title: UT BMDM-PHLPP1

status: Public on Dec 31 2025

type: SRA

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

country: China

institute: Naval medical university

library_source: genomic

data_processing:
Genome mapping was performed using Bowtie (version:0.12.8) and clean reads were compared to reference genome mm10. MACS (version 2.2.7.1) was applied to call peak.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameter was set as fold change ≥ 2 or≤ 1/2 and P value < 0.05, and the differences between the obtained peakswere annotated.
The annotation program was the same as the above peak annotation program, including different peak location information, annotation information, etc.
Assembly: mm10
Supplementary files format and content: narrowPeak file that includes information of PHLPP1-binding DNA
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml).

extract_protocol:
CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions. Briefly, WT BMDMs were stimulated with IL-4 and then harvested after PBS wash. Cells (1 × 105) were bound with concanavalin A-coated magnetic beads and then incubated with antibodies against PHLPP1 (ProteinTech) at 4 °C overnight. On the next day, samples were incubated with a second antibody and then with Hyperactive pA/G-Transposon for 1 h. DNA was treated with TTBL at 37 °C for 1 h and extracted.
The librarys were constructed by purified DNA, and amplified using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the product instructions.

treatment_protocol: WT and Phlpp1 deficient BMDMs were stimulated with IL-4 (20ng/ml) for 4 hours

tag: tissue

value: bone marrow

tag: cell type

value: Mouse primary bone marrow-derived macrophages

tag: treatment

value: untreated


title: GC_WT2

city: Badalona

first: Maribel

last: Parra

state: Barcelona

address: Ctra. de Can Ruti, Camí de les Escoles, s/n

department: Lymphocyte Development and Disease

country: Spain

institute: Josep Carreras Leukaemia Research Institute

library_source: transcriptomic

data_processing:
Quality control of the samples was performed with the FASTQC tool
Paired-end reads were aligned to the murine reference genome (GRCm38) using STAR (version 2.7.0a).
A count table file indicating the number of reads per gene in each sample was generated using HTSeq (version 0.10.0).
Genes with no or very low expression were filtered out and differentially expressed genes were identified using DESeq2.
Assembly: Genome Reference Consortium Mouse Build 38 (GRCm38-mm10).
Supplementary files format and content: Tab-delimited text file include normalized count values obtained using DESeq2

molecule: total RNA

source_name: Spleen

growth_protocol: Cells were extracted from fresh murine spleens and sorted to obtain purified germinal center B cells.

extract_protocol:
Total RNA was extracted at IRB Genomics Unit (Barcelona).
Low input library was performed in all samples.
Paired-end mode with 100bp read length. 50 milion paired-end reads were generated per each sample

treatment_protocol: HDAC7 knockout cells have a floxed Hdac7 and a CRE recombinase activated depending on Cgamma-1 gene promotor.

value: Spleen

tag: cell line

value: germinal center B cells

value: wild-type

tag: strain

tag: genotype

value: wildtype


title: GC_WT4


title: GC_WT1


title: GC_KO1

value: HDAC7 knockout


title: CH15

city: Berlin

first: Frederik

middle: Richard

last: Heinrich

state: Berlin

address: Chariteplatz 1

department: Bioinformatics

country: Germany

description: Naive Th cells

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by feature featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw counts for genes.

molecule: polyA RNA

source_name: spleen

extract_protocol:
isolation protocol: Succesive CD4+ and C62L+ T cell isolation using positive selection with MACS Beads from wildtype mouse splenocytes. Cells were either harvested directly, or activated for 48 hrs with anti-CD3 and anti-CD28 under Th1, Th2 or Th17 polarizing conditions and the cultured for 1 week or repeatedly restimulated with anti-CD3 and anti-CD28 and cultured for 4 weeks. After each week the viable cells were collected by Ficoll grandient centrifugation.
FACS sort: none, viable cells were obtained by Ficoll gradient centrifugation
RNA isolation protocol: RNA of cells was extracted using RNeasy Plus Micro Kit (Qiagen) and RNA quality was assessed by an Agilent 2100 Bioanalyzer.
Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

value: C57BL/6J background

value: Naive Th cells

tag: age

value: 0 weeks

tag: sorting strategy

value: viable cells


title: CH16

description: Th1 cells after 1 week

value: 1 week


title: CH13

description: Th17 cells after 1 week


title: CH11

description: Th2 cells after 1 week


title: CH12

description: Th2 cells after 4 weeks

value: 4 weeks


title: CH14

description: Th17 cells after 4 weeks


title: CH10

description: Th2 cells after 4 weeks


title: CH9

description: Th2 cells after 1 week


title: GC_KO2


title: CH8

description: Th1 cells after 4 weeks


title: CH7

description: Naive Th cells


title: CH6

description: Th1 cells after 1 week


title: CH5

description: Th17 cells after 4 weeks


title: CH4

description: Th17 cells after 1 week


title: CH2

description: Th1 cells after 1 week


title: CH3

description: Th1 cells after 4 weeks


title: IL-4 BMDM-PHLPP1

value: IL-4(20ng/ml) for 4h


title: I-

first: Chunxing

last: Zheng

address: 320 Yueyang Rd.

institute: Shanghai Institute of Nutrition and Health

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (Reads N rate < 10%, q20 > 90%)
Sequence after trimmed was mapped to mm8 whole genome using soap2.21 with parameters  -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Inguinal adipose tissues were collected and digested. Mature adipocytes were separated by centrifuge. The SVF cells in the pellets were prepared for FACS afterwards. Total RNA was extracted with TRIZOL reagent.
Total RNA from sorted cell subsets was treated with DNase I. Messenger RNA was enriched with Oligo (dT) magnetic beads and fragmented before reverse transcription and second-strand cDNA synthesis. The cDNA libraries were then purified, ligated with adaptors, and amplified. Quality of the cDNA libraries were evaluated (Agilient 2100 Bioanalyzer) prior to high-throughput sequencing (Illumina HiSeq 2000).

treatment_protocol: Mice were fed with high-fat diet containing 60 Kcal % fat (D12492, Research Diets, New Brunswick, NJ) for 16 weeks.

value: Inguinal adipose tissue

tag: mice treatment

value: 16-weeks high-fat diet


title: GC_KO3


title: GC_KO4


title: I+G-


title: Adi

source_name: Mature adipocytes


title: MTX-H3K4-INPUT-BR1

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

country: USA

institute: SUNY Upstate Medical University

description:
Library name: MTX-H3K4-INPUT-BR1
MTX-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with MTX at IC50 conc (Control for MTX-H3K4-ChIP_BR1).
H3K4_MTX_BR1_Log2IPtoIC.bw

data_processing:
alignment by Bowtie2, bamCompare by deepTools to log2 normalize IP to IC (input control) signals
Assembly: sacCer3
Supplementary files format and content: BAM and BigWIg
Supplementary files format and content: BigWig files were made from ChIP and INPUT from each sample, therefore each bw file is associated with two bam files (ChIP and INPUT)

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: WT yeast cells from the W303 background were grown either in YEPD or SC media at 30 °C.

extract_protocol:
300ml of cells were collected for each treatment  gropu. Post-harvest, the cells were resuspenced in a small volume to help with crosslinking. Cross-linked cell pellets were lysed to isolate the DNA which was then sonicated. For INPUT samples 10% of total DNA per samples was set aside. Remaining 90% of genomic DNA was then subjected to immunoprecipitation using antibodies specific to H3K36me3 and H3K4me3 residues. The IP'ed DNA was then purified, and subjected to library construction.
Cells growth (in YPD or SC) and drug administration at IC50 were performed as described for Figure S1.  ChIP was performed as described with modifications (Joshi et al, 2022).  Briefly, 300 ml of cells were collected by centrifugation, and after resuspension in 35 ml of fresh media (YPD or SC), protein-DNA crosslinking was done by the addition of formaldehyde at 1%, followed by incubation at room temperature with gentle rotation for 25 m.  The crosslinking reaction was quenched by 125 mM glycine and incubation for 5 m.  Cells were washed once each with cold 1X PBS and 50 mM HEPES, then snap-frozen prior to storage at -80°C.  To extract the DNA, the frozen cells pellets were thawed in 300 µl of lysis buffer (50 mM HEPES/KOH, pH7.5, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 140 mM NaCl, 1X Halt Protease and Phosphatase Inhibitor cocktail (Thermo Scientific)) on ice.  Each thawed cell pellet was then distributed into three screw-capped microcentrifuge tubes and volume was increased to 300 µl with lysis buffer.  To each tube 300 µL of glass beads were added and samples were treated in a homogenizer at 4°C for six cycles of 30 s each, with 3 m intermittent resting on ice.  Cell lysis was monitored by microscopy every two cycles.  At ~80% cell lysis, the cell lysates were collected by centrifugation at 1,400 g for 3 m, after puncturing the bottom of the tube with a heated needle.  Cell lysates were then sonicated for 10 m at 10 % duty factor, 200 cycles/burst, and 75 W peak power to obtain DNA fragments between 200-600 bps.  The sonicated cell lysates were centrifuged at 15,000 g for 20 m at 4°C to remove cell debris.  The volume of the supernatant was increased to 1 ml with lysis buffer, followed by collecting a 40-µl aliquot as “Input”, a 50-µl aliquot for agarose gel electrophoresis to check DNA fragment size, and the remainder 910 µl for IP.  The 50-ml aliquot was reversed crosslinked overnight in a 65°C water bath, then DNA was purified using a Qiagen PCR column purification kit.  DNA was analyzed on a 1.5% agarose gel.  The 910-ml aliquot was pre-cleared by incubation with anti-rabbit M280 magnetic beads (Invitrogen Cat # 11203D) according to manufacturer’s recommendation.  The pre-cleared lysates (eluate) were then incubated with magnetic beads conjugated with 5 µg of anti-H3K4me3 (Abcam #ab8580), or anti-H3K36me3 (Abcam #ab9050), or rabbit IgG (Bethyl lab #120-101) for IP at 4°C overnight, followed by washing once each with wash buffer 1 (50 mM HEPES/KOH, pH 7.5, 1 mM EDTA, 1% Triton X100, 0.1% Sodium deoxycholate, 140 mM NaCl, 1X protease inhibitor cocktail, 1X phosphatase inhibitor cocktail), wash buffer 2 (50 mM HEPES/KOH, ph 7.5, 1 mM EDTA, 1% Triton X100, 0.1% Sodium deoxycholate, 500 mM NaCl, 1X protease inhibitor cocktail, 1X phosphatase inhibitor cocktail), wash buffer 3 (0.25 M LiCl, 0.5% NP-40, 0.5 % Sodium deoxycholate, 1mM EDTA, 10 mM Tris-HCl pH 8.0) and TE 0.1, for 3, 3, 15 and 3 m, respectively at 4°C.  The protein-bound DNA was eluted from the beads by 160 µl elution buffer (0.85X TE pH 8.0, 1% SDS, 0.25 M NaCl) and incubation in a 65°C water bath for 30 m with gentle vortexing every 5-10 mins.  Henceforth the IP and Input DNA were processed together, after adjusting the volume of Input DNA with elution buffer (~120 µl) to obtain the same volume as IP DNA.  The DNA was digested with 800 ng of DNase-free RNaseA at 37°C for 2 h, followed by 14 µl of Proteinase K (10 mg/ml) at 65°C overnight to reverse crosslinks.  The liberated DNA was purified using phenol/chloroform extraction and ethanol precipitation using 3 µl of glycogen (20 µg/µl) as a carrier.  The resulting DNA pellet was dissolved in 30 µl and 100 µl of TE 0.1 respectively, for IP and Input DNA.  DNA library construction was performed as described previously (Joshi et al, 2021) and sequencing performed on Hi-Seq 2500 (2x150 bp).  ChIP-seq data were processed similarly as for Break-seq and the relative amount of ChIP was calculated as the Log2 ratio of signal from the ChIP to that from the Input control using MACS2 and deepTools (Ramírez et al, 2016), respectively.

treatment_protocol: Cells were grown to an OD~0.3 before addition of either the replication inhibitor or vehicle control. Post addition of the either, the cells were continued to grow for the determined IC50 timepoint prior to harvesting.

