title: NPC1-/- mouse O4+ cells H3K27ac

description: ChIP-seq for H3K27ac performed on O4-positive cells (oligodendrocyte lineage) collected from mice lacking functional NPC1 at 16-days of age. Cells from 6 mice were pooled together for a single analysis

data_processing:
Reads were alligned using the Burrows-Wheeler Aligner algorithm on default settings
Duplicate reads were removed and uniquely mapped reads with a mapping quality score of at least 25 were used.
The number of test tags were normalized for each sample with Drosophila spike-in tags
Alignments were extended in silico at their 3'-ends to a length of 200bp and assigned to 32-nt bins along the genome. The resulting histograms were stored as BigWigs.
Assembly: mouse mm10
Supplementary files format and content: BigWig

source_name: brain

extract_protocol:
Cells were isolated from brains of 16-day-old mice by magnetic-activated cell sorting using microbeads targeting the antigen O4 and were immediately flash frozen. Cell pellets from 6 mice were pooled together and fixed with 1% formaldehyde for 15 minutes and quenched with glycine. After cell lysis, chromatin was sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA was prepared by treating aliquots of chromatin with RNase, proteinase K, and heat, followed by ethanol precipitation. Soluble chromatin for H3K27me3 ChIP-seq was spiked-in with soluble Drosophila chromatin equivalent to 5-10% of mouse chromatin. The mix of suble chromatin was incubated with 4 ug of antibody against H3K27me3 or H3K27ac. Complexed were eluted with SDS buffer. ChIP-DNA was purified with phenol-chloroform extraction. *Drosophila spike-in was used for H3K27me3, but not H3K27ac
libraries were prepared by consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. These steps were done with an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: O4+ oligodendrocyte

tag: chip antibody

value: H3K27ac (ActiveMotif)


title: Control_3_Chd-521

status: Public on May 31 2023

type: SRA

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

country: USA

institute: Indiana University

library_source: transcriptomic

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10 UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: mm10
Supplementary files format and content: preprocessed_tpm

molecule: total RNA

organism: Mus musculus

source_name: Pancreatic beta cells

extract_protocol:
RNA was isolated from FACS-purified β cells using the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher). The DNAse treated RNA was analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 8.0 were used for cDNA synthesis and library preparation.
cDNA was first synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Clontech Laboratories, Inc.). A dual indexed cDNA library was then prepared using Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. The average size of the library insert was approximately 300-400 bp

tag: tissue

value: Pancreatic beta cells

tag: cell type

value: beta cell

tag: genotype

value: Control


title: WT mouse O4+ cells H3K27ac

city: Ann Arbor

first: Andrew

last: Lieberman

state: MI

address: 1150 W Medical Center Drive

department: Pathology

institute: University of Michigan

description: ChIP-seq for H3K27ac performed on O4-positive cells (oligodendrocyte lineage) collected from WT mice at 16-days of age. Cells from 6 mice were pooled together for a single analysis

library_source: genomic

molecule: genomic DNA

value: brain

tag: cell line

value: primary cells

value: wild-type


title: SK-Mel-28_miR-134-3p_rep2

type: RNA

city: Greifswald

first: Theresa

last: Kordaß

state: Mecklenburg-Vorpommern

address: Ferdinand-Sauerbruch Straße DZ7 5.05

department: Surgical Research Laboratory

country: Germany

institute: Univserity Medicine Greifswald

hyb_protocol: was performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany

data_processing: data was quantile normalized (enforces the individual hybridizations to have equal intensity distributions) across all hybridizations on BeadArray(s); performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany

label: biotin

organism: Homo sapiens

source_name: cell line

extract_protocol: After 48 h, cells were harvested for RNA isolation using an RNAeasy kit (Qiagen, Hilden, Germany).

treatment_protocol: SK-Mel-28 cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format.

tag: transfected with


title: SK-Mel-28_miR-127-5p_rep1

scan_protocol: was performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany


title: SK-Mel-28_control_miRNA_rep2

label_protocol: was performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany


title: Npc1-/- mouse O4+ cells H3K27me3

description: ChIP-seq for H3K27me3 performed on O4-positive cells (oligodendrocyte lineage) collected from mice lacking functional NPC1 at 16-days of age. Cells from 6 mice were pooled together for a single analysis

value: H3K27me3 (ActiveMotif; 39155)


title: WT mouse O4+ cells H3K27me3

description: ChIP-seq for H3K27me3 performed on O4-positive cells (oligodendrocyte lineage) collected from WT mice at 16-days of age. Cells from 6 mice were pooled together for a single analysis


title: SK-Mel-28_miR-4672_rep1


title: SK-Mel-28_miR-1293_rep1


title: SK-Mel-28_miR-6514-3p_rep1


title: SK-Mel-28_miR-34b-3p_rep1


title: SK-Mel-28_miR-3116_rep1


title: SK-Mel-28_miR-6859-3p_rep1


title: Control_1_Chd-385


title: Control_2_Chd-493


title: Cacna1s-/-_hindlimb_skeletal_muscle_E18.5 [snRNA-seq]

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software 2.0.0 provided by 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hindlimb skeletal muscle

extract_protocol:
Hindlimb skeletal muscles (without skin and bone) were dissected, snap-frozen, and stored in liquid nitrogen.  For the E14.5 embryo, 56 hindlimbs were pooled together. For the E18.5, 14 hindlimbs were pooled together. For the P5, 8 hindlimbs were pooled together. For the adult, 4 hindlimbs were pooled together. For E18.5 Cacna1s-/-, 26 hindlimbs were pooled together. Skeletal muscles were thawed for 5 min on ice. Muscles were minced with scissors in 1 ml cold lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NonidetTM P40, 1mM DTT, 1U/μl RNase inhibitor in Nuclease-Free Water). After 2 min, 4 ml of cold lysis buffer were added, and muscles were lysed for 5 min at +4 °C. 10 ml of cold wash buffer (PBS, BSA 2%, and 0.2 U/μl RNase inhibitor from Roche) was added, and the lysate was dounced with 20 strokes of loose pestle. The homogenate was filtered with 70 μm and 40 μm cell strainers. Nuclei were pelleted by centrifugation for 5 min at 500 × g at +4 °C. Nuclei were resuspended in 0.5ml of wash buffer and 2μl of PCM1 antibody (Sigma-Aldrich HPA023374) to stain the myonuclei. After 15 min, nuclei were pelleted by centrifugation for 5 min at 500 × g at +4 °C. Nuclei were resuspended in 0.5ml of wash buffer and 2μl of PCNA antibody (Biolegend 682203) to stain all the nuclei and 1μl of secondary antibody red Goat anti-rabbit against PCM1. After 15 min nuclei were pelleted by centrifugation for 5 min at 500 × g at +4 °C. Then the nuclei were resuspended in 300μl of wash buffer and filtered with 30μm cell strainers.
Library was performed according to the manufacter’s instructions (Next GEM single-cell Multiome ATAC+ Gene expression kit). Briefly, Post GEM-incubation Cleanup using DynaBeads MyOne Silane Beads was followed by Pre-Amplification PCR (72 °C for 5 min, 98 °C for 3 min, cycled 7 × 98 °C for 20 s, 63 °C for 30 s, 72 °C for 1 min). After cleanup with SPRIselect Reagent Kit, ATAC library was generated (98 °C for 45 s, cycled 8 × 98 °C for 20 s, 67 °C for 30 s, 72 °C for 20 s) and purified with SPRIselect Reagent Kit. The fragment size estimation of the resulting ATAC libraries was assessed with Agilent TapeStation D1000 HS (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific). SnATAC-seq libraries were then sequenced by pair with a HighOutput flowcel using an Illumina Nextseq 500 with the following mode: Read 1N - 63 cycles, i7 index – 8 cycles, i5 index - 24 cycles *(8 dark cycles and 16 cycles on i5), Read 2N - 63 cycles. SnRNA-seq libraries were constructed by performing the following steps: cDNA Amplification, SPRIselect cleanup, Fragmentation, End reair and A tailing, SPRIselect cleanup, and Adaptor ligation, SPRIselect cleanup, Samplex index PCR and SPRIselect cleanup size selection. The fragment size estimation of the resulting libraries was assessed with Agilent TapeStation D1000 (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific).

value: hindlimb skeletal muscle

tag: strain/genotype

value: Cacna1s-/- C57bl6n

tag: age


title: WT_hindlimb_skeletal_muscle_Adult [snRNA-seq]

description: 10x Genomics

value: WT C57bl6n

value: Adult


title: KO3

data_processing:
The pooled libraries were then denatured and neutralized before loading to NovaSeq 6000 sequencer at 300 pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 100 x 106 reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).
Assembly: mm10
Supplementary files format and content: peaks.narrowPeak

extract_protocol:
A total of 27,000-80,000 Tomato+ mature β-cells were collected for ATAC-Sequencing. Cells were first lysed to collect nuclei by incubating with 100 μL lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 0.10% Nonidet P40 Substitute, 0.01% Digitonin, 1% BSA, 1 mM DTT, 40 U/uL RNase Inhibitor) for 3 minutes, centrifuging at 300 rcf for 5 minutes at 4°C, and discarding the supernatant. The resulting nuclei were then washed with 1 mL wash buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.10% Tween-20, 1% BSA, 1 mM DTT, 40 U/μl RNase Inhibitor) and centrifuged at 200 rcf for 5 minutes at 4°C for 2-3 times. The final nuclei, ranging from 14,000-45,000 in number, were used for tagmentation and library preparation
Nuclei were immediately suspended in 50 μL tagmentation reaction using 2xTD buffer (Illumina, FC-121-1030) and Nextera Tn5 Transposase enzyme (Illumina, FC-121-1030). Fragments greater than 600 bp were excluded in library preparation. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity


title: Arid1a_knockout_rep2 [RNA-seq]

city: Goettingen

first: Zhe

last: Zhang

state: Niedersachsen

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology & GI oncology

institute: University Medical Center, Goettingen

data_processing:
Single-end 50bp reads were aligned to mouse genome MGSCv37/mm9 by TopHat (Version 2.1.1)
Transcripts were counted by htseq-count (Version 0.9.1)
Transcripts normalization and differential expression analysis were performed by Cuffnorm (Version 2.2.1.2) and Cuffdiff (version 2.2.1.5) with FDR cutoff 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts corresponding with gene names

