title: Control SCC7 cells

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

description: Library name: SCC7_no

data_processing:
FASTQ files produced by Illimina NovaSeq6000 were imported to CLC Genomics Workbench software (ver.22.0.1).
The 3' end of the sequenced read was trimmed by one nucleotide. Reads with more than 2 ambiguous nucleotides and reads with low quality scores were removed using CLC Genomics Workbench software (ver.22.0.1).
Trimmed sequence reads were mapped to GRCh37 release-75 using CLC genomics workbench with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.22.0.1).
Assembly: GRCh37
Supplementary files format and content: Csv files include RPKM and TPM values for each sample.

source_name: Mouse squamous cell carcinoma

extract_protocol:
Total RNA was isolated from the each sample using the RNeasy Mini Kit (Qiagen). Polyadenylated mRNA was purified using oligo dT beads included in the NEBNext Poly (A) mRNA Magnet Isolation Module (New England Biolabs, NEB). Purified mRNA was used for the construction of sequencing libraries using NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
The purified mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences included in NEBNext Multiplex Oligos for Illumina were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Tapestation 4200 D1000 (Agilent). The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NovaSeq6000 DNA sequencer with 50 bp paired-end cycle sequencing kit (Illumina).

value: Mouse squamous cell carcinoma

value: untreated


title: Taf1_WT_Uninduced_Replicate 2

status: Public on Jul 16 2025

type: SRA

city: Rockville

first: SAKSHI

last: SINGH

state: Maryland

address: 6 center drive , Bldg 6

department: NICHD-DIR

country: USA

institute: NIH

library_source: genomic

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Histone H3, H3-K18ac, Rpb1, Gcn4, TBP and Taf1 were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Assembly: SacCer3
Supplementary files format and content: Bigwig files

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM). For anchor away strains, cells were treated with rapamycin for 90 min before adding SM or no SM.

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-histone H3 (Abcam #ab1791) and H3-K18ac (Sigma 07-354), anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-Taf1(rom Joseph Reese's lab), anti-Rpb1 (Biolegend, Cat#664906). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

tag: tissue

value: Whole cells

tag: cell line

tag: chip antibody

value: Taf1 (J.C Reese)

tag: genotype

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]

tag: treatment

value: Formaldehyde-fixed and sonicated


title: BlaER1, IFNAR, TAK, REP1

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description: Library name: IFNAR_TAK_REP1

library_source: transcriptomic

data_processing:
Reads were alignred with STAR
Alignments were filtered with samtools on MAPQ30
Counts table were generated with FeaturesCounts on Gencode v34 annotations
Assembly: hg38
Supplementary files format and content: bigWig and tabulated text file

molecule: total RNA

organism: Homo sapiens

growth_protocol: WT, IFNAR1-/- IFNAR2-/-,and  IFNAR1-/- IFNAR2-/-MORC3-/- BlaER1 cell lines were previously described in {Gaidt et.al DOI 10.1038/s41586-021-04054-5}. They were maintained in suspension at approximately 10e6 cells per mL in RPMI+Glutamax (GIBCO) supplemented with 10% FBS, penicillin/streptomycin, 25mM HEPES, 1mM sodium pyruvate and 2-mercaptoethanol. When indicated, cells were treated with the SUMOi TAK-981 at a final concentration of 100nM.

extract_protocol:
Total RNA was extracted using 1mL Trizol reagent and 100uL 1-Bromo-3-chloropropane (BCP). The upper phase was collected, and RNA was precipitated using 2-propanol, washed with 80% ethanol, resuspended in water and quantified. cDNA was generated using 1ug RNA and a High-Capacity cDNA Reverse Transcription Kit (Applied  Biosystems) and diluted in 200uL water.
Total RNA-seq libraries were generated using Library prep stranded total RNA Ribozero Plus Ligation (Illumina) following manufacturer’s instructions

value: IFNAR-/-

value: TAK (100nM)


title: Healthy control-3, left colon, infliximab

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FASTQs were trimmed using cutadapt following specific NEXTflexTM recomendations.
We used bowtie 1.01 to align reads against the human genome (GRCh38) no allowing mismatches.
Mapped reads were quantified to known mature microrna ( miRBase version 22) using Partek E/M method.
microrna filtering based on the rule of 10 count in at least 1 sample, log-transformation using the Limma voom function using TMM followed by quantile normalisations.
Assembly: GRCh38
Supplementary files format and content: Quantified read counts

source_name: left colon

growth_protocol: Sample collection was carried out in sterile vials and stored in ice-cold complete medium (composed of RPMI 1640 from Sigma Aldrich, 100 μg/ml penicillin/streptomycin, 2 mM L-glutamine, 50 μg/mL gentamicin and 10% foetal bovine serum).

extract_protocol:
To evaluate the quantity and quality of miRNAs, we used Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Cat. #Q32855).
Sequencing libraries for miRNAs were prepared with “NEXTflexTM Small RNA-Seq Kit v3” (©Bioo Scientific Corp. Catalog #5132-05))

treatment_protocol: Biopsies were then washed in HBSS buffer and cultured in complete medium at 37ºC for 18 hours, either in the presence of infliximab (4 ml complete medium + 4 µL infliximab stock at 10 mg/mL), or just in a control medium (4 ml complete medium). After culturing, all samples were introduced in 250 μl RNAlater solution and stored at -80ºC.

value: left colon

tag: subject

value: Healthy control

value: infliximab


title: Healthy control-3, left colon, basal

value: basal


title: SCC7 cells treated with AGE

country: Japan

description: Library name: SCC7_AGE

organism: Mus musculus

tag: cell type

value: treated with AGE


title: Taf1_WT_Uninduced_Replicate 1


title: BlaER1, IFNAR MORC3, DMSO, REP2

description: Library name: IFNAR_MORC3_DMSO_REP2

value: IFNAR-/- MORC3-/-

value: DMSO


title: BlaER1, IFNAR, DMSO, REP3

description: Library name: IFNAR_DMSO_REP3


title: BlaER1, IFNAR, DMSO, REP2

description: Library name: IFNAR_DMSO_REP2


title: H3-K18ac_gcn5∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] gcn5[delta]::kanMX4


title: Healthy control-3, terminal ileum, infliximab

source_name: terminal ileum

value: terminal ileum


title: PD7591-shALK7-3

city: Gangneung

first: Yujin

last: Kwon

country: South Korea

institute: Korea Institute of Science and Technology

description: Library name: Sample 6

data_processing:
The quality of raw reads was assessed with FastQC (version 0.11.9), and the quality scores were > Q30, indicating high quality.
Clean reads with high-quality scores were processed using the Tuxedo protocol  with TopHat2 (version 2.1.1) and Cufflinks.
Assembly: Reads for each sample were aligned to the mouse reference genome using TopHat2.
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel file includes transcript per million reads (TPM) for each Sample

source_name: pancreatic ductal adenocarcinoma

growth_protocol: The primary murine pancreatic cancer cell line, YFP PD7591 (a gift from Dr. Ben Stanger, University of Pennsylvania), was isolated from primary tumors of a genetically engineered mouse model (Kras-G12D p53-/- YFP Rosa) and cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 50 μg/mL streptomycin and 50 I.U./mL penicillin.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol Reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer's protocol.
RNA-seq libraries were prepared using a TruSeq Standard mRNA Sample Prep Kit (Illumina) according to the manufacturer's protocol.

value: pancreatic ductal adenocarcinoma

value: primary murine pancreatic cancer cell

value: ALK7 knockdown


title: BlaER1, IFNAR, DMSO, REP1

description: Library name: IFNAR_DMSO_REP1


title: Healthy control-3, terminal ileum, basal


title: BlaER1, WT, TAK, REP4

description: Library name: WT_TAK_REP4

value: WT


title: PD7591-shALK7-1

description: Library name: Sample 4


title: H3-K18ac_spt8∆_Induced_Replicate 3

value: Whole cells

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt8[delta]::kanMX4


title: H3-K18ac_gcn5∆_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: Healthy control-2, left colon, infliximab


title: Healthy control-4, terminal ileum, infliximab


title: BlaER1, WT, TAK, REP3

description: Library name: WT_TAK_REP3

value: TAK (100nM)


title: PD7591-shALK7-2

description: Library name: Sample 5


title: Taf1_WT_Uninduced_Replicate 3

value: Taf1 (J.C Reese)

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]


title: PD7591-shC-3

description: Library name: Sample 3


title: PD7591-shC-2

description: Library name: Sample 2


title: Healthy control-2, left colon, basal

value: left colon

value: Healthy control


title: BlaER1, WT, TAK, REP2

description: Library name: WT_TAK_REP2


title: BlaER1, WT, TAK, REP1

description: Library name: WT_TAK_REP1


title: Healthy control-2, terminal ileum, infliximab

value: infliximab


title: PD7591-shC-1

description: Library name: Sample 1


title: H3-K18ac_spt8∆_Induced_Replicate 1


title: Healthy control-2, terminal ileum, basal

value: basal


title: Healthy control-1, left colon, infliximab


title: Duo_WT_Full4

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

description: Library name: Duo_WT_Full4

data_processing:
FASTQC
TRIMMOMATIC
hisat2
samtools
featureCounts
DEseq2
Assembly: Mus_musculus.GRCm38.102.gtf
Supplementary files format and content: TXT file and raw counts

molecule: polyA RNA

source_name: Duodenum

extract_protocol:
Trizol
PolyA selection for mRNA species (eukaryotic)

value: Duodenum


title: H3-K18ac_spt3∆_Induced_Replicate 2

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt3[delta]::kanMX4


title: BlaER1, WT, DMSO, REP3

description: Library name: WT_DMSO_REP3

value: DMSO


title: Duo_WT_Full3

description: Library name: Duo_WT_Full3


title: H3-K18ac_spt3∆_Induced_Replicate 1


title: BlaER1, WT, DMSO, REP4

description: Library name: WT_DMSO_REP4


title: Healthy control-1, left colon, basal


title: H3-K18ac_spt3∆_Induced_Replicate 3


title: BlaER1, WT, DMSO, REP2

description: Library name: WT_DMSO_REP2


title: Duo_WT_Full2

description: Library name: Duo_WT_Full2


title: H3-K18ac_WT_Induced_Replicate 3


title: Healthy control-1, terminal ileum, infliximab

value: terminal ileum


title: BlaER1, WT, DMSO, REP1

description: Library name: WT_DMSO_REP1


title: H3-K18ac_spt8∆_Induced_Replicate 2


title: Healthy control-1, terminal ileum, basal


title: Serie10, BlaER1 IFNAR_MORC3 Monocytes, ChIP H3K9me3, REP2

description:
Library name: serie10_BlaER1_IFNAR_MORC3_mono_H3K9me3_rep2
Serie 10

data_processing:
reads were aligned on mm10 or hg38 with bowtie2
alignments were filtered with samtools on MAPQ30.
PCR ducplicates were removed with Picard tools
Bigwig werer generated with Deeptools BamCoverage with CPM normalization
Assembly: hg38
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: RAW 264.7 mouse macrophages were maintained in DMEM+Glutamax (GIBCO) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin. When indicated, cells were treated with the SUMOylation inhibitor (SUMOi) ML-792(MedChemExpress) at a final concentration of 2,5uM. WT, IFNAR1-/- IFNAR2-/- and IFNAR1-/- IFNAR2-/-MORC3-/- BlaER1 cell lines were previously described in {Gaidt et.al DOI 10.1038/s41586-021-04054-5}. They were maintained in suspension at approximately 10e6 cells per mL in RPMI+Glutamax (GIBCO) supplemented with 10% FBS, penicillin/streptomycin, 25mM HEPES, 1mM sodium pyruvate and 2-mercaptoethanol. When indicated, cells were treated with the SUMOi TAK-981 at a final concentration of 100nM.

