title: Brain, control, biological replicate 1

value: Mammary adenocarcinoma cells

value: E0771-GFP (AAV)

value: No treatment


title: S21

status: Public on Jul 16 2025

type: SRA

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

country: USA

institute: University of Virginia

description:
Library name: KO4339-6-1_S21
counts_Jan_2023.csv.gz

library_source: transcriptomic

data_processing:
Sequencing quality was assessed using Fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next, the bioinformatic tool cutadap (Martin, 2011) was used to remove adapter sequences, trim low-quality bases, and filter short reads. Lastly, processed reads were mapped to the mouse reference genome (GRCm39) using STAR v2.6.1(Dobin et al., 2013) and reads that map onto each gene will be quantified using the featureCounts tool included in Subread software package (https://subread.sourceforge.net/). The generated count table was imported to R to perform differential gene expression (DEG) analysis using the DESeq2 package (Love, Huber, & Anders, 2014). Lowly expressed genes were filtered out, retaining genes with at least 15 counts in 14 or more samples to improve data robustness. Variance stabilizing transformation (VST) was applied to normalize the dataset for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: tsv

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was isolated from CD11b-positive microglial cells by using Direct-zol RNA Miniprep Plus (Product #: R2072; Zymo Research, USA) according to manufacturer’s instruction. The isolated RNA was immediately frozen at -80°C and sent to sequence
RNA-seq library preparation was performed using Poly(A) selection, where polyadenylated mRNA transcripts were selectively enriched and the sequencing was performed in the Illumina's NovaSeq platform with 30 million read pairs per sample.

treatment_protocol: WT and P2RY12 deficient littermate mice were subjected to an intraperitoneal (i.p.) injection of LPS (1 mg/kg)

tag: tissue

value: Brain

tag: cell type

value: Microglia

tag: genotype

value: wt

tag: treatment

value: lps

tag: batch

value: Total RNA


title: Col-10ACC-4h-rep2

city: Shanghai

first: Lin

last: Li

address: 220 Handan Road

country: China

institute: Fudan university

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. (Reference: [1] Chen S ,  Zhou Y ,  Chen Y , et al. fastp : an ultra-fast all-in-one FASTQ preprocessor. 2018.)
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. (Reference: [2] Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature methods, 2015, 12(4): 357-360.)
The mapped reads of each sample were assembled by StringTie in a reference-based approach. (Reference: [3] Pertea M, Pertea G M, Antonescu C M, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nature biotechnology, 2015, 33(3): 290-295.)
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM[4] was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2[5] or DEGseq[6]. DEGs with |log2FC|≧1 and FDR＜ 0.05(DESeq2 ) or FDR ＜ 0.001(DEGseq) were considered to be significantly different expressed genes. (Reference: [4] Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011;12:323.)
In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value＜0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and Python scipy software, respectively. (Reference: [5] Love M I, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome biology, 2014, 15(12): 550.[6] Wang L, Feng Z, Wang X, et al. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data[J]. Bioinformatics, 2009, 26(1): 136-138.)
Assembly: TAIR10 (ensemble_55)
Supplementary files format and content: XLS; Quantitative annotation results table of gene tpm expression

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: The Col-0/etr1-1 seedlings grown under white light for 6 hours, then turned to dark condition at 22°C for 4 days.

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). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (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 (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s 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, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X Plus sequencer (2 × 150bp read length).

treatment_protocol: 4-day-old dark-grown seedlings were transferred to 1/2 MS liquid medium complemented with 30 μM PFT-α, 10 μM ACC or 1‰ DMSO (v/v) for 4 h, and whole seedlings were collected.

value: whole seedlings

value: wildtype

value: 10 uM ACC for 4 h


title: dgcn5_H3K4ac

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

library_source: genomic

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
BedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Candida albicans SC5314 (PRJNA10701)
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Candida albicans

source_name: yeast cell

growth_protocol: C. albicans were grown in YPD  media (1% yeast extracts, 2% peptone, 2% glucose) and harvested during the exponential growth phase, at an OD600 of 1.0 for yeast growth. To prepare hyphal status cells, C. albicans grown in YPD were harvested at OD600 of 0.9 and transferred to preheated YPD containing 10% FBS. Hyphal formation was induced by incubating cells at 37°C with shaking.

extract_protocol:
Cells were crosslinked using 1% formaldehyde for 5 minutes. Before sonication, the cells were treated with zymolyase to produce spheroplasts.
ChIP-seq libraries were prepared using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (NEB, E6240, following the manufacturer’s instructions. 10 ng of ChIPed DNA was used as starting material.

value: yeast cell

tag: chip antibody

value: acetyl H3K4

value: YPD


title: PK10-49

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

description: TLS-poor

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
Pertek®Flow® was used for trimming, QC, alignment by STAR - 2.7.8a
Assembly: hg38_ensembl_release91_v2
Supplementary files format and content: Tab determined text file which include Normalized_counts from DESeq2

organism: Homo sapiens

source_name: Tumor tisseue

extract_protocol:
Archived PDAC FFPE tumor samples were categorized as TLS-positive or TLS-negative based on H&E staining. Under a microscope, the tumor areas were marked using a marker on the bottom side of the H&E-stained slide glasses. The non-stained FFPE slides, which were serial sections of the H&E-stained sections, were used for tumor tissue collection. When scraping the non-stained FFPE tissues, the H&E-stained slide (with the marked tumor areas) was stacked beneath the non-stained FFPE slide. Using the markers visible through the stacked slides, only the tumor tissues were carefully scraped and collected from the non-stained FFPE sections. Total RNA was extracted from FFPE slides using Qiagen RNeasy FFPE kit following anufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA).
rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Tumor tisseue


title: dset1_H3K4ac_rep2


title: Col-10ACC-4h-rep1


title: dset1_H3K4ac_rep1


title: PK10-51

description: TLS-poor


title: WT_H3K4ac_rep2

value: clinical isolate


title: Col-30PFTα-4h-rep3

value: 30 uM PFT-{alpha} for 4 h


title: S18

description:
Library name: KO4339-5-3_S18
counts_Jan_2023.csv.gz

value: ns


title: PK17-16

description: TLS-poor


title: Col-30PFTα-4h-rep2


title: PK18-78

description: TLS-rich


title: PK17-62

description: TLS-poor


title: WT_hypha_H3K4ac_rep2

value: YPD supplemented with 10% serum, 37℃, 30 min


title: WT_H3K4ac_rep1


title: Col-30PFTα-4h-rep1


title: S17

description:
Library name: KO4339-5-2_S17
counts_Jan_2023.csv.gz


title: S16

description:
Library name: KO4339-4-5_S16
counts_Jan_2023.csv.gz

value: ko


title: PK17-21

description: TLS-poor


title: PK17-52

description: TLS-poor


title: S15

description:
Library name: KO4339-4-4_S15
counts_Jan_2023.csv.gz

value: Brain


title: dset1_H3K4me3


title: S20

description:
Library name: KO4339-5-5_S20
counts_Jan_2023.csv.gz

value: Microglia


title: Col-mock-4h-rep2

value: DMSO for 4 h


title: WT_hypha_3H_H3K4me3_rep2

value: YPD supplemented with 10% serum, 37℃, 3 h


title: S14

description:
Library name: KO4339-4-3_S14
counts_Jan_2023.csv.gz

value: lps

value: Total RNA


title: WT_hypha_3H_H3K4me3_rep1


title: bone_marrow metastasis rep 4

city: Baltimore

first: Da

last: Peng

state: Maryland

address: 733 North Broadway, MRB 653

institute: Johns Hopkins University

data_processing:
Sequence reads were trimmed for low quality sequence using trim-galore.
Trimmed sequence reads were quantified using Salmon.
Assembly: hg38
Supplementary files format and content: txt file includes raw count matrix for each sample
Supplementary files format and content: csv file includes sample table for each sample

source_name: Ewing sarcoma

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit according to manufacturer's instructions.
Using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420L) and a normalized RNA input between 200pg-50ng a template switching method is used to generate cDNAs. The NEB Ultra II FS workflow is used for fragmentation, end repair, dA-tailing, adapter ligation and PCR. Indexed libraries that meet appropriate cut-offs for both quantity and quality are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: Ewing sarcoma

tag: cell line


title: bone_marrow metastasis rep 3


title: dgcn5_hypha_H3K4me3_rep2


title: Col-mock-4h-rep1

value: whole seedlings

value: wildtype


title: S13

description:
Library name: KO4339-4-2_S13
counts_Jan_2023.csv.gz


title: S19

description:
Library name: KO4339-5-4_S19
counts_Jan_2023.csv.gz

value: wt


title: gcn5△ _Induced_Replicate_3

city: Rockville

first: SAKSHI

last: SINGH

address: 6 center drive , Bldg 6

department: NICHD-DIR

institute: NIH

description:
Library name: SS-10423-2_24
MATa his3∆1 leu2∆ met15∆ ura3∆ gcn5∆::kanMX4

data_processing:
The RNA-sequencing reads were aligned to the S. cerevisiae reference genome S288C (assembly version: SacCer3) using STAR aligner PCR duplicates were removed using samtools. The total number of reads obtained from ERCC alignment was used to calculate the size factor for each sample, and reads corresponding to yeast genes were normalized by the size factors.
To identify the differentially expressed genes DeSeq2 analysis was performed using 3 biological replicates of each strain
Assembly: SacCer3
Supplementary files format and content: RNAseq_SpikeIn_Fragment_Counts_04-21-25.csv

