title: genome-wide sgl silencer-seq, rep1

description:
screen
36bp

data_processing:
Paired-end sequencing reads were aligned to the D. melanogaster reference genome BDGP R5/dm3 using Bowtie (version 1.2.2, (Langmead et al., 2009)) allowing 3 mismatches with the options: “‐v 3 ‐m 1 –best –strata –X 2000”. Mapped read pairs were collapsed by coordinates (start, end, strand) and by unique molecular identifiers (UMI) to distinguish PCR duplicates from reads originating from distinct RNA molecules with identical sequence. Fragments with identical coordinates were considered as duplicates if their UMIs differed by < 3 out of the 10 nucleotides. Genome coverage per sample was calculated using genomeCoverageBed from bedtools (version 2.27.1, Quinlan and Hall, 2010). BigWig files were created using the wigToBigWig utility from KentUtils (Kent et al., 2010).
To identify silencer-seq depleted regions in the genome (“dips” instead of peaks), first position-specific coverage for each sample and each strand were calculated separately using the coverage() function of the GenomicRanges R package (version 1.34.0, (Lawrence et al., 2013)). Afterwards, the log2 fold change and hypergeometric p‐value between coverage in experiment and input samples were determined. Loci with log2 fold change ≤ (-1.58) – corresponding to a 3-fold depletion over input – and hypergeometric p‐value ≤ 0.001 were collapsed into continuous depleted regions using the reduce() function.
genome build/assembly: BDGP R5/dm3
processed data files format and content: genomic coverage of silencer-seq screen or input samples in bigWig format
processed data files format and content: silencer-seq dip calls as tsv files containing genomic regions of significant coverage depletion relative to input (collapsed regions with ≥ 3-fold depletion and hypergeometric p‐value ≤ 0.001)

value: cells electroporated with genome-wide sgl silencer-seq library


title: genome-wide sgl silencer-seq, rep2

status: Public on Nov 19 2024

type: SRA

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

description:
screen
36bp

library_source: other

molecule: other

organism: Drosophila melanogaster

source_name: Schneider S2

growth_protocol: D. melanogaster Schneider S2 cells were cultured in Schneider’s Medium (Gibco, cat. no. 21720-024) supplemented with 10% heat-inactivated fetal bovine serum (Sigma-Aldrich, cat. no. F7524) at 27°C and 0.4% CO2.

extract_protocol:
Total RNA was isolated after cell lysis (Qiagen Tissue Ruptor) using the Qiagen RNeasy Maxi Kit. The entire total RNA samples were subjected to mRNA isolation by Dynabeads Oligo-dT25 beads (Invitrogen).
UMI-STARR-Seq libraries were UMI-tagged and prepared for NGS as previously described (Arnold et al., 2013, Neumayr et al., 2019).

treatment_protocol:
The sugarless (sgl) or hamlet (ham) S2 cell developmental enhancer (Zabidi et al., 2015) as 599bp sequences was introduced directly upstream of the Drosophila synthetic core promoter (DSCP) in the original STARR-seq vector (pSTARR-seq_fly Addgene #71499, Arnold et al., 2013) to obtain two different silencer-seq vectors.
A D. melanogaster genome-wide silencer-seq library in the sgl enhancer vector and two focused silencer-seq libraries (containing approximately 10Mb D. melanogaster genomic DNA from bacterial artificial chromosomes (BACs) covering ≈6% of the genome) in the sgl and ham vectors were produced by cloning roughly 500-800bp sheared genomic DNA or BAC fragments downstream of the reporter open reading frame, as described previously (Arnold et al., 2013).
For genome-wide and BAC-scale silencer-seq screens, the libraries were electroporated (MaxCyte STX Scalable Transfection System, 0.1ug DNA per one million cells) into exponentially growing S2 cells (80-90% confluency) in two biological replicates (200 million cells per BAC library replicate; 800-1600 million cells per genome-wide library replicate) after one cell washing step in a 1:1 mix of HyClone MaxCyte Electroporation Buffer with Schneider’s Medium (with no supplements).
Twenty-four hours after library transfection, cells were havested and the samples processed like regular UMI-STARR-seq (Arnold et al., 2013, Neumayr et al., 2019).

tag: cell line

value: Schneider S2

tag: fraction

value: screen

tag: treatment


title: CG11247 (Saft) ChIP-seq, cl.1, rep1, input

library_source: genomic

data_processing:
Reads from S2 cell ChIP-seq experiments were trimmed to a uniform length of 36 nucleotides, applying a standard quality setting (-Q33) using TrimGalore (version 0.6.2, (Krueger, n.d.)) and FASTX-Toolkit (version 0.0.14, (Hannon, 2010)). Trimmed reads were then aligned to the D. melanogaster reference genome BDGP R5/dm3 using Bowtie (version 1.2.2, (Langmead et al., 2009)). Following alignment, the read counts were normalized on a per million basis and bigwig files were generated with an extended read length setting of 150 nucleotides using bedtools (version 2.27.1, (Quinlan and Hall, 2010)).
Peak calling was performed with MACS2 (version 2.1.2.1, (Zhang et al., 2008)) separately in both replicates and per clonal cell line.
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage in FLAG-ChIP or input samples (either separately for each replicate or both replicates merged in one file) in bigWig format
Supplementary files format and content: narrowPeak files of MACS2 called peaks for each replicate

molecule: genomic DNA

extract_protocol:
For each sample and replicate, 50 million 80-90% confluent S2 cells were harvested, washed with PBS, cross-linked in 1% formaldehyde at room temperature for 10 min and quenched with 125mM glycine. For nuclei isolation, cells were incubated in cell lysis buffer (50mM Tris pH8, 2mM EDTA, 0.5% NP-40, 10% glycerol, cOmplete Protease Inhibitor Cocktail (Roche)) for 10min at 4°C. After pelleting, nuclei were lysed in 50mM Tris pH8, 10mM EDTA, 1% SDS and cOmplete Protease Inhibitor Cocktail (Roche) for 15min. Chromatin fragments between 200-1000bp were obtained through sonication (E220 Focused-ultrasonicator, Covaris). Chromatin from approximately 30 million cells was immunoprecipitated overnight at 4°C with the anti-FLAG M2 (Merck, F1804) antibody. Antibody-bound chromatin was loaded on 40ul magnetic Dynabeads (1:1 mix of Protein G and A beads, Invitrogen) for 1h 4°C, washed twice in low-salt, high-salt, LiCl and TE buffer and eluted with 1% SDS, 100mM NaHCO3, 5mM DTT in water. Subsequently, samples were decrosslinked overnight at 65°C and treated with RNase A and proteinase K.
DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo Research), according to manufacturer’s instructions. Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

treatment_protocol:
The endogenous CG7372/Phaser or CG11247/Saft ORF was homozygously tagged with a FLAG-AID peptide in OsTir1 S2 cells as previously described (Hendy et al., 2022; Serebreni et al., 2023).
cells were left untreated (i.e. no protein depletion)

tag: genotype

value: OsTir1, Saft_FLAG-AID

tag: clone

value: 9C (clone 1)

tag: chip antibody


title: CG11247 (Saft)-AID MNase-seq, untreated, rep1

data_processing:
Reads of the MNase-seq experiments were trimmed to a uniform length of 36 nucleotides, applying a standard quality setting (-Q33) using TrimGalore (version 0.6.2, (Krueger)) and FASTX-Toolkit (version 0.0.14, (Hannon, 2010)). Trimmed reads were then aligned to the D. melanogaster reference genome BDGP R5/dm3 using Bowtie (version 1.2.2, (Langmead et al., 2009)). Following alignment, the read counts were normalized on a per million basis and bigwig files were generated with an extended read length setting of 150 nucleotides using bedtools (version 2.27.1, (Quinlan and Hall, 2010)).
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage per replicate and condition in bigWig format
Supplementary files format and content: genomic coverage of merged replicates per condition in bigWig format

extract_protocol:
MNase-seq in the Saft-AID cell line was performed as described previously (Hendy et al., 2022) in two biological replicates, starting with 50 million cells per sample and condition and using 1% (instead of 0.75%) NP-40 for nuclei permeabilization. The MNase reaction with 0.1 units of micrococcal nuclease (Merck) per sample was carried out for 25 minutes at 37°C, carefully vortexing samples every 5 min. Digested DNA was purified and size-selected as described previously (Hendy et al., 2022).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