value: WT

tag: background

tag: media

value: SC

value: MTX

tag: molecule

value: INPUT DNA

tag: biological replicate


title: MTX-H3K4-ChIP-BR2

description:
Library name: MTX-H3K4-ChIP-BR2
MTX-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with MTX at IC50 conc.
H3K4_MTX_BR2_Log2IPtoIC.bw

value: ChIP DNA


title: MTX-H3K4-INPUT-BR2

description:
Library name: MTX-H3K4-INPUT-BR2
MTX-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with MTX at IC50 conc (Control for MTX-H3K4-ChIP_BR2).
H3K4_MTX_BR2_Log2IPtoIC.bw


title: MTX-H3K36-INPUT-BR1

description:
Library name: MTX-H3K36-INPUT-BR1
MTX-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with MTX at IC50 conc (Control for MTX-H3K36-ChIP_BR1).
H3K36_MTX_BR1_Log2IPtoIC.bw


title: MTX-H3K36-ChIP-BR2

description:
Library name: MTX-H3K36-ChIP-BR2
MTX-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with MTX at IC50 conc.
H3K36_MTX_BR2_Log2IPtoIC.bw


title: MMS-H3K4-INPUT-BR1

description:
Library name: MMS-H3K4-INPUT-BR1
MMS-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with MMS at IC50 conc (Control for MMS-H3K4-ChIP_BR1).
H3K4_MMS_BR1_Log2IPtoIC.bw

value: YEPD

value: MMS


title: MMS-H3K4-ChIP-BR2

description:
Library name: MMS-H3K4-ChIP-BR2
MMS-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with MMS at IC50 conc.
H3K4_MMS_BR2_Log2IPtoIC.bw


title: MMS-H3K4-INPUT-BR2

description:
Library name: MMS-H3K4-INPUT-BR2
MMS-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with MMS at IC50 conc (Control for MMS-H3K4-ChIP_BR2).
H3K4_MMS_BR2_Log2IPtoIC.bw


title: MMS-H3K4-ChIP-BR1

description:
Library name: MMS-H3K4-ChIP-BR1
MMS-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with MMS at IC50 conc.
H3K4_MMS_BR1_Log2IPtoIC.bw


title: MMS-H3K36-INPUT-BR1

description:
Library name: MMS-H3K36-INPUT-BR1
MMS-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with MMS at IC50 conc (Control for MMS-H3K36-ChIP_BR1).
H3K36_MMS_BR1_Log2IPtoIC.bw


title: MMS-H3K36-INPUT-BR2

description:
Library name: MMS-H3K36-INPUT-BR2
MMS-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with MMS at IC50 conc (Control for MMS-H3K36-ChIP_BR2).
H3K36_MMS_BR2_Log2IPtoIC.bw


title: MMS-H3K36-ChIP-BR1

description:
Library name: MMS-H3K36-ChIP-BR1
MMS-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with MMS at IC50 conc.
H3K36_MMS_BR1_Log2IPtoIC.bw


title: MMS-H3K36-ChIP-BR2

description:
Library name: MMS-H3K36-ChIP-BR2
MMS-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with MMS at IC50 conc.
H3K36_MMS_BR2_Log2IPtoIC.bw


title: HU-H3K4-INPUT-BR1

description:
Library name: HU-H3K4-INPUT-BR1
HU-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with HU at IC50 conc (Control for HU-H3K4-ChIP_BR1).
H3K4_HU_BR1_Log2IPtoIC.bw

value: HU


title: HU-H3K4-INPUT-BR2

description:
Library name: HU-H3K4-INPUT-BR2
HU-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with HU at IC50 conc (Control for HU-H3K4-ChIP_BR2).
H3K4_HU_BR2_Log2IPtoIC.bw


title: HU-H3K4-ChIP-BR2

description:
Library name: HU-H3K4-ChIP-BR2
HU-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with HU at IC50 conc.
H3K4_HU_BR2_Log2IPtoIC.bw


title: CH1

description: Naive Th cells

value: C57BL/6J background


title: HU-H3K4-ChIP-BR1

description:
Library name: HU-H3K4-ChIP-BR1
HU-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with HU at IC50 conc.
H3K4_HU_BR1_Log2IPtoIC.bw


title: HU-H3K36-INPUT-BR1

description:
Library name: HU-H3K36-INPUT-BR1
HU-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with HU at IC50 conc (Control for HU-H3K36-ChIP_BR1).
H3K36_HU_BR1_Log2IPtoIC.bw


title: HU-H3K36-ChIP-BR2

description:
Library name: HU-H3K36-ChIP-BR2
HU-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with HU at IC50 conc.
H3K36_HU_BR2_Log2IPtoIC.bw


title: HU-H3K36-INPUT-BR2

description:
Library name: HU-H3K36-INPUT-BR2
HU-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with HU at IC50 conc (Control for HU-H3K36-ChIP_BR2).
H3K36_HU_BR2_Log2IPtoIC.bw


title: I+G+


title: DOX-H3K4-INPUT-BR2

description:
Library name: DOX-H3K4-INPUT-BR2
DOX-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with DOX at IC50 conc (Control for DOX-H3K4-ChIP_BR2).
H3K4_DOX_BR2_Log2IPtoIC.bw

value: DOX


title: DOX-H3K4-INPUT-BR1

description:
Library name: DOX-H3K4-INPUT-BR1
DOX-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with DOX at IC50 conc (Control for DOX-H3K4-ChIP_BR1).
H3K4_DOX_BR1_Log2IPtoIC.bw


title: DOX-H3K36-INPUT-BR2

description:
Library name: DOX-H3K36-INPUT-BR2
DOX-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with DOX at IC50 conc (Control for DOX-H3K36-ChIP_BR2).
H3K36_DOX_BR2_Log2IPtoIC.bw


title: MTX-H3K36-INPUT-BR2

description:
Library name: MTX-H3K36-INPUT-BR2
MTX-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with MTX at IC50 conc (Control for MTX-H3K36-ChIP_BR2).
H3K36_MTX_BR2_Log2IPtoIC.bw


title: DOX-H3K4-ChIP-BR1

description:
Library name: DOX-H3K4-ChIP-BR1
DOX-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with DOX at IC50 conc.
H3K4_DOX_BR1_Log2IPtoIC.bw


title: MTX-H3K4-ChIP-BR1

description:
Library name: MTX-H3K4-ChIP-BR1
MTX-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with MTX at IC50 conc.
H3K4_MTX_BR1_Log2IPtoIC.bw


title: DOX-H3K36-INPUT-BR1

description:
Library name: DOX-H3K36-INPUT-BR1
DOX-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with DOX at IC50 conc (Control for DOX-H3K36-ChIP_BR1).
H3K36_DOX_BR1_Log2IPtoIC.bw


title: DOX-H3K36-ChIP-BR1

description:
Library name: DOX-H3K36-ChIP-BR1
DOX-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with DOX at IC50 conc.
H3K36_DOX_BR1_Log2IPtoIC.bw


title: MTX-H3K36-ChIP-BR1

description:
Library name: MTX-H3K36-ChIP-BR1
MTX-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with MTX at IC50 conc.
H3K36_MTX_BR1_Log2IPtoIC.bw


title: DOX-H3K36-ChIP-BR2

description:
Library name: DOX-H3K36-ChIP-BR2
DOX-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with DOX at IC50 conc.
H3K36_DOX_BR2_Log2IPtoIC.bw


title: CPT-H3K4-INPUT-BR1

description:
Library name: CPT-H3K4-INPUT-BR1
CPT-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with CPT at IC50 conc (Control for CPT-H3K4-ChIP_BR1).
H3K4_CPT_BR1_Log2IPtoIC.bw

value: CPT


title: CPT-H3K4-ChIP-BR2

description:
Library name: CPT-H3K4-ChIP-BR2
CPT-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with CPT at IC50 conc.
H3K4_CPT_BR2_Log2IPtoIC.bw


title: CPT-H3K4-ChIP-BR1

description:
Library name: CPT-H3K4-ChIP-BR1
CPT-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with CPT at IC50 conc.
H3K4_CPT_BR1_Log2IPtoIC.bw


title: CPT-H3K36-INPUT-BR2

description:
Library name: CPT-H3K36-INPUT-BR2
CPT-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with CPT at IC50 conc (Control for CPT-H3K36-ChIP_BR2).
H3K36_CPT_BR2_Log2IPtoIC.bw


title: CPT-H3K36-ChIP-BR1

description:
Library name: CPT-H3K36-ChIP-BR1
CPT-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with CPT at IC50 conc.
H3K36_CPT_BR1_Log2IPtoIC.bw


title: CPT-H3K36-ChIP-BR2

description:
Library name: CPT-H3K36-ChIP-BR2
CPT-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with CPT at IC50 conc.
H3K36_CPT_BR2_Log2IPtoIC.bw


title: CPT-H3K36-INPUT-BR1

description:
Library name: CPT-H3K36-INPUT-BR1
CPT-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with CPT at IC50 conc (Control for CPT-H3K36-ChIP_BR1).
H3K36_CPT_BR1_Log2IPtoIC.bw


title: CM-H3K4-INPUT-BR2

description:
Library name: CM-H3K4-INPUT-BR2
CM-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for CM-H3K4-ChIP-BR2)
H3K4_CM_BR2_Log2IPtoIC.bw

value: 0.1 N NaOH


title: CM-H3K4-INPUT-BR1

description:
Library name: CM-H3K4-INPUT-BR1
CM-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for CM-H3K4-ChIP-BR1)
H3K4_CM_BR1_Log2IPtoIC.bw


title: CM-H3K4-ChIP-BR1

description:
Library name: CM-H3K4-ChIP-BR1
CM-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo MTX-H3K4-ChIP-BR1)
H3K4_CM_BR1_Log2IPtoIC.bw


title: CM-H3K36-INPUT-BR1

description:
Library name: CM-H3K36-INPUT-BR1
CM-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for CM-H3K36-ChIP-BR1)
H3K36_CM_BR1_Log2IPtoIC.bw


title: CM-H3K36-ChIP-BR1

description:
Library name: CM-H3K36-ChIP-BR1
CM-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo MTX-H3K36-ChIP-BR1)
H3K36_CM_BR1_Log2IPtoIC.bw


title: CM-H3K4-ChIP-BR2

description:
Library name: CM-H3K4-ChIP-BR2
CM-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo MTX-H3K4-ChIP-BR2)
H3K4_CM_BR2_Log2IPtoIC.bw


title: CD-H3K4-INPUT-BR2

description:
Library name: CD-H3K4-INPUT-BR2
CD-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for CD-H3K4-ChIP-BR2)
H3K4_CD_BR2_Log2IPtoIC.bw


title: HU-H3K36-ChIP-BR1

description:
Library name: HU-H3K36-ChIP-BR1
HU-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with HU at IC50 conc.
H3K36_HU_BR1_Log2IPtoIC.bw


title: CM-H3K36-ChIP-BR2

description:
Library name: CM-H3K36-ChIP-BR2
CM-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo MTX-H3K36-ChIP-BR2 )
H3K36_CM_BR2_Log2IPtoIC.bw


title: CD-H3K4-ChIP-BR2

description:
Library name: CD-H3K4-ChIP-BR2
CD-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo DOX-H3K4-ChIP-BR2)
H3K4_CD_BR2_Log2IPtoIC.bw


title: DOX-H3K4-ChIP-BR2

description:
Library name: DOX-H3K4-ChIP-BR2
DOX-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with DOX at IC50 conc.
H3K4_DOX_BR2_Log2IPtoIC.bw


title: CM-H3K36-INPUT-BR2

description:
Library name: CM-H3K36-INPUT-BR2
CM-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for CM-H3K36-ChIP-BR2)
H3K36_CM_BR2_Log2IPtoIC.bw


title: CD-H3K4-INPUT-BR1

description:
Library name: CD-H3K4-INPUT-BR1
CD-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for CD-H3K4-ChIP-BR1)
H3K4_CD_BR1_Log2IPtoIC.bw


title: CD-H3K36-ChIP-BR2

description:
Library name: CD-H3K36-ChIP-BR2
CD-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo DOX-H3K36-ChIP-BR2 )
H3K36_CD_BR2_Log2IPtoIC.bw


title: CD-H3K36-INPUT-BR2

description:
Library name: CD-H3K36-INPUT-BR2
CD-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for CD-H3K36-ChIP-BR2)
H3K36_CD_BR2_Log2IPtoIC.bw


title: CD-H3K36-INPUT-BR1

description:
Library name: CD-H3K36-INPUT-BR1
CD-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for CD-H3K36-ChIP-BR1)
H3K36_CD_BR1_Log2IPtoIC.bw


