title: microorganism,mutant-coculture,24h,rep2

value: H. alvei H4 {delta}luxI +P. fluorescens ACTT13525


title: CLFT044_rep3

status: Public on Jan 31 2024

type: SRA

city: Riverside

first: Jason

last: Stajich

state: California

address: 900 Univeristy Avenue

department: Microbiology and Plant Pathology

country: USA

institute: University of California, Riverside

library_source: transcriptomic

data_processing:
Reads were aligned to reference genomes GCA_000149865.1 and  JAQIHF000000000 using Hisat2  v2.2.1
Raw read counts were generated with FeatureCounts from Rsubread (Liao, Smyth, and Shi 2019) and TPM values were calculated with edgeR (Robinson, McCarthy, and Smyth 2010)
Assembly: GCA_000149865.1 and  JAQIHF000000000
Supplementary files format and content: comma separated files containing transcript counts for each sample when aligning to the reference genome GCA_000149865.1
Supplementary files format and content: comma separated file containing transcript counts for each sample when aligning to the reference genome JAQIHF000000000

molecule: polyA RNA

organism: Batrachochytrium dendrobatidis

source_name: fungi

growth_protocol: 5e5 zoospores from Bd strains CLFT044, CLFT061, CLFT067, CLFT071, CLFT085, and JEL423 were inoculated on 1% Tryptone agar and incubated at 18C for seven days.

extract_protocol:
RNA was extracted using TRIzol following manufacturer's protocols and incorporating a 12 hour isopropanol precipitation to increase yields.
mRNA library preparation (poly A enrichment) at Novogene

tag: cell type

value: fungi

tag: genotype

tag: treatment

value: Bd-BRAZIL


title: 8032-S52_S52_L002

city: 5841 S Maryland Ave. MC3026

first: Eric

middle: M

last: Thompson

state: IL

institute: The University of Chicago

description: X21584 G207 24hr

data_processing:
Sample fastq file quality metrics were assessed via FastQC v0.11.9 and MultiQC v1.11. Paired-end reads were aligned to the GRCh38.p14 human reference genome via STAR v2.7.2b with default parameter settings. Post-alignment quality metrics were assessed via the log file output of STAR. Quantification and generation of the raw counts matrix were performed by featureCounts v1.6.3. The raw counts matrix was then normalized, and differential expression was calculated via DeSeq2 R package v1.36.0.
Assembly: GRCh38.p14
Supplementary files format and content: Single .csv file contains gene counts for all samples with each sample containing two entries; one for each sequencing lane (L001 and L002)

molecule: total RNA

organism: Homo sapiens

source_name: X21584 pediatric high grade glioma

growth_protocol: D283,D324, D556, D456: DMEM-12 plus 10% FNS, 1% NEAA, 1% glutamine; X21584: neurobasal medium plus FGF, EGF, B-27 supplement, L-glutamine, amphotericin, and gentamicin; D341: Improved MEM Zinc option.

extract_protocol:
The Sequencing and Genomic Technologies (SGT) Core Facility at Duke University performed RNA sequencing. The SGT Core Facility extracted total RNA from cell pellets using the RNeasy Plus Mini Kit from Qiagen (catalog #: 74134). mRNA was enriched from total RNA and reverse-transcribed into cDNA to build sequencing libraries using the KAPA mRNA HyperPrep Kit from Roche (KK8581).
Libraries were pooled to equimolar concentrations and sequenced on the NovaSeq 6000 S2 flow cell to produce 50 bp paired-end reads.

value: pediatric high grade glioma cell line

tag: cell line

tag: time


title: vehicle, ALN-treated, 2wks of daily loading, rep7,cancellous bone,L [A49]

city: Ithaca

first: Marjolein

last: van der Meulen

state: NY

address: Weill Hall

department: BME

institute: Cornell University

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample

organism: Mus musculus

source_name: cancellous bone

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols

tag: tissue

value: cancellous bone

tag: limb

value: L

tag: age

value: 28 wks


title: vehicle, ALN-treated, 2wks of daily loading, rep7,cancellous bone,Right [A53]

value: Right


title: pMacs, WT, M, O, IFN-treated, replicate 3

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

data_processing:
Reads were aligned to mouse genome GRCm39/v107 with STAR v2.7.9a
Gene counts were generated from bam files using Rsamtools v2.16.0 and the summarizeOverlaps function with the GenomicAlignments v1.36.0 package in R
Differential genes were analyzed with DESeq2 v1.40.2 in R using default settings.
Gene ontology enrichment analysis was performed with goseq v1.52.0 in R.
Assembly: GRCm39/v107
Supplementary files format and content: comma-separated text file includes FPKM values for each sample
Supplementary files format and content: comma-separated text file includes raw count values for each sample

source_name: primary peripheral macrophages

growth_protocol: Peritoneal macrophages were harvested from mice that had received a 1 ml intraperitoneal administration of 3% Brewer thioglycolate broth 72 hours prior collection. Mice also received Buprenorphine Sustained-Release every 48 hours for pain relief. Mice were sacrificed via cervical dislocation and abdomen sprayed with 70% Ethanol. The skin of the abdomen was split along the midline, taking care to avoid puncturing or cutting the abdominal cavity. 10 mL of cold RPMI media (Gibco; 11875119) was injected into the peritoneal cavity using a 27G needle. After gentle massaging of the peritoneal cavity, as much fluid was withdrawn as possible from the peritoneal cavity using a 25G needle and 10 mL syringe. Aspirated fluid was passed through a 70uM nylon filter onto 50mL falcon and pre-wet with 5mL of HBSS-/-. Filters were then washed twice with 5mL of HBSS-/- and then tubes spun at 400x g for 5 minutes at 4°C. Supernatant was aspirated and pellet resuspended in 3 mL pre-warmed growth media (RPMI, 10% FBS, 1% Pen-Strep). Cells were counted and viability recorded using trypan-blue exclusion on an automated cell-counter (Countess™; Thermo). Volume growth media was adjusted so that cells were plated at 5 x 105/mL in 6-, 24- or 96-well plates depending on the intended assay. Cells were incubated at 37°C, 5% CO2 for a minimum of 2-to-3 hours to allow macrophages to adhere. Wells were washed twice with sterile PBS to remove non-adherent cells and new, pre-warmed growth media added.

extract_protocol:
RNA from approximately 2-4 x 106 cells was isolated. RNeasy mini kit (Qiagen) was used according to manufacturer’s instructions. Briefly, 10 µL of β-mercaptoethanol was added to every 1 mL of RLT buffer. 350 µL was added to each well and cells homogenized manually with a mini cell scraper. Cell lysate was transferred to an RNAase free Eppendorf and an equal volume of 70% ethanol was added to each sample. Samples were loaded into supplier columns and centrifuged at 11,000 x g for 30 seconds and flow through discarded. 350 µL RW1 buffer was added to each column and centrifuged at 11,000 x g for 15 seconds and flow through discarded. RW1 buffer was added and columns centrifuged at 11,000 x g for 15 seconds. RPE buffer was added to columns, centrifuged for 11,000 x g for 30 seconds, repeated, and 30 µL RNase-free water was added and RNA was eluted. RNA concentration was quantified and 260/230 and 260/280 ratios recorded using a spectrophotometer. RIN values were assessed to ensure RNA integrity using Agilent RNA 6000 Nano Kit (Agilent) and Agilent 2100 Bioanalyzer
RNA was sent to the Interdisciplinary Center for Biotechnology Research (ICBR) core at the University of Florida, where library preparation was performed following the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina manual and 2x150bp paired-end sequencing completed on an Illumina NovaSeq 6000 (Illumina).

treatment_protocol: For cells requiring ex vivo stimulation, 100U of IFNγ (R&D) or vehicle (H2O) was added for 18 hours. For co-treatments, a final concentration of 40 nM Bafilomycin A1 (Sigma) and 100 nM PF360 (PF-06685360; MedChem) was used.

tag: Sex

value: M

value: old

value: primary peripheral macrophages

value: wild-type

value: interferon-gamma


title: vehicle, ALN-treated, 2wks of daily loading, rep7,cortical bone,L [A50]

source_name: cortical bone

value: cortical bone


title: pMacs, WT, M, O, IFN-treated, replicate 2


title: vehicle, ALN-treated, 2wks of daily loading, rep6,cortical bone,Right [A46]


title: 8032-S51_S51_L002

description: X21584 G207 8hr


title: microorganism,coculture,24h,rep3

city: Dalian

first: Yanan

last: Wang

state: Liaoning

address: Ganjingzi District

country: China

institute: Dalian Polytechnic University

data_processing:
clean data (clean reads) were obtained by removing  reads containing adapter, reads containing N base and low quality reads from  raw data.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Rockhopper was used to identify novel genes, operon, TSS, TTS and Cis_x0002_natural antisense transcripts.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq R package
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package and used KOBAS3 software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: 569
Supplementary files format and content: H. alvei H4WT and P. fluorescens ATCC13525
Supplementary files format and content: H. alvei H4ΔluxI and P. fluorescens ATCC13525

organism:
Pseudomonas fluorescens
Hafnia alvei

source_name: H. alvei H4 WT + P. fluorescens ACTT13525

extract_protocol:
The RNA was harvested from H. alvei H4WT/ΔluxI and P. fluorescens ATCC13525
Total RNA was used as input material for the RNA sample preparations. For  prokaryotic samples, mRNA was purified from total RNA using probes to  remove rRNA.

tag: strain


title: vehicle, ALN-treated, 2wks of daily loading, rep6,cancellous bone,Right [A45]


title: pMacs, WT, M, O, IFN-treated, replicate 1


title: vehicle, ALN-treated, 2wks of daily loading, rep8,cancellous bone,L [A57]


title: pMacs, WT, M, O, untreated, replicate 2

value: untreated


title: 8032-S51_S51_L001

description: X21584 G207 8hr


title: microorganism,coculture,24h,rep2

value: H. alvei H4 WT + P. fluorescens ACTT13525


title: pMacs, WT, F, Y, untreated, replicate 3

value: F

value: young


title: microorganism,coculture,24h,rep1


title: 8032-S50_S50_L002

description: X21584 G207 8hr


title: 8032-S50_S50_L001

description: X21584 G207 8hr


title: 8032-S52_S52_L001

description: X21584 G207 24hr


title: pMacs, WT, F, Y, untreated, replicate 1


title: microorganism,mutant-coculture,24h,rep1

source_name: H. alvei H4 {delta}luxI +P. fluorescens ACTT13525


title: vehicle, ALN-treated, 2wks of daily loading, rep5,cortical bone,Right [A38]


title: vehicle, ALN-treated, 2wks of daily loading, rep6,cancellous bone,L [A41]


title: 8032-S4_S4_L002

description: D324 G207 8hr

source_name: D324 medulloblastoma

value: medulloblastoma cell line


title: 8032-S4_S4_L001

description: D324 G207 8hr


title: pMacs, WT, F, Y, IFN-treated, replicate 3


title: pMacs, WT, F, Y, IFN-treated, replicate 2


title: vehicle, ALN-treated, 2wks of daily loading, rep5,cortical bone,L [A34]


title: vehicle, ALN-treated, 2wks of daily loading, rep5,cancellous bone,L [A33]


title: pMacs, WT, F, Y, IFN-treated, replicate 1


title: 8032-S49_S49_L001

description: X21584 G207 8hr


title: 8032-S49_S49_L002

description: X21584 G207 8hr


title: vehicle, ALN-treated, 2wks of daily loading, rep4,cortical bone,Right [A30]


title: vehicle, ALN-treated, 2wks of daily loading, rep6,cortical bone,L [A42]


title: fls2_flg22_10h_2

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

data_processing:
RNA-seq was performed on the HiseqX platform at Macrogen.
Reads were quality filtered by fastp (ver. 0.19.7) with the parameters -A -x -f 8 -q 30.
Arabidopsis genome indexes were generated by STAR (ver. 2.6.1b) using the the paremeters --runMode genomeGenerate --genomeDir /home/user/ngs/data1/At_genome_sjdbOverhang139/ --genomeFastaFiles Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --sjdbGTFfile Arabidopsis_thaliana.TAIR10.34.gtf --sjdbOverhang 139 --runThreadN 8
Reads were mapped by STAR (ver. 2.6.1b) with the parameters --runMode alignReads --genomeDir /home/user/ngs/data1/At_genome_sjdbOverhang139/ --runThreadN 8 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3, and transformed to a count per gene per library by featureCounts (ver. 1.6.0) with the parameters -s 1 -t exon -g gene_id -a /home/user/ngs/data1/At_genome/Arabidopsis_thaliana.TAIR10.34.gtf.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Arabidopsis thaliana

source_name: Seven-day-old plants

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 16 h light period on 1/2 MS 25mM sucrose agar media.