treatment_protocol:
The endogenous CG11247/Saft ORF was homozygously tagged with a FLAG-AID peptide in OsTir1 S2 cells as previously described (Hendy et al., 2022; Serebreni et al., 2023).
Cells were left untreated (i.e. no protein depletion) or treated with auxin (indole-3-acetic acid, IAA) for 48h to deplete the AID-tagged CG11247/Saft protein

value: mock


title: CG11247 (Saft)-AID RNA-seq S2, 24h auxin, rep1

description:
75bp
CG9C_raw_counts.tsv

library_source: transcriptomic

data_processing:
Reads of the Schneider S2 cell Saft-AID RNA-seq experiment were processed and aligned to the D. melanogaster reference genome BDGP R5/dm3 using the nf-core/slamseq pipeline (version 1.0.0, (Neumann et al., 2019; Ewels et al., 2020)) with options '--quantseq 1 --multimappers 1’.
genome build/assembly: BDGP R5/dm3
processed data files format and content: tab-delimited text files with raw counts for all samples per tissue or cell line

molecule: total RNA

extract_protocol:
Following auxin-mediated Saft protein depletion for the specified durations, 2 million cells were harvested per sample by centrifugation at 300 g for 5 min and washed once with PBS. Total RNA was isolated and DNase I treated after cell lysis with the RNA isolation kit provided by the VBC core facilities, which uses a lysis step based on guanidine thiocyanate (adapted from (Boom et al., 1990)) and SpeedBeads magnetic carboxylate modified particles (Merck) and eluted in 50ul water.
cDNA libraries from 500ng total RNA were prepared with the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer's protocol.

treatment_protocol: The endogenous CG11247/Saft ORF was homozygously tagged with a FLAG-AID peptide in OsTir1 S2 cells as previously described (Hendy et al., 2022; Serebreni et al., 2023). Cells were treated with 500µM auxin (indole-3-acetic acid, IAA) for 24h or 48h or left untreated (solvent only). Cells were treated with 500µM auxin (indole-3-acetic acid, IAA) for 24h or 48h or left untreated (solvent only).

value: 24h auxin (IAA)


title: CG11247 (Saft) ChIP-seq, cl.1, rep1

value: FLAG M2 (Merck, F1804)


title: CG11247 (Saft)-AID RNA-seq S2, 48h auxin, rep1

description:
75bp
CG9C_raw_counts.tsv

value: 48h auxin (IAA)


title: CG11247 (Saft)-AID RNA-seq S2, untreated, rep1

description:
75bp
CG9C_raw_counts.tsv


title: CG11247 (Saft)-AID MNase-seq, 48h auxin, rep2


title: CG11247 (Saft)-AID RNA-seq S2, 24h auxin, rep2

description:
75bp
CG9C_raw_counts.tsv


title: CG11247 (Saft)-AID MNase-seq, 48h auxin, rep1


title: genome-wide sgl silencer-seq, input

description:
input
36bp

value: input

value: PCR amplified inserts of genome-wide sgl silencer-seq library


title: CG11247 (Saft)-AID MNase-seq, untreated, rep2


title: CG11247 (Saft) ChIP-seq, cl.1, rep2


title: CG7372 (Phaser) ChIP-seq, rep2

value: OsTir1, Phaser_FLAG-AID


title: CG11247 (Saft) ChIP-seq, cl.2, rep2, input

value: 4H (clone 2)


title: CG11247 (Saft) ChIP-seq, cl.2, rep2


title: CG11247 (Saft) ChIP-seq, cl.1, rep2, input


title: CG7372 (Phaser) ChIP-seq, rep1


title: CG11247 (Saft) ChIP-seq, cl.2, rep1


title: CID006584-1-reup

city: Oxford

first: Tom

last: Thomas

address: Old Road Campus, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic single cell

data_processing:
Cell Ranger v3.1.0 was used to align reads to reference (GRCh38-3.0.0) and generate feature- barcode matrices from the Chromium single-cell RNA-seq output.
Assembly: GRCh38-3.0.0
Supplementary files format and content: We have provided filtered matrices containing the outputs of the Cell Ranger pipeline in .h5 format for each sample as outlined above.

organism: Homo sapiens

source_name: gut

extract_protocol:
Gut and synovial tissue samples and PBMCs were thawed into warm IMDM media with 10% FBS and washed. Gut samples were EDTA-treated pre-digestion with rotation for 15 min to remove dead/damaged epithelial cells, and then dissociated enzymatically with Liberase TM and DNase into a single-cell suspension with rotation. Thawed synovial samples were digested in Liberase TL and DNase in warm media for 30 min, with agitation. All cell samples were strained and washed twice with PBS with 0.4% bovine serum albumin (BSA). Live cells were counted using acridine orange/propidium iodide and ≤ 10,000 cells were loaded per 10X Chromium channel.
The GEX 3’ V3 protocol was followed.

tag: tissue

value: gut

tag: librarytype

value: 3 prime v3.1

tag: cellsloaded

tag: disease

value: UC

tag: disease duration

tag: patient

tag: site

value: Rectum

tag: inflammation

value: Inflamed

value: Pre

tag: age

tag: Sex

value: F

tag: ethnicity

value: Caucasian

tag: match

value: No

tag: batch

tag: inflammation score


title: CID006581-1-reup

tag: treatment


title: CID006579-1-reup


title: CID006583-1-reup


title: CG7372 (Phaser) ChIP-seq, rep1, input

tag: cell line

value: Schneider S2

tag: genotype

tag: clone


title: BAC STARR-seq, ctrl, RpS12, input

description:
36bp
DSCP_merged_RpS12_BAC32_input.bw

data_processing:
Paired-end sequencing reads were aligned to the D. melanogaster reference genome BDGP R5/dm3 and the artificial D. pseudoobscura BAC region genome using Bowtie (version 1.2.2, (Langmead et al., 2009)) allowing 3 mismatches with the options: “‐v 3 ‐m 1 –best –strata –X 2000”. Mapped read pairs were collapsed by coordinates (start, end, strand) and by unique molecular identifiers (UMI) to distinguish PCR duplicates from reads originating from distinct RNA molecules with identical sequence. Fragments with identical coordinates were considered as duplicates if their UMIs differed by < 3 out of the 10 nucleotides. Genome coverage per sample was calculated using genomeCoverageBed from bedtools (version 2.27.1, Quinlan and Hall, 2010). BigWig files were created using the wigToBigWig utility from KentUtils (Kent et al., 2010).
For spike-in normalization of sample reads, a scaling factor per sample (BAC STARR-seq, ctrl, rep1 = 1.409819401; BAC STARR-seq, ctrl, rep2 = 1.667366961; BAC STARR-seq, DLM3, rep1 = 0.779454999; BAC STARR-seq, DLM3, rep2 = 0.848202481) was calculated by normalizing the ratio of total unique spike-in reads to total unique sample reads by the minimum ratio among all samples and adjusting for sample library size.
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage of STARR-seq input and spike-in normalized screen samples in bigWig format
Library strategy: STARR-seq

treatment_protocol:
The spz4 DLM3 silencer (530bp sequence) was cloned into the two original DSCP and RpS12 STARR-seq vectors (pSTARR-seq_fly Addgene #71499 and pSTARR-seq_fly-RpS12 Addgene #71504) downstream of the reporter polyA site (using PciI).
Focused STARR-seq libraries from 500-800bp BAC fragments (covering approximately 8Mb or 5% of the D. melanogaster genome) were created in the pSTARR-seq-DSCP-DLM3 and pSTARR-seq-RpS12-DLM3 vectors, as well as in the two corresponding original STARR-seq plasmids without the silencer (Addgene #71499 and #71504), as described previously (Arnold et al., 2013). Additionally, two focused spike-in libraries were derived by cloning sheared BACs containing D. pseudoobscura genomic sequences into the DSCP and RpS12 STARR-seq vectors.
For each condition (+/– silencer) and replicate, 20ug of focused pre-mixed STARR-seq libraries (equimolar dm3 BAC DSCP/RpS12  library mix spiked with 1% equimolar dp3 BAC DSCP/RpS12 library mix) were electroporated into 200 million exponentially growing S2 cells (80-90% confluency; MaxCyte STX Scalable Transfection System) after one cell washing step in a 1:1 mix of HyClone MaxCyte Electroporation Buffer with Schneider’s Medium (with no supplements).
Twenty-four hours after library transfection, cells were havested and the samples processed like regular UMI-STARR-seq (Arnold et al., 2013, Neumayr et al., 2019).

