title: Hek293T,NSP14,Questin,Day 3

city: Hangzhou

first: Wei

last: Xie

address: No. 866 Yuhangtang Road, West Lake District

institute: Zhejiang University

description: Library name: NSP14-2

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost: 3 deletion cost: 3 length faction: 0.8 similarity faction: 0.8)
Read count extraction and normalization were performed usingCLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: treatment

growth_protocol: Hek293t cells were maintained in DMEM suppiemented with 10% fetal bovine serum (FBS) and antibiodics in humidied atmosphere with 5% CO2 at 37℃.

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

treatment_protocol: The recombinant pLVX-EF1α-HA-NSP14-IRES-EGFP-Puro plasmid was transiently transfected into HEK293T mammalian cells when the cell density reached 60%.

value: embryonic kidney

value: Epithelial-like cell

value: WT

value: TRANSFECTION


title: Hek293T,NSP14,DMSO,Day 2

status: Public on Dec 31 2024

type: SRA

country: China

description: Library name: NSP-DMSO-1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: GSC923 cells, Control, 24 hours, Biological replicate 3

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

country: USA

institute: National Cancer Institute

data_processing:
The samples have 51 to 67 million pass filter reads with more than 96% of bases above the quality score of Q30
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR
the gene expression quantification analysis was performed for all samples using STAR/RSEM tools
Assembly: Human hg38
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and passed the quality control of the Agilent RNA ScreenTape syste
TruSeq Stranded mRNA Kit

value: IDH WT

value: Control


title: Hek293T,NSP14,Day 3

description: Library name: mx-1-10uM-2


title: Hek293T,NSP14,Questin,Day 2

description: Library name: NSP14-1


title: Hek293T,NSP14,Day 2

description: Library name: mx-1-10uM-1


title: Hek293T,EGFP,Day 3

description: Library name: EGFP-2

source_name: control


title: GSC923 cells, Control, 24 hours, Biological replicate 2


title: Hek293T,EGFP,Day 2

description: Library name: EGFP-1


title: GSC923 cells, Control, 24 hours, Biological replicate 1


title: MB7433 strain (DHB4 ΔdegP + pAL-FevREco105-CYTO-FLAG) treated at 42°C, replicate 3

city: Ipswich

first: Augusto

middle: Emanuel

last: Garcia

state: MA

address: 240 County Rd

department: Research

institute: New England Biolabs

data_processing:
To remove reads mapping to rRNA, the reads were first aligned to a custom .fasta file containing the DNA sequences coding for rRNA in the complete genome reference of Escherichia coli K-12 strain DHB4 (GenBank accession CP014270.1) using Bowtie2 version 2.3.4.1 set for paired-end reads through Galaxy.
The remaining reads (unaligned reads from previous step) were aligned to Escherichia coli str. K-12 substr. MG1655 complete genome reference (NCBI Reference Sequence accession NC_000913.3) using Bowtie2 (version 2.3.4.1) set for paired-end reads, with >80% of the reads aligning concordantly exactly 1 time through Galaxy.
Aligned reads were summarized using featureCounts from the subread package (version 1.6.4) through Galaxy, using the “Unstranded” setting, to obtain a table of counts for each of the annotation features labelled as “gene” in the NC_000913.3.gff3 file downloaded directly from NCBI. Genes labelled with locus_tag were converted to gene names through the curated annotations in Ecocyc database using Ecocyc SmartTables tools.
The obtained tables of counts were imported into RStudio and analyzed using DESeq2 (version 1.28.1) Counts from replicates were compared using PCA plots. Based on the dissimilarities among replicates observed in these plots, one of the 30°C replicates was dropped for each of the MB7409, MB7410 and MB7434 strains.
For Differential Expression of Genes in DESeq2, the conditions compared were the following:  At 30°C  MB7410 vs MB7409  MB7434 vs MB7409  MB7180 vs MB7050  MB7433 vs MB7050  At 42°C  MB7410 vs MB7409  MB7434 vs MB7409  MB7180 vs MB7050  MB7433 vs MB7050
Genome_build: NC_000913.3
Supplementary_files_format_and_content: The log2FoldChange and p-adj values for each gene for each comparison, obtained by differential expression analysis from DESeq2, were merged into a single matrix.

organism: Escherichia coli K-12

growth_protocol: Cells were grown overnight in 5ml LB media + 10µg cloramphenicol and diluted 1/100 into 15ml of the same media in a 25ml flask. These cultures were grown for 4 hours until they reached exponential phase before applying treatment (changing temperature)

extract_protocol:
1.5ml of each culture was harvested by centrifugation and total RNA was extracted using RNAeasy Mini Kit (Qiagen cat#74104) including the DNAse treatment step with RNase-Free DNase Set (Qiagen cat#79254) following the vendor guidelines. An extra DNase treatment step was added after extraction using DNase I (RNase-free, New England Biolabs cat#M0303S) and RNA was purified using Monarch® RNA Cleanup Kit (New England Biolabs cat#T2040L) eluting in 10µl. Concentration was measured using QubitTM dsDNA BR Assay Kits (Invitrogen cat#Q32850) on a Qubit 2.0 Fluorometer, and the RNA Integrity Number (RIN) was corroborated to be >9 using RNA 6000 Nano Kit (Agilent cat#5067-1511) on an Agilent 2100 Bioanalyzer System.
For samples MB7409, MB7410 and MB7434 treated at 30°C: library preparation, sequencing and analysis was performed by CD genomics. Firstly, the ribosomal RNA depletion was performed using NEBNext® rRNA Depletion Kit (Bacteria, New England Biolabs cat#E7860S). The rRNA-depleted RNA was purified by 2x RNAClean XP beads (Beckman Coulter) and eluted in 45ul of nuclease-free water. The purified RNA was then mixed with 4ul of NEBNext First Strand Synthesis Reaction Buffer and 1ul of random primers. The reaction was incubated at 94C for 12 mins for fragmentation. Subsequently, to perform first strand cDNA synthesis, 8ul of NEBNext Strand Specificity Reagent and 2ul of NEBNext First Strand Synthesis Enzyme Mix was added to the reaction and the reaction was incubated at 25C 10 mins, 42C 30 mins, 70C 15 mins. Second strand reaction was then performed by adding 8ul of NEBNext Second Strand Synthesis Reaction Buffer with dUTP Mix (10X), 4ul of NEBNext Second Strand Synthesis Enzyme Mix, and 48ul of nuclease-free water. The reaction was incubated at 16C 1hr. The cDNA was purified by 1.8x SPRIselect Beads (Beckman Coulter) and eluted in 50ul of nuclease-free water. The reaction was incubated at 16C 1hr. The cDNA was purified by 1.8x SPRIselect Beads (Beckman Coulter) and eluted in 50ul of nuclease-free water. Subsequently, end prep reaction was performed by adding 7ul of NEBNext Ultra II End Prep Reaction Buffer and 3ul of NEBNext Ultra II End Prep Enzyme Mix into 50 ul purified cDNA. Endprep reaction was incubated at 20C 30 mins and 65C 20 mins. Adaptor ligation reaction was then performed by adding 1ul of NEBNext Ligation Enhancer, 30ul of NEBNext Ultra II Ligation Master Mix, and 2.5ul of NEBNext Adaptor, diluted to 0.5uM in Adaptor Dilution Buffer. The mix was incubated at 20C 15 mins. 3ul of USER Enzymer (New England Biolabs) was then added to the ligation product and the reaction was incubated at 37C 15 mins. The ligated product was purified by SPRIselect Beads (Beckman Coulter) and eluted in 15ul of nuclease-free water. PCR was carried out by adding 25ul of NEBNext Ultra II Q5 Master Mix, 5ul of i5 Primer, and 5ul of i7 Primer into 15ul of purified ligated product. PCR was performed at 98C 30 seconds, 15 cycles of 98C 10 seconds and 65C 75 seconds, and a final extension at 65C 5 mins.  The final library was then purified by SPRIselect Beads and loaded into Illumina NovaSeq6000 paired end 150 bp mode for sequencing. For the rest of the samples: Ribosomal RNA was removed from the total RNA with NEBNext® rRNA Depletion Kit (Bacteria, New England Biolabs cat#E7860S). Libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs cat#E7760L) using oligos for indexing from NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, New England Biolabs cat#E6440S). Final library quality and concentration was estimated using High Sensitivity DNA Kit (Agilent cat#5067-4626) on an Agilent 2100 Bioanalyzer System and all the libraries were pooled at 4nM in 20uL and sequenced on the Illumina Nextseq 500 Mid Output 2x75+8i+8i  following the manufacturer's protocols.

treatment_protocol: After reaching exponential phase (first 4 hours of growth), cells were grown in the conditions specified for each sample (either 0.5h or 1h at at either 30°C or 42°C).

tag: strain

value: [delta]degP

tag: plasmid

tag: growth time and  temperature

value: 4h at 30°C

tag: treatment time and temperature

value: 1h at 42°C


title: MB7433 strain (DHB4 ΔdegP + pAL-FevREco105-CYTO-FLAG) treated at 42°C, replicate 2


title: NT2-1_TCR

city: Munich

first: Klaus

last: Dornmair

address: Grosshaderner Strasse 9

department: Institute of Clinical Neuroimmunology

country: Germany

institute: University Hospital LMU Munich

description: 10x Genomics

data_processing:
Raw data obtained from sequencing was pre-processed and aligned to the human reference genome GRCh38-2020-A using Cell Ranger (10 Genomics, v6.0.2).
Pre-processed data were then further processed and analysed in JupyterLab (v3.2.1) using an R kernel (R v4.1.3and the R package Seurat (v4.1.1). In summary, data from GEX and CSP (=ADT) libraries were combined for each sample and quality-filtered to remove low-quality cells, doublets, and dead cells. Cells were kept if the contained >500 and <20,000 RNA molecules, >200 and <2,500 genes, and ≤7.5% mitochondrial RNA. Read counts from GEX and CSP assays were normalized by sample using the NormalizeData-function with normalization-method set to “LogNormalize” and “CLR”, respectively. .
CD8+ and CD4+ T-cell subsets were identified based on normalized CSP (=ADT) barcode read count data. Cells that were at ≥1.5-fold enriched in CD8A compared to CD4 were assigned the cell type CD8+ T cells. Conversely, cells that were at least 1.5-fold depleted in CD8A compared to CD4 were assigned the cell type CD4+ T cells. The remaining cells were assigned to CD8+ T cells if their normalized CD8A RNA count in the RNA assay was ≥0.8 and CD4 expression was <0.2, and to CD4+ T cells if the opposite was the case. Cells that could not be assigned to CD4+ T cells or CD8+ T cells and cells that expressed no TCR chain were categorized as ambiguous
Assembly: GRCh38-2020-A
Supplementary files format and content: Cellranger output files: mRNA+ADT_matrix.mtx.gz,  mRNA+ADT_barcodes.tsv.gz,  mRNA+ADT_features.tsv.gz
Supplementary files format and content: Cellranger output files: TCR_filtered_contig_annotations.csv, TCR_clonotypes.csv

source_name: cerebrospinal fluid cells

extract_protocol:
Single cells from CSF were labelled with barcoded antibodies targeting CD4 or CD8A (cell surface protein (CSP) staining with antibody-derived tags (ADT)) using the TotalSeq-C with 10x Feature Barcoding Technology (Biolegend) as described in 10x Genomics protocol CG000149 (Rev B).
Single-cell gene expression (GEX), T-cell receptor (TCR), and cell surface protein (CSP = antibody-derived tags (ADT)) libraries were prepared using the 10x Genomics platform according to protocol CG000208 (Rev F). All antibody-labelled CSF cells from each sample were used as input. Nuclease-free water was added to the barcode antibody-labelled cells to a final volume of 37.8 µL and the protocol was carried out with minor alterations: TE buffer (Affymetrix #J75793) was used instead of elution buffer EB. ThermoScientific 2x Phusion MasterMix with HF (#F-531) was used instead of the Amplification Master Mix at step 4.1 and 4.3.
OTHER: scRNAseq, CITE-seq, TCRseq