extract_protocol:
Cells were collected and fixed in 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched using glycine at a final concentration of 125mM for 5 minutes. Cells were washed twice in ice cold PBS. For fragmentation by sonication, cells were lysed in nuclei extraction buffer (250mM sucrose, 10mM Tris-HCl, 10mM MgCl2, 1% Triton X-100, 5mM 2-mercaptoethanol, and cOmplete protease inhibitor cocktail (Roche)) for 10 minutes on ice. The extracted nuclei were resuspended in nuclei lysis buffer (50mM Tris-HCl, 10mM EDTA, 0,2% SDS, and cOmplete protease inhibitor cocktail (Roche)), and sonicated with a Bioruptor Pico (Diagenode) using 6 cycles (30 sec on, 30 sec off), until chromatin fragments reached a size of around 300 base pairs (bp). For fragmentation by Micrococcal Nuclease (Mnase) digestion, cells were lysed with SimpleChIP® Enzymatic Cell Lysis Buffers A & B (Cell signaling) following manufacturer’s instructions. Nuclei were incubated with Mnase (Cell signaling) for 20 minutes at 37°C, until the chromatin fragments were digested to the size of 150 to 450 bp.
ChIP-seq libraries were prepared using Diagenode MicroPlex kit following manufacturer’s instructions

value: no treatment

tag: batch

value: Abcam ab8898


title: active Crohn´s disease-10, left colon, infliximab

data_processing:
Raw reads were trimmed with skewer followed by quality control analysis via FastQC.
Trimmed reads were aligned hg38 via STAR v2.7.1 aligner indexed to GENCODE v26 GTF library using -quantMode GeneCounts for feature counting.
Gene filtering based on the rule of 10 count in at least 1 sample, log-transformation using the Limma voom function using TMM followed by quantile normalisations.
Assembly: GRCh38
Supplementary files format and content: Quantified raw read counts

extract_protocol:
To evaluate the quantity and quality of mRNAs, we used Agilent RNA 6000 Nano Chips (Agilent Technologies, Cat. #5067-1511).
Total RNA (mRNA plus lncRNA) sequencing libraries were prepared using “Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus” kit (Illumina, Inc. Part # 20040525) following the “Illumina Stranded total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide”.
Total RNA (mRNA plus lncRNA)

value: active Crohn's disease


title: H3-K18ac_WT_Induced_Replicate 1

value: Whole cells


title: H3-K18ac_WT_Induced_Replicate 2


title: H3-K18ac_WT_Uninduced_Replicate 3


title: Serie10, BlaER1 IFNAR_MORC3 Monocytes,  ChIP H3K9me3, REP1

description:
Library name: serie10_BlaER1_IFNAR_MORC3_mono_H3K9me3_rep1
Serie 10


title: Serie10, BlaER1 IFNAR Monocytes, ChIP H3K9me3, REP2

description:
Library name: serie10_BlaER1_IFNAR_mono_H3K9me3_rep2
Serie 10

value: IFNAR-/-


title: active Crohn´s disease-10, left colon, basal


title: Duo_KI_Half5

description: Library name: Duo_KI_Half5


title: active Crohn´s disease-10, terminal ileum, infliximab


title: Serie10, BlaER1 IFNAR Monocytes, ChIP H3K9me3, REP1

description:
Library name: serie10_BlaER1_IFNAR_mono_H3K9me3_rep1
Serie 10


title: active Crohn´s disease-10, terminal ileum, basal


title: Duo_KI_Half2

description: Library name: Duo_KI_Half2


title: H3-K18ac_WT_Uninduced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: H3-K18ac_WT_Uninduced_Replicate 2


title: Serie10, BlaER1 IFNAR_MORC3 Monocytes, Input, REP2

description:
Library name: serie10_BlaER1_IFNAR_MORC3_mono_input_rep2
Serie 10


title: active Crohn´s disease-9, left colon, infliximab


title: Duo_WT_Full1

description: Library name: Duo_WT_Full1


title: Serie10, BlaER1 IFNAR_MORC3 Monocytes,  Input, REP1

description:
Library name: serie10_BlaER1_IFNAR_MORC3_mono_input_rep1
Serie 10


title: Duo_KI_Half3

description: Library name: Duo_KI_Half3


title: Duo_KI_Half1

description: Library name: Duo_KI_Half1


title: Duo_KI_Half7

description: Library name: Duo_KI_Half7


title: H3_gcn5∆_Induced_Replicate 2

value: anti-histone H3 (Abcam ab1791)

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] gcn5[delta]::kanMX4


title: Duo_WT_Half7

description: Library name: Duo_WT_Half7


title: H3_gcn5∆_Induced_Replicate 1


title: Duo_KI_Half6

description: Library name: Duo_KI_Half6


title: H3_gcn5∆_Induced_Replicate 3


title: Serie10, BlaER1 IFNAR Monocytes, Input, REP2

description:
Library name: serie10_BlaER1_IFNAR_mono_input_rep2
Serie 10


title: Serie10, BlaER1 IFNAR Monocytes, Input, REP1

description:
Library name: serie10_BlaER1_IFNAR_mono_input_rep1
Serie 10


title: H3_spt8∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt8[delta]::kanMX4


title: active Crohn´s disease-9, terminal ileum, infliximab


title: active Crohn´s disease-9, left colon, basal

value: left colon


title: Duo_WT_Half6

description: Library name: Duo_WT_Half6


title: Duo_WT_Half5

description: Library name: Duo_WT_Half5


title: H3_spt8∆_Induced_Replicate 2


title: Serie9, BlaER1 WT Monocytes, TAK, ChIP H3K4me3, REP1

description:
Library name: serie9_BlaER1_WT_mono_TAK_H3K4me3_rep1
Serie 9

value: WT

value: TAK (100nM)

value: Active Motif 39159


title: Serie9, BlaER1 WT Monocytes, TAK, ChIP H3K4me3, REP2

description:
Library name: serie9_BlaER1_WT_mono_TAK_H3K4me3_rep2
Serie 9


title: Duo_WT_Half4

description: Library name: Duo_WT_Half4

value: Duodenum


title: H3_spt8∆_Induced_Replicate 1


title: H3_spt3∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt3[delta]::kanMX4


title: Duo_WT_Half3

description: Library name: Duo_WT_Half3


title: Serie9, BlaER1 WT Monocytes, DMSO, ChIP H3K4me3, REP1

description:
Library name: serie9_BlaER1_WT_mono_ctrl_H3K4me3_rep1
Serie 9

value: DMSO


title: Duo_WT_Half2

description: Library name: Duo_WT_Half2


title: H3_spt3∆_Induced_Replicate 2


title: active Crohn´s disease-8, terminal ileum, basal

value: terminal ileum

value: basal


title: Duo_WT_Half1

description: Library name: Duo_WT_Half1


title: Serie9, BlaER1 WT Monocytes, TAK, ChIP H3K27me3, REP2

description:
Library name: serie9_BlaER1_WT_mono_TAK_H3K27me3_rep2
Serie 9

value: Millipore 07–449


title: active Crohn´s disease-9, terminal ileum, basal

value: active Crohn's disease


title: H3_spt3∆_Induced_Replicate 1

value: Whole cells


title: Serie9, BlaER1 WT Monocytes, TAK, ChIP H3K27me3, REP1

description:
Library name: serie9_BlaER1_WT_mono_TAK_H3K27me3_rep1
Serie 9


title: Duo_KI_Con4

description: Library name: Duo_KI_Con4


title: H3_WT_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]


title: Duo_KI_Con3

description: Library name: Duo_KI_Con3


title: H3_WT_Induced_Replicate 2

value: Formaldehyde-fixed and sonicated


title: active Crohn´s disease-7, left colon, basal


title: active Crohn´s disease-7, terminal ileum, infliximab

value: infliximab


title: active Crohn´s disease-8, left colon, infliximab


title: Serie9, BlaER1 WT Monocytes, DMSO, ChIP H3K27me3, REP2

description:
Library name: serie9_BlaER1_WT_mono_ctrl_H3K27me3_rep2
Serie 9


title: Serie9, BlaER1 WT Monocytes, DMSO, ChIP H3K27me3, REP1

description:
Library name: serie9_BlaER1_WT_mono_ctrl_H3K27me3_rep1
Serie 9


title: active Crohn´s disease-7, terminal ileum, basal


title: Duo_KI_Con2

description: Library name: Duo_KI_Con2


title: Serie9, BlaER1 WT Monocytes, TAK, ChIP CTCF, REP2

description:
Library name: serie9_BlaER1_WT_mono_TAK_CTCF_rep2
Serie 9

value: Active Motif 61932


title: H3_WT_Induced_Replicate 1

value: anti-histone H3 (Abcam ab1791)


title: active Crohn´s disease-8, left colon, basal

value: left colon


title: Duo_KI_Con1

description: Library name: Duo_KI_Con1


title: Serie9, BlaER1 WT Monocytes, DMSO, ChIP H3K4me3, REP2

description:
Library name: serie9_BlaER1_WT_mono_ctrl_H3K4me3_rep2
Serie 9

value: WT


title: active Crohn´s disease-8, terminal ileum, infliximab


title: active Crohn´s disease-6, left colon, infliximab


title: Serie9, BlaER1 WT Monocytes, TAK, ChIP CTCF, REP1

description:
Library name: serie9_BlaER1_WT_mono_TAK_CTCF_rep1
Serie 9

value: TAK (100nM)


title: H3_WT_Uninduced_Replicate 2


title: active Crohn´s disease-6, left colon, basal


title: active Crohn´s disease-7, left colon, infliximab


title: Serie9, BlaER1 WT Monocytes, DMSO, ChIP CTCF, REP2

description:
Library name: serie9_BlaER1_WT_mono_ctrl_CTCF_rep2
Serie 9


title: Duo_WT_Con3

description: Library name: Duo_WT_Con3


title: H3_WT_Uninduced_Replicate 1


title: Serie9, BlaER1 WT Monocytes, DMSO, ChIP CTCF, REP1

description:
Library name: serie9_BlaER1_WT_mono_ctrl_CTCF_rep1
Serie 9


title: Duo_WT_Con2

description: Library name: Duo_WT_Con2


title: Rpb1_gcn5∆_Induced_Replicate 3

value: anti-Rpb1 (Biolegend, Cat#664906)

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] gcn5[delta]::kanMX4


title: active Crohn´s disease-5, left colon, infliximab


title: Serie9, BlaER1 WT Monocytes, TAK, Input, REP2

description:
Library name: serie9_BlaER1_WT_mono_TAK_input_rep2
Serie 9


title: Rpb1_gcn5∆_Induced_Replicate 2


title: active Crohn´s disease-6, terminal ileum, infliximab


title: H3_WT_Uninduced_Replicate 3


title: Duo_WT_Con1

description: Library name: Duo_WT_Con1

value: Duodenum


title: active Crohn´s disease-5, left colon, basal


title: active Crohn´s disease-5, terminal ileum, infliximab


title: Rpb1_spt8∆_Induced_Replicate 2

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt8[delta]::kanMX4


title: LPS_NZM rep1

city: Hangzhou

first: Kaiyu

last: Liang

address: Qingchun East Road

department: Sir Run Run Shaw Hospital

country: China

institute: Zhejiang University

description: Library name: LPS_NZM1

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturer's instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
The RNA-seq transcriptome librariy was prepared following Illumina Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: Bone marrow

value: BMDM

value: wild type

value: LPS+NZM


title: Rpb1_spt8∆_Induced_Replicate 1

value: Whole cells


title: LPS_NZM rep3

description: Library name: LPS_NZM3


title: Rpb1_gcn5∆_Induced_Replicate 1


title: Serie9, BlaER1 WT Monocytes, DMSO, Input, REP2

description:
Library name: serie9_BlaER1_WT_mono_ctrl_input_rep2
Serie 9

value: DMSO


title: Duo_WT_Con4

description: Library name: Duo_WT_Con4


title: active Crohn´s disease-5, terminal ileum, basal

value: terminal ileum

value: active Crohn's disease

value: basal


title: Serie8, BlaER1 IFNAR Monocytes, ChIP SUMO2/3, REP2

description:
Library name: serie8_BlaER1_IFNAR_mono_SUMO2/3_rep2
Serie 8

value: IFNAR-/-

value: no treatment

value: Abcam ab3742


title: Serie9, BlaER1 WT Monocytes, TAK, Input, REP1

description:
Library name: serie9_BlaER1_WT_mono_TAK_input_rep1
Serie 9

value: WT

value: TAK (100nM)


title: Rpb1_spt3∆_Induced_Replicate 3

value: anti-Rpb1 (Biolegend, Cat#664906)