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:
Total RNA isolation was carried out using Hot-Phenol Method followed by DNAse1 digestion and RNA clean up using  RNA clean up using RNA Clean and Concentrator kit . Prior to library preparation For spike in normalization of the RNA, an equal amount (2.4 l of 1:100 fold dilution) of ERCC spike-in mix (Thermo Fisher #4456740) was added to 1.2 ug of RNA samples of each strain.
RNA-sequencing libraries preparation was performed by NHLBI-genome sequencing core using the Illumina TrueSeq stranded mRNA Library Prep Kit. Ribo-depletion was performed to remove the rRNA using Qiagen FastSelect Yeast rRNA Depletion Kit, followed by paired-end sequencing using the Novaseq-X platform.

value: Whole cells


title: dgcn5_hypha_H3K4me3_rep1

value: yeast cell


title: bone marrow metastasis rep 2


title: gcn5△ _Induced_Replicate_1

description:
Library name: SS-10423-2_22
MATa his3∆1 leu2∆ met15∆ ura3∆ gcn5∆::kanMX4


title: gcn5△ _Induced_Replicate_2

description:
Library name: SS-10423-2_23
MATa his3∆1 leu2∆ met15∆ ura3∆ gcn5∆::kanMX4


title: WT_hypha_H3K4me3_rep2

value: clinical isolate


title: primary tumor


title: Col-mock-4h-rep3


title: S11

description:
Library name: KO4339-3-4_S11
counts_Jan_2023.csv.gz


title: WT_hypha_H3K4me3_rep1


title: S10

description:
Library name: KO4339-3-3_S10
counts_Jan_2023.csv.gz


title: spt8△ _Induced_Replicate_3

description:
Library name: SS-10423-2_18
MATa his3∆1 leu2∆ met15∆ ura3∆ spt8∆::kanMX4


title: lung metastasis rep 4


title: spt8△_Induced_Replicate_2

description:
Library name: SS-10423-2_17
MATa his3∆1 leu2∆ met15∆ ura3∆ spt8∆::kanMX4


title: dgcn5_H3K4me3_rep2

value: YPD


title: lung metastasis rep 3


title: dgcn5_H3K4me3_rep1


title: S9

description:
Library name: KO4339-3-2_S9
counts_Jan_2023.csv.gz

value: ns


title: lung metastasis rep 2


title: WT_H3K4me3_rep2


title: lung metastasis rep 1


title: spt3△ _Induced_Replicate_3

description:
Library name: SS-10423-1_12
MATa his3∆1 leu2∆ met15∆ ura3∆ spt3∆::kanMX4


title: S7

description:
Library name: KO4339-2-4_S7
counts_Jan_2023.csv.gz


title: WT_H3K4me3_rep1


title: bone marrow metastasis rep 1


title: spt3△_Induced_Replicate_2

description:
Library name: SS-10423-1_11
MATa his3∆1 leu2∆ met15∆ ura3∆ spt3∆::kanMX4


title: S12

description:
Library name: KO4339-3-5_S12
counts_Jan_2023.csv.gz


title: dset1_H3K4me2


title: spt3△ _Induced_Replicate_1

description:
Library name: SS-10423-1_10
MATa his3∆1 leu2∆ met15∆ ura3∆ spt3∆::kanMX4


title: WT_hypha_H3K4me2_rep2

value: YPD supplemented with 10% serum, 37℃, 30 min


title: SMARCB1_MuT_2

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

data_processing:
Raw reads were filtered and mapped to human RefSeq  using Hisat2 (version:2.0.4).
Assembly: GRCh38
Supplementary files format and content: Readcount values of mRAN expression for the whole detected genes.

source_name: IOMM-Lee

extract_protocol:
Total RNA of IOMM-Lee cells was extracted using TRIzol (Invitrogen, CA, USA) according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®).
Agilent 4200 bioanalyzer was used to evaluate the concentration and size distribution of cDNA library, followed by sequencing with an Illumina Novaseq6000.

value: IOMM-Lee

value: meningioma

value: K364T-mutated SMARCB1 overexpression


title: S4

description:
Library name: KO4339-1-5_S4
counts_Jan_2023.csv.gz

value: Brain

value: Microglia


title: S3

description:
Library name: KO4339-1-4_S3
counts_Jan_2023.csv.gz


title: S5

description:
Library name: KO4339-2-2_S5
counts_Jan_2023.csv.gz

value: lps


title: SMARCB1_MuT_1


title: SMARCB1_MuT_3


title: WT _Induced_Replicate_3

description:
Library name: SS-10423-1_6
MATa his3∆1 leu2∆ met15∆ ura3∆

value: WT


title: WT_hypha_H3K4me2_rep1


title: WT_H3K4me2_rep2


title: spt8△ _Induced_Replicate_1

description:
Library name: SS-10423-2_16
MATa his3∆1 leu2∆ met15∆ ura3∆ spt8∆::kanMX4


title: S8

description:
Library name: KO4339-2-5_S8
counts_Jan_2023.csv.gz

value: Total RNA


title: SMARCB1_WT_3

value: WT SMARCB1 overexpression


title: S6

description:
Library name: KO4339-2-3_S6
counts_Jan_2023.csv.gz


title: WT _Induced_Replicate_1

description:
Library name: SS-10423-1_4
MATa his3∆1 leu2∆ met15∆ ura3∆


title: S2

description:
Library name: KO4339-1-3_S2
counts_Jan_2023.csv.gz


title: S1

description:
Library name: KO4339-1-2_S1
counts_Jan_2023.csv.gz


title: WT_H3K4me2_rep1


title: dset1_H3K4me1


title: WT_Uninduced_Replicate_3

description:
Library name: SS-10423-1_3
MATa his3∆1 leu2∆ met15∆ ura3∆


title: SMARCB1_WT_1


title: WT_Uninduced_Replicate_2

description:
Library name: SS-10423-1_2
MATa his3∆1 leu2∆ met15∆ ura3∆


title: SMARCB1_WT_2


title: H3K4M H3WT, rep2

city: Boston

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

description: Library name: LK_WT_K4M_rep2

data_processing:
Sequenced reads were aligned against the mm10 reference genome using BWA. Alignments were filtered for uniquely mapped none-mitochondrial reads and duplicates were removed.
BigWig files were generated using deeptools with CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Bone marrow

growth_protocol: No in vitro culture was involved.

extract_protocol:
Tagmentated DNA was extracted with a phenol chloroform isoamyl alcohol method and resuspended with 1mM Tris-HCl 0.01mM EDTA.
CUT&Tag was performed as previously described in Kaya-Okur (2020). In brief, 100,000 bead-bound cells per sample were permeabilized and incubated with primary antibodies targeting the desired epitopes (anti-K4M (ReMAb Biosciences, 31-1250-00S, RM363), anti-H3K4me3 (Active motif, Cat No.39060), anti-H3K4me1 (LifeTech, 710795), anti-H3K27ac (Activ Motif, Cat No.39133), H3K27me3 (CST, C36B11, #9733). After incubation with secondary antibody (Guinea Pig anti-Rabbit IgG, antibodies online ABIN101961) to amplify local abundance of immunoglobulins, protein A/G-tethered transposase (pAG-Tn5, Epicypher) was added and bound in situ at target loci. After tagmentation and DNA clean-up, libraries were prepared by PCR amplification with barcoded Illumina-compatible primers. Tapestation 2200 analysis using High Sensitivity D5000 ScreenTape (Agilent) was performed to confirm successful library preparation before sequencing.

treatment_protocol: Mice harboring K-to-M mutation were induced with Doxycycline for 2 weeks and myeloid progenitor cells (Lineage-/cKit+/Sca1-) were sorted from bone marrow.

value: Bone marrow

value: Myeloid progenitors

value: Induce Dox for 2 weeks


title: active Crohn´s disease-10, 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: active Crohn's disease

value: infliximab


title: H3K4M H3WT, rep1

description: Library name: LK_WT_K4M_rep1


title: WT _Induced_Replicate_2

description:
Library name: SS-10423-1_5
MATa his3∆1 leu2∆ met15∆ ura3∆

value: Whole cells


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

value: basal


title: WT_hypha_H3K4me1_rep1

value: yeast cell

value: clinical isolate

value: YPD supplemented with 10% serum, 37℃, 30 min


title: SCLC_patient_4

city: Patras

first: Athanasios

middle: Nasir

last: Shaukat

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

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 analyzed using the smallRNA plugin of the Torrent Suite Software (v. 5.12)
The filtered miRNA counts were uploaded to 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: mirbase (build 20)
Supplementary files format and content: limma-voom ouput in xlsx format

source_name: plasma-derived exosomes (EV)

extract_protocol:
Exosomes were isolated using the EXO-Prep exosome precipitation kit (HansaBioMed Life Sciences, Tallinn, Estonia) according to the manufacturer’s instructions. The pelleted exosomes were resuspended directly into Trizol reagent (15596026, Invitrogen) with one 30-second pulse with LABSONIC M sonicator (Sartorius) to homogenize the solutions. Subsequently, the RNA was isolated according to the manufacturer’s instructions with one minor modification of addition of Linear Acrylamide (AM9520, Invitrogen) in the aqueous phase to a final concentration of 20μg/ml
Small RNA libraries were prepared with the Ion Total-RNA seq kit v2 (4479789, Ion Torrent) according to the manufacturer for small RNA libraries without enrichment (Rev. B.0)

value: plasma-derived exosomes (EV)

tag: disease state

value: SCLC


title: H3K4M H3K4M, rep2

description: Library name: LK_K4M_K4M_rep2


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

source_name: terminal ileum

value: terminal ileum


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


title: WT_H3K4me1_rep2

value: YPD


title: SCLC_patient_2


title: H3K4M H3K4M, rep1

description: Library name: LK_K4M_K4M_rep1


title: SCLC_patient_3


title: Serie3, RAW 264.7, 24h ML, ChIP H3K9me3, REP2

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description:
Library name: serie3_raw_ML_H3K9me3_rep2
Serie 3