value: cerebrospinal fluid cells

value: primary cells

value: untreated

tag: library type

value: TCR


title: NT1-14_TCR

description: 10x Genomics


title: NT1-13_TCR

description: 10x Genomics


title: NT2-1_GEX

description: 10x Genomics

value: mRNA, ADT

tag: adt

value: TotalSeq-C0072 anti-human CD4 Antibody, TotalSeq-C0046 anti-human CD8 Antibody


title: MB7433 strain (DHB4 ΔdegP + pAL-FevREco105-CYTO-FLAG) treated at 42°C, replicate 1


title: MB7180 strain (DHB4 ΔdegP + pAL-FevRCit-CYTO-FLAG) treated at 42°C, replicate 1

value: pAL-FevRCit-CYTO-FLAG


title: MB7050 strain (DHB4 ΔdegP + pAL-0) treated at 42°C, replicate 3

description:
MB7180-42-FevRcit.xlsx
MB7433-42-FevReco105.xlsx


title: MB7180 strain (DHB4 ΔdegP + pAL-FevRCit-CYTO-FLAG) treated at 42°C, replicate 2


title: NT1-3_TCR

description: 10x Genomics


title: NT1-3_GEX

description: 10x Genomics


title: MB7180 strain (DHB4 ΔdegP + pAL-FevRCit-CYTO-FLAG) treated at 42°C, replicate 3


title: NT1-13_GEX

description: 10x Genomics


title: MB7050 strain (DHB4 ΔdegP + pAL-0) treated at 42°C, replicate 2


title: MB7050 strain (DHB4 ΔdegP + pAL-0) treated at 42°C, replicate 1


title: MB7433 strain (DHB4 ΔdegP + pAL-FevREco105-CYTO-FLAG) treated at 30°C, replicate 3

value: 1h at 30°C


title: 226_TGcrush

city: Würzburg

first: Chi Wang

last: Ip

address: Josef-Schneider-Str. 11

department: Department of Neurology

institute: University Hospital Würzburg

data_processing:
Reads were first processed using cutadept (version 2.1)
The reference genome was expanded by incorporating the NCBI RefSeq Rattus norvegicus Genome Rnor_6.0 (https://www.ncbi.nlm.nih.gov/genome/?term=txid10116), along with the sequence for the mutated human TOR1A gene (OMIM: 605204.0001)
Subsequently, the reads were aligned to the processed sequences through STAR (version STAR_2.6.1a_08-27)
The quantification of reads was conducted using featureCounts from the Subread package (version 1.6.3)
Differential expression analysis was carried out employing DESeq2 (version 1.22.2)
Assembly: reference genome: NCBI RefSeq Rattus norvegicus Genome Rnor_6.0 (https://www.ncbi.nlm.nih.gov/genome/?term=txid10116)/ Sequence for the mutated human TOR1A gene (OMIM: 605204.0001)

organism: Rattus norvegicus

source_name: Striatum

growth_protocol: Rats were housed under standard conditions (21°C, 12-hour light/dark cycle) with free access to food and water

extract_protocol:
mRNA of snap-frozen tissue was isolated by using the RNeasy Micro Kit (Qiagen, Hilden, Germany)
Library preparation was performed by using the Illumina TruSeq stranded mRNA Sample Preparation Guide (Illumina, San Diego, CA, USA)
Single-end sequencing was performed with a read length of 75 nt in two runs of two times 14 libraries (28 samples)

treatment_protocol: A right-sided sciatic nerve crush injury for 30 seconds was performed

value: Striatum

tag: Sex

value: male

tag: time

value: 12 weeks post injury

value: {delta}ETorA

value: sciatic nerve crush


title: Hek293T,NSP14,DMSO,Day 3

description: Library name: NSP-DMSO-2

value: embryonic kidney

value: Epithelial-like cell

value: WT

value: TRANSFECTION


title: 222_TGcrush


title: 223_TGcrush


title: MB7433 strain (DHB4 ΔdegP + pAL-FevREco105-CYTO-FLAG) treated at 30°C, replicate 2

value: [delta]degP

value: 4h at 30°C


title: MB7180 strain (DHB4 ΔdegP + pAL-FevRCit-CYTO-FLAG) treated at 30°C, replicate 3


title: MB7433 strain (DHB4 ΔdegP + pAL-FevREco105-CYTO-FLAG) treated at 30°C, replicate 1


title: 194_TGnaive

value: naive


title: MB7180 strain (DHB4 ΔdegP + pAL-FevRCit-CYTO-FLAG) treated at 30°C, replicate 1


title: 220_TGcrush


title: MB7180 strain (DHB4 ΔdegP + pAL-FevRCit-CYTO-FLAG) treated at 30°C, replicate 2


title: 214_TGcrush


title: MB7050 strain (DHB4 ΔdegP + pAL-0) treated at 30°C, replicate 3

description:
MB7180-30-FevRcit.xlsx
MB7433-30-FevReco105.xlsx


title: MB7050 strain (DHB4 ΔdegP + pAL-0) treated at 30°C, replicate 2


title: NT1-14_GEX

description: 10x Genomics

value: cerebrospinal fluid cells

value: primary cells

value: untreated


title: 192_TGnaive


title: MB7050 strain (DHB4 ΔdegP + pAL-0) treated at 30°C, replicate 1


title: 191_TGnaive


title: MB7434 strain (DHB4 + pAL-FevREco105-CYTO-FLAG) treated at 42°C, replicate 3

value: Wild-type

value: 4h at 42°C

value: 0.5h at 42°C


title: MB7434 strain (DHB4 + pAL-FevREco105-CYTO-FLAG) treated at 42°C, replicate 2


title: MB7410 strain (DHB4 + pAL-FevRCit-CYTO-FLAG) treated at 42°C, replicate 3

value: pAL-FevRCit-CYTO-FLAG


title: 189_TGnaive

value: Striatum

value: male

value: 12 weeks post injury


title: 190_TGnaive

value: {delta}ETorA


title: 188_TGnaive


title: MB7410 strain (DHB4 + pAL-FevRCit-CYTO-FLAG) treated at 42°C, replicate 2


title: 209_WTcrush

value: wt

value: sciatic nerve crush


title: 207_WTcrush


title: 206_WTcrush


title: 193_TGnaive


title: 219_TGcrush


title: 205_WTcrush


title: 203_WTcrush


title: HCoEpC treated with PD0325901 and AG490

city: Rome

first: Probiomics

state: RM

address: via Montpellier 1

country: Italy

institute: Probiomics s.r.l

library_source: genomic

data_processing:
Raw sequencing data were basecalled with the standalone Guppy basecaller (v.6.4.6) using the high accuracy model "dna_r9.4.1_450bps_modbases_5mc_cg_hac.cfg" that also calls 5’methycytosine in the CpG context. The reads with a q score < 7 were discarded.
Specifying the reference genome sequence (Gencode hg38) with the --align_ref parameter, Guppy generates mapped or unmapped bam files.
The bam files were then converted to bed format with modbam2bed 0.7.0 aggregating the methylation levels between the strands.
Assembly: hg38
Supplementary files format and content: Bismark.cov files include the counts of methylated and unmethylated cytosines
Library strategy: DNA-seq

molecule: genomic DNA

source_name: epithelium

growth_protocol: Primary human colonic epithelial cells (HCoEpC; iXCells Biotechnologies) were cultured in Epithelial Cell Growth Medium (iXCells Biotechnologies, Cat# MD-0041).  Prior infection or treatments, 5 × 104 HCoEpC were seeded /well in 6-well plates and grown up to 80% confluency. B95–8 is an EBV positive marmoset cell line, that was cultured in RPMI 1640 (Sigma-Aldrich, St Louis, MO, USA, R0883), 10% fetal bovine serum (FBS; SigmaAldrich, F7524), 2 mM glutamine (Aurogene, Rome, Italy, AU-X0550), 100 mg/ml streptomycin and 100 U/ml penicillin (Aurogene, AUL0022), in 5% CO2-saturated humidity at 37 ◦C.

extract_protocol:
Genomic DNA was purified with PureLink genomic DNA mini kit (Invitrogen, #K182001) from 10^6 EBV-infected and uninfected HCoEpC, pretreated or not with PAA or PD/AG, and was sheared to ~6 kb fragment size using Covaris G tubes. DNA concentration was assessed using the dsDNA BR assay on a Qubit fluorometer (Thermo Fisher)
Nanopore sequencing libraries were prepared using the native library prep kit SQK-LSK110 according to the manufacturer’s instructions. The library of each sample was loaded into an R9.4.1 MinION flow cell (FLO-MIN106) and sequenced on an ONT MinION device with MinKNOW acquisition software version v.22.10.10. The samples were run for a maximum duration of 72 hours.

treatment_protocol: For the infected conditions (V, PD-AG-V, and PAA-V), 5 × 10^4 HCoEpC were exposed to 10^7 EBV DNA copies isolated from the B95–8 cells treated with 12- O-tetradecanoylforbol-13-acetate (TPA, 30 ng/ml, Sigma-Aldrich; P8139) and Sodium-butyrate (3 mM, Sigma-Aldrich; B5887) for 96 h to activate EBV lytic cycle. After one hour incubation at 37°C, HCoEpC were spinoculated at 1400 rpm for 1 hour at 37 °C. Subsequently, the supernatant was replaced with fresh Epithelial Cell Growth Medium and the cells were grown at 37°C for 72 hours. Next, the ELITE MGB kit (ELITech) was used to evaluate HCoEpC infection. For the pretreated and treated conditions (PD-AG-V, PAA-V, PD-AG, and PAA). PD0325901 (1 μM, PD, MedChemExpress, HY-10,254) and AG490 (20 μM, AG, Millipore #658411) were used to inhibit ERK1/2 and STAT3 in the PD-AG-V and PD-AG conditions, while the phosphonoacetic acid (500 μM, PAA, Sigma-Aldrich, #284,270) was used as an EBV DNA replication and late gene expression inhibitor in the PAA-V and PAA conditions. Finally, uninfected HCoEpC were used as control.

value: epithelium

value: Primary human colonic epithelial cells (HCoEpC)

value: treated with PD0325901 and AG490


title: MB7409 strain (DHB4 + pAL-0) treated at 42°C, replicate 2

description:
MB7410-42-FevRcit.xlsx
MB7434-42-FevReco105.xlsx


title: 202_WTnaive

value: naive


title: HCoEpC treated with phosphonoacetic acid

value: treated with phosphonoacetic acid


title: HCoEpC infected with EBV

value: infected with EBV


title: MB7434 strain (DHB4 + pAL-FevREco105-CYTO-FLAG) treated at 42°C, replicate 1


title: HCoEpC pretreated with PD0325901 and AG490 before EBV infection


title: 199_WTnaive


title: 200_WTnaive


title: 187_TGnaive


title: MB7410 strain (DHB4 + pAL-FevRCit-CYTO-FLAG) treated at 42°C, replicate 1


title: 198_WTnaive


title: 201_WTnaive


title: ArfGAP2f/f diABZI 3

city: Philadelphia

first: Samuel

last: Chauvin

state: PA

address: 518 Johnson Pavilion, 3610 Hamilton Walk

department: Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: Library name: Sample 12

data_processing:
Pseudoalignment reference was prepared against known coding and non-coding transcripts for GRCm39 release 110 (Ensembl).
We generated decoy files from the hardmasked version of the GRCm39 genome. The decoy was used when generating the pseudoalignment index with salmon (v1.4.0).
We pseudoaligned the paired reads to this index using salmon (v1.4.0) with the options libType ISR, seqBias, gcBias, validateMappings, and 50 bootstraps.
The quantification file was created using the wasabi R package (v1.0.1).
Differential expression analysis was performed using the sleuth package (v0.30.1) in R (v4.3.1).
Assembly: GRCm39
Supplementary files format and content: Excel sheet with TPM values for each sample.