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt3[delta]::kanMX4

value: Formaldehyde-fixed and sonicated


title: Serie8, BlaER1 IFNAR Monocytes, ChIP SUMO2/3, REP1

description:
Library name: serie8_BlaER1_IFNAR_mono_SUMO2/3_rep1
Serie 8


title: LPS rep3

description: Library name: LPS3

value: Bone marrow

value: LPS


title: LPS rep2

description: Library name: LPS2

value: BMDM

value: wild type


title: active Crohn´s disease-4, left colon, infliximab

value: left colon

value: infliximab


title: active Crohn´s disease-4, left colon, basal


title: active Crohn´s disease-6, terminal ileum, basal

value: terminal ileum


title: Serie8, BlaER1 IFNAR Monocytes, Input, REP2

description:
Library name: serie8_BlaER1_IFNAR_mono_input_rep2
Serie 8


title: LPS rep1

description: Library name: LPS1


title: LPS_NZM rep2

description: Library name: LPS_NZM2

value: LPS+NZM


title: active Crohn´s disease-4, terminal ileum, infliximab

value: active Crohn's disease


title: Control rep3

description: Library name: Control3

value: Vehicle


title: Rpb1_WT_Induced_Replicate 3

value: Whole cells

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]


title: Serie8, BlaER1 IFNAR Monocytes, Input, REP1

description:
Library name: serie8_BlaER1_IFNAR_mono_input_rep1
Serie 8

value: IFNAR-/-

value: no treatment


title: active Crohn´s disease-4, terminal ileum, basal

value: basal


title: Serie9, BlaER1 WT Monocytes, DMSO, Input, REP1

description:
Library name: serie9_BlaER1_WT_mono_ctrl_input_rep1
Serie 9

value: WT

value: DMSO


title: Control rep2

description: Library name: Control2

value: Bone marrow


title: Serie7, BlaER1 WT Monocytes, TAK, ChIP H3.3, REP2

description:
Library name: serie7_BlaER1_WT_mono_TAK_H3_3_rep2
Serie 7

value: TAK (100nM)

value: Abcam ab176840


title: active Crohn´s disease-3, left colon, infliximab


title: Control rep1

description: Library name: Control1

value: BMDM

value: wild type


title: Serie7, BlaER1 WT Monocytes, TAK, ChIP H3.3, REP1

description:
Library name: serie7_BlaER1_WT_mono_TAK_H3_3_rep1
Serie 7


title: Rpb1_WT_Induced_Replicate 1

value: anti-Rpb1 (Biolegend, Cat#664906)

value: Formaldehyde-fixed and sonicated


title: active Crohn´s disease-3, left colon, basal

value: left colon


title: Serie7, BlaER1 WT Monocytes, DMSO, ChIP H3.3, REP2

description:
Library name: serie7_BlaER1_WT_mono_ctrl_H3_3_rep2
Serie 7


title: Aged_NZM rep3

description: Library name: Aged_NZM3

value: BMSC


title: Rpb1_WT_Uninduced_Replicate 3


title: active Crohn´s disease-3, terminal ileum, infliximab

value: terminal ileum

value: active Crohn's disease

value: infliximab


title: Rpb1_spt3∆_Induced_Replicate 2

value: Whole cells

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt3[delta]::kanMX4


title: Serie7, BlaER1 WT Monocytes, DMSO, ChIP H3.3, REP1

description:
Library name: serie7_BlaER1_WT_mono_ctrl_H3_3_rep1
Serie 7


title: Aged_NZM rep2

description: Library name: Aged_NZM2


title: Rpb1_WT_Uninduced_Replicate 2

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]


title: active Crohn´s disease-3, terminal ileum, basal

value: basal


title: Aged_NZM rep1

description: Library name: Aged_NZM1


title: Serie7, BlaER1 WT Monocytes, TAK, Input, REP2

description:
Library name: serie7_BlaER1_WT_mono_TAK_input_rep2
Serie 7

value: WT


title: Rpb1_WT_Uninduced_Replicate 1


title: Rpb1_spt3∆_Induced_Replicate 1


title: active Crohn´s disease-2, left colon, infliximab


title: Serie7, BlaER1 WT Monocytes, TAK, Input, REP1

description:
Library name: serie7_BlaER1_WT_mono_TAK_input_rep1
Serie 7


title: Aged rep3

description: Library name: Aged3

value: Bone marrow


title: active Crohn´s disease-2, left colon, basal


title: Gcn4_spt8∆_Induced_Replicate 3

value: Gcn4 (lab generated)

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt8[delta]::kanMX4


title: Rpb1_WT_Induced_Replicate 2


title: Serie7, BlaER1 WT Monocytes, DMSO, Input, REP2

description:
Library name: serie7_BlaER1_WT_mono_ctrl_input_rep2
Serie 7

value: DMSO


title: Gcn4_spt8∆_Induced_Replicate 2


title: active Crohn´s disease-2, terminal ileum, basal


title: Serie7, BlaER1 WT Monocytes, DMSO, Input, REP1

description:
Library name: serie7_BlaER1_WT_mono_ctrl_input_rep1
Serie 7


title: active Crohn´s disease-1, left colon, infliximab


title: Exosomal small RNA, LFD biological replicate 3

city: Boston

first: Gerald

middle: V

last: Denis

state: MA

address: 72 East Concord Street

institute: Boston University

data_processing:
Sequencing reads were processed to remove adapters and low-quality sequences using in-house processing from Novogene.
Cleaned reads were aligned to the mouse reference genome (Ensembl v108, GRCm39) using Bowtie.
Small RNA sequences were identified and annotated using miRBase v22.
Gene expression counts were calculated using miREvo and mirdeep.
Differential expression analysis between HFD and LFD groups was performed using DESeq2.
Assembly: Ensembl v108, Mus musculus, GRCm39 primary assembly.
Supplementary files format and content: Tab-delimited text files containing miRNA gene counts for each sample.

source_name: Plasma

extract_protocol:
Exosomal RNA was purified using phenol extraction followed by ethanol precipitation. The RNA quality and integrity were evaluated using the Agilent 2100 Bioanalyzer. The resulting RNA was sequenced by Novogene, which performs additional quality control steps to ensure data accuracy, including RNA integrity checks and quantification. RNA within the 25–200 nucleotide range was selected for library preparation.
Libraries were prepared using the Abclonal Small RNA Library Prep Kit for Illumina.

treatment_protocol: Exosomes were isolated from plasma samples collected from HFD and LFD mice following 12 weeks of diet intervention.

value: Plasma

value: Exosomes

value: WT C57BL/6J

value: Low-Fat Diet


title: Serie6, BlaER1 WT Lymphocytes, TAK, ChIP MORC3, REP2

description:
Library name: serie6_BlaER1_WT_lympho_TAK_MORC3_rep2
Serie 6

value: TAK (100nM)


title: Gcn4_spt8∆_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: Aged rep1

description: Library name: Aged1

value: BMSC

value: wild type


title: active Crohn´s disease-1, left colon, basal

value: left colon

value: active Crohn's disease


title: Serie6, BlaER1 WT Lymphocytes, TAK, ChIP MORC3, REP1

description:
Library name: serie6_BlaER1_WT_lympho_TAK_MORC3_rep1
Serie 6


title: Gcn4_gcn5∆_Induced_Replicate 3

value: Whole cells

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] gcn5[delta]::kanMX4


title: Exosomal small RNA, LFD biological replicate 2


title: Gcn4_gcn5∆_Induced_Replicate 2


title: active Crohn´s disease-1, terminal ileum, infliximab

value: terminal ileum

value: infliximab


title: Gcn4_gcn5∆_Induced_Replicate 1

value: Gcn4 (lab generated)


title: active Crohn´s disease-1, terminal ileum, basal

value: basal


title: Serie6, BlaER1 WT Lymphocytes, DMSO, ChIP MORC3, REP1

description:
Library name: serie6_BlaER1_WT_lympho_ctrl_MORC3_rep1
Serie 6

value: WT

value: DMSO


title: Exosomal small RNA, HFD biological replicate 3

value: Plasma

value: Exosomes

value: High-Fat Diet


title: Gcn4_spt3∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt3[delta]::kanMX4


title: quiescent Crohn´s disease-10, left colon, infliximab

value: quiescent Crohn's disease


title: Serie6, BlaER1 WT Lymphocytes, TAK, Input, REP2

description:
Library name: serie6_BlaER1_WT_lympho_TAK_input_rep2
Serie 6

value: TAK (100nM)


title: Exosomal small RNA, HFD biological replicate 2

value: WT C57BL/6J


title: Aged rep2

description: Library name: Aged2

value: Bone marrow

value: BMSC

value: wild type


title: quiescent Crohn´s disease-10, left colon, basal

value: left colon


title: Gcn4_spt3∆_Induced_Replicate 2

value: Whole cells

value: Formaldehyde-fixed and sonicated


title: Serie6, BlaER1 WT Lymphocytes, TAK, Input, REP1

description:
Library name: serie6_BlaER1_WT_lympho_TAK_input_rep1
Serie 6


title: Exosomal small RNA, HFD biological replicate 1


title: quiescent Crohn´s disease-10, terminal ileum infliximab

value: terminal ileum

value: infliximab


title: Gcn4_spt3∆_Induced_Replicate 1

value: Gcn4 (lab generated)


title: Serie6, BlaER1 WT Lymphocytes, DMSO, Input, REP2

description:
Library name: serie6_BlaER1_WT_lympho_ctrl_input_rep2
Serie 6

value: WT

value: DMSO


title: Aged Replicate 2 (snRNAseq)

city: New York

first: Genomics-core-facility

last: WCM

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded extraction, and gene UMI counting were made using the Cell Ranger software v7.1.0
Assembly: mm10
Supplementary files format and content: Cellranger output files:

molecule: nuclear RNA

source_name: Liver

extract_protocol:
Nuclei were isolated from snap frozen mouse liver tissues according to a previously published protocol (dx.doi.org/10.17504/protocols.io.bhpej5je), for a total of two replicates for the young and aged conditions. Briefly, samples were prepared by incubating fresh tissue chunks in HypoThermosol FRS solution (Sigma Aldrich, cat. no. H4416) for 15 minutes on ice, followed by a 30-minute incubation in Cryostor CS10 cryopreservation medium (Stemcell Technologies, cat. no. 7930) on ice, subsequently transferred to a cryo-freezing container overnight at -80° C and then to liquid nitrogen storage. Frozen liver tissue was minced into small chunks and homogenized in a refrigerated Dounce homogenizer using lysis buffer prepared according to the protocol’s instructions. After thorough homogenization, lysate was transferred into a 15-mL Falcon tube through a 40 mM cell strainer and samples were spun for 5 minutes at 500g at 4° C. Nuclei were counted using a hemocytometer and 10, 000 nuclei per sample were loaded onto the Chromium Single Cell 3′ Chip (10X Genomics, USA) and processed with the Chromium Controller (10X Genomics, USA).
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10X Chromium).