extract_protocol:
Total RNAs were extracted using Sepazol-RNA I Super G (Nacalai tesque), followed by RQ1 RNase-Free DNase  (Promega) treatment.
Libraries were prepared from 500 ng of total RNA. BrAD-seq (Townsley et al., 2015) was used to to create strand specific 3-prime digital gene expression.

treatment_protocol: Six-day-old Arabidopsis plants were transferred into 1/2 liquid media with 25 mM sucrose (for flg22) or without sucrose (for 2-deoxy-d-glucose) for 1 day, and treated with 1μM flg22 or 1mM 2-deoxy-d-glucose

tag: replicate


title: 8032-S48_S48_L002

description: X21584 control

value: control


title: pMacs, WT, F, O, untreated, replicate 5


title: pMacs, WT, F, Y, untreated, replicate 2


title: pMacs, WT, F, O, untreated, replicate 4


title: vehicle, ALN-treated, 2wks of daily loading, rep4,cancellous bone,Right [A29]


title: vehicle, ALN-treated, 2wks of daily loading, rep5,cancellous bone,Right [A37]


title: 8032-S48_S48_L001

description: X21584 control

value: pediatric high grade glioma cell line


title: vehicle, ALN-treated, 2wks of daily loading, rep4,cancellous bone,L [A25]

value: cancellous bone


title: 8032-S47_S47_L002

description: X21584 control


title: pMacs, WT, F, O, untreated, replicate 3


title: pMacs, WT, F, O, untreated, replicate 2


title: 8032-S47_S47_L001

description: X21584 control


title: vehicle, ALN-treated, 2wks of daily loading, rep3,cortical bone,Right [A22]


title: pMacs, WT, F, O, untreated, replicate 1


title: 8032-S46_S46_L002

description: X21584 control


title: pMacs, WT, F, O, IFN-treated, replicate 5


title: 8032-S46_S46_L001

description: X21584 control


title: vehicle, ALN-treated, 2wks of daily loading, rep3,cancellous bone,Right [A21]


title: pMacs, WT, F, O, IFN-treated, replicate 4


title: vehicle, ALN-treated, 2wks of daily loading, rep3,cortical bone,L [A18]

value: L


title: 8032-S45_S45_L002

description: D456 G207 24hr

source_name: D456 pediatric high grade glioma


title: vehicle, ALN-treated, 2wks of daily loading, rep4,cortical bone,L [A26]

value: 28 wks


title: pMacs, WT, F, O, IFN-treated, replicate 3


title: 8032-S45_S45_L001

description: D456 G207 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep2,cortical bone,Right [A14]

value: Right


title: pMacs, WT, F, O, IFN-treated, replicate 2


title: vehicle, ALN-treated, 2wks of daily loading, rep2,cancellous bone,Right [A13]


title: 8032-S44_S44_L001

description: D456 G207 24hr


title: 8032-S44_S44_L002

description: D456 G207 24hr


title: pMacs, WT, F, O, IFN-treated, replicate 1


title: 8032-S43_S43_L002

description: D456 G207 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep3,cancellous bone,L [A17]


title: vehicle, ALN-treated, 2wks of daily loading, rep2,cancellous bone,L [A09]


title: pMacs, R1441C KI, M, Y, untreated, replicate 2

value: M

value: R1441C knock-in


title: Infinium Array: PGCLC BPS 1uM rep 2

type: genomic

city: San Antonio

first: Jake

middle: Dean

last: Lehle

state: TX

address: 16631 Vance Jackson Rd APT#1220

department: NDRB

institute: The University of Texas at San Antonio

description: Infinium Array PGCLC BPS 1uM in EtOH rep 2

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip Array using standard Illumina Infinium HD Methylation protocol.

scan_protocol: Arrays were imaged using iScan reader using standard recommended Illumina scanner setting

data_processing: SeSAMe software v1.20.0

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Mouse PGCLC

label_protocol: Standard Illumina Protocol

growth_protocol: See the publication for a full description of specific growth protocols for each cell types included in the study.

extract_protocol: Genomic DNA was bisulfite-converted with the EZ DNA Methylation Kit (D5001) and modified according to the manufacturer’s recommendations (Zymo Research, CA USA & Illumina, CA USA).

treatment_protocol: For all cell types except PGCLCs, 1 μM BPS was added to media gassed with 5% CO2, 5% O2, and balanced N2 and then injected into sealed T-25 cell culture flasks and left to incubate for 24 hours. The media was gassed to ensure enrichment to 5% CO2, which is normally regulated by the cell incubator, limiting the potential for the pH to change in the media during this exposure period due to the absorption of CO2 by incubating cells. Following 24 hours of exposure, media containing BPS was removed and cells were washed and allowed to recover in fresh untreated media (without BPS or EtOH) for 24 hours prior to harvesting. PGCLCs were not suitable for this exposure paradigm as EpiLCs undergo differentiation to PGCLCs in cell aggregates formed in low-adherence round-bottom 96 well plates and cannot be maintained in T-25 sealed flasks. Therefore, diluted BPS was added to PGCLC media and added to cells in round-bottom 96 well plates to incubate for 24 hours prior to a shortened wash and “chase” period of 8 hours prior to cell sorting.

tag: gender

value: Male

value: BPS 1uM


title: Infinium Array: PGCLC BPS 1uM rep 1

description: Infinium Array PGCLC BPS 1uM in EtOH rep 1


title: Infinium Array: PGCLC con rep 1

description: Infinium Array PGCLC control (EtOH) rep 1

value: Control


title: Infinium Array: PGCLC BPS 1uM rep 3

description: Infinium Array PGCLC BPS 1uM in EtOH rep 3


title: vehicle, ALN-treated, 2wks of daily loading, rep2,cortical bone,L [A10]

value: cortical bone


title: 8032-S42_S42_L002

description: D456 G207 8hr


title: vehicle, ALN-treated, 2wks of daily loading, rep1,cancellous bone,Right [A05]


title: Infinium Array: PGCLC con rep 2

description: Infinium Array PGCLC control (EtOH) rep 2


title: Infinium Array: Granulosa BPS 1uM rep 1

description: Infinium Array Granulosa BPS 1uM in EtOH rep 1

source_name: Mouse Granulosa Cells

value: Female


title: Infinium Array: Granulosa BPS 1uM rep 2

description: Infinium Array Granulosa BPS 1uM in EtOH rep 2


title: pMacs, R1441C KI, M, Y, IFN-treated, replicate 3

value: primary peripheral macrophages

value: interferon-gamma


title: Infinium Array: PGCLC con rep 3

description: Infinium Array PGCLC control (EtOH) rep 3


title: Infinium Array: Sertoli BPS 1uM rep 2

description: Infinium Array Sertoli BPS 1uM in EtOH rep 2

source_name: Mouse Sertoli Cells


title: Infinium Array: Granulosa con rep 3

description: Infinium Array Granulosa control (EtOH) rep 3


title: Infinium Array: Granulosa BPS 1uM rep 3

description: Infinium Array Granulosa BPS 1uM in EtOH rep 3


title: pMacs, R1441C KI, M, Y, untreated, replicate 3

value: young

value: untreated


title: vehicle, ALN-treated, 2wks of daily loading, rep1,cancellous bone,L [A01]


title: vehicle, ALN-treated, 2wks of daily loading, rep1,cortical bone,L [A02]


title: Infinium Array: Granulosa con rep 2

description: Infinium Array Granulosa control (EtOH) rep 2


title: pMacs, R1441C KI, M, Y, IFN-treated, replicate 1


title: Infinium Array: Sertoli BPS 1uM rep 1

description: Infinium Array Sertoli BPS 1uM in EtOH rep 1


title: Infinium Array: Sertoli BPS 1uM rep 3

description: Infinium Array Sertoli BPS 1uM in EtOH rep 3


title: 8032-S42_S42_L001

description: D456 G207 8hr


title: 8032-S43_S43_L001

description: D456 G207 24hr


title: Infinium Array: Granulosa con rep 1

description: Infinium Array Granulosa control (EtOH) rep 1


title: vehicle, ALN-treated, 2wks of daily loading, rep1,cortical bone,Right [A06]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,cortical bone,Right [591]


title: pMacs, R1441C KI, M, Y, untreated, replicate 1


title: 8032-S41_S41_L001

description: D456 G207 8hr


title: pMacs, R1441C KI, M, O, untreated, replicate 2

value: old


title: 8032-S41_S41_L002

description: D456 G207 8hr

value: pediatric high grade glioma cell line


title: pMacs, R1441C KI, M, O, untreated, replicate 3


title: Infinium Array: Sertoli con rep 1

description: Infinium Array Sertoli control (EtOH) rep 1


title: 8032-S3_S3_L002

description: D324 control

value: medulloblastoma cell line

value: control


title: 8032-S40_S40_L002

description: D456 G207 8hr


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,cancellous bone,Right [576]

value: cancellous bone

value: 28 wks


title: 8032-S40_S40_L001

description: D456 G207 8hr


title: Infinium Array: Prelim iPSC BPS 100uM rep 3

description: Infinium Array Preliminary iPSC BPS 100uM in EtOH rep 3

source_name: Mouse iPSC


title: Infinium Array: Prelim iPSC BPS 100uM rep 2

description: Infinium Array Preliminary iPSC BPS 100uM in EtOH rep 2


title: pMacs, R1441C KI, M, O, IFN-treated, replicate 5

value: M


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,cortical bone,Right [577]

value: Right


title: Infinium Array: Sertoli con rep 2

description: Infinium Array Sertoli control (EtOH) rep 2

value: Male


title: 8032-S3_S3_L001

description: D324 control


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,cortical bone,L [570]

value: L


title: pMacs, R1441C KI, M, O, IFN-treated, replicate 4

value: R1441C knock-in


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,cortical bone,Right [563]

value: cortical bone


title: pMacs, R1441C KI, M, O, untreated, replicate 1


title: 8032-S39_S39_L001

description: D456 control


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,cancellous bone,Right [562]


title: Infinium Array: Prelim iPSC BPS 100uM rep 1

description: Infinium Array Preliminary iPSC BPS 100uM in EtOH rep 1

value: BPS 1uM


title: pMacs, R1441C KI, M, O, IFN-treated, replicate 2

value: primary peripheral macrophages


title: 8032-S38_S38_L002

description: D456 control


title: pMacs, R1441C KI, M, O, IFN-treated, replicate 3

value: interferon-gamma


title: 8032-S39_S39_L002

description: D456 control


title: vehicle, vehicle, 2wks of daily loading, rep10,cortical bone,Right [549]


title: Infinium Array: Prelim iPSC BPS 50uM rep 3

description: Infinium Array Preliminary iPSC BPS 50uM in EtOH rep 3

value: Control


title: pMacs, R1441C KI, M, O, IFN-treated, replicate 1


title: pMacs, R1441C KI, M, Y, IFN-treated, replicate 2

value: young


title: 8032-S38_S38_L001

description: D456 control


title: vehicle, vehicle, 2wks of daily loading, rep6,cancellous bone,Right [548]