tag: fraction

tag: core promoter

value: PCR amplified inserts of input library


title: CID006577-1-reup

tag: tissue

tag: librarytype

tag: cellsloaded

tag: disease

value: M

value: Yes


title: CG7372 (Phaser) ChIP-seq, rep2, input

tag: chip antibody


title: CID006576-1-reup

value: CD

tag: disease duration

tag: patient

tag: site

tag: inflammation

value: Post

tag: age


title: CID006580-1-reup

tag: Sex

tag: ethnicity

tag: match

tag: batch

tag: inflammation score


title: CID006571-1-reup

tag: treatment


title: CID006582-1-reup


title: CID006568-1-reup


title: CID006567-1-reup


title: CID006566-1-reup


title: CID006575-1-reup


title: CID006562-1-reup


title: UCSF IDH-mutant astrocytoma #201 initial

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

country: USA

institute: Stanford University School of Medicine

description: IDH-mutant astrocytoma tumor

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: Astrocytoma, IDH-mutant

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using disposable biopsy punches.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients. 14 tumors were from the initial diagnostic surgical procedure prior to any radiation or chemotherapy treatment, and 17 tumors were from a subsequent surgery for recurrence/progressive disease usually following radiation and/or chemotherapy.

tag: tumor status

value: paired

tag: tumor category

value: initial


title: CID006558-1-reup

tag: tissue

value: gut

tag: librarytype


title: CID006573-1-reup

value: 3 prime v3.1

tag: cellsloaded

tag: disease


title: CID006565-1-reup

value: UC

tag: disease duration


title: CID005782-1-reup

value: Healthy

value: #N/A

tag: patient

value: Rectum


title: CID006572-1-reup

tag: site

value: Inflamed

value: Pre


title: CID006563-1-reup

tag: inflammation

value: F

value: Caucasian


title: CID006561-1-reup

tag: age

value: No


title: CID006578-1-reup

tag: Sex

value: M


title: CID006559-1-reup

tag: ethnicity

value: Yes


title: CID005781-1-reup

tag: match


title: mch_male

city: Köln

first: Jens

middle: C

last: Brüning

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

country: Germany

institute: Max Planck Institute for Metabolism Research

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse reference genome GRCm38 and counted using cellranger (cellranger-6.1.2; 10x Genomics).
Cells were filtered to have at least 800 unique molecular identifiers, 500 unique genes and a rate of mitochondrial RNA below 5%. The remaining 11,242 cells were processed using the Seurat R package (v4.4.0) using a pipeline with default settings for variable feature detection (1000 highly variable features), PCA (50 PCs), UMAP calculation and Louvain clustering (resolution = 1) for cluster detection (v4.3.0).
The scArches algorithm was used to transfer labels for all hypothalamic cell types from HypoMap onto the data set. Each initial cluster was annotated using the HypoMap label with the highest percentage of cells in that cluster and subsequently all clusters with a high percentage of non-neuronal or non-MCH neuron labels were removed. The remaining 7,590 MCH-neurons were re-processed using the same Seurat pipeline with a lower highly variable feature number (500) and clustering resolution (0.8), resulting in 10 subclusters.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated files for barcodes(cells), genes and matrix file for processed counts corresponding to the data set used in the analysis. Matrix contains data in format genes x cells.
Supplementary files format and content: Supplementary files: Final processed and filtered data set as Seurat (.rds) and anndata (.h5ad) files.

molecule: nuclear RNA

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
After decapitation, the brain was removed, and the hypothalami of MCH-Cre; lsl-ZsGreen mice were dissected and frozen in liquid nitrogen immediately. On single nuclei preparation day, individual hypothalami tissue were lysed in 1ml of ice-cold EZ PREP buffer (D8938, Sigma). The tissue was homogenized with a glass dounce, twice at 250 rpm and 12 times at 1000 rpm and incubated on ice for 5 min. Nuclei were centrifuged at 500 g, 5 min after addition of 4 mL of nuclear lysis buffer and incubated on ice for 5 min. The supernatant was discarded, and the pellet was resuspended in 4 mL nucleus suspension buffer (NSB, 1x PBS, 0.01% BSA, and 0.1% RNase inhibitor (352235, Clontech). Nuclei were centrifuged at 500 g for 2 min. The supernatant was discarded and isolated nuclei were resuspended in 300 μl NSB and then filtered through a 30 μm cell strainer into sorting tubes for flow cytometry sorting on a BD FACSAria IIIu.
Nuclei suspension was stained with DAPI (1:1000, 62248, Thermo Fisher Scientific) as nuclear marker. ZsGreen positive nuclei + DAPI positive nuclei were collected as MCH neuron nuclei. A FACSAria IIIu was used for gating and sorting nuclei. Single nuclei were identified based on side scatter (SSC-A) and DAPI fluorescence (area versus width). ZsGreen fluorescence was detected with 488 nm excitation and 530 nm emission.
Sequencing libraries were generated using 10x Genomics Chromium Single-Cell 3′ Reagent kit v3 according to the standardized protocol. Paired-end sequencing was performed using an Illumina NovaSeq 6000.

treatment_protocol: Mice were housed in individually ventilated cages (IVCs) within a controlled environment at 22°C – 24°C and a 12-hr light/12-hr dark cycle. Mice were checked daily to verify animal health and the health status monitoring of the animal facility was performed quarterly every year. Mice were housed in groups of not more than 5 mice per cage after weaning. Animals received ad libitum access standard rodent chow (ssniff V1554, 59494 Soest, Germany) and water. Mice were age-matched between experimental groups for both males and females.

value: hypothalamus

tag: genotype

value: MCH-Cre; lsl-ZsGreen

tag: strain

value: male


title: mch_female

description: 10x Genomics

value: female


title: CID005778-1-reup

value: gut

tag: treatment

tag: batch

tag: inflammation score


title: Old_BKO_02

city: Minneapolis

first: Anna

last: Carey

state: Minnesota

address: 312 Church Street SE

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

data_processing:
Analysis of read count matrices was performed using Seurat version 4.3.1 in R. Cells with mitochondrial RNA <15% and an R² of 0.95 for nCount_RNA vs. nFeature_RNA were included. Each sample was normalized using ‘NormalizeData’, and the top 2000 highly variable genes were selected with ‘FindVariableFeatures’. Dimensional reduction and clustering followed the standard Seurat workflow with ‘ScaleData’ and ‘RunPCA’. The top 50 principal components, identified by ‘ElbowPlot’, were used for UMAP visualization via ‘RunUMAP’ and finding nearest neighbors. Clusters and subclusters were identified using the Louvain algorithm with a resolution of 0.2.
Differentially expressed genes (DEGs) were identified by comparing normalized expressed RNAs for each model to RNAs expressed in control cells via the function ‘FindMarkers’ and then merging the results. When comparing clusters, the function ‘FindAllMarkers’ was employed to find marker genes that characterized a specific cluster compared to all other clusters. A minimum of 100 cells from a sample group in a cluster was required for downstream analysis.
Before gene set enrichment analysis (GSEA) or over-representation analysis (ORA), common gene symbols were converted into Entrez gene ids and ensemble ids using the R package biomart, version 3.18, using the dataset "mmusculus_gene_ensembl"16,17. ORA of Gene Ontology (GO) and Reactome (version 1.34.0) terms was conducted using ClusterProfiler (version 3.18.1) using DEGs with an absolute average Log fold change >0 and adjusted p-values <0.05 where analysis occurred separately for up and down-regulated genes using the ‘enrichGO’ and ‘enrichPathway’ functions18,19’20,21. Using the same DEG lists, Reactome Pathway Analysis was employed for GSEA using the function ‘GSEA’ and the Reactome IL-1 family signaling enrichment gene set.
Assembly: GRCh38
Supplementary files format and content: rds objects processed through Seruat

source_name: CD45+ live cells from visceral white adipose tissue (vWAT)

extract_protocol:
RNA was isolated using the Invitrogen purelink RNA micro kit (cat#12183-016) and processed as per manufacturer’s instructions.
Single-cell libraries were prepared in triplicate with >85% cell viability confirmed by trypan blue staining. Cells were resuspended in MEM with 10% FBS at 1200 cells/uL. Library construction used Chromium Next GEM Single Cell 3ʹ dual index Kits v3.1 with Chip G (10x Genomics). About 10,000 single cells were loaded to generate gel bead-in-emulsions (GEMs), lysed, and RNA was barcoded and reverse-transcribed. GEMs were broken, and cDNA was prepared following the manufacturer’s protocol. cDNA quality was assessed with the Agilent Bioanalyzer and Pico-green. Libraries underwent QC by shallow-sequencing on an Illumina NextSeq and final sequencing on an Illumina Nova Seq S4 capturing ~20,000 paired-end reads per cell. Sequencing libraries were converted into feature-barcode matrices using Cell Ranger (10x Genomics, version 5.0.0) and mapped to GRCh38.