value: Liver

tag: strain

tag: Sex

value: Male

tag: age


title: Aged Replicate 1 (snRNAseq)

description: 10X Genomics


title: Serie6, BlaER1 WT Lymphocytes, DMSO, Input, REP1

description:
Library name: serie6_BlaER1_WT_lympho_ctrl_input_rep1
Serie 6


title: quiescent Crohn´s disease-9, left colon, infliximab


title: Serie5, BlaER1 WT Lymphocytes, ChIP H3K9me3, REP2

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_H3K9me3_rep2
Serie 5

value: no treatment

value: Abcam ab8898


title: quiescent Crohn´s disease-9, left colon, basal

value: quiescent Crohn's disease

value: basal


title: Exosomal small RNA, LFD biological replicate 1

value: Plasma

value: Exosomes

value: WT C57BL/6J

value: Low-Fat Diet


title: Young Replicate 2 (snRNAseq)

description: 10X Genomics

value: wild type


title: Gcn4_WT_Induced_Replicate 1

value: Whole cells

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]

value: Formaldehyde-fixed and sonicated


title: Serie5, BlaER1 WT Lymphocytes, ChIP H3K9me3, REP1

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_H3K9me3_rep1
Serie 5


title: Serie6, BlaER1 WT Lymphocytes, DMSO, ChIP MORC3, REP2

description:
Library name: serie6_BlaER1_WT_lympho_ctrl_MORC3_rep2
Serie 6


title: Young Replicate 1 (snRNAseq)

description: 10X Genomics


title: Gcn4_WT_Uninduced_Replicate 3

value: Gcn4 (lab generated)


title: Serie5, BlaER1 WT Lymphocytes, ChIP MORC3, REP4

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_MORC3_rep4
Serie 5

value: WT


title: Gcn4_WT_Uninduced_Replicate 2


title: CFs, CCL4, rep3

city: Hefei

first: He

last: Sun

state: Anhui province

address: No. 678, Furong Road, Shushan District

department: Department of Cardiothoracic Surgery

institute: The Second Affiliated Hospital of Anhui Medical University

data_processing:
Mapped reads of each sample were assembled using StringTie (version 2.1.6) with default parameters. The transcriptomes from all samples were merged using gffcompare (version 0.9.8) to create a comprehensive transcriptome. StringTie and Ballgown were then used to estimate transcript expression levels and calculate FPKM (fragments per kilobase of transcript per million mapped reads) values.
Assembly: GRCm38
Supplementary files format and content: tab-delimited csv files include FPKM values for each Sample

source_name: primary cell

extract_protocol:
Total RNA was extracted using Trizol reagent and assessed for quantity and purity with a Bioanalyzer 2100.
High-quality RNA (RIN > 7.0) was used for library construction. mRNA was purified from 5 µg of total RNA using Dynabeads Oligo (dT) and fragmented with the Magnesium RNA Fragmentation Module. RNA fragments were reverse-transcribed into cDNA using SuperScript™ II Reverse Transcriptase and converted into U-labeled second-stranded DNAs with E. coli DNA polymerase I and RNase H. These were ligated to dual-index adapters and size-selected with AMPureXP beads. After UDG treatment, the products were PCR-amplified and sequenced with 2×150 bp paired-end reads on an Illumina NovaSeq 6000.

value: primary cell

value: cardiac fibroblasts

value: carbon tetrachloride(CCL4)


title: quiescent Crohn´s disease-9, terminal ileum, basal

value: terminal ileum


title: CFs, CCL4, rep2


title: Serie5, BlaER1 WT Lymphocytes, ChIP MORC3, REP3

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_MORC3_rep3
Serie 5

value: no treatment


title: quiescent Crohn´s disease-8, left colon, infliximab

value: left colon

value: quiescent Crohn's disease

value: infliximab


title: Serie5, BlaER1 WT Lymphocytes, ChIP MORC3, REP2

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_MORC3_rep2
Serie 5


title: Gcn4_WT_Uninduced_Replicate 1


title: Gcn4_WT_Induced_Replicate 3


title: quiescent Crohn´s disease-8, left colon, basal

value: basal


title: TBP_spt8∆_Induced_Replicate 3

value: TBP ( J.C. Reese)

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt8[delta]::kanMX4


title: CFs, CCL4, rep1


title: Gcn4_WT_Induced_Replicate 2


title: Serie5, BlaER1 WT Lymphocytes, ChIP MORC3, REP1

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_MORC3_rep1
Serie 5


title: CFs, Control, rep3

value: control


title: Serie5, BlaER1 WT Lymphocytes, Input, REP4

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_input_rep4
Serie 5


title: TBP_spt8∆_Induced_Replicate 2

value: Whole cells


title: quiescent Crohn´s disease-10, terminal ileum basal


title: CFs, Control, rep2


title: TBP_spt8∆_Induced_Replicate 1


title: quiescent Crohn´s disease-8, terminal ileum, basal


title: CFs, Control, rep1


title: TBP_gcn5∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] gcn5[delta]::kanMX4


title: quiescent Crohn´s disease-7, left colon, infliximab


title: quiescent Crohn´s disease-8, terminal ileum, infliximab


title: scMultiome_sgSatb1_ATAC

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Singular Genomics G4 seqeuncing platform

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: matrix and fragment files were genreated using Cell Ranger-Arc (10x Genomics)
Library strategy: Multiome

source_name: Spleen

extract_protocol:
control and SATB1-defiient P14 cells were sorted on day 21 post LCVM-Cl13 infection, then nucelei of these cells were isolated using "Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing". Nuclei were encapsulated with GEM using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits and follwing the 10x protocols
Libraries were constructed following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Protocol

value: Spleen

value: P14 CD8+ primary T cells

value: Satb1 CRISPR KO


title: Serie5, BlaER1 WT Lymphocytes, Input, REP2

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_input_rep2
Serie 5

value: WT


title: quiescent Crohn´s disease-9, terminal ileum, infliximab


title: quiescent Crohn´s disease-7, left colon, basal


title: Serie5, BlaER1 WT Lymphocytes, Input, REP1

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_input_rep1
Serie 5


title: TBP_gcn5∆_Induced_Replicate 2

value: Formaldehyde-fixed and sonicated


title: quiescent Crohn´s disease-7, terminal ileum, infliximab


title: scMultiome_sgCtrl_ATAC

value: CRISPR control


title: TBP_gcn5∆_Induced_Replicate 1


title: Serie4, BlaER1 IFNAR_MORC3 Monocytes, ChIP MORC3, REP2

description:
Library name: serie4_BlaER1_IFNAR_MORC3_mono_MORC3_rep2
Serie 4


title: quiescent Crohn´s disease-7, terminal ileum, basal

value: terminal ileum


title: scMultiome_sgCtrl_RNA


title: scMultiome_sgSatb1_RNA


title: TBP_spt3∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] spt3[delta]::kanMX4


title: TBP_spt3∆_Induced_Replicate 2


title: Serie4, BlaER1 IFNAR_MORC3 Monocytes,  ChIP MORC3, REP1

description:
Library name: serie4_BlaER1_IFNAR_MORC3_mono_MORC3_rep1
Serie 4

value: no treatment


title: Serie4, BlaER1 IFNAR Monocytes, ChIP MORC3, REP2

description:
Library name: serie4_BlaER1_IFNAR_mono_MORC3_rep2
Serie 4

value: IFNAR-/-


title: quiescent Crohn´s disease-6, left colon, infliximab

value: left colon

value: quiescent Crohn's disease

value: infliximab


title: Serie5, BlaER1 WT Lymphocytes, Input, REP3

description:
Library name: serie5_BlaER1_WT_lympho_ctrl_input_rep3
Serie 5


title: TBP_spt3∆_Induced_Replicate 1

value: TBP ( J.C. Reese)


title: sgCtrl_rep5

data_processing:
Raw sequencing data was processed by nf-core/rnaseq pipeline v3.8.1 (Ewels et al., 2020; Philip et al., 2022) using Salmon for pseudo-alignment and quantification.
Assembly: mm10
Supplementary files format and content: a combined csv file including raw counts for every sample

extract_protocol:
Total RNA was extracted with RNeasy Plus Micro Kit (Qiagen).
RNA-seq libraries were prepared following the SMART-seq2 protocol (Picelli et al., 2014)

value: sgCtrl RNP


title: sgCtrl_rep4


title: quiescent Crohn´s disease-6, left colon, basal

value: basal


title: Serie4, BlaER1 IFNAR Monocytes,  ChIP MORC3, REP1

description:
Library name: serie4_BlaER1_IFNAR_mono_MORC3_rep1
Serie 4


title: TBP_WT_Induced_Replicate 3

value: Whole cells

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta]


title: Serie4, BlaER1 WT Monocytes, TAK, ChIP H3K9me3, REP2

description:
Library name: serie4_BlaER1_WT_mono_TAK_H3K9me3_rep2
Serie 4

value: TAK (100nM)

value: Abcam ab8898


title: quiescent Crohn´s disease-6, terminal ileum, infliximab


title: sgCtrl_rep3

value: Spleen

value: P14 CD8+ primary T cells


title: quiescent Crohn´s disease-6, terminal ileum, basal


title: TBP_WT_Induced_Replicate 2

value: Formaldehyde-fixed and sonicated


title: TBP_WT_Induced_Replicate 1


title: Serie4, BlaER1 WT Monocytes, TAK, ChIP H3K9me3, REP1

description:
Library name: serie4_BlaER1_WT_mono_TAK_H3K9me3_rep1
Serie 4

value: WT


title: sgCtrl_rep2

value: CRISPR control


title: Serie4, BlaER1 WT Monocytes, DMSO, ChIP H3K9me3, REP2

description:
Library name: serie4_BlaER1_WT_mono_ctrl_H3K9me3_rep2
Serie 4

value: DMSO


title: sgCtrl_rep1


title: quiescent Crohn´s disease-5, left colon, infliximab


title: quiescent Crohn´s disease-5, left colon, basal


title: TBP_WT_Uninduced_Replicate 3


title: sgSatb_rep5

value: CRISPR SATB1 KO

value: sgSatb1 RNP


title: Serie4, BlaER1 WT Monocytes, DMSO, ChIP H3K9me3, REP1

description:
Library name: serie4_BlaER1_WT_mono_ctrl_H3K9me3_rep1
Serie 4


title: sgSatb_rep4


title: TBP_WT_Uninduced_Replicate 1


title: TBP_WT_Uninduced_Replicate 2


title: sgSatb_rep3


title: quiescent Crohn´s disease-5, terminal ileum, infliximab

value: terminal ileum

value: quiescent Crohn's disease


title: Serie4, BlaER1 WT Monocytes, TAK, ChIP MORC3, REP4

description:
Library name: serie4_BlaER1_WT_mono_TAK_MORC3_rep4
Serie 4


title: quiescent Crohn´s disease-5, terminal ileum, basal


title: Serie4, BlaER1 WT Monocytes, TAK, ChIP MORC3, REP3

description:
Library name: serie4_BlaER1_WT_mono_TAK_MORC3_rep3
Serie 4


title: quiescent Crohn´s disease-4, terminal ileum, infliximab

value: infliximab


title: Sperm,RamF4_508_10, Control

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description: Library name: RamF4_508_10

data_processing:
Trimming (TrimGalore)
Alignment (Bismark)
Differential methylation analysis (methylKit R package)
Annotation
Assembly: Oar_rambouillet v1.0
Supplementary files format and content: Bismark coverage files-cytosine reports / methylation counts

organism: Ovis aries

source_name: Sperm

extract_protocol:
Genomic DNA was extracted from sperm samples using the Quick-DNA Miniprep Plus (Zymo Research, CA, US).
DNA samples were bisulfite-treated with the Zymo EZ DNA Methylation-Lightning kit, followed by library preparation using Illumina universal adapter sequences and Pico Methyl-Seq Library Prep Kit (Zymo Research).