source_name: Pancreas

extract_protocol:
The pancreas of 8-week-old p48-Cre and Arid1afl/fl;p48-Cre mice were harvested in ice-cold HBSS, dissociated by surgical scissors in a 10 cm cell culture dish filled with 5 ml cold HBSS and centrifuged at low speed (300 rpm, 5 min) to remove blood vessels and adipose tissue. The remaining explant was digested in 5 ml solution 2 at 37 ºC for 20 min, pipetted every 2 min using a 10 ml pipette. The tissue-containing tube was washed with 10 ml solution 1 and centrifuged (300 rpm, 5 min) before adding a second time of solution 2 and cultivated at 37 ºC for 10 min. Next, tissue suspension was transferred into a new 50 ml tube by filtering through a 100 µm cell strainer and the tissue fragments were ground using a syringe plunger. The remaining cells were collected by washing the mesh with two times of 10 ml solution 1 and pelleted. Recovering was achieved by easing the acinar cells in 5 ml solution 3 containing 10% FCS for 1 hour at 37 ºC and total RNA was extracted by TRIzol method.
Libraries were prepared from 500 ng RNA utilizing Truseq RNA Library Prep Kit v2 following manufacturer’s instructions. mRNA was captured by RNA purification beads and eluted. The first strand and second strand cDNA were synthesized and the overhangs of the fragments were repaired into blunt ends. The 3’ end was added with a single adenine to prevent mutual ligation during the following adapter conjugation. Finally, the DNA fragments with both flow-cell-hybridization adapters were amplified and the library was quantified by Agilent Bioanalyzer 2100. Size selection was optional if the main population of the library exceeds the appropriate size for sequencing or small fragments such as primer-dimers exist.

value: Primary acinar cells

tag: strain

value: post natal 8 weeks


title: Arid1a_knockout_rep3 [RNA-seq]


title: Control_4_Chd-524


title: KO2


title: FA0mg_ND.2

city: Philadelphia

first: Margie

last: Clapper

state: PA

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description: non-neoplastic colon epithelium form colitic mice treated with 0 mg folic acid

data_processing:
Raw reads were aligned to mm10 genome using bowtie
Raw counts in each known gene from the Ensembl database were enumerated using htseq-count from the HTSeq package
Genome_build: mm10
Supplementary_files_format_and_content: raw count in tab-delimited format

source_name: non-neoplastic, 0mg folic acid, rep2

growth_protocol: Mice were fed a diet containing folic acid 2 mg/kg chow, followed by carcinogen azoxymethane injection. Colitis was induced in all mice using 4 cycles of DSS. Immediately after the first DSS treatment, mice were randomized to receive folic acid 0 or 8 mg/kg chow for 16 weeks. At the end of study, mice were euthanized and colons were collected and process for gene expression analyses

extract_protocol:
Cells were microdissected from paraffin-embedded tissues usig Leica LMD6500 system.  RNA was isolated using the RecoverAllTM total Nucleic Acid Isolation for FFPE kit.  RNA concentration and quality were determined on an Agilent 2100 Bioanalyzer using RNA 6000 Pico chips.
Libraries were generated using SMARTerÒ Stranded RNA-Seq Kit V2- Pico Input Mammalian with 40 ng total RNA. Libraries were quantified using a Qubit ds DNA HS kit and size distribution validated on the Agilent 2100. Bioanalyzer using the Agilent High Sensitivity DNA kit.

treatment_protocol: AOM was injected at 7 weeks of age and DSS treatment was initiated at 9 weeks of age for 4 cycles (each cycle = 7 days of 2% DSS in drinking water plus 14 days of untreated water). At 11 weeks of age, mice were randomly assigned to receive folic acid at 0 or 8 mg/kg chow for 16 weeks.  Mice were euthanized at 27 weeks of age.  Colons were fixed in 10% formalin and processed for embedding.

value: laser microdissected non-neoplasitc colon epitheila cells

value: Swiss Webster

tag: treatment

value: 0 mg folic acid


title: KO1


title: FA0mg_ND.4

source_name: non-neoplastic, 0mg folic acid,rep 4


title: CN3


title: Arid1a_wt_rep2 [RNA-seq]


title: CN2


title: WT_hindlimb_skeletal_muscle_E14.5 [snRNA-seq]

description: 10x Genomics


title: Arid1a_wt_rep1 [RNA-seq]


title: WT_hindlimb_skeletal_muscle_E18.5 [snRNA-seq]

description: 10x Genomics


title: UK022 EPZ + IFNy

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

description:
raw counts and TPM
22Ei

data_processing:
Sequencing and base-calling were performed by BGI (Beijing Genomics Institute)
Sequencing reads were trimmed and filtered using Trimmomatic(V0.39) to remove adapters and low quality reads. Reads from human and mouse samples were mapped to Ensembl GRCm38 transcripts annotation (release 82), using RSEM (v1.3.2) and STAR (2.6.1d) with default settings.

source_name: Lung tumor organoids

growth_protocol: Patient derived tumoroids were grown in Matrigel plus cocktail media

extract_protocol:
Matrigel was dissolved by Dispase and the cell pellets were collected.  RNA was extracted using Absolutely RNA Nanoprep kits (Agilent).
RNA libraries were prepared for sequencing using BGI protocols.

treatment_protocol: Patient derived tumoroids were treated with 5uM EPZ6438 for 9 days followed by 2 days of EPZ6438 + 20 ng/mL IFNy

value: Lung tumor organoids

value: malignant epithelial

value: WT

value: IFNy + EPZ6438


title: CN1

value: Pancreatic beta cells

value: beta cell

value: Control


title: WT_hindlimb_skeletal_muscle_Adult [snATAC-seq]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software 2.0.0 by 10X Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: Cacna1s-/-_hindlimb_skeletal_muscle_E18.5 [snATAC-seq]

description: 10x Genomics


title: UK022 GSK + IFNy

description:
raw counts and TPM
22Gi

value: IFNy + GSK126


title: WT_hindlimb_skeletal_muscle_P5 [snATAC-seq]

description: 10x Genomics

value: hindlimb skeletal muscle


title: UK022 IFNy

description:
raw counts and TPM
22i

value: IFNy


title: WT_hindlimb_skeletal_muscle_E18.5 [snATAC-seq]

description: 10x Genomics

value: WT C57bl6n


title: WT_hindlimb_skeletal_muscle_P5 [snRNA-seq]

description: 10x Genomics


title: Arid1a_knockout_rep1 [RNA-seq]


title: Quadriceps, normal muscles, scRNAseq

city: Chengdu

first: Xiaokai

last: Li

state: Sichuan

address: Huiming road #211

country: China

institute: Sichuan Agricultural University

description: 10x Genomics

data_processing:
Raw sequencing data were processed using the CellRanger analysis pipeline (v7.0.1). A custom reference (mm10 pre-mRNA) was built for reads alignment in accordance with 10x Genomics recommendations, and all reads were mapped to the reference genome using the STAR with default setting. The mapped reads with valid barcodes and unique molecular identifiers (UMIs) were used to generate the gene-barcode matrix.
Further analysis was performed using the Seurat package (v4.1.1). For each sample, single-nucleus transcriptomes with fewer than 200 or more than 4,000 genes or more than 0.8% mitochondria genes were further filtered out from the analysis. Genes detected in less than 3 nuclei were also removed.
The resulting expression matrix of each sample was normalized using the NormalizeData function. Then, the IntegrateData function was applied to integrate datasets, and the ScaleData function was used to scale the data.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Quadriceps

extract_protocol:
The quadriceps muscle from WT and PTRF KO mice at 3 months of age were processed according to the previously described muscle nuclear isolation protocol with modifications. Quadriceps muscles were isolated from mice, minced immediately on ice with a scalpel, and placed in lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 in Nuclease-Free H2O). The minced tissue was further homogenized using a Dounce grinder for 10-12 strokes gently on ice, avoiding bubble formation. The homogenate was sequentially filtered through 70 and 40 mm cell strainers (Biologix) and centrifuged (×1000 g) for 5 min at 4℃ to pellet the nuclei. The pellet was resuspended with 1 mL of ice-cold wash buffer (PBS containing 2% BSA and 0.2 U/μL RNase inhibitor) and then filtered through the 20μm cell strainer before centrifugation (×500 g) for 5 min at 4℃. The collected nuclei were resuspended in 100μL of cold wash buffer, and the purity of nuclei suspensions was confirmed by microscopy with DAPI staining.
snRNA-seq libraries were generated using Chromium Next GEM Single Cell 3′ Gene Expression v3.1 kit (10× Genomics) according to the manufacturer’s protocol. Gel Beads and Partitioning Oil were then dispensed into corresponding wells separately in a chip. We then performed emulsion droplet generation reverse transcription at 53℃ for 45 min and inactivated at 85℃ for 5 min. The cDNA was then purified from the broken droplet and amplified in a PCR reaction. The amplified cDNA products were then cleaned, fragmented, end-repaired, A-tailed, and ligated to the sequencing adapter. Finally, the indexed PCR was performed to amplify the DNA representing 3ʹ polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. Sequencing was performed on an Illumina NovaSeq system with the pair-end sequencing settings Read1: -28 bp and Read2: -150bp.