title: CD-H3K36-ChIP-BR1

description:
Library name: CD-H3K36-ChIP-BR1
CD-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo DOX-H3K36-ChIP-BR1)
H3K36_CD_BR1_Log2IPtoIC.bw


title: CC-H3K4-INPUT-BR2

description:
Library name: CC-H3K4-INPUT-BR2
CC-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for CC-H3K4-ChIP-BR2)
H3K4_CC_BR2_Log2IPtoIC.bw

value: 1N NaoH


title: CC-H3K4-INPUT-BR1

description:
Library name: CC-H3K4-INPUT-BR1
CC-H3K4-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for CC-H3K4-ChIP-BR1)
H3K4_CC_BR1_Log2IPtoIC.bw


title: CD-H3K4-ChIP-BR1

description:
Library name: CD-H3K4-ChIP-BR1
CD-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo DOX-H3K4-ChIP-BR1)
H3K4_CD_BR1_Log2IPtoIC.bw


title: CC-H3K4-ChIP-BR2

description:
Library name: CC-H3K4-ChIP-BR2
CC-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo CPT-H3K4-ChIP-BR2)
H3K4_CC_BR2_Log2IPtoIC.bw


title: CPT-H3K4-INPUT-BR2

description:
Library name: CPT-H3K4-INPUT-BR2
CPT-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with CPT at IC50 conc (Control for CPT-H3K4-ChIP_BR2).
H3K4_CPT_BR2_Log2IPtoIC.bw


title: CC-H3K36-INPUT-BR2

description:
Library name: CC-H3K36-INPUT-BR2
CC-H3K36-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for CC-H3K36-ChIP-BR2)
H3K36_CC_BR2_Log2IPtoIC.bw


title: CC-H3K4-ChIP-BR1

description:
Library name: CC-H3K4-ChIP-BR1
CC-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo CPT-H3K4-ChIP-BR1)
H3K4_CC_BR1_Log2IPtoIC.bw


title: CC-H3K36-INPUT-BR1

description:
Library name: CC-H3K36-INPUT-BR1
CC-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for CC-H3K36-ChIP-BR1)
H3K36_CC_BR1_Log2IPtoIC.bw


title: CC-H3K36-ChIP-BR2

description:
Library name: CC-H3K36-ChIP-BR2
CC-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo CPT-H3K36-ChIP-BR2 )
H3K36_CC_BR2_Log2IPtoIC.bw


title: CC-H3K36-ChIP-BR1

description:
Library name: CC-H3K36-ChIP-BR1
CC-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo CPT-H3K36-ChIP-BR1)
H3K36_CC_BR1_Log2IPtoIC.bw


title: C0-H3K4-INPUT-BR2

description:
Library name: C0-H3K4-INPUT-BR2
C0-H3K4-INPUT-BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for C0-H3K4-ChIP-BR2)
H3K4_C0_BR2_Log2IPtoIC.bw


title: C0-H3K4-ChIP-BR2

description:
Library name: C0-H3K4-ChIP-BR2
C0-H3K4-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo HU-H3K4-ChIP-BR2 and MMS-H3K4-ChIP-BR2)
H3K4_C0_BR2_Log2IPtoIC.bw


title: C0-H3K4-ChIP-BR1

description:
Library name: C0-H3K4-ChIP-BR1
C0-H3K4-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo HU-H3K4-ChIP-BR1 and MMS-H3K4-ChIP-BR1)
H3K4_C0_BR1_Log2IPtoIC.bw


title: C0-H3K36-INPUT-BR1

description:
Library name: C0-H3K36-INPUT-BR1
C0-H3K36-INPUT-BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for C0-H3K36-ChIP-BR1)
H3K36_C0_BR1_Log2IPtoIC.bw


title: C0-H3K36-INPUT-BR2

description:
Library name: C0-H3K36-INPUT-BR2
C0-H3K36-INPUT--BR2 denotes BR2 genomic DNA sample treated with AgD H2O (Control for C0-H3K36-ChIP-BR2)
H3K36_C0_BR2_Log2IPtoIC.bw


title: CPT-SET2-BR3

description:
Library name: CPT-SET2-BR3
CPT-SET2-BR3 denotes BR3  ChIP-seq sample treated with CPT 100 microgm/ml (Treatment  for CC-SET2-BR3)
SET2_CPTtoCC_BR3.bw

data_processing:
*library strategy: Break-seq
alignment by Bowtie2, bamCompare by deepTools to normalize CPT to CC samples
Assembly: sacCer3
Supplementary files format and content: BAM and BigWIg
Supplementary files format and content: BigWig files were made from CPT and CC samples for each strain, therefore each bw file is associated with two bam files.

growth_protocol: WT/ mutant (rpd3∆, set1∆, set2∆)  yeast cells from the W303 background were grown either in YEPD or SC media at 30 °C.

extract_protocol:
10^8 cells prewashed with 50mM EDTA were embedded into each agarose plug (0.5% Incert agarose in 50mM EDTA).  The cells were then spheroplasted for 4h at 37 °C with gentle shaking, followed by an overnight incubation with LDS. The cells were then washed twice for 30 min each  with 0.2 X NDS and TE pH8.0 for 30 min each.
Agarose plugscontaining DNA were washed once with TE pH 8.0, followed by in-gel labeling using biotin tagged dATP.  Plugs containing labelled DNA were then digested with β-agarase to digest the agarose.  The eluted DNA was then sonicated to using Covaris M220 sonicator to get an average fragment size of 300 bp.  The  sonicated DNA was end repaied followed by dA Tailing. The biotinylated, endrepaired and dA Tailed DNA was subjected to IP using M270 Dynabeads to caputed the biotin labeled DNA fragments. The captured DNA was then subjected to library construction by attaching Solexa adaptors to the ends using T4 DNA ligase. 400 ng of the DNA was then subjectedto PCR amplification using KAPA Hotstart Ready Mix (KAPA) using a unique sequencing primer per sample.  The amplified DNA was then purified using AMPure beads to remove free adaptors.  The libraries were then sequenced on Illumina Hi-Seq 2500 platform  (150 bp paired-end reads).

treatment_protocol: Cells were grown to an OD~0.3 before addition of either the replication inhibitor or vehicle control.  Post addition of the either,  the cells were continued to grow for the determined IC50 timepoint prior to harvesting.

value: DNA DSBs


title: C0-H3K36-ChIP-BR2

description:
Library name: C0-H3K36-ChIP-BR2
C0-H3K36-ChIP-BR2 denotes BR2 ChIP-seq sample treated with AgD H2O (Control fo HU-H3K36-ChIP-BR2 and MMS-H3K36-ChIP-BR2)
H3K36_C0_BR2_Log2IPtoIC.bw


title: C0-H3K36-ChIP-BR1

description:
Library name: C0-H3K36-ChIP-BR1
C0-H3K36-ChIP-BR1 denotes BR1 ChIP-seq sample treated with AgD H2O (Control fo HU-H3K36-ChIP-BR1 and MMS-H3K36-ChIP-BR1)
H3K36_C0_BR1_Log2IPtoIC.bw


title: CPT-WT-BR3

description:
Library name: CPT-WT-BR3
CPT-WT-BR3 denotes BR2  ChIP-seq sample treated with CPT 100 microgm/ml (Treatment  for CC-WT-BR3)
WT_CPTtoCC_BR3.bw


title: CPT-SET2-BR2

description:
Library name: CPT-SET2-BR2
CPT-SET2-BR2 denotes BR2  ChIP-seq sample treated with CPT 100 microgm/ml (Treatment  for CC-SET2-BR2)
SET2_CPTtoCC_BR2.bw


title: CPT-WT-BR2

description:
Library name: CPT-WT-BR2
CPT-WT-BR2 denotes BR2  ChIP-seq sample treated with CPT 100 microgm/ml (Treatment  for CC-WT-BR2)
WT_CPTtoCC_BR2.bw


title: CPT-RPD3-BR3

description:
Library name: CPT-RPD3-BR3
CPT-RPD3-BR3 denotes BR3  ChIP-seq sample treated with CPT 100 microgm/ml (Treatment  for CC-RPD3-BR3 )
RPD3_CPTtoCC_BR3.bw


title: 2-2-MTX-16

description:
2-2-MTX
2-2-MTX-16 denotes BR2TR2 DNA-seq sample treated with 150 µg/mL MTX

data_processing:
library strategy: DNA-seq
alignment by Bowtie2, peakcalling by MACS2 bdgdiff
Assembly: sacCer3
Supplementary files format and content: bed, bdgdiff

extract_protocol:
10 ml cell pellets were collected per conditions and were snap frozen at stored at -80°C. DNA was isolated from each cell pellet using Yeast Smash and Grab method. Briefly, to each cell pellet in an eppendorf tube 300 µL of glass beads, 200 µL of lysis buffer (10 mM Tris pH 8.0, 1 mM EDTA, 100 mM NaCl, 1% SDA, 2% Triton X-100) and 200 µL of 1:1 phenol chloroform was added.  The cells were vortexed for 2 mins followed by adding another 200 µL of TE pH 8.0 and continued vortexing for a few seconds.  The tubes were then centrifuged at 13,500 rpm for 5 mins after which the top aqueous layer was transferred to a fresh tube. Two volumes of 100% ethanol was added and the tubes were centrifuged at 13,500 rpm for 2-3 mins at RT to pellet the DNA.  The DNA pellet was washed with ice cold 70% ethanol.  The pellets were then dried and the DNA pellet was resuspended in 50 µL TE pH 8.0.
The eluted DNA was then sonicated to using Covaris M220 sonicator to get an average fragment size of 300 bp.  The  sonicated DNA was end repaied followed by dA Tailing. The sonicated, endrepaired and dA Tailed DNA was subjected to library construction by attaching Solexa adaptors to the ends using T4 DNA ligase. 400 ng of the DNA was then subjectedto PCR amplification using KAPA Hotstart Ready Mix (KAPA) using a unique sequencing primer per sample.  The amplified DNA was then purified using AMPure beads to remove free adaptors.  The libraries were then sequenced on Illumina Hi-Seq 2500 platform  (150 bp paired-end reads).

tag: technical replicate


title: CC-RPD3-BR3

description:
Library name: CC-RPD3-BR3
CC-RPD3-BR3 denotes BR3  ChIP-seq sample treated with AgD H2O (Control for CPT-RPD3-BR3 )
RPD3_CPTtoCC_BR3.bw

value: 1N NaOH


title: CC-SET2-BR2

description:
Library name: CC-SET2-BR2
CC-SET2-BR2 denotes BR2  ChIP-seq sample treated with AgD H2O (Control for CPT-SET2-BR2)
SET2_CPTtoCC_BR2.bw


title: CPT-RPD3-BR2

description:
Library name: CPT-RPD3-BR2
CPT-RPD3-BR2 denotes BR2  ChIP-seq sample treated with CPT 100 microgm/ml (Treatment  for CC-RPD3-BR2)
RPD3_CPTtoCC_BR2.bw


title: CC-SET2-BR3

description:
Library name: CC-SET2-BR3
CC-SET2-BR3 denotes BR3  ChIP-seq sample treated with AgD H2O (Control for CPT-SET2-BR3)
SET2_CPTtoCC_BR3.bw


title: 2-1-MTX-15

description:
2-1-MTX
2-1-MTX-15 denotes BR2TR1 DNA-seq sample treated with 150 µg/mL MTX


title: CC-WT-BR2

description:
Library name: CC-WT-BR2
CC-WT-BR2 denotes BR2  ChIP-seq sample treated with AgD H2O (Control for CPT-WT-BR2)
WT_CPTtoCC_BR2.bw


title: CC-WT-BR3

description:
Library name: CC-WT-BR3
CC-WT-BR3 denotes BR2  ChIP-seq sample treated with AgD H2O (Control for CPT-WT-BR3)
WT_CPTtoCC_BR3.bw


title: 1-1-MTX-13

description:
1-1-MTX
1-1-MTX-13 denotes BR1TR1 DNA-seq sample treated with 150 µg/mL MTX


title: CC-RPD3-BR2

description:
Library name: CC-RPD3-BR2
CC-RPD3-BR2 denotes BR2  ChIP-seq sample treated with AgD H2O (Control for CPT-RPD3-BR2)
RPD3_CPTtoCC_BR2.bw


title: 1-2-MTX-14

description:
1-2-MTX
1-2-MTX-14 denotes BR1TR2 DNA-seq sample treated with 150 µg/mL MTX


title: 2-2-CM-12

description:
2-2-CM
2-2-CM-12 denotes BR2TR2 DNA-seq sample treated with 0.1N NAOH (Control for MTX)

value: 0.1N NaOH


title: C0-H3K4-INPUT-BR1

description:
Library name: C0-H3K4-INPUT-BR1
C0-H3K4-INPUT--BR1 denotes BR1 genomic DNA sample treated with AgD H2O (Control for C0-H3K4-ChIP-BR1)
H3K4_C0_BR1_Log2IPtoIC.bw


title: 2-2-DOX-8

description:
2-2-DOX
2-2-DOX-8 denotes BR2TR2 DNA-seq sample treated with 25 µg/mL DOX


title: 1-1-CM-9

description:
1-1-CM
1-1-CM-9 denotes BR1TR1 DNA-seq sample treated with 0.1N NAOH (Control for MTX)


title: mouse keratinocyte, HdR4

city: Kyoto

first: Satoshi

last: NAKAMIZO

state: Kyoto

address: 54 Shogoin-Kawahara, Sakyo

country: Japan

institute: Kyoto University

description: Library name: Hc4

data_processing:
Sequenced reads were quantified using Genomon (version .2.63, genomon: http://genomon.hgc.jp/exome/index.html) against the Mus musculus transcriptome (GRCm38).
Assembly: GRCm38
Supplementary files format and content: The comma-separated CSV file contains the raw counts for each sample.

