrA_IPTG = 0M, biol rep 4


title: manLAM 1

description: DMSO and PAMP treatments


title: Total cell wall lipid extracts 2

description: DMSO and PAMP treatments


title: WT H3K4me3 D0 ESC CUT&Tag repeat 3


title: PIM6 3

description: DMSO and PAMP treatments


title: sample.30832394_EcN_SensorArrayOnly_IPTG = 0M, biol rep 4


title: MCM2-2A H3K4me3 D0 ESC CUT&Tag repeat 3


title: PIM6 2

description: DMSO and PAMP treatments


title: WT H3K4me3 D0 ESC CUT&Tag repeat 2


title: miRNA-seq dataset: PR8-infected IFNLR-/- mouse #1

description:
FDK236_LP1
DIinfKOmice_miRNAseq_counts.txt


title: miRNA-seq dataset: PR8-infected IFNLR-/- mouse #3

description:
FDK254_LP3
DIinfKOmice_miRNAseq_counts.txt


title: sample.30832393_Escherichia_coli_Nissle_WT_IPTG = 0M, biol rep 4


title: miRNA-seq dataset: PR8-infected IFNLR-/- mouse #5

description:
FDK255_LP5
DIinfKOmice_miRNAseq_counts.txt


title: sample.30832392_EcN_NOTgate_PhlF_IPTG = 0M, biol rep 3


title: WT H3K4me3 D0 ESC CUT&Tag repeat 1


title: SL-1 2

description: DMSO and PAMP treatments


title: sample.30832391_EcN_NOTgate_BetI_IPTG = 0M, biol rep 3


title: miRNA-seq dataset: DI222-treated IFNAR-/- mouse #4

description:
DG4595_ADI4
DIinfKOmice_miRNAseq_counts.txt

source_name: Whole lungs of DI222-treated IFNAR-/- mouse

value: IFNAR-/-


title: SL-1 1

description: DMSO and PAMP treatments


title: MCM2-2A H3K9me3 D0 ESC CUT&Tag repeat 3

value: Anti-H3K9me3 Antibody (ab8898)


title: sample.30832390_EcN_NOTgate_IcaR_IPTG = 0M, biol rep 3


title: miRNA-seq dataset: DI222-treated IFNAR-/- mouse #3

description:
DG4567_ADI3
DIinfKOmice_miRNAseq_counts.txt

value: Lung


title: TDM 3

description: DMSO and PAMP treatments

value: TDM


title: miRNA-seq dataset: DI222-treated IFNAR-/- mouse #5

description:
DG4599_ADI5
DIinfKOmice_miRNAseq_counts.txt

value: DI222 co-treatment


title: sample.30832389_EcN_NOTgate_AmeR_IPTG = 0M, biol rep 3


title: TDM 2

description: DMSO and PAMP treatments


title: MCM2-2A H3K9me3 D0 ESC CUT&Tag repeat 1

value: ESC


title: miRNA-seq dataset: DI222-treated IFNAR-/- mouse #2

description:
DG4474_ADI2
DIinfKOmice_miRNAseq_counts.txt


title: WT H3K9me3 D0 ESC CUT&Tag repeat 3


title: sample.30832388_EcN_NOTgate_LitR_IPTG = 0M, biol rep 3


title: miRNA-seq dataset: DI222-treated IFNAR-/- mouse #1

description:
DG4460_ADI1
DIinfKOmice_miRNAseq_counts.txt


title: miRNA-seq dataset: PR8-infected IFNLR-/- mouse #2

description:
FDK216_LP2
DIinfKOmice_miRNAseq_counts.txt

value: PR8-only infection


title: TDM 1

description: DMSO and PAMP treatments


title: sample.30832387_EcN_NOTgate_QacR_IPTG = 0M, biol rep 3


title: miRNA-seq dataset: PR8-infected IFNAR-/- mouse #5

description:
DG4597_AP5
DIinfKOmice_miRNAseq_counts.txt


title: PDIM 2

description: DMSO and PAMP treatments

value: PDIM


title: miRNA-seq dataset: PR8-infected IFNAR-/- mouse #4

description:
DG4593_AP4
DIinfKOmice_miRNAseq_counts.txt


title: PIM6 1

description: DMSO and PAMP treatments

value: monocyte differentiated to macrophages with PMA


title: WT H3K9me3 D0 ESC CUT&Tag repeat 2


title: PDIM 1

description: DMSO and PAMP treatments


title: sample.30832385_EcN_NOTgate_BM3R1_IPTG = 0M, biol rep 3


title: WT H3K9me3 D0 ESC CUT&Tag repeat 1


title: miRNA-seq dataset: PR8-infected IFNAR-/- mouse #3

description:
DG4565_AP3
DIinfKOmice_miRNAseq_counts.txt


title: DMSO 2

description: DMSO and PAMP treatments

value: DMSO


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag repeat 3

value: DMEM/F12 _serum

value: MCM2-2A mutant

value: Anti-H3K27me3 Antibody (CST_9733)