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: WT

value: Abcam ab8898


title: WT_H3K4me1_rep1


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


title: WT_hypha_H3K4me1_rep2


title: dset1_hypha_15_rep1

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
Assembly: Candida albicans SC5314 (PRJNA10701)
Supplementary files format and content: total counts, total normalized_counts

source_name: hyphae

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA (MN, MN740955) according to the protocol of the manufacturer. For sequencing, mRNA was captured using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
A strand-specific sequencing libraries were synthesized using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (NEB, E7420) according to the instruction manual.

value: hyphae

value: YPD supplemented with 10% serum, 37℃, 15 min


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


title: Healthy_donor_1

value: normal


title: Serie3, RAW 264.7, DMSO, ChIP H3K9me3, REP2

description:
Library name: serie3_raw_ctrl_H3K9me3_rep2
Serie 3

value: DMSO


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

value: active Crohn's disease


title: Serie3, RAW 264.7, 24h ML, ChIP H3K9me3, REP1

description:
Library name: serie3_raw_ML_H3K9me3_rep1
Serie 3


title: dset1_hypha_rep3


title: WT_Uninduced_Replicate_1

description:
Library name: SS-10423-1_1
MATa his3∆1 leu2∆ met15∆ ura3∆


title: dset1_hypha_rep2


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


title: Marmoset, Mutant, 2

city: Tokyo

first: Maria

last: Harbers

address: 7-3-1 Hongo, Bunkyo-ku

department: Graduate School of Medicine

country: Japan

institute: The University of Tokyo

data_processing:
Low-quality (< 20 base pairs) and adapter sequences were trimmed using the Trimmomatic software (version 0.38)  with the following parameters: ILLUMINACLIP: path/to/adapter. fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were mapped to the reference genome (mCaljac.1.2.pat.X) using the RNA-seq aligner STAR software (Version 2.7.10a)
Assembly: mCaljac.1.2.pat.X
Supplementary files format and content: comma-separated values (csv) files including raw counts for each sample

organism: Callithrix jacchus

source_name: brain

extract_protocol:
Brain tissues were homogenized in a homogenizer with TRIzol reagent and incubated at room temperature for 5 minutes. Chloroform equivalent to 20% of Trizol solution was added to the homogenate, mixed, and left at room temperature for 3 minutes, then centrifuged at 12,000 x g for 10 minutes at 4°C to remove insoluble material (extracellular membrane, polysaccharides, and polymeric DNA). The supernatant was transferred to a new tube, mixed with an equal volume of 2-propanol, and centrifuged at 12,000 × g for 15 min at 4°C. The precipitate was rinsed with 70% ethanol and dissolved in TE buffer. The resulting total RNA was subjected to DNA degradation using DNase I.
Sequencing libraries from bulk tissues were prepared with NEBNext™ Poly(A) mRNA Magnetic Isolation Module and NEBNext™ UltraTM II Directional RNA Library Prep Kit.

value: brain

value: mutant


title: Serie3, RAW 264.7, DMSO, ChIP H3K9me3, REP1

description:
Library name: serie3_raw_ctrl_H3K9me3_rep1
Serie 3


title: Serie3, RAW 264.7, ChIP SUMO2/3, REP2

description:
Library name: serie3_raw_ctrl_SUMO2/3_rep2
Serie 3

value: Abcam ab3742


title: Marmoset, Mutant, 1


title: dset1_hypha_rep1


title: Serie3, RAW 264.7, ChIP SUMO2/3, REP1

description:
Library name: serie3_raw_ctrl_SUMO2/3_rep1
Serie 3


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

value: left colon

value: basal


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

value: infliximab


title: WT_hypha_rep3

value: clinical isolate

value: YPD supplemented with 10% serum, 37℃, 30 min


title: Marmoset, Control, 2

value: wild-type


title: Marmoset, Control, 1


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

value: terminal ileum


title: WT_hypha_15_rep1


title: Serie3, RAW 264.7, 24h ML, Input, REP1

description:
Library name: serie3_raw_ML_input_rep1
Serie 3

value: WT


title: Serie3, RAW 264.7, 24h ML, Input, REP2

description:
Library name: serie3_raw_ML_input_rep2
Serie 3


title: WT_hypha_rep2


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


title: WT_hypha_rep1


title: PC-4

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

description:
Library name: PC-4
column name in raw_counts_All samples.csv:PC-4

data_processing:
Raw RNAseq data were provided in FASTQ format. The quality of raw RNAseq reads was assessed using the FastQC program . High-quality reads were aligned to the mouse reference genome (NCBI Build 37) using Bowtie2  and Tophat  with default parameters and the Ensembl Gene transfer format (GTF) file. Gene expression levels were estimated in FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: mouse reference genome (NCBI Build 37)
Supplementary files format and content: csv file with FPKM for each samples

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, 15596018) followed by RNeasy Plus Mini Kit (Qiagen, 74136). Samples that passed RNA quality control were subjected to Ultra-Low Input RNAseq at GENWIZ.
Library was constructed using the Illumina Nextera XT kit and sequencing (2x150bp) was performed on the Illumina platform.

treatment_protocol: Skeletal muscle single cell suspension was incubated with PDGFRβ-APC (eBioscience, 17-1402-82), CD31-FITC (Biolegend, 103108), and CD45-FITC (eBioscience, 11-0451-85) for 30 minutes on ice. The cells were washed in ice-cold sorting buffer and resuspended in sorting buffer supplemented with DAPI. Next, the samples were filtered through a 40 µm cell strainer and run through a MoFlo Astrios EQ (Beckman Coulter) cell sorter. Single-color controls were used to perform compensation, and fluorescence-minus-one controls were used to set the gating boundaries. Pericytes and SMCs were gated as DAPIlowFITC-APC+tdTomato- and DAPIlowFITC-APC+tdTomato+ cells, respectively.

value: skeletal muscle

value: pericytes


title: PC-3

description:
Library name: PC-3
column name in raw_counts_All samples.csv:PC-3


title: Serie3, RAW 264.7, Input, REP2

description:
Library name: serie3_raw_ctrl_input_rep2
Serie 3


title: dset1_yeast_rep2

source_name: whole yeast

value: whole yeast

value: YPD


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


title: dset1_yeast_rep1


title: Serie3, RAW 264.7, Input, REP1

description:
Library name: serie3_raw_ctrl_input_rep1
Serie 3

value: DMSO


title: SCLC_patient_1

value: plasma-derived exosomes (EV)

value: SCLC


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

value: active Crohn's disease


title: PC-2

description:
Library name: PC-2
column name in raw_counts_All samples.csv:PC-2


title: PC-1

description:
Library name: PC-1
column name in raw_counts_All samples.csv:PC-1


title: Serie2, RAW 264.7, ChIP Morc3, REP2

description:
Library name: serie2_raw_ctrl_Morc3_rep2
Serie 2

value: no treatment


title: WT_yeast_rep2


title: Serie2, RAW 264.7, ChIP Morc3, REP1

description:
Library name: serie2_raw_ctrl_Morc3_rep1
Serie 2


title: SMC-4

description:
Library name: SMC-4
column name in raw_counts_All samples.csv:SMC-4

value: smooth muscle cells


title: WT_yeast_rep1


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


title: Serie2, RAW 264.7, Input, REP2

description:
Library name: serie2_raw_ctrl_input_rep2
Serie 2


title: Serie2, RAW 264.7, Input, REP1

description:
Library name: serie2_raw_ctrl_input_rep1
Serie 2


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

value: left colon


title: U-2 OS WT, baseline (parallel to 11j treatment) 0 hours, rep 3

city: Columbus

first: Jacob

middle: William

last: Smith

state: oh

address: 484 W 12th Ave

department: Chemistry and Biochemistry

institute: The Ohio State University

description: Library name: WT_NMDi_baseline_dT_BC1006_PB

data_processing:
Reads basecalled with Dorado v0.9.6
Reads demultiplexed through a custom pipeline to identify the barcode sequences.
Reads trimmed and aligned to reference genome (GRCh38.p14) using minimap2 with the 'splice' preset.
Genes assigned through custom script to pick the GRCh38.p14 genome annotation with the best overlap with the minimap2 alignment.
Genes with an alignment consisting of >80% matches to the genome were excluded to remove some errant alignments.
Genes counted per sample.
Assembly: GRCh38.p14
Supplementary files format and content: csv file includes raw counts for each sample

source_name: U-2 OS

growth_protocol: Grown in DMEM supplemented with 10% FBS, 100 units/mL penicillin/streptomycin, and 2mM L-glutamine at 37C with 100% humidity and 5% CO2

extract_protocol:
RNA isolated with TRIzol and chloroform, followed by purification with a spin-column kit (RNA Clean & Concentrator-5, Zymo Research #R1015).
polyA-RNA was reverse transcribed with poly-dT barcoded oligos and PCR amplified in the manner of SMARTer cDNA synthesis. This cDNA was multiplexed, cleaned, and prepared via the Oxford Nanopore Ligation Sequencing v14 kit.

treatment_protocol: Cells treated with DMSO-solubilized tunicamycin to 5µg/mL, DMSO-solubilized NMD inhibitor 11j to 0.5μM, blue light at 250 μW/cm2, or anti-XBP1 siRNA.