source_name: Skin

extract_protocol:
Total RNA was isolated from directly from culture plates using RNeasy mini kit.
RNA-sequencing libraries were generated using NEBNext Ultra II RNA Library kit for Illumina (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions and sequenced on the NovaSeq 6000 platform (Illumina, San Diego, CA).

value: Skin

value: HdR


title: 1-2-DOX-6

description:
1-2-DOX-6
1-2-DOX-6 denotes BR1TR2 DNA-seq sample treated with 25 µg/mL DOX

value: WT

value: SC


title: mouse keratinocyte, HdR3

description: Library name: Hc3


title: 1-1-DOX-5

description:
1-1-DOX
1-1-DOX-5 denotes BR1TR1 DNA-seq sample treated with 25 µg/mL DOX


title: mouse keratinocyte, HdR1

description: Library name: Hc1


title: 2-2-CD-4

description:
2-2-CD
2-2-CD-4 denotes BR2TR1DNA-seq sample treated with AgD H2O (Control for DOX)


title: mouse keratinocyte, WT4

description: Library name: Wc4


title: 1-2-CD-2

description:
1-2-CD
1-2-CD-2 denotes BR1TR2 DNA-seq sample treated with AgD H2O (Control for DOX)


title: 2-1-CD-3

description:
2-1-CD
2-1-CD-3 denotes BR2TR1 DNA-seq sample treated with AgD H2O (Control for DOX)


title: mouse keratinocyte, WT2

description: Library name: Wc2


title: mouse keratinocyte, WT1

description: Library name: Wc1


title: 2-2-AD-16

description:
2-2-AD
2-2-AD-16 denotes BR2TR2 DNA-seq sample treated with 50 µg/mL AD

value: AD


title: 1-1-CD-1

description:
1-1-CD
1-1-CD-1 denotes BR1TR1 DNA-seq sample treated with AgD H2O (Control for DOX)


title: 2-1-CM-11

description:
2-1-CM
2-1-CM-11 denotes BR2TR1 DNA-seq sample treated with 0.1N NAOH (Control for MTX)


title: 1-1-AD-18-B

description:
1-1-AD
1-1-AD-18-B denotes BR1TR1 DNA-seq sample treated with 50 µg/mL AD


title: 1-2-AD-14

description:
1-2-AD
1-2-AD-14 denotes BR1TR2 DNA-seq sample treated with 50 µg/mL AD


title: 2-1-AD-15

description:
2-1-AD
2-1-AD-15 denotes BR2TR1 DNA-seq sample treated with 50 µg/mL AD


title: C57 BL6/J skin wound edge, D1, PBS association 1/3

city: New York

first: Dr. Shruti

last: Naik

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description: Library name: PBS_24_1

data_processing:
The demultiplexed FASTQ files were first trimmed to remove adaptor sequences using trimmomatic.
Reads were aligned to mm10 / Grcm38 genome using STAR aligner
Generated raw gene counts for each sample using featureCounts funciton from subreads package.
Assembly: mm10
Supplementary files format and content: csv file containing raw genes counts per sample
Supplementary files format and content: a csv file containing normalized gene counts (DESeq2 median of ratios) normalized.

source_name: skin wound edge

extract_protocol:
Total RNA was extracted using the Direct-zol RNA kit (Zymo Research) as per manufacturer’s instructions.
RNA was shipped to Novogene for library prep and sequencing. Paired end RNA Sequencing was performed using NovaSeq X Plus System. FASTQ files were generated and were demultiplexed.

treatment_protocol: Total skin wound edge was dissected and flash frozen in liquid nitrogen and 4 wound edges were pooled per sample.

value: skin wound edge

value: C57 BL6/J

value: PBS


title: C57 BL6/J skin wound edge, D1, PBS association 2/3

description: Library name: PBS_24_2


title: C57 BL6/J skin wound edge, D1, S. aureus LAC association 3/3

description: Library name: LAC_24_3

value: S. aureus LAC


title: C57 BL6/J skin wound edge, D1, S. aureus LAC association 2/3

description: Library name: LAC_24_2


title: 1-2-CM-10

description:
1-2-CM
1-2-CM-10 denotes BR1TR2 DNA-seq sample treated with 0.1N NAOH (Control for MTX)


title: 2-1-DOX-7

description:
2-1-DOX
2-1-DOX-7 denotes BR2TR1 DNA-seq sample treated with 25 µg/mL DOX


title: 2-1-CA-11

description:
2-1-CA
2-1-CA-11 denotes BR2TR1 DNA-seq sampletreated with 2%  acetone as solvent

value: 2% Acetone


title: C57 BL6/J skin wound edge, D1, PBS association 3/3

description: Library name: PBS_24_3


title: 1-1-CA-9

description:
1-1-CA
1-1-CA-9 denotes BR1TR1 DNA-seq sampletreated with 2%  acetone as solvent


title: AML-12 Cell RNA rep2

city: Townsville

first: Lionel

last: Hebbard

state: QLD

address: 1 James Cook Dr, Douglas QLD 4811

country: Australia

institute: James Cook University

description: Library name: AML-12_cell_2_RNA

data_processing:
RNA: Trimmomatic v0.39; Bowtie2 v2.5.4; RSEM v1.3.3
DNA: GATKv4.5.0.0; HaplotypeCaller; ANNOVAR v2020-06-08
Assembly: GRCm39
Supplementary files format and content: RNA: RSEM isoforms.results and genes.results
Supplementary files format and content: DNA: Annotated VCF

source_name: Liver

extract_protocol:
RNA: Isolate II RNA Mini Kit (BIO-52073, Meridian Bioscience). DNA: Monarch gDNA Extraction Kit (T3010G, New England Biolabs)
RNA: PolyA Purification; Fragmentation; Random Priming; dUTP Strand Marking; Adapter Ligation; Amplification. DNA: Fragmentation; End Repair and A-Tailing; Adapter Ligation; Size Selection; Amplification

value: Liver

value: Hepatocyte

value: Untreated

tag: batch


title: 2-2-CPT-8

description:
2-2-CPT
2-2-CPT-8 denotes BR2TR2 DNA-seq sample treated with 100µg/mL CPT

value: YEPD

value: CPT


title: 1-2-CA-10

description:
1-2-CA
1-2-CA-10 ddenotes BR1TR2 DNA-seq sampletreated with 2%  acetone as solvent


title: mouse keratinocyte, HdR2

description: Library name: Hc2


title: 2-1-CPT-7

description:
2-1-CPT
2-1-CPT-7 denotes BR2TR1 DNA-seq sample treated with 100µg/mL CPT


title: A52 Cell DNA rep1

description: Library name: A52_cell_DNA

source_name: Hepatocellular Carcinoma

value: Hepatocellular Carcinoma


title: 1-2-CPT-6

description:
1-2-CPT
1-2-CPT-6 denotes BR1TR2 DNA-seq sample treated with 100µg/mL CPT


title: AML-12 Cell RNA rep1

description: Library name: AML-12_cell_1_RNA


title: A52 Cell RNA rep2

description: Library name: A52_cell_2_RNA


title: mouse keratinocyte, WT3

description: Library name: Wc3


title: 1-1-CPT-5

description:
1-1-CPT
1-1-CPT-5 denotes BR1TR1 DNA-seq sample treated with 100µg/mL CPT


title: 2-2-CA-12

description:
2-2-CA
2-2-CA-12 denotes BR2TR2 DNA-seq sampletreated with 2%  acetone as solvent


title: C57 BL6/J skin wound edge, D1, S. aureus LAC association 1/3

description: Library name: LAC_24_1


title: 2-1-CC-3

description:
2-1-CC
2-1-CC-3 denotes BR2TR1 DNA-seq sample treated with 1N NAOH (Control for CPT)

value: 1N NaoH


title: A52 Cell RNA rep1

description: Library name: A52_cell_1_RNA


title: 2-2-CC-4

description:
2-2-CC
2-2-CC-4 denotes BR2TR2 DNA-seq sample treated with 1N NAOH (Control for CPT)


title: A52 Tissue RNA rep4

description: Library name: A52_tissue_4_RNA


title: 1-2-CC-2

description:
1-2-CC
1-2-CC-2 denotes BR1TR2 DNA-seq sample treated with 1N NAOH (Control for CPT)


title: A52 Tissue RNA rep3

description: Library name: A52_tissue_3_RNA


title: A52 Tissue RNA rep5

description: Library name: A52_tissue_5_RNA


title: 1-1-CC-1

description:
1-1-CC
1-1-CC-1 denotes BR1TR1 DNA-seq sample treated with 1N NAOH (Control for CPT)


title: 2-1-MMS-8

description:
2-1-MMS
2-1-MMS-8 denotes BR2TR1 DNA-seq sample treated with 0.002% MMS

value: MMS


title: A52 Tissue RNA rep1

description: Library name: A52_tissue_1_RNA


title: 2-2-MMS-12

description:
2-2-MMS
2-2-MMS-12 denotes BR2TR2 DNA-seq sample treated with 0.002% MMS


title: A52 Tissue RNA rep2

description: Library name: A52_tissue_2_RNA


title: Kidney_oxa_5

city: St Louis

first: Mikhail

last: Berezin

state: Missouri

address: 4515 McKinley  Ave

institute: Washington University in St. Louis

description:
Library name: Kidney_oxa_5
kidney oxaliplatin biological replicate 5