title: miRNA-seq dataset: PR8-infected IFNAR-/- mouse #2

description:
DG4478_AP2
DIinfKOmice_miRNAseq_counts.txt


title: DMSO 1

description: DMSO and PAMP treatments


title: sample.30832384_EcN_NOTgate_HlyIIR_IPTG = 0M, biol rep 3


title: sample.30832383_EcN_NOTgate_PsrA_IPTG = 0M, biol rep 3


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag repeat 2


title: miRNA-seq dataset: PR8-infected IFNAR-/- mouse #1

description:
DG4446_AP1
DIinfKOmice_miRNAseq_counts.txt


title: MCM2-2A H3K27me3 D0 ESC CUT&Tag repeat 1


title: sample.30832382_EcN_SensorArrayOnly_IPTG = 0M, biol rep 3


title: RNA-seq dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #3

description:
DJA267_DODI3
DIinfKOmice_mRNAseq_counts.txt

extract_protocol:
Whole lungs were homogenized in QIAzol. The total RNA was extracted using miRNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-free DNase (Qiagen), followed by poly(A) mRNA enrichment.
The enriched poly(A) mRNAs were subject to RNA-seq library preparatin with NEBNext Ultra II RNA library prep kit for Illumina following the manufacturer’s protocol.

value: IFNAR-/- IFNLR-/-


title: LC5a

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
align with cellranger
Assembly: hg38/GRCh38

source_name: Lung

extract_protocol:
10x genomics chromium 3' Next GEM  single cell RNAseq kit
follow 10x genomics instruction


title: LC5b


title: LC4


title: WT H3K27me3 D0 ESC CUT&Tag repeat 2

value: WT


title: RNA-seq dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #2

description:
DJA268_DODI2
DIinfKOmice_mRNAseq_counts.txt


title: WT H3K27me3 D0 ESC CUT&Tag repeat 1


title: sample.30832386_EcN_NOTgate_AmtR_IPTG = 0M, biol rep 3

value: TRUE


title: sample.30832381_Escherichia_coli_Nissle_WT_IPTG = 0M, biol rep 3


title: sample.30832379_EcN_NOTgate_BetI_IPTG = 0M, biol rep 2


title: LC3b


title: wild type Rabbit, replicate 2,miRNA [TD_3]

city: Shanghai

first: hu

last: xiaolin

state: Shanghai

address: south congqing road 227#

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Adapters, low-quality reads (percentages of base quality lower than 15 higher than 20%), reads with unknown base higher than 5% were removed with SOAPnuke V1.5.2
Clean reads were mapped to reference genome with HISAT2 V2.0.4  with default parameters. Then, gene expressions were quantified by RSEM V1.1.17  and HTSeq V1.99.2
Supplementary files format and content: GCA_000003625.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oryctolagus cuniculus

source_name: femoral head

extract_protocol:
5 μg RNA of each sample were utilized with ribosomal RNA removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, United States)
NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, United States)

value: femoral head


title: RNA-seq dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #3

description:
DJA263_DOP3
DIinfKOmice_mRNAseq_counts.txt


title: wild type Rabbit, replicate 2,miRNA [TD_2]


title: LC3a


title: RNA-seq dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #2

description:
DJA247_DOP2
DIinfKOmice_mRNAseq_counts.txt


title: wild type Rabbit, replicate 1,miRNA [TD_1]


title: LC2b


title: RNA-seq dataset: DI222-treated IFNLR-/- mouse #4

description:
FDK263_LDI4
DIinfKOmice_mRNAseq_counts.txt

value: IFNLR-/-


title: Perthes' disease Rabbit, replicate 5,miRNA [TB_5]

value: Perthes' disease


title: WT H3K27me3 D0 ESC CUT&Tag repeat 3


title: sample.30832376_EcN_NOTgate_LitR_IPTG = 0M, biol rep 2


title: LC1b

value: Lung


title: LC2a


title: RNA-seq dataset: DI222-treated IFNLR-/- mouse #3

description:
FDK237_LDI3
DIinfKOmice_mRNAseq_counts.txt


title: Perthes' disease Rabbit, replicate 4,miRNA [TB_4]


title: sample.30832374_EcN_NOTgate_AmtR_IPTG = 0M, biol rep 2


title: Perthes' disease Rabbit, replicate 2,miRNA [TB_2]


title: Perthes' disease Rabbit, replicate 3,miRNA [TB_3]