treatment_protocol: F3 and F4 rams are descendants of methionine supplemented and control F0 rams

value: Sperm

value: descendant of control ram

value: control


title: Sperm,RamF4_515_24, Control

description: Library name: RamF4_515_24


title: quiescent Crohn´s disease-4, left colon, infliximab

value: left colon


title: Serie4, BlaER1 WT Monocytes, TAK, ChIP MORC3, REP2

description:
Library name: serie4_BlaER1_WT_mono_TAK_MORC3_rep2
Serie 4

value: TAK (100nM)


title: quiescent Crohn´s disease-4, left colon, basal

value: basal


title: Serie4, BlaER1 WT Monocytes, DMSO, ChIP MORC3, REP4

description:
Library name: serie4_BlaER1_WT_mono_ctrl_MORC3_rep4
Serie 4


title: Serie4, BlaER1 WT Monocytes, TAK, ChIP MORC3, REP1

description:
Library name: serie4_BlaER1_WT_mono_TAK_MORC3_rep1
Serie 4


title: quiescent Crohn´s disease-4, terminal ileum, basal


title: Sperm, RamF4_437_6, Control

description: Library name: RamF4_437_6


title: Serie4, BlaER1 WT Monocytes, DMSO, ChIP MORC3, REP3

description:
Library name: serie4_BlaER1_WT_mono_ctrl_MORC3_rep3
Serie 4


title: quiescent Crohn´s disease-3, left colon, infliximab


title: Sperm,RamF4_392_11, Treatment

description: Library name: RamF4_392_11

value: descendant of methionine supplemented ram

value: treatment


title: Sperm, RamF4_442_3, Treatment

description: Library name: RamF4_442_3


title: P14, sgSatb1 rep3

description: Singular Genomics G4 seqeuncing platform

data_processing:
Raw sequencing data was processed by nf-core/atacseq pipeline v1.2.2 (Ewels et al., 2020; Patel et al., 2022) in which reads were aligned to mm10 genome by BWA, BedGraph and  bigwig files were generated by BEDTools and bedGraphToBigWig, and peak calling was done by MACS2.
Assembly: mm10
Supplementary files format and content: bigWig, Bedgraph

extract_protocol:
P14 T cells were FACS-sorted from spleens on day 21 p.i. Nuclei were extracted using  cold ATAC-RSB buffer (10nM Tris-HCl Ph7.4, 10mM NaCl, 3mM MgCl2) containing 0.1% Tween-20.
ATAC-seq library was constructed following the Omni-ATAC protocol (Corces, M Ryan et al. Nature Methods, 2017).

treatment_protocol: Naive P14 CD8 T cells isolated from mouse spleens were transfected with CRISPR ribonucleoprotein (RNP)  to knock out CD19 (sgCtrl) as control or Satb1 (sgSatb1). 2500 transfected CD45.1+ P14 T cells were transferred to CD45.1- C57BL/6 mice followed by LCMV Clone 13 infection. P14 T cells were FACS-sorted from  spleens on day 21 p.i. and extracted nucei were used for ATAC-seq library construction following the Omni-ATAC protocol (Nature Methods, 2017).

value: Spleen

value: P14 CD8+ primary T cells

value: Satb1 CRISPR KO


title: P14, sgSatb1 rep4


title: Serie4, BlaER1 WT Monocytes, DMSO, ChIP MORC3, REP2

description:
Library name: serie4_BlaER1_WT_mono_ctrl_MORC3_rep2
Serie 4

value: WT

value: DMSO


title: P14, sgSatb1 rep2

value: sgSatb1 RNP


title: P14, sgSatb1 rep1


title: Sperm, RamF4_365_12, Control

description: Library name: RamF4_365_12


title: quiescent Crohn´s disease-3, terminal ileum, infliximab

value: terminal ileum


title: sgSatb_rep2

value: CRISPR SATB1 KO


title: quiescent Crohn´s disease-3, left colon, basal

value: quiescent Crohn's disease


title: sgSatb_rep1


title: Serie4, BlaER1 IFNAR_MORC3 Monocytes,  Input, REP1

description:
Library name: serie4_BlaER1_IFNAR_MORC3_mono_input_rep1
Serie 4

value: no treatment


title: P14, sgCtrl rep4

value: CRISPR control

value: sgCtrl RNP


title: Sperm, RamF4_362_4, Control

description: Library name: RamF4_362_4

value: Sperm

value: descendant of control ram

value: control


title: quiescent Crohn´s disease-2, left colon, infliximab

value: left colon

value: infliximab


title: quiescent Crohn´s disease-3, terminal ileum, basal

value: basal


title: Sperm, RamF4_345_5, Treatment

description: Library name: RamF4_345_5

value: descendant of methionine supplemented ram

value: treatment


title: Serie4, BlaER1 IFNAR Monocytes, Input, REP2

description:
Library name: serie4_BlaER1_IFNAR_mono_input_rep2
Serie 4

value: IFNAR-/-


title: Sperm, RamF4_337_9, Treatment

description: Library name: RamF4_337_9


title: Serie4, BlaER1 WT Monocytes, DMSO, ChIP MORC3, REP1

description:
Library name: serie4_BlaER1_WT_mono_ctrl_MORC3_rep1
Serie 4

value: WT

value: DMSO


title: P14, sgCtrl rep2

value: Spleen

value: P14 CD8+ primary T cells


title: quiescent Crohn´s disease-2, terminal ileum, infliximab

value: terminal ileum

value: quiescent Crohn's disease


title: Serie4, BlaER1 WT Monocytes, TAK, Input, REP4

description:
Library name: serie4_BlaER1_WT_mono_TAK_input_rep4
Serie 4

value: TAK (100nM)


title: Serie4, BlaER1 IFNAR_MORC3 Monocytes, Input, REP2

description:
Library name: serie4_BlaER1_IFNAR_MORC3_mono_input_rep2
Serie 4

value: no treatment


title: P14, sgCtrl rep3

value: CRISPR control

value: sgCtrl RNP


title: Sperm,RamF3_482_4, Control

description: Library name: RamF3_482_4

value: Sperm

value: descendant of control ram

value: control


title: quiescent Crohn´s disease-1, left colon, infliximab

value: left colon

value: infliximab


title: Sperm,RamF4_319_23, Treatment

description: Library name: RamF4_319_23

value: descendant of methionine supplemented ram

value: treatment


title: quiescent Crohn´s disease-2, left colon, basal

value: basal


title: Mm, forelimb, E13.5, wt, scRNA, Rep2

city: Berlin

first: Christian

middle: A.

last: Feregrino

address: Ihnestraße 63

country: Germany

institute: MPI - Molecular Genetics

data_processing:
The different single-cell RNA-sequencing libraries were processed using 10X Genomics CellRanger v6.0.211 and our custom genome annotations for C. perspicillata and M. musculus. Individual count matrices were filtered for quality based on relative UMI counts (removed >4*mean and <0.2*median of the sample), percentage of ribosomal UMIs (removed >median + 3*MAD & <median + 3*MAD), and relation of UMI count/genes detected (removed <0.15 & UMI count <2/3). The filtered datasets were integrated in a species / limb manner (e.g. all Mouse FL datasets together). For this we used Seurat v4.3.012, first Log normalizing each dataset with a factor of 10’000 and scoring the cell cycle state of each cell. Then, using the SCTransform tool we regressed the percentage of ribosomal UMIs, the UMI count, and the S and G2M cycle score of each cell. Using the top 25% integration features, we found integration anchors using the SCT normalization, 20 first dimensions and a k.filter of 100. These anchors were used with the tool IntegrateData.
Assembly: mm39, carPer2
Supplementary files format and content: h5ad

source_name: forelimb

extract_protocol:
For single-cell gene expression analysis, mouse and bat embryonic limb tissues were dissected and dissociated with trypsin. Cells were filtered through a 40 µm Flowmi Cell Strainer (Merck, #BAH136800040) and pelleted at 300 x g at 4°C for 5 minutes. Cells were resuspended in 1 volume 0.04% BSA/PBS and dehydrated by slowly adding 9 volumes of 100% methanol. Samples were stored at -80 °C until library preparation
For rehydration, dehydrated cells were centrifuged at 1000 x g at 4°C for 10 minutes and washed twice in 1 mL of rehydration buffer (1 % BSA, 0.4 U/µL Ambion RNse Inhibitor (Invitrogen, #AM1682) and 0.2 U/µL SUPERaseIn RNase Inhibitor (Invitrogen, #AM2696) in 1x DPBS). After the second wash, cells were resuspended in rehydration buffer, counted and diluted to a concentration of 1,000 cells/µL. Single cell gene expression libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, #PN-1000121) according to the manufacturer’s instructions. The aimed target cell recovery in each experiment was 10,000 cells.  To generate Gel Beads-in-emulsion (GEMs), reactions were assembled in a Chromium Next GEM Chip G (10X Genomics, #PN-1000121). Chips were run on a Chromium Controller X/iX. Sample indices were added to the cDNAs via PCR using the Single Index Kit T Set A (10X Genomics, #PN-1000213) or Dual Index Kit TT Seat A (10X Genomics, #PN-1000215). Library concentration was measured by Qubit dsDNA HS Assay Kit (Invitrogen, #Q33231) and quality was assessed using Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent, #5067-4626). Finally, scRNA-seq libraries were sequenced on a Illumina NovaSeq 6000 with asynchronous 28 bp / 90 bp paired-end reads. Single-cell experiments were performed in biological duplicates.

value: forelimb

tag: Stage

value: wildtype


title: Serie4, BlaER1 IFNAR Monocytes, Input, REP1

description:
Library name: serie4_BlaER1_IFNAR_mono_input_rep1
Serie 4

value: IFNAR-/-


title: Sperm,RamF3_504_11, Treatment

description: Library name: RamF3_504_11


title: Mm, hindlimb, E13.5, wt, scRNA, Rep2

source_name: hindlimb

value: hindlimb


title: Sperm,RamF3_489_9, Treatment

description: Library name: RamF3_489_9


title: quiescent Crohn´s disease-1, left colon, basal

value: quiescent Crohn's disease


title: quiescent Crohn´s disease-2, terminal ileum, basal

value: terminal ileum


title: Mm, hindlimb, E13.5, wt, scRNA, Rep1


title: Mm, hindlimb, E12.5, wt, scRNA, Rep2


title: Serie4, BlaER1 WT Monocytes, TAK, Input, REP1

description:
Library name: serie4_BlaER1_WT_mono_TAK_input_rep1
Serie 4

value: WT

value: TAK (100nM)


title: Mm, hindlimb, E12.5, wt, scRNA, Rep1


title: P14, sgCtrl rep5

value: Spleen

value: P14 CD8+ primary T cells

value: CRISPR control

value: sgCtrl RNP


title: Sperm,RamF3_399_5, Treatment

description: Library name: RamF3_399_5

value: Sperm


title: Sperm,RamF3_446_12, Control

description: Library name: RamF3_446_12

value: descendant of control ram

value: control


title: Serie4, BlaER1 WT Monocytes, TAK, Input, REP2

description:
Library name: serie4_BlaER1_WT_mono_TAK_input_rep2
Serie 4


title: Healthy control-10, left colon, infliximab

value: left colon

value: Healthy control

value: infliximab


title: Sperm,RamF3_391_3, Treatment

description: Library name: RamF3_391_3

value: descendant of methionine supplemented ram

value: treatment


title: Mm, forelimb, E13.5, wt, scRNA, Rep1

value: forelimb

value: wildtype


title: Serie4, BlaER1 WT Monocytes, DMSO, Input, REP4

description:
Library name: serie4_BlaER1_WT_mono_ctrl_input_rep4
Serie 4

value: DMSO


title: quiescent Crohn´s disease-1, terminal ileum, basal

value: terminal ileum

value: quiescent Crohn's disease

value: basal


title: Serie4, BlaER1 WT Monocytes, DMSO, Input, REP2

description:
Library name: serie4_BlaER1_WT_mono_ctrl_input_rep2
Serie 4

value: WT


title: Mm, forelimb, E12.5, wt, scRNA, Rep2


title: quiescent Crohn´s disease-1, terminal ileum, infliximab


title: Sperm,RamF3_339_10, Control

description: Library name: RamF3_339_10


title: Mm, forelimb, E12.5, wt, scRNA, Rep1


title: Serie4, BlaER1 WT Monocytes, DMSO, Input, REP3

description:
Library name: serie4_BlaER1_WT_mono_ctrl_input_rep3
Serie 4


title: Serie4, BlaER1 WT Monocytes, DMSO, Input, REP1

description:
Library name: serie4_BlaER1_WT_mono_ctrl_input_rep1
Serie 4


title: Sperm, RamF3_362_23, Treatment

description: Library name: RamF3_362_23


title: Healthy control-10, terminal ileum, basal


title: Serie4, BlaER1 WT Monocytes, TAK, Input, REP3

description:
Library name: serie4_BlaER1_WT_mono_TAK_input_rep3
Serie 4

value: TAK (100nM)