value: Quadriceps

value: 3 months old


title: UK022 EPZ

description:
raw counts and TPM
22E


title: SK-Mel-28_miR-224-3p_rep2


title: SK-Mel-28_miR-134-3p_rep1


title: SK-Mel-28_miR-224-3p_rep1


title: WT_hindlimb_skeletal_muscle_E14.5 [snATAC-seq]

description: 10x Genomics


title: P14, Stat5CA

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
P14 CD8 T cells transduced with a retrovirus encoding STAT5CA and isolated from LCMV Cl13 infected mice at D27p.i.
10x Genomics

data_processing:
Sample demultiplexing, alignment, filtering and creation of a UMI count matrix were performed using Cell Ranger software v.4.0.0 (10x Genomics). A Seurat object was created from the UMI count matrix using Seurat_4.0.5.80 Cells with fewer than 200 or greater than 2500 detected genes were excluded from downstream analysis as of cells with >10% of mitochondrial gene counts. Genes which expression was detected in 3 cells or less were excluded
A total of 920 P14 Empty and 302 P14 STAT5CA cells passed filters with an average sequencing depth of 1984 genes per cell and were considered for downstream analysis. Counts were normalized by total expression in the corresponding cell using the “LogNormalize” function and default scaling factor of 10,000 to give counts per million. Top 2000 variable features were determined using the “vst” selection method. Linear dimensional reduction (PCA) was performed on scaled variable features and features from the 20 most significant PCs were used as input for unsupervised clustering using the “FindNeighbors” and “FindClusters” functions of Seurat with a resolution of 0.3
Differentially expressed genes were identified by the Seurat function “FindAllMarkers” with min.pct=0.25 and logfc.threshold=0.25
Seurat clusters were used as features to calculate module scores of single cells using the “AddModuleScore” of Seurat_4.0.5. Module scores for each of the gene signatures were used to color the UMAP projection
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: P14 CD8 T cells

growth_protocol: Splenocytes from recipient mice were pooled from duplicate experiments and CD8 T cell enrichment was performed using EasySeptm CD8+ T cell isolation Kit (StemCell). Enriched CD8 T cells were stained and P14 populations of interest were sorted at 4oC in 1.5ml Eppendorf tubes containing 50% FBS RPMI as described above

extract_protocol:
Sorted samples were topped with cold PBS 0.04% BSA, centrifuge for 5’ 350g at 4oC, washed two times in cold PBS and resuspended in 50-100ul of cold PBS. Samples were counted, down-sampled and equivalent number of cells (6300) between samples were loaded into the Chip (Chromium Next GEM Chip G) of a Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index, 10x Genomics) and run onto a Chromium Controller
Samples were then processed according to manufacturer’s protocol. cDNA libraries were prepared using the Dual Index TT Set A (10x Genomics) and the number of indexing PCR cycles was adjusted to the cDNA input ,Libraries were quantified by qPCR using a KAPA Library Quant Kit (KAPA Biosystems). Normalized libraries were pooled (2.5nM), loaded onto a NovaSeq 6000 SP Reagent Kit (100 cycles, Illumina) for a final concentration of 450pM and paired-end sequencing was performed on a NovaSeq 6000 (Illumina).

value: P14 CD8 T cells


title: SK-Mel-28_miR-3126-5p_rep1


title: Quadriceps, PTRF KO muscles, scRNAseq

description: 10x Genomics

value: PTRF knockout


title: P14, Empty

description:
P14 CD8 T cells transduced with an Empty (control) retrovirus and isolated from LCMV Cl13 infected mice at D27p.i.
10x Genomics

value: Empty


title: UK022 Vehicle

description:
raw counts and TPM
22V

value: Vehicle


title: RNAseq_EµMyc_2hours_DMSO_Replicate_3

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the mouse reference genome (Mm10) using HISAT2 (v2.1.0) with default parameters.
Read counting across genomic features (exons) was performed using featureCounts (part of the subread package) prior to differential gene expression analysis using the limma/voom workflow.
Gene set enrichment analyses were performed using GSEA software (Broad Institute) and enrichment plots were plotted in Rstudio.
Assembly: Mm10
Supplementary files format and content: Raw (non-normalized) gene expression counts matrix in CSV format

source_name: B-cell lymphoma

growth_protocol: Eµ-Myc lymphoma (Clone #4242) cells were grown in vitro under standard culture conditions.

extract_protocol:
Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions.
Sequencing libraries were prepared from 500ng RNA using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria). Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.

treatment_protocol: Samples were treated in biological triplicate in the presence of JQ1 (1µM), RG6146 (2.5µM), or DMSO vehicle.

value: Eu-Myc Clone 4242

tag: timepoint

value: 2 hours

tag: treatment+dose

value: DMSO


title: RNAseq_EµMyc_2hours_DMSO_Replicate_2


title: Tox2, OPC

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

data_processing:
Salmon was used to align, normalize, and tabulate reads
Assembly: RefSeq mm10
Supplementary files format and content: TPMs

source_name: iPSC-derived oligodendrocyte progenitor cells (OPCs)

growth_protocol: OPCs were cultured in DMEM F12 supplemented with N2max B27 Fdf2 and Pdgfa

extract_protocol:
Phenol-chloroform with TRIzol
Total RNA submitted to Novogene for library preparation and sequencing

treatment_protocol: Compared control OPCs treated with vehicle (DMSO) to OPCs treated with methyltrioctylammonium chloride and tributyltetradecylphosphonium chloride

value: Incubation with tributyltetradecylphosphonium chloride


title: RNAseq_EµMyc_2hours_DMSO_Replicate_1


title: UK057 EPZ + IFNy

description:
raw counts and TPM
57Ei

value: Lung tumor organoids

value: malignant epithelial

value: WT

value: IFNy + EPZ6438


title: Tox1, OPC

value: iPSC-derived oligodendrocyte progenitor cells (OPCs)

value: Incubation with methyltrioctylammonium chloride


title: P14, IL2Rb ortho

description:
P14 CD8 T cells transduced with a retrovirus encoding an orthogonal IL2R and isolated from LCMV Cl13 infected mice at D26p.i. Mice were treated with ortho IL-2 from D21-25
10x Genomics


title: RNAseq_EµMyc_2hours_RG6146_Replicate_3


title: UK057 IFNy

description:
raw counts and TPM
57i

value: IFNy


title: MaMel-02_mock_rep3

treatment_protocol: MaMel-02 cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format.

value: mock


title: MaMel-02_miR-1293_rep2


title: Control, OPC

value: Incubation with vehicle (DMSO)


title: RNAseq_EµMyc_2hours_RG6146_Replicate_2


title: MaMel-02_mock_rep2


title: UK057 EPZ

description:
raw counts and TPM
57EPZ


title: MaMel-02_mock_rep1


title: UK022 GSK

description:
raw counts and TPM
22G


title: RNAseq_EµMyc_2hours_RG6146_Replicate_1


title: Maf_biol rep1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
After quality control using FastQC tool, reads were trimed for adapter sequence and were aligned to mm10 reference genome using bowtie2 (Version 2.3.2) with default settings.
Picard (Version 2.10.3) was then used to remove duplicated reads.
HOMER software was used for .bigWig generation.
HOMER software was used for peak calling. For Maf ChIPseq, default setting was used except with -style factor, for H3K27ac ChIPseq, fdr was set to 1e-3 and -style histone was used.
For heatmap generation, merge .bed file for each condition were generated and the summit .bed used as input for ngs.plot.r R package.
Assembly: GRCm38 - mm10
Supplementary files format and content: bigWig, .bed format peaks called by HOMER (except for Input sample)

source_name: Adult skeletal muscle

extract_protocol:
Nuclei were fixed with 4% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sheared on a Bioruptor Pico (Diagenode) for 10 cycles (30 sec on/ 30 sec off for each cycle) at 4°C
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB. 10 ng of DNA was used as starting material for input samples and 1 ng for ip samples. Libraries were amplified using 15 cycles for ip samples and 12 cycles for input on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

value: Adult skeletal muscle

tag: tissue type

value: Gastrocnemius and quadriceps

value: Maf (Bethyl Laboratories, A300-613A)


title: UK057 GSK

description:
raw counts and TPM
57GSK


title: RNAseq_EµMyc_2hours_JQ1_Replicate_3

value: JQ1, 1uM


title: MaMel-02_miR-3126-5p_rep3


title: MaMel-02_miR-1293_rep1


title: UK057 GSK + IFNy

description:
raw counts and TPM
57Gi

value: IFNy + GSK126


title: H3K27Ac_ biol rep2

value: H3K27Ac (Diagenode, C15410196)


title: UK057 Vehicle

description:
raw counts and TPM
57V

value: Vehicle


title: MaMel-02_miR-1293_rep3


title: RNAseq_EµMyc_2hours_JQ1_Replicate_2

value: Eu-Myc Clone 4242

value: 2 hours


title: MaMel-02_miR-4672_rep3


title: MaMel-02_miR-3126-5p_rep2


title: MaMel-02_miR-3126-5p_rep1


title: MaMel-02_miR-4672_rep1


title: H3K27Ac_biol rep1


title: MaMel-02_miR-3116_rep3


title: SK-Mel-28_control_miRNA_rep1


title: UK022 IFNy + EPZ ChIP

description:
raw counts and TPM
22Ei ChIP

value: Lung tumor organoids

value: malignant epithelial


title: RNAseq_EµMyc_2hours_JQ1_Replicate_1


title: Input biol rep2


title: Maf_biol rep2


title: Liver niche PDX_late4

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

data_processing:
Gene_count_matrix_ankl1, sequenced reads were trimmed with fastp v0.19.8, mapped to GRCh38 with Hisat2 v2.2.1, and counted with StringTie v2.1.4.
Liver_niche data, sequenced reads were mapped to hg38 or mm10 with bowtie v1.1.1 and CASTIN, then counted with CASTIN.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-deliminated text files including raw counts and normalized counts for every gene.

source_name: Liver niche PDX

extract_protocol:
Livers were removed from healthy mice or PDX mice, and RNA was harvested using Sepasol-RNA I Super G (nacalai tesque, Cat#09379-55).
RNA library was constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat#E7760L) following the manufacturer's protocol.