treatment_protocol: Young (3m) and old (20 month) old female mice were treated with 0.1 mg/kg LPS (E. coli O111-B2) for 4 hours prior to euthanization by cervical dislocation under anaesthesia and harvest of visceral white adipose tissue (vWAT); vWAT was digested using collagenase II digestion buffer and a single cell suspension of the stromovascular fraction was isolated and stained prior to fluorescence associated cell sorting for the CD45+ live cell population.

tag: tissue

tag: developmental stage

value: Old

value: C57BL/6 CD19cre+ IL1R1 fl/fl (BKO)

value: In vivo 4 hour 0.1 mg/kg LPS


title: CID005780-1-reup

tag: librarytype

value: 3 prime v3.1

tag: cellsloaded

value: Healthy

value: #N/A


title: CID005777-1-reup

tag: disease

tag: disease duration


title: CID005776-1-reup

tag: patient

tag: site


title: BAC sgl silencer-seq, input

data_processing:
Paired-end sequencing reads were aligned to the D. melanogaster reference genome BDGP R5/dm3 using Bowtie (version 1.2.2, (Langmead et al., 2009)) allowing 3 mismatches with the options: “‐v 3 ‐m 1 –best –strata –X 2000”. Mapped read pairs were collapsed by coordinates (start, end, strand) and by unique molecular identifiers (UMI) to distinguish PCR duplicates from reads originating from distinct RNA molecules with identical sequence. Fragments with identical coordinates were considered as duplicates if their UMIs differed by < 3 out of the 10 nucleotides. Genome coverage per sample was calculated using genomeCoverageBed from bedtools (version 2.27.1, Quinlan and Hall, 2010). BigWig files were created using the wigToBigWig utility from KentUtils (Kent et al., 2010).
To identify silencer-seq depleted regions in the genome (“dips” instead of peaks), first position-specific coverage for each sample and each strand were calculated separately using the coverage() function of the GenomicRanges R package (version 1.34.0, (Lawrence et al., 2013)). Afterwards, the log2 fold change and hypergeometric p‐value between coverage in experiment and input samples were determined. Loci with log2 fold change ≤ (-1.58) – corresponding to a 3-fold depletion over input – and hypergeometric p‐value ≤ 0.001 were collapsed into continuous depleted regions using the reduce() function.
Assembly: BDGP R5/dm3
Supplementary files format and content: genomic coverage of silencer-seq screen or input samples in bigWig format
Supplementary files format and content: silencer-seq dip calls as tsv files containing genomic regions of significant coverage depletion relative to input (collapsed regions with ≥ 3-fold depletion and hypergeometric p‐value ≤ 0.001)
Library strategy: STARR-seq

tag: cell line

value: Schneider S2

tag: fraction

value: input

value: PCR amplified inserts of focused BAC sgl silencer-seq library


title: Old_BKO_03

value: CD45+ live cells from visceral white adipose tissue (vWAT)


title: CID005779-1-reup

tag: inflammation

tag: age

tag: Sex

value: F

tag: ethnicity

value: Caucasian

value: No


title: Old_BKO_01

tag: genotype

tag: treatment


title: CID005775-1-reup

value: M

tag: match

tag: batch

tag: inflammation score


title: CID006570-1-reup

tag: tissue

tag: librarytype

value: UC

value: Rectum

value: Inflamed

value: Post


title: CID005774-1-reup

value: gut

tag: cellsloaded

tag: disease

value: CD

value: Yes


title: CID006569-1-reup

value: 3 prime v3.1

tag: disease duration

tag: patient


title: Old_WT_02

tag: developmental stage

value: Old

value: C57BL/6 CD19cre- IL1R1 fl/fl (WT)

value: In vivo 4 hour 0.1 mg/kg LPS


title: Old_WT_01


title: Young_WT_02

value: Young


title: CID005772-1-reup

tag: site

value: Pre


title: Lung, hashtags A, Hashtag

city: Berlin

first: Bastian

last: Opitz

address: Augustenburgerplatz 1

department: Department of Infectious Diseases, Respiratory Medicine and Critical Care

institute: Charité – Universitätsmedizin Berlin

description:
10x genomics
ivo1_barcodes.tsv.gz
ivo1_features.tsv.gz
ivo1_matrix.mtx.gz

data_processing:
Cellranger pipeline
Assembly: mm10
Supplementary files format and content: Tab separated values files and  matrix files

molecule: protein

source_name: Lung

extract_protocol:
mice were infected and after 18 hours lungs were digested to single cells and objected to 10x scRNAseq
Library construction was performed following manufacturers instructions (10x)

value: Lung

tag: group

value: control group and diabetic group

value: infected with S.pneumoniae

tag: library type

value: HTO


title: CID005771-1-reup

tag: inflammation

tag: age

tag: Sex

value: M

value: Caucasian


title: CID005770-1-reup

value: Rectum

tag: treatment

value: F

tag: ethnicity


title: Lung, hashtags B, Hashtag

description:
10x genomics
ivo2_barcodes.tsv.gz
ivo2_features.tsv.gz
ivo2_matrix.mtx.gz


title: Lung, cells B, GEX

value: mRNA


title: CID005769-1-reup

value: gut

value: CD

value: Post

tag: match

tag: batch


title: CID005768-1-reup

tag: tissue

value: 3 prime v3.1

value: Inflamed

value: Yes

tag: inflammation score


title: SA-21-IP

city: Tianjing

first: Jiayu

last: Yu

address: Weijin street

country: China

institute: Nankai university

description: OE S564A

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software,clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N（poly-N≥6） and 3’low- quality（＜20） reads from raw data. At the same time, Q20,Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling,software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width,fold enrichment, significant level and peak summit number per peak were all displayed.
Peak related genes can be confirmed by Peak Annotator(PeakAnalyzer), and then Gene Ontology (GO) enrichment analysis of performed to identify the function enrichment results. GO enrichment analysis was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value less than 0.05 were considered significantly enriched by peak related genes.
Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2.
Assembly: mm10
Supplementary files format and content: bigWig ,narrow peak

source_name: Inner cell mass

growth_protocol: Mouse ESCs were cultured in Dulbecco’s Modified Eagle Media (DMEM, GIBCO) supplemented with 15% fetal bovine serum (HyClone), 1% nonessential amino acids (Invitrogen), 1% penicillin and streptomycin (Invitrogen), 1% L-glutamine (Invitrogen), 1% β-mercaptoethanol (Sigma), and 1000 units/ml leukemia inhibitor factor (LIF). ESCs were plated on 0.2% gelatin-coated dishes and maintained in a 5% CO2 humidified incubator (Thermo Fisher) at 37 °C.

extract_protocol:
Total RNA was purified using the RNeasy Mini Kit (QIAGEN)
The fragment distribution and concentration of RNAs（after immunoprecipitation） were detected using an Agilent 2100 bioanalyzer (Agilent) and simpliNano spectrophotometer (GE Healthcare).Then, immunoprecipitated RNA or Input was used for library construction with NEBNext® Ultra™II RNA Library Prep Kit for Illumina®(New England Biolabs, E7770). Library quality was assessed on the Agilent Bioanalyzer 2100 system.
The libraries were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.