title: C34, skin, control, 0

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

description: Library name: C34

data_processing:
Reads were mapped with STAR software (v.2.7.8a) against the human reference genome GRCh38 using the GRCh38.p13 Ensembl annotation.
The table of counts was obtained with featureCounts function in the package subread (v.2.0.3).
Counts were normalized with log2 counts per million (CPM) with the edgeR package (v.3.40.2) with a prior.count=3. Genes with more than 10 counts in at least 9 samples were kept.
Assembly: GRCh38
Supplementary files format and content: counts

source_name: skin

growth_protocol: Skin biopsies were incubated with RNAlater during maximum 1 week

extract_protocol:
Total RNA was extracted from  skin biopsies with Genelute mammalian total RNA kit from Sigma- Aldrich (cat. No. RTN350). Tissue was disrupted and digested in the Lysis buffer with proteinase K (P4850, Sigma-Aldrich) and 2-mercaptoethanol (M3148, Sigma-Aldrich) incubating it for 10 minutes at 55ºC.  After washing and centrifugation several times to remove contaminants, RNA was eluted with 50 μl of Elution buffer. Two commercial kits were tested. This kit obtained the best performance in total RNA recovered and integrity of the sample. The samples were used immediately or stored at -80ºC for future use.
Samples were processed according to Truseq RNA Exome protocol from Illumina (Document #10000000039582 v01 March 2018) following steps from 1 to 6_Enrich DNA Fragments page 18. Afterwards, samples were processed using Illumina RNA preparation with enrichment Tagmentation protocol (Document #1000000124435 v03 April 2021) following steps from 6_Normalize Library page 15 to the end of the protocol. Samples were enriched with Illumina Exome Panel and Unique Dual Index from NEBNext were used. The initial total RNA input for every sample was 100 nanograms measured with Qubit 4.0. 200 nanograms of each amplified sample was enriched in pools up to 3 samples, libraries profiles were checked by 2100 Bioanalyzer. All samples amplified enough to continue with the process. Final enriched libraries were quantified by 2100 Bioanalyzer (DNA 1000 kit). Samples were sequenced in a NextSeq2000 from Illumina with an estimated output of 25 million reads/sample and a read length of 2x50bp.
Exome RNA capture

treatment_protocol: No other treatments other than keeping in RNAlater

value: skin

tag: condition

value: control skin

tag: allergen

tag: technician

value: B

value: female


title: Healthy control-10, left colon, basal

value: left colon


title: Healthy control-9, left colon, basal

value: Healthy control


title: Mm, forelimb, E12.5, Tbx3, scRNA, Rep2


title: Sperm, RamF3_337_6, Control

description: Library name: RamF3_337_6

value: Sperm

value: descendant of control ram

value: control


title: Sperm, RamF3_329_24, Control

description: Library name: RamF3_329_24


title: edited_rich_1

city: Patras

first: Adamantia

last: Kouvela

address: Asklipiou 1

country: Greece

institute: Department of Biochemistry, School of Medicine, University of Patras

description:
Library name: Sample3
limma _ Normalised counts.tabular

data_processing:
Adapters were trimmed with Trimmomatic.
The resulting fastq files were uploaded to the Galaxy web platform through the usegalaxy.eu public server
The differential gene expression was calculated with limma-voom (v3.50.1)
Assembly: Staphylococcus aureus RN4220
Supplementary files format and content: limma _ Normalised counts.tabular

organism: Staphylococcus aureus

source_name: Staphylococcus aureus RN4220

extract_protocol:
Total RNA was extracted using FastRNA Pro Blue kit (MP Biomedicals) according to the manufacturer’s protocol. The samples were treated with DNase I and the quality of the RNA was visualized using agarose gel electrophoresis. Ribosomal RNA (rRNA) was depleted using the S. aureus Ribo-seq riboPOOL kit (SiTOOLs Biotech) according to the manufacturer’s instructions.
RNA was fragmented using 50 mM bicarbonate buffer for 8 minutes at 96 °C. Fragmented RNA was subsequently treated with dephosphorylation and phosphorylation (deP/P) steps to enable small RNA library construction. Small RNA sequencing libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs), following the manufacturer’s protocol. Libraries were sequenced on the Illumina NextSeq 1000 platform in the Epitranscriptomics and RNA Sequencing Core, Université de Lorraine.

value: Staphylococcus aureus RN4220

value: edited


title: Mm, forelimb, E12.5, Meis2, scRNA, Rep2

value: forelimb


title: control_rich_2

description:
Library name: Sample2
limma _ Normalised counts.tabular


title: C26, skin, control, 0

description: Library name: C26


title: Mm, hindlimb, E11.5, wt, scRNA, Rep2

value: hindlimb

value: wildtype


title: Healthy control-9, left colon, infliximab

value: infliximab


title: Healthy control-9, terminal ileum, infliximab

value: terminal ileum


title: edited_rich_2

description:
Library name: Sample4
limma _ Normalised counts.tabular


title: C32, skin, control, 0

description: Library name: C32


title: edited_small_rep_2

description:
Library name: Sample8
limma_small_50+.xlsx
limma_small_30-50.xlsx
limma_small_15-30.xlsx

library_source: other

data_processing:
Basecalling, de-multiplexing and filtering of low quality reads was performed within the Torrent Suite 5.12.3
The resulting fastq files were uploaded to the Galaxy web platform through the usegalaxy.eu public server
The differential gene expression was calculated with limma-voom (v3.50.1)
Assembly: Staphylococcus aureus RN4220
Supplementary files format and content: limma-voom ouput in xlsx format

molecule: other

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s protocol after sonication with the LABSONIC M sonicator (Sartorius, Göttingen, Germany). The samples were treated with DNase I and the quality of the RNA was visualized using agarose gel electrophoresis. Ribosomal RNA (rRNA) was depleted using the RiboMinusTM Bacteria 2.0 Transcriptome Isolation Kit (Thermo Fisher Scientific).
cDNA libraries were prepared from 100 ng rRNA-depleted RNA using the Ion Total RNA-Seq v2 Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Briefly, RNAs were digested with RNase III to produce 200 nt RNA fragments, which were successively treated for adapter ligation, reverse transcription, and 14 cycles of PCR amplification using the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific). The quantity of the libraries was measured with the Qubit 1x dsDNA HS Assay Kit (Thermo Fisher Scientific) and the size distribution was assessed using the Agilent High Sensitivity DNA Kit on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Template preparation and the Ion chip 540™ loading were performed on the Ion Chef system using the Ion 540™ Chef kit. The single-end sequencing was carried out on an Ion GeneStudio S5 sequencer. RNA sequencing analysis was performed in biological duplicates. For the sequencing of small RNAs, total RNA was run onto a 12% UREA-PAGE and the <150 nt RNA fraction was gel extracted . The library preparation procedure was the same as in the case of the total transcriptome analysis, except for the steps of ribosomal RNA depletion and RNase III treatment.


title: C24, skin, control, 0

description: Library name: C24

value: male


title: control_rich_1

description:
Library name: Sample1
limma _ Normalised counts.tabular


title: Healthy control-9, terminal ileum, basal

value: basal


title: Mm, forelimb, E12.5, Tbx3, scRNA, Rep1


title: Mm, hindlimb, E11.5, wt, scRNA, Rep1


title: Healthy control-10, terminal ileum, infliximab


title: Healthy control-8, left colon, infliximab


title: C6A, skin, control, 0

description: Library name: C6A

value: skin

value: control skin

value: A


title: Healthy control-8, left colon, basal

value: left colon


title: C31, skin, control, 0

description: Library name: C31

value: B

value: female


title: Mm, forelimb, E12.5, Meis2, scRNA, Rep1


title: Mm, forelimb, E11.5, wt, scRNA, Rep1


title: C23, skin, control, 0

description: Library name: C23


title: edited_small_rep_1

description:
Library name: Sample7
limma_small_50+.xlsx
limma_small_30-50.xlsx
limma_small_15-30.xlsx


title: C21, skin, control, 0

description: Library name: C21


title: Mm, forelimb, E11.5, wt, scRNA, Rep2


title: control_small_rep_2

description:
Library name: Sample6
limma_small_50+.xlsx
limma_small_30-50.xlsx
limma_small_15-30.xlsx


title: C20, skin, control, 0

description: Library name: C20


title: Mm, RNAseq, wildtype, E15.5, developing distal hindlimb, Rep2

data_processing:
Read mapping to mm39 and Carollia perspicillata reference genomes was performed using the STAR_2.6.1d software20 with the following options: --chimSegmentMin 10 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.05 --outSAMmode NoQS --outFilterMismatchNmax 10. For samples obtained from transgenic animals the transgene sequence was temporarily merged with the genome annotation using the option -add. For each sample, read counts per gene were obtained via the R function “featureCounts”, with the parameter --countReadPairs -s 2. For visualization, CPM normalized bigwig files were created using the “bamCoverage” tool from deepTools21 or read counts were normalized to reads per kilobase million (RPKM) based on the number of uniquely mapped reads.
Differentially expressed genes (DEGs) were identified from featureCounts count matrices using DESeq2 v1.38.3 (R v4.2.2)22. For each comparison, replicate quality was assessed using PCA and Euclidean distance between samples. When necessary, outlier replicates were removed from further analysis. Lowly expressed genes were then filtered using edgeR v3.40.2 filterbyexpr23 and non-annotated transcripts were removed to ensure 1-to-1 comparisons between the species. Counts were normalized and differential expression calculated as log2 fold change (LFC) from the mean of normalized counts. Genes were assigned as differentially expressed for LFC larger than ±0.5 and adjusted Wald test p value below 0.05.
Assembly: mm39, carPer2
Supplementary files format and content: counts

extract_protocol:
Limbs from mice and bats were dissected in ice cold PBS, snap frozen in liquid nitrogen and stored at -80°C until further processing.
Total RNA was extracted using RNeasy Mini Kit (Quiagen, #74106) or RNeasy Micro Kit (Quiagen, #74004) according to the manufacturer's instructions. Limb samples derived from E11.5 and E13.5 as well as CS15 and CS17 embryos were directly homogenized in RTL buffer supplemented with 1% β-Mercaptoethanol and applied to spin columns. Limb tissues from older embryonic stages (E15.5 and CS19) were crushed in liquid nitrogen using Bel-Art SP Scienceware Liquid Nitrogen-Cooled Mini Mortar prior to homogenization. Genomic DNA was removed using the RNase-Free DNase Set (Quiagen, 79254). For gene expression analysis, samples were poly-A enriched and libraries were prepared using the Kapa HyperPrep Kit (Roche, #07962347001). RNA libraries were sequenced on a Novaseq2 with 100 bp paired-end reads. RNA-seq experiments were performed at least in biological duplicates.