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Assembly: Ensembl release 101
Supplementary files format and content: Comma Separated CSV file containing the raw gene counts for all samples

source_name: Kidney

extract_protocol:
For Kidney samples, total RNA was extracted with PureLink RNA mini kit following manufactors' instructions. For bone marrow, RNA was extracted with Trizol followed by column-based purification using PureLink column.
Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Mice were treated with 5% dextrose or 10 mg/kg oxaliplatin i.p. for 8 weeks

value: Kidney

value: 10 mg/kg oxaliplatin


title: Kidney_oxa_4

description:
Library name: Kidney_oxa_4
kidney oxaliplatin biological replicate 4


title: Kidney_oxa_3

description:
Library name: Kidney_oxa_3
kidney oxaliplatin biological replicate 3


title: 2-2-HU-15-B

description:
2-2-HU
2-2-HU-15-B denotes BR2TR2 DNA-seq sample treated with 50mM HU

value: WT

value: HU


title: 1-1-MMS-5

description:
1-1-MMS
1-1-MMS-5 denotes BR1TR1 DNA-seq sample treated with 0.002% MMS


title: Kidney_oxa_2

description:
Library name: Kidney_oxa_2
kidney oxaliplatin biological replicate 2


title: 1-2-MMS-10

description:
1-2-MMS
1-2-MMS-10 denotes BR1TR2 DNA-seq sample treated with 0.002% MMS


title: 2-1-HU-14-B

description:
2-1-HU
2-1-HU-14-B denotes BR2TR1 DNA-seq sample treated with 50mM HU


title: Kidney_oxa_1

description:
Library name: Kidney_oxa_1
kidney oxaliplatin biological replicate 1


title: Kidney_ctrl_5

description:
Library name: Kidney_ctrl_5
kidney control biological replicate 5

value: control (5% dextrose)


title: 1-1-HU-4

description:
1-1-HU
1-1-HU-4 denotes BR1TR1 DNA-seq sample treated with 50mM HU


title: Kidney_ctrl_4

description:
Library name: Kidney_ctrl_4
kidney control biological replicate 4


title: 1-2-HU-3

description:
1-2-HU
1-2-HU-3 denotes BR1TR2 DNA-seq sample treated with 50mM HU


title: Kidney_ctrl_3

description:
Library name: Kidney_ctrl_3
kidney control biological replicate 3


title: 2-2-C0-9

description:
2-2-C0
2-2-C0-9 denotes BR2TR2 DNA-seq sample treated with AgD H2O (Control for HU and MMS)


title: Kidney_ctrl_2

description:
Library name: Kidney_ctrl_2
kidney control biological replicate 2


title: 2-1-C0-6

description:
2-1-C0
2-1-C0-6 denotes BR2TR1 DNA-seq sample treated with AgD H2O (Control for HU and MMS)


title: 1-2-C0-4

description:
1-2-C0
1-2-C0-4 denotes BR1TR2 DNA-seq sample treated with AgD H2O (Control for HU and MMS)


title: 1-1-C0-2

description:
1-1-C0
1-1-C0-2 denotes BR1TR1 DNA-seq sample treated with AgD H2O (Control for HU and MMS)


title: SGMHT-1

city: Chongqing

first: huina

last: lu

address: No. 6 Panxi Seventh Branch Road, Jiangbei District, Chongqing

institute: CHONGQING TRADITIONAL CHINESE MEDICINE HOSPITAL

description: Library name: SGMHT-1

library_source: transcriptomic single cell

data_processing:
Raw reads are demultiplexed and mapped to the reference genome using the 10× Genomics Cell Ranger pipeline, and downstream single-cell analyses are performed using Cell Ranger and Seurat(Macosko et al., 2015).
For each gene and cell barcode, unique molecule identifiers were calculated to construct digital expression matrixes. Genes expressed in more than three cells were considered as expressed genes by secondary filtering with Seurat, requiring a minimum of 200 expressed genes per cell and filtering out some foreign cells.
The feature barcode matrix was generated and the clustering and gene expression analysis were conducted using Cell Ranger default parameter settings.
Data normalization, dimensionality reduction, clustering and differential expression analysis were performed using the Seurat package, and the dataset was synthesized using the Seurat alignment method canonical correlation analysis (CCA)(Butler et al., 2018).
Highly variable genes were selected and the principal components were used to graph. GO and KEGG pathway enrichment analyses were performed on marker genes by clusterProfiler R package. Intercellular communication analysis was performed using the R package CellChat with default parameters, based on the CellChatDB mouse database. Single-cell trajectory analysis was performed using Monocle 2 to identify significant translational relationships among cell types.
Assembly: mouse reference genome (GRCm38.94)
Supplementary files format and content: no
Supplementary files format and content: no

source_name: lung

extract_protocol:
Lung tissue was cut into small pieces and digested using trypsin, followed by filtration through a cell strainer to remove undigested tissue fragments, thereby obtaining a single-cell suspension.
The cell suspension was loaded into a Chromium microfluidic chip with 3' (v3.1) chemistry and barcoded using a 10× Chromium Controller. RNA from barcoded cells was subsequently reverse transcribed and sequencing libraries were constructed using reagents in the Chromium Single Cell 3' v3.1 kit according to the manufacturer's instructions. Sequencing was performed using Illumina NovaSeq6000.

value: lung

value: wt

value: SMD group1


title: D6

description:
Library name: D6
Prednisone group 6

library_source: other

data_processing:
Raw data was truncated to remove barcode and primer sequences, and reads from each sample were spliced using FLASH to obtain raw tags(Magoc and Salzberg, 2011).
The spliced Raw Tags were filtered by fastp software to obtain high-quality tags, which were compared with the SILVA 138.1 database (https://www.arb-silva.de/) to remove the chimeric sequences and obtain the final effective tags.
The Effective Tags were clustered using vsearch v2.14.2(Rognes et al., 2016), and the sequences were clustered into operational taxonomic units (OTUs) with 97% identity, and the representative sequences in the OTUs were filtered at the same time.
Species annotation analysis was performed with GreenGene data using RDP Classifier v2.2 to obtain taxonomic information. Alpha diversity index analyses were performed using Qiime software (Version 1.9.1)(Bokulich et al., 2018), and Unifrac distances were calculated and UPGMA clustering trees were constructed. Linear discriminant analysis effect size (LEfSe) analyses were performed using LEfSe software(Segata et al., 2011) with the default setting of 2 for the LDA Score filter.
Functional annotation prediction of OTUs was performed using PICRUSt2(Douglas et al., 2020). Relationships between environmental factors and species abundance were analyzed based on the Spearman correlation.
Assembly: no
Supplementary files format and content: no
Supplementary files format and content: no
Library strategy: 16S rRNA-seq

molecule: other

source_name: stool samples

extract_protocol:
Genomic DNA was extracted from stool samples using the E.Z.N.A.® Stool DNA Kit (D4015, OMEGA) for high-throughput 16S rRNA gene sequencing. The bacterial universal primers 341F-CCTAYGGRBGCASCAG; and 806R-GGGACTACNNGGTTATTAAT were selected for amplification of the V3-V4 region of the bacterial 16S rRNA gene by PCR, and the PCR products were verified by 2% agarose gel electrophoresis(Hess et al., 2011).
library construction was performed using the NEB Next® Ultra™ II FS DNA Free PCR Library Preparation Kit (New England Biolabs). Purified amplicons were subjected to PE250 sequencing on a NovaSeq 6000 system.

value: stool samples

value: Prednisone group 6

value: no


title: 2-1-MTX-15 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-MTX
2-1-MTX-15 denotes BR2TR1 Break-seq sample treated with 150 µg/mL MTX
MTX treated sample.

data_processing:
*library strategy: Break-seq
alignment by Bowtie2, peakcalling by MACS2 bdgdiff
Assembly: sacCer3
Supplementary files format and content: bed, bdgdiff

value: SC

value: MTX


title: Kidney_ctrl_1

description:
Library name: Kidney_ctrl_1
kidney control biological replicate 1


title: Model-1

description: Library name: Model-1

value: model 1


title: D5

description:
Library name: D5
Prednisone group 5

value: Prednisone group 5


title: D4

description:
Library name: D4
Prednisone group 4

value: Prednisone group 4


title: D3

description:
Library name: D3
Prednisone group 3

value: Prednisone group 3


title: 1-1-MTX-13 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-MTX
1-1-MTX-13 denotes BR1TR1 Break-seq sample treated with 150 µg/mL MTX
MTX treated sample.


title: D2

description:
Library name: D2
Prednisone group 2

value: Prednisone group 2


title: 1-2-MTX-14 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-MTX
1-2-MTX-14 denotes BR1TR2 Break-seq sample treated with 150 µg/mL MTX
MTX treated sample.


title: 2-2-MTX-16 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-MTX
2-2-MTX-16 denotes BR2TR2 Break-seq sample treated with 150 µg/mL MTX
MTX treated sample.


title: 2-1-CM-11 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-CM
2-1-CM-11 denotes BR2TR1 Break-seq sample treated with 0.1N NAOH (Control for MTX)
Vehicle control treated control sample for MTX. Hence, no processed files for these.

value: 0.1N NaOH


title: 1-2-CM-10 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-CM
1-2-CM-10 denotes BR1TR2 Break-seq sample treated with 0.1N NAOH (Control for MTX)
Vehicle control treated control sample for MTX. Hence, no processed files for these.

value: WT


title: D1

description:
Library name: D1
Prednisone group 1

value: Prednisone group 1


title: 2-2-CM-12 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-CM
2-2-CM-12 denotes BR2TR2 Break-seq sample treated with 0.1N NAOH (Control for MTX)
Vehicle control treated control sample for MTX. Hence, no processed files for these.


title: 1-1-CM-9 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-CM
1-1-CM-9 denotes BR1TR1 Break-seq sample treated with 0.1N NAOH (Control for MTX)
Vehicle control treated control sample for MTX. Hence, no processed files for these.


title: C5

description:
Library name: C5
SMD group 5

value: SMD group 5


title: C6

description:
Library name: C6
SMD group 6

value: SMD group 6


title: 2-2-DOX-8 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-DOX
2-2-DOX-8 denotes BR2TR2 Break-seq sample treated with 25 µg/mL DOX
DOX treated sample.

value: DOX


title: C3

description:
Library name: C3
SMD group 3

value: wt

value: SMD group 3


title: 2-1-DOX-7 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-DOX
2-1-DOX-7 denotes BR2TR1 Break-seq sample treated with 25 µg/mL DOX
DOX treated sample.


title: 1-2-DOX-6 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-DOX-6
1-2-DOX-6 denotes BR1TR2 Break-seq sample treated with 25 µg/mL DOX
DOX treated sample.


title: 1-1-DOX-5 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-DOX
1-1-DOX-5 denotes BR1TR1 Break-seq sample treated with 25 µg/mL DOX
DOX treated sample.


title: C2

description:
Library name: C2
SMD group 2

value: stool samples

value: SMD group 2


title: C1

description:
Library name: C1
SMD group 1

value: SMD group 1

value: no


title: 2-1-CD-3 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-CD
2-1-CD-3 denotes BR2TR1 Break-seq sample treated with AgD H2O (Control for DOX)
Vehicle control treated control sample for DOX. Hence, no processed files for these.

value: SC


title: 2-2-CD-4 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-CD
2-2-CD-4 denotes BR2TR2 Break-seq sample treated with AgD H2O (Control for DOX)
Vehicle control treated control sample for DOX. Hence, no processed files for these.


title: 1-2-CD-2 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-CD
1-2-CD-2 denotes BR1TR2 Break-seq sample treated with AgD H2O (Control for DOX)
Vehicle control treated control sample for DOX. Hence, no processed files for these.


title: B6

description:
Library name: B6
model 6

value: model 6


title: B5

description:
Library name: B5
model 5

value: model 5


title: 1-1-CD-17-B [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-CD
1-1-CD-17-B denotes BR1TR1 Break-seq sample treated with AgD H2O (Control for DOX)
Vehicle control treated control sample for DOX. Hence, no processed files for these.


title: B4

description:
Library name: B4
model 4

value: model 4


title: 2-2-AD-16 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-AD
2-2-AD-16 denotes BR2TR2 Break-seq sample treated with 50 µg/mL AD
AD treated sample.

value: AD


title: B3

description:
Library name: B3
model 3

value: model 3


title: B1

description:
Library name: B1
model 1

value: model 1


title: 2-1-AD-15 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-AD
2-1-AD-15 denotes BR2TR1 Break-seq sample treated with 50 µg/mL AD
AD treated sample.

value: WT


title: A5

description:
Library name: A5
control 5

value: control 5


title: 2-1-CA-11 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-CA
2-1-CA-11  denotes BR2TR1 Break-seq sample treated with 2% acetone (Control for AD)
Vehicle control treated control sample for AD. Hence, no processed files for these.

value: 2% Acetone


title: 2-2-CA-12 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-CA
2-2-CA-12  denotes BR2TR2 Break-seq sample treated with 2% acetone (Control for AD)
Vehicle control treated control sample for AD. Hence, no processed files for these.


title: B2

description:
Library name: B2
model 2

value: model 2


title: C4

description:
Library name: C4
SMD group 4

value: wt

value: SMD group 4


title: 1-2-AD-14 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-AD
1-2-AD-14 denotes BR1TR2 Break-seq sample treated with 50 µg/mL AD
AD treated sample.


title: 1-1-AD-18-B [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-AD
1-1-AD-18-B denotes BR1TR1 Break-seq sample treated with 50 µg/mL AD
AD treated sample.


title: A4

description:
Library name: A4
control 4

value: stool samples

value: control 4


title: A6

description:
Library name: A6
control 6

value: control 6


title: 1-2-CA-10 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-CA
1-2-CA-10 denotes BR1TR2 Break-seq sample treated with 2% acetone (Control for AD)
Vehicle control treated control sample for AD. Hence, no processed files for these.