organism: Mus musculus

source_name: Bone marrow-derived macrophages

growth_protocol: Day 7 bone marrow-derive macrophages were culutred in D10 with M-CSF (20 ng/mL) at 37˚C with 5% CO2.

extract_protocol:
RNA was isolated using the Qiagen Rneasy Mini kit with on-column Dnase treatment.
Libraries were prepared using the NEBNext poly(A) mRNA enrichment and RNA library prep kits (New England Biolabs) according to manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO (vehicle) or diABZI (100 nM) for 24 hours.

value: Bone marrow-derived macrophages

value: diABZI


title: 210_WTcrush


title: 196_WTnaive


title: MB7409 strain (DHB4 + pAL-0) treated at 42°C, replicate 3

value: Wild-type

value: 4h at 42°C


title: 195_WTnaive


title: ArfGAP2f/f diABZI 1

description: Library name: Sample 10


title: HCoEpC untreated and uninfected (negative control)


title: HCoEpC pretreated with phosphonoacetic acid before EBV infection


title: MB7409 strain (DHB4 + pAL-0) treated at 42°C, replicate 1

value: 0.5h at 42°C


title: ArfGAP2f/f diABZI 2

description: Library name: Sample 11


title: ArfGAP2f/f vehicle 2

description: Library name: Sample 8

value: Vehicle


title: ArfGAP2f/f vehicle 3

description: Library name: Sample 9


title: CAG-Cre ArfGAP2f/f diABZI 3

description: Library name: Sample 6

value: CAG-Cre ArfGAP2f/f


title: CFP-FIB2 replicate 2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Raw FASTQ files were analyzed by the "clip" module of pRNASeqTools (https://github.com/grubbybio/pRNASeqTools) with default parameters. First, raw reads were trimmed to remove 3' adapters and mapped to Araport11.
Second, peaks were called by CLIPper using the default parameters for each replicate. All peaks were combined, and reads assigned to these peaks were counted for differential peak identification using an R package DESeq2.
Genome_build: Araport 11
Supplementary_files_format_and_content: BED files indicating the identified peaks

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings for CLIP seq were grown on Murashige and Skoog (MS) plates containing 1% (v/w) sucrose and 0.7% (v/w) agar at 23°C under long day conditions for 14 days.

extract_protocol:
RNAs were extracted using ehonal precipitation after proteinase K digestion. NEBNext Small RNA Library Prep Set (Cat#E7330L) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using protocols described in "Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation, Cell Research (2015) 25:864-876. doi:10.1038/cr.2015.77"

treatment_protocol: UV-crosslinked

tag: developmental stage

value: 14-day-old seedlings

tag: cultivar

value: seedlings


title: CFP-FIB2 replicate 3


title: CFP-FIB2 replicate 4


title: CFP-FIB2 replicate 1


title: CAG-Cre ArfGAP2f/f diABZI 2

description: Library name: Sample 5


title: GFP-FIB1 replicate 3


title: GFP-FIB1 replicate 4


title: CAG-Cre ArfGAP2f/f vehicle 3

description: Library name: Sample 3


title: CAG-Cre ArfGAP2f/f diABZI 1

description: Library name: Sample 4


title: CAG-Cre ArfGAP2f/f vehicle 2

description: Library name: Sample 2


title: GFP-FIB1 replicate 1


title: GFP replicate 4

value: GFP


title: GFP replicate 3


title: GFP replicate 2


title: om2

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The 12 libraries were sequenced in two batches in Illumina NextSeq 1000 instrument with single-lane P3 flow cell, and 28 & 90 cycles for R1 and R2 reads resp. Basecall data (bcl files) was processed to demultiplex and generate fastq files and trim adapters and filter reads, with nf-core demultiplex pipeline 1.4.1 in NextFlow 23.10.1 in Singularity with BCL Convert 4.2.7 and fastp 0.23.4 using default pipeline options. The fastq data was then processed in CellRanger 8.0.0 with default options on 10X Genomics's cloud platform with GRCm39-2024-A transcriptome reference.
Assembly: mGRCm39
Supplementary files format and content: unfiltered (raw) matrix in h5 format generated by CellRanger

molecule: nuclear RNA

source_name: Lung

extract_protocol:
Nucleus isolation from frozen tissue was performed as described in publication with PMC ID 9437562. Briefly, dounce homogenization followed by centrifugation was used to collect nuclei.
Kits and protocols for Single Cell 3' Gene Expression from 10X Genomics were used as per manufacturer's recommendations.

value: Lung

value: All

value: Left lower lung lobe

value: High-fat diet

tag: age in_days_at_sacrifice

tag: weight in_grams_at_sacrifice

tag: sequencing run

value: Male


title: om1

description: 10X Genomics

tag: tissue

tag: cell line


title: om3

description: 10X Genomics

tag: cell type

tag: genotype


title: GFP replicate 1


title: of3

description: 10X Genomics

tag: strain

tag: treatment

value: Female


title: ArfGAP2f/f vehicle 1

description: Library name: Sample 7


title: nm2

description: 10X Genomics

value: Control diet


title: CAG-Cre ArfGAP2f/f vehicle 1

description: Library name: Sample 1

value: Bone marrow-derived macrophages


title: GFP-FIB1 replicate 2


title: nf1

description: 10X Genomics


title: nf2

description: 10X Genomics


title: BC56-100-3

first: Gengwei

last: Wu

state: Zhejiang

address: No.298, Desheng Middle Road

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: NCBI_Cucumber_9930_V3
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

organism: Cucumis sativus

source_name: leave

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: leave

tag: age

value: 21 days old

value: BC56 and 100 mM NaCl


title: BC56-100-2


title: BC56-100-1


title: of2

description: 10X Genomics

value: Wild-type


title: of1

description: 10X Genomics


title: BC56-2


title: nm3

description: 10X Genomics


title: nm1

description: 10X Genomics


title: nf3

description: 10X Genomics


title: obese rat subcutaneous, biological rep5

type: RNA

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

country: Canada

institute: University of Guelph

description: gene expression data from obese rat subcutaneous

hyb_protocol: For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Rat Gene 2.1 ST array strips on the Affymetrix Hyb Oven 640, according to the manufacturer’s instructions. Strips were then washed and stained on the Affymetrix FS 450, according to the manufacturer’s instructions.

scan_protocol: Strips were scanned on the Affymetrix Scanner 3000 7G, following the manufacturer's default settings.

data_processing: RMA background correction and normalization.

label: biotin

source_name: obese rat subcutaneous

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA according to the manufacturer's instructions.

growth_protocol: Male ZDF rats (Charles River, St-Constant, QC, Canada) were housed in individual cages, with a reverse 12h:12h light–dark cycle, and were provided with food and water ad libitum. Lean control rats were fed a standard chow (Purina 5008 diet; Purina, St Louis, MO, USA). Obese rats were provided a stock diet for 6 weeks.

extract_protocol: Tissue samples were homogenized using homogenizing beads and TRIzol (Thermo Fisher Scientific Inc., California, USA). Total RNA was then extracted using the RNeasy Mini Kit (Qiagen, Toronto, Canada), which included the optional DNase step, according to manufacturer instructions.

treatment_protocol: Samples were immediately frozen in liquid nitrogen after extraction from animals. Samples were thawed on ice immediately before commencing RNA extraction.

value: Zucker

value: subcutaneous

tag: group

value: obese


title: obese rat subcutaneous, biological rep1


title: obese rat subcutaneous, biological rep2


title: obese rat subcutaneous, biological rep4


title: resveratrol rat subcutaneous, biological rep5

description: gene expression data from resveratrol rat subcutaneous

source_name: resveratrol rat subcutaneous

value: resveratrol


title: rosiglitazone rat subcutaneous, biological rep4

description: gene expression data from rosiglitazone rat subcutaneous

source_name: rosiglitazone rat subcutaneous

value: rosiglitazone


title: rosiglitazone rat subcutaneous, biological rep2


title: rosiglitazone rat subcutaneous, biological rep3


title: CK-100-3

value: 100 mM NaCl


title: resveratrol rat subcutaneous, biological rep3


title: resveratrol rat subcutaneous, biological rep2


title: obese rat subcutaneous, biological rep3


title: resveratrol rat subcutaneous, biological rep4


title: rosiglitazone rat subcutaneous, biological rep5


title: CK-100-2


title: BC56-3


title: CK-3

value: untreated


title: CK-2


title: rosiglitazone rat subcutaneous, biological rep1


title: resveratrol rat subcutaneous, biological rep1


title: BC56-1


title: CK-1


title: lean control rat subcutaneous, biological rep3

description: gene expression data from lean control rat subcutaneous

source_name: lean control rat subcutaneous

value: lean control


title: lean control rat subcutaneous, biological rep2


title: lean control rat subcutaneous, biological rep4


title: lean control rat subcutaneous, biological rep5


title: CK-100-1


title: lean control rat subcutaneous, biological rep1


title: obese rat retroperitoneal, biological rep5

description: gene expression data from obese rat retroperitoneal

source_name: obese rat retroperitoneal

value: retroperitoneal


title: 180_Duodenum

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

hyb_protocol: Nanostring GX protocol

scan_protocol: Nanostring nCounter platform

data_processing: nSolver 4.0 software

label_protocol: Nanostring GX protocol

extract_protocol: miRvana

value: Male

tag: maternal antibiotic administration

value: none (control)

tag: diet

value: Standard

tag: tissue type

value: Duodenum


title: 15_Duodenum

tag: Sex

value: Female

value: interperitoneal (IP)

value: Western


title: 71_Duodenum


title: 181_Duodenum


title: obese rat retroperitoneal, biological rep1


title: rosiglitazone rat retroperitoneal, biological rep5

description: gene expression data from rosiglitazone rat retroperitoneal

source_name: rosiglitazone rat retroperitoneal


title: resveratrol rat retroperitoneal, biological rep2

description: gene expression data from resveratrol rat retroperitoneal

source_name: resveratrol rat retroperitoneal


title: homo_LN_blood_03

city: Changsha

first: Yang

last: Jia

address: renmin road No.139

institute: the second xiangya hospital of central south university

description: lncRNA

hyb_protocol: The labeled lncRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs  have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: Peripheral Blood