value: U-2 OS

value: epithelial ostersarcoma

value: baseline (parallel to 11j treatment)

tag: time

value: 0 hours

tag: biological replicate


title: SMC-3

description:
Library name: SMC-3
column name in raw_counts_All samples.csv:SMC-3


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

value: basal


title: H3K4M HSPCs

description: Library name: K4M_LSK

library_source: transcriptomic single cell

data_processing:
sequenced reads were aligned to the mm10 reference genome using CellRanger version 7.0.0.
The filtered reads assigned to cell barcodes were analyzed with the R package Seurat, version 5.1.0
All cells with fewer than 900 and more than 6,000 genes expressed were removed, as well as all genes expressed in fewer than 3 cells. Further, only cells with less than 10% percentage mitochondria expression were retained
The data was normalized using SCTransform (Hafemeister and Satija 2019), decomposed using PCA. Layers were integrated using Anchor-based CCA integration. UMAP (McInnes 2020)  embeddings were then computed using the first 20 dimensions as input.
Assembly: mm10
Supplementary files format and content: RDS objects with counts, and PCA and UMAP reductions

extract_protocol:
Cells (1000 cells/μl) were resuspended with PBS and were loaded into Chromium 10x system.
scRNA-seq libraries were generated from approximately 5000 cells per sample using Chromium 10x instrument with version 3.0 kit.

treatment_protocol: Competitive bone marrow transplanted mice harboring H3WT or H3K4M were induced with Doxycycline for 2 weeks and CD45.2+ HSPCs (lineage-/cKit+/Sca1+) and MyPs (lineage-/cKit+/Sca1-) were sorted from bone marrow.

value: Bone marrow

value: Hematopoietic stem and progenitor cells

value: Induce Dox for 2 weeks


title: U-2 OS WT, baseline (parallel to 11j treatment) 0 hours, rep 2

description: Library name: WT_NMDi_baseline_dT_BC1005_PB

value: WT


title: U-2 OS WT, 0.5µM SMG1 inhibitor 11j 2 hours, rep 3

description: Library name: WT_NMDi_2h_dT_BC1012_PB

value: 0.5µM SMG1 inhibitor 11j

value: 2 hours


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

value: terminal ileum

value: infliximab


title: SMC-1

description:
Library name: SMC-1
column name in raw_counts_All samples.csv:SMC-1

value: skeletal muscle


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

value: active Crohn's disease


title: H3K4M MyPs

description: Library name: K4M_LK

value: Myeloid progenitors


title: U-2 OS WT, 0.5µM SMG1 inhibitor 11j 2 hours, rep 2

description: Library name: WT_NMDi_2h_dT_BC1011_PB


title: H3WT HSPCs

description: Library name: WT_LSK


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

value: left colon


title: H3WT MyPs

description: Library name: WT_LK


title: U-2 OS WT, baseline (parallel to 11j treatment) 0 hours, rep 1

description: Library name: WT_NMDi_baseline_dT_BC1004_PB

value: U-2 OS


title: ATAC H3WT, rep2

data_processing:
Reads were aligned to the mm10 genome using BWA with default parameters for paired-end reads
BigWig files were generated using deeptools with CPM normalization
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
DNA was extracted using MiniElute Kit according to the manufacturer’s instructions.
ATAC-seq was performed as previously described (Buenrostro et al., 2013). 60,000 cells were washed once with 100μl PBS and resuspended in 50μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10min at 500 g at 4°C, followed by the addition of 50μl transposition reaction mix (25μl TD buffer, 2.5μl Tn5 Transposase and 22.5μl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MiniElute Kit (QIAGEN). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Integrity for libraries was checked on a TapeStation before sequencing.


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


title: U-2 OS WT, 0.5µM SMG1 inhibitor 11j 2 hours, rep 1

description: Library name: WT_NMDi_2h_dT_BC1010_PB

value: epithelial ostersarcoma


title: U-2 OS Opto-IRE1, blue light + siXBP1 24 hours, rep 3

description: Library name: Opto-IRE1_siXBP1_24hLight_dT_BC1006_PB

value: blue light + siXBP1

value: 24 hours


title: Sorted fibroblast from Vipr2-KO mice,PACAP,rep3

city: Jinan

first: Shi-chen

last: Fu

state: Shandong

address: No. 107 Wenhua West Road

department: Department of Gastroenterology

institute: Qilu Hospital of Shandong University

description: Library name: Sample12

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp. And the low quality reads were removed to obtain the clean reads.  FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2.
Assembly: The clean reads were mapped to the Mus musculus genome using HISAT2.
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: mouse colonic fibroblast

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: mouse colonic fibroblast

value: PACAP (100nM) in PBS


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

value: basal


title: Sorted fibroblast from Vipr2-KO mice,Vehicle,rep3

description: Library name: Sample9

value: vehicle (PBS)


title: Sorted fibroblast from Vipr2-KO mice,PACAP,rep1

description: Library name: Sample10


title: Sorted fibroblast from Vipr2-KO mice,PACAP,rep2

description: Library name: Sample11


title: SMC-2

description:
Library name: SMC-2
column name in raw_counts_All samples.csv:SMC-2

value: smooth muscle cells


title: ATAC H3WT, rep1

value: Bone marrow

value: Induce Dox for 2 weeks


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

value: terminal ileum


title: U-2 OS Opto-IRE1, blue light + siXBP1 24 hours, rep 2

description: Library name: Opto-IRE1_siXBP1_24hLight_dT_BC1005_PB


title: Sorted fibroblast from Vipr2-KO mice,Vehicle,rep2

description: Library name: Sample8


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

value: infliximab


title: ATAC H3K4M, rep2


title: U-2 OS Opto-IRE1, blue light + siXBP1 24 hours, rep 1

description: Library name: Opto-IRE1_siXBP1_24hLight_dT_BC1004_PB


title: ATAC H3K4M, rep1


title: U-2 OS Opto-IRE1, blue light + siXBP1 6 hours, rep 3

description: Library name: Opto-IRE1_siXBP1_6hLight_dT_BC1003_PB

value: 6 hours


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

value: active Crohn's disease


title: Sorted fibroblast from wild-typre mice,PACAP,rep3

description: Library name: Sample6

value: wild-type


title: ATAC H3K4M/K27M, rep2

value: Myeloid progenitors


title: Sorted fibroblast from wild-typre mice,PACAP,rep2

description: Library name: Sample5


title: U-2 OS Opto-IRE1, blue light + siXBP1 6 hours, rep 2

description: Library name: Opto-IRE1_siXBP1_6hLight_dT_BC1002_PB

value: U-2 OS


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


title: ATAC H3K4M/K27M, rep1


title: U-2 OS Opto-IRE1, blue light + siXBP1 6 hours, rep 1

description: Library name: Opto-IRE1_siXBP1_6hLight_dT_BC1001_PB

value: epithelial ostersarcoma


title: Sorted fibroblast from wild-typre mice,PACAP,rep1

description: Library name: Sample4


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


title: ATAC H3K27M, rep2


title: Sorted fibroblast from wild-typre mice,Vehicle,rep3

description: Library name: Sample3


title: U-2 OS Opto-IRE1, blue light + siXBP1 0 hours, rep 3

description: Library name: Opto-IRE1_siXBP1_baseline_dT_BC1009_PB

value: blue light + siXBP1

value: 0 hours


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


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

value: left colon


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


title: Sorted fibroblast from wild-typre mice,Vehicle,rep2

description: Library name: Sample2

value: mouse colonic fibroblast


title: Sorted fibroblast from Vipr2-KO mice,Vehicle,rep1

description: Library name: Sample7


title: ATAC H3K27M, rep1


title: U-2 OS Opto-IRE1, blue light + siXBP1 0 hours, rep 2

description: Library name: Opto-IRE1_siXBP1_baseline_dT_BC1008_PB


title: H3K4me3 H3WT, rep2

data_processing:
*library strategy: CUT&Tag
Sequenced reads were aligned against the mm10 reference genome using BWA. Alignments were filtered for uniquely mapped none-mitochondrial reads and duplicates were removed.
BigWig files were generated using deeptools with CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig


title: Sorted fibroblast from wild-typre mice,Vehicle,rep1

description: Library name: Sample1


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


title: Calm1N98S/N98S mouse_3

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

country: Taiwan

institute: National Taiwan University

description: Library name: Calm1N98S/N98S mouse RNASeq_3

data_processing:
Sequence reads were mapped to the mouse genome (mm10) with Hisat2,  allowing up to two mismatches. Sequence reads aligned to the mouse genome were imported into Partek Genomics Suite version 6.6 (Partek, St Louis, MO) for sequence read clustering, counting and annotation.
Assembly: mm10
Supplementary files format and content: FPKM data for all RefSeq transcripts in each sample (in .txt format)

source_name: heart

extract_protocol:
Total RNA was extracted from the left ventricular tissues of Calm1+/+, Calm1N98S/+ and Calm1N98S/N98S (N = 3 per genotype per group) with Trizol (Thermo Scientific)
Agilent RNA 6000 Nano Kit and Agilent 2100 bioanalyzer (Agilent Technologies) were utilized to assess the quality and integrity of the total RNA samples. Only RNA samples with an RNA integrity number of at least 8 were used for subsequent library construction and sequencing. Mouse left ventricular RNA (1 g total RNA for each sample) sequencing libraries were constructed using a SureSelect Strand-Specific RNA library prep kit (Agilent Technologies)