treatment_protocol: In Dcp1a KO cells, overexpressing different forms of mutants including Dcp1a WT, S563A, and S563D

value: Inner cell mass

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: genotype

value: OE S564A


title: Old_WT_03

value: CD45+ live cells from visceral white adipose tissue (vWAT)

value: Old

value: C57BL/6 CD19cre- IL1R1 fl/fl (WT)

value: In vivo 4 hour 0.1 mg/kg LPS


title: CID005765-1-reup

tag: librarytype

tag: cellsloaded

tag: disease

tag: disease duration

tag: patient

value: Pre

value: Caucasian


title: CID005767-1-reup

tag: site

tag: inflammation

value: F


title: CID005766-1-reup

value: Rectum

tag: age

tag: Sex


title: CID005764-1-reup

value: gut

tag: treatment

tag: ethnicity


title: CID005763-1-reup

value: CD

tag: match

tag: batch


title: SA-21-input

description: OE S563A

tag: tissue

value: OE S563A


title: WT-19-input

description: OE WT

tag: cell line

value: WT

value: OE WT


title: WT-19-IP

description: OE WT

tag: cell type


title: 7d_CSP

city: Chicago

first: Veronica

last: Locher

state: IL

institute: University of Chicago

description:
7d_matrix.mtx.gz
7d_barcodes.tsv.gz
7d_features.tsv.gz

data_processing:
alignment performed with cell ranger count
Assembly: GRCm39
Supplementary files format and content: processed data files contains  detected cell-associated barcodes in MEX format. Each  matrix element is the number of UMIs associated with a feature (row) and a barcode (column).
Library strategy: CITE-seq

extract_protocol:
Lungs were harvested from control and β-glucan-treated mice and mechanically disrupted with scissors before being treated with Collagenase Type I, DNAse I and elastase (Worthington) for 30 minutes at 37°C. Cells were then passed through a 100 µm cell strainer and red blood cells were lysed. Single cell suspensions were stained with TotalSeq-tagged anti-CD45 and anti-Ly6G (Biolegend) according to the manufacturer’s instructions.
Single-cell GEXs and CSP libraries were generated using a Chromium Controller instrument (10x Genomics). Sequencing libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10x Genomics), according to the manufacturer’s instructions. GEX libraries were amplified with a thermal cycler for 13 cycles and CSP libraries for 10 cycles.
paired scRNA-seq and CITE-seq

value: Lung

value: 7 days post b-glucan

tag: library type

value: ADT


title: Young_WT_01

tag: developmental stage

value: Young

tag: genotype


title: CID005762-1-reup

tag: librarytype

value: 3 prime v3.1

tag: cellsloaded

tag: disease

value: Post

value: Yes

tag: inflammation score


title: CID005773-1-reup

tag: disease duration

tag: patient

tag: site

tag: inflammation

value: M


title: 4d_CSP

description:
4d_matrix.mtx.gz
4d_barcodes.tsv.gz
4d_features.tsv.gz

tag: treatment

value: 4 days post b-glucan


title: CID005760-1-reup

value: Pre

tag: age

tag: Sex

tag: ethnicity

value: Caucasian

tag: match


title: NTC_CSP

description:
NTC_matrix.mtx.gz
NTC_barcodes.tsv.gz
NTC_features.tsv.gz

tag: tissue

value: NTC


title: CID005759-1-reup

value: gut

value: Inflamed

value: F

tag: batch


title: 7d_GEX

tag: library type

value: mRNA


title: Lung, cells A, GEX

tag: group

value: control group and diabetic group

value: infected with S.pneumoniae


title: CID005758-1-reup

tag: librarytype

value: CD


title: CID005757-1-reup

tag: cellsloaded


title: 4d_GEX

value: Lung


title: CID005756-1-reup

tag: disease


title: E14 PD-2

data_processing:
The quality control was assessed through FastQC software , and low-quality reads were filtered by Trimmomatic software . The clean reads were mapped to the mouse reference genome mm10 using Bowtie2 software with the default parameter.
The reads length in 20-40 bp were retained for subsequent analysis. rRNA and tRNA reads were removed by aligning reads with the rRNA and tRNA reference sequence on NCBI database using the bowtie2 software with parameters bowtie2 –q –un-gz. The remaining reads were aligned to the mouse mm10 genome using STAR software.
The mapped RPFs reads were quantified as FPKMTranslation using Cufflinks software . The corresponding transcriptomic analysis yielded FPKMTranscription. Translational efficiency was calculated as the ratio of FPKMTranslation over FPKMTranscription.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample
Library strategy: Ribo-seq

extract_protocol:
Cells were lysed and digested with RNase I (Thermo Fisher). The ribosome-protected RNA fragments (RPFs) were purified by size-exclusion chromatography with MicroSpin S-400 HR columns (GE Healthcare Life Sciences).  rRNAs were depleted from RPFs using the rRNA depletion kit (QIAGEN).
Sequencing libraries were generated using the NEBNext Multiplex Small RNA Library Prep Kit (New England Biolabs) for Illumina, and sequenced by Novogene.

treatment_protocol: Mouse ESCs were cultured with DMSO (Sigma) or 1 μM PD (Selleck) for 3 passages.

value: Inner cell mass

tag: cell line

tag: cell type

value: Embryonic stem cells

tag: genotype

value: WT

value: PD treatment


title: SD-10-IP

description: OE S564D

value: OE S564D


title: NTC_GEX


title: E14 PD-1


title: E14 DMSO-2

value: DMSO treatment


title: CID005754-1-reup

value: 3 prime v3.1

tag: disease duration

tag: patient

tag: site

value: Rectum

value: Post

value: M

value: Yes

tag: inflammation score


title: SD-10-input

description: OE S563D

tag: treatment

value: OE S563D


title: CID005753-1-reup

value: gut

tag: inflammation

tag: age

tag: Sex

tag: ethnicity

value: Caucasian


title: CID005752-1-reup

tag: tissue

tag: match

tag: batch


title: CID005755-1-reup

tag: librarytype

tag: cellsloaded

value: Inflamed

value: Pre

value: F


title: Dcp1a KO-2 EB

data_processing:
The raw reads were trimmed to remove adapters and then aligned to mouse reference genome mm10 using STAR software with the default parameter.
Expression level of individual genes was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks software.
Differentially expressed genes (DEGs) were defined by the Cufflinks software with fold change >2 and p-value < 0.05.
For alternative splicing (AS) analysis, AS events were identified using a robust and flexible detection software rMATS . The differential AS events were filtered with the criteria: the Inclusion Level difference > 0.25, and the p value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Total RNA was purified using the RNeasy Mini Kit (QIAGEN). Cytoplasmic and nuclear RNA was isolated using the Cytoplasmic & Nuclear RNA Purification Kit (Norgen Biotek).
RNA-seq library preparation were constructed by Novogene (Tianjin) following standard protocols. Libraries were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Inner cell mass

tag: cell line

value: Dcp1a KO

value: Dcp1a KO withdrawal LIF


title: CID005761-1-reup

tag: disease

value: CD


title: Dcp1a KO-1 EB

tag: cell type

value: Embryonic stem cells

tag: genotype


title: CID005750-1-reup

tag: disease duration

tag: patient


title: E14-EB

value: WT

value: WT withdrawal LIF


title: E14 DMSO-1

value: DMSO treatment


title: CID005751-1-reup

value: 3 prime v3.1

tag: site

value: Post

tag: inflammation score


title: CID005749-1-reup

tag: inflammation

tag: treatment

value: M

value: Yes


title: Dcp1a KO-2


title: Dcp1a KO-1


title: CID005748-1-reup

value: gut

tag: age

tag: Sex


title: CID005747-1-reup

tag: tissue

tag: ethnicity

value: Caucasian


title: CID005746-1-reup

value: UC

value: Rectum

value: Inflamed

tag: match

tag: batch


title: CID005745-1-reup

tag: librarytype

tag: cellsloaded

value: Sigmoid

value: F


title: E14-1

value: Inner cell mass

tag: cell line


title: E14 PD 0h-2

tag: cell type

value: PD treatment with Actinomycin D treated 0h


title: CID005744-1-reup

tag: disease

value: No


title: E14 DMSO 0h-2

value: Embryonic stem cells

tag: genotype

value: WT

value: DMSO treatment with Actinomycin D treated 0h


title: E14 PD 8h-1

value: PD treatment with Actinomycin D treated 8h


title: CID005742-1-reup

value: 3 prime v3.1

tag: disease duration

tag: patient

value: Pre


title: CID005741-1-reup

tag: site

value: Post

value: M

value: Yes

tag: inflammation score


title: E14 PD 0h-1

tag: treatment


title: E14 DMSO 8h-1

value: DMSO treatment with Actinomycin D treated 8h


title: E14 PD Nuclear-1

value: PD treatment


title: E14 DMSO Nuclear-1

value: DMSO treatment


title: E14 PD Cyto-1

molecule: cytoplasmic RNA


title: CID005738-1-reup

value: gut

value: UC

value: Rectum

tag: inflammation

value: Inflamed

tag: age

value: Caucasian


title: CID005739-1-reup

tag: tissue

tag: Sex


title: CID005740-1-reup

value: Sigmoid

tag: ethnicity

tag: match


title: CID005737-1-reup

tag: librarytype

tag: batch


title: CID005736-1-reup

tag: cellsloaded


title: CID005735-1-reup

value: Afro-Carribean


title: E14 DMSO 0h-1

value: Inner cell mass

tag: cell line

tag: cell type

value: Embryonic stem cells

value: WT

value: DMSO treatment with Actinomycin D treated 0h


title: E14 PD 8h-2

tag: genotype

value: PD treatment with Actinomycin D treated 8h


title: CID005733-1-reup

value: 3 prime v3.1

tag: disease

tag: disease duration

value: Post

value: M


title: CID005734-1-reup

tag: patient

tag: site

value: Yes


title: RNA-seq-silicosis-N136

city: Taiyuan

first: ting

last: liu

address: NO.85 Jiefang South Road, Yingze District

institute: The First Clinical Medical College of Shanxi Medical University

description: sample of silicosis

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using trimmomatic 0.39.
The filtered reads of mRNA and lncRNA were mapped to the Mus_musculus.GRCm39.106 using hisat2; the filtered reads of circRNA were mapped to the Mus_musculus.GRCm39.106 using bowtie2.
The counted and normalized expression of lncRNA, and mRNA and circRNA were estimated using all mapped reads by featureCounts v2.0.0.
Differentially expressed merged transcripts were quantified using DESeq2 1.36.0.
Assembly: Mus_musculus.GRCm39.106
Supplementary files format and content: csv files include gene count values for each Sample.