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent lncRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: whole blood

tag: gender

value: female

tag: disease state

value: lupus nephritis


title: obese rat retroperitoneal, biological rep3

value: Zucker

value: obese


title: obese rat retroperitoneal, biological rep2


title: resveratrol rat retroperitoneal, biological rep3

value: resveratrol


title: obese rat retroperitoneal, biological rep4


title: 14_Duodenum


title: 135_Duodenum


title: homo_control_blood_01

description: lncRNA

value: healthy


title: homo_LN_blood_02

description: lncRNA

value: male


title: homo_control_blood_02

description: lncRNA


title: 21_Duodenum


title: resveratrol rat retroperitoneal, biological rep4


title: resveratrol rat retroperitoneal, biological rep5


title: homo_LN_blood_01

description: lncRNA


title: 134_Duodenum


title: rosiglitazone rat retroperitoneal, biological rep4

value: rosiglitazone


title: rosiglitazone rat retroperitoneal, biological rep2

value: retroperitoneal


title: rosiglitazone rat retroperitoneal, biological rep3


title: homo_control_blood_03

description: lncRNA


title: resveratrol rat retroperitoneal, biological rep1


title: rosiglitazone rat retroperitoneal, biological rep1


title: 121_Duodenum

value: Male


title: 120_Duodenum


title: 116_Duodenum


title: 197_WTnaive

value: Striatum

tag: time

value: 12 weeks post injury

value: wt

value: naive


title: 112_Duodenum

value: none (control)

value: Duodenum


title: 65_Duodenum

value: Female

value: Standard


title: lean control rat retroperitoneal, biological rep4

description: gene expression data from lean control rat retroperitoneal

source_name: lean control rat retroperitoneal

value: lean control


title: 45_Duodenum

value: Oral

value: Western


title: 62_Duodenum


title: 39_Duodenum


title: 46_Duodenum


title: 37_Duodenum


title: lean control rat retroperitoneal, biological rep3

value: Zucker


title: lean control rat retroperitoneal, biological rep5


title: 28_Duodenum


title: 29_Duodenum


title: lean control rat retroperitoneal, biological rep2


title: 147_Duodenum


title: 145_Duodenum


title: lean control rat retroperitoneal, biological rep1


title: obese rat epididymal, biological rep3

description: gene expression data from obese rat epididymal

source_name: obese rat epididymal

value: epididymal

value: obese


title: obese rat epididymal, biological rep4


title: resveratrol rat epididymal, biological rep5

description: gene expression data from resveratrol rat epididymal

source_name: resveratrol rat epididymal

value: resveratrol


title: 144_Duodenum


title: 46_Colon

value: Colon


title: 45_Colon


title: obese rat epididymal, biological rep1


title: resveratrol rat epididymal, biological rep4


title: 181_Ileum

value: Male

value: Ileum


title: 173_Duodenum


title: 180_Ileum


title: 173_Ileum


title: 62_Colon


title: obese rat epididymal, biological rep5


title: resveratrol rat epididymal, biological rep1


title: 147_Ileum


title: 145_Ileum


title: 144_Ileum


title: 135_Ileum


title: obese rat epididymal, biological rep2


title: rosiglitazone rat epididymal, biological rep4

description: gene expression data from rosiglitazone rat epididymal

source_name: rosiglitazone rat epididymal

value: rosiglitazone


title: lean control rat epididymal, biological rep4

description: gene expression data from lean control rat epididymal

source_name: lean control rat epididymal


title: resveratrol rat epididymal, biological rep2


title: rosiglitazone rat epididymal, biological rep5


title: rosiglitazone rat epididymal, biological rep3


title: resveratrol rat epididymal, biological rep3


title: rosiglitazone rat epididymal, biological rep2


title: rosiglitazone rat epididymal, biological rep1


title: lean control rat epididymal, biological rep5


title: lean control rat epididymal, biological rep1


title: lean control rat epididymal, biological rep3


title: lean control rat epididymal, biological rep2


title: 134_Ileum


title: 112_Jejunum

value: Jejunum


title: Aged_CTRL1 (without CNV)

city: Tianjin

first: Xue

last: Dong

state: TIANJIN

address: Qixiangtai Road

department: Department of Pharmacology

institute: Tianjin Medical University

description: 10x Genomics

data_processing:
Raw data were input and filtered with the Cell Ranger pipeline (10× Genomics)
Unique molecular identifier (UMI) count tables from control and CNV mice were loaded into R and processed using the Seurat R package (version 4.1.1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina+choroid

extract_protocol:
Choroid-sclera and retina were digested separately in a papain solution (40U papain / 10mL DPBS) for 45 minutes. Papain was then neutralized in a trypsin inhibitor solution (0.15% ovomucoid in DPBS) and the tissue was triturated to generate a single-cell suspension. Following trituration, the cells were pelleted, resuspended, and filtered through a 40μm Nitex mesh filter to eliminate any clumped cells. Dissociated cells from retinas were finally incubated with PE anti-mouse CD73 (127206, Biolegend, US) followed by anti-PE microbeads (130-048-801, Miltenyi Biotec, US) to deplete rods. Single cell suspensions from retina and choroid-sclera were mixed and diluted at a concentration of 200 cells/μL in 0.2% BSA/DPBS for loading into 10x Genomics Chromium.
Droplet generation and cDNA libraries were completed by Novogene company (Beijing,China).

treatment_protocol: Mice with age 6-8 weeks or over 18 months were induced CNV with laser photocoagulation (532 nm, 200 mW, 0.150 s, 100 μm; Vovus Spectra, Lumenis, US) using a slit lamp delivery system and a cover glass as a contact lens.

value: retina+choroid

value: > 18 months

value: WT

tag: condition

value: control


title: 62_Ileum

value: Female

value: Standard


title: 46_Ileum

value: Oral


title: naïve bladder, immune cell, scRNAseq

city: Hefei

first: Lu

last: Li

address: #373, Huangshan Road

institute: University of Science and Technology of China

description: 10x Genomics

data_processing:
For data processing, low quality cells were first filtered using Seurat (version 3.1.4). Cells with mitochondrial RNA content greater than 25% or with fewer than 200 genes were all excluded. A total of 5362 bladder CD45+cells that passed rigorous quality control were used for the downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bladder

extract_protocol:
Mouse bladder was dissected into small pieces, followed by digestion in RPMI 1640 medium containing 0.34 U/mL Liberase and 10 μg/mL DNase I for 1 h at 37°C. The tissue suspension was filtered through a 70 μm nylon mesh strainer and washed in cold PBS twice.The bladder single-cell suspension was obtained from a pool of 5 naïve 8-10weeks adult female C57BL/6 mice and sorted for CD45+ immune cells at a purity higher than 95% (Beckman MoFlo Astrios EQ).
The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000) according to the manufacturer’s instructions.

value: Bladder

value: Immune cells

value: wild type


title: 45_Ileum

value: Western


title: 181_Colon

value: none (control)


title: 180_Colon

value: Colon


title: Young_CNV

description: 10x Genomics

value: 6-8 weeks

value: CNV


title: Young_CTRL1 (without CNV)

description: 10x Genomics


title: SIR-S20

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

library_source: other

data_processing:
Adaptors were removed from sequencing read files from miRNA fractions using the clip_adaptors.pl module of mirdeep219. All sequence data were subjected to quality control by fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html). Sequence read files from mRNA fractions were trimmed down to 50 bp to remove the poor-quality sequences at the ends. Sequence read files were further collapsed based on sequence identity and annotated for miRNA by mapping to miRbase version 2120 using the miraligner module of seqbuster. Reads passing QC standards were mapped to the GRCm38 mouse reference genome assembly using TopHat v2.0.13 (Bowtie v2.0.6) with supplied annotations at parameters (--min-anchor 8, --min-isoform-fraction 0.15). The raw count of mapped reads to genes was determined using the htseq-count utility (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html. Isomirs were identified using the R isomiRs library of the seqbuster package. Differential expression between groups of genes or miRNAs was assessed using DESEQ2.
Assembly: mm10
Supplementary files format and content: M1B_M54B_mRNAs_counts.xlsx : total gene counts
Supplementary files format and content: M1A_M54A_miRNAs_counts.xlsx : total expression counts
Supplementary files format and content: SIR_S3_to_S20_counts.xlsx : total expression counts
Supplementary files format and content: SIR_S23_S24_S29_S30_counts.xlsx : total expression counts
Supplementary files format and content: SIR_S33_S34_counts.xlsx : total expression counts

molecule: other

source_name: lung

extract_protocol:
For RIP-seq analysis, the lungs of infected mice were perfused with formaldehyde to form crosslinks between miRNAs, MREs and individual proteins of bound RNA induced silencing complexes (RISCs). Crosslinked miRNA-mRNA-RISC complexes were immunoprecipitated by the addition of an antibody against AGO2, one component of RISC, and magnetic beads conjugated to protein A . Additional samples received either an antibody against IgG, as a negative control, or no antibody (labeled as 10% input), as a positive control. Protein-RNA complexes isolated from each sample were washed and eluted from the magnetic beads, crosslinks were reversed and protein components were digested. For SIR analysis, lungs from late-stage pulmonary adenocarcinoma animals infected with either adenoCre or adeno were formaldehyde crosslinked. Crosslinked miRNA-MRE complexes were isolated by the addition of a SIR probe followed by streptavidin beads. After extensive washing, complexes were eluted, crosslinks were reversed and the liberated miRNAs were sequenced. As positive controls, sequencing libraries were also generated from 10% of the starting input from each sample.
Sequencing libraries were constructed starting with the entire pellet of RIP or SIR RNA, using TruSeq Small RNA kits from Illumina (San Diego, CA), following manufacturer’s instructions. Two different gel fragments were isolated from each gel of RIP samples. The first fragment, containing miRNAs, corresponded to a size of 145 bps-160 bps, including ligated adapters. The second fragment of each gel, containing immunoprecipitated mRNA targets, corresponded to a size of 160 bps-500 bps, including ligated adapters. Only one gel fragment, containing miRNAs corresponding to a size of 145 bps-160 bps, including ligated adapters, was isolated from each SIR sample. Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies, Santa Clara, CA) and quantitative PCR (KAPA Biosystems, Wilmington, MA), according to the manufacturers’ instructions.
RIP-seq libraries were pooled and sequenced on a MiSeq 50 base pair single-read flow cell using v2 reagents (Illumina, San Diego, CA). SIR libraries were also pooled and sequenced on either a HiSeq2500 high output 100 base pair paired-end flow cell using TruSeq SBS v3 reagents or on a NextSeq500 high output 75 base pair single-read flow cell using v2 reagents (Illumina, San Diego, CA).

treatment_protocol: We obtained two strains of mice: B6.129S4-Krastm4Tyj/J (stock #008179), referred to as K, and B6.129P2-Trp53tm1Brn/J (stock #008462), referred to as P. Both K and P mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and were interbred to create mice that were heterozygous for the KrasG12D allele and homozygous for the floxed Trp53 allele, referred to as KP. Male K and KP mice underwent one of three different experimental treatments at 6-7 weeks of age. The first treatment group of each mouse strain, referred to as early-stage tumor (ET) or late-stage tumor (LT), respectively, received intranasal administration of 5x106 PFU of adenovirusCre (Viral Vector Core, University of Iowa, Iowa City, IA).  The second group received 5x106 PFU of adenovirus (Viral Vector Core, University of Iowa, Iowa City, IA) while the third group was not infected. Collectively, K animals from the second and third groups are referred to early-stage normal (EN) and KP animals from the second and third groups are referred to late-stage normal (LN). Animals in the first two treatment groups were anesthetized with intraperitoneal injections of tribromoethanol (400 mg/kg body weight) prior to viral instillation. Animals in all three treatment groups were harvested 16 weeks later, at 22 weeks of age.