value: liver


title: Liver niche PDX_late3


title: UK022 EPZ ChIP

description:
raw counts and TPM
22E ChIP

value: WT


title: R+D-C226

city: Guangzhou

first: Xinyu

last: Wang

state: Guangdong

address: Zhongshan 2nd Road

department: Department of Immunology

institute: Sun-yat sen University

description: C57BL/6J mouse model bearing MC38 tumors

data_processing:
Hisat2 v2.1.0,Stringtie-1.3.5
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality, and then trimmed sequence reads were mapped to GrCM38 using Hisat2 with default parameters
Read count extraction and normalization were performed using stringtie and the DEseq2 package
Assembly: GRCM38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Tumor

extract_protocol:
Total RNA was extracted from tumor tissue with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol:
Eight-week-old C57BL/6J mice were inoculated with MC38 cells (1× 106 cells per mouse) via subcutaneous injection into the left flank. For monotherapy, the mice were randomly grouped and intraperitoneally injected with (1) PBS, (2) 14 µg DOX (0.56 mg/kg), (3) 14 µg DPD (0.56 mg/kg) and (4) 20 µg Ru-PD-L1 (0.80 mg/kg) for every 3 days started at day9. For combinational therapy, the mice were treated with 14 µg DPD (or DOX) by peritumoral injection 6 hours after the administration of Ru-PD-L1.
The tumor-bearing mice were euthanized, and the tumor tissues were harvested at day 20 after tumor inoculation.

value: Tumor

tag: agent

value: R+D

tag: model

value: MC38 tumors


title: UK022 Vehicle ChIP

description:
raw counts and TPM
22V ChIP


title: MaMel-02_miR-3116_rep2


title: MaMel-02_miR-3116_rep1


title: Atorva3

city: Hefei

first: Zhenghong

address: 443 Huangshan road

institute: University of Science and Technology of China

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM(v1.2.12).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human umbilical vein endothelial cells

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol.

treatment_protocol: HUVECs were treated with DMSO or atorvastatin (10μM) for 24 hours.

value: Human umbilical vein endothelial cells

value: atorvastatin


title: R+D-C219


title: Liver niche PDX_late1


title: R+X-C225

value: R+X


title: Liver niche Ct3

source_name: Liver niche Ct


title: R+X-C206


title: Atorva2


title: Liver niche Ct2


title: Input biol rep1

value: Adult skeletal muscle

value: Gastrocnemius and quadriceps


title: Veh3

value: vehicle


title: Atorva1


title: Liver niche Ct1


title: RP-C218

value: RP


title: UK022 IFNy ChIP

description:
raw counts and TPM
22i ChIP

value: IFNy


title: RP-C201


title: Veh2


title: Liver niche PDX_late2


title: MaMel-02_miR-6859-3p_rep3


title: MBD3+ ES cell population Hi-C rep5

city: Cambridge

first: Ernest

last: Laue

address: 80 Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Cut&Run:
Cut&Run data was trimmed using trim_galore and then aligned using Bowtie standard parameters to the Mus Musculus reference genome (mm10).
Cut&Run bigwig tracks were calculated using BedTools and bedGraphToBigWig with standard parameters.
The coverage was calculated with computeMatrix reference-point with options --binSize 10.
Peaks were called using MACS2 to be at FDR 1% and above 5-fold enrichment.
Hi-C
Population Hi-C was mapped to the genome using NucProcess (https://github.com/tjs23/nuc_processing) and analysed further using NucTools (https://github.com/tjs23/nuc_tools).
Genome_build: UCSC GRCm38/mm10
Supplementary_files_format_and_content: Bigwig files were generated for Cut&Run datasets.
Supplementary_files_format_and_content: Population Hi-C txt file (.txt) is a tab-separated text format containing all the chromosomal coordinates for Hi-C contacts and the number observed (chromosome_A start position_A end position_A chromosome_B start position_B end position_B number observed).

source_name: MBD3+ ES cell population Hi-C

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatin-coated plates in 2i/LIF conditions as described (Ying et al., 2008).

extract_protocol:
Cut&Run experiments were carried out according to Meers et al., (2019) using a Drosophila genomic DNA spike-in and “input” controls consisting of samples which were processed in parallel with the Cut&Run samples but with untethered MNase.
Population Hi-Cs were carried out as previously outlined (Stevens et al., Nature, 2017). 5-10 million Haploid mouse ES cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Cut&Run experiments were carried out according to Meers et al., (2019) using a Drosophila genomic DNA spike-in and “input” controls consisting of samples which were processed in parallel with the Cut&Run samples but with untethered MNase.
Hi-C libraries were prepared as previously outlined (Stevens et al., Nature, 2017). Briefly, sonicated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. Biotinylated junctions were captured on streptavidin M-280 dynabeads and the blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~300-700 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: background

value: Mouse embryonic stem cells

tag: culture conditions


title: DPD-C217

value: DPD


title: Veh1


title: MBD3+ ES cell population Hi-C rep4


title: DPD-C214


title: MaMel-02_miR-34b-3p_rep3


title: MBD3+ ES cell population Hi-C rep2


title: DOX-C222

value: DOX


title: MaMel-02_miR-6859-3p_rep1


title: DOX-C227


title: Negative_2

city: Durham

first: Victoria

last: Jeffers

state: NH

address: 46 College Rd

department: MCBS

institute: UNH

data_processing:
Basecalls were performed using bcl2fastq 2.20.0 for Nextseq output.
cutadapt v3.4 was used to trim sequencing primers and reads with fewer than 30bp after trimming
Mapping against the reference was performed with hisat2 v2.1.0 with the parameters "--no-discordant --no-spliced-alignment --phred33 --no-unal --no-mixed"
Peaks were called with MACS3 v3.0.0a6 with parameters "-f BAMPE -g 6.2e7 -B -q 0.01"
Assembly: ToxoDB-52_TgondiiME49
Supplementary files format and content: bigWig, insert corresponding to mapped read pairs
Supplementary files format and content: narrowPeak, MACS3 output
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: Tachyzoites

growth_protocol: Parasites were maintained in primary human foreskin fibroblasts in 1%FBS, DMEM at 37C, 5%CO2

extract_protocol:
Ten million (1x10^7) parasites were centrifuged 2000xg for 10min and the parasite pellet used directly with the CUT&Tag-IT Assay Kit (Active Motif 53160). Our experimental sample used TgBDP13xHA parasites and 1ul of a 1:50 dilution of the rabbit anti-HA primary antibody (Cell Signaling 3724T). The negative control sample used ΔKu80 parasites (the parental line) with the same primary antibody conditions. Samples were incubated with primary antibody overnight at 4°C.
After tagmentation, DNA was extracted, purified on a column and libraries were amplified by PCR usinf i5&i& indexed primers

treatment_protocol: No change in treatment prior to extraction

value: Tachyzoites


title: Ctrl-C223

value: Ctrl


title: BDP1_rep3


title: BDP1_rep2


title: MaMel-02_miR-34b-3p_rep1

data_processing: data was quantile normalized (enforces the individual hybridizations to have equal intensity distributions) across all hybridizations on BeadArray(s); performed by GPCF core facility of German Cancer Research center (DKFZ) Heidelberg, Germany

source_name: cell line


title: MaMel-02_miR-6859-3p_rep2


title: MaMel-02_miR-34b-3p_rep2


title: MaMel-02_miR-134-3p_rep3


title: non-CIN rep6

city: Bedford Park

first: Stephen

middle: L

last: Gregory

state: South Australia

address: Sturt Road

department: Molecular Medicine

country: Australia

institute: Flinders University

data_processing:
CLC Genomics Workbench 20 adaptor trimming
Reads below 15bp discarded
Mapped to Drosophila genome, default settings
Assembly: Drosophila genome BDGP6.22.98
Supplementary files format and content: Excel spreadsheet containing RPKM and differential expression

organism: Drosophila melanogaster

source_name: 3rd instar larvae

growth_protocol: standard growth media

extract_protocol:
RNEasy Plus minipreps
Illumina rRNA depleted TrueSeq

treatment_protocol: no treatment

value: 3rd instar larvae


title: non-CIN rep5


title: non-CIN rep4


title: H3K9ac


title: MaMel-02_miR-134-3p_rep2

extract_protocol: After 48 h, cells were harvested for RNA isolation using an RNAeasy kit (Qiagen, Hilden, Germany).


title: MBD3+ ES cell population Hi-C rep3


title: Negative_1


title: MaMel-02_miR-4672_rep2


title: BDP1_rep1


title: Mouse cortical neurons, erinacine S, 48 hrs, rep3

city: Hsinchu

first: Chun-Yu

last: Lin

address: No. 75 Po-Ai St.

department: Department of Biological Science and Technology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The sequence was directly determined using Illumina's sequencing-by-synthesis (SBS) technology.
Sequencing data (FASTQ reads) were generated based on Illumina's basecalling program bcl2fastq v2.20.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding window approach.
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
Hisat2 is used for mapping sequencing reads to genomes.
To Convert SAM file to BAM file format, Samtools, a suite of programs for interacting with high-throughput sequencing data, was used.
TPM values were calculated from filtered mapped reads using Stringtie (v2.1.3) with the default setting.
Assembly: GRCm38.p5
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: brain

growth_protocol:
Embryos from timed pregnant C57BL/6J adult mice (E17.5) were used. Mouse brains were collected from the embryos, the meninges were carefully removed, and the cortexes were isolated under the dissecting microscope. Cortexes were incubated with 5 mL of digestion medium (0.25% trypsin-EDTA, 10 mM HEPES) at 37 °C for 30 minutes and dissociated mechanically via trituration. Dissociated cortical neurons were filtered by cell strainer before centrifuged at 80 g for 10 mins at room temperature.
The cell pellet was resuspended in the cortical neuron plating medium (Minimum Essential Medium supplemented with 5% fetal bovine serum, 0.6% D-glucose, and 2 mM L-glutamine). 1×10^4 or 8×10^4 neurons were plated into each well of a 96-well or 24-well plate in the cortical neuron plating medium. After 3 hours of incubation, the cortical neuron plating medium was replaced with 100 µL or 250 µL of the cortical neuron maintenance medium (neurobasal medium supplemented with 1× B27 and 0.5 mM L-glutamine).

extract_protocol:
Total RNAs were extracted from cortical neurons using Blood/Cell total RNA mini kit (RB050, Geneaid, Taiwan) according to the manufacturer's instructions. Reverse transcription was performed using RevertAid First Strand cDNA Synthesis Kit (K1621, Thermo Scientific, Waltham, MA) according to the manufacturer's instructions.
The SureSelect Strand-Specific RNA Library Preparation Kit (Agilent, Santa Clara, CA) was used for library construction followed by AMPure XP Beads size selection. The sequence was directly determined using Illumina’s sequencing-by-synthesis (SBS) technology.