value: heart


title: U-2 OS Opto-IRE1, 5µg/mL tunicamycin 2 hours, rep 3

description: Library name: Opto-IRE1_2hTunicamycin_dT_BC1012_PB

value: 5µg/mL tunicamycin

value: 2 hours


title: H3K4me3 H3WT, rep1

value: Bone marrow


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

value: basal


title: H3K4me1 H3WT, rep2

value: Induce Dox for 2 weeks


title: U-2 OS Opto-IRE1, 5µg/mL tunicamycin 2 hours, rep 2

description: Library name: Opto-IRE1_2hTunicamycin_dT_BC1011_PB


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

value: infliximab


title: H3K4me1 H3WT, rep1


title: Calm1N98S/N98S mouse_1

description: Library name: Calm1N98S/N98S mouse RNASeq_1


title: U-2 OS Opto-IRE1, 5µg/mL tunicamycin 2 hours, rep 1

description: Library name: Opto-IRE1_2hTunicamycin_dT_BC1010_PB


title: H3K27me3 H3WT, rep2


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


title: Calm1N98S/+ mouse_3

description: Library name: Calm1N98S/+ mouse RNASeq_3


title: U-2 OS WT, 5µg/mL tunicamycin 2 hours, rep 3

description: Library name: WT_2hTunicamycin_dT_BC1009_PB

value: WT


title: U-2 OS WT, 5µg/mL tunicamycin 2 hours, rep 2

description: Library name: WT_2hTunicamycin_dT_BC1008_PB


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

value: terminal ileum

value: active Crohn's disease


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


title: H3K27ac H3WT, rep2

value: Myeloid progenitors


title: Calm1N98S/+ mouse_2

description: Library name: Calm1N98S/+ mouse RNASeq_2


title: Calm1N98S/+ mouse_1

description: Library name: Calm1N98S/+ mouse RNASeq_1


title: U-2 OS WT, 5µg/mL tunicamycin 2 hours, rep 1

description: Library name: WT_2hTunicamycin_dT_BC1007_PB

value: U-2 OS


title: U-2 OS Opto-IRE1, blue light + siXBP1 0 hours, rep 1

description: Library name: Opto-IRE1_siXBP1_baseline_dT_BC1007_PB

value: epithelial ostersarcoma


title: Calm1(+/+) mouse_3

description: Library name: WT Calm1 mouse RNASeq_3

value: wild type


title: U-2 OS Opto-IRE1, blue light 24 hours, rep 3

description: Library name: Opto-IRE1_24hLight_dT_BC1006_PB

value: blue light

value: 24 hours


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

value: left colon


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


title: H3K4me3 H3K4M, rep2


title: H3K27ac H3WT, rep1


title: Calm1(+/+) mouse_2

description: Library name: WT Calm1 mouse RNASeq_2

value: heart


title: Calm1N98S/N98S mouse_2

description: Library name: Calm1N98S/N98S mouse RNASeq_2


title: U-2 OS Opto-IRE1, blue light 24 hours, rep 2

description: Library name: Opto-IRE1_24hLight_dT_BC1005_PB


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


title: Calm1(+/+) mouse_1

description: Library name: WT Calm1 mouse RNASeq_1


title: U-2 OS Opto-IRE1, blue light 24 hours, rep 1

description: Library name: Opto-IRE1_24hLight_dT_BC1004_PB


title: H3K4me1 H3K4M, rep2


title: U-2 OS Opto-IRE1, blue light 2 hours, rep 3

description: Library name: Opto-IRE1_2hLight_dT_BC1003_PB


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

value: quiescent Crohn's disease


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


title: chx10cre_ptbp1_cko_scRNA

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

description:
Library name: chx10cre_ptbp1_cko
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

data_processing:
Single cell RNA-seq: Sequencing results were processed through the Cell Ranger 7.0.1 pipeline (10x Genomics) with default parameters. Seurat V4 was used to perform downstream analysis following the standard pipeline.
Assembly: mm10
Supplementary files format and content: Cell-by-gene count matrix for all the samples as csv
Supplementary files format and content: Metadata for the cell-by-gene count matrix as csv

source_name: Retina

extract_protocol:
Papain dissociation to prepare single cell suspension
scRNA-Seq following 10x Genomics 3' version 3.1 capture guideline

value: Retina

tag: age

value: 30 days

tag: library type

value: mRNA


title: H3K4me1 H3K4M, rep1

value: Bone marrow

value: Induce Dox for 2 weeks


title: chx10cre_scRNA

description:
Library name: chx10cre
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: H3K27me3 H3WT, rep1


title: U-2 OS Opto-IRE1, blue light 2 hours, rep 2

description: Library name: Opto-IRE1_2hLight_dT_BC1002_PB

value: 2 hours


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

value: terminal ileum

value: infliximab


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

value: basal


title: H3K27me3 H3K4M, rep2

value: Myeloid progenitors


title: H3K27me3 H3K4M, rep1


title: C2C12 myotubes stimulated with dexamethasone, treated with GW8510, rep2

city: Beijing

first: Yutong

last: Chen

address: 38 Xueyuan Road

institute: Peking University Health Science Center

description: Library name: SAMPLE 8

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Mouse C2C12 myoblast were cultured by dulbecco's modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution in an incubator 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were maintained with DMEM containing 2% horse serum (Solarbio, S9050) and replaced every 48 hours for 6 days. To induce muscle atrophy in vitro, C2C12 was stimulated with 10 μM dexamethasone (TargetMol, T1076) or 20 ng/ml TNFα (novoprotein, CF09) for 24 hours. Then, C2C12 was treated with DMSO or GW8510 (2 μM, dissolved in 0.1% DMSO) for another 24 hours.

value: Mouse myoblasts

value: WT

value: dexamethasone and GW8510


title: C2C12 myotubes stimulated with dexamethasone, treated with GW8510, rep3

description: Library name: SAMPLE 9


title: U-2 OS Opto-IRE1, blue light 6 hours, rep 3

description: Library name: Opto-IRE1_6hLight_dT_BC1012_PB

value: U-2 OS

value: epithelial ostersarcoma

value: blue light

value: 6 hours


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

value: left colon

value: quiescent Crohn's disease


title: U-2 OS Opto-IRE1, blue light 6 hours, rep 2

description: Library name: Opto-IRE1_6hLight_dT_BC1011_PB


title: H3K4me3 H3K4M, rep1


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


title: H3K27ac H3K4M, rep2


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


title: H3K27ac H3K4M, rep1


title: C2C12 myotubes stimulated with dexamethasone, treated with GW8510, rep1

description: Library name: SAMPLE 7


title: U-2 OS Opto-IRE1, blue light 6 hours, rep 1

description: Library name: Opto-IRE1_6hLight_dT_BC1010_PB


title: U-2 OS WT, blue light 6 hours, rep 3

description: Library name: WT_6hLight_dT_BC1009_PB


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


title: C2C12 myotubes stimulated with dexamethasone, rep2

description: Library name: SAMPLE 5

value: dexamethasone


title: H3K4me3 H3K27M, rep2

value: Bone marrow


title: C2C12 myotubes stimulated with dexamethasone, rep1

description: Library name: SAMPLE 4


title: H3K4me1 H3K27M, rep2

value: Induce Dox for 2 weeks


title: C2C12 myotubes, Control, rep3

description: Library name: SAMPLE 3

value: DMSO


title: U-2 OS WT, blue light 6 hours, rep 1

description: Library name: WT_6hLight_dT_BC1007_PB


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


title: U-2 OS WT, blue light 6 hours, rep 2

description: Library name: WT_6hLight_dT_BC1008_PB


title: U-2 OS Opto-IRE1, blue light 2 hours, rep 1

description: Library name: Opto-IRE1_2hLight_dT_BC1001_PB

value: 2 hours


title: C2C12 myotubes, Control, rep2

description: Library name: SAMPLE 2


title: H3K4me1 H3K27M, rep1


title: C2C12 myotubes, Control, rep1

description: Library name: SAMPLE 1


title: H3K27me3 H3K27M, rep2


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

value: terminal ileum

value: infliximab


title: U-2 OS Opto-IRE1, baseline 0 hours, rep 2

description: Library name: Opto-IRE1_baseline_dT_BC1005_PB

value: baseline

value: 0 hours


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

value: basal


title: C2C12 myotubes stimulated with dexamethasone, rep3

description: Library name: SAMPLE 6

value: Mouse myoblasts

value: WT


title: U-2 OS Opto-IRE1, baseline 0 hours, rep 1

description: Library name: Opto-IRE1_baseline_dT_BC1004_PB

value: U-2 OS

value: epithelial ostersarcoma


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


title: U-2 OS WT, baseline 0 hours, rep 3

description: Library name: WT_baseline_dT_BC1003_PB


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


title: mouse orthotopic tumor,Xevinapant treatment

first: Qiong

last: Wu

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

description:
Library name: Xevinapant-pool-RNA
10X Genomics

data_processing:
Principal component analysis was performed on the integrated data and a shared nearest neighbor (SNN) graph was constructed using the first 40 principal components. Clusters were identified using the by Louvain clustering implemented in FindClusters function at resolution=0.8. Uniform manifold approximation and projection (UMAP) was used to visualize gene expression and clusters. Differential expression analysis for each cluster was performed using FindAllMarkers function in Seurat with default settings. Clusters were further annotated by comparing differential genes with canonical markers. Gene signatures for each cluster were listed in Supplemental Table. For marker gene dot plot, gene-level average expression was calculated for each cluster and then Z-score normalized. Differential expression analysis was performed followed by gene set enrichment analysis (GSEA) that compared Xeivinapant vs. Vehicle mice within different cell type/subtype. Genes were ranked based on -log10(p-value)*(sign of log2(fold-change)) resulted from the differential analysis, with most up-regulated genes at the top and most down-regulated genes at the bottom. Pre-ranked GSEA was performed on gene rankings using R package fgsea , against Gene signatures from Hallmark, GO-biological processes and canonical pathways databases from MsigDB.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Single cell suspension was extracted from tumors using 10X Genomics Sample Preparation Kit (Cat#1000414) following the manufacture's instruction.
Sequencing reads were mapped against mm10 mouse transcriptome and processed for UMI counting using Cell Ranger (v3.0, 10X Genomics). Barcodes with UMI counts were imported to Seurat v4.0 for downstream analysis. Cells with less than 200 genes detected, with greater than 10% mitochondrial UMIs, or with complexity score (log10GenesPerUMI) less than 0.8 were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet, DoubletFinder, and scDblFinder, using 0.08% doublet rate for every 1,000 cells. Cells identified as doublets by more than one method were removed. Raw UMI counts were log normalized and the top 5,000 variable genes were detected in each sample separately. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring function. Individual mice samples were further integrated to remove batch effects using IntegrateData function in Seurat with anchor.features =8,000. Scaled z-scores for each gene were calculated using ScaleData regressing against total reads count, mitochondrial UMIs percentage, cell cycle phases, and log10GenesPerUMI.