title: 1-1-CA-9 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-CA
1-1-CA-9 denotes BR1TR1 Break-seq sample treated with 2% acetone (Control for AD)
Vehicle control treated control sample for AD. Hence, no processed files for these.


title: 2-2-CPT-8 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-CPT
2-2-CPT-8 denotes BR2TR2 Break-seq sample treated with 100µg/mL CPT
CPT treated sample.

value: YEPD

value: CPT


title: A2

description:
Library name: A2
control 2

value: control 2

value: no


title: A3

description:
Library name: A3
control 3

value: control 3


title: lungD5

description: Library name: lungD5

data_processing:
Adapter sequences, reads containing N, and reads with Qphred ≤ 20 were removed using fastp(Chen et al., 2018).
Subsequently, clean reads were aligned to the mouse reference genome (GRCm38.94) using HISAT2 software(Kim et al., 2019).
The number of reads mapping to the exon region of each gene was calculated by FeatureCounts(Liao et al., 2014), and accordingly, as well as the gene length, the expression level of each gene in the sample was calculated.
Further, differentially expressed genes (DEGs) were analyzed using the DESeq2 package(Love et al., 2014), and the thresholds for significant differential expression were set at false discovery rate (FDR) < 0.05 and log2(Fold Change) | > 1.
DEGs were analyzed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome and Disease Ontology (DO) enrichment analysis using clusterProfiler(Wu et al., 2021), and Genome Enrichment Analysis (GSEA) for all genes(Subramanian et al., 2005).
Assembly: mouse reference genome (GRCm38.94)

extract_protocol:
Total RNA was extracted from lung tissue samples using TRIzol reagent, and the purity, concentration and integrity of RNA were assessed using a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), a Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA) and agarose gel electrophoresis, respectively.
Sequencing libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions, and PE150 sequencing was performed on the NovaSeq 6000 platform.

value: lung

value: Prednisone group 1


title: A1

description:
Library name: A1
control 1

value: control 1


title: 1-2-CPT-6 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-CPT
1-2-CPT-6 denotes BR1TR2 Break-seq sample treated with 100µg/mL CPT
CPT treated sample.

value: WT


title: 2-1-CPT-7 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-CPT
2-1-CPT-7 denotes BR2TR1 Break-seq sample treated with 100µg/mL CPT
CPT treated sample.


title: lungD3

description: Library name: lungD3

value: Prednisone group 3


title: 1-1-CPT-5 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-CPT
1-1-CPT-5 denotes BR1TR1 Break-seq sample treated with 100µg/mL CPT
CPT treated sample.


title: lungD4

description: Library name: lungD4

value: Prednisone group 4


title: 2-2-CC-4 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-CC
2-2-CC-4 denotes BR2TR2 Break-seq sample treated with 1N NAOH (Control for CPT)
Vehicle control treated control sample for CPT. Hence, no processed files for these.

value: 1N NaoH


title: lungD2

description: Library name: lungD2

value: wt

value: Prednisone group 2


title: lungD1

description: Library name: lungD1


title: 2-1-CC-3 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-CC
2-1-CC-3 denotes BR2TR1 Break-seq sample treated with 1N NAOH (Control for CPT)
Vehicle control treated control sample for CPT. Hence, no processed files for these.


title: 1-2-CC-2 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-CC
1-2-CC-2 denotes BR1TR2 Break-seq sample treated with 1N NAOH (Control for CPT)
Vehicle control treated control sample for CPT. Hence, no processed files for these.


title: lungC5

description: Library name: lungC5

value: SMD group 5


title: 1-1-CC-16-B [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-CC
1-1-CC-16-B denotes BR1TR1 Break-seq sample treated with 1N NAOH (Control for CPT)
Vehicle control treated control sample for CPT. Hence, no processed files for these.


title: lungC3

description: Library name: lungC3

value: SMD group 3


title: lungC4

description: Library name: lungC4

value: SMD group 4


title: lungC2

description: Library name: lungC2

value: SMD group 2


title: 1-2-MMS-10 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-MMS
1-2-MMS-10 denotes BR1TR2 Break-seq sample treated with 0.002% MMS
MMS treated sample.

value: YEPD

value: MMS


title: 1-1-MMS-5 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-MMS
1-1-MMS-5 denotes BR1TR1 Break-seq sample treated with 0.002% MMS
MMS treated sample.


title: 2-1-MMS-8 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-MMS
2-1-MMS-8 denotes BR2TR1 Break-seq sample treated with 0.002% MMS
MMS treated sample.


title: 2-2-MMS-12 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-MMS
2-2-MMS-12 denotes BR2TR2 Break-seq sample treated with 0.002% MMS
MMS treated sample.


title: lungB4

description: Library name: lungB4

value: model 4

value: no


title: lungC1

description: Library name: lungC1

value: lung

value: SMD group 1


title: 2-2-HU-15-B [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-HU
2-2-HU-15-B denotes BR2TR2 Break-seq sample treated with 50mM HU
HU treated sample.

value: HU


title: lungB3

description: Library name: lungB3

value: model 3


title: 2-1-HU-14-B [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-HU
2-1-HU-14-B denotes BR1TR2 Break-seq sample treated with 50mM HU
HU treated sample.

value: WT


title: lungB5

description: Library name: lungB5

value: model 5


title: lungB2

description: Library name: lungB2

value: model 2


title: 1-1-HU-4 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-HU
1-1-HU-4 denotes BR1TR1 Break-seq sample treated with 50mM HU
HU treated sample.


title: lungA5

description: Library name: lungA5

value: wt

value: control 5


title: 2-2-C0-9 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-2-C0
2-2-C0-9 denotes BR2TR2 Break-seq sample treated with AgD H2O (Control for HU and MMS)
Vehicle control treated control sample for HU and MMS. Hence, no processed files for these.


title: lungA4

description: Library name: lungA4

value: control 4


title: lungA3

description: Library name: lungA3

value: control 3


title: 1-2-C0-13-B [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-C0
1-2-C0-13-B denotes BR1TR2 Break-seq sample treated with AgD H2O (Control for HU and MMS)
Vehicle control treated control sample for HU and MMS. Hence, no processed files for these.


title: lungA1

description: Library name: lungA1

value: control 1


title: BMDM, Nab-Paclitaxe

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

description: Library name: BMDM-NP

data_processing:
Adapter sequences were trimmed for both forward and reverse reads using cutadapt. Read quality was assessed using fastQC (v 0.11.9). Trimmed sequences were aligned to the mouse reference genome mm10, the human reference genome hg38. The resulting SAM files were converted to a binary format (BAM), sorted by queryname, and indexed using samtools.
Assembly: hg38 and mm10
Supplementary files format and content: bigWig

source_name: BMDM

extract_protocol:
ATAC-seq was performed using a modified method based on Corces et al. Cell were lysed and transposed simultaneously in 25 µL of transposition mix in Tagment DNA Buffer. The transposition was incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. After tagmentation, the reactions were stopped with addition of stop buffer. The transposed DNA fragments were purfied by DNA Purification Kits and amplified using PCR.
The final libraries were purified using pure beads and quantified using a Qubit 2.0 Fluorometer. Puried DNA libraries were sequenced on a Illimina Novaseq platform.

value: BMDM

value: Mouse bone marrow-derived macrophages

value: Nab-Paclitaxe


title: BMDM, DMSO

description: Library name: BMDM-D

value: DMSO


title: lungB1

description: Library name: lungB1

value: model 1

value: no


title: Pep_CUMS

city: Nanjing

first: Dandan

last: Xu

state: Jiangsu Province

address: No.87 Dingjiaqiao

institute: Southeast University

description: Library name: sample3

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0)
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: mm10
Supplementary files format and content: gene_fpkm.xls

source_name: prelimbic cortex

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent
VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction

value: prelimbic cortex


title: RAW264.7, miR192-LNP, LPS 24hr, rep3

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku

department: Department of Immunology

institute: Kumamoto University

description: Library name: miR192_24hr_3

data_processing:
Sequence reads were trimmed adaptor sequence and low quality sequence using trim galore(0.6.10).
Trimmed sequence reads were mapped to GRCm39 using STAR(2.7.11b).
Read count extraction were performed using featureCounts(v2.0.8)
Assembly: GRCm39
Supplementary files format and content: csv file include raw counts data

growth_protocol: RAW264.7 cells were maintained in DMEM (high glucose) supplemented with 10% fetal bovine serum (FBS), penicillin and streptomycin with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Kits(Zymo Research) and 1ug total RNA was used for library construction.
NEBNext® UltraTM ll Directional RNA Library Prep Kit was used for library preparation.

treatment_protocol: RAW264.7 cells were pretreated with miR-192-LNP or negative control miRNA (NC)-LNP (containing 100 pmol miRNA) for 24 hours, followed by stimulation with 200 ng/mL LPS for an additional 24 hours.


title: RAW264.7, miR192-LNP, LPS 24hr, rep2

description: Library name: miR192_24hr_2


title: Con_CUMS

description: Library name: sample1


title: BMDM, Paclitaxe

description: Library name: BMDM-P

value: Paclitaxe


title: 2-1-C0-6 [Break-seq]

description:
DNA double strand breaks (DSBs)
2-1-C0
2-1-C0-6 denotes BR2TR1 Break-seq sample treated with AgD H2O (Control for HU and MMS)
Vehicle control treated control sample for HU and MMS. Hence, no processed files for these.

value: YEPD


title: 1-1-C0-2 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-1-C0
1-1-C0-2 denotes BR1TR1 Break-seq sample treated with AgD H2O (Control for HU and MMS)
Vehicle control treated control sample for HU and MMS. Hence, no processed files for these.

value: WT


title: lungA2

description: Library name: lungA2

value: lung

value: control 2


title: Circ_CUMS

description: Library name: sample2


title: RAW264.7, miR192-LNP, LPS 24hr, rep1

description: Library name: miR192_24hr_1


title: RAW264.7, NC-LNP, LPS 24hr, rep3

description: Library name: NC_LNP_24hr_3


title: 1-2-HU-3 [Break-seq]

description:
DNA double strand breaks (DSBs)
1-2-HU
1-2-HU-3 denotes BR1TR2 Break-seq sample treated with 50mM HU
HU treated sample.

value: HU


title: Volunteer BA01033_Timepoint D07

type: RNA

city: Barcelona

first: Gemma

last: Moncunill

address: Rosselló 153

department: Malaria

institute: ISGlobal

description: Gene expression data from Volunteer BA01033_Timepoint D07

hyb_protocol: Affymetrix WT Terminal Labeling and Hybridization

scan_protocol: Affymetrix GeneTitan® system was used

data_processing: Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics”

label: Biotin

organism: Homo sapiens

source_name: Sample Volunteer BA01033_Timepoint D07

label_protocol: Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

extract_protocol: QIAamp RNA Blood Mini Kit

treatment_protocol: Homogenized cell lysates from a middle step were stored at -80°C