treatment_protocol:
For RNA-seq assays, 6.5×10^6 neurons were plated into the 15-cm culture dishes. After 3 hours of incubation, the cortical neuron plating medium was replaced with 20 mL of the cortical neuron maintenance medium.
After incubating for 1 additional hour, 20 mL of erinacine S solution (final concentration 1 μg/mL) was added into each culture dish. Dissociated cortical neurons were maintained in a 37 °C, 5% CO2 incubator for 16 or 48 hours.

value: brain

value: primary cortical neuron

value: 1 μg/mL erinacine S treatment

tag: time

value: 48 hrs


title: non-CIN rep3

tag: tissue


title: non-CIN rep2


title: Mouse cortical neurons, erinacine S, 48 hrs, rep2

tag: cell type


title: Nuli-1_t15_assay3

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
cDNA reads quality and trimming: The quality of the cDNA reads was analyzed using FastQC (0.11.8). Adapters and poor quality sequences were trimmed using Trimmomatic (v0.39).
Alignment: Paired-end reads were aligned to the LUZ19 (NC_010326.1), P. aeruginosa PAO1 (NC_002516.2), and Human reference genomes (assembly GRCh38.p13) using the BWA-MEM aligner. SAMtools (v1.9) was used to process the alignment files and assess mapping quality. Next, the aligned read pairs (fragments) were assigned to the genomic features of the phage and the host using featureCounts. Counts were normalized using FPKM values.
Normalization: Reads that mapped to the human genome and bacterial rRNA reads (60-80%) were removed in silico. Subsequently, fragment counts were first normalized by gene length and next by the number of non-ribosomal read pairs in each sample to obtain FPKM values
statistics: Samples variance was analyzed using Principal Component Analysis (PCA) in R. Differential gene expression analysis was performed using a negative binomial distribution test from the DESeq2 Bioconductor package in R. An ANOVA test was performed to identify the most significantly up- or down-regulated genes.
Assembly: NC_010326.1), P. aeruginosa PAO1 (NC_002516.2)
Supplementary files format and content: csv files containing the FPKM (non-rRNA) values for each sample

organism: Pseudomonas aeruginosa PAO1

source_name: 15 min infected- P. aeruginosa PAO1 (DSM22644) adhered to Nuli-1 cell line (ATCC® CRL-4011™), with Pseudomonas LUZ19 phage

growth_protocol: P. aeruginosa PAO1 overnight cultures were whased with PBS and ajusted to OD=0.13 in MCCM media. 1 mL of bacterial suspenssion was added to each well of a six-well plate, containing a confluent monolayer of Nuli-1 epithelial cells, bacterial adhesion was allowed for 1h at 37°C .

extract_protocol:
At each time point of phage infection, the complex cell mixture was collected and total RNA was extracted using Purelink RNA Mini Kit (Invitrogen). MICROBEnrichTM kit was used to remove human RNA.
Mammalian RNA-depleted samples (n=3 per condition) were directly used to deplete bacterial rRNA and cDNA libraries construction following Ribo-zero (Illumina) manufacturer’s recommendations. Successful rRNA depletion was verified on a Bioanalyzer using the DNA High sensitivity kit (Agilent) and the final concentrations were determined using the Qubit 4 Fluorometer (Invitrogen).
Samples were processed immediately, according to Illumina Stranded Total RNA Prep with Ribo-Zero Plus TruSeq Stranded mRNA Library Prep recommendations. In the end, cDNA libraries were evaluated on a Bioanalyzer (Agilent) to confirm average fragments between the range of 200-300 bp, and final concentrations were measured on a Qubit. The libraries’ normalization and pooling were performed according to MiniSeq System Denature and Dilute Libraries Guide: protocol A from Illumina. For each run, a library of three samples with equimolar amounts was combined with PhiX control (spike-in of 0.5-2%) and paired-end sequenced (2×75 bp) on an in-house Illumina Miniseq sequencer. After a first sequencing run, specific samples were re-sequenced to increase the sequencing depth of the phage and bacterial transcriptomes and improve the statistic power to detect differentially expressed genes.

treatment_protocol: Non-aderent bacteria were removed and phage LUZ19 was added at a final MOI=75 (except in the control, t=0 min).

tag: cell type_used_for_cell_adherence

value: human airway epithelium of normal genotype

value: 15 min with phage

tag: phage moi


title: Ctrl-C204

value: Tumor

value: MC38 tumors


title: Mouse cortical neurons, erinacine S, 48 hrs, rep1


title: Nuli-1_t15_assay2


title: Mouse cortical neurons, DMSO, 48 hrs, rep3

value: DMSO solvent control treatment


title: non-CIN rep1

tag: genotype


title: Nuli-1_t15_assay1


title: CIN rep5


title: Mouse cortical neurons, DMSO, 48 hrs, rep2


title: MaMel-02_miR-134-3p_rep1

first: Theresa

address: Ferdinand-Sauerbruch Straße DZ7 5.05

institute: Univserity Medicine Greifswald

tag: cell line

tag: transfected with


title: MaMel-02_control_miRNA_rep2

value: control


title: MaMel-02_control_miRNA_rep3


title: MaMel-02_control_miRNA_rep1


title: Nuli-1_t10_assay3

source_name: 10 min infected- P. aeruginosa PAO1 (DSM22644) adhered to Nuli-1 cell line (ATCC® CRL-4011™), with Pseudomonas LUZ19 phage

value: 10 min with phage


title: CIN rep4


title: MDA-MB-231_mock_rep3

treatment_protocol: MDA-MB-231 cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format.

value: mock


title: CIN rep3


title: Nuli-1_t10_assay2


title: Mouse cortical neurons, erinacine S, 16 hrs, rep3

tag: strain

value: 16 hrs


title: Mouse cortical neurons, DMSO, 48 hrs, rep1

tag: treatment


title: Mouse cortical neurons, erinacine S, 16 hrs, rep2


title: CIN rep2


title: MDA-MB-231_mock_rep2


title: CIN rep1


title: Nuli-1_t10_assay1


title: Mouse cortical neurons, erinacine S, 16 hrs, rep1


title: Nuli-1_t5_assay3

source_name: 5 min infected- P. aeruginosa PAO1 (DSM22644) adhered to Nuli-1 cell line (ATCC® CRL-4011™), with Pseudomonas LUZ19 phage

value: 5 min with phage


title: MDA-MB-231_mock_rep1


title: Nuli-1_t5_assay1


title: BOVIODH2

city: Poznan

first: Piotr

last: Pawlak

address: Wolynska 33

department: Department of Genetics And Animal Breeding

country: Poland

institute: Poznan University of Life Sciences

data_processing:
Adapters from raw reads were trimmed with cutadapt (v1.18). Trimmed reads were mapped to cow Ensemble genome (ARS-UCD1.2) with STAR (v2.7.9a). All reads mapped to exons were counted using featureCounts (v2.0.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: txt file with raw counts

organism: Bos taurus

source_name: blastocyst stage embryo

extract_protocol:
Smarter Ultra Low Input RNA v4 Clontech
Illumina Nextera XT according to Manufacturer

value: blastocyst stage embryo

value: IO+DHEA


title: Nuli-1_t5_assay2


title: MDA-MB-231_miR-6514-5p_rep3

city: Greifswald

last: Kordaß


title: BOVIODH1


title: Mouse cortical neurons, DMSO, 16 hrs, rep2


title: MDA-MB-231_miR-6514-5p_rep1


title: MDA-MB-231_miR-6514-5p_rep2


title: Nuli-1_t0_assay3

source_name: P. aeruginosa PAO1 (DSM22644) adhered to Nuli-1 cell line (ATCC® CRL-4011™)

value: untreated

value: phage wasn't added


title: MDA-MB-231_miR-6859-3p_rep3


title: MDA-MB-231_miR-3126-5p_rep3


title: MDA-MB-231_miR-6859-3p_rep2


title: MDA-MB-231_miR-6859-3p_rep1


title: BOVETO3

value: Etomoxir


title: BOVETO2


title: MDA-MB-231_miR-3126-5p_rep1


title: Mouse cortical neurons, DMSO, 16 hrs, rep1

value: brain

value: primary cortical neuron


title: Nuli-1_t0_assay1

value: human airway epithelium of normal genotype


title: ABI5_5X180_rep2 (small RNA-Seq)

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

description:
TAIR10_pseudo_2x180.reference.fa
TAIR10_pseudo_5x180.reference.fa

data_processing:
The small RNA sequencing data were trimmed using Trimmomatic (v.0.39) and then mapped to the pseudo-genome sequence with insertion of 2x180 or 5x180 in TAIR10 and called small RNA using ShortStack version 3.8.5 with parameter setting "--mincov 1rpm --pad 75 --mismatches 0 --nohp".
Assembly: pseudo-genome sequence with insertion of 2x180 or 5x180 in TAIR10
Supplementary files format and content: bw

organism: Arabidopsis thaliana

source_name: Seedling, long day condition (16h light and 8h dark), 1-week old

growth_protocol: Plants were grown on 1/2 X MS agar (0.8%) + 1% sucrose

extract_protocol:
Total RNA extraction was performed by using TRIzol reagent (Invitrogen, #15596026)
The small RNA sequencing libraries were prepared with Real Seq Bioscience RealSeqR-AC Kit (500-00012) following the related protocol
Small RNA-Seq

value: whole seedling

value: 5xCEN180 repeats knocked-in at ABI5 intron1 in Columbia-0 background

tag: fraction

value: small RNA


title: Nuli-1_t0_assay2


title: Mettl14 cKO, m6A IP

city: Stanford

first: Yue

last: Sun

state: CA

address: 290 Jane Stanford Way

institute: Stanford University

data_processing:
Remove sequencing adaptor, low quality bases and filter out low quality bases using Cutadapt and Fastp.
Aligning reads to Mus musculus genome (Version: v96) using Bowtie2.
Peak calling using exomePeak and annotated with ChIPseeker for IP samples.
M6A-enriched motifs were identified using MEME and HOMER.
RNA expression levels for input samples were calculated using StringTie. Differential expression analysis was performed between control and Mettl14-cKO input samples with edgeR.
Assembly: Ensembl release 96, Mus musculus
Supplementary files format and content: bigWig (except for Input sample)

source_name: retina

extract_protocol:
Total RNAs of control and Mettl14-cKO retinas were extracted using Trizol following the manufacturer's procedure. mRNAs were isolated from ~50 ug of total RNA with poly-T oligo coated magnetic beads (Invitrogen) and fragmented into ~ 100 nt using divalent cations under elevated temperature. M6A-enriched mRNAs were immunoprecipitated by incubate with anti m6A antibody (No.202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) with 0.5 μg/μl BSA at 4 °C for 2 h, followed by incubate with protein-A beads. M6A-enriched mRNAs were eluted with free m6A (6.7mM m6A in IP buffer) and precipitated with 75% ethanol. Both IP and input RNAs are subjected to cDNA library preparations and sequencing.
strand-specific m6A-seq libraries were prepared by dUTP method. Post amplification libraries were size selected at ~100±50 bp.