title: pMacs, R1441C KI, F, Y, untreated, replicate 5

value: F

value: untreated


title: 8032-S37_S37_L002

description: D456 control

value: pediatric high grade glioma cell line


title: Infinium Array: Prelim iPSC BPS 1uM rep 3

description: Infinium Array Preliminary iPSC BPS 1uM in EtOH rep 3


title: Infinium Array: Prelim iPSC BPS 50uM rep 1

description: Infinium Array Preliminary iPSC BPS 50uM in EtOH rep 1


title: pMacs, R1441C KI, F, Y, untreated, replicate 4


title: Infinium Array: Prelim iPSC BPS 50uM rep 2

description: Infinium Array Preliminary iPSC BPS 50uM in EtOH rep 2


title: 8032-S36_S36_L002

description: D283 G207 24hr

source_name: D283 medulloblastoma

value: medulloblastoma cell line


title: pMacs, R1441C KI, F, Y, untreated, replicate 2


title: Infinium Array: Sertoli con rep 3

description: Infinium Array Sertoli control (EtOH) rep 3


title: vehicle, vehicle, 2wks of daily loading, rep4,cortical bone,L [542]


title: 8032-S36_S36_L001

description: D283 G207 24hr


title: vehicle, vehicle, 2wks of daily loading, rep5,cancellous bone,Right [520]

value: cancellous bone


title: 8032-S37_S37_L001

description: D456 control

value: control


title: vehicle, vehicle, 2wks of daily loading, rep3,cancellous bone,L [541]

value: 28 wks


title: pMacs, R1441C KI, F, Y, untreated, replicate 1


title: vehicle, vehicle, 2wks of daily loading, rep3,cortical bone,L [514]


title: pMacs, R1441C KI, F, Y, untreated, replicate 3


title: StsDa01_ssDNA_rep4

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

library_source: genomic

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text/bed files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq

organism: Escherichia coli

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus

extract_protocol:
E. coli C2566 genomic DNA was purified using Monarch Genomic DNA Purification Kit (NEB Ipswich, MA), GM12878 genomic DNA was obtained from Coriell Cell Repositories (Camden, NJ).
Input DNA was sheared to 300 bp using the Covaris S2 instrument. Sheared material was transferred to a PCR strip tube to begin library construction. NEBNext DNA Ultra II Reagents (NEB, Ipswich, MA) were used according to the manufacturer’s instructions for end repair, A-tailing, and adaptor ligation. The custom made Pyrollo-dC adaptor (NEB Organic Synthesis Division, Ipswich MA), where all dCs are replaced with Pyrollo-dC, was used. The ligated samples were purified using NEBNext Sample Purification Beads  according to the manufacturer’s instructions. For ssDNA libraries, prior to deamination the DNA was denatured by heating at 90oC for 10 minutes followed by cooling for 2 minutes on ice. The DNA was then deaminated using 1 µL of PURExpress (NEB, Ipswich, MA) synthesized deaminase protein following manufacturer's recommendations for 1 hour at 37oC. Then 1 µL of Thermolabile Proteinase K (NEB, Ipswich, MA) was added and incubated for 30 min at 37oC followed by 10 min at 60oC. Then the library was amplified using NEBNext Q5U Master Mix (NEB, Ipswich, MA, USA). Paired-end sequencing of 150 cycles (2 x 75 bp) was performed for all the sequencing runs.
DNA sequencing of deaminated double-stranded and single-stranded DNA


title: vehicle, vehicle, 2wks of daily loading, rep2,cancellous bone,L [513]


title: 8032-S34_S34_L002

description: D283 G207 24hr


title: StsDa01_dsDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: StsDa01_ssDNA_rep3


title: pMacs, R1441C KI, F, Y, IFN-treated, replicate 2


title: vehicle, vehicle, 2wks of daily loading, rep4,cortical bone,Right [507]

value: Right


title: 8032-S35_S35_L002

description: D283 G207 24hr


title: SsdA_ssDNA_rep2


title: StsDa01_dsDNA_rep1


title: Infinium Array: Prelim iPSC BPS 1uM rep 1

description: Infinium Array Preliminary iPSC BPS 1uM in EtOH rep 1

value: Male


title: pMacs, R1441C KI, F, Y, IFN-treated, replicate 1

value: R1441C knock-in


title: 8032-S35_S35_L001

description: D283 G207 24hr


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,cancellous bone,Right [590]


title: SsdA_ssDNA_rep1


title: pMacs, R1441C KI, F, O, untreated, replicate 5

value: old


title: pMacs, R1441C KI, F, O, untreated, replicate 4


title: Infinium Array: Prelim iPSC BPS 1uM rep 2

description: Infinium Array Preliminary iPSC BPS 1uM in EtOH rep 2

value: BPS 1uM


title: Infinium Array: Prelim iPSC con rep 3

description: Infinium Array Preliminary iPSC control (EtOH) rep 3


title: SsdA_dsDNA_rep1


title: vehicle, vehicle, 2wks of daily loading, rep4,cancellous bone,Right [506]


title: 8032-S33_S33_L001

description: D283 G207 8hr


title: SsdA_dsDNA_rep2


title: 8032-S34_S34_L001

description: D283 G207 24hr


title: Infinium Array: Prelim iPSC con rep 1

description: Infinium Array Preliminary iPSC control (EtOH) rep 1


title: RaDa01_ssDNA_rep2


title: pMacs, R1441C KI, F, O, untreated, replicate 1

value: primary peripheral macrophages


title: 8032-S33_S33_L002

description: D283 G207 8hr


title: vehicle, vehicle, 2wks of daily loading, rep3,cortical bone,Right [493]

value: cortical bone


title: Infinium Array: Prelim iPSC con rep 2

description: Infinium Array Preliminary iPSC control (EtOH) rep 2

value: Control


title: 8032-S32_S32_L002

description: D283 G207 8hr


title: pMacs, R1441C KI, F, O, untreated, replicate 3


title: pMacs, R1441C KI, F, O, untreated, replicate 2


title: 8032-S31_S31_L002

description: D283 G207 8hr


title: vehicle, vehicle, 2wks of daily loading, rep2,cortical bone,L [486]

value: L


title: RaDa01_dsDNA_rep2


title: RaDa01_ssDNA_rep1


title: pMacs, R1441C KI, F, O, IFN-treated, replicate 4

value: F

value: interferon-gamma


title: pMacs, R1441C KI, F, O, IFN-treated, replicate 5


title: vehicle, vehicle, 2wks of daily loading, rep5,cortical bone,Right [521]


title: MGYPDa23_ssDNA_rep4


title: 8032-S32_S32_L001

description: D283 G207 8hr


title: RaDa01_dsDNA_rep1


title: 8032-S30_S30_L002

description: D283 control


title: 8032-S31_S31_L001

description: D283 G207 8hr


title: vehicle, vehicle, 2wks of daily loading, rep2,cancellous bone,Right [478]


title: pMacs, R1441C KI, F, O, IFN-treated, replicate 3


title: vehicle, vehicle, 2wks of daily loading, rep3,cancellous bone,Right [492]


title: 8032-S30_S30_L001

description: D283 control


title: MGYPDa23_ssDNA_rep3


title: pMacs, R1441C KI, F, O, IFN-treated, replicate 2


title: vehicle, vehicle, 2wks of daily loading, rep1,cortical bone,Right [465]


title: pMacs, R1441C KI, F, O, IFN-treated, replicate 1


title: vehicle, vehicle, 2wks of daily loading, rep1,cancellous bone,Right [464]


title: MGYPDa23_dsDNA_rep2


title: MGYPDa23_dsDNA_rep3


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,cortical bone,L [444]

value: 27 wks


title: 8032-S2_S2_L002

description: D324 control

value: medulloblastoma cell line


title: 8032-S2_S2_L001

description: D324 control


title: MGYPDa17_ssDNA_rep3


title: LN, chikv-2, 24hpi (re-analyzed)

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
re-analysis of GSM5322186
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz

data_processing: Single-cell RNA-seq libraries were processed using the 10X Genomics cellranger software (5.0.1). Analysis was performed using the R package Seurat (4.0.0). Cell type identification was performed with clustifyr (1.0.0) using references built from published data.

source_name: Lymph node

growth_protocol: Mice were housed and bred at the University of Colorado School of Medicine under specific pathogen-free conditions and were distributed randomly into groups containing approximately even division of sexes for experiments. WT male mice were purchased commercially and were age matched and distributed randomly across groups. Mice 4 weeks of age were used in all experiments. All mouse experiments were performed under animal biosafety level 2 or 3 conditions, as appropriate.

extract_protocol:
At 24 hpi the draining popliteal lymph node from mock- or CHIKV-inoculated mice were pooled into individual replicates (3 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click’s medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37C. After incubation, digested tissues were clarified by passing through a 100 μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042-401) columns according to the manufacturer’s instructions with the following modifications: (1) we used 25% of the recommended volume of anti-PE microbeads and (2) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemocytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry.
Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128)

treatment_protocol: WT C57BL/6 mice were mock-inoculated (n = 3) or inoculated with 10e3 PFU of CHIKV (n = 3) in the left rear footpad.

value: Lymph node

value: WT

tag: inoculation

value: chikv

value: 24 hpi


title: LN, chikv-3, 24hpi (re-analyzed)

description:
re-analysis of GSM5322187
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz


title: 8032-S29_S29_L002

description: D283 control

value: control


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep7,cortical bone,Right [437]

value: Right


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep6,cancellous bone,L [443]

value: cancellous bone


title: MGYPDa17_ssDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: LN, chikv-1, 24hpi (re-analyzed)

description:
re-analysis of GSM5322185
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz


title: LN, mock-3, 24hpi (re-analyzed)

description:
re-analysis of GSM5322184
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz

value: mock


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,cortical bone,L [430]


title: MGYPDa17_dsDNA_rep4


title: 8032-S28_S28_L002

description: D283 control


title: MGYPDa17_dsDNA_rep3


title: 8032-S29_S29_L001

description: D283 control


title: LN, mock-2, 24hpi (re-analyzed)

description:
re-analysis of GSM5322183
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,cancellous bone,L [429]


title: LbsDa01_ssDNA_rep2


title: 8032-S27_S27_L002

description: D341 G207 24hr

source_name: D341 medulloblastoma


title: LN, mock-1, 24hpi (re-analyzed)

description:
re-analysis of GSM5322182
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz


title: 8032-S28_S28_L001

description: D283 control


title: LbsDa01_ssDNA_rep1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep6,cortical bone,Right [423]


title: LbsDa01_dsDNA_rep2


title: LbsDa01_dsDNA_rep1


title: LN CD45- cells, chikv-2-8hpi_enriched

description:
Single-cell RNA-seq library from the Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128), libraries enriched for molecules aligning to the CHIKV genome
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz

library_source: transcriptomic single cell

data_processing:
Single-cell RNA-seq libraries were processed using the 10X Genomics cellranger software (5.0.1). Analysis was performed using the R package Seurat (4.2.0).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files

extract_protocol:
At 8 h post-infection the draining popliteal lymph node from mock- or CHIKV-inoculated mice was pooled into individual replicates (2 replicates; LNs from 5 mice pooled per replicate). Lymph nodes were mechanically homogenized using a 22G needle in Click’s medium (Irvine Scientific, 9195) supplemented with 5 mg/mL liberase DL (Roche, 05401160001) and 2.5 mg/mL DNase (Roche 10104159001) for 1 h at 37°C. After incubation, digested LNs were clarified by passing through a 100-μm cell strainer. Cell suspensions were enriched for CD45- cells by labeling cells with PE-conjugated anti-mouse CD45 (30-F11), CD140A (APA5), and Ter119 (Ter119) monoclonal antibodies and subsequent depletion of PE-labeled cells using Miltenyi anti-PE microbeads (130-048-801) and Miltenyi MACS LS (130-042- 401) columns according to the manufacturer’s instructions with the following modifications: (i) We used 25% of the recommended volume of anti-PE microbeads, and (ii) we subjected the CD45- enriched cell fraction to a second MACS LS column. All cell suspensions post-column enrichment were enumerated using a hemacytometer. Cell fractions throughout the procedure were analyzed for PE-labeled cell depletion and enrichment of CD45- cells by flow cytometry.
Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128)

treatment_protocol: WT C57BL/6 mice were mock-inoculated (n = 2) or inoculated with 10^3 PFU of CHIKV (n = 2) in the left rear footpad.