value: lung

value: adeno


title: SIR-S19


title: 173_Colon

value: Male


title: SIR-S14


title: SIR-S17


title: SIR-S18


title: SIR-S13


title: 15_Jejunum

value: interperitoneal (IP)

value: Jejunum


title: 14_Jejunum


title: SIR-S12


title: Aged_CNV

description: 10x Genomics

value: retina+choroid

value: > 18 months

value: WT


title: SIR-S11


title: 135_Colon


title: 71_Jejunum

value: Female

value: Standard


title: 145_Colon

value: Oral


title: 134_Colon


title: SIR-S10

value: Cre


title: 147_Colon

value: Western


title: 65_Jejunum

value: none (control)


title: SIR-S9


title: 45_Jejunum


title: 46_Jejunum


title: SIR-S8


title: 39_Jejunum


title: SIR-S7


title: 37_Jejunum


title: SIR-S3


title: RIP_miRNA-M54A_LS_T_Cre_INPUT_replicate 3


title: RIP_miRNA-M53A_LS_T_Cre_IgG_replicate 3


title: 29_Jejunum


title: RIP_miRNA-M52A_LS_T_Cre_AGO2_replicate 3


title: SIR-S4


title: 28_Jejunum


title: 173_Jejunum


title: RIP_miRNA-M49A_LS_T_Cre_AGO2_replicate 2


title: RIP_miRNA-M50A_LS_T_Cre_IgG_replicate 2


title: RIP_miRNA-M51A_LS_T_Cre_INPUT_replicate 2


title: 147_Jejunum


title: 71_Cecum

extract_protocol: miRNeasy

value: Cecum


title: 144_Jejunum


title: RIP_miRNA-M48A_LS_T_Cre_INPUT_replicate 1


title: RIP_miRNA-M47A_LS_T_Cre_IgG_replicate 1


title: 62_Cecum


title: 65_Cecum


title: RIP_miRNA-M46A_LS_T_Cre_AGO2_replicate 1


title: 45_Cecum


title: RIP_miRNA-M45A_LS_N_Adeno_INPUT_replicate 3


title: H2AK5ac_PR9_REP2

type: genomic

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin immunoprecipitation of H2AK5ac in PR9 cells (2nd biological replicate).

hyb_protocol: Hybridization is performed for 16 - 20 hours at 42°C.

scan_protocol: NimbleGen two-color arrays are scanned with a GenePix 4000B Scanner, to obtain images from for the 532nm and 635nm wavelengths.

data_processing: Data is pre-processed by NimbleGen Services using the NimbleGen NimbleScan software. Pair reports contain the raw data, listing the probe intensities of each array. Scaled Log2-Ratio Data is calculated for each sample from the experimental and reference conditions.

source_name: PR9_input_dna (control)

label_protocol: Experimental samples are labeled with Cy5, total DNA samples used as reference are labeled with Cy3 using 9mer primers that have Cy3 and Cy5 dyes attached and Klenow added.

extract_protocol: Qiagen dna extraction

tag: fraction

value: non-immunoprecipitated DNA

value: PR9 cell line

value: immunoprecipitated DNA

tag: antibody


title: H2AK5ac_PR9_REP1

description: Chromatin immunoprecipitation of H2AK5ac in PR9 cells (1st biological replicate).

tag: cell line


title: 145_Jejunum


title: 46_Cecum


title: H2AK5ac_CD4+

description: Chromatin immunoprecipitation of H2AK5ac in CD4+ cells.

source_name: CD4+_input_dna (control)

value: CD4+ cell line


title: 37_Cecum


title: 29_Cecum


title: RIP_miRNA-M43A_LS_N_Adeno_AGO2_replicate 3

tag: tissue

value: lung

value: adeno


title: RIP_miRNA-M42A_LS_N_Adeno_INPUT_replicate 2

tag: genotype


title: H2A.ZK(4-7-11)ac_CD4+

description: Chromatin immunoprecipitation of H2A.ZK(4-7-11) in CD4+ cells.


title: RIP_miRNA-M40A_LS_N_Adeno_AGO2_replicate 2


title: RIP_miRNA-M41A_LS_N_Adeno_IgG_replicate 2


title: 147_Cecum

tag: strain

value: Male


title: RIP_miRNA-M38A_LS_N_Adeno_IgG_replicate 1

tag: treatment


title: 28_Cecum


title: 145_Cecum


title: 173_Cecum


title: 144_Cecum


title: RIP_miRNA-M37A_LS_N_Adeno_AGO2_replicate 1


title: 180_Stomach

value: Stomach


title: RIP_miRNA-M36A_LS_N_Un_INPUT_replicate 3

value: uninfected


title: RIP_miRNA-M34A_LS_N_Un_AGO2_replicate 3


title: 181_Stomach


title: RIP_miRNA-M35A_LS_N_Un_IgG_replicate 3


title: RIP_miRNA-M33A_LS_N_Un_INPUT_replicate 2


title: 173_Stomach


title: 147_Stomach


title: 144_Stomach


title: 145_Stomach


title: RIP_miRNA-M31A_LS_N_Un_AGO2_replicate 2


title: 135_Stomach


title: RIP_miRNA-M30A_LS_N_Un_INPUT_replicate 1


title: 121_Stomach

value: interperitoneal (IP)


title: 134_Stomach


title: RIP_miRNA-M39A_LS_N_Adeno_INPUT_replicate 1


title: RIP_miRNA-M29A_LS_N_Un_IgG_replicate 1


title: RIP_miRNA-M28A_LS_N_Un_AGO2_replicate 1


title: RIP_miRNA-M27A_ES_T_Cre_INPUT_replicate 3


title: RIP_miRNA-M25A_ES_T_Cre_AGO2_replicate 3


title: 116_Stomach


title: RIP_miRNA-M24A_ES_T_Cre_INPUT_replicate 2


title: 62_Stomach

value: Female


title: 65_Stomach

value: Standard


title: RIP_miRNA-M23A_ES_T_Cre_IgG_replicate 2


title: RIP_miRNA-M22A_ES_T_Cre_AGO2_replicate 2


title: 46_Stomach

value: Oral


title: 45_Stomach


title: RIP_miRNA-M20A_ES_T_Cre_IgG_replicate 1

value: Cre


title: RIP_miRNA-M21A_ES_T_Cre_INPUT_replicate 1


title: 37_Stomach

value: Western


title: 29_Stomach

value: none (control)


title: RIP_miRNA-M19A_ES_T_Cre_AGO2_replicate 1


title: 39_Stomach


title: 28_Stomach


title: RIP_miRNA-M18A_ES_N_Adeno_INPUT_replicate 3


title: 21_Stomach


title: 15_Stomach


title: RIP_miRNA-M26A_ES_T_Cre_IgG_replicate 3


title: RIP_miRNA-M16A_ES_N_Adeno_AGO2_replicate 3


title: RIP_miRNA-M15A_ES_N_Adeno_INPUT_replicate 2


title: 71_Ileum

value: Ileum


title: RIP_miRNA-M14A_ES_N_Adeno_IgG_replicate 2


title: 65_Ileum


title: RIP_miRNA-M12A_ES_N_Adeno_INPUT_replicate 1


title: RIP_miRNA-M13A_ES_N_Adeno_AGO2_replicate 2


title: RIP_miRNA-M11A_N_Adeno_IgG_replicate 1


title: 37_Ileum


title: 29_Ileum


title: RIP_miRNA-M8A_ES_N_Un_IgG_replicate 3


title: RIP_miRNA-M7A_ES_N_Un_AGO2_replicate 3


title: RIP_miRNA-M17A_ES_N_Adeno_IgG_replicate 3


title: RIP_miRNA-M10A_ES_N_Adeno_AGO2_replicate 1


title: 21_Ileum


title: RIP_miRNA-M6A_ES_N_Un_INPUT_replicate 3


title: 121_Ileum


title: 14_Stomach


title: 14_Ileum


title: 15_Ileum


title: 112_Stomach


title: RIP_miRNA-M5A_ES_N_Un_IgG_replicate 2


title: RIP_miRNA-M44A_LS_N_Adeno_IgG_replicate 3


title: RIP_miRNA-M4A_ES_N_Un_AGO2_replicate 2


title: 120_Ileum


title: 116_Ileum


title: 112_Ileum


title: RIP_miRNA-M3A_ES_N_Un_INPUT_replicate 2


title: 120_Colon

value: Colon


title: RIP_miRNA-M2A_ES_N_Un_IgG_replicate 1


title: 28_Ileum


title: RIP_miRNA-M9A_ES_N_Un_INPUT_replicate 3


title: RIP_miRNA-M1A_ES_N_Un_AGO2_replicate 1


title: RIP_mRNA-M54B_LS_T_Cre_INPUT_replicate 1


title: 116_Colon


title: 112_Colon


title: RIP_mRNA-M53B_LS_T_Cre_IgG_replicate 3


title: 071_Colon


title: RIP_mRNA-M51B_LS_T_Cre_INPUT_replicate 1


title: RIP_mRNA-M52B_LS_T_Cre_AGO2_replicate 3


title: RIP_mRNA-M49B_LS_T_Cre_AGO2_replicate 2


title: RIP_mRNA-M50B_LS_T_Cre_IgG_replicate 2


title: RIP_mRNA-M48B_LS_T_Cre_INPUT_replicate 1


title: RIP_mRNA-M46B_LS_T_Cre_AGO2_replicate 1


title: RIP_mRNA-M47B_LS_T_Cre_IgG_replicate 1


title: 121_Colon


title: 037_Colon


title: 029_Colon


title: RIP_mRNA-M45B_LS_N_Adeno_INPUT_replicate 3


title: RIP_mRNA-M44B_LS_N_Adeno_IgG_replicate 3


title: 028_Colon


title: 014_Colon


title: 021_Colon


title: RIP_mRNA-M43B_LS_N_Adeno_AGO2_replicate 3


title: 1377_infected

city: Providence

first: Alan

last: Morrison

state: RI

address: 830 Chalkstone Ave

institute: Ocean State Research Institute

description:
Library name: 1377_infected
03_02FNOSRI_1377I_RNA_mm_41

data_processing:
The number of fragments overlapping predefined genomic features of interest (e.g. genes) are counted. For DGE assays: aligned reads were quantified at the annotated 3’ end of genes.
After obtaining the gene expression count matrix, we perform differential analyses to identify statistically significant differential genes using DESeq2. The following lists the pre-processing steps before differential calling.
Data Normalization: DESeq2 expects un-normalized count matrix of sequencing fragments. The DESeq2 model internally corrects for library size using their median-of-ratios method.
Filtering before multiple testing adjustment: we perform a minimal pre-filtering to keep only rows that have at least 10 reads total. After a differential test has been applied to each gene, the p-value of each gene is calculated and adjusted to control the number of false positives among all discoveries at a proper level. This procedure is known as multiple testing adjustment. During this process, DESeq2 by default filters out statistical tests (i.e. genes) that have low counts by a statistical technique called independent filtering. It uses the average counts of each gene (i.e. baseMean), across all samples, as its filter criterion, and it omits all genes with average normalized counts below a filtering threshold from multiple testing adjustment. This filtering threshold is automatically determined to maximize detection power (i.e. maximize the number of differential genes detected) at a specified false discovery rate (FDR).
Gene enrichment analysis is performed to identify biological pathways, gene ontology terms, or other functional categories that are enriched in the set of genes of interest. GSEA analysis is performed using clusterProfiler. We select differentially expressed genes between pairwise comparisons as input for gene enrichment analysis. More specifically, DEGs are grouped into up-regulated and down-regulated gene sets. Then gene ontology (GO) analysis is performed for the selected gene sets to identify enriched functional categories. Key parameters setting in clusterProfiler for GSEA analsysis: pvalueCutoff = 1, qvalueCutoff = 1 in enrichGO.
Assembly: mm10
Supplementary files format and content: fastq files are raw reads and bam files are processed reads.
Supplementary files format and content: Bam files are binary files containing reads and alignment information. BAM-index files with extension *.bam.bai. These are index files that need to be located in the same directory as the BAM file for certain BAM file visualizations.