value: tumor

value: mGSC

value: GBM stem cell

value: Xevinapant


title: mouse orthotopic tumor, vehicle treatment

description:
Library name: Vehicle-pool-RNA
10X Genomics

value: Vehicle


title: H3K4me3 H3K27M, rep1

value: Bone marrow

value: Myeloid progenitors

value: Induce Dox for 2 weeks


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

value: left colon

value: quiescent Crohn's disease


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

value: terminal ileum

value: infliximab


title: H3K27ac H3K27M, rep1


title: U-2 OS WT, baseline 0 hours, rep 2

description: Library name: WT_baseline_dT_BC1002_PB

value: baseline

value: 0 hours


title: H3K4me3 H3K4M/K27M, rep2


title: P-Mn/TI@mHSA2

city: Tianjin

first: Yi

last: Li

address: Nankai

institute: Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: MOT2

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus.GRCm38
Supplementary files format and content: Excel files include FPKM values for each Sample

extract_protocol:
Cell was collected, and total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: macrophage

value: therapy


title: U-2 OS WT, baseline 0 hours, rep 1

description: Library name: WT_baseline_dT_BC1001_PB

value: U-2 OS

value: epithelial ostersarcoma

value: WT


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

value: basal


title: H3K4me3 H3K4M/K27M, rep1


title: U-2 OS Opto-IRE1, baseline 0 hours, rep 3

description: Library name: Opto-IRE1_baseline_dT_BC1006_PB


title: TBP_spt8∆,TAF1-AA, with Rapamycin_Induced_Replicate 3

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

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)

value: Whole cells

value: TBP ( J.C. Reese)

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4 spt8[delta]::natMX4

value: Formaldehyde-fixed and sonicated


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

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


title: H3K27me3 H3K27M, rep1

extract_protocol:
Tagmentated DNA was extracted with a phenol chloroform isoamyl alcohol method and resuspended with 1mM Tris-HCl 0.01mM EDTA.
CUT&Tag was performed as previously described in Kaya-Okur (2020). In brief, 100,000 bead-bound cells per sample were permeabilized and incubated with primary antibodies targeting the desired epitopes (anti-K4M (ReMAb Biosciences, 31-1250-00S, RM363), anti-H3K4me3 (Active motif, Cat No.39060), anti-H3K4me1 (LifeTech, 710795), anti-H3K27ac (Activ Motif, Cat No.39133), H3K27me3 (CST, C36B11, #9733). After incubation with secondary antibody (Guinea Pig anti-Rabbit IgG, antibodies online ABIN101961) to amplify local abundance of immunoglobulins, protein A/G-tethered transposase (pAG-Tn5, Epicypher) was added and bound in situ at target loci. After tagmentation and DNA clean-up, libraries were prepared by PCR amplification with barcoded Illumina-compatible primers. Tapestation 2200 analysis using High Sensitivity D5000 ScreenTape (Agilent) was performed to confirm successful library preparation before sequencing.

value: Bone marrow

value: Myeloid progenitors

value: Induce Dox for 2 weeks


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

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))

value: left colon

value: quiescent Crohn's disease


title: H3K4me1 H3K4M/K27M, rep1


title: TBP_spt8∆,TAF1-AA, with Rapamycin_Induced_Replicate 2


title: H3K4me1 H3K4M/K27M, rep2


title: TBP_spt8∆,TAF1-AA, with  Rapamycin_Induced_Replicate 1


title: P-Mn@mHSA3

description: Library name: MO3


title: P-Mn@mHSA2

description: Library name: MO2


title: P-Mn@mHSA1

description: Library name: MO1


title: H3K27ac H3K27M, rep2


title: H3K27me3 H3K4M/K27M, rep2


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

value: terminal ileum

value: infliximab


title: P-Mn/TI@mHSA3

description: Library name: MOT3

value: macrophage


title: TBP_spt8∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 3


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


title: PBS3

description: Library name: M3

value: control


title: H3K27me3 H3K4M/K27M, rep1


title: PBS2

description: Library name: M2


title: TBP_spt8∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 2


title: TBP_spt8∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 1


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


title: H3K27ac H3K4M/K27M, rep1


title: PBS1

description: Library name: M1


title: P-Mn/TI@mHSA1

description: Library name: MOT1

value: therapy


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


title: TBP_spt3∆,TAF1-AA, with Rapamycin_Induced_Replicate 3

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4 spt3[delta]::natMX4


title: RNA H3WT, rep2

data_processing:
Transcriptome mapping was performed with STAR using the Ensembl annotation of the mm10 reference genome.
Read counts for individual genes were generated using HTSeq. Only genes with CPM > 1 for at least one sample were included in the analyses.
Assembly: mm10
Supplementary files format and content: Table with RPKM values for each sample

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen).
RNA-seq libraries were constructed from polyadenosine (polyA)-selected RNA using NEBNext Ultra Directional RNA library prep kit for Illumina (New England BioLabs). Libraries were amplified for 14 cycles. Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit. Libraries were quantified using the Kapa Biosystems Library Quantification kit (KK4828) and the BioRad CFX96 instrument. Each lane of sequencing was pooled with unique barcodes. Pooled libraries are also quantified using the Kapa Biosystems Library Quantification kit (KK4828) and the BioRad CFX96 instrument.


title: TBP_spt3∆,TAF1-AA, with Rapamycin_Induced_Replicate 2


title: RNA H3WT, rep1


title: TBP_spt3∆,TAF1-AA, with  Rapamycin_Induced_Replicate 1


title: RNA H3K4M, rep2


title: HBP1 CKO_24hrs post-cerulein_284 (Test)

city: PORTLAND

first: JUNGSUN

last: KIM

state: OR

address: KCRB 5001.51, 2720 SW Moody Ave

institute: Oregon Health & Science University

description:
Library name: Test_24h_284
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequincing data were processed using 10x Genomics Space Ranger to generate FASTQ files
Sequences were aligned to mm10 genome using Space Ranger default settings
Gene expression level of RefSeq coding genes were quantified using Space Ranger default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of genes ID
Supplementary files format and content: matrix.mtx.gz : gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue imag
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: cytassist_image.tiff: Cytassist image of tissue
Supplementary files format and content: aligned_tissue_image.jpg: aligned image of tissue
Supplementary files format and content: tissue_positions.csv : list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: pancreas

growth_protocol: mice in normal feeding

extract_protocol:
Collected pancreata were fixed with 4% PFA overnight, paraffinated, and mounted onto a glass slide as a four-μm section.
Spatial transcriptome sequuincing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Kit according to manufacturer's protocol

treatment_protocol: Pancreatitis was induced in 8–10-week-old mice via seven hourly intraperitoneal injections of 50 µg/kg cerulein, and pancreata were collected 24 hrs, 48 hrs, and 7 days after the last cerulein injection.

value: pancreas

value: Originally derived from C57BL/6J, backcrossed onto the C57Bl/6J background

value: p48Cre; HBP1flox/flox

value: 24hrs after cerulein


title: TBP_spt3∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 3

value: Whole cells

value: TBP ( J.C. Reese)


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


title: RNA H3K4M/K27M, rep2

value: Bone marrow


title: H3K27ac H3K4M/K27M, rep2

value: Myeloid progenitors


title: HBP1 CKO_24hrs post-cerulein_286 (Test)

description:
Library name: Test_24h_286
FFPE Spatial transcriptome sequencing


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

value: basal


title: TBP_spt3∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 2

value: Formaldehyde-fixed and sonicated


title: RNA H3K4M, rep1

value: Induce Dox for 2 weeks


title: RNA H3K4M/K27M, rep1


title: TBP_spt3∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 1


title: HBP1 WT_48hrs post-cerulein_274 (Control)

description:
Library name: Con_48h_274
FFPE Spatial transcriptome sequencing

value: 48hrs after cerulein


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

value: left colon

value: quiescent Crohn's disease

value: infliximab


title: HBP1 WT_24hrs post-cerulein_287 (Control)

description:
Library name: Con_24h_287
FFPE Spatial transcriptome sequencing


title: HBP1 WT_24hrs post-cerulein_256 (Control)

description:
Library name: Con_24h_256
FFPE Spatial transcriptome sequencing


title: RNA H3K27M, rep2


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

value: terminal ileum


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


title: MKO_5

city: Charlottesville

first: Anwaruddin

last: Mohammad

address: Pinn Hall

institute: University of Virginia

description:
Library name: 9_166_027_S62
counts.csv.gz

data_processing:
Sequencing quality was assessed using Fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next, the bioinformatic tool cutadap (Martin, 2011) was used to remove adapter sequences, trim low-quality bases, and filter short reads. Lastly, processed reads were mapped to the mouse reference genome (GRCm39) using STAR v2.6.1(Dobin et al., 2013) and reads that map onto each gene will be quantified using the featureCounts tool included in Subread software package (https://subread.sourceforge.net/). The generated count table was imported to R to perform differential gene expression (DEG) analysis using the DESeq2 package (Love, Huber, & Anders, 2014). Lowly expressed genes were filtered out, retaining genes with at least 15 counts in 14 or more samples to improve data robustness. Variance stabilizing transformation (VST) was applied to normalize the dataset for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: tsv

source_name: Brain

extract_protocol:
RNA was isolated from CD11b-positive microglial cells by using Direct-zol RNA Miniprep Plus (Product #: R2072; Zymo Research, USA) according to manufacturer’s instruction. The isolated RNA was immediately frozen at -80°C and sent to sequence
RNA-seq library preparation was performed using Poly(A) selection, where polyadenylated mRNA transcripts were selectively enriched and the sequencing was performed in the Illumina's NovaSeq platform with 30 million read pairs per sample.