value: Lymph node stromal cells

tag: infection

value: CHIKV infected

value: 8 hpi

tag: enriched


title: 8032-S27_S27_L001

description: D341 G207 24hr


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep7,cancellous bone,Right [422]


title: 8032-S26_S26_L001

description: D341 G207 24hr


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,cancellous bone,L [415]

value: L


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,cortical bone,L [416]

value: cortical bone


title: LN CD45- cells, chikv-1-8hpi_enriched

value: enriched for molecules aligning to the CHIKV genome


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep8,cancellous bone,Right [436]

value: 27 wks


title: LN CD45- cells, mock-2_enriched

value: mock infected


title: 8032-S25_S25_L002

description: D341 G207 24hr

value: medulloblastoma cell line


title: BaDa02_ssDNA_rep4


title: LN CD45- cells, mock-1_enriched

value: Lymph node

value: WT


title: BaDa02_ssDNA_rep3


title: BaDa02_dsDNA_rep2


title: vehicle, vehicle, 2wks of daily loading, rep1,cancellous bone,L [485]

value: 28 wks


title: LN CD45- cells, mock-2

description:
Single-cell RNA-seq library from the Next GEM single-cell 3′ GEM library and gel bead kit v3.1 (1000128)
morrison_count_matrix.tsv.gz
morrison_metadata.tsv.gz

value: no


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,cortical bone,Right [409]

value: Right


title: 8032-S24_S24_L001

description: D341 G207 8hr


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,cortical bone ,L [388]


title: BaDa02_dsDNA_rep3


title: 8032-S25_S25_L001

description: D341 G207 24hr


title: AvDa02_ssDNA_rep2


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep6,cancellous bone,Right [408]

value: cancellous bone


title: AvDa02_ssDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: 8032-S26_S26_L002

description: D341 G207 24hr


title: AvDa02_dsDNA_rep2


title: LN CD45- cells, chikv-1-8hpi


title: LN CD45- cells, chikv-2-8hpi


title: RNA-seq-siMat2a_2

city: Los Angeles

first: Wentao

last: Yang

address: 1441 Eastlake Ave

institute: university of southern california

data_processing:
The cutadapt (https://cutadapt.readthedocs.org/en/stable/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) tools wrapped in Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) were used to trim low quality bases (Q<20) and adapter for raw sequences.
RNA-seq data were mapped to the mm10 (GRCm38) genome of mouse and ERCC reference using Tophat2 (2.1.1)
Duplicated reads for pair-end data were then removed by SAMtools (v1.9)
Annotation of mRNA (GRCm38 v99) was downloaded from Ensembl database. LncRNA annotation was downloaded from NONCODE database and repeat annotation was downloaded from Homer (v4.10). All three annotations were merged into one for gene annotation. Fragment (or template) count for each feature was performed by using featureCounts with parameters “-g 'gene_id' -p  -M -O --fraction -C -F GTF -T 64 -s 0”
Fragment counts were transformed to fragments per kilobase of transcript per million (FPKM) by using edgeR
Assembly: mm10 (GRCm38)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mouse embryonic stem cells

extract_protocol:
Total RNAs were extracted by the RNeasy mini kit (QIAGEN).
Samples were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, #E7760L), NEBNext rRNA Depletion Dit (Human/Mouse/Rat) (NEB, #E6310X), NEBNext Multiplex Oligos for Illumina (NEB, #E6440L) and ERCC RNA Spike-In control Mix (Thermo Fisher Scientific, #4456740).

value: mouse embryonic stem cells


title: RNA-seq-siMat2a_1


title: 8032-S24_S24_L002

description: D341 G207 8hr


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,cancellous bone,Right [394]

source_name: cancellous bone


title: 8032-S22_S22_L002

description: D341 G207 8hr


title: 8032-S23_S23_L001

description: D341 G207 8hr


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,cortical bone,Right [381]


title: 8032-S23_S23_L002

description: D341 G207 8hr


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,cancellous bone,L [387]


title: AvDa01_ssDNA_rep4


title: AvDa02_dsDNA_rep1


title: RNA-seq-siCtr_2


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,cortical bone,L [374]


title: RNA-seq-siCtr_1


title: vehicle, vehicle, 2wks of daily loading, rep2,cortical bone,Right [479]


title: 8032-S21_S21_L002

description: D341 control

value: control


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,cancellous bone,Right [380]


title: 8032-S22_S22_L001

description: D341 G207 8hr


title: RNA-seq-MYCi_2


title: AvDa01_ssDNA_rep3


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,cortical bone,Right [367]


title: RNA-seq-MYCi_1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,cancellous bone,L [373]


title: 8032-S20_S20_L002

description: D341 control


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,cancellous bone,Right [366]


title: RNA-seq-LowSAM50uM_2


title: 8032-S20_S20_L001

description: D341 control


title: AvDa01_dsDNA_rep3


title: AvDa01_dsDNA_rep4


title: LN CD45- cells, mock-1

value: Lymph node stromal cells


title: AaDa02_ssDNA_rep4


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,cortical bone,Right [353]


title: RNA-seq-LowSAM50uM_1


title: 8032-S1_S1_L002

description: D324 control


title: RNA-seq-LowSAM25uM_2


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,cancellous bone,L [345]


title: AaDa02_ssDNA_rep3


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,cancellous bone,Right [352]


title: AaDa02_dsDNA_rep2


title: 8032-S19_S19_L002

description: D341 control


title: 8032-S19_S19_L001

description: D341 control


title: 8032-S21_S21_L001

description: D341 control


title: AaDa02_dsDNA_rep1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,cancellous bone,Right [338]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,cortical bone,Right [339]


title: PvmDa01_ssDNA_rep2


title: 8032-S18_S18_L002

description: D556 G207 24hr

source_name: D556 medulloblastoma


title: RNA-seq-H2O_2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep6,cortical bone,L [332]

source_name: cortical bone


title: 8032-S18_S18_L001

description: D556 G207 24hr


title: PvmDa01_dsDNA_rep2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,cancellous bone,L [331]


title: PvmDa01_ssDNA_rep1


title: RNA-seq-H2O_1


title: PvmDa01_dsDNA_rep1


title: PTH-pretreated, vehicle, 1wk of daily loading, rep5,cortical bone,Right [325]


title: RNA-seq-EedKO_2


title: 8032-S17_S17_L002

description: D556 G207 24hr


title: 8032-S17_S17_L001

description: D556 G207 24hr


title: RNA-seq-LowSAM25uM_1


title: PdDa01_ssDNA_rep2


title: 8032-S1_S1_L001

description: D324 control


title: RNA-seq-Het_1


title: PdDa01_ssDNA_rep1


title: 8032-S16_S16_L001

description: D556 G207 24hr


title: RNA-seq-ETO_2


title: 8032-S16_S16_L002

description: D556 G207 24hr


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,cancellous bone,L [289]


title: RNA-seq-ETO_1


title: PdDa01_dsDNA_rep1


title: RNA-seq-DMSO_2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,cortical bone,Right [283]


title: RNA-seq-DMSO_1


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,cancellous bone,Right [282]


title: 8032-S15_S15_L002

description: D556 G207 8hr


title: 8032-S14_S14_L002

description: D556 G207 8hr


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,cancellous bone,Right [324]


title: PbDa02_ssDNA_rep1


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,cortical bone,L [276]


title: RNA-seq-EedKO_1


title: 8032-S14_S14_L001

description: D556 G207 8hr


title: PTH-pretreated, vehicle, 1wk of daily loading, rep5,cortical bone,L [290]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,cortical bone,Right [269]


title: 8032-S15_S15_L001

description: D556 G207 8hr


title: PbDa02_dsDNA_rep2


title: CRISPR-seq-TSC-1

data_processing:
The cutadapt (https://cutadapt.readthedocs.org/en/stable/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) tools wrapped in Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) were used to trim low quality bases (Q<20) and adapter for raw sequences.
The refined reads were subsequently aligned to the mouse genome (mm10) using Bismark2 with its default settings.
‘bismark_methylation_extractor’ function was employed to calculate the percentage of methylated CpG calls over the total number of calls for each specific site.
A robust coverage exceeding 100x was attained for the examined CpG sites, ensuring a highly reliable analysis.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bedgraph for the CpG methylation sites of Elf5 promoter

source_name: Trophoblast stem Cells

extract_protocol:
Genomic DNA was extracted using the phenol/chloroform/isoamyl alcohol (25:24:1 ratio) method. Genomic DNA was subjected to DNA bisulfite conversion using the Methylation-GoldTM Kit (ZYMO RESEARCH, #D5005). DNA were then used for PCR amplification using the NEB Taq DNA polymerase (NEB, #M0273S). The PCR products were then purified by the QIAquick PCR purification kit (Qiagen, #28104).
Paired-end Tru-Seq compatible Illumina libraries were prepared by the Center for Computational and Integrative Biology (CCIB) DNA Core at Massachusetts General Hospital. Briefly, partial Illumina compatible adapters with unique barcodes were ligated onto each sample during library construction. Subsequently, a low-cycle PCR amplification step completeed the addition of the full-length adapter sequences.

value: Trophoblast stem Cells


title: PbDa02_dsDNA_rep1


title: PdDa01_dsDNA_rep2


title: PbDa01_ssDNA_rep2


title: 8032-S13_S13_L002

description: D556 G207 8hr


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,cortical bone,Right [255]


title: 8032-S13_S13_L001

description: D556 G207 8hr


title: CRISPR-seq-iTSC-2

source_name: Induced trophoblast stem cells

value: Induced trophoblast stem cells


title: CRISPR-seq-iTSC-1


title: PbDa02_ssDNA_rep2


title: PbDa01_ssDNA_rep1


title: 8032-S12_S12_L002

description: D556 control


title: PbDa01_dsDNA_rep2


title: CRISPR-seq-ESC-1

source_name: embryonic stem cells

value: embryonic stem cells


title: 8032-S12_S12_L001

description: D556 control


title: PbDa01_dsDNA_rep1


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,cortical bone,L [262]

value: cortical bone

value: L


title: CRISPR-seq-TSC-2


title: 8032-S11_S11_L002

description: D556 control


title: 8032-S10_S10_L002

description: D556 control


title: HWAT; scRNAseq

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

institute: The second xiangya hospital of central south university

description: 10X Genomics

data_processing:
The Cell Ranger software was obtained from 10× Genomics website.  Alignment, filtering, barcode counting, and UMI counting were performed with cell ranger count module on the raw sequencing data to generate a gene-barcode matrix for subsequent analysis.
The output of Cell Ranger filtered gene expression matrix were analyzed by R software with the Seurat package.
Before the downstream analysis, a step-by-step quality-filtering process was used to remove low-quality nuclei. First, mitochondrial reads were filtered on the threshold of 15%, the UMIs were filtered on the threshold of 1000, detected features were filtered on the threshold of 300, and the ratio of the number of UMIs to features was filtered with a threshold of 2.5. Second, outlier detection was performed using PCA calculated from quality metrics in Scater38. Third, genes expressed in fewer than ten nuclei were removed. Fourth, the nuclei were clustered using Seurat39, and clusters with fewer UMIs low features, or high doublet scores40 were removed iteratively.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peri-heart white adipose tissue