source_name: macrophage

growth_protocol: BMDMs were obtained by in vitro differentiation of primary femur and tibia bone marrow cells using an established protocol. In brief, femurs and tibias from the indicated mouse lines mice were dissected, cleaned, disinfected in 70% ethanol, and washed with fully supplemented RPMI 1640 medium. Red blood cells were removed by ammonium-chloride potassium lysis buffer and subsequent centrifugation. Remaining BM cells were then cultured at a density of 3.5 × 106 cells/10cm Petri dish in fully supplemented RPMI with 30% (vol/vol) L929 cell-conditioned medium. Cells were matured to phenotypic macrophages over 6-7 days as confirmed by >98% expression of F4/80 and CD68. Non-adherent cells were washed away with PBS while adherent cells were recovered by gentle pipetting in PBS with 1mM EDTA.

extract_protocol:
For RNA extraction, cells were collected and placed in TRIzol™ for SARS-CoV-2 inactivation. RNA was extracted from TRIzol™ and then column purified (QIAGEN, RNeasy Kit 74106). 2μg total RNA was used for the contstruction of the sequecncing libraries.
The paired-end 150 sequencing reads generated by Illumina sequencing are mapped to the genome using the STAR algorithm with default settings. Alignment information for each read is stored in the BAM format. nfcore/rnaseq pipeline is applied to perform the alignment.

treatment_protocol:
Polarization of BMDMs was carried out by incubation with LPS (100ng/mL) and IFN-γ (50ng/mL) for 18 hours.
Following polarization, BMDMs were incubated with SARS-CoV-2 dosed at an MOI of 0.1 or mock vehicle control for 24 hours.

tag: cell type

value: macrophage

value: infected


title: 1377_mock

description:
Library name: 1377_mock
09_02FNOSRI_1377M_RNA_mm_47

value: mock


title: 1376_infected

description:
Library name: 1376_infected
02_02FNOSRI_1376I_RNA_mm_40


title: RIP_mRNA-M42B_LS_N_Adeno_INPUT_replicate 2

value: lung


title: RIP_mRNA-M41B_LS_N_Adeno_IgG_replicate 2

value: adeno


title: 1375_mock

description:
Library name: 1375_mock
07_02FNOSRI_1375M_RNA_mm_45


title: 015_Colon


title: RIP_mRNA-M40B_LS_N_Adeno_AGO2_replicate 2


title: 065_Colon


title: preWT-CTX

city: Suwon

first: Kyoung

last: Cho

state: Gyeonggi-do (41)

address: 154-2 Gwanggyosanro, Youngtong-gu

department: Life Science

country: South Korea

institute: Kyonggi University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

value: brain

value: cortex

value: WT (littermate)

value: 8-week (normal)


title: RIP_mRNA-M38B_LS_N_Adeno_IgG_replicate 1


title: preWT-STR

value: striatum


title: RIP_mRNA-M37B_LS_N_Adeno_AGO2_replicate 1


title: RIP_mRNA-M36B_LS_N_Un_INPUT_replicate 3

value: uninfected


title: RIP_miRNA-M32A_LS_N_Un_IgG_replicate 2


title: RIP_mRNA-M35B_LS_N_Un_IgG_replicate 3


title: preHD-STR(2)

value: 8-week (pre-symptom)


title: RIP_mRNA-M34B_LS_N_Un_AGO2_replicate 3


title: 1376_mock

description:
Library name: 1376_mock
08_02FNOSRI_1376M_RNA_mm_46


title: preHD-CTX(2)


title: preHD-CTX


title: RIP_mRNA-M33B_LS_N_Un_INPUT_replicate 2


title: RIP_mRNA-M32B_LS_N_Un_IgG_replicate 2


title: 1375_infected

description:
Library name: 1375_infected
01_02FNOSRI_1375I_RNA_mm_39


title: postHD_CTX(2)

value: 13-week (post-symptom)


title: RIP_mRNA-M30B_LS_N_Un_INPUT_replicate 1


title: postHD-STR(2)


title: postHD-CTX


title: RIP_mRNA-M29B_LS_N_Un_IgG_replicate 1


title: RIP_mRNA-M39B_LS_N_Adeno_INPUT_replicate 1


title: postHD-STR


title: RIP_mRNA-M28B_LS_N_Un_AGO2_replicate 1


title: postWT-CTX

value: 13-week (normal)


title: RIP_mRNA-M27B_ES_T_Cre_INPUT_replicate 3

value: Cre


title: postWT-STR


title: RIP_mRNA-M25B_ES_T_Cre_AGO2_replicate 3


title: RIP_mRNA-M24B_ES_T_Cre_INPUT_replicate 2


title: RIP_mRNA-M23B_ES_T_Cre_IgG_replicate 2


title: RIP_mRNA-M21B_ES_T_Cre_INPUT_replicate 1


title: RIP_mRNA-M19B_ES_T_Cre_AGO2_replicate 1


title: RIP_mRNA-M18B_ES_N_Adeno_INPUT_replicate 3


title: RIP_mRNA-M31B_LS_N_Un_AGO2_replicate 2


title: preHD-STR


title: RIP_mRNA-M17B_ES_N_Adeno_IgG_replicate 3


title: RIP_mRNA-M15B_ES_N_Adeno_INPUT_replicate 2


title: RIP_mRNA-M16B_ES_N_Adeno_AGO2_replicate 3


title: RIP_mRNA-M22B_ES_T_Cre_AGO2_replicate 2


title: RIP_mRNA-M14B_ES_N_Adeno_IgG_replicate 2


title: RIP_mRNA-M12B_ES_N_Adeno_INPUT_replicate 1


title: RIP_mRNA-M13B_ES_N_Adeno_AGO2_replicate 2


title: RIP_mRNA-M9B_ES_N_Un_INPUT_replicate 3


title: RIP_mRNA-M11B_ES_N_Adeno_IgG_replicate 1


title: 120_Stomach

value: Male

value: interperitoneal (IP)

value: Western

value: Stomach


title: Mac-WT_NGsc3

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
10× Genomics Cell Ranger 7.1 mkfastq wrapper was used to perform sample demultiplexing and generate fastq files. Demultiplexed fastq files generated by the Genomics Core were analyzed by the Bioinformatics Shared Resource (Bioinformatics | UAMS Winthrop P. Rockefeller Cancer Institute) with the 10x Genomics Cell Ranger (version 6.0.2) count function for sequence alignment using STAR to the mm10-3.0.0 mouse reference genome. The Seurat toolkit ([Seurat; [45-47]) was used to pre-process the raw counts generated by Cell Ranger to filter out low-quality cells, cell doublets, and cells with a high percentage of mitochondrial genes. Cells with unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less 200 unique features, total gene counts more than more the 75th percentile plus 1.5 times the IQR or less than 1000 counts, and/or mitochondrial feature percentage more the 75th percentile plus 1.5 times the IQR or less than the 25th percentile minus 1.5 times the IQR were filtered out of the data. The data were then scaled by regressing the variables associated with cell death and cell cycling using Seurat vars.to.regress function. Counts were normalized using SCTransform and PCA was performed on the scaled data. The 2000 highest variable features were selected using Seurat FindVariableFeatures functionand principal-components analysis (PCA) was performed and used for downstream analysis by visualizing the variance explained. A  Uniform Manifold Approximation and Projection (UMAP) was used to visualize the clustering results [48]. Seurat FindNeighbors and FindClusters functions were used to label clusters based on the visual clustering in the projections, and the FindAllMarkers function identified markers that define clusters by differential expression.These gene markers were compared with known markers in order to assign appropriate cell type labels. Differential expression analysis was performed using FindMarkers function with the MAST test, a GLM framework that treats cellular detection rate as a covariate [49].
Assembly: mm10-3.0.0 mouse reference genome
Supplementary files format and content: .fastq Illumina reads
Supplementary files format and content: 10x Genomics filtered feature matrix .h5

source_name: Lung

growth_protocol: All cell lines were purchased from ATCC (Manassas, VA, USA). The human MDA-MB-231, and the murine 4T1 and E0771 breast cancer cell lines were cultured in a base medium supplemented with 10% heat-inactivated fetal bovine serum (cat. no. S11150H; R&D System Inc.), 50 units/ml penicillin plus 50 μg/ml streptomycin (cat. no. 30-001-CI; Corning). The base medium for MDA-MB-231 and 4T1 cells was Gibco DMEM (cat. no. 11965092; ThermoFisher Scientific), and for E0771 cells, the base medium was Gibco RPMI 1640 Medium (cat. no. 2240089; ThermoFisher Scientific). Human breast cancer tissues were provided by the Cooperative Human Tissue Network (CHTN, https://www.chtn.org/), and primary human breast cancer cells were established by conditional reprogramming as described previously [42, 43].  Tumor growth in mice: PyMT-SR-A+/+ [B6.FVB-Tg(MMTV-PyVT)634Mul/LellJ (RRID:IMSR_JAX:022974; The Jackson Laboratory, Bar Harbor, ME) [44]] were crossed with SR-A-/- mice [B6.Cg-Msr1tm1Csk/J (RRID:IMSR_JAX:006096, The Jackson Laboratory)] to create PyMT-SR-A-/- mice. Colonies were maintained at UAMS by breeding hemizygous male PyMT mice with female WT C57Bl/6 or SR-A-/- mice. Female mice that were hemizygous for the MMTV-PyMT transgene were used for experiments.

extract_protocol:
NGS libraries were prepared from the single-cell suspensions using the 10X Genomics NextGEM 3’ assay and sequenced on the NextSeq 500 using Illumina SBS reagents. Library quality was assessed, and cell number and viability were determined using Trypan Blue exclusion to target 10,000 cells per sample with 20,000 reads per cell.
10X Genomics NextGEM 3’ assay

treatment_protocol: To test the possibility that SR-A actively induces a tumor-supportive macrophage phenotype and actively contributes to breast cancer progression, we crossed the mouse mammary tumor virus-polyoma middle-T (PyMT) transgenic mouse model of spontaneous breast cancer [41] with SR-A knockout (SR-A-/-) mice to generate PyMT-SR-A-/- mice. PyMT expression in breast epithelial cells results in 100% of female PyMT mice developing hyperplastic lesions that rapidly progress to premalignant adenoma/mammary intraepithelial neoplasia (MIN), which are often accompanied by focal macrophage infiltration, and then to early and advanced carcinomas [41]. We then compared tumor latency, metastasis, and TAM phenotype in PyMT-SR-A-/- and control (PyMT-SR-A+/+) mice to determine the contributions of SR-A in breast tumors. We found that SR-A expression was associated with decreased tumor latency, increased metastasis, and induction of a tumor-supportive TAM phenotype.