title: sample.30832375_EcN_NOTgate_QacR_IPTG = 0M, biol rep 2


title: RNA-seq dataset: DI222-treated IFNAR-/- IFNLR-/- mouse #1

description:
DJA260_DODI1
DIinfKOmice_mRNAseq_counts.txt


title: Input_CC885(Hsap)_B, Ribo-seq

city: Martinsried/Planegg

first: Martin

last: Mueller

address: Am Klopferspitz 18

country: Germany

institute: MPI of Biochemistry

description:
Counts_HEK293_CC885_ribo.txt
Input_CC885B

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts
Library strategy: Ribo-seq

source_name: embryonic kidney

growth_protocol: The Bristol strain N2 was used as wild-type. Strains used in this study are listed in the Key Resource Table. Worms were grown on nematode growth medium (NGM) seeded with OP50 bacteria and maintained at 20°C unless otherwise indicated. For liquid culture, worm eggs were collected by bleaching and synchronized populations of L1 larvae were obtained by overnight growth in M9 medium. The L1 larvae were grown in S Basal in presence of OP50 bacteria.

extract_protocol:
C. elegans  Synchronized nematodes were transferred to 1 l S-Basal and grown in liquid culturentil D1 of adulthood or until D6, when indicated. FUdR (200 µM) was added when the culture had reached the L4/young adult stage. After thorough washing in M9, the nematodes were frozen in lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide) by dropwise transfer into liquid nitrogen. The nematodes were lysed with a Retsch Cryomill MM400 at 30 Hz for 3 times 90 s with cooling between cycles. The lysate was cleared for 10 min at 20,000 x g and 4oC. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.  HEK293T cells  HEK293T cells were seeded into 15 cm plates 24 h prior to treatment. The cells were treated with 10 nM CC-885 and 20 μg/ml G418 for 4 h. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.
C. elegans  The procedure for immunoprecipitation (IP) of GCN-1 bound ribosomes was adapted from {Matsuo, 2021 #75}. Nematodes were synchronized by bleaching. L1 larvae were transferred to 1 L S-Basal. The animals were harvested at D1 of adulthood. Bacteria were removed by repeated washes in M9. In the last washing step, M9 was replaced by lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide). After a quick spin, the worms were flash frozen in liquid nitrogen. The frozen worms were lysed with a Retsch cryomill MM400 at 30 Hz as above. The lysate was thawed on ice and clarified by centrifugation at 4,000 x g for 10 min at 4oC. Protein concentration was determined by Bradford assay. The supernatant fraction (80 mg of total protein) was partially digested with 3 units per 1 mg RNA RNase I (Epicenter) at 4oC for 1 h. Ribosomes were pelleted through a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC and resuspended in lysis buffer supplemented with 10% glycerol. The IP was performed at 4oC for 1 h using M2 anti-FLAG magnetic agarose beads (Invitrogen). The beads were washed 10 times with lysis buffer and bound material was digested with 12.5 units of RNase I (Epicenter) at 23oC for 45 min (strong RNase I treatment). Ribosome protected mRNA fragments were eluted by adding TRIzol reagent (Invitrogen). Libraries were prepared as previously described (McGlincy, 2017 #78) and sequenced on an Illumina NextSeq 500 system.  HEK293T cells  Cells (treated with CC-885 or untreated) were harvested, washed with PBS and lysed by trituration through a 26 G needle for 10 times in lysis buffer (20 mM Tris, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, 1 % Triton-X 100). The lysate was cleared at 4,000 x g for 10 min and an equivalent of 5 mg RNA input was digested with 15 units of RNAse I. The digested lysate was then layered over a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) and centrifuged at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC. The pelleted ribosomes were resuspended in lysis buffer supplemented with 10 % glycerol and incubated with GCN1 antibody (A301-843A, Thermo Fisher) coupled to protein G Dynabeads (10003D, Invitrogen) (5 µg antibody per 50 µl of protein G beads) for 2 h at 4oC. The beads were washed 10 times and digested with 4 units RNAse I for 45 min at 23oC. RPFs were isolated by TRIzol and libraries were prepared as previously described (McGlincy, 2017).

treatment_protocol: HEK293T cells were cultured in DMEM (Thermo Scientific, 11995073) supplemented with 10% FBS (Gibco, 10270106) at 5% CO2 and 37°C. Subsequently, cells were treated with 10 nM CC-885 and 20ug/ul G418 for 4 hours.