extract_protocol:
All the mice used in this study were 10-week-old male C57BL/6J purchased from Slac Laboratory Animal Company (Shanghai, China). All mice were housed in an environment with controlled temperature and a 12:12 hour light/dark cycle. Before collecting WAT, the mice were anesthetized and infused with PBS heparin sodium solution (77mg/L) to remove blood from adipose tissue. Next, SWAT, NWAT, EWAT, HWAT, and MWAT were collected and the adjacent lymph nodes were removed from SWAT and MWAT. SWAT, EWAT, and NWAT from six mice were pooled for nuclear isolation and snRNA-seq experiments, MWAT from 10 mice for nuclear isolation and snRNA-seq experiments, and HWAT from 20 mice for nuclear isolation and snRNA-seq experiments.
After nuclear separation, at least 8000 nuclei were immediately loaded onto the 10x Genomics Chromium controller (10X Genomics, PN110203). The libraries were prepared according to the manufacturer's instructions, using 10x Genomics single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074).  The libraries were finally sequenced using the Illumina Novaseq 6000 sequencer at a depth of at least 20,000 reads per nucleus with a pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).
snRNAseq

value: Peri-heart white adipose tissue

value: male

value: adipocytes (ADs), immune cells (ICs), endothelial cells (ECs), mesothelial cells (MCs), fibro-adipogenic progenitor cells (FAPs), and pericytes

tag: diet

value: chow diet

value: C57BL/9J wild type


title: MmgDa02_ssDNA_rep2


title: NWAT; scRNAseq

description: 10X Genomics

source_name: Perirenal white adipose tissue

value: Perirenal white adipose tissue

value: C57BL/8J wild type


title: MmgDa02_ssDNA_rep1


title: CRISPR-seq-ESC-2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,cortical bone,Right [241]

value: Right

value: 27 wks


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,cancellous bone,Right [254]

value: cancellous bone


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,cancellous bone,Right [240]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,cortical bone,L [234]


title: MWAT; scRNAseq

description: 10X Genomics

source_name: Mesenteric white adipose tissue

value: Mesenteric white adipose tissue

value: C57BL/7J wild type


title: MmgDa02_dsDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,cancellous bone,L [233]


title: APOA4-KO cells, Hypoxia3, 48H

city: Hangzhou

first: yusen

last: wei

institute: Zhejiang University

description:
gene_count_matrix.csv
genes_fpkm_expression.csv

data_processing:
Fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 to map reads to the reference genome of the Ensembl GRCh38.p13 reference genome (release 109). The mapped reads of each sample were assembled using StringTie with default parameters.  StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: the Ensembl GRCh38.p13 reference genome (release 109)
Supplementary files format and content: Matrix table with raw gene counts and FPKM value for every sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min.
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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp.

value: APOA4 knockout

value: Hypoxia


title: MmgDa02_dsDNA_rep1


title: SWAT; scRNAseq

description: 10X Genomics

source_name: Subcutaneous white adipose tissue

value: Subcutaneous white adipose tissue

value: C57BL/6J wild type


title: 8032-S10_S10_L001

description: D556 control

value: medulloblastoma cell line

value: control


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,cortical bone,L [248]

value: cortical bone

value: L


title: LsfDa01_ssDNA_rep2


title: 8032-S11_S11_L001

description: D556 control


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,cancellous bone,L [247]


title: APOA4-KO cells, Hypoxia2, 48H


title: vehicle, ALN-treated, 1wk of daily loading, rep5,cortical bone,L [220]


title: APOA4-KO cells, Hypoxia1, 48H


title: vehicle, ALN-treated, 1wk of daily loading, rep3,cancellous bone,L [219]


title: vehicle, ALN-treated, 1wk of daily loading, rep1,cortical bone,Right [213]


title: LsfDa01_ssDNA_rep1


title: APOA4-KO cells, Hypoxia3, 24H


title: LsfDa01_dsDNA_rep2


title: BMSCs, Dmp1KOFgf23cKO3

city: Chicago

first: Valentin

last: David

state: Illinois

address: 320 E Superior Street

department: Medicine

institute: Northwestern University

description: 10X Genomics

data_processing:
After the initial demultiplexing we used Seurat HTODemux function to separate the data in 12 separate samples. Using the barcodes for each sample, data was demultiplexed in individual samples (bam, matrix, features and barcodes) using the 10 Genomics CellRanger with barcode-sample-assignment attribute. Alignment was performed against the mm10-2020-A build using both exonic and intronic reads.
Data from each individual sample was processed into a Seurat Object and mitochondiral percentage was calculated. Data from each sample was merged into a single Seurat Object, normalized using SCT transform and mitochondrial percentage was regressed.
Seurat clusters were called using 50 npcs, 1:30 umap reduction on the SCT assay and FindClusters function at the resolution of 0.8. Celltypes were detemined using differentially expressed gene markers in clusters.
An osteoblast subcluster was created from the intitial Seurat object and used for to determine the genes differentially expressed in osteoblastic clusters.
Assembly: mm10
Supplementary files format and content: Tab separated matrix, features and barcodes(cells) files.
Supplementary files format and content: FGF23 regulated and DMP1 regulated differential expression with corrected p value (BD FDR p<0.1).

source_name: Bone Marrow

growth_protocol: Cells were cultured for 21 days in αMEM medium supplemented with 10% FBS (Corning, New York, USA), 10 U/ml penicillin, 100 μg/ml streptomycin (Thermo Fisher Scientific, Whaltman, USA), 10 mM β-glycerophosphate, and 50 μg/ml ascorbic acid (Sigma-Aldrich, St. Louis, USA) to induce differentiation.

extract_protocol:
Collected cells were isolated after 5 min Trypsin 1X incubation. Cells were incubated with 7-Aminoactinomycin D (7AAD) for 10 minutes and kept on ice until fluorescence sorting. Live cells (7AAD negative) were  filtered through a 40 µm nylon mesh, and isolated cells were loaded into the 10X Chromium system and libraries were constructed using Chromium Single Cell 3’ Reagent Kit (v3) according to the manufacturer’s protocol. Libraries were subsequently sequenced on a NovaSeq 6000 Sequencing System (Illumina).
Samples were multiplexed using the CellPlex kit (1 separate reaction per genotype) (10X Genomics).The sequencing data were demultiplexed using the Cell Ranger 7.0.1 pipeline  (10x Genomics).

value: Bone Marrow

value: Primary cells

value: cell culture


title: APOA4-KO cells, Hypoxia2, 24H


title: APOA4-KO cells, Hypoxia1, 24H


title: vehicle, ALN-treated, 1wk of daily loading, rep4,cortical bone,L [206]


title: BMSCs, Dmp1KOFgf23cKO1

description: 10X Genomics


title: BMSCs, Dmp1KO4

description: 10X Genomics


title: HgmDa02_ssDNA_rep2


title: APOA4-KO cells, Control2, 0H

value: NO


title: BMSCs, Dmp1KO2

description: 10X Genomics


title: HgmDa02_dsDNA_rep2


title: vehicle, ALN-treated, 1wk of daily loading, rep6,cortical bone,L [178]

value: 27 wks


title: HgmDa02_ssDNA_rep1


title: BMSCs, Dmp1KOFgf23cKO4

description: 10X Genomics


title: EWAT; scRNAseq

description: 10X Genomics

source_name: Epididymal white adipose tissue

value: Epididymal white adipose tissue

value: male

value: adipocytes (ADs), immune cells (ICs), endothelial cells (ECs), mesothelial cells (MCs), fibro-adipogenic progenitor cells (FAPs), and pericytes

value: chow diet


title: HgmDa02_dsDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: vehicle, ALN-treated, 1wk of daily loading, rep2,cancellous bone,L [177]

value: cancellous bone


title: APOA4-KO cells, Control1, 0H

value: APOA4 knockout


title: BMSCs, Dmp1KOFgf23cKO2

description: 10X Genomics


title: LsfDa01_dsDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep3,cancellous bone,Right [212]

value: Right


title: HepG2 cells, Hypoxia3, 48H

value: WT

value: Hypoxia


title: BMSCs, Fgf23cKO4

description: 10X Genomics


title: HgmDa01_ssDNA_rep2


title: HgmDa01_ssDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep3,cortical bone,L [192]

value: cortical bone


title: BMSCs, Dmp1KO3

description: 10X Genomics


title: APOA4-KO cells, Control3, 0H


title: HepG2 cells, Hypoxia1, 48H


title: BMSCs, Dmp1KO1

description: 10X Genomics


title: HgmDa01_dsDNA_rep2


title: HepG2 cells, Hypoxia2, 48H


title: BMSCs, Fgf23cKO2

description: 10X Genomics


title: vehicle, ALN-treated, 1wk of daily loading, rep1,cortical bone,L [136]

value: L


title: vehicle, ALN-treated, 1wk of daily loading, rep2,cortical bone,L [171]


title: HepG2 cells, Hypoxia3, 24H


title: vehicle, ALN-treated, 1wk of daily loading, rep1,cancellous bone,L [135]


title: HepG2 cells, Hypoxia2, 24H


title: HgmDa01_dsDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep1,cancellous bone,Right [114]


title: BMSCs, Fgf23cKO1

description: 10X Genomics

value: Bone Marrow


title: BMSCs, WT4

description: 10X Genomics

value: Primary cells


title: CgmDa01_ssDNA_rep2


title: HepG2 cells, Hypoxia1, 24H


title: vehicle, vehicle, 1wk of daily loading, rep4,cortical bone,L [108]


title: vehicle, ALN-treated, 1wk of daily loading, rep2,cancellous bone,Right [170]


title: BMSCs, WT3

description: 10X Genomics

value: cell culture


title: CgmDa01_dsDNA_rep2


title: CgmDa01_ssDNA_rep1


title: vehicle, vehicle, 1wk of daily loading, rep4,cortical bone,Right [101]


title: BMSCs, Fgf23cKO3

description: 10X Genomics


title: BMSCs, WT2

description: 10X Genomics


title: HepG2 cells, Control2, 0H

value: NO


title: CgmDa01_dsDNA_rep1


title: vehicle, vehicle, 1wk of daily loading, rep5,cancellous bone,Right [100]

value: 27 wks


title: BMSCs, WT1

description: 10X Genomics


title: BcDa02_ssDNA_rep2


title: vehicle, vehicle, 1wk of daily loading, rep3,cortical bone,L [94]


title: BMSCs, AM48_S48, Dmp1KO/Fgf23cKO

data_processing:
StrandNGS 4.0 was used for alignment and differential expression
Sequenced reads were trimmed for adaptor sequence,  masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Strand NGS 4.0
Reads were filtered using the Filter by Read Metrics filter with the following parameters: Quality threshold >= 20; N's allowed in read <= 0; Number of multiple matches allowed <= 1; Removed non-primary multiply mapped reads; Removed reads that are failing vendor's QC.
Strand specific reads: false. Max EM Iterations: 1000. Convergence criterion for EM: 0.001.
Normalization Type = Deseq.  Threshold for normalization = 1. Baseline type =  median of all samples
Assembly: mm10/Annotation: UCSC Transcripts (2018.02.25)
Supplementary files format and content: Matrix table with raw and normalized gene counts for every gene and every sample and differential group expression.
Supplementary files format and content: FGF23 regulated and DMP1 regulated differential expression with corrected p value (BD FDR p<0.1).

extract_protocol:
We isolated total RNA from cell cultures using TRI reagent (Waltham, MA, USA) and purified RNA using RNeasy kit (Qiagen, Germantown, MD, USA) and submitted 1 µg of total RNA for sequencing.
Libraries were prepared according to Illumina's instructions.  Total RNA library for each individual sample was prepared using the TruSeq Total RNA-Seq Library Preparation Kit (Illumina, San Diego, CA), and the bar-coded cDNA libraries were sequenced for 50 bp PE reads using Illumina NovaSeq 6000.