value: Brain

value: Microglia

value: ko

value: Total RNA


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


title: HBP1 CKO_48hrs post-cerulein_285 (Test)

description:
Library name: Test_48h_285
FFPE Spatial transcriptome sequencing

value: pancreas

value: Originally derived from C57BL/6J, backcrossed onto the C57Bl/6J background

value: p48Cre; HBP1flox/flox


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


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


title: RNA H3K27M, rep1

value: Bone marrow


title: TBP_TAF1-AA, with Rapamycin_Induced_Replicate 2

first: SAKSHI

last: SINGH

address: 6 center drive , Bldg 6

institute: NIH

source_name: Whole cells

value: Whole cells

value: TBP ( J.C. Reese)

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4


title: MWT_4

description:
Library name: 8_178_015_S61
counts.csv.gz

value: wt


title: TBP_TAF1-AA, with Rapamycin_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


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


title: LCC9_4_OHT_5, m6A, direct RNA-seq

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Sequencing was performed on the MinION Mk1C (MC-112610) using a FLO-MIN106 flow cell with an SQK-RNA002 Kit (Oxford Nanopore Technologies). The specified run length was set to 75 h
Quality control (QC) of the raw sequence data was performed using FastQC
The sequence files were directly aligned to the Human transcriptome (Ensembl v107) using minimap2, generating alignment files in bam format
The fast5 and fastq files were indexed together using nanopolish for signal-level analysis and signal events were aligned to sequence data using nanopolish eventalign
The reads were analyzed for m6A modifications using m6Anet
Assembly: hg38
Supplementary files format and content: comma-delimited results from m6Anet

growth_protocol: MCF-7 and LCC9 BC cells were maintained in IMEM and supplemented with 10% FBS (MCF-7) or 5% FBS (LCC9) and 1% Pen/Strep with 5%CO2 ar 37C

extract_protocol:
PolyA+ mRNA was isolated according to manufacturer’s instructions using the Dynabeads mRNA Direct Purification Kit
Direct RNA libraries were prepped using the direct-RNA chemistry sequencing kit (SQK-RNA002)

treatment_protocol: All BC cells were serum starved in IMEM -Phenol Red-free medium, supplemented with 5% DCC-FBS and 1% PS for 72 h prior to treatment. Following 72 h incubation in SS media, the cells were treated with vehicle control (DMSO), or 100 nM 4-OHT for 24 h in SS media

value: TAM-resistant MCF-7 derivitive

value: WT


title: MKO_4

description:
Library name: 7_190_003_S60
counts.csv.gz


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

value: quiescent Crohn's disease

value: basal


title: MWT_3

description:
Library name: 6_107_086_S59
counts.csv.gz

value: Brain


title: LCC9_4_OHT_4, m6A, direct RNA-seq


title: TBP_TAF1-AA, w/o Rapamycin_Induced_Replicate 3

city: Rockville


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

value: left colon

value: infliximab


title: TBP_TAF1-AA, with Rapamycin_Induced_Replicate 3


title: LCC9_4_OHT_3, m6A, direct RNA-seq


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


title: TBP_TAF1-AA, w/o Rapamycin_Induced_Replicate 1


title: MKO_3

description:
Library name: 5_119_074_S58
counts.csv.gz

value: Microglia

value: ko

value: Total RNA


title: MKO_2

description:
Library name: 4_131_062_S57
counts.csv.gz


title: Taf1-AA_spt8∆,TAF1-AA, with Rapamycin_Induced_Replicate 3

value: Taf1 (J.C Reese)

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4 spt8[delta]::natMX4


title: MKO_1

description:
Library name: 2_143_050_S56
counts.csv.gz


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

value: terminal ileum


title: LCC9_4_OHT_1, m6A, direct RNA-seq


title: LCC9_DMSO_5, m6A, direct RNA-seq

value: DMSO (Control)


title: Taf1-AA_spt8∆,TAF1-AA, with Rapamycin_Induced_Replicate 2

value: Whole cells


title: FKO_5_rep1

description:
Library name: 20_104_089_S23
counts.csv.gz


title: LCC9_DMSO_4, m6A, direct RNA-seq


title: FKO_5

description:
Library name: 20_104_089_S72
counts.csv.gz


title: Taf1-AA_spt8∆,TAF1-AA, with  Rapamycin_Induced_Replicate 1


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


title: Taf1-AA_spt8∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 3


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


title: TBP_TAF1-AA, w/o Rapamycin_Induced_Replicate 2

value: TBP ( J.C. Reese)

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4


title: FWT_5_rep1

description:
Library name: 19_116_077_S22
counts.csv.gz

value: wt


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


title: LCC9_4_OHT_2, m6A, direct RNA-seq

value: TAM-resistant MCF-7 derivitive

value: WT


title: FWT_5

description:
Library name: 19_116_077_S71
counts.csv.gz


title: Taf1-AA_spt8∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: LCC9_DMSO_2, m6A, direct RNA-seq


title: FKO_4_rep1

description:
Library name: 18_128_065_S21
counts.csv.gz

value: Brain


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

value: quiescent Crohn's disease

value: basal


title: LCC9_DMSO_1, m6A, direct RNA-seq


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

value: infliximab


title: Taf1-AA_spt3∆,TAF1-AA, with Rapamycin_Induced_Replicate 3

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4 spt3[delta]::natMX4


title: Healthy control-10, left colon, infliximab

value: left colon

value: Healthy control


title: FKO_4

description:
Library name: 18_128_065_S70
counts.csv.gz

value: Microglia

value: ko

value: Total RNA


title: MCF_7_4_OHT_4, m6A, direct RNA-seq

value: Breast Cancer Luminal A subtype


title: Healthy control-10, left colon, basal


title: Taf1-AA_spt3∆,TAF1-AA, with Rapamycin_Induced_Replicate 2

value: Whole cells

value: Taf1 (J.C Reese)


title: MCF_7_4_OHT_5, m6A, direct RNA-seq


title: Healthy control-10, terminal ileum, infliximab

value: terminal ileum


title: MCF_7_4_OHT_3, m6A, direct RNA-seq


title: Taf1-AA_spt3∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 3


title: LCC9_DMSO_3, m6A, direct RNA-seq

value: TAM-resistant MCF-7 derivitive

value: DMSO (Control)


title: FKO_3

description:
Library name: 16_140_053_S69
counts.csv.gz


title: MCF_7_4_OHT_2, m6A, direct RNA-seq

value: WT


title: FWT_3_rep1

description:
Library name: 15_152_041_S19
counts.csv.gz

value: Brain

value: wt


title: Taf1-AA_spt3∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 2

value: Formaldehyde-fixed and sonicated


title: Taf1-AA_spt8∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 2

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4 spt8[delta]::natMX4


title: FKO_3_rep1

description:
Library name: 16_140_053_S20
counts.csv.gz


title: Healthy control-9, left colon, infliximab

value: infliximab


title: FKO_2

description:
Library name: 14_106_087_S67
counts.csv.gz


title: Healthy control-9, left colon, basal

value: left colon

value: basal


title: MCF_7_4_OHT_1, m6A, direct RNA-seq


title: Healthy control-9, terminal ileum, infliximab

value: Healthy control


title: MCF_7_DMSO_4, m6A, direct RNA-seq


title: FWT_3

description:
Library name: 15_152_041_S68
counts.csv.gz

value: Microglia


title: MCF_7_DMSO_5, m6A, direct RNA-seq


title: Taf1-AA_spt3∆,TAF1-AA, with  Rapamycin_Induced_Replicate 1

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4 spt3[delta]::natMX4


title: Taf1-AA_TAF1-AA, with Rapamycin_Induced_Replicate 3

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4


title: FWT_2

description:
Library name: 13_118_075_S66
counts.csv.gz

value: Total RNA


title: MCF_7_DMSO_3, m6A, direct RNA-seq

value: Breast Cancer Luminal A subtype


title: Taf1-AA_TAF1-AA, with Rapamycin_Induced_Replicate 2

value: Whole cells

value: Taf1 (J.C Reese)


title: FKO_1

description:
Library name: 12_130_063_S65
counts.csv.gz

value: ko


title: Taf1-AA_spt3∆,TAF1-AA, w/o Rapamycin_Induced_Replicate 1


title: Healthy control-9, terminal ileum, basal

value: terminal ileum


title: Healthy control-8, left colon, infliximab


title: Taf1-AA_TAF1-AA, w/o Rapamycin_Induced_Replicate 3


title: MCF_7_DMSO_2, m6A, direct RNA-seq

value: WT

value: DMSO (Control)