value: embryonic kidney

tag: ip antibody

value: Input (Hsapiens)


title: sample.30832380_EcN_NOTgate_PhlF_IPTG = 0M, biol rep 2


title: sample.30832373_EcN_NOTgate_BM3R1_IPTG = 0M, biol rep 2


title: RNA-seq dataset: DI222-treated IFNLR-/- mouse #2

description:
FDK256_LDI2
DIinfKOmice_mRNAseq_counts.txt

value: DI222 co-treatment


title: RNA-seq dataset: DI222-treated IFNLR-/- mouse #1

description:
FDK218_LDI1
DIinfKOmice_mRNAseq_counts.txt


title: Input_CC885(Hsap)_A, Ribo-seq

description:
Counts_HEK293_CC885_ribo.txt
Input_CC885A


title: sample.30832378_EcN_NOTgate_IcaR_IPTG = 0M, biol rep 2


title: Perthes' disease Rabbit, replicate 1,miRNA [TB_1]


title: sample.30832372_EcN_NOTgate_HlyIIR_IPTG = 0M, biol rep 2


title: sample.30832377_EcN_NOTgate_AmeR_IPTG = 0M, biol rep 2


title: RNA-seq dataset: PR8-infected IFNLR-/- mouse #6

description:
FDK261_LP6
DIinfKOmice_mRNAseq_counts.txt

value: PR8-only infection


title: RNA-seq dataset: PR8-infected IFNAR-/- IFNLR-/- mouse #1

description:
DJA258_DOP1
DIinfKOmice_mRNAseq_counts.txt


title: Input_Untreated(Hsap)_B, Ribo-seq

description:
Counts_HEK293_Untreated_ribo.txt
Input_NTCB

value: Untreated


title: Rhesus37136B

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

data_processing:
Illumina base-calling and demultiplexing with BCL-2-Fastq.
Trimmed FASTQ files were generated using the Cell Ranger v3.1.0 (10x Genomics) mkfastq command using default parameters. Alignment of trimmed reads, filtering, and UMI counting were performed using CellRanger v3.1.0 count function using mouse GRCm38 (mm10), human GRCh38 (hg38), Papio anubis (olive baboon) Panubis1.0 (Ensemble GCA_008728515.1) and rhesus macaque Mmul_10 (Ensemble GCA_003339765.3) references.
Gene expression matrices for each dataset were imported into Seurat (v3.2.3) and merged by species to produce aggregated gene-barcode matrices which were subsequently filtered, normalized and used for cell clustering.
Assembly: Papio anubis (olive baboon) Panubis1.0 (Ensemble GCA_008728515.1) and rhesus macaque Mmul_10 (Ensemble GCA_003339765.3)
Supplementary files format and content: A single gene-barcode matrix file (MTX). Each sparse matrix is stored in Market Exchange Format (MEX), which contains TSV files with features (genes) and barcode sequences corresponding to row and column indices, respectively.

organism: Macaca mulatta

source_name: Testis

extract_protocol:
Donor cells were recovered from olive baboon and rhesus macaque testes using  two-step enzymatic digestion approach.  Briefly, testicular parenchyma were digested with 1mg/ml Collagenase Type IV (Worthington Biochemicals) for 2-3 minutes at 37°C, washed with Hank’s Buffered Salt Solution (HBSS) to remove interstitial cells, digested with 0.25% trypsin/EDTA containing 1.4mg/ml DNase I (Sigma) for 7-9 minutes at 37°C, and quenched with 10% FBS. Testis cell suspensions were filtered through a nylon mesh to generate a single-cell suspension.  Single-cell transcriptomes were generated using the 10x Genomics Chromium Cell Gene Expression kit (v2 chemistry) per manufacturer recommendations (Zheng et al., 2017) at the UTSA Genomics Core as previously described (Hermann et al., 2018). For each replicate, we targeted collection of 5,000 single-cell gelbead emulsions (GEMs) containing single cells and generated libraries as per manufacturer recommendations (Zheng et al., 2017). Libraries were sequenced at the Genome Sequencing Facility (GSF) at Greehey Children’s Cancer Research Institute at UT Health San Antonio (UTHSA) on a HiSeq2500 (Illumina) instrument.
10x Genomics Single-cell 3' libraries were prepared according to manufacturer recommendations (Single Cell 3' v3 chemistry for 37979, Single Cell 3' v2 chemistry for all others).

treatment_protocol: Animal were untreated and testes obtained at necropsy for another purpose

value: Testis

value: Testicular cells

tag: library type

value: 10x Genomics 3' single-cell Gene Expression


title: sample.30832371_EcN_NOTgate_PsrA_IPTG = 0M, biol rep 2


title: Rhesus37136A


title: sample.30832370_EcN_SensorArrayOnly_IPTG = 0M, biol rep 2


title: RNA-seq dataset: PR8-infected IFNLR-/- mouse #4

description:
FDK239_LP4
DIinfKOmice_mRNAseq_counts.txt


title: GCN1-IP_CC885(Hsap)_B, Ribo-seq

description:
Counts_HEK293_CC885_ribo.txt
IPB_CC885

value: GCN1 antibody CAT#A301-843A


title: LC1a


title: Primordial germ cells, Lin28-bKO, rep3

city: Fukuoka

first: Seung June

last: Kwon

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Graduate School of Systems Life Sciences