source_name: lung

growth_protocol: After 90 days of experimental treatment, the lungs of mouse were excised and immediately snap-frozen with liquid nitrogen.

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

treatment_protocol: The silica-treated silicosis mice model was constructedby a single intratracheal instillation of 8 mg of silica in 40 μL sterile normal saline.

value: lung

tag: treatment

value: silicosis

tag: strain


title: RNA-seq-silicosis-N129

description: sample of silicosis


title: RNA-seq-silicosis-N138

description: sample of silicosis


title: CID005732-1-reup

value: gut

value: UC

tag: inflammation

value: Pre

tag: age

tag: inflammation score


title: CID005731-1-reup

tag: tissue

tag: Sex

tag: ethnicity


title: CID005743-1-reup

tag: librarytype

value: Rectum

value: Inflamed

value: F

value: Caucasian

tag: match

tag: batch


title: E14 DMSO 8h-2

value: Inner cell mass

tag: cell line

tag: cell type

value: Embryonic stem cells

value: DMSO treatment with Actinomycin D treated 8h


title: RNA-seq-control-C9

description: sample of control

value: control


title: RNA-seq-control-C8

description: sample of control


title: CID005729-1-reup

value: 3 prime v3.1

tag: cellsloaded

tag: disease


title: RNA-seq-control-C7

description: sample of control


title: CID005728-1-reup

tag: disease duration

tag: patient

value: Sigmoid

value: Post

value: No


title: CID005727-1-reup

tag: site

tag: treatment


title: BMDM_UT_Chrom_RNA-seq_R2

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: BMDM untreated

data_processing:
All samples were analysed following the Nextflow pipeline that can be freely downloaded from https://github.com/fgualdr/mmrnaseq. Briefly:
Reads were quality filtered according to the illumina pipeline
Reads were aligned to the mouse mm10 genome using STAR v. 2.7.9a
Bigwig files were generated using deeptools v. 3.5.1 and scaled accoding to a pre-defined invariant set of peaks (see Gualdrini et al. 2016)
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Mouse  Bone-Marrow derived Macrophages (BMDM)

growth_protocol: Bone marrow derived macrophage (BMDM) cultures were carried out as described before (Curina et al., 2017).

extract_protocol:
Chromatin-associated RNA was extracted as described (Comoglio et al., 2019). Briefly, 5-15x106 BMDM cells were lysed with ice-cold 10 mM Tris-HCl (pH 7.5), 0.05% NP-40, and 150 mM NaCl buffer for 5 min. The lysate was then layered on 2.5 vol of a chilled sucrose cushion and centrifuged at 14,000 rpm for 10 min at 4°C. The nucleus pellet was gently washed with ice-cold PBS/1 mM EDTA and then resuspended in a 20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, and 50% glycerol buffer by gentle flicking of the tube. An equal volume of a cold 10 mM HEPES (pH 7.6), 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, and 1% NP-40 buffer was added. The tube was gently vortexed and then centrifuged at 14,000 rpm for 2 min at 4°C. The chromatin pellet was then dissolved in TRIzol (Invitrogen). Chromatin-associated RNA was purified with TRIzol with an additional phenol/ chloroform extraction step prior to precipitation.
We used 60-100 ng of the nascent RNA for cDNA-library synthesis using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina RS-122-9007) with the ribosomal depletion step. Libraries were quantified with the Quantifluor reagent (Promega cat. E2670) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the high-sensitivity assay HD5000 (Agilent cat. 5067-5592). cDNA libraries were sequenced on an Illumina NovaSeq platform with 51-bp paired-end reads.

treatment_protocol: Cells were treated with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL. Trichostatin A (TSA, cat. no. S1045, Selleck) was added for 30 min. Spermine Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) was used at 0.5 mM for 15 min before TSA or LPS treatment.

tag: genotype

value: untreated

tag: molecule subtype

value: Chromatin-associated RNA


title: BMDM_UT_Chrom_RNA-seq_R3

description: BMDM untreated

value: Mouse  Bone-Marrow derived Macrophages (BMDM)


title: CID005726-1-reup

value: gut

value: UC

tag: inflammation

tag: age

value: Yes

tag: inflammation score


title: E14 DMSO Cyto-1

tag: tissue

value: WT

value: DMSO treatment


title: BMDM_UT_Chrom_RNA-seq_R1

description: BMDM untreated


title: CID005722-1-reup

tag: librarytype

tag: Sex

value: F

tag: ethnicity

value: Caucasian


title: CID005725-1-reup

value: Pre

tag: match

tag: batch


title: CID005723-1-reup

tag: cellsloaded


title: BMDM_NO_TSA_Chrom_RNA-seq_R3

description: BMDM pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes followed by 20minutes  Trichostatin A (TSA, cat. no. S1045, Selleck)  stimulation

tag: cell type

value: 15min NO + 20min TSA


title: BMDM_TSA_Chrom_RNA-seq_R1

description: BMDM treated for 20minutes with Trichostatin A (TSA, cat. no. S1045, Selleck)

value: 20min TSA


title: CID005724-1-reup

value: 3 prime v3.1

tag: disease

tag: disease duration

value: Rectum


title: BMDM_TSA_Chrom_RNA-seq_R3


title: BMDM_TSA_Chrom_RNA-seq_R2


title: CID005721-1-reup

tag: patient

tag: site

value: Inflamed


title: BMDM_NO_Chrom_RNA-seq_R3

description: BMDM pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes

tag: genotype

tag: treatment

value: 15min NO


title: BMDM_NO_TSA_Chrom_RNA-seq_R1

tag: molecule subtype


title: CID005730-1-reup

tag: inflammation

tag: age

value: M

value: Afro-Carribean


title: CID005720-1-reup

tag: tissue

value: Sigmoid

tag: inflammation score


title: BMDM_NO_Chrom_RNA-seq_R2

value: Mouse  Bone-Marrow derived Macrophages (BMDM)

value: Chromatin-associated RNA


title: CID005717-1-reup

value: gut

tag: librarytype

value: UC

value: Post

tag: Sex

value: Yes


title: BMDM_NO_Chrom_RNA-seq_R1


title: CID005718-1-reup

tag: ethnicity

value: Caucasian

tag: match


title: CID005715-1-reup

tag: cellsloaded

value: Pre

tag: batch


title: BMDM_NO_LPS_Chrom_RNA-seq_R3

description: BMDM pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes followed by 1h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

tag: cell type

value: 15min NO + 1h LPS


title: BMDM_NO_TSA_Chrom_RNA-seq_R2

value: 15min NO + 20min TSA


title: BMDM_NO_LPS_Chrom_RNA-seq_R2


title: CID005716-1-reup

value: 3 prime v3.1

tag: disease

tag: disease duration


title: CID005714-1-reup

tag: patient

tag: site


title: CID005713-1-reup

tag: treatment


title: BMDM_LPS_Chrom_RNA-seq_R3

description: BMDM treated for 1h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

tag: genotype

value: 1h LPS

tag: molecule subtype


title: CID005712-1-reup

value: Healthy

value: #N/A

value: Rectum

tag: inflammation

tag: age

value: No


title: CID005711-1-reup

tag: tissue

value: M

tag: inflammation score


title: BMDM_LPS_Chrom_RNA-seq_R2

value: Mouse  Bone-Marrow derived Macrophages (BMDM)


title: BMDM_LPS_Chrom_RNA-seq_R1

value: Chromatin-associated RNA


title: CID005710-1-reup

value: gut

tag: librarytype

tag: Sex


title: RAW 264.7_NOLPS

data_processing:
All samples were analysed following the Nextflow pipeline that can be freely downloaded from https://github.com/fgualdr/mmchipseq. Briefly:
Reads were quality filtered according to the illumina pipeline
Reads were aligned to the mouse mm10 genome using STAR v. 2.7.9a
Peaks were called using MACS2 v. 2.2.7.1
Bigwig files were generated using deeptools v. 3.5.1 and scaled accoding to a pre-defined invariant set of peaks (see Gualdrini et al. 2016)
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: RAW 264.7 cells (from ATCC) were cultured in DMEM with 10% North American serum,1% pen/strep (cat. no. P4333, Sigma), and 1% L-Glutamax (cat. no. 35050061, Gibco). Cell lines were authenticated by the Tissue Culture Facility of the European Institute of Oncology using the GenePrint10 system (Promega) and routinely screened for mycoplasma contamination.