title: Healthy control-8, left colon, basal


title: Taf1-AA_TAF1-AA, w/o Rapamycin_Induced_Replicate 2

value: Formaldehyde-fixed and sonicated


title: MWT_1_rep1

description:
Library name: 1_155_038_S18
counts.csv.gz

value: Brain

value: wt


title: Healthy control-10, terminal ileum, basal


title: Healthy control-8, terminal ileum, infliximab

value: infliximab


title: Taf1-AA_TAF1-AA, w/o Rapamycin_Induced_Replicate 1


title: MWT_1

description:
Library name: 1_155_038_S55
counts.csv.gz


title: Healthy control-8, terminal ileum, basal

value: basal


title: FWT_1

description:
Library name: 11_142_051_S64
counts.csv.gz


title: MCF_7_DMSO_1, m6A, direct RNA-seq


title: Serie8, BlaER1 IFNAR_MORC3 Monocytes, ChIP SUMO2/3, REP2

description:
Library name: serie8_BlaER1_IFNAR_MORC3_mono_SUMO2/3_rep2
Serie 8

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

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

value: Abcam ab3742


title: Serie8, BlaER1 IFNAR_MORC3 Monocytes, ChIP SUMO2/3, REP1

description:
Library name: serie8_BlaER1_IFNAR_MORC3_mono_SUMO2/3_rep1
Serie 8


title: Taf1_gcn4∆_Induced_Replicate 3

value: MATa his3[delta]1 leu2[delta] met15[delta] ura3[delta] gcn4[delta]::kanMX4


title: Taf1_gcn4∆_Induced_Replicate 2


title: Taf1-AA_TAF1-AA, with Rapamycin_Induced_Replicate 1

value: MATa his3-[delta]1 leu2-[delta]0 met15-[delta]0 ura3-[delta]0 fpr1[delta]::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 TAF1-FRB ::hphMX4


title: MWT_5

description:
Library name: 10_154_039_S63
counts.csv.gz

value: Microglia

value: Total RNA


title: Healthy control-7, left colon, basal

value: left colon

value: Healthy control


title: Serie8, BlaER1 IFNAR_MORC3 Monocytes, Input, REP2

description:
Library name: serie8_BlaER1_IFNAR_MORC3_mono_input_rep2
Serie 8


title: Healthy control-7, left colon, infliximab


title: Healthy control-7, terminal ileum, infliximab


title: Taf1_gcn5∆_Induced_Replicate 3

value: Whole cells

value: Taf1 (J.C Reese)

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


title: G4

city: Shaanxi

first: Yilin

last: Zhang

address: 8P8R+27G, Shiji Blvd, Qindu District, Xianyang, Shaanxi, China

institute: Shaanxi University of Chinese Medicine

description: Library name: sample14

data_processing:
Filtering: Reads containing adapters, reads with over 10% unknown nucleotides (N), and low-quality reads (with more than 50% bases having Q-value ≤ 20) were removed using fastp (version 0.18.0).  rRNA Removal: Bowtie2 (version 2.2.8) was used to map reads to the ribosome RNA (rRNA) database, and rRNA-mapped reads were removed.  Alignment with Reference Genome: Clean reads were aligned to a reference genome using HISAT2.  Gene Abundance Quantification: Gene expression was quantified using StringTie (v1.3.1) and RSEM for calculating FPKM and TPM values.
Assembly: Reference genome details are not provided explicitly in the document, but the alignment was done using HISAT2 with a reference genome index.
Supplementary files format and content: The processed data likely includes FPKM and TPM values calculated for gene expression and variations across samples. The exact file formats (e.g., FASTQ, BAM) are not specified but may include sequencing data and gene expression quantification files.

source_name: colon

extract_protocol:
RNA Extraction: Total RNA was extracted using the Trizol reagent kit (Invitrogen, Carlsbad, CA, USA). The RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and RNase free agarose gel electrophoresis.  mRNA Enrichment: Eukaryotic mRNA was enriched using Oligo(dT) beads for eukaryotic samples or Ribo-ZeroTMMagnetic Kit (Epicentre, Madison, WI, USA) for prokaryotic samples.  Fragmentation and cDNA Synthesis: mRNA was fragmented and reversed transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530, New England Biolabs, Ipswich, MA, USA).  Library Construction and Sequencing: The cDNA was end repaired, an A base was added, and Illumina sequencing adapters were ligated. The library was then amplified by PCR and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
The cDNA fragments were purified using AMPure XP Beads (1.0X), end-repaired, A-tailed, and ligated with Illumina adapters.  The final library was amplified by PCR.

value: colon

value: C57BL/6 mouse colon tissue

value: Colon epithelial cells

value: WT

value: WMW-H


title: Taf1_gcn4∆_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: Serie8, BlaER1 IFNAR_MORC3 Monocytes, Input, REP1

description:
Library name: serie8_BlaER1_IFNAR_MORC3_mono_input_rep1
Serie 8

value: no treatment


title: Serie11, THP1, TAK, ChIP MORC3, REP2

description: Library name: THP1_TAK_MORC3_rep2

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 were generated with Deeptools BamCoverage with CPM normalization
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: THP1 human monocytes and were maintained in suspension at approximately 106 cells per ml in RPMI+Glutamax (GIBCO) supplemented with 10% FBS, penicillin/streptomycin, 25 mM HEPES, 1 mM sodium pyruvate and 2-mercaptoethanol. For THP1 macrophage differentiation, cells were treated with Phorbol 12-myristate 13-acetate (PMA, abcam) to a final concentration of 50 nM. When indicated, cells were treated with DMSO or TAK-981 to a final concentration of 500nM.

treatment_protocol: PMA 50nM TAK-981 500nM

value: PMA 50nM, TAK 500nM


title: G5

description: Library name: sample15


title: G3

description: Library name: sample13


title: Serie11, THP1, TAK, ChIP MORC3, REP1

description: Library name: THP1_TAK_MORC3_rep1


title: Healthy control-7, terminal ileum, basal

first: Ana

last: Aransay

address: Parque tecnologico de Bizkaia, Building 801-A

institute: CIC bioGUNE

value: terminal ileum

value: basal


title: Healthy control-6, left colon, infliximab

value: infliximab


title: G2

description: Library name: sample12


title: Taf1_gcn5∆_Induced_Replicate 2


title: Serie11, THP1, DMSO, ChIP MORC3, REP2

description: Library name: THP1_ctrl_MORC3_rep2

value: PMA 50nM, DMSO


title: G1

description: Library name: sample11


title: Taf1_gcn5∆_Induced_Replicate 1


title: Healthy control-6, left colon, basal

value: left colon


title: M5

description: Library name: sample10

value: AOM/DSS


title: Serie11, THP1, DMSO, ChIP MORC3, REP1

description: Library name: THP1_ctrl_MORC3_rep1


title: Healthy control-6, terminal ileum, infliximab

value: Healthy control


title: Taf1_spt8∆_Induced_Replicate 3

value: Whole cells

value: Taf1 (J.C Reese)

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


title: Serie11, THP1, TAK, Input, REP2

description: Library name: THP1_TAK_input_rep2


title: Healthy control-6, terminal ileum, basal


title: M4

description: Library name: sample9

value: colon

value: C57BL/6 mouse colon tissue


title: Serie11, THP1, TAK, Input, REP1

description: Library name: THP1_TAK_input_rep1

value: WT


title: Taf1_spt8∆_Induced_Replicate 2


title: M3

description: Library name: sample8

value: Colon epithelial cells


title: Taf1_spt8∆_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: Healthy control-5, left colon, infliximab


title: Taf1_spt3∆_Induced_Replicate 3

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


title: Healthy control-5, left colon, basal


title: Serie11, THP1, DMSO, Input, REP2

description: Library name: THP1_ctrl_input_rep2


title: Taf1_spt3∆_Induced_Replicate 2


title: BlaER1, IFNAR MORC3, DMSO, REP3

description: Library name: IFNAR_MORC3_DMSO_REP3

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

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-/- MORC3-/-

value: DMSO


title: K5

description: Library name: sample5

value: Control


title: Healthy control-5, terminal ileum, infliximab

value: terminal ileum

value: infliximab


title: M1

description: Library name: sample6


title: K4

description: Library name: sample4


title: Taf1_spt3∆_Induced_Replicate 1


title: Serie11, THP1, DMSO, Input, REP1

description: Library name: THP1_ctrl_input_rep1

value: PMA 50nM, DMSO


title: Taf1_WT_Induced_Replicate 3

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


title: K3

description: Library name: sample3


title: Healthy control-4, left colon, infliximab

value: left colon

value: Healthy control


title: Healthy control-5, terminal ileum, basal

value: basal


title: Taf1_WT_Induced_Replicate 2

value: Whole cells

value: Taf1 (J.C Reese)


title: BlaER1, IFNAR MORC3, DMSO, REP1

description: Library name: IFNAR_MORC3_DMSO_REP1


title: Healthy control-4, left colon, basal


title: BlaER1, IFNAR, TAK, REP3

description: Library name: IFNAR_TAK_REP3

value: IFNAR-/-

value: TAK (100nM)


title: K2

description: Library name: sample2

value: colon

value: C57BL/6 mouse colon tissue

value: Colon epithelial cells

value: WT


title: Taf1_WT_Induced_Replicate 1

value: Formaldehyde-fixed and sonicated


title: Healthy control-4, terminal ileum, basal


title: BlaER1, IFNAR, TAK, REP2

description: Library name: IFNAR_TAK_REP2


title: K1

description: Library name: sample1

value: Control


title: M2

description: Library name: sample7

value: AOM/DSS