institute: Kyushu University

description:
lin28bko3
DESeqResult_LIN28AKO_Ctrl.xlsx

data_processing:
Quality control of raw reads (containing adapters or N > 10%) was done by cell innovator (Fukuoka, Japan).
Reference genome (GRCg6a) index building and alignment were conducted utilizing HISAT2 (2.1.0).
Read counts are extracted by featureCounts (2.0.3) taking advantage of GRCg6a.106.gtf from Ensembl genome browser.
After count matrix was filtered (sum of all conditions >= 10), normalization and DEG analyses were conducted by DESeq2 (1.36.0) on R (4.2.1).
EdgeR (3.38.4) and EnhancedVolcano (1.14.0) were used for MDS and volcano plots, respectively.
Assembly: galGal6
Supplementary files format and content: tab-delimited text files include filtered raw inputs for DESeq2 analyses
Supplementary files format and content: excel files include results of the DESeq2 analyses

organism: Gallus gallus

source_name: PGC

extract_protocol:
Total RNA was harvested using Nucleospin RNA Plus kit (Takara) from control and lin28-KO PGCs.
RNA-seq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) following manufacturer's protocols.

value: PGC

value: Lin28B knockout


title: GCN1-IP_CC885(Hsap)_A, Ribo-seq

description:
Counts_HEK293_CC885_ribo.txt
IPA_CC885

value: WT


title: sample.30832368_EcN_NOTgate_PhlF_IPTG = 0M, biol rep 1

data_processing:
Sequencing reads were trimmed using Trimmomatic (Bolger et al., 2014)
Using theBurrows-Wheeler alignment tool (Li and Durbin, 2009), reference sequences were indexed and all trimmed reads were aligned to the indexed reference
Gene expression tables were constructed from the aligned reads using featureCounts (Liao et al., 2014) and normalized to fragments per kilobase of transcript per million mapped reads (FPKM). Samples with fewer than 5 x 106 mapped reads were excluded
Using custom Python code (see https://github.com/VoigtLab/EcN_analysis),  differentially expressed genes were identified. Mapped reads at each nucleotide position were normalized where tRNA regions were removed before calculating the total number of mapped nucleotides used for normalizing RNA-seq profiles.
Assembly: E. coli Nissle 1917 genome (NCBI CP007799)
Supplementary files format and content: comma-separated values (CSV) file includes FPKM values for all samples

value: TRUE


title: RNA-seq dataset: PR8-infected IFNLR-/- mouse #3

first: Matthew

last: Chung

address: 50 South Dr

description:
FDK254_LP3
DIinfKOmice_mRNAseq_counts.txt


title: GCN1-IP_Untreated(Hsap)_B, Ribo-seq

description:
Counts_HEK293_Untreated_ribo.txt
IPB_NTC


title: sample.30832369_Escherichia_coli_Nissle_WT_IPTG = 0M, biol rep 2


title: Primordial germ cells, Lin28-bKO, rep1

description:
lin28bko1
DESeqResult_LIN28AKO_Ctrl.xlsx


title: RNA-seq dataset: PR8-infected IFNLR-/- mouse #2

description:
FDK216_LP2
DIinfKOmice_mRNAseq_counts.txt


title: GCN1-IP_Untreated(Hsap)_A, Ribo-seq

description:
Counts_HEK293_Untreated_ribo.txt
IPA_NTC


title: sample.30832367_EcN_NOTgate_BetI_IPTG = 0M, biol rep 1


title: Primordial germ cells, Lin28-aKO, rep3

description:
lin28ako3
DESeqResult_LIN28AKO_Ctrl.xlsx

value: Lin28A knockout


title: sample.30832366_EcN_NOTgate_IcaR_IPTG = 0M, biol rep 1


title: sample.30832365_EcN_NOTgate_AmeR_IPTG = 0M, biol rep 1


title: D0 and D8, scRNAseq

first: Deepak

last: Mishra

address: 77 Massachusetts Avenue

institute: MIT

description:
D8
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, genes.tsv, matrix.mtx).