value: retina

value: Mettl14 fl/fl;Chx10-Egfp/Cre

tag: rna-ip antibody

value: m6A antibody (Synaptic Systems, #202003)


title: Mettl14 cKO, input


title: BOVKONW2

value: Control


title: ABI5_5X180_rep1 (small RNA-Seq)


title: Mettl14 WT, input

value: Mettl14 fl/fl or fl/wt


title: BOVCONW1


title: Mouse cortical neurons, DMSO, 16 hrs, rep3

value: DMSO solvent control treatment

value: 16 hrs


title: Mettl14 WT, m6A IP


title: ABI5_2X180_with_Donor_DNA_rep2 (small RNA-Seq)

value: 2xCEN180 repeats knocked-in at ABI5 intron1 with donor DNA and pEC-Cas9 transgene background


title: BOVETO1

value: blastocyst stage embryo


title: ABI5_2X180_with_Donor_DNA_rep1 (small RNA-Seq)


title: MDCK cells, p27, Day5, biol rep 3

city: Chicago

first: John

last: Devany

state: IL

address: 929 E 57th St

department: Physics

institute: The University of Chicago

data_processing:
Kallisto v0.46.1
Assembly: CanFam 3.1
Supplementary files format and content: .xls files with number of reads and TPM for each sample

organism: Canis lupus familiaris

source_name: MDCK

growth_protocol: MDCK cells obtained from the lab of James Nelson were grown in DMEM with 10% FBS, 4mM glutamine, and 200ng/ul Doxycycline

extract_protocol:
Macherey-Nagel NucleoSpin RNA was used according to the manufacturer protocol
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using an TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (illumine provided reagents and protocols)

treatment_protocol: Seeded 4x10^5 cells on a 22x22mm coverslip coated with a collagen gel. Replaced medium daily for 5 days.

value: MDCK

value: epithelial cells

value: mEmerald-p27 1-176


title: MDCK cells, p27ck, Day5, biol rep 3

value: snaptag-p27ck 1-176


title: MDCK cells, p27, Day5, biol rep 2


title: ABI5_2X180_rep2 (small RNA-Seq)

value: 2xCEN180 repeats knocked-in at ABI5 intron1 in Columbia-0 background


title: Single-truBKO_rep2

first: Christopher

middle: Daniel

last: Katanski

institute: University of Chicago

data_processing:
Next, read2 was used to map with bowtie2 (version 2.3.3.1) with the following parameters: “-q -p 10 -local -no-unal”. Reference genome was a curated fasta of mature E. coli tRNAs with CCA added from gtRNADB.
Bowtie2 output sam files were further processed with custom python script to count the number of reads mapping to each template - script availibe here: https://github.com/ckatanski/Ecoli_trmA_truB.
Bowtie2 output sam files were also converted to bam files, then sorted using samtools. Next IGV was used to collapse reads into 1 nt window. IGV output .wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/MSRR-seq). The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools ( https://github.com/pysam-developers/pysam) to sum all reads that mapped to each gene. Data was visualized with custom R scripts (available on GitHub at ttps://github.com/ckatanski/Ecoli_trmA_truB)
Assembly: E. coli K12 substrain MG1655 tRNA reference genome: http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/bacteria/Esch_coli_K_12_MG1655_3/
Supplementary files format and content: tsv tab separated value - "trace" data indicated pileup, mutation rate, and indel rates at every position along each tRNA in the reference genome
Supplementary files format and content: tsv tab separated value - "count" data indicate the number of reads mapped to each sequence in the tRNA reference genome
Library strategy: MSR-seq

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: E. coli cultures were grown from single colonies overnight in LB media containing 50 µg/mL kanamycin (ΔtrmA, ΔtruB, and ΔtrmAΔtruB strains) or lacking antibiotic (wildtype). Saturated cultures were centrifuged, resuspended in fresh LB media containing 2% (w/v) sodium formate, and cultures were prepared in LB media containing 2% (w/v) sodium formate at an OD600 of ~0.1. Cultures were grown at 37°C until reaching an OD600 between 0.3 and 0.4, when 15 mL of each culture was harvested by centrifugation, shock frozen, and stored at -80°C until RNA extraction.

extract_protocol:
Total RNA was extracted from cell pellets using TRIzol (Invitrogen) using the manufacturer’s instructions. In brief, cell pellets were resuspended in 3 mL TRIzol, followed addition of 0.6 mL chloroform. Following centrifugation, the aqueous layer was transferred to a new tube and precipitated with isopropanol. The resulting RNA was washed several times with 70% ethanol and resuspended in water.
Total RNA was used to sequence tRNA with MSR-seq as described previously (PMID: 35513407). Briefly,  RNA samples treated to beta elimination to assay for tRNA charging, then RNA was ligated to barcoded adaptors. Then reverse transcription was performed with SSIV overnight. cDNA was ligated to another adaptor followed by indexing PCR and illumina sequencing
PMID: 35513407

value: Escherichia coli

value: deltatruB


title: ABI5_2X180_rep1 (small RNA-Seq)

value: whole seedling

value: small RNA


title: Single-trmAKO_rep3

value: deltatrmA


title: Single-truBKO_rep3


title: Single-truBKO_rep1


title: ABI5_2X180nrpd1a_rep2 (small RNA-Seq)

value: nrpd1a-3 T-DNA knock-out mutant in ABI5 with 2xCEN180 knock-in background


title: MDCK cells, p27, Day5, biol rep 1


title: MDCK cells, p27ck, Day5, biol rep 2


title: ABI5_2X180nrpd1a_rep1 (small RNA-Seq)


title: Single-trmAKO_rep2


title: MDCK cells, p27ck, Day5, biol rep 1


title: MDA-MB-231_miR-4672_rep2


title: MDA-MB-231_miR-3126-5p_rep2


title: MDA-MB-231_miR-34b-3p_rep2


title: MDA-MB-231_miR-4672_rep3


title: MDA-MB-231_miR-34b-3p_rep3


title: Single-trmAKO_rep1


title: ABI5_2X180ibm1_rep2 (small RNA-Seq)

value: ibm1-5  T-DNA knock-out mutant in ABI5 with 2xCEN180 knock-in background


title: MDA-MB-231_miR-4672_rep1


title: Whole blood, CPP-Se group, 30 Days, biol rep 3

city: Chongqing

first: Wang

middle: Wen

last: Can

address: No. 18, Food City Avenue

institute: Chongqing Sweet Pet Products Co., Ltd

data_processing:
Illumina Casava software (version: 2.19 ) used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software (version: 0.19.7, parameter: fastp -g -q 5 -u 50 -n 15 -l 150)
Trimmed sequence reads were mapped to the reference genome  using hisat2  software (version:2.0.5, parameter: hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>] ).
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript  sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: ROS_Cfam_1.0
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Whole blood

extract_protocol:
RNA was harvested using trizol reagent (Ambion). 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®  following manufacturer's protocols.

value: Whole blood

value: fed with CPP-Se

value: Day 30


title: Whole blood, CPP-Se group, 30 Days, biol rep 2


title: ABI5_2X180ibm1_rep1 (small RNA-Seq)


title: MDA-MB-231_miR-34b-3p_rep1


title: Single-WT_rep3

value: wildtype


title: Single-WT_rep2


title: Single-WT_rep1


title: Whole blood, CPP-Se group, 30 Days, biol rep 1


title: BCG_WT_SCV2_D7, replicate 3

city: Baltimore

first: Rulin

state: Maryland

address: 1650 Orleans Street

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
Cell Ranger v4.0.0 was used to demultiplex the FASTQ reads and align them to the Mesocricetus auratus gemone.
Assembly: BCM_Maur_2.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mesocricetus auratus

source_name: lung, BCG vaccinated, SARS-CoV-2 infection

extract_protocol:
Whole right lung superior lobe was isolated from each animal, mouse lung dissociation kit (Miltenyi Biotec) was used with some additional modifications. Following single cell preparation, cell suspensions were applied to a MACS Smart Strainer (70 μm) and washed twice with 10 ml of DMEM. Cells were pelleted by spinning at 300 × g for a total of 7 minutes at 4°C. Cells were resuspended in 1ml DMEM containing 200 μl DNase (1μg/μl) for 5 minutes at room temperature. Cells were washed by adding 10 ml sterile PBS containing 0.5% BSA and pelleted at 4°C. The RBC lysis was carried out using 1X RBC lysis solution (Miltenyi Biotec; 130-094-183) in a total volume of 1ml for 10 minutes at 4°C. Cells were resuspended in 10 ml chilled DPBS containing 0.5% BSA and pelleted subsequently. Cells were filtered using 35 μm Falcon cell strainer and transferred to a 2 ml lo-binding tube in a total volume of 1ml DPBS containing 0.04% BSA.
Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index) (CG000315).