value: Lung

value: PyMT-SR-A+/+

value: Wild Type lung cells


title: RIP_mRNA-M10B_ES_N_Adeno_AGO2_replicate 1

value: lung

value: adeno


title: RIP_mRNA-M26B_ES_T_Cre_IgG_replicate 3


title: RIP_mRNA-M7B_ES_N_Un_AGO2_replicate 3


title: RIP_mRNA-M8B_ES_N_Un_IgG_replicate 3


title: Mac-SrA-Neg_NGsc3

value: PyMT-SR-A-/-

value: epCAM+ tumor cells


title: RIP_mRNA-M3B_ES_N_Un_INPUT_replicate 1


title: RIP_mRNA-M4B_ES_N_Un_AGO2_replicate 2


title: RIP_mRNA-M2B_ES_N_Un_IgG_replicate 1


title: RIP_mRNA-M1B_ES_N_Un_AGO2_replicate 1


title: RIP_mRNA-M20B_ES_T_Cre_IgG_replicate 1


title: Sciatic nerve, mutant, postnatal day 21, biol rep 4 [2022A384]

city: Marseille

first: Heather

middle: C

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

country: France

institute: INSERM/Aix-Marseille Univ

data_processing:
The quality of sequencing reads was assessed using fastQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads were aligned on the GRCm39 mouse reference genome using STAR (v2.7.2b). Bam files were indexed and sorted using Samtools (v1.7). After mapping, the number of reads per feature ( GENCODE v34 annotations) was determined using StringTie v2.1.6.
Genes differentially expressed between conditions were identified using a Wald test in the DESeq2 package (v1.34.0). Transcripts with an adjusted P-value for FDR (False Discovery Rate) below 0.05 were assigned as significantly differentially expressed.
Assembly: GRCm39
Supplementary files format and content: Tab-separated text, gene count matrix

source_name: sciatic nerve

growth_protocol: Heterozygous mice bearing the P0-Cre recombinase allele (derived from B6N.FVB-Tg(Mpz-cre)26Mes/J, RRID:IMSR_JAX:017927, Feltri ML et al., 1999, PMID: 10586237) were bred to heterozygous mice bearing a T1799A mutation in a floxed construct containing an alternative exon 15 within the Braf locus (RRID:IMSR_JAX:017928, Mercer et al., 2005, PMID: 16357158)

extract_protocol:
Sciatic nerves on postnatal days 5 (P5) or 21 (P21) were lysed using ceramic beads in the FastPrep-24™ homogenizer (MP Biomedicals) at 6 m/s for 50 sec and total RNA extracted with the RNeasy Lipid Tissue Mini Kit (#74804; Qiagen). RNA concentrations were measured on a NanoDrop (NanoDrop TM 1000 Spectrophotometer; Thermo Fisher Scientific).
Librairies were constructed following the instructions of the KAPA mRNA HyperPrep kit (Roche, #KR1352-v7.21) using 1 μg total RNA. After conversion to cDNA, librairies were multiplexed after ligation of a 6 basepair index and PCR amplification. Quality and quantity of librairies were assessed individually before multiplexing using a Bioanalyzer High Sensitivity DNA microfluidics chip (Agilent Technologies) and quantified spectrophotometrically on a Qubit™ using the dsDNA High Sensitivity Kit (Thermofisher). Normalized equimolar quantities of cDNA librairies were loaded using a total of 400 pM on an Illumina NextSeq 500 sequencer.
RNA-seq for Differential Gene Expression, 25 M paired-end sequences, 2*76 basepair reads per sample

treatment_protocol: Progeny were genotyped. Mice bearing composite heterozygous Mpz-Cre and defloxed Braf alleles were termed "mutant" and other genotypes were termed "controls". Mice were born in appropriate Mendelian ratios. Single sciatic nerves were dissected away from conjunctive tissue and flash-frozen at -80°C for RNA-sequencing from euthanized animals at postnatal days 5 or 21.

value: sciatic nerve

tag: Stage

value: postnatal day 21

value: mutant


title: Sciatic nerve, mutant, postnatal day 21, biol rep 3 [2022A383]


title: Sciatic nerve, control, postnatal day 21, biol rep 3 [2022A313]

value: control


title: H2A119Ub_Low_Gln

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Library strategy: CUT&Tag

source_name: KPC1199 cells

extract_protocol:
Briefly, tumor cell were generated and collected after 72 hours of glutamine starvation.CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme).
DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme)

value: KPC1199 cells

value: pancreatic tumor cells

tag: chip antibody

value: 0.4 mmol/L gln


title: K36me3_Cont

value: 2 mmol/L gln


title: Sciatic nerve, control, postnatal day 21, biol rep 4 [2022A314]


title: Sciatic nerve, mutant, postnatal day 21, biol rep 2 [2022A219]


title: H2A119Ub_Cont


title: Sciatic nerve, control, postnatal day 5, biol rep 4 [2022A213]

value: postnatal day 5


title: K27me3_Cont


title: Sciatic nerve, control, postnatal day 5, biol rep 3 [2022A211]


title: K27Ac_Low_Gln


title: K27Ac_Cont


title: Sciatic nerve, mutant, postnatal day 5, biol rep 2 [2022A208]


title: RIP_mRNA-M5B_ES_N_Un_IgG_replicate 2

value: uninfected


title: RIP_mRNA-M6B_ES_N_Un_INPUT_replicate 2


title: Sciatic nerve, mutant, postnatal day 5, biol rep 4 [2022A212]


title: K4me3_Low_Gln


title: Low_Gln_3

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size were calculated using a protocol from Chepeleve et al., Nucleic Acids Research, 2009.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

extract_protocol:
Briefly, tumor cell were generated and collected after 72 hours of glutamine starvation.
RNA libraries were prepared for sequencing using standard illumina protocols.


title: Sciatic nerve, mutant, postnatal day 5, biol rep 1 [2022A206]


title: Low_Gln_2


title: K4me3_Cont


title: Sciatic nerve, control, postnatal day 5, biol rep 2 [2022A209]


title: Low_Gln_1


title: Sciatic nerve, mutant, postnatal day 21, biol rep 1 [2022A202]


title: K36me3_Low_Gln


title: Cont_3


title: K27me3_Low_Gln


title: Sciatic nerve, mutant, postnatal day 5, biol rep 3 [2022A210]


title: Sciatic nerve, control, postnatal day 21, biol rep 1 [2022A200]


title: Sciatic nerve, control, postnatal day 21, biol rep 2 [2022A203]


title: input_KO2 macrophage

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Reads were aligned to Mus musculus reference genome mm10 using bowtie2
The SAM files were converted to the BAM format using Samtools.
Picardtools (http://broadinstitute.Github.io/picard) were used to remove PCR duplicates.
The BAM files were converted to bigwig files by deepTools for visualization and heatmaps.
For camparison across CUT&Tag samples with a spike-in genome, the bigwig files were normalized to spike-in genome coverage
Assembly: mm10
Supplementary files format and content: bigWig (except for input sample)
Library strategy: CUT&Tag

source_name: Bone marrow-derived macrophages

growth_protocol: Dulbecco's modified Eagle's medium (DMEM, HyClone,Logan, UT, USA) supplemented with 10% (v/v) fetal bovine serum (Gibco, Grand Island, NY, USA), 1% (w/v) sodium pyruvate, 1% (w/v) HEPES, 100 U/ml pen/strep, 20% L929 cell conditioned media and 5% horse serum

extract_protocol:
Mixed cells were washed and resuspended with PBS prior to light fixation with 0.1% formaldehyde/PBS. Concanavalin A beads were prepared and washed with binding buffer combined with macrophage-HEK293T mixed cells, and rotated at room temperature for 20 min. The bead- cells complex was suspended with primary antibody (H3K27me3) in ice-cold antibody for overnight at 4 °C. The mixture was then washed with Dig-wash buffer followed by the addition of secondary for 30 min. The mixture was washed again with Dig-wash buffer and subjected to binding reaction of pAG-Tn5 adaptor complex in Dig-300 buffer for 1 h at room temperature. After washed with Dig-300 buffer, the mixture was suspended with Tagmentation buffer for tagmentation reaction for 45 min at 37 °C. The tagmented DNA was eluted and purified using SPRI beads (Beckman Coulter). The DNA was amplified by PCR reaction using Q5 Hot Start High-Fidelity 2x Master Mix (NEB).
Libraries were prepared by Custom Barcodes Adapter 1 (index i5) and Custom Barcodes Adapter 2 (index i7). Libraries were amplified by 17 cyles on thermocycler. Libraries were purified and quantified by SPRIselect (Beckman Coulter, B23319) and library quantification kit (Takara Bio, 638324), respectively.

treatment_protocol: BMDMs were primed with Salmonella spp lipopolysaccharide (LPS; Sigma Aldrich, St. Louis, MO, USA) at 100 ng/ml for 24 h. After the priming, the medium was replaced with fresh DMEM complete medium, and the cells were rested for 48 h. The resting step was followed by LPS (10 ng/ml) stimulation for the indicated times

value: Bone marrow-derived macrophages

value: Macrophage

value: Eed KO

value: LPS tolerance


title: Cont_2


title: input_KO1 macrophage


title: CLP-GA3

city: Hangzhou

first: Xiao

last: Yan

address: No.2318 Yuhangtang Road

institute: Hangzhou Normal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data(raw reads) of fastq format were firstly processed through in-houseperl scripts.In this step,clean data(clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat 2v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat 2v2.0.5.
Feature Counts 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 readscount mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
The isolated islets are quickly put into liquid nitrogen and stored at low temperature. TRIzol (Invitrogen, Waltham, Massachusetts, USA) was used to isolate total RNA from islets according to the manufacturer's protocol. The amount of total RNA was measured with Nanodrop 2000 (Thermo Scientific, Waltham, Massachusetts, USA), and the quality was evaluated by 1% agarose gel electrophoresis, and stained with 4S Red Plus nucleic acid stain (Sango, Shanghai, China).
RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit.

treatment_protocol: C57BL/6J mice treated with gallic acid or vehicle were subjected to cecal ligation and puncture (CLP).

value: Liver

tag: age

value: 8–10 weeks old

value: wild type

value: cecal ligation and puncture (CLP)+Gallic acid


title: Cont_1


title: input_WT2 macrophage

value: WT


title: Sciatic nerve, control, postnatal day 5, biol rep 1 [2022A207]

value: sciatic nerve


title: input_WT1 macrophage


title: CLP-GA5


title: CLP2

value: cecal ligation and puncture (CLP)


title: H3K27me3_KO1 macrophage

value: H3K27me3, CST


title: H3K27me3_WT2 macrophage


title: GA3

value: Sham operation+Gallic acid


title: GA2


title: Con4

value: Sham operation


title: RNA_NK_rep3

city: Chicago

first: Benjamin

last: McDonald

state: IL

address: 924 E. 57th Street BSLC

institute: University of Chicago

data_processing:
Raw sequence reads were proceed through FastQC
and  aligned to mouse genome Mus_musculus.GRCm39.108
Assembly: Mus_musculus.GRCm39.108

source_name: Bone marrow

extract_protocol:
RNA extraction and cDNA synthesis were processed with SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio).
Libraries were constructed using Nextera XT DNA library preparation kit (Illumina)

value: Bone marrow

value: lymphocytes


title: GA1


title: RNA_NK_rep5


title: H3K27me3_KO2 macrophage


title: Con2


title: RNA_NK_rep4


title: RNA_NK_rep6


title: RNA_NK_rep2


title: RNA_NKP_rep6


title: CLP-GA7


title: Con1


title: CLP3


title: RNA_NKP_rep5


title: RNA_NKP_rep4


title: RNA_NKP_rep3


title: CLP1


title: RNA_NKP_rep2


title: H3K27me3_WT1 macrophage


title: vWATpE2_RNAseq_1

city: Sherbrooke

first: Nicolas

last: Gévry

state: Québec

address: 2500, boulevard de l'Université

department: Biologie

institute: Université de Sherbrooke

data_processing:
For RNA-seq : Normalized expression data were obtained using the RNAseq mugqic pipeline from McGill University (https://bitbucket.org/mugqic/mugqic) with mm10 genome assembly. Expression analysis was performed on medium and highly expressed genes (cut-off with FPKM > 100).
For ChIP-seq : Trimmed ChIPseq raw data were aligned to mm10 assembly using bwa tool v0.7.12. Only sequences that mapped once to the genome with a mapping quality score >10 were further analysed. Peaks were called by MACS tool v2.1.0 using a threshold p-value of 0.0025.
Genome_build: mm10
Supplementary_files_format_and_content: bed (narrowPeak) files were generated using MACS tool. Bedgraph files were generated using HOMER's maketagdirectory and makeUCSCfiles tools. Xlsx file combined FPKM data from th RNA-seq experiments, FPKM were obtained by the cufflink tool, sample 1 respresents vehicule-treated vWAT samples and sample 2 represents estradiol-treated vWAT samples.