source_name: Personal Genome Project iPS cell line PGP1 (hu43860C) obtainable from Coriell (GM23338)

extract_protocol:
For dissociation of organoids into single cells for staining, these organoids were incubated in 50 microliters 2.5% trypsin (Corning) supplemented with 10 mM EDTA (Sigma-Aldrich) for 2 minutes. Well contents were transferred to 1.7 mL tubes and 500 microliters PBS was added to tubes and centrifuged at 300 x g for 4 minutes. Supernatant was aspirated and 50 microliters of Collagenase 4 (STEMCELL Technologies) was added prior to suspension being mechanically agitated by 15 strokes with a P-1000 and 15 strokes with a P-200. Suspension was incubated for 10 minutes prior to mechanical agitation by 30 strokes with a P-200. 750 microliters PBS was added prior to centrifugation at 300 x g for 4 minutes. Supernatant was aspirated and cells were resuspended in 50 microliters before being passed through a 40-micron strainer into a 2.0 mL tube. Cells were washed with 200 microliter PBS and centrifuged at 300 x g for 4 minutes with supernatant discarded before counting.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics) by MIT BioMicroCenter Core. Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: D0 and D8 differentiating hiPSCs


title: RNA-seq dataset: DI222-treated IFNAR-/- mouse #4

institute: NIAID (National Institute of Allergy and Infectious Diseases)

description:
DG4595_ADI4
DIinfKOmice_mRNAseq_counts.txt

value: IFNAR-/-


title: Input_Untreated(Hsap)_A, Ribo-seq

description:
Counts_HEK293_Untreated_ribo.txt
Input_NTCA


title: Primordial germ cells, Lin28-aKO, rep2

description:
lin28ako2
DESeqResult_LIN28AKO_Ctrl.xlsx


title: RNA-seq dataset: PR8-infected IFNLR-/- mouse #5

description:
FDK255_LP5
DIinfKOmice_mRNAseq_counts.txt

value: Lung

value: IFNLR-/-


title: D0 and D5, scRNAseq

description:
D5
10x Genomics

value: D0 and D5 differentiating hiPSCs


title: Primordial germ cells, Lin28-aKO, rep1

description:
lin28ako1
DESeqResult_LIN28AKO_Ctrl.xlsx


title: RNA-seq dataset: DI222-treated IFNAR-/- mouse #3

description:
DG4567_ADI3
DIinfKOmice_mRNAseq_counts.txt

value: DI222 co-treatment


title: Primordial germ cells, Control, rep3

description:
control3
DESeqResult_LIN28AKO_Ctrl.xlsx
DESeqResult_LIN28BKO_Ctrl.xlsx

value: WT (control vector)


title: RNA-seq dataset: DI222-treated IFNAR-/- mouse #2

description:
DG4474_ADI2
DIinfKOmice_mRNAseq_counts.txt


title: Primordial germ cells, Lin28-bKO, rep2

description:
lin28bko2
DESeqResult_LIN28AKO_Ctrl.xlsx


title: D0 and D3, scRNAseq

description:
D3
10x Genomics

value: D0 and D3 differentiating hiPSCs


title: RNA-seq dataset: PR8-infected IFNLR-/- mouse #1

description:
FDK236_LP1
DIinfKOmice_mRNAseq_counts.txt

value: PR8-only infection


title: RNA-seq dataset: DI222-treated IFNAR-/- mouse #1

description:
DG4460_ADI1
DIinfKOmice_mRNAseq_counts.txt


title: Primordial germ cells, Control, rep1

description:
control1
DESeqResult_LIN28AKO_Ctrl.xlsx
DESeqResult_LIN28BKO_Ctrl.xlsx


title: sample.30832362_EcN_NOTgate_AmtR_IPTG = 0M, biol rep 1


title: RNA-seq dataset: DI222-treated IFNAR-/- mouse #5

description:
DG4599_ADI5
DIinfKOmice_mRNAseq_counts.txt


title: sample.30832361_EcN_NOTgate_BM3R1_IPTG = 0M, biol rep 1


title: Pre-Oxalate (43.1)

city: Birmingham

first: Tanecia

last: Mitchell

state: AL

address: 720 20th Street South, 816E

department: Urology

institute: University of Alabama at Birmingham

data_processing:
Basecalling was performed using Illumina bcl2fastq version 2.18.0.12
STAR version 2.6.1b was used to align the raw FASTQ files to the reference genome using parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate; --outSAMattributes All
Transcript abundances were estimated using HTSeq count version 0.11.0 using parameters -r pos; -t exon -i gene_id; -a 10; -s no; -f bam
Differential expression between post-oxalate group vs pre-oxalate group were performed uasing DESeq2 version 1.20.0 using default parameters
Genome_build: GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file contatining raw transcript abundances for each gene in each sample

source_name: Monocytes

extract_protocol:
Monocytes were purified from blood using magnetic bead isolation from Miltenyi Biotech. RNA was purified using the Maxwell Simply RNA kit (Promega) per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary blood cells

value: Leukocytes

tag: cell types

value: Monocytes


title: RNA-seq dataset: PR8-infected IFNAR-/- mouse #5

description:
DG4597_AP5
DIinfKOmice_mRNAseq_counts.txt

source_name: Whole lungs of PR8-infected IFNAR-/- mouse


title: Post-Oxalate (43.2)