title: HepG2 cells, Control1, 0H


title: RPS2-RESCUE ADAR2dd_TORIN-1_Replicate-3

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

description:
epr_volcano_plot_values.tsv
epr_cds_3_fusion_joined.tsv

data_processing:
remove adapter with Cutadapt
align to genome using STAR 2.7.6
calculate edits per read (EPR)
Assembly: GRCh38
Supplementary files format and content: epr_volcano_plot_values.tsv
Supplementary files format and content: epr_cds_3_fusion_joined.tsv

source_name: Kidney

extract_protocol:
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Ilumina TruSeq Stranded mRNA Library Prep (Cat #  20020594)

value: Kidney

tag: rps2-rbe fusion

value: RPS2-RESCUE ADAR2dd

tag: agent

value: doxycycline-induced expression


title: vehicle, vehicle, 1wk of daily loading, rep4,cancellous bone,L [93]


title: BMSCs, AM47_S47, Dmp1KO/Fgf23cKO

tag: cell type

tag: genotype


title: RPS2-RESCUE ADAR2dd_TORIN-1_Replicate-2

tag: cell line

tag: treatment


title: BMSCs, AM46_S46, Dmp1KO/Fgf23cKO

tag: tissue


title: vehicle, vehicle, 1wk of daily loading, rep4,cancellous bone,Right [86]

tag: limb


title: HepG2 cells, Control3, 0H

tag: time


title: BMSCs, AM45_S45, Dmp1KO/Fgf23cKO


title: vehicle, vehicle, 1wk of daily loading, rep3,cortical bone,Right [87]

tag: age


title: BcDa02_dsDNA_rep1

source_name: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BcDa02_dsDNA_rep2


title: RPS2-RESCUE ADAR2dd_TORIN-1_Replicate-1


title: RPS2-TadA-7.10 (V82G)_TORIN-1_Replicate-3


title: PpDa04_ssDNA_rep2


title: vehicle, vehicle, 1wk of daily loading, rep3,cancellous bone,Right [72]


title: PpDa04_ssDNA_rep1


title: RPS2-TadA-7.10 (V82G)_TORIN-1_Replicate-2


title: BMSCs, AM44_S44, Dmp1KO


title: BMSCs, AM43_S43, Dmp1KO


title: vehicle, vehicle, 1wk of daily loading, rep2,cortical bone,Right [59]


title: BcDa02_ssDNA_rep1


title: PpDa04_dsDNA_rep2


title: RPS2-TadA-7.10 (V82G)_TORIN-1_Replicate-1


title: vehicle, vehicle, 1wk of daily loading, rep2,cortical bone,L [66]


title: RPS2-APOBEC1_TORIN-1_Replicate-3


title: PpDa04_dsDNA_rep1


title: BMSCs, AM42_S42, Dmp1KO


title: BMSCs, AM41_S41, Dmp1KO


title: PpDa03_ssDNA_rep2


title: RPS2-APOBEC1_TORIN-1_Replicate-2


title: BMSCs, AM40_S40, Fgf23cKO


title: vehicle, vehicle, 1wk of daily loading, rep2,cancellous bone,Right [30]


title: vehicle, vehicle, 1wk of daily loading, rep2,cancellous bone,L [23]


title: RPS2-APOBEC1_TORIN-1_Replicate-1


title: RPS2-TadA-8e_TORIN-1_Replicate-3


title: PTH-pretreated, vehicle, 2wks of daily loading, rep7,lymph node,L [666]

source_name: lymph node

value: lymph node

value: 28 wks


title: PpDa03_dsDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: PpDa03_dsDNA_rep1


title: BMSCs, AM38_S38, Fgf23cKO


title: BMSCs, AM37_S37, Fgf23cKO


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,lymph node,L [652]


title: MsddA_ssDNA_rep2


title: RPS2-TadA-8e_TORIN-1_Replicate-2


title: BMSCs, AM36_S36, WT


title: BMSCs, AM35_S35, WT


title: MsddA_ssDNA_rep1


title: RPS2-TadA-8e_TORIN-1_Replicate-1


title: vehicle, vehicle, 1wk of daily loading, rep3,cancellous bone,L [51]

value: cancellous bone


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,lymph node,Right [659]

value: Right


title: RPS2-RESCUE ADAR2dd_DMSO_Replicate-2

value: DMSO


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,lymph node,L [638]


title: BMSCs, AM34_S34, WT

value: WT


title: MsddA_dsDNA_rep2


title: RPS2-RESCUE ADAR2dd_DMSO_Replicate-1


title: PpDa03_ssDNA_rep1


title: RPS2-RESCUE ADAR2dd_DMSO_Replicate-3


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,lymph node,Right [631]


title: MsddA_dsDNA_rep1


title: BMSCs, AM33_S33, WT


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,lymph node,L [624]


title: BMSCs, AM39_S39, Fgf23cKO


title: MGYPDa26_ssDNA_rep2


title: RPS2-TadA-7.10 (V82G)_DMSO_Replicate-3


title: RPS2-TadA-7.10 (V82G)_DMSO_Replicate-2


title: liver, HFD, NLRP6 KO, rep3

city: Xinxiang

first: Wei

last: Hong

state: Henan

address: Xiangyang road no.688

institute: Sanquan College Of Xinxiang Medical University

data_processing:
IlluminaCasava 2.19 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl 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.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: liver

growth_protocol: Mice were fed a normal diet until they were 8 weeks old.

extract_protocol:
Liver tissue was frozen in liquid nitrogen, and and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ RNA Library Prep Kit for Illumina

treatment_protocol: The experimental group was fed with high-fat diet for 12 weeks, while the control group continued to eat normally.

value: liver

value: NLRP6 knockout

value: high fat diet


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,lymph node,Right [603]


title: RPS2-TadA-7.10 (V82G)_DMSO_Replicate-1


title: MGYPDa26_ssDNA_rep1


title: MGYPDa26_dsDNA_rep2


title: liver, HFD, NLRP6 KO, rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,lymph node,L [596]

value: L


title: MGYPDa26_dsDNA_rep1


title: RPS2-APOBEC1_DMSO_Replicate-2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,lymph node,Right [589]


title: liver, HFD, WT, rep3


title: RPS2-APOBEC1_DMSO_Replicate-3


title: MGYPDa23_ssDNA_rep2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,lymph node,Right [575]


title: liver, HFD, WT, rep2


title: RPS2-APOBEC1_DMSO_Replicate-1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,lymph node,Right [561]


title: RPS2-TadA-8e_DMSO_Replicate-3


title: liver, HFD, WT, rep1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,lymph node,L [610]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,lymph node,L [568]


title: liver, ND, NLRP6 KO, rep3

value: normal diet


title: MGYPDa23_dsDNA_rep1


title: MGYPDa23_ssDNA_rep1


title: RPS2-TadA-8e_DMSO_Replicate-2


title: vehicle, vehicle, 2wks of daily loading, rep8,lymph node,L [554]


title: MGYPDa21_ssDNA_rep2


title: MGYPDa21_ssDNA_rep1


title: liver, ND, NLRP6 KO, rep2


title: RPS2-TadA-8e_DMSO_Replicate-1


title: liver, HFD, NLRP6 KO, rep2


title: liver, ND, NLRP6 KO, rep1


title: vehicle, vehicle, 2wks of daily loading, rep7,lymph node,L [540]


title: liver, ND, WT, rep3


title: vehicle, vehicle, 2wks of daily loading, rep6,lymph node,Right [533]


title: RBFOX2-TadA-7.10 (V82G)_Replicate-3

description:
Hugo_F2
cu_RBFOX2-TadA-7.10_V82G_.tsv
ai_RBFOX2-TadA-7.10_V82G_.tsv
cu_RBFOX2-TadA-7.10_V82G_cleaned.tsv
ai_RBFOX2-TadA-7.10_V82G_cleaned.tsv

data_processing:
remove adapter with Cutadapt
align to human genome using STAR 2.7.6a
SAILOR analysis of data for C-to-U edits
SAILOR analysis of data for A-to-I edits
Assembly: GRCh38
Supplementary files format and content: cleaned =  RBFOX2-rBE data  with the rBE only edit clusters present in all three replicates were substracted
Supplementary files format and content: ai = A-to-I edits
Supplementary files format and content: ct = C-to-U edits
Supplementary files format and content: both = both A-to-I and C-to-U edits considered simultaneously

value: immortalized cell line

tag: rbe construct

value: RBFOX2-TadA-7.10 (V82G)


title: RBFOX2-TadA-7.10 (V82G)_Replicate-2

description:
Hugo_F1
cu_RBFOX2-TadA-7.10_V82G_.tsv
ai_RBFOX2-TadA-7.10_V82G_.tsv
cu_RBFOX2-TadA-7.10_V82G_cleaned.tsv
ai_RBFOX2-TadA-7.10_V82G_cleaned.tsv

value: Kidney

tag: replicate


title: MGYPDa21_dsDNA_rep2


title: RBFOX2-TadA-7.10 (V82G)_Replicate-1

description:
Hugo_E8
cu_RBFOX2-TadA-7.10_V82G_.tsv
ai_RBFOX2-TadA-7.10_V82G_.tsv
cu_RBFOX2-TadA-7.10_V82G_cleaned.tsv
ai_RBFOX2-TadA-7.10_V82G_cleaned.tsv


title: liver, ND, WT, rep2


title: MGYPDa21_dsDNA_rep1


title: vehicle, vehicle, 2wks of daily loading, rep5,lymph node,L [512]

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample


title: liver, ND, WT, rep1


title: TadA-7.10 (V82G) only_Replicate-3

description:
Hugo_E7
cu_TadA-7.10_V82G_only.tsv
ai_TadA-7.10_V82G_alone.tsv

value: TadA-7.10 (V82G) only


title: vehicle, vehicle, 2wks of daily loading, rep6,lymph node,L [526]


title: FlDa01_ssDNA_rep2


title: vehicle, vehicle, 2wks of daily loading, rep4,lymph node,L [498]


title: RNA-seq-Het_2

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells


title: vehicle, vehicle, 2wks of daily loading, rep5,lymph node,Right [505]

value: lymph node


title: TadA-7.10 (V82G) only_Replicate-1

description:
Hugo_E5
cu_TadA-7.10_V82G_only.tsv
ai_TadA-7.10_V82G_alone.tsv

value: doxycycline-induced expression


title: TadA-7.10 (V82G) only_Replicate-2

description:
Hugo_E6
cu_TadA-7.10_V82G_only.tsv
ai_TadA-7.10_V82G_alone.tsv


title: FlDa01_dsDNA_rep2

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: Δ/DN Rep4 - US

city: Montreal

first: Anastasia

last: Nijnik

state: Quebec

address: Rm 368 - 3649 Promenade Sir William Osler

department: Physiology

country: Canada

institute: McGill University

data_processing:
The quality of the sequencing reads was confirmed using the FastQC tool (Babraham Bioinformatics), and low-quality bases were trimmed from the read extremities using Trimmomatic v.0.33.The reads were then mapped to the mouse UCSC mm39 reference genome assembly using Hisat2 v2.2.1. Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters.
We retained genes that had an expression level of at least 5 counts per 106 reads (CPM) in at least 3 of the samples, and performed quantile normalization with the preprocessCore package to remove batch effects. TMM normalization and differential gene expression analyses were conducted using the edgeR Bioconductor package. Dimension reduction analysis was performed using the Principal Component and Partial Least Squares regression method.
Pairwise comparisons were performed between the genotypes or between the treatments, and genes with changes in expression ≥ |1.5| fold and Benjamini-Hochberg adjusted p values ≤ 0.01 were considered significant.
For data visualization in Integrative Genomics Viewer (IGV) bigwig files were generated using a succession of genomeCoverageBed and wigToBigWig tools and scaled per 10x106 exon-mapped reads. Gene ontology (GO) enrichment analyses on differentially expressed gene clusters were performed with DAVID Bioinformatics Resources 6.8, and Gene Set Enrichment Analysis (GSEA) was performed with GSEA tool v4.3.2 using MSigDB v2022.1 with default configuration and permutation within gene sets.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include feature counts for each sample, where rRNA have been excluded.

source_name: Bone marrow derived cells

growth_protocol: For BMDC derivation, mouse bone marrow was resuspended at 107 cells/mL and seeded dropwise at 75 μLs per well into 6-well non-tissue culture treated plates (Fisher Scientific) containing 3 mL/well of RPMI-1640 media, with 10% fetal calf serum (FCS) (both from ThermoFisher Scientific), 2 mM L-glutamine (Wisent), 100 U/mL penicillin/streptomycin (Wisent), 50 μM β-mercaptoethanol (Millipore-Sigma), and 20 ng/mL granulocyte-macrophage colony-stimulating factor (GM-CSF, 315-03, Peprotech) The cultures were fed with fresh media at days 3 and 6.