source_name: vWAT

extract_protocol:
Tissue were removed and flash freezed in liquid nitrogen. RNA were extracted using the direct-zol RNA Miniprep kit (R2052, Zymo Research). For ChIP experiment, nuclei were first isolated and sonicated, then a anti-ERα antibody (sc543, Santa Cruz Biotechnology) was used to purified ERα enrichied chromatin.
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols. Shortly, RNA-seq librairies were prepared following Baby, V. et al. (PMID: 28893065) procedure. ChIP-seq librairies were produced as proviously describe in Bianco, S. et al. (PMID: 25435372).

treatment_protocol: Mice were treated with estradiol or vehicule before sacrifices

value: vWAT

value: Estradiol

value: 10 weeks


title: vWATmE2_RNAseq_2

value: Vehicule


title: vWATmE2_RNAseq_1


title: vWATpE2_RNAseq_2


title: vWATpE2_RNAseq_3


title: RNA_NKP_rep1


title: LiverpE2_ERa_ChIPseq_2

description:
LiverpE2_ERa_ChIPseq.narrowPeak
LiverpE2_ERa_ChIPseq.ucsc.bedGraph.gz


title: LiverpE2_ERa_ChIPseq_1


title: RNA_ILCP_rep6


title: BATpE2_ERa_ChIPseq_1

description:
BATpE2_ERa_ChIPseq.narrowPeak
BATpE2_ERa_ChIPseq.ucsc.bedGraph.gz

source_name: BAT

value: BAT


title: RNA_ILCP_rep5


title: RNA_NK_rep1


title: RNA_ILCP_rep4


title: scWATpE2_ERa_ChIPseq_3

description:
scWATpE2_ERa_ChIPseq.narrowPeak
scWATpE2_ERa_ChIPseq.ucsc.bedGraph.gz

source_name: scWAT

value: scWAT


title: scWATpE2_ERa_ChIPseq_2


title: scWATpE2_ERa_ChIPseq_1


title: vWATmE2_H3K27ac_ChIPseq_2

description:
vWATmE2_H3K27ac_ChIPseq.narrowPeak
vWATmE2_H3K27ac_ChIPseq.ucsc.bedGraph.gz


title: RNA_ILCP_rep2


title: RNA_ILCP_rep1


title: RNA_EILP_rep5


title: vWATmE2_H3K27ac_ChIPseq_1


title: vWATpE2_H3K27ac_ChIPseq_2

description:
vWATpE2_H3K27ac_ChIPseq.narrowPeak
vWATpE2_H3K27ac_ChIPseq.ucsc.bedGraph.gz


title: vWATpE2_H3K27ac_ChIPseq_1


title: RNA_EILP_rep4


title: RNA_EILP_rep3


title: vWATmE2_ERa_ChIPseq_2

description:
vWATmE2_ERa_ChIPseq.narrowPeak
vWATmE2_ERa_ChIPseq.ucsc.bedGraph.gz


title: RNA_EILP_rep2


title: vWATmE2_ERa_ChIPseq_1


title: RNA_EILP_rep1


title: Fibro Rep 2

city: PHILADELPHIA

first: MONTSERRAT

last: ANGUERA

address: 380 S. University Ave, Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania

description:
XCI is skewed; Cast X chromosome will always be inactive
SupplementaryTable_4.xlsx

data_processing:
For allele specific alignment: SNPsplit was used to identify SNPs that differ between the Castaneus and 129S1 or B6 genomes and to generate an mm10 genome in which all differential SNPs are N-masked. Spliced Transcripts Alignment to a Reference (STAR) was used to align reads to the N-Masked Genome and aligned reads were then separated into "Cast" and "129S1" or "B6" reads using SNPsplit.
Aligned reads were quantified using FeatureCounts (subread-2.0.0).
Diploid RPKM was calculated, genes are expressed if RPKM >1
Haploid gene expression of expressed genes was calculated in allele-specific reads per 10 million uniquely mapped (SRPM), genes considered expressed from inactive X if SRPM > 2
Binomial model of escape probablity calculated, 95% confidence interval was applied to genes passing RPKM and SRPM filters; if 95% confidence interval is > 0 gene was considered as escaping XCI
Assembly: 129S1/SvlmJ (accession# ERS076385) and CAST/EiJ (accession# ERS076381) genomes, assembled by Sanger Institute Mouse Genomes Project https://www.sanger.ac.uk/data/mouse-genomes-project/
Supplementary files format and content: .TXT files containing raw outputs generated by FeatureCounts (subread-2.0.0), 2/sample, allele-specific, whole genome
Supplementary files format and content: .CSV files containing final list of escape genes with processed read counts; columns contain gene name, mean diploid RPKM for naïve and stim, mean SRPM for each X allele in naïve and stim, and the Xi/Xa ratio of SRPM for naïve and stim

source_name: ear

extract_protocol:
phenol/chloroform isolation (TRIzol)
Illumina TruSeq Stranded Total RNA LT kit

treatment_protocol: in vitro stimulated cells were treated with 1uM CpG for 12hrs or 24hrs before collection

value: ear

value: female

value: Fibroblasts

value: F1 B6/Cast; Xist+/-


title: vWATpE2_ERa_ChIPseq_1

description:
vWATpE2_ERa_ChIPseq.narrowPeak
vWATpE2_ERa_ChIPseq.ucsc.bedGraph.gz


title: vWATpE2_ERa_ChIPseq_3


title: vWATpE2_ERa_ChIPseq_2


title: B6 B Cell Stim 24 hour Rep 3

description:
XCI is skewed; Cast X chromosome will always be inactive
SupplementaryTable_3.xlsx

source_name: spleen

value: spleen

value: CD23+ B cells

value: in vitro CpG 24hrs


title: Fibro Rep 1


title: Fibro Rep 3


title: vWATpE2_ERa_ChIPseq_4


title: B6 B Cell Stim 24 hour Rep 2


title: nhr131_F17_biol_rep5

city: San Francisco

first: Kaveh

last: Ashrafi

state: CA

department: Physiology

institute: UCSF

data_processing:
Galaxy EC2 instance
FASTq groomer
TopHat2 ( paired end, mate-inner-distance: 150 bp, stdev 40 bp )
HTSeq-counts
Assembly: WS235
Supplementary files format and content: comma separated value, Raw_counts.csv

organism: Caenorhabditis elegans

source_name: whole animal_L4_stage

growth_protocol: C. elegans were cultured from synchronized L1 stage animals in liquid culture until the L4 stage

extract_protocol:
C. elegans were extracted directly with trizol, total RNA purified using spin columns with on column DNAse digestion (Zymo Research)
Total RNA was converted into Illumina adapter ligated cDNA using Nextflex polyA beads in conjunction with the NextFlex Rapid Directional RNA-Seq Kit (Bioo Scientific/Perkin-Elmer)

treatment_protocol: 4 hr before harvest, liquid cultures were treated with either F17 or DMSO alone

value: whole animal_L4_stage


title: B6 B Cell Stim 12 hour Rep 3

description:
XCI is skewed; Cast X chromosome will always be inactive
SupplementaryTable_2.xlsx

value: in vitro CpG 12hrs


title: nhr131_F17_biol_rep4


title: B6 B Cell Stim 24 hour Rep 1


title: nhr131_F17_biol_rep3


title: nhr131_F17_biol_rep2


title: RNA_ILCP_rep3

value: Bone marrow

value: WT


title: B6 B Cell Stim 12 hour Rep 2


title: nhr131_F17_biol_rep1


title: B6 B Cell Stim 12 hour Rep 1


title: B6 B Cell Naïve Rep 3

description:
XCI is skewed; Cast X chromosome will always be inactive
SupplementaryTable_1.xlsx


title: B6 B Cell Naïve Rep 2


title: nhr131_DMSO_biol_rep4

value: DMSO


title: nhr131_DMSO_biol_rep2


title: B6 B Cell Naïve Rep 1


title: D0.5 Stim B cell rep 2

description: XCI is skewed; Cast X chromosome will always be inactive

data_processing:
HiC-Pro v2.8.9 was used for allele-specific analysis, SNP files were downloaded from Sanger Institiute Mouse Genomes Project for each strain, SNP files were used to mask mm9 reference genome (UCSC Genome Browser), alignment to mask genome was performed using Bowtie2 and the custom SNP-masked index. Parameters for alignment were: (global parameters: --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end –reorder; local parameters: --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end –reorder). Unampped reads, non-uniquely mapped reads, PCR duplicates were filtered out
Raw cis contact matrices at 30kb were assembled, replicates for each condition were merged then balanced using Knight-Ruiz balancing. For each balanced matrix, simple scalar normalization, where a simple scalar size factor for each pixel was calculated based on genomic distance between pairs of bins.
For domain calling, 3DNetMod was used to identify TADs and subTADs on the balanced Hi-C matrices binned at 30kb resolution. Data was log transformed and chunked into 6Mb regions with 4Mb overlap between adjacent regions, and into 3Mb regions with 2Mb overlap. Sparse regions, where a chunked region contained zero counts for 1/3 of all pixels on the diagnal or contained consecutive zeros for more than 1500kb distance, were filtered out. High confidence domains were identified as consecutive gamma steps resulting in the same number of communitues (mean per 20 partitions) with a minimum plateu size of 16 and 8 for 6Mb and 3Mb chinked regions. 6Mb and 3Mb chunked regions were merged and domains smaller than or equal to 150kb were filtered out. Final unique boundary locations were made by merging redudent domains and colocalizing boundary locaitons. Domains were considered redundant if two domains were within =/- 60kb on both boundary edges. Boundary locations were colocalized to share a single consistent boundary if the gap between adjacent boundaries was less than 7.5% of the domain size of each of the boundaries or if boundaries were located within 60 kb of each other.
Assembly: C57BL/6NJ (accession #ERS076384) and CAST/EiJ (accession# ERS076381) genomes, assembled by Sanger Institute Mouse Genomes Project https://www.sanger.ac.uk/data/mouse-genomes-project/, mm9 (https://hgdownload.soe.ucsc.edu/downloads.html#mouse)
Supplementary files format and content: .gz files containing all valid pairs for either the whole genome or for each X allele (active X and inactive X) for all replicates and timepoints
Supplementary files format and content: .npz files of merged replicates containing balanced files for each X allele (active X and inactive X), and .txt files of merged replicates containing bias for each X allele at 30kb and 200kb resolution

extract_protocol:
Arima HiC+ kit was used to prepare samples with no changes to protocol (Arima Genomics, San Diego, CA, USA), 2 million cells/replicate (n=2 mice per timepoint)
KAPA HyperPrep kit (07962312001, Roche) with modifications provided by Arima Genomics

treatment_protocol: in vitro stimulated cells were treated with 1uM CpG for 12hr and 24hrs before collection

value: Female

value: CD23+ B Cell

value: F1 C57BL6/Cast; Xist+/-

value: 1uM CpG for 12hrs


title: nhr131_DMSO_biol_rep1


title: WT_F17_biol_rep5

value: wild type


title: nhr131_DMSO_biol_rep3


title: D0.5 Stim B cell rep 1


title: WT_F17_biol_rep3


title: WT_F17_biol_rep4


title: SIR-S34

source_name: lung

value: lung

value: Cre


title: WT_F17_biol_rep2


title: liver, HSS100_2

city: Goyang

first: Hee-sung

last: Chae

state: Gyeonggi-do

address: Dongguk-ro 32

department: Department of pharmacy

institute: Dongguk university

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA)according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

value: liver

value: High fat diet with Schisandrin C plus simvastatin100 mg/kg


title: liver, HSS100_1