extract_protocol:
MED1 ChIP-seq was carried out as previously described (Gualdrini et al., 2022). Briefly, cells were were scraped in PBS, incubated for 45 min with 2 mM DSG in PBS, washed twice, and then incubated with 1% formaldehyde in PBS for 10 min followed by quenching with 125 mM glycine and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Branson Ultrasonics Sonifier, lysates were incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen) previously coupled with tetra-acetylated histone H4 (cat. no. 06866, Millipore)  MED1 antibody (cat.no. A300-793A, Bethyl). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycho- late). Immunoprecipitated chromatin was eluted and cross-link-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen) and then quantified with QuantiFluor (cat. no. E2670, Promega).
DNA libraries were prepared as previously described (Austenaa et al., 2021). The purified DNA libraries were quantified with the Quantifluor reagent (cat. no. E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent). DNA libraries were diluted to a working concentration of 4 nM and 50-bp single reads sequenced on an Illumina Novaseq6000 platform.

treatment_protocol: Cells were treated with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 100 ng/mL (RAW 264.7 cells) with or without Spermine Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) was used at 0.5 mM for 15 min before TSA or LPS treatment.

tag: cell line

value: Mouse monocyte/macrophage-like cells


title: UT_R3

description: BMDM untreated

treatment_protocol: Cells were treated with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL. iNOS inhibitor 1400W (1400W, cat. no. CAY-81520, Cayman Chemical)  added 30 min before macrophage activation.

value: untreated


title: CID005708-1-reup

tag: cellsloaded

value: UC

value: Inflamed

value: Post

tag: ethnicity

tag: match

value: Yes


title: CID005719-1-reup

tag: disease

value: Pre

value: F

value: Caucasian

tag: batch


title: CID005707-1-reup

value: 3 prime v3.1

tag: disease duration

tag: patient

value: Sigmoid


title: CID005706-1-reup

tag: site

tag: treatment


title: UT_R2

description: BMDM untreated

tag: cell type

tag: genotype

tag: molecule subtype


title: LPS_8h_R3

description: BMDM treated for 8h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

value: 8h LPS


title: CID005705-1-reup

tag: tissue

value: Rectum

tag: inflammation

tag: age


title: UT_R1

description: BMDM untreated


title: CID005704-1-reup

tag: librarytype

tag: Sex

value: M

tag: inflammation score


title: LPS_8h_R2

value: Mouse  Bone-Marrow derived Macrophages (BMDM)


title: CID004758-1-reup

tag: cellsloaded

value: CD

tag: ethnicity


title: LPS_8h_R1

value: Chromatin-associated RNA


title: LPS_16h_R3

description: BMDM treated for 16h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

value: 16h LPS


title: CID004757-1-reup

value: gut

tag: disease

tag: match


title: BMDM_NO_LPS_Chrom_RNA-seq_R1

value: 15min NO + 1h LPS


title: CID004755-1-reup

tag: disease duration

tag: batch


title: CID004756-1-reup

tag: patient

tag: site

value: Inflamed


title: LPS_16h_R1

tag: cell type

tag: treatment


title: CID005709-1-reup

value: Healthy

value: #N/A

value: No


title: CID004754-1-reup

value: Pre

value: Yes


title: RAW 264.7_LPS

tag: cell line

value: Mouse monocyte/macrophage-like cells


title: CID004753-1-reup

tag: tissue

value: 3 prime v3.1

value: Caucasian


title: CID004752-1-reup

tag: inflammation


title: INH_R2

tag: genotype

value: 30min INOS inhibitor

tag: molecule subtype


title: INH_LPS_8h_R3

description: BMDM pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes followed by 8h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

value: 30min INOS inhibitor + 8h LPS


title: CID004750-1-reup

tag: librarytype

value: UC

value: Rectum

value: Post

tag: age

tag: Sex

value: F


title: INH_LPS_8h_R2

value: Mouse  Bone-Marrow derived Macrophages (BMDM)

value: Chromatin-associated RNA


title: CID004749-1-reup

value: gut

tag: cellsloaded

value: Sigmoid

tag: ethnicity

tag: inflammation score


title: INH_LPS_8h_R1


title: CID004747-1-reup

tag: disease

tag: disease duration

value: Inflamed

tag: match


title: INH_LPS_16h_R3

description: BMDM pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes followed by 16h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

value: 30min INOS inhibitor + 16h LPS


title: CID004748-1-reup

tag: patient

tag: site

tag: batch


title: INH_LPS_16h_R2

tag: cell type

tag: treatment


title: CID004746-1-reup

tag: tissue

tag: inflammation

value: Pre


title: LPS_16h_R2

tag: genotype

value: 16h LPS

tag: molecule subtype


title: INH_LPS_16h_R1


title: CID004745-1-reup

tag: librarytype

tag: age

value: Yes


title: BMDM_UT_R2

description: BMDM untreated

data_processing:
Reads were quality filtered according to the illumina pipeline
Paired-end Spike-in tetra-acetylated histone H4 ChIP-seq was analyzed similar to previous reports (Orlando et al., 2014). Briefly the genome sequence of both the mouse (mm10 assembly) and the Drosophila genomes (assembly dm6) were concatenated to produce a chimeric combined genome, with the Drosophila chromosomes re-named to include the “_dm6” suffix.
Custom Bowtie2 index was generated using the chimeric genome and used to sequence in pair-end mode each sample (with the following commands “-X 1000 -k 2 -t --phred33 -p 8 -q”). Mapped reads were then filtered by keeping reads mapped in proper pair and removing those unmapped, having mate unmapped, and failing quality. Duplicated reads were then removed using samtools markdup function. Finally reads split into mm10 and dm6 based on the chromosome suffix which was at the end removed.
ChIP-seq peaks were identified using MACS2 (version 2.2.6) with parameters “‐‐keep-dup ‘all’ ‐‐call-summits ‐‐nomodel ‐‐nolambda ‐‐extsize 300”. Reference set of peaks was identified selecting significant peaks per-samples in addition to being consistent between replicated (overlapping area of at least 50% between replicates).
ChIP-seq scaling factors were computed either identifying internal invariant peaks as previously described (Gualdrini et al., 2016) or using solely the reads mapping to the dm6 genome (as described in Orlando et al., 2014).
Assembly: mm10, dm6
Supplementary files format and content: bigWig

extract_protocol:
tetra-acetylated histone H4 ChIP-seq was carried out as previously described (Gualdrini et al., 2022). Briefly, 5x106 BMDM cells were fixed with 1% formaldehyde (cat. no. 252549, Merck) for 10 min at room temperature and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Branson Ultrasonics Sonifier, lysates were incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen) previously coupled with tetra-acetylated histone H4 (cat. no. 06866, Millipore)  antibody. tetra-acetylated histone H4 ChIP-seq, 1 μg of chromatin was supplemented with 5% spike-in of S2 Drosophila chromatin (prepared in the same manner). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycho- late). Immunoprecipitated chromatin was eluted and cross-link-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen) and then quantified with QuantiFluor (cat. no. E2670, Promega).
DNA libraries were prepared as previously described (Austenaa et al., 2021). The purified DNA libraries were quantified with the Quantifluor reagent (cat. no. E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent). DNA libraries were diluted to a working concentration of 4 nM and 50-bp single reads sequenced on an Illumina Novaseq6000 platform.