title: Healthy control-8, terminal ileum, infliximab

value: Healthy control


title: Healthy control-8, terminal ileum, basal


title: C18, skin, control, 0

description: Library name: C18


title: Mm, RNAseq, wildtype, E15.5, developing distal hindlimb, Rep1


title: Healthy control-7, left colon, infliximab


title: Mm, RNAseq, wildtype, E15.5, developing distal forelimb, Rep4


title: edited_long_rep_2

description:
Library name: Sample4
limma-voom_long.xlsx


title: edited_long_rep_1

description:
Library name: Sample3
limma-voom_long.xlsx


title: Mm, RNAseq, wildtype, E15.5, developing distal forelimb, Rep3


title: control_long_rep_2

description:
Library name: Sample2
limma-voom_long.xlsx

value: control


title: C15, skin, control, 0

description: Library name: C15


title: C13, skin, control, 0

description: Library name: C13


title: Healthy control-6, left colon, infliximab


title: Mm, RNAseq, wildtype, E15.5, developing distal forelimb, Rep2


title: Healthy control-6, terminal ileum, infliximab


title: C12, skin, control, 0

description: Library name: C12


title: Mm, RNAseq, Tbx3, E12.5, developing distal forelimb, Rep5


title: Cp, chiropatagium, right, CS18, wt, scRNA, Rep1

organism: Carollia perspicillata

source_name: chiropatagium

value: chiropatagium


title: C16, skin, control, 0

description: Library name: C16


title: Healthy control-6, left colon, basal


title: Healthy control-7, terminal ileum, basal


title: Mm, RNAseq, wildtype, E15.5, developing distal forelimb, Rep1


title: Cp, chiropatagium, left, CS18, wt, scRNA, Rep2


title: Healthy control-7, left colon, basal


title: 9, skin, control, 0

description: Library name: 9

value: C


title: Cp, chiropatagium, right, CS18, wt, scRNA, Rep2


title: Healthy control-7, terminal ileum, infliximab


title: Mm, RNAseq, Tbx3, E12.5, developing distal forelimb, Rep4

value: forelimb


title: control_small_rep_1

description:
Library name: Sample5
limma_small_50+.xlsx
limma_small_30-50.xlsx
limma_small_15-30.xlsx

value: Staphylococcus aureus RN4220


title: C11, skin, control, 0

description: Library name: C11


title: control_long_rep_1

description:
Library name: Sample1
limma-voom_long.xlsx


title: 8, skin, control, 0

description: Library name: 8


title: Mm, RNAseq, Tbx3, E12.5, developing distal forelimb, Rep3


title: Cp, chiropatagium, left, CS18, wt, scRNA, Rep1

value: wildtype


title: Healthy control-6, terminal ileum, basal


title: Cp, hindlimb, CS17, wt, scRNA, Rep1

value: hindlimb


title: Healthy control-5, left colon, infliximab

value: infliximab


title: Healthy control-5, terminal ileum, infliximab

value: terminal ileum


title: Mm, RNAseq, Tbx3, E12.5, developing distal forelimb, Rep2


title: Cp, hindlimb, CS17, qt, scRNA, Rep2


title: 5, skin, control, 0

description: Library name: 5


title: Mm, RNAseq, Meis2, E12.5, developing distal forelimb, Rep4


title: Cp, hindlimb, CS15, wt, scRNA, Rep2


title: Cp, hindlimb, CS15, wt, scRNA, Rep1


title: Mm, RNAseq, Meis2, E12.5, developing distal forelimb, Rep5


title: Healthy control-4, left colon, basal

value: basal


title: 48, skin, allergic contact dermatitis, nickel

description: Library name: 48

value: skin

value: allergic contact dermatitis

value: nickel


title: Mm, RNAseq, Meis2, E12.5, developing distal forelimb, Rep1


title: Cp, forelimb, CS17, wt. scRNA, Rep2


title: Cp, forelimb, CS17, wt,  scRNA, Rep1


title: Healthy control-5, terminal ileum, basal


title: Healthy control-5, left colon, basal

value: left colon


title: Healthy control-4, left colon, infliximab


title: Mm, RNAseq, Meis2, E12.5, developing distal forelimb, Rep3


title: 46, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 46

value: B


title: 50, skin, allergic contact dermatitis, formaldehyde

description: Library name: 50

value: formaldehyde

value: female


title: 49, skin, allergic contact dermatitis, nickel

description: Library name: 49


title: Mm, RNAseq, Tbx3, E12.5, developing distal forelimb, Rep1


title: 47, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 47


title: Mm, RNAseq, Meis2, E12.5, developing distal forelimb, Rep2


title: 7, skin, control, 0

description: Library name: 7

value: control skin

value: male


title: Cp, forelimb, CS15, wt, scRNA, Rep2


title: Healthy control-4, terminal ileum, infliximab

value: Healthy control


title: Cp, RNAseq, wildtype, CS19, developing distal hindlimb, Rep3


title: Healthy control-2, left colon, infliximab


title: ST#15-D4

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

description:
ST#15 D Combination-4
counts.txt
gene_list.txt

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). The parameters were as follows:
1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases.
After the removal of the reads that contained adaptor contamination, low quality bases, and undetermined bases by Cutadapt, sequence quality was verified using FastQC. HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/, StringTie was used for assembled. To estimate the expression levels of all transcripts, StringTie and ballgrwn were used. The mRNA differential expression analysis was performed by R package DESeq2 between two different groups (and by R package edgeR between two samples). The mRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed mRNAs. The heatmap was generated with the top 100 genes exhibiting the most significant FDR in DESeq2 analysis. Z scores of the normalized value were applied to pheatmap package (version=1.0.12).
Partek Flow software was used for following data processing and analysis. Raw data was trimmed,  alignment by STAR with mm39 - Ensembl Transcripts release 108 , Gene count was further normalized by DEseq2.
Assembly: mm39 - Ensembl Transcripts release 108
Supplementary files format and content: "Partek_ST_23Normalized_counts.csv" : normalized count of DEseq2 was caliculated and shown in the file  "Partek_ST_23Normalized_counts.csv"
Supplementary files format and content: "counts.txt" : Experiment #ST#15 and #ST#23 has been processed for batch collection by General linear model Batch effect adjustment on PartekFlow software. Normalized count of DEseq2 was caliculated. Data is shown in  "counts.txt".
Supplementary files format and content: " gene_list.txt": GSEA from combined data of ST#15 amd ST#23 has been caliculated on Partek Flow software as B ADU-S100 vs A control, C anti-LTbRAb vs A control, D combination vs A control. Gene list and GSEA data is shown as " gene_list.txt"

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Mouse tumors from KxPxCx injection

value: Combination


title: Healthy control-3, terminal ileum, basal


title: Healthy control-4, terminal ileum, basal


title: Healthy control-3, left colon, infliximab


title: Cp, RNAseq, wildtype, CS19, developing distal hindlimb, Rep4

value: wildtype


title: Healthy control-3, terminal ileum, infliximab


title: Mm, RNAseq, wildtype, E12.5, developing distal forelimb, Rep2

value: forelimb


title: Mm, RNAseq, wildtype, E12.5, developing distal forelimb, Rep4


title: 42, skin, allergic contact dermatitis, nickel

description: Library name: 42


title: 43, skin, allergic contact dermatitis, nickel

description: Library name: 43


title: 44, skin, allergic contact dermatitis, formaldehyde

description: Library name: 44


title: Mm, RNAseq, wildtype, E12.5, developing distal forelimb, Rep3


title: ST#15-D5

description:
ST#15 D Combination-5
counts.txt
gene_list.txt


title: Healthy control-3, left colon, basal


title: 40, skin, allergic contact dermatitis, formaldehyde

description: Library name: 40

value: A


title: Cp, forelimb, CS15, wt, scRNA, Rep1


title: Mm, RNAseq, wildtype, E12.5, developing distal forelimb, Rep1


title: Cp, RNAseq, wildtype, CS19, developing distal hindlimb, Rep1

value: hindlimb


title: Cp, RNAseq, wildtype, CS19, developing distal forelimb, Rep1


title: Cp, RNAseq, wildtype, CS19, developing distal hindlimb, Rep2


title: 39, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 39

value: methylisothiazolinone


title: Cp, RNAseq, wildtype, CS19, developing distal forelimb, Rep2


title: Healthy control-2, left colon, basal

value: basal


title: 38, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 38

value: skin

value: allergic contact dermatitis


title: ST#15-D3

description:
ST#15 D Combination-3
counts.txt
gene_list.txt


title: Mm, RNAseq, wildtype, E12.5, developing distal forelimb, Rep5


title: 45, skin, allergic contact dermatitis, nickel

description: Library name: 45

value: nickel


title: 41, skin, allergic contact dermatitis, formaldehyde

description: Library name: 41


title: Healthy control-2, terminal ileum, infliximab

value: terminal ileum

value: infliximab


title: 37, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 37

value: B

value: female


title: Cp, developing  forelimb, CS16, wt, HiC, Rep3

data_processing:
For read processing, the Carollia perspicillata reference genome (carPer2) was indexed with the short read aligner BWA 0.7.1737 . Raw reads from sequenced Hi-C libraries were then processed using the Juicer pipeline v1.5.638. The three replicates were processed independently and subsequently merged after filtering and deduplication.  Hi-C maps with various bin sizes were generated using Juicer tools 1.11.0938 using the parameter pre -q 30. For displaying Hi-C maps as heatmaps, KR normalized maps with 5 kb bin size were used.
Topologically associated domains (TADs) were called using Hi-C data of Carollia perspicillata embryonic fibroblasts with the software TopDom39 (KR normalized, resolution: 50 kb, window size: 10).
Assembly: mm39, carPer2
Supplementary files format and content: txt, bed
Supplementary files format and content: HiC nodups file produced by Juicer

extract_protocol:
Fibroblast cells or limb cells were dissociated and 1x10^6 or 5x10^5 cells were used for library processing.
Cells were fixed in 2% formaldehyde in 10%FCS/PBS. After cell lysis, chromatin was digested with DpnII enzyme (NEB, #R0543), digested ends were marked with biotin-14-dATP (Invitrogen, #19524016) and subsequently ligated. Crosslinking was reversed, DNA precipitated and sheared to a fragment size of 300-600 bp using a S-Series 220 Covaris sonicator. The biotin-containing fragments were pulled down with Dynabeads MyOne Streptavidin T1 beads (Invitrogen, #65602) and ends were repaired using Klenow Fragment DNA polymerase I (NEB, #M0210) and T4 DNA polymerase (NEB, #M0203). Adaptors were added to DNA fragments using NEBNext Multiplex Oligos for Illumina kit (NEB, # E7335S) and sequencing indices were added by PCR using NEBNext Ultra II Q5Master Mix (NEB, #M0544) . Hi-C libraries were generated as three technical replicates and sequenced on a NovaSeq2 as 100bp paired-end reads.


title: Healthy control-2, terminal ileum, basal


title: 36, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 36


title: Cp, developing forelimb, CS16, wt, HiC, Rep2


title: Healthy control-1, left colon, infliximab

value: left colon


title: Cp, developing forelimb, CS16, wt, HiC, Rep1


title: ST#15-D1

description:
ST#15 D Combination-1
counts.txt
gene_list.txt


title: Healthy control-1, left colon, basal

value: Healthy control


title: Healthy control-1, terminal ileum, infliximab


title: Cp, fibroblast, wt, HiC, Rep1

description: TADs_Fibroblast_carPer2_merged_50K.TopDom_10.bed

data_processing:
For read processing, the Carollia perspicillata reference genome (carPer2) was indexed with the short read aligner BWA 0.7.1737 . Raw reads from sequenced Hi-C libraries were then processed using the Juicer pipeline v1.5.638. The three replicates were processed independently and subsequently merged after filtering and deduplication.  Hi-C maps with various bin sizes were generated using Juicer tools 1.11.0938 using the parameter pre -q 30. For displaying Hi-C maps as heatmaps, KR normalized maps with 5 kb bin size were used.
Topologically associated domains (TADs) were called using Hi-C data of Carollia perspicillata embryonic fibroblasts with the software TopDom39 (KR normalized, resolution: 50 kb, window size: 10).
Assembly: mm39, carPer2
Supplementary files format and content: txt, bed

source_name: embryonic fibroblast

value: embryonic fibroblast


title: ST#15-C5

description:
ST#15 C anti-LTbR Ab-5
counts.txt
gene_list.txt

value: Mouse tumors from KxPxCx injection

value: Combination


title: Cp, fibroblast, wt, HiC, Rep3

value: wildtype


title: ST#15-C4

description:
ST#15 C anti-LTbR Ab-4
counts.txt
gene_list.txt


title: 35, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 35


title: Cp, fibroblast, wt, HiC, Rep2


title: Healthy control-1, terminal ileum, basal

data_processing:
Raw reads were trimmed with skewer followed by quality control analysis via FastQC.
Trimmed reads were aligned hg38 via STAR v2.7.1 aligner indexed to GENCODE v26 GTF library using -quantMode GeneCounts for feature counting.
Gene filtering based on the rule of 10 count in at least 1 sample, log-transformation using the Limma voom function using TMM followed by quantile normalisations.
Assembly: GRCh38
Supplementary files format and content: Quantified raw read counts