tag: group

tag: phase

value: B

tag: route

value: IM

tag: Sex

value: Male


title: BMDM, PBS

description: Library name: BMDM-PB

tag: cell type

tag: treatment

value: PBS


title: RAW264.7, NC-LNP, LPS 24hr, rep2

description: Library name: NC_LNP_24hr_2

tag: cell line


title: Volunteer BA01033_Timepoint M0

description: Gene expression data from Volunteer BA01033_Timepoint M0

source_name: Sample Volunteer BA01033_Timepoint M0


title: Volunteer BA01063_Timepoint D07

description: Gene expression data from Volunteer BA01063_Timepoint D07

source_name: Sample Volunteer BA01063_Timepoint D07

value: Female


title: Volunteer BA01069_Timepoint D01

description: Gene expression data from Volunteer BA01069_Timepoint D01

source_name: Sample Volunteer BA01069_Timepoint D01


title: Volunteer BA01069_Timepoint D07

description: Gene expression data from Volunteer BA01069_Timepoint D07

source_name: Sample Volunteer BA01069_Timepoint D07


title: Volunteer BA01033_Timepoint D01

description: Gene expression data from Volunteer BA01033_Timepoint D01

source_name: Sample Volunteer BA01033_Timepoint D01


title: Volunteer BA01069_Timepoint M0

description: Gene expression data from Volunteer BA01069_Timepoint M0

source_name: Sample Volunteer BA01069_Timepoint M0


title: Volunteer BA01069_Timepoint D-1

description: Gene expression data from Volunteer BA01069_Timepoint D-1

source_name: Sample Volunteer BA01069_Timepoint D-1


title: RAW264.7, NC-LNP, LPS 24hr, rep1

description: Library name: NC_LNP_24hr_1


title: Volunteer BA01033_Timepoint D-1

description: Gene expression data from Volunteer BA01033_Timepoint D-1

source_name: Sample Volunteer BA01033_Timepoint D-1


title: RAW264.7, nonLNP, LPS 24hr, rep3

description: Library name: LNPnon_24hr_3


title: Volunteer BA01063_Timepoint D-1

description: Gene expression data from Volunteer BA01063_Timepoint D-1

source_name: Sample Volunteer BA01063_Timepoint D-1


title: RAW264.7, nonLNP, LPS 24hr, rep1

description: Library name: LNPnon_24hr_1


title: RAW264.7, nonLNP, LPS 24hr, rep2

description: Library name: LNPnon_24hr_2


title: Volunteer BA01055_Timepoint M0

description: Gene expression data from Volunteer BA01055_Timepoint M0

source_name: Sample Volunteer BA01055_Timepoint M0


title: Volunteer BA01063_Timepoint M0

description: Gene expression data from Volunteer BA01063_Timepoint M0

source_name: Sample Volunteer BA01063_Timepoint M0


title: RAW264.7, miR192-LNP, LPS 0hr, rep3

description: Library name: miR192_0hr_3


title: RAW264.7, NC-LNP, LPS 0hr, rep3

description: Library name: NC_LNP_0hr_3

value: NC-LNP


title: RAW264.7, miR192-LNP, LPS 0hr, rep2

description: Library name: miR192_0hr_2


title: RAW264.7, NC-LNP, LPS 0hr, rep2

description: Library name: NC_LNP_0hr_2


title: RAW264.7, nonLNP, LPS 0hr, rep3

description: Library name: LNPnon_0hr_3


title: RAW264.7, nonLNP, LPS 0hr, rep2

description: Library name: LNPnon_0hr_2


title: Volunteer BA01063_Timepoint D01

description: Gene expression data from Volunteer BA01063_Timepoint D01

source_name: Sample Volunteer BA01063_Timepoint D01


title: RAW264.7, miR192-LNP, LPS 0hr, rep1

description: Library name: miR192_0hr_1


title: Volunteer BA01055_Timepoint D01

description: Gene expression data from Volunteer BA01055_Timepoint D01

source_name: Sample Volunteer BA01055_Timepoint D01


title: Volunteer BA01040_Timepoint M0

description: Gene expression data from Volunteer BA01040_Timepoint M0

source_name: Sample Volunteer BA01040_Timepoint M0


title: Volunteer BA01040_Timepoint D07

description: Gene expression data from Volunteer BA01040_Timepoint D07

source_name: Sample Volunteer BA01040_Timepoint D07


title: HealthyCtrl-1, HT5

first: Jun

last: Wang

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description: Library name: HealthyCtrl

data_processing:
We imported filtered sequencing data from CellRanger into R (4.2.1) via Read10X function of Seurat package (v5.0.3). Starting from 14,479 input cells, we implemented HTODemux() function to perform demultiplexing with different hashtag oligos (HTOs). After getting rid of either “doublets” or negative hashtag binding possibly due to non-specific binding, 7,139 cells were determined as “singlet” and proceed to subsequent analysis following standard workflow of Seurat vignette. A quality control was then performed on the cells to calculate the number of genes, UMIs and the proportion of mitochondrial genes for each cell using Seurat v4.0.3 and the cells with low number of covered genes (gene-count < 200) and high mitochondrial counts (mt-genes > 5%) were filtered out. The data (6,681 cells) was then normalized (log normalized), scaled, and variable features (dispersed genes) were used to perform principal component analysis (PCA). The first 20 PCs were used to find neighbors and clusters, using the FindNeighbors and FindClusters functions (resolution at 1.2). We then performed Uniform Manifold Approximation and Projection (UMAP) on the first 20 PCs. 17 clusters were generated afterwards. After removing two clusters (#15,16), we could categorize these cells into 9 groups including B cells, CD4 T cells (or NKT cells), CD8 T cells, Kupffer cells, Macrophages, mDC, Neutrophils, pDC and Resident Macrophages. We could further used split.by() function to divide these subpopulations into PBS (HTO1&2), BiTS (HTO3&4), and Ctrl (HTO5) with bar plots showing its distributions. CD8 T cells cluster was further divided into four subclusters including Tcm, Teff, Trm, Trm-2. Top 15 markers genes by FindAllMarker() function or biased gene list from references were introduced to plot the heat map. We also used Addmodule function to calculate the “Effector Signature” and “Memory Signature” in CD8 T cells cluster using gene list. Lastly, pseudotime analysis using monocle (v3) was performed to generate the possible trajectories.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: Seurat object

source_name: liver

extract_protocol:
Livers were homogenized by mechanical disruption and subsequently CD45+ cells were isolated (MiltenyiBiotec). Cells from each mouse were hashtagged (Biolegend) and libraries were prepared using 12k cells/mouse
Single cells were encapsulated into emulsion droplets using Chromium X Controller (10x Genomics) and subsequent scRNA-seq, libraries were constructed using Chromium Next GEM Single Cell 5’v2 Reagent Kit (PN-1000263) according to the manufacturer protocol. Briefly, cell populations were hashtagged using BioLegend Type C oligo-tagged antibodies and counted using a BioRad TC20 Automated Cell Counter. Cells were then pooled and placed in each channel of a Next GEM Chip, loaded onto the Chromium instrument and an emulsion was created. Reverse transcription and library preparation were performed on a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad).  cDNA was amplified 13 cycles and evaluated on an Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies).  Final Gene Expression, TCR and Cell Surface Protein libraries were amplified 14, 8 and 8 cycles respectively and visualized on an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).  Individual libraries were diluted to 2nM and pooled for sequencing. Pools were sequenced with a 10B 100 cycle run kit (26bp Read1, 10bp Index1, 10bp Index2 and 91bp Read2) on the NovaSeq X+ Sequencing System (Illumina).

tag: tissue

value: liver


title: Volunteer BA01048_Timepoint D-1

description: Gene expression data from Volunteer BA01048_Timepoint D-1

source_name: Sample Volunteer BA01048_Timepoint D-1

tag: age


title: Volunteer BA01048_Timepoint M0

description: Gene expression data from Volunteer BA01048_Timepoint M0

source_name: Sample Volunteer BA01048_Timepoint M0


title: Volunteer BA01048_Timepoint D07

description: Gene expression data from Volunteer BA01048_Timepoint D07

source_name: Sample Volunteer BA01048_Timepoint D07


title: Volunteer BA01048_Timepoint D01

description: Gene expression data from Volunteer BA01048_Timepoint D01

source_name: Sample Volunteer BA01048_Timepoint D01


title: BiTS-2, HT4

description: Library name: BiTS-2


title: PBS-2, HT2

description: Library name: PBS-2


title: Volunteer BA01055_Timepoint D07

description: Gene expression data from Volunteer BA01055_Timepoint D07

source_name: Sample Volunteer BA01055_Timepoint D07


title: PBS-1, HT1

description: Library name: PBS-1


title: Volunteer BA01035_Timepoint M0

description: Gene expression data from Volunteer BA01035_Timepoint M0

source_name: Sample Volunteer BA01035_Timepoint M0


title: Volunteer BA01040_Timepoint D-1

description: Gene expression data from Volunteer BA01040_Timepoint D-1

source_name: Sample Volunteer BA01040_Timepoint D-1


title: Volunteer BA01055_Timepoint D-1

description: Gene expression data from Volunteer BA01055_Timepoint D-1

source_name: Sample Volunteer BA01055_Timepoint D-1


title: RAW264.7, NC-LNP, LPS 0hr, rep1

description: Library name: NC_LNP_0hr_1


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate 4

city: Cleveland

first: Brian

last: Kim

state: OHIO

address: 10900 Euclid Ave

institute: Case Western Reserve University

data_processing:
Signal intensities were converted to base calls during a run using the system's Real Time Analysis (RTA) software. Sample de-multiplexing and alignment to mm10 genome was performed by Illumina's CASAVA 1.8.2 software suite.
Reads per genome coverage (RPGC)- normalized bigWig and bedgraph files were generated using the bamcoverage functions in deeptools version 3.4.3.
Peaks were called using MACS2 version 2.2.7.2
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Cell line

extract_protocol:
ATAC-seq genomic DNA was extracted using ATAC-seq kit (Active Motif)
Library was constructed per protocol of ATAC-seq kit (Active Motif). Tagmented DNA was amplified for 10 cycles then DNA was cleaned using SPRI magnetic beads. DNA was size selected for less than 1000bp and extracted using Qiagen Qiaquick Gel extraction kit. Samples were quantified by KAPA.

value: Cell line

value: adipocyte

tag: genotype

value: Tgf-b1. Tgf-b1 Free


title: BiTS-1, HT3

description: Library name: BiTS-1


title: Volunteer BA01067_Timepoint M0

description: Gene expression data from Volunteer BA01067_Timepoint M0

source_name: Sample Volunteer BA01067_Timepoint M0


title: RAW264.7, nonLNP, LPS 0hr, rep1

description: Library name: LNPnon_0hr_1


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate 2


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate 1


title: Volunteer BA01040_Timepoint D01

description: Gene expression data from Volunteer BA01040_Timepoint D01

source_name: Sample Volunteer BA01040_Timepoint D01


title: 3T3-L1 cells, Tgf-b1 Free treated, 14 days, duplicate 3


title: 3T3-L1 cells, Tgf-b1 treated, 4 Days, duplicate 3


title: Volunteer BA01035_Timepoint D-1

description: Gene expression data from Volunteer BA01035_Timepoint D-1

source_name: Sample Volunteer BA01035_Timepoint D-1


title: Volunteer BA01035_Timepoint D01

description: Gene expression data from Volunteer BA01035_Timepoint D01

source_name: Sample Volunteer BA01035_Timepoint D01


title: 3T3-L1 cells, Tgf-b1 treated, 4 Days, duplicate 2


title: Volunteer BA01058_Timepoint M0

description: Gene expression data from Volunteer BA01058_Timepoint M0

source_name: Sample Volunteer BA01058_Timepoint M0


title: 3T3-L1 cells, Tgf-b1 treated, 4 Days, duplicate 1


title: Volunteer BA01058_Timepoint D01

description: Gene expression data from Volunteer BA01058_Timepoint D01

source_name: Sample Volunteer BA01058_Timepoint D01


title: Volunteer BA01067_Timepoint D07

description: Gene expression data from Volunteer BA01067_Timepoint D07

source_name: Sample Volunteer BA01067_Timepoint D07


title: Volunteer BA01067_Timepoint D-1

description: Gene expression data from Volunteer BA01067_Timepoint D-1

source_name: Sample Volunteer BA01067_Timepoint D-1


title: Volunteer BA01035_Timepoint D07

description: Gene expression data from Volunteer BA01035_Timepoint D07

source_name: Sample Volunteer BA01035_Timepoint D07


title: Volunteer BA01067_Timepoint D01

description: Gene expression data from Volunteer BA01067_Timepoint D01

source_name: Sample Volunteer BA01067_Timepoint D01


title: Volunteer BA01058_Timepoint D07

description: Gene expression data from Volunteer BA01058_Timepoint D07

source_name: Sample Volunteer BA01058_Timepoint D07


title: 3T3-L1 cells, PBS treated, duplicate 1


title: 3T3-L1 cells, PBS treated, duplicate 3


title: Ctrl_synovium_12weeks

city: Sinagawa-ku

first: Kazuhiro

last: Shibusaka

state: Tokyo-to

address: 1-5-8, Hatanodai,1st building, 343

institute: showa university

data_processing:
Reads from scRNA-seq were processed using Cell Ranger software v7.0.0 (10x Genomics) with default parameters for each sample. In brief, alignment to the reference genome, UMI (unique molecular identifier) collapsing, UMI counting, and initial quality control were performed. Filtered gene expression matrices containing only cellular barcodes were generated during this step.
Assembly: mm10
Supplementary files format and content: tab-separated barcodes files