title: Input(Cele)_B_disome

data_processing:
Sequencing reads were demultiplexed and trimmed using a custom awk script. Barcodes used for Ribo-seq - replicate A: ATCGT; replicate B: AGCTA
The UMI were extracted using UMI-tools using the option ‘--extract-method=regex --bc-pattern="^(?P<umi_1>.{2}).+(?P<umi_2>.{6})$"’, which serves to remove duplicated reads arising from library amplification. The clipped reads were then mapped against ncRNA/rRNA indices using Bowtie2 (v2.4.2) with the parameters ‘-N 1 -L 15’. Unaligned reads were mapped against the genome using STAR (v2.7.10a) with parameters ‘--outFilterMismatchNmax 2 --quantMode TranscriptomeSAM GeneCounts --outSAMattributes MD NH --outFilterMultimapNmax 1’. The P-site offset and metagene plots were computed using the R package “riboWaltz” (Lauria, 2018). Transcript enrichment was calculated with the R package “DESeq2” (Love, 2014) or “DEBrowser” (Kucukural, 2019).
Assembly: hg38 and WBcel235(ce11)
Supplementary files format and content: tab-delimited text file with raw counts or comma-delimited text file with half-lives and CPM
Library strategy: Ribo-seq

organism: Caenorhabditis elegans

extract_protocol:
C. elegans  Synchronized nematodes were transferred to 1 l S-Basal and grown in liquid culturentil D1 of adulthood or until D6, when indicated. FUdR (200 µM) was added when the culture had reached the L4/young adult stage. After thorough washing in M9, the nematodes were frozen in lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide) by dropwise transfer into liquid nitrogen. The nematodes were lysed with a Retsch Cryomill MM400 at 30 Hz for 3 times 90 s with cooling between cycles. The lysate was cleared for 10 min at 20,000 x g and 4oC. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.  HEK293T cells  HEK293T cells were seeded into 15 cm plates 24 h prior to treatment. The cells were treated with 10 nM CC-885 and 20 μg/ml G418 for 4 h. Ribosome protected fragments (RPFs) were recovered, and libraries were prepared as previously described {McGlincy, 2017 #78}.
C. elegans  The procedure for immunoprecipitation (IP) of GCN-1 bound ribosomes was adapted from {Matsuo, 2021 #75}. Nematodes were synchronized by bleaching. L1 larvae were transferred to 1 L S-Basal. The animals were harvested at D1 of adulthood. Bacteria were removed by repeated washes in M9. In the last washing step, M9 was replaced by lysis buffer (25 mM Hepes-KOH pH 7.4, 100 mM KoAC, 10 mM MglCl2, 0.5 mM DTT, 2x EDTA free protease inhibitor, 0.1 U/μL SUPERase*In, 100 μg/mL cycloheximide). After a quick spin, the worms were flash frozen in liquid nitrogen. The frozen worms were lysed with a Retsch cryomill MM400 at 30 Hz as above. The lysate was thawed on ice and clarified by centrifugation at 4,000 x g for 10 min at 4oC. Protein concentration was determined by Bradford assay. The supernatant fraction (80 mg of total protein) was partially digested with 3 units per 1 mg RNA RNase I (Epicenter) at 4oC for 1 h. Ribosomes were pelleted through a sucrose cushion (1 M, 20 U/mL SUPERase*In (Invitrogen)) at 55.000 rpm in a SW 55 Ti rotor (Beckman Coulter) for 2 h at 4oC and resuspended in lysis buffer supplemented with 10% glycerol. The IP was performed at 4oC for 1 h using M2 anti-FLAG magnetic agarose beads (Invitrogen). The beads were washed 10 times with lysis buffer and bound material was digested with 12.5 units of RNase I (Epicenter) at 23oC for 45 min (strong RNase I treatment). Ribosome protected mRNA fragments were eluted by adding TRIzol reagent (Invitrogen). Libraries were prepared as previously described (McGlincy, 2017 #78) and sequenced on an Illumina NextSeq 500 system.  HEK293T cells  SLAM-seq was performed using the Lexogen SLAM-seq kinetics kit following the manufacturer's instructions.
Ribo-seq (disome) and mRNAseq (SLAMseq)

treatment_protocol: HEK293T cells were cultured in DMEM (Thermo Scientific, 11995073) supplemented with 10% FBS (Gibco, 10270106) at 5% CO2 and 37°C.