title: 32, skin, allergic contact dermatitis, formaldehyde

description: Library name: 32

value: formaldehyde


title: 33, skin, allergic contact dermatitis, formaldehyde

description: Library name: 33


title: ST#15-C2

description:
ST#15 C anti-LTbR Ab-2
counts.txt
gene_list.txt


title: Cp, H3K27ac, developing distal hindlimb, wt, Input, CS19,  Rep1

description:
H3K27ac_D-HL_CS19_carPer2_WT_merged_-IP.bw
diff_dFL_vs_dHL_dHL.bed
diff_dFL_vs_dHL_common.bed

data_processing:
Read mapping of the sequenced samples to mouse and bat reference genomes (mm39 / carPer2) was performed using the STAR_2.6.1d software20. Reads were then filtered and sorted and duplicates were removed using SAMtools27. For visualization, CPM normalized bigwig files were created using deepTools “bamCoverage” tool21. Input samples were substracted using deepTools bamCompare
The coverage of dFL-specific acetylation regions relative to the acetylation regions shared between dFL/dHL was calculated for each TAD. Differential acetylation regions between dFL and dHL, as well as acetylation regions common in both conditions, were predicted from ChIP-seq alignments using macs2 (ref 28) bdgdiff command with the following parameter: -l 800 -g 500 and a likelihood ratio cutoff of 1000.
Meis2 binding signal of one of our dFL replicates was aggregated by TADs. The signal (area under the curve) was calculated using deepTools pyBigwig (ref 21). By analyzing the second derivative of the density distribution of the signal by TAD, we found the dividing point to the subpopulation of enriched TADs. The same procedure was carried out for the coverage length of the acetylation peaks. Genes were categorized as "Cytoskeleton”, "ECM”, or "Transcription Factor” using the Uniprot database, if the Keywords included the terms "Cytoskeleton”, "Extracellular matrix”, or ("DNA-binding” OR “Transcription regulation”) respectively.
Assembly: carPer2, mm39
Supplementary files format and content: bigwig, narrowPeak, bed

extract_protocol:
Mouse and bat embryonic limbs were dissected and fixed in 1% formaldehyde in 10% FCS/PBS and subsequently snap-frozen and stored at −80°C until further processing
Chromatin immunoprecipitations were performed using the iDeal ChIP-seq Kit for Histones (Diagenode, #C01010051) and iDeal ChIP-seq Kit for Transcription Factors (Diagenode, #C01010055) according to the manufacturer's instructions. Briefly, fixed limbs were lysed and sonicated using a Bioruptor Plus Sonication device (45 cycles, 30s on, 30s off, at high power setting) in provided buffers. 5 µg sheared chromatin were used for histone immunoprecipitation with 1µg of anti-H3K27ac (Diagenode, #C15410174). For Meis2 immunoprecipitation, 20 µg of sheared chromatin were used with two anti-Meis antibodies simultaneously, one recognizing the conserved C-terminal domain of Meis1a and Meis2a and the other recognizing all Meis2 isoforms as previously described26. 2µg of each antibody were used per immunoprecipitation. Antibodies were generously provided by Dr. Miguel Torres. Libraries were prepared using the Kapa HyperPrep Kit (Roche, #07962347001) and libraries were sequenced on a NovaSeq2 with 100bp paired-end reads. ChIP-seq experiments were performed in biological duplicates.

value: hindlimb


title: PRKG_KO_2

data_processing:
Reads were mapped with STAR software (v.2.7.8) against the human reference genome GRCh38 using the GRCh38.p13 Ensembl annotation.
The table of counts was obtained with featureCounts function in the package subread (v.2.0.3).
Counts were normalized with log2 counts per million (CPM) with the edgeR package (v.3.40.2) with a prior.count=3. Genes with more than 10 counts in at least 3 samples were kept.
Assembly: GRCh38
Supplementary files format and content: counts

growth_protocol: RH4 cells were manteined in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
NGS libraries with polyA capture were prepared according to the manual NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina ® , section 1 (NEB #E7760) (New England Biolabs) (Version 5.0, 12/22)

treatment_protocol: sh cell lines were estable transfected and selected with puromucyn.

value: FP-RMS

value: knock out_PRKG1


title: 31, skin, allergic contact dermatitis, formaldehyde

description: Library name: 31

value: skin

value: male


title: Cp, H3K27ac, developing distal hindlimb, wt, Input, CS19, Rep2


title: PRKG_KO_3


title: ST#15-C1

description:
ST#15 C anti-LTbR Ab-1
counts.txt
gene_list.txt


title: ST#15-D2

description:
ST#15 D Combination-2
counts.txt
gene_list.txt


title: 34, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 34

value: allergic contact dermatitis

value: methylisothiazolinone


title: ST#15-C3

description:
ST#15 C anti-LTbR Ab-3
counts.txt
gene_list.txt


title: PRKG_KO_1


title: Cp, H3K27ac, developing distal hindlimb, wt, CS19, Rep2

value: anti-H3K27ac (Diagenode, #C15410174)


title: ST#15-B5

description:
ST#15 B ADU-S100-5
counts.txt
gene_list.txt


title: 29, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 29

value: B


title: Cp, H3K27ac, developing distal hindlimb, wt, CS19, Rep1


title: ST#15-B4

description:
ST#15 B ADU-S100-4
counts.txt
gene_list.txt


title: SCRCtrl_3

value: SCRCtrl

value: knock out_control


title: 28, skin, allergic contact dermatitis, formaldehyde

description: Library name: 28

value: female


title: Cp, H3K27ac, developing distal forelimb, wt, Input, CS19, Rep2

description:
H3K27ac_D-FL_CS19_carPer2_WT_merged_-IP.bw
diff_dFL_vs_dHL_dFL.bed
diff_dFL_vs_dHL_common.bed

value: forelimb


title: SCRCtrl_2


title: ST#15-B2

description:
ST#15 B ADU-S100-2
counts.txt
gene_list.txt

value: Mouse tumors from KxPxCx injection


title: 26, skin, allergic contact dermatitis, formaldehyde

description: Library name: 26


title: SCRCtrl_1


title: 25, skin, allergic contact dermatitis, nickel

description: Library name: 25

value: nickel


title: ST#15-B1

description:
ST#15 B ADU-S100-1
counts.txt
gene_list.txt

value: Combination


title: Cp, H3K27ac, developing distal forelimb, wt, CS19, Rep2

value: wildtype


title: ST#15-B3

description:
ST#15 B ADU-S100-3
counts.txt
gene_list.txt


title: 24, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 24


title: Sh2_3

value: knock down_PRKG1_#1


title: Cp, H3K27ac, developing distal forelimb, wt, CS19, Rep1


title: ST#15-A5

description:
ST#15 A control-5
counts.txt
gene_list.txt


title: 23, skin, allergic contact dermatitis, methylisothiazolinone

description: Library name: 23


title: ST#15-A4

description:
ST#15 A control-4
counts.txt
gene_list.txt


title: Cp, Meis2, developing distal hindlimb, wt, Input, CS19, Rep2

description:
Meis2_D-HL_CS19_carPer2_WT_-IP_merged.bw
Meis2_carPer_CS19_dist_hindlimb.narrowPeak

value: hindlimb


title: Sh2_1

value: FP-RMS


title: 30, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 30

value: skin


title: 22, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 22


title: ST#15-A3

description:
ST#15 A control-3
counts.txt
gene_list.txt


title: Sh1_2

value: knock down_PRKG1_#2


title: Sh1_3


title: Cp, Meis2, developing distal hindlimb, wt, CS19, Rep2

value: Meis1a+Meis2 (Delgado et al., 2021)


title: 21, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 21

value: allergic contact dermatitis


title: ST#15-A1

description:
ST#15 A control-1
counts.txt
gene_list.txt


title: Cp, H3K27ac, developing distal forelimb, wt, Input, CS19, Rep1


title: Cp, Meis2, developing distal hindlimb, wt, CS19, Rep1


title: S100LTbRAb_8

description:
ST#23 D Combination-8
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: Sh1_1


title: ShCtrl_3

value: ShCtrl#LKO

value: knock down_control


title: 18, skin, allergic contact dermatitis, nickel

description: Library name: 18

value: B


title: Cp, Meis2, developing distal forelimb, wt, Input, CS19, Rep2

description:
Meis2_D-FL_CS19_carPer2_WT_merged-IP.bw
Meis2_carPer_CS19_dist_forelimb.narrowPeak


title: Cp, Meis2, developing distal forelimb, wt, Input, CS19, Rep1


title: 19, skin, allergic contact dermatitis, nickel

description: Library name: 19


title: Sh2_2


title: 17, skin, allergic contact dermatitis, nickel

description: Library name: 17


title: ShCtrl_2


title: S100LTbRAb_7

description:
ST#23 D Combination-7
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: S100LTbRAb_6

description:
ST#23 D Combination-6
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: ShCtrl_1


title: Cp, Meis2, developing distal forelimb, wt, CS19, Rep2


title: 16, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 16

value: C


title: S100LTbRAb_5

description:
ST#23 D Combination-5
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: Cp, Meis2, developing distal forelimb, wt, CS19, Rep1


title: S100LTbRAb_4

description:
ST#23 D Combination-4
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: ST#15-A2

description:
ST#15 A control-2
counts.txt
gene_list.txt


title: 15, skin, allergic contact dermatitis, nickel

description: Library name: 15

value: female


title: 20, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 20


title: hep-S biol rep 3

city: Guangzhou

first: Wu

last: Haibin

address: Waihuan east road

institute: South china university of technology

data_processing:
Sequencing was performed by Novogene (China) on an Illumina HiSeq X-Tensequencer with 150 bp paired- end sequencing reaction.
The reads were mapped to the human reference genome using HISAT2.
Reads Counts for each gene in each sample were counted by featureCounts, and FPKM (Fragments Per Kilobase Millon Mapped Reads) and then were calculated to estimate the expression level of genes in each sample.
Assembly: GRCh38
Supplementary files format and content: raw counts for each sample

source_name: P-heporgs

extract_protocol:
Total RNA of  HB-orgs and P-hep-orgs  were extracted using RNAiso Plus kit according to the manufacturer’s instructions.
The cDNA libraries for RNA sequencing were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB).

value: H9 differentiated cells

value: P-heporgs

value: static condition


title: Cp, Meis2, developing distal hindlimb, wt, Input, CS19, Rep1


title: hep-S biol rep 2


title: Cp, ATAC-seq, developing forelimb, CS17, Rep2

description: ATAC-seq_FL_CS17_carPer2_WT.genrich_peaks_0.05.narrowPeak

data_processing:
For processing, adaptors were trimmed with the cutadapt tool34 and reads were mapped to indexed reference genomes (mm39/carPer2) using Bowtie235. Reads were then filtered, sorted and duplicates removed according to ChIP-seq processing. Reproducible peaks were called using Genrich with default parameters.
Assembly: carPer2
Supplementary files format and content: narrowPeak

extract_protocol:
Bat limbs were dissected and dissociated with trypsin.
50,000 cells per reaction were lysed and isolated nuclei were incubated with Tn5 Transposase (Illumina, #20034197) for transposition. DNA fragments were purified and barcoded adaptors were added via PCR. Fragments were purified and sequenced as 100 bp paired-end reads on a NovaSeq 6000 system. ATAC-seq experiments were performed in biological duplicates.

value: forelimb


title: hep-S biol rep 1


title: Cp, ATAC-seq, developing forelimb, CS17, Rep1

value: wildtype


title: 13, skin, allergic contact dermatitis, nickel

description: Library name: 13

value: nickel


title: S100LTbRAb_3

description:
ST#23 D Combination-3
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt

value: Mouse tumors from KxPxCx injection

value: Combination


title: S100LTbRAb_2

description:
ST#23 D Combination-2
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: S100LTbRAb_1

description:
ST#23 D Combination-1
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt


title: 12, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 12

value: skin


title: 11, skin, allergic contact dermatitis, 2-hydroxyethylmethacrylate

description: Library name: 11


title: hep-D biol rep 3

value: dynamic condition


title: hep-D biol rep 2


title: LTbRAb_8

description:
ST#23 C anti-LTbR Ab-8
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt

value: anti-LTbRAb


title: LTbRAb_7

description:
ST#23 C anti-LTbR Ab-7
Partek_ST_23Normalized_counts.csv
counts.txt
gene_list.txt