extract_protocol:
RNA was extracted using the EZ-10 DNAaway RNA kit (Bio Basic), according to the manufacturer’s protocol, and quantified with NanoDrop (ThermoFisher Scientific). cDNA was prepared using the Moloney murine leukemia virus (MMLV) reverse-transcription kit and quantitative PCRs run on a StepOnePlus instrument with PowerSYBR master mix (all from ThermoFisher Scientific). Primers were purchased from Integrated DNA Technologies.
RNA yields and quality were assessed using Bioanalyzer (Agilent). rRNA depletion and library preparation were performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche).

treatment_protocol: After 8-9 days, BMDCs were harvested and seeded at 106 cells/mL for stimulation with lipopolysaccharide (LPS, E. coli O111:B4, Millipore-Sigma), polyinosinic–polycytidylic acid (poly(I:C), Millipore-Sigma), or (1→3)-β-D-glucan from Alcaligenes faecalis (Millipore-Sigma).

value: Bone marrow derived cells

value: Bone marrow defived dendritic cells (BMDCs)

value: {delta}/DN

value: US


title: Δ/DN Rep4 - LPS

value: LPS


title: vehicle, vehicle, 2wks of daily loading, rep4,lymph node,Right [491]

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols

value: Right

value: 28 wks


title: FlDa01_dsDNA_rep1


title: RBFOX2-RESCUE ADAR2dd_Replicate-3 (E4)

description:
Hugo_E4
cu_RBFOX2-RESCUE_ADAR2dd.tsv
ai_RBFOX2-RESCUE_ADAR2dd.tsv
both_ai_and_cu_RBFOX2-RESCUE_ADAR2dd.tsv
cu_RESCUE_ADAR2dd_only.tsv
ai_RESCUE_ADAR2dd_only.tsv
both_ai_and_cu_RESCUE_ADAR2dd_alone.tsv

value: RBFOX2-RESCUE ADAR2dd


title: FlDa01_ssDNA_rep1


title: Δ/DN Rep3 - US


title: CsDa01_ssDNA_rep2


title: Δ/DN Rep3 - LPS


title: vehicle, vehicle, 2wks of daily loading, rep3,lymph node,Right [477]


title: RBFOX2-RESCUE ADAR2dd_Replicate-2 (E3)

description:
Hugo_E3
cu_RBFOX2-RESCUE_ADAR2dd.tsv
ai_RBFOX2-RESCUE_ADAR2dd.tsv
both_ai_and_cu_RBFOX2-RESCUE_ADAR2dd.tsv
cu_RESCUE_ADAR2dd_only.tsv
ai_RESCUE_ADAR2dd_only.tsv
both_ai_and_cu_RESCUE_ADAR2dd_alone.tsv


title: CsDa01_ssDNA_rep1


title: Δ/DN Rep2 - US


title: RBFOX2-RESCUE ADAR2dd_Replicate-1 (E2)

description:
Hugo_E2
cu_RBFOX2-RESCUE_ADAR2dd.tsv
ai_RBFOX2-RESCUE_ADAR2dd.tsv
both_ai_and_cu_RBFOX2-RESCUE_ADAR2dd.tsv
cu_RESCUE_ADAR2dd_only.tsv
ai_RESCUE_ADAR2dd_only.tsv
both_ai_and_cu_RESCUE_ADAR2dd_alone.tsv


title: vehicle, vehicle, 2wks of daily loading, rep2,lymph node,L [470]

value: L


title: CsDa01_dsDNA_rep2


title: Δ/DN Rep2 - LPS


title: vehicle, vehicle, 2wks of daily loading, rep2,lymph node,Right [463]


title: vehicle, vehicle, 2wks of daily loading, rep3,lymph node,L [484]


title: vehicle, vehicle, 2wks of daily loading, rep1,lymph node,L [456]


title: TadA-8e only_Replicate-2

description:
Hugo_D8
cu_TadA-8e_alone.tsv
ai_RBFOX2-TadA-8e_only.tsv

value: immortalized cell line

value: TadA-8e only


title: Δ/DN Rep1 - LPS


title: CsDa01_dsDNA_rep1


title: TadA-8e only_Replicate-1

description:
Hugo_D7
cu_TadA-8e_alone.tsv
ai_RBFOX2-TadA-8e_only.tsv

value: Kidney


title: TadA-8e only_Replicate-3

description:
Hugo_E1
cu_TadA-8e_alone.tsv
ai_RBFOX2-TadA-8e_only.tsv


title: BlDa01_ssDNA_rep2


title: vehicle, vehicle, 2wks of daily loading, rep1,lymph node,Right [449]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep7,lymph node,L [442]

value: 27 wks


title: RBFOX2-TadA-8e_Replicate-3

description:
Hugo_B7
cu_RBFOX2-TadA-8e.tsv
ai_RBFOX2-TadA-8e.tsv
cu_FOX2-TadA-8e_cleaned.tsv
ai_RBFOX2-TadA-8e_cleaned.tsv


title: Δ/+ Rep3 - US

value: {delta}/+


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,lymph node,Right [435]

value: lymph node


title: Δ/+ Rep4 - US


title: BlDa01_ssDNA_rep1


title: AshDa01_ssDNA_rep2


title: BlDa01_dsDNA_rep1


title: Δ/+ Rep3 - LPS


title: RBFOX2-TadA-8e_Replicate-1

description:
Hugo_B5
cu_RBFOX2-TadA-8e.tsv
ai_RBFOX2-TadA-8e.tsv
cu_FOX2-TadA-8e_cleaned.tsv
ai_RBFOX2-TadA-8e_cleaned.tsv

value: doxycycline-induced expression


title: RBFOX2-TadA-8e_Replicate-2

description:
Hugo_B6
cu_RBFOX2-TadA-8e.tsv
ai_RBFOX2-TadA-8e.tsv
cu_FOX2-TadA-8e_cleaned.tsv
ai_RBFOX2-TadA-8e_cleaned.tsv


title: Δ/+ Rep2 - US


title: Δ/DN Rep1 - US


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep6,lymph node,L [428]


title: AshDa01_ssDNA_rep1

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: BlDa01_dsDNA_rep2


title: Δ/+ Rep2 - LPS

value: Bone marrow derived cells


title: RBFOX2-RESCUE ADAR2dd_Replicate-2 (B3)

description:
Hugo_B3
ai_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv
cu_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv
both_ai_and_cu_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv


title: AshDa01_dsDNA_rep2


title: Δ/+ Rep1 - US

value: Bone marrow defived dendritic cells (BMDCs)


title: APOBEC1 only_Replicate-3

description:
Hugo_D6
cu_APOBEC1_only.tsv
ai_APOBEC1_only.tsv

value: APOBEC1 only


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep5,lymph node,L [414]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,lymph node,Right [407]


title: AshDa01_dsDNA_rep1


title: RBFOX2-RESCUE ADAR2dd_Replicate-1 (B2)

description:
Hugo_B2
ai_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv
cu_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv
both_ai_and_cu_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv


title: AaDa02_ssDNA_rep2


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,lymph node,L [400]


title: Δ/+ Rep1 - LPS


title: APOBEC1 only_Replicate-2

description:
Hugo_D5
cu_APOBEC1_only.tsv
ai_APOBEC1_only.tsv


title: Social Isolation Sed Cohort 2

city: New York

first: Miklos

last: Toth

address: 1300 York Ave

institute: Weill Cornell Medicine

description: 10X Genomics

data_processing:
Brain: Raw sequencing data was processed using the CellRanger v6.0.0 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Qiagen RNeasy kit
PL mPFC was dissected from mice and RNA extracted using Qiagen RNeasy Micro kit
Libraries were constructed according to manufacterer protocols by the Weill Cornell Epigenomics Core using the Chromium Single Cell 3' Reagent V3 kit.

value: Brain

value: PL mPFC

tag: Sex

value: Male

tag: gestational day


title: d21_HcDa01_ssDNA_rep2


title: AaDa02_ssDNA_rep1


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep4,lymph node,Right [421]

value: Right


title: Social Isolation Run Cohort 2

description: 10X Genomics


title: APOBEC1 only_Replicate-1

description:
Hugo_D4
cu_APOBEC1_only.tsv
ai_APOBEC1_only.tsv


title: RBFOX2-APOBEC1_Replicate-3

description:
Hugo_A3
cu_RBFOX2-APOBEC1.tsv
ai_RBFOX2-APOBEC1.tsv
cu_RBFOX2-APOBEC1_cleaned.tsv
ai_RBFOX2-FOX2-APOBEC1_cleaned.tsv


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep3,lymph node,L [386]


title: Group House Sed Cohort 2

description: 10X Genomics


title: Group House Run Cohort 2

description: 10X Genomics


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,lymph node,Right [365]


title: d21_HcDa01_dsDNA_rep2


title: RBFOX2-RESCUE ADAR2dd_Replicate-3 (B4)

description:
Hugo_B4
ai_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv
cu_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv
both_ai_and_cu_RBFOX2-RESCUE_ADAR2dd_cleaned.tsv

value: RBFOX2-RESCUE ADAR2dd


title: d21_HcDa01_ssDNA_rep1


title: RBFOX2-APOBEC1_Replicate-2

description:
Hugo_A2
cu_RBFOX2-APOBEC1.tsv
ai_RBFOX2-APOBEC1.tsv
cu_RBFOX2-APOBEC1_cleaned.tsv
ai_RBFOX2-FOX2-APOBEC1_cleaned.tsv


title: Group House Sed Cohort 1

description: 10X Genomics


title: RBFOX2-APOBEC1_Replicate-1

description:
Hugo_A1
cu_RBFOX2-APOBEC1.tsv
ai_RBFOX2-APOBEC1.tsv
cu_RBFOX2-APOBEC1_cleaned.tsv
ai_RBFOX2-FOX2-APOBEC1_cleaned.tsv


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,lymph node,Right [393]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep1,lymph node,L [344]

value: L


title: Group House Run Cohort 1

description: 10X Genomics


title: No Enzyme_Replicate-4

data_processing:
remove adapter with Cutadapt
align to human genome using STAR 2.7.6a
align unmapped reads from above to 12X MS2 stem-loop reporter mRNA using STAR 2.7.6a
SAILOR analysis of data for C-to-U edits
SAILOR analysis of data for A-to-I edits
Assembly: GRCh38
Assembly: 12X MS2 stem-loop reporter mRNA
Supplementary files format and content: The processed data files are in .bed format. They contain SAILOR-identified C-to-U or A-to-I edit information for endogenous transcripts (*non.construct.bed) and the 12X stem-loop-bearing-bearing reporter mRNA (*reporter.construct.bed).

value: immortalized cell line


title: Treg cells, Srci1, Day5 [Treg-Srci1-3]

city: Guangzhou

first: Tao

last: Xu

address: Forested street

institute: Sun Yat-Sen University

data_processing:
Quality control for the raw reads was performed with fastq
Raw reads were trimmed for adaptor sequence/low-quality sequence using fastq
Trimmed sequence reads were mapped to GRCm38(vM23) using STAR (v2.7.9a )
Read count extraction and normalization were performed using RSEM (v1.3.3 )
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Treg cells, Srci1, Day5

growth_protocol: CD4 naïve T cells (CD4+CD25−CD62highCD44low) were sorted from mice spleen and lymphonode. Approximately 0.4 million cells were plated into 48-well-plates coated with anti-mouse CD3 (clone 145-2C11, eBioscience) (2 μg/ml) and anti-mouse CD28 (clone 37.51, eBioscience) (1 μg/ml). The differentiation conditions for T cells are as followed: 0.5 ng/ml (or indicated) TGFβ, 200 U/ml mouse IL-2, 1 μg/ml anti-IFNγ and 1 μg/ml anti-mouse IL-4 for Treg, 2.5 ng/ml TGFβ, 10 ng/ml mouse IL-1β, 10 ng/ml mouse IL-6, 10 ng/ml mouse IL-23, 1 μg/ml anti-mouse IFNγ, and 1 μg/ml anti-mouse IL-4 for TH17.