value: Input (Cele)


title: RNA-seq dataset: PR8-infected IFNAR-/- mouse #4

description:
DG4593_AP4
DIinfKOmice_mRNAseq_counts.txt


title: sample.30832360_EcN_NOTgate_HlyIIR_IPTG = 0M, biol rep 1


title: Pre-Oxalate (27.1)


title: Input(Cele)_A_disome


title: sample.30832359_EcN_NOTgate_PsrA_IPTG = 0M, biol rep 1


title: RNA-seq dataset: PR8-infected IFNAR-/- mouse #3

description:
DG4565_AP3
DIinfKOmice_mRNAseq_counts.txt


title: Post-Oxalate (11.2)


title: sample.30832364_EcN_NOTgate_LitR_IPTG = 0M, biol rep 1


title: GCN-1-IP(Cele)_B_disome

value: FLAG M2


title: sample.30832358_EcN_SensorArrayOnly_IPTG = 0M, biol rep 1


title: RNA-seq dataset: PR8-infected IFNAR-/- mouse #2

description:
DG4478_AP2
DIinfKOmice_mRNAseq_counts.txt


title: sample.30832363_EcN_NOTgate_QacR_IPTG = 0M, biol rep 1


title: Pre-Oxalate (11.1)


title: Primordial germ cells, Control, rep2

description:
control2
DESeqResult_LIN28AKO_Ctrl.xlsx
DESeqResult_LIN28BKO_Ctrl.xlsx

value: PGC


title: sample.30832357_Escherichia_coli_Nissle_WT_IPTG = 0M, biol rep 1

value: TRUE


title: GCN-1-IP(Cele)_A_disome


title: RNA-seq dataset: PR8-infected IFNAR-/- mouse #1

description:
DG4446_AP1
DIinfKOmice_mRNAseq_counts.txt


title: Post-Oxalate (27.2)


title: myoblasts_D4_chrRNA_rep1

status: Public on May 14 2023

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

data_processing:
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: *_polyA_estimates.tsv: text files containing the poly(A) tail length estimate for each read
Supplementary files format and content: *_splicing_status_per_read.txt: text files containing the overall splicing status of each read
Supplementary files format and content: *_hg38_multi_introns_isoforms_counts.txt or hg38_multi_introns_counts.txt: text files containing the per-intron splicing status for each intron in each read
Supplementary files format and content: *_hg38_multi_exons_isoforms_counts.txt: text files containing the per-exon splicing status for each exon in each read

molecule: nuclear RNA

source_name: myoblasts

extract_protocol:
Qiagen miRNeasy
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002) or targeted PCR amplification of gene interest and DNA nanopore sequencing (SQK-LSK109)

value: myoblasts

tag: pcr-amplified gene


title: HeLa_chrRNA_rep2a

source_name: HeLa

extract_protocol:
Qiazol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002) or targeted PCR amplification of gene interest and DNA nanopore sequencing (SQK-LSK109)

value: HeLa


title: HeLa_chrRNA_rep1b


title: myoblasts_D0_chrRNA_rep2


title: HeLa_chrRNA_rep1a


title: HeLa_CRISPR_IFRD2_ex6

value: CRISPR-Cas9 sgRNAs IFRD2 exon6


title: HeLa_CRISPR_IFRD2_ex5

value: CRISPR-Cas9 sgRNAs IFRD2 exon5


title: HeLa_CRISPR_IFRD2_ex5-ex6_rep2

value: CRISPR-Cas9 sgRNAs IFRD2 exon5, exon6


title: HeLa_CRISPR_clone_int4-int8C

value: CRISPR-Cas9 sgRNAs IFRD2 intron4, intron8C


title: HeLa_CRISPR_non_targeting_pool_rep2

value: CRISPR-Cas9 non-targeting sgRNA


title: myoblasts_D4_chrRNA_rep2


title: HeLa_CRISPR_IFRD2_int8B-int8C

value: CRISPR-Cas9 sgRNAs IFRD2 intron8B, intron8C


title: HeLa_CRISPR_IFRD2_int7-int8A

value: CRISPR-Cas9 sgRNAs IFRD2 intron7, intron8A


title: HeLa_CRISPR_IFRD2_int8A-int8B

value: CRISPR-Cas9 sgRNAs IFRD2 intron8A, intron8B


title: HeLa_CRISPR_IFRD2_int7-int8C

value: CRISPR-Cas9 sgRNAs IFRD2 intron7, intron8C


title: HeLa_CRISPR_IFRD2_ex7-int8C

value: CRISPR-Cas9 sgRNAs IFRD2 exon7, intron8C


title: HeLa_CRISPR_IFRD2_int6-int7

value: CRISPR-Cas9 sgRNAs IFRD2 intron6, intron7


title: HeLa_CRISPR_IFRD2_int6-ex7

value: CRISPR-Cas9 sgRNAs IFRD2 intron6, exon7


title: HeLa_CRISPR_IFRD2_ex7-int7

value: CRISPR-Cas9 sgRNAs IFRD2 exon7, intron7