value: lung

value: tissue dissociated cells

value: BCG vaccinated

tag: infection

value: SARS-CoV-2 infection

value: D7 post-challenge


title: BCG_WT_SCV2_D7, replicate 2

description: 10x Genomics


title: Whole blood, Control group, 30 Days, biol rep 3

value: fed without CPP-Se


title: BCG_WT_SCV2_D7, replicate 1

description: 10x Genomics


title: Whole blood, Control group, 30 Days, biol rep 2


title: Whole blood, Control group, 30 Days, biol rep 1


title: SCV2_D7, replicate 2

description: 10x Genomics

source_name: lung, Unvaccinated, SARS-CoV-2 infection

value: Unvaccinated


title: Double-trmAtruBKO_rep2

value: Escherichia coli

value: deltatrmAdeltatruB


title: Double-trmAtruBKO_rep1


title: SCV2_D7, replicate 1

description: 10x Genomics


title: Double-WT_rep3


title: Double-WT_rep2


title: BCG_WT_SCV2_D4, replicate 3

description: 10x Genomics

value: D4 post-challenge


title: Double-trmAtruBKO_rep3


title: BCG_WT_SCV2_D4, replicate 2

description: 10x Genomics


title: Double-WT_rep1


title: BCG_WT_SCV2_D4, replicate 1

description: 10x Genomics


title: Yeast W303, pab1 and pbp1 deletions, replicate 3

city: Worcester

first: Kotchaphorn

last: Mangkalaphiban

state: MA

address: 368 Plantation St.

institute: University of Massachusetts Medical School

description:
pab1d_pbp1d_rep3
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv

library_source: other

data_processing:
library strategy: ribosome profiling/Ribo-Seq
NEXTFLEX adapters were trimmed from reads using cutadapt v1.9; reads < 23 bp (15 bp RPF + 4 bp 5'UMI + 4 bp 3' UMI) were discarded.
Reads (excluding the UMIs) that were mapped to non-protein coding sequences were discarded.
PCR duplicates were identified by the combination of 4 bp UMIs on the ends of the reads and removed using UMI-tools software (Smith et al., 2017) with default algorithm ("directional").
De-deuplicated reads were aligned to the transcriptome (https://github.com/Jacobson-Lab/yeast_transcriptome_v5) and transcript abundance quantified using RSEM v1.3.0 and bowtie v 1.0.0 (paramters: strandedness forward, 15 nt seed length, reads with more than 2 mismatches in the seed region and/or mapped to more than 10 places are discarded)
Assembly: R64-2-1
Supplementary files format and content: Wig files, generated by RSEM, contained coverage data.
Supplementary files format and content: Comma-delimited files contain either RPKM values or read count either at a gene or isoform level for all samples.

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in 1 L of YEPD at 30C with shaking.

extract_protocol:
Whole cell lysates were treated with RNaseI (Invitrogen) and ultracentrifuged through a sucrose cusion to isolate 80S ribosomes. Ribosome-protected mRNA fragments (RPFs) were isloated from 80S ribosomes using miRNeasy kit (QIAGEN), size selected for RNAs < 200 nt, and 3'-dephosphorylated/5'phosphorylated by T4 polynucleotide kinase (NEB).
Sequencing libraries were prepared using NEXTFLEX Small RNA-Seq Kit v3 (Perkin Elmer), skipping the first denaturation step and replacing it with hybridization of oligos from the QIAseq FastSelect - rRNA Yeast kit (QIAGEN).

value: pab1 and pbp1 deletions


title: MDA-MB-231_miR-224-3p_rep1

state: Mecklenburg-Vorpommern


title: MDA-MB-231_miR-224-3p_rep3


title: SCV2_D4, replicate 2

description: 10x Genomics


title: MDA-MB-231_miR-134-3p_rep2


title: MDA-MB-231_miR-134-3p_rep3


title: MDA-MB-231_miR-224-3p_rep2


title: MDA-MB-231_control_miRNA_rep3

value: control


title: Yeast W303, pbp1 deletion, replicate 3

description:
PAB1_pbp1d_rep3
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv

value: pbp1 deletion


title: S9 - TBHQ WT

city: Amherst

first: Alicia

middle: R

last: Timme-Laragy

address: 637 N PLEASANT ST

department: Environmental Health Sciences

institute: University of Massachusetts-Amherst

data_processing:
Raw fastq sequencing files were uploaded to the Galaxy web public server, and the following tool were applied to analyze the data: “Concatenate datasets tail-to-head” tool, “fastp” tool for preprocessing, read alignment with the “HISAT2” tool to zebrafish genome GRCz11, “Infer Experiment” and the “Convert GTF to BED12” tools for correct strand alignment,  “MultiQC” tool for mapping statistics, “StringTie” tool to create gene counts, “DESeq2” for differential gene expression analyses, “Filter” tool to view the results for protein coding genes, and other visualization tools prepare and interpret data.
Assembly: GRCz11
Supplementary files format and content: txt file (tab delimited) with DESeq2 normalized counts of each sample listed by Ensembl ID and GeneSymbol

organism: Danio rerio

source_name: whole fish

growth_protocol: Adult Nrf2a wildtype (nrf2a+/+) and mutant (nrf2afh318/fh318) zebrafish were housed on a 14 h:10 h light:dark cycle in a recirculating Aquaneering system maintained at 28.5°C and fed twice daily with GEMMA Micro 300. Embryos were collected from breeding tanks with a 2:1 female:male ratio. Embryos were collected within 3 h post-breeding, washed, and stored in 0.3 x Danieu’s solution in an incubator with the same light and temperature conditions as the adult fish.

extract_protocol:
Zebrafish were anesthetized in an ice water bath, decapitated, and the bodies were sectioned into four pieces before being transferred to into FastPrep homogenization tubes containing 500 µL TRIzol Reagent (Invitrogen, Carlsbad, California). The contents were sonicated for 3-4 seconds 3 times, before adding additional 250 µL TRIzol. Again, the contents were sonicated for 3-4 seconds 3 times, and 250 µL TRIzol was added (total TRIzol was 1 mL). The contents were then sonicated 3-4 seconds 3-5 times, depending on if the contents were completely sonicated. RNA was isolated using TRIzol Reagent and RNA Clean & Concentrator kit with in-column DNase-I treatment (Zymo Research, Irvine, CA) and stored at -80°C till further processing.
Total RNA was used to isolate poly(A) mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module, and libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). The quantity of library was assayed using Qubit DNA HS assay (Life Technologies, Carlsbad, CA), and quality was analyzed on Bioanalyzer (Agilent Technologies Inc, Santa Clara, CA).

treatment_protocol: At 3 days post fertilization (dpf), zebrafish were screened for normal development. At 5 dpf, the larvae were separated into eight groups (n=15) and transferred into 3 L tanks and housed in the same light and temperature conditions as the adult fish. At this timepoint, control EtOH and 5% tBHQ feed was prepared; 97% tert-Butylhydroquinone (tBHQ; Acros Organic, Catalog #AC150820050 and Sigma-Aldrich, Sigma #380202) was dissolved in 96% ethanol (EtOH), then atomized onto a single layer of GEMMA Micro 75 zebrafish (Skretting, Westbrook, ME) and dried. For both Nrf2a wildtype and mutant larvae, four tanks were assigned to the 5% tBHQ feed and the other four tanks were assigned to the control feed and were fed until collection at at roughly 7 months post-fertilization.

value: whole fish

tag: age

value: 7 months post-fertilization

tag: Sex

value: male

value: Nrf2a wr

value: 5% tBHQ diet


title: SCV2_D4, replicate 1

description: 10x Genomics

value: lung

value: tissue dissociated cells


title: S12 - ETOH WT

value: EtOH control diet


title: S8 -TBHQ WT


title: S11 - ETOH WT

value: female


title: S10 - ETOH WT


title: S7 - TBHQ WT


title: MDA-MB-231_miR-134-3p_rep1

department: Surgical Research Laboratory


title: CTL_CTL_Low

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 bd Laurier

country: Canada

institute: Université Laval

hyb_protocol: Affymetrix Pico protocol

scan_protocol: Affymetrix Pico protocol

data_processing: Bioconductor pipeline (oligo, affycoretools, pd.clariom.s.human packages)

label: Direct-zol RNA kit

source_name: untreated dental plaque cells

label_protocol: Affymetrix Pico protocol

growth_protocol: Immortalized HGF-1 were cultivated in DMEM supplemented with 10% heat-inactivated (HI)-FBS, 4 mM L-glutamine and 100 ug/ml penicillin/streptomycin + 0.25 ug/ml amphotericin B at 37C in 5% CO2. Human U937 monocytes (ATCC CRL1593.2) were cultivated in RPMI medium supplemented with 10% HI-FBS and 100 ug/ml penicillin/streptomycin + 0.25 ug/ml amphotericin B at 37C in 5% CO2. Two weeks prior the experiments, the cells were maintained in their culture media containing either 5 mM or 25 mM glucose. The coculture model was composed of immortalized HGF-1 overlaid with U937-macrophages-like cells. An arbitrary ratio of 10:1 macrophages to fibroblasts was used. U937 monocytes were differentiated into macrophages-like cells in presence of 50 ng/ml of phorbol 12-myristate 13-acetate (PMA) for 72h. Macrophages-like cells were then washed to remove non-adherence cells, harvested by scraping, suspended in their culture medium and placed over the immortalized HGF-1. The coculture model was incubated overnight at 37C in 5% CO2 to allow macrophages adhesion prior to stimulation

extract_protocol: The cells were washed with ice-cold PBS and the RNA extracted from the coculture models using the Direct-zol RNA extraction kit from Zymo Research

treatment_protocol: The subgingival microbiomes samples were used to stimulate the gingival coculture model cultivated either in 5 mM or 25 mM glucose concentration for 24h. Untreated coculture models served as negative controls.

tag: glucose

value: Low

tag: group

value: Control


title: MDA-MB-231_control_miRNA_rep1

source_name: cell line


title: MDA-MB-231_control_miRNA_rep2


title: BCG_WT, replicate 3

description: 10x Genomics

source_name: lung, BCG vaccinated, without SARS-CoV-2 infection

value: BCG vaccinated

value: without SARS-CoV-2 infection

tag: time

value: D30 post-vaccination


title: BCG_WT, replicate 2

description: 10x Genomics

tag: tissue


title: S6 - TBHQ M

value: Nrf2a m/m


title: S5 - TBHQ M


title: Bio10_Perio_Low

source_name: Patient with periodontitis, gingival fibroblasts and macrophages, co-cultured with 5 mM glucose

value: Periodontitis


title: S4 - TBHQ M


title: Bio10_Perio_High

source_name: Patient with periodontitis, gingival fibroblasts and macrophages, co-cultured with 25 mM glucose .