extract_protocol:
T cells were harvested on Day5 and total RNA were extracted using TRIzol™ Reagent. RNA purity were measured by Nano Drop. The concentration of RNA was determined by Qubit RNA Br (broad-range) Assay Kit, and the integrity of RNA was detected by RNA ScreenTape. mRNA were isolated using the NEBNext® Poly(A)mRNA Magnetic Isolation Module kit.
The mRNA library was constructed with the NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® sequencing platform.

treatment_protocol: Indicated concentration of Srci1 was added into culture 24 hours after initial plating.

value: T cell from LNs and spleen

value: Treg

value: wild type

value: Day 5


title: PTH-pretreated, vehicle, 1wk of daily loading, rep6,lymph node,L [316]

value: lymph node

value: 27 wks


title: d16_HmDa02_ssDNA_rep2

data_processing:
basecalls were performed using Illumina RTA software and fastq files were generated from the BCL files using Picard’s basecallstofastq.
Reads were trimmed for adaptor sequence and low quality bases at the 3' end using the trim_galore program.
The trimmed read sequences were C to T converted and were then mapped to the a composite reference including E.coli and all the control sequences using the Bismark program with the default Bowtie2 settings.
The first 5 bp at the 5’ end of R2 reads were removed to reduce end-repair errors and aligned read pairs that shared the same alignment ends were regarded as PCR duplicates and were discarded.
The numbers of Ts (converted not methylated) and Cs (unconverted modified) of each covered cytosine position were then calculated from the remaining good quality alignments using Bismark methylation extractor.
Assembly: E. coli C2566, human hg38
Supplementary files format and content: tab-delimited text/bed files include genomic coordinates, number of Cs and number of Ts and sequence contexts of covered cytosines.
Library strategy: SEM-seq

value: E. coli C2566, phage lambda, plasmid pRSSM1.PleII, phage XP12, phage T4 AGT-, and Adenovirus


title: No Enzyme_Replicate-3

value: Kidney

value: doxycycline-induced expression


title: Treg cells, Srci1, Day5 [Treg-Srci1-2]


title: PTH-pretreated, ALN-treated, 1wk of daily loading, rep2,lymph node,L [372]


title: Treg cells, Srci1, Day5 [Treg-Srci1-1]


title: d16_HmDa02_dsDNA_rep2


title: d16_HmDa02_dsDNA_rep1


title: Treg cells, DMSO, Day5 [Treg-DMSO-3]

source_name: Treg cells, DMSO, Day5

value: DMSO


title: MCP-APOBEC3A (Y132G/K30R)_Replicate-2


title: MCP-APOBEC3A (Y132G/K30R)_Replicate-1


title: ScDa03_ssDNA_rep2


title: Treg cells, DMSO, Day5 [Treg-DMSO-2]


title: d21_HcDa01_dsDNA_rep1


title: MCP-evoAPOBEC1_Replicate-2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,lymph node,Right [267]


title: Treg cells, DMSO, Day5 [Treg-DMSO-1]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,lymph node,Right [281]


title: MCP-evoAPOBEC1_Replicate-1


title: ScDa03_ssDNA_rep1


title: d16_HmDa02_ssDNA_rep1


title: PTH-pretreated, vehicle, 1wk of daily loading, rep5,lymph node,Right [309]


title: MCP-TadA-7.10 (V82G)_Replicate-2


title: ScDa03_dsDNA_rep2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,lymph node,Right [253]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep2,lymph node,L [260]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep4,lymph node,L [302]


title: MCP-TadA-7.10 (V82G)_Replicate-1


title: TH17 cells, Srci1, Day5 [TH17-Srci1-3]

source_name: TH17 cells, Srci1, Day5


title: TH17 cells, Srci1, Day5 [TH17-Srci1-2]


title: PTH-pretreated, vehicle, 1wk of daily loading, rep3,lymph node,L [288]


title: TH17 cells, Srci1, Day5 [TH17-Srci1-1]


title: MCP-APOBEC1 (STAMP)_Replicate-4


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,lymph node,L [232]


title: PsDa01_ssDNA_rep2


title: PsDa01_ssDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep6,lymph node,L [218]


title: MCP-ADARcd (E488Q) (hyperTRIBE)_Replicate-2


title: TH17 cells, DMSO, Day5 [TH17-DMSO-2]

source_name: TH17 cells, DMSO, Day5


title: vehicle, ALN-treated, 1wk of daily loading, rep5,lymph node,L [204]


title: TH17 cells, DMSO, Day5 [TH17-DMSO-3]


title: MCP-APOBEC1 (STAMP)_Replicate-3


title: ScDa03_dsDNA_rep1


title: PsDa01_dsDNA_rep1


title: TH17 cells, DMSO, Day5 [TH17-DMSO-1]


title: TH17 cells, STAT3 KO, Day5 [TH17-STAT3KO-3]

source_name: TH17 cells, STAT3 KO, Day5

value: STAT3-fl/fl CD4-cre


title: vehicle, ALN-treated, 1wk of daily loading, rep6,lymph node,Right [197]


title: MCP-ADARcd (E488Q) (hyperTRIBE)_Replicate-1


title: PfDa01_ssDNA_rep1


title: PfDa01_ssDNA_rep2


title: MCP-TadA-TadA-8e_Replicate-2


title: vehicle, ALN-treated, 1wk of daily loading, rep4,lymph node,L [176]


title: PfDa01_dsDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep4,lymph node,Right [169]


title: PsDa01_dsDNA_rep2


title: vehicle, ALN-treated, 1wk of daily loading, rep5,lymph node,Right [183]


title: PfDa01_dsDNA_rep2


title: MCP-TadA-7.10_Replicate-1


title: TH17 cells, STAT3 KO, Day5 [TH17-STAT3KO-2]


title: TH17 cells, STAT3 KO, Day5 [TH17-STAT3KO-1]


title: MCP-TadA-8.20_Replicate-2


title: PTH-pretreated, vehicle, 1wk of daily loading, rep1,lymph node,Right [225]


title: RIP-Seq Peritoneal macrophages 12

city: Hang Zhou

address: Huansha Roud

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm39.104 whole genome usingBWA (v 0.7.12)with parameters BWA mem ( v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment,significant level and peak summit number per peak were all displayed.
Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: Mus_musculus_Ensemble_GRCm39.104
Supplementary files format and content: tab-delimited text files  peak  for each Sample

source_name: Peritoneal macrophages

growth_protocol: Peritoneal macrophages  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal macrophages were incubated with IFN-G for 0 hour，24hours and 48 hours.

tag: sample type

value: total RNA

value: Peritoneal macrophages

value: IFN-G


title: MCP-TadA-TadA-8e_Replicate-1


title: vehicle, ALN-treated, 1wk of daily loading, rep3,lymph node,L [162]

city: Ithaca


title: RIP-Seq Peritoneal macrophages 11


title: MCP-TadA-7.10_Replicate-2


title: RIP-Seq Peritoneal macrophages 10


title: NoDa01_ssDNA_rep1


title: NoDa01_dsDNA_rep1


title: vehicle, ALN-treated, 1wk of daily loading, rep2,lymph node,L [148]


title: NoDa01_dsDNA_rep2


title: vehicle, ALN-treated, 1wk of daily loading, rep3,lymph node,Right [155]

value: Right


title: RIP-Seq Peritoneal macrophages 9


title: MCP-APOBEC1 (STAMP)_Replicate-2


title: MCP-TadA-8e_Replicate-2


title: NoDa01_ssDNA_rep2


title: vehicle, ALN-treated, 1wk of daily loading, rep1,lymph node,L [120]

value: L


title: MGYPDa14_ssDNA_rep2


title: vehicle, ALN-treated, 1wk of daily loading, rep1,lymph node,Right [113]


title: vehicle, ALN-treated, 1wk of daily loading, rep2,lymph node,Right [127]


title: RIP-Seq Peritoneal macrophages 6

value: Ac4C-binding RNA


title: RIP-Seq Peritoneal macrophages 7


title: MGYPDa14_ssDNA_rep1


title: vehicle, vehicle, 1wk of daily loading, rep6,lymph node,L [106]


title: MCP-RESCUE-S ADAR2dd_Replicate-2

value: immortalized cell line


title: MCP-TadA-8.20_Replicate-1


title: MGYPDa14_dsDNA_rep1


title: RIP-Seq Peritoneal macrophages 5


title: MCP-RESCUE-S ADAR2dd_Replicate-1


title: RIP-Seq Peritoneal macrophages 8


title: MCP-TadA-8e_Replicate-1


title: MCP-RESCUE ADAR2dd_Replicate-2


title: vehicle, vehicle, 1wk of daily loading, rep4,lymph node,Right [85]


title: RIP-Seq Peritoneal macrophages 3


title: MGYPDa11_ssDNA_rep2


title: MGYPDa11_ssDNA_rep1


title: RIP-Seq Peritoneal macrophages 2


title: RIP-Seq Peritoneal macrophages 1


title: MCP-APOBEC1 (STAMP)_Replicate-1


title: MGYPDa11_dsDNA_rep2


title: vehicle, vehicle, 1wk of daily loading, rep3,lymph node,Right [71]


title: MCP-RESCUE ADAR2dd_Replicate-1


title: No Enzyme_Replicate-2


title: MGYPDa14_dsDNA_rep2


title: MGYPDa11_dsDNA_rep1


title: vehicle, vehicle, 1wk of daily loading, rep2,lymph node,Right [57]


title: vehicle, vehicle, 1wk of daily loading, rep3,lymph node,L [50]


title: T9_Transection, Triceps Brachii Muscle, Rep6

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Raw fastq was aligned to mouse reference genome GRCm38 with hisat2 v2.1.0.  Gene wise counts were generated with featureCounts from the subread package v1.5.1 for genes annotated by ensembl Mus_musculus.GRCm38.102, counting the primary alignment in the case of multimapped reads.  Raw counts were normalized by voom
Assembly: GRCm38
Supplementary files format and content: voom normalized counts

source_name: Triceps Brachii Muscle

extract_protocol:
Mouse skeletal muscle tissue (~30 mg) was homogenized in Trizol reagent (Invitrogen) and extracted using RNeasy mini kit (Qiagen) according to manufacturer’s instructions. Total RNA concentration and integrity were determined by 260/280 and 260/230 nanodrop absorbance, as well as QUBIT and RNA6000 PicoAssay.
mRNA libraries were generated using NEBNext® Ultra™ II Directional (stranded) RNA library prep kit for Illumina (NEB #E7760L) and NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490). 200 ng total RNA was used for library input, fragmentation occurred for 10 minutes, and 12X PCR cycles were run. Library quality was assessed using High Sensitivity DNA Bioanalyzer and libraries were then sequenced by NovaSeq6000 SP Paired-End 150bp format at a sequencing depth of ~20 million reads per lane per sample.

value: Triceps Brachii Muscle

value: Male

tag: disease

value: T9 Transection SCI

tag: timepoint

value: 3 days post surgery


title: T9_Transection, Triceps Brachii Muscle, Rep5


title: vehicle, vehicle, 1wk of daily loading, rep5,lymph node,L [92]

first: Marjolein

last: van der Meulen

address: Weill Hall

institute: Cornell University

value: lymph node

value: 27 wks


title: RIP-Seq Peritoneal macrophages 4


title: No Enzyme , No Reporter_Replicate-2

value: Kidney


title: vehicle, vehicle, 1wk of daily loading, rep2,lymph node,L [36]


title: No Enzyme_Replicate-1

value: doxycycline-induced expression


title: T9_Transection, Triceps Brachii Muscle, Rep4


title: No Enzyme , No Reporter_Replicate-1