source_name: Synovium

extract_protocol:
The articular disk containing synovium was carefully removed from the joint cavity and separated from the surrounding tissue using tweezers and scissors under a stereomicroscope. The synovial membrane was then collected and minced in ice-cold PBS. The minced tissue was subsequently cultured in FCS (fetal calf serum)-free RPMI 1640 medium and digested with constant stirring at 37°C for 15 minutes. The cells were isolated by filtering through 70 μm and 40 μm strainers, followed by centrifugation
The library was prepared according to the manufacturer's instructions (single cell 3' v1 protocol, 10x Genomics). Briefly, synovium tissue cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in each individual GEM was reverse transcribed into cDNA, which included an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate-sized fragments were selected using SPRIselect reagent for subsequent library construction. An Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: Synovium

value: female

value: Control


title: Young_PICS

city: Novato

first: Fei

last: Wu

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: 10x Genomics

data_processing:
Post sequencing, to align read and generate feature barcode matrices raw data was subjected to the Cell Ranger pipeline 6.1.2.
Assembly: mm10-2020-A
Supplementary files format and content: Market Exchange Format (MEX) matrix

source_name: Spleen

extract_protocol:
Mice were euthanized using CO2 fixation prior to collecting organs, blood, and lymphoid organs. Spleens were processed into single cell suspensions and filtered through 40 µm cell strainer followed by hemolysis. Cells were blocked with Fc-block CD16/32 (93) and stained with viability dye zombie aqua, CD45 (30-F11), TCRB (17A2), B220 (6D5) (BioLegend), using methods described above for surface staining. For collection of singlet cells, live CD45+ TCRB+ CD19- T cells, live CD45+ TCRB- CD19+ B cells, and live CD45+ TCRB+ CD19+ PICs were sorted using a MoFlo Astrios Sorting Machine, at the Princess Margaret Hospital Flow Cytometry Facility, University Health Network (Toronto, Canada), and collected into Eppendorf tubes containing a 500 uL cushion of RPMI-1640 (Wisent) with 10% heat-inactivated FBS (Wisent). Samples were processed according to protocols for 5’ v2 chemistry 10X Genomics at the Princess Margaret Genomics Centre.
Library construction was performed according to the manufacturer's instructions (single cell 5' v2 protocol, 10X genomics).

treatment_protocol: Wild-type mice were aged to either 5-months of age (young) or 24-months of age (aged) prior to sacrifice

value: Spleen

value: B-T PICs

value: WT C57BL6J Mice

value: Young


title: Young_B_Cells

description: 10x Genomics

value: B Cells


title: MS_synovium_12weeks

value: WT

value: Mechanical Stress


title: 3T3-L1 cells, PBS treated, duplicate 2

value: PBS


title: Volunteer BA01051_Timepoint D07

description: Gene expression data from Volunteer BA01051_Timepoint D07

source_name: Sample Volunteer BA01051_Timepoint D07

value: B

value: IM

value: Female


title: ADD_synovium_12weeks

value: Articular Disc Displacement


title: Volunteer BA01051_Timepoint M0

description: Gene expression data from Volunteer BA01051_Timepoint M0

source_name: Sample Volunteer BA01051_Timepoint M0


title: Aged_PICS

description: 10x Genomics

value: Aged


title: Aged_T_Cells

description: 10x Genomics

value: T Cells


title: Volunteer BA01051_Timepoint D01

description: Gene expression data from Volunteer BA01051_Timepoint D01

source_name: Sample Volunteer BA01051_Timepoint D01


title: Volunteer BA01051_Timepoint D-1

description: Gene expression data from Volunteer BA01051_Timepoint D-1

source_name: Sample Volunteer BA01051_Timepoint D-1


title: Aged_B_Cells

description: 10x Genomics


title: Volunteer BA01044_Timepoint M0

description: Gene expression data from Volunteer BA01044_Timepoint M0

source_name: Sample Volunteer BA01044_Timepoint M0

value: Male


title: Volunteer BA01044_Timepoint D-1

description: Gene expression data from Volunteer BA01044_Timepoint D-1

source_name: Sample Volunteer BA01044_Timepoint D-1


title: koAfLaeB_2

first: Zili

last: Song

address: Beichen West Road 1

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Library name: Sample8

data_processing:
Data quality control by fastp software (version 0.19.7)
The reads was quickly and accurately compared with the reference genome using HISAT2 software.
Read count extraction and normalization were performed using subread software.
Assembly: GCA_000150145.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus fumigatus

source_name: Mycelium

growth_protocol: A. fumigatus was cultured on GMM medium at 25℃ for 5 days.

extract_protocol:
RNA was harvested using TRIzol reagent (Invitrogen), 1.3 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

value: Mycelium

value: Mycelium Cell

value: AfLaeB knockout

value: metabolic differentiation

value: Day 5


title: koAfLaeB_3

description: Library name: Sample9


title: Volunteer BA01044_Timepoint D01

description: Gene expression data from Volunteer BA01044_Timepoint D01

source_name: Sample Volunteer BA01044_Timepoint D01


title: Volunteer BA01044_Timepoint D07

description: Gene expression data from Volunteer BA01044_Timepoint D07

source_name: Sample Volunteer BA01044_Timepoint D07


title: Young_T_Cells

description: 10x Genomics

value: Spleen

value: WT C57BL6J Mice

value: Young


title: Volunteer BA01039_Timepoint M0

description: Gene expression data from Volunteer BA01039_Timepoint M0

source_name: Sample Volunteer BA01039_Timepoint M0


title: Volunteer BA01058_Timepoint D-1

description: Gene expression data from Volunteer BA01058_Timepoint D-1

source_name: Sample Volunteer BA01058_Timepoint D-1


title: Volunteer BA01039_Timepoint D-1

description: Gene expression data from Volunteer BA01039_Timepoint D-1

source_name: Sample Volunteer BA01039_Timepoint D-1


title: Volunteer BA01039_Timepoint D07

description: Gene expression data from Volunteer BA01039_Timepoint D07

source_name: Sample Volunteer BA01039_Timepoint D07


title: Volunteer BA01039_Timepoint D01

description: Gene expression data from Volunteer BA01039_Timepoint D01

source_name: Sample Volunteer BA01039_Timepoint D01


title: koAfCsdA_3

description: Library name: Sample6

value: AfCsdA knockout


title: Volunteer BA01037_Timepoint D-1

description: Gene expression data from Volunteer BA01037_Timepoint D-1

source_name: Sample Volunteer BA01037_Timepoint D-1


title: koAfCsdA_2

description: Library name: Sample5


title: koAfLaeB_1

description: Library name: Sample7


title: AfWT_3

description: Library name: Sample3

value: A. fumigatus wild type


title: koAfCsdA_1

description: Library name: Sample4


title: AfWT_2

description: Library name: Sample2


title: AfWT_1

description: Library name: Sample1


title: Volunteer BA01037_Timepoint D01

description: Gene expression data from Volunteer BA01037_Timepoint D01

source_name: Sample Volunteer BA01037_Timepoint D01

value: B


title: Volunteer BA01037_Timepoint D07

description: Gene expression data from Volunteer BA01037_Timepoint D07

source_name: Sample Volunteer BA01037_Timepoint D07

value: IM


title: genomic DNA from H3K27M-mutant hemispheric glioma

type: genomic

city: Hidaka

first: Mitsuaki

middle: Shirahata

last: Shirahata

state: Saitama

department: Neurosurgery/Neuro-oncology

institute: Saitama Medical University International Medical Center

hyb_protocol: Bisulphite converted DNA was hybridized to human Infinium Methylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy3 and Cy5

source_name: Genomic DNA

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from surgical resected tissue using Maxwell® RSC Tissue DNA Kit (Promega) according to standard instructions

value: Genomic DNA


title: Volunteer BA01043_Timepoint D01

description: Gene expression data from Volunteer BA01043_Timepoint D01

source_name: Sample Volunteer BA01043_Timepoint D01

value: IV

value: Female


title: Volunteer BA01043_Timepoint D07

description: Gene expression data from Volunteer BA01043_Timepoint D07

source_name: Sample Volunteer BA01043_Timepoint D07


title: C19

city: Taiyuan

first: Yue

last: Sui

state: --- Select One ---

address: No.85 of South Jiefang Road, Yingze District, Taiyuan, Shanxi, China

institute: First Hospital of Shanxi Medical University

hyb_protocol: Using the EZ DNA Methylation Kit (D5001, Zymo) for bisulfite transformation of genomic DNA, the methylated cytosine remains unchanged, while the unmethylated cytosine is converted to uracil. The detection process of the Illumina Infinium MethylationEPIC v2.0 BeadChip mainly includes the following steps:   (1) Isothermal displacement amplification of DNA transformed by bisulfite using random primers and polymerase;   (2) Fragmentation of amplified products;   (3) The fragmented products were hybridized with the Illumina Infinium MethylationEPIC v2.0 BeadChip, and the target region sequences were captured by the specific probe on the BeadChip, and then used as templates for single base extension and fluorescence labeling;   (4) The probe fluorescence labeling data is captured by scanning with Iscan platform.

scan_protocol: BeadArray Reader and standard  Illumina scanner setting

data_processing: Packages in R version 4.4.0

label: other

source_name: DNA from normal control

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from the fresh-frozen tissue samples were extracted by the DNA extraction kit (DP304-02, Tiangen).

value: rectal mucosa

tag: disease state

value: normal control


title: Volunteer BA01043_Timepoint M0

description: Gene expression data from Volunteer BA01043_Timepoint M0

source_name: Sample Volunteer BA01043_Timepoint M0


title: Volunteer BA01037_Timepoint M0

description: Gene expression data from Volunteer BA01037_Timepoint M0

source_name: Sample Volunteer BA01037_Timepoint M0


title: Volunteer BA01043_Timepoint D-1

description: Gene expression data from Volunteer BA01043_Timepoint D-1

source_name: Sample Volunteer BA01043_Timepoint D-1


title: C17


title: Volunteer BA01065_Timepoint D-1

description: Gene expression data from Volunteer BA01065_Timepoint D-1

source_name: Sample Volunteer BA01065_Timepoint D-1


title: Volunteer BA01065_Timepoint D07

description: Gene expression data from Volunteer BA01065_Timepoint D07

source_name: Sample Volunteer BA01065_Timepoint D07


title: C18


title: Volunteer BA01065_Timepoint D01

description: Gene expression data from Volunteer BA01065_Timepoint D01

source_name: Sample Volunteer BA01065_Timepoint D01


title: Volunteer BA01065_Timepoint M0

description: Gene expression data from Volunteer BA01065_Timepoint M0

source_name: Sample Volunteer BA01065_Timepoint M0


title: Volunteer BA01054_Timepoint D01

description: Gene expression data from Volunteer BA01054_Timepoint D01

source_name: Sample Volunteer BA01054_Timepoint D01

value: Male


title: Volunteer BA01054_Timepoint D-1

description: Gene expression data from Volunteer BA01054_Timepoint D-1

source_name: Sample Volunteer BA01054_Timepoint D-1


title: GC cells-2_N

city: Shanghai

first: Pengshan

last: Zhang

state: Shanghai

address: No. 650, Xinsongjiang Road

institute: Shanghai General Hospital

description:
Gene expression after 24hr under normoxia
823_H.normalized

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Gastric cancer cell line-2, normoxia,24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: TRIzol reagent (Life Technologies, USA) according to the manufacturer’s protocol

treatment_protocol: Two different gastric cancer cell lines were cultured in a hypoxia chamber with 1% O2, 94% N2 and normoxia at 37°C for 24h, then RNA-seq were performed to examine the circRNA expression profiles.

value: Gastric cancer cell line-2


title: Volunteer BA01054_Timepoint D07

description: Gene expression data from Volunteer BA01054_Timepoint D07

source_name: Sample Volunteer BA01054_Timepoint D07


title: Volunteer BA01054_Timepoint M0

description: Gene expression data from Volunteer BA01054_Timepoint M0

source_name: Sample Volunteer BA01054_Timepoint M0


title: Volunteer BA01046_Timepoint D07

description: Gene expression data from Volunteer BA01046_Timepoint D07

source_name: Sample Volunteer BA01046_Timepoint D07


title: C15


title: Volunteer BA01046_Timepoint M0

description: Gene expression data from Volunteer BA01046_Timepoint M0

source_name: Sample Volunteer BA01046_Timepoint M0


title: Volunteer BA01036_Timepoint M0

description: Gene expression data from Volunteer BA01036_Timepoint M0

source_name: Sample Volunteer BA01036_Timepoint M0