value: High


title: Yeast W303 WT, replicate 3

description:
PAB1_PBP1_rep3
pab1_strains_RPF_RSEM_FPKM_genes.results.csv
pab1_strains_RPF_RSEM_FPKM_isoforms.results.csv
pab1_strains_RPF_RSEM_expected_count_genes.results.csv
pab1_strains_RPF_RSEM_expected_count_isoforms.results.csv

value: WT


title: S2 - ETOH M

value: whole fish

value: 7 months post-fertilization


title: S3 - ETOH M

value: male


title: S1 - ETOH M


title: CTL_CTL_High


title: Bio9_Healthy_Low

source_name: Healthy patient, gingival fibroblasts and macrophages, co-cultured with 5 mM glucose

value: Healthy


title: Bio9_Healthy_High

source_name: Healthy patient, gingival fibroblasts and macrophages, co-cultured with 25 ML glucose


title: vaccinated+SVCV, scRNAseq

city: Hangzhou

first: Chongbin

last: Hu

state: Zhejiang Province

address: 866 Yuhangtang Rd

department: College of Life Sciences

institute: Zhejiang University

description: 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: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Leukocytes were collected from the spleen samples through Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation as previously described.[58a, 62] Briefly, zebrafish were anesthetized by MS222 after 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh (Greiner Bio-OneGmbH, Germany). The cell suspension was suspended in Leibovitz's L-15 Medium (L-15, Gibco) supplemented with penicillin (100 U/ml, Sigma-Aldrich), streptomycin (100 μg/ml, Sigma-Aldrich) and heparin sodium (10 U/ml, Sigma-Aldrich). The cell suspension was slowly added into a Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation, centrifuged at 1,200 g for 25 min, and the cell layer of the interface was carefully aspirated and then washed with ice-cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue (Sigma, St. Louis, MO, USA), which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: leukocyte

value: Spleen

value: AB

value: 5-7 weeks old


title: Bio6_Perio_Low

value: Low


title: Kdm6a-KO1

city: Shanghai

first: Xu

last: Wang

address: No. 639, Zhizaoju Road

institute: Shanghai Jiao Tong university, School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BMDM

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kdm6a KO

value: LPS

value: macrophage


title: Kdm6a-KO2


title: Kdm6a-KO3


title: Bio8_Healthy_High

source_name: Healthy patient, gingival fibroblasts and macrophages, co-cultured with 25 mM glucose


title: Bio6_Perio_High


title: BCG_WT, replicate 1

description: 10x Genomics

value: lung

value: tissue dissociated cells

value: BCG vaccinated

value: without SARS-CoV-2 infection

value: D30 post-vaccination


title: Kdm6a-WT3

value: Kdm6a WT


title: PBS, scRNAseq

description: 10x Genomics


title: Kdm6a-WT1


title: Bio8_Healthy_Low


title: C5ar1 KO neutrophils_D2 pi_Mouse 4

status: Public on May 30 2023

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

state: MD

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

data_processing:
Gene-level counts were filtered to remove low-expression genes (keeping genes with >15 counts in at least one sample). Differential gene expression was evaluated using limma (DOI: 10.1093/nar/gkv007). Differentially expressed genes were defined as genes with a fold change of at least ±2 in either direction at false discovery rate (FDR) less than 0.01. Pathway enrichment analysis for differentially expressed genes of C5ar1–/– versus C5ar1+/+ phagocytes was performed using GSEA.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed reads displayed as log2(RPKM) values.

source_name: C5ar1 KO neutrophils

extract_protocol: RNA was isolated from the sorted cells using the Trizol reagent (Thermo Fisher) and further processed using a clean-up and concentration micro-elute kit (RNA Clean-Up and Concentration Micro-Elute kit, Norgen Cat# 61000), as per manufacturer's instructions. cDNA was amplified using the SMART-Seq v4 UltraLow Input RNA kit (Takara Bio, San Jose, CA) and sequencing libraries were prepared using the Nextera XT (Illumina, San Diego, CA). Multiplexed libraries were sequenced on a HiSeq3000 instrument (Illumina, San Diego, CA) in 50-bp single-end mode and mapped using STAR (v2.5.2).

treatment_protocol: Single cell suspensions were prepared from WT and C5ar1–/– kidneys of mice infected with C. albicans at day 2 post-infection. Macrophages and neutrophils were stained using sterile anti-mouse antibodies against CD45 (clone 30-F11, Biolegend), Ly6G (clone 1A8, Biolegend), CD11b (clone M1/70, Biolegend), MHCII (clone M5/114.15.2, Thermo Fisher), F4/80 (clone BM8, Biolegend), CD3 (clone 145-2C11, Biolegend), CD19 (clone 1D3, Biolegend), and NKp46 (clone 29A1.4, Biolegend). Macrophages were defined as CD45+ CD3/CD19/NKp46/Ly6G- MHCIIhi F4/80+ CD11b+ , while and neutrophils were defined as CD45+ Ly6G+ CD11b+  and were FACS-sorted with purity of >90% into RPMI supplemented with 10% FBS and penicillin/streptomycin. The sorted cells were centrifuged at 300 xg for 5 minutes at 4 °C, resuspended in Trizol (QIAGEN, Germantown, MD) and and stored at -80 °C until further use.

tag: genotype/variation

value: neutrophils


title: C5-DNCB

first: Qinyu

last: Tang

address: 389 Xincun Road, Putuo District, Shanghai, China

institute: Tongji University

description: Gene expression of dorsal skin in BALB/c mice with atopic dermatitis

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min.

scan_protocol: The slides were scanned on an Agilent G2505C microarray scanner using one color scan.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The raw intensities were log2 transformed and quantile normalized. After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained. Multiple probes from the same small RNA (miRNA/tsRNA/pre-miRNA/tRNA/ snoRNA) were averaged and consolidated into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by filtering at the indicated fold change (FC) and statistical significance (p-value) thresholds. Hierarchical clustering, scatter plots, and volcano plots were generated by R software.

source_name: dorsal skin

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

extract_protocol: If included in the service, total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis. Please see “RNA_QC&Labeling_QC.pdf” for the sample QC results.

value: skin

value: female

value: DNCB


title: C5ar1 KO neutrophils_D2 pi_Mouse 3


title: Bio5_Perio_Low

value: Periodontitis


title: A6-normal

description: Gene expression of dorsal skin in control BALB/c mice

value: control


title: C6-DNCB


title: C3-DNCB


title: C5ar1 KO neutrophils_D2 pi_Mouse 2


title: Bio3_Perio_High

value: High


title: SVCV, scRNAseq

description: 10x Genomics

value: leukocyte

value: Spleen

value: AB

value: 5-7 weeks old


title: C5ar1 KO neutrophils_D2 pi_Mouse 1


title: A5-normal


title: C5ar1 WT neutrophils_D2 pi_Mouse 3

source_name: C5ar1 WT neutrophils

value: wild type


title: Bio4_Healthy_High

value: Healthy


title: C5ar1 WT neutrophils_D2 pi_Mouse 4


title: C5ar1 KO macrophages_D2 pi_mouse 4

source_name: C5ar1 KO macrophages

value: macrophages


title: C5ar1 WT neutrophils_D2 pi_Mouse 1


title: C5ar1 WT neutrophils_D2 pi_Mouse 2


title: C5ar1 KO macrophages_D2 pi_mouse 3


title: Bio5_Perio_High


title: C5ar1 KO macrophages_D2 pi_mouse 2


title: C5ar1 KO macrophages_D2 pi_mouse 1


title: Bio7_Healthy_High


title: C5ar1 WT macrophages_D2 pi_mouse 3

source_name: C5ar1 WT macrophages


title: C5ar1 WT macrophages_D2 pi_mouse 4


title: C5ar1 WT macrophages_D2 pi_mouse 1


title: A3-normal


title: MDA-MB-468_INPUT

city: Cleveland

first: Ruth

last: Keri

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

description: Total DnA input

data_processing:
fastq files were aligned to version hg19 for both the RNA-Seq and the ChIP-Seq.
For RNA-Seq, Differential expression was determined using the DESeq2 R package, where differentially expressed genes were deemed significantly changed if the Benjamini-Hochberg adjusted p-value was <0.05.
For ChIP-Seq, quality filter with FastQ. Reads were aligned to hg19 using Bowtie2. Data was sorted, indexed and filtered with Samtools-1.3.1. Peaks were called with MACS2. Rank ordering of super-enhancers (ROSE) was used to rank enhancers in hg19 with a stitch size of 12.5 kb. MACS2 was then used to make bedgraphs that were converted to wig files.
Genome_build: hg19

source_name: epithelial breast cancer cell line; derived from metasatic pleural effusion

growth_protocol: MDA-MB-231 and MDA-MB-468 cells were cultured in RPMI-1640 supplmented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody. Libraries were prepared using the ThruPlex DNA-seq kit from Rubicon Genomics using 20ng of ChIP DNA. Two unique tags were used. Two final pools were made. Each library was QC'ed using Qbit HS dsDNA kit for concentration and Agilent Bioanalyzer DNA HS chip for quality and fragment size. DNA was pooled based on qubit concentration, and qPCR was performed using Kappa Biosystems Illumina LIbrary Quant kit on the pool for nM concentration. DNA was then loaded onto an Illumina HiSeq 2500 50bp rapid run v2 flowcell.

treatment_protocol: Cells were treated with either vehicle or THZ1 for 48hrs for the RNA-Seq. Cells were not treated for the ChIP-Seq

value: epithelial breast cancer cell line

value: no treatment


title: MDA-MB-468_2_H3K27Ac_ChIP

description: DNA immunoprecipitated with antibodies against H3K27Ac


title: MDA-MB-468_1_H3K27Ac_ChIP


title: Bio3_Perio_Low

value: Low


title: Bio7_Healthy_Low