treatment_protocol: Cells were treated with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL. Trichostatin A (TSA, cat. no. S1045, Selleck) was added for 10, 20 and 30 min. Spermine Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) was used at 0.5 mM for 15 min before TSA or LPS treatment.

tag: strain

value: untreated


title: CID004744-1-reup

value: 3 prime v3.1

tag: cellsloaded

tag: Sex

value: M

tag: ethnicity

value: Caucasian


title: BMDM_UT_R1

description: BMDM untreated


title: INH_R3

value: 30min INOS inhibitor


title: BMDM_TSA_R2

value: 20min TSA


title: CID004743-1-reup

tag: disease

value: UC

tag: disease duration

value: Post

value: No

tag: inflammation score


title: BMDM_TSA_R1

value: Mouse  Bone-Marrow derived Macrophages (BMDM)


title: BMDM_NO_TSA_R2

value: 15min NO + 20min TSA


title: BMDM_NO_TSA_R1


title: CID004738-1-reup

value: gut

value: CD

tag: patient

tag: site

value: Rectum

tag: match


title: CID004741-1-reup

tag: treatment

value: Pre

tag: batch


title: INH_R1

tag: cell type

value: Chromatin-associated RNA


title: CID004751-1-reup

tag: tissue

tag: inflammation

value: Yes


title: CID004740-1-reup

tag: librarytype

value: Inflamed


title: CID004737-1-reup

value: 3 prime v3.1

tag: age


title: CID004739-1-reup

value: M


title: BMDM_NO_R2

tag: strain

value: 15min NO


title: BMDM_NO_R1


title: CID004736-1-reup

tag: cellsloaded

value: Caucasian


title: BMDM_NO_LPS_R1

value: 15min NO + 1h LPS


title: BMDM_LPS_R2

value: 1h LPS


title: CID004733-1-reup

tag: Sex


title: CID004732-1-reup

tag: ethnicity


title: CID004735-1-reup

tag: disease

value: Post


title: CID004734-1-reup

tag: disease duration


title: BMDM_LPS_R1


title: shLUC_TSA_R2

description: BMDM infected with Lentivirus expressing non-targeting shRNA treated with 20minutes with Trichostatin A (TSA, cat. no. S1045, Selleck)

data_processing:
Reads were quality filtered according to the illumina pipeline
Paired-end Spike-in H3K27ac ChIP-seq was analyzed similar to previous reports (Orlando et al., 2014). Briefly the genome sequence of both the mouse (mm10 assembly) and the Drosophila genomes (assembly dm6) were concatenated to produce a chimeric combined genome, with the Drosophila chromosomes re-named to include the “_dm6” suffix.
Custom Bowtie2 index was generated using the chimeric genome and used to sequence in pair-end mode each sample (with the following commands “-X 1000 -k 2 -t --phred33 -p 8 -q”). Mapped reads were then filtered by keeping reads mapped in proper pair and removing those unmapped, having mate unmapped, and failing quality. Duplicated reads were then removed using samtools markdup function. Finally reads split into mm10 and dm6 based on the chromosome suffix which was at the end removed.
ChIP-seq peaks were identified using MACS2 (version 2.2.6) with parameters “‐‐keep-dup ‘all’ ‐‐call-summits ‐‐nomodel ‐‐nolambda ‐‐extsize 300”. Reference set of peaks was identified selecting significant peaks per-samples in addition to being consistent between replicated (overlapping area of at least 50% between replicates).
ChIP-seq scaling factors were computed either identifying internal invariant peaks as previously described (Gualdrini et al., 2016) or using solely the reads mapping to the dm6 genome (as described in Orlando et al., 2014).
Assembly: mm10, dm6
Supplementary files format and content: bigWig

growth_protocol: Bone marrow derived macrophage (BMDM) cultures were carried out as described before (Curina et al., 2017). Cells were infected with lentivirus expressing either non-targeting shRNA (shNT) or shRNA targeting MED14.

extract_protocol:
H3K27ac ChIP-seq was carried out as previously described (Gualdrini et al., 2022). Briefly, 5x106 BMDM cells were fixed with 1% formaldehyde (cat. no. 252549, Merck) for 10 min at room temperature and lysed to prepare nuclear extracts.. After chromatin shearing by sonication with a Branson Ultrasonics Sonifier, lysates were incubated overnight at 4°C with protein G Dynabeads (cat. no.10009D, Invitrogen) previously coupled with H3K27ac (cat. no. ab4729, Abcam)  antibody. 1 μg of chromatin was supplemented with 5% spike-in of S2 Drosophila chromatin (prepared in the same manner). After immunoprecipitation, beads were recovered using a magnetic stand and washed with RIPA buffer (50 mM HEPES-KOH at pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycho- late). Immunoprecipitated chromatin was eluted and cross-link-reverted overnight at 65°C. DNA was purified with QIAquick PCR purification kit (cat. no. 28106, Qiagen) and then quantified with QuantiFluor (cat. no. E2670, Promega).
DNA libraries were prepared as previously described (Austenaa et al., 2021). The purified DNA libraries were quantified with the Quantifluor reagent (cat. no. E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the high-sensitivity assay HD5000 (cat. no. 5067-5592, Agilent). DNA libraries were diluted to a working concentration of 4 nM and 50-bp single reads sequenced on an Illumina Novaseq6000 platform.

tag: strain background

value: 20min TSA


title: shLUC_UT_R2

description: BMDM infected with Lentivirus expressing non-targeting shRNA untreated

value: Mouse  Bone-Marrow derived Macrophages (BMDM)

value: untreated


title: shLUC_UT_R1


title: CID004731-1-reup

value: gut

tag: patient

tag: inflammation score


title: CID004742-1-reup

value: UC

tag: site

tag: match


title: shLUC_NO_TSA_R2

description: BMDM infected with Lentivirus expressing non-targeting shRNA pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes followed by 20minutes with Trichostatin A (TSA, cat. no. S1045, Selleck)

tag: treatment

value: 15min NO + 20min TSA


title: CID004729-1-reup

value: CD

tag: batch


title: CID004728-1-reup

tag: tissue


title: CID004730-1-reup

value: Rectum

tag: inflammation


title: shLUC_NO_TSA_R1

tag: cell type


title: BMDM_NO_LPS_R2


title: shLUC_TSA_R1


title: CID004725-1-reup

tag: librarytype

value: Pre

tag: age

value: Yes


title: shLUC_NO_R1

description: BMDM infected with Lentivirus expressing non-targeting shRNA pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes


title: CID004727-1-reup

value: 3 prime v3.1

tag: cellsloaded


title: CID004726-1-reup

value: Inflamed

tag: Sex

value: M


title: shLUC_NO_LPS_R2

description: BMDM infected with Lentivirus expressing non-targeting shRNA pre-treateed with Nonoate (NO donor, cat, no. CAY-82150, Cayman Chemical) for 15minutes followed by 1h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL


title: shLUC_NO_LPS_R1


title: shLUC_NO_R2

value: 15min NO


title: CID004723-1-reup

value: F

tag: ethnicity

value: Caucasian


title: CID004722-1-reup

tag: disease

value: Post


title: CID004720-2-reup

tag: disease duration


title: shLUC_LPS_R2

description: BMDM infected with Lentivirus expressing non-targeting shRNA and treated for 1h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL

tag: strain background

value: 1h LPS


title: shLUC_LPS_R1

value: Mouse  Bone-Marrow derived Macrophages (BMDM)


title: CID004719-1-reup

tag: patient


title: shA1_TSA_R2

value: 20min TSA


title: CID004718-1-reup

value: gut

tag: inflammation score


title: shA1_TSA_R1


title: shA1_UT_R1

value: untreated


title: CID004715-1-reup

tag: site

value: Sigmoid

value: No


title: shA1_UT_R2


title: CID004713-1-reup

value: CD

tag: match


title: shA1_NO_TSA_R2

tag: treatment

value: 15min NO + 20min TSA


title: shA1_NO_TSA_R1


title: shA1_NO_R2


title: shA1_NO_R1


title: CID004711-1-reup

value: Rectum

value: Pre

value: Yes

tag: batch


title: shA1_NO_LPS_R2

value: 15min NO + 1h LPS


title: CID004714-1-reup

tag: tissue

value: 3 prime v3.1

value: M


title: CID004724-1-reup

tag: inflammation

value: F

value: Caucasian


title: CID004710-1-reup

value: Inflamed


title: CID004708-1-reup


title: shA1_NO_LPS_R1

tag: cell type

value: Mouse  Bone-Marrow derived Macrophages (BMDM)


title: shA1_LPS_R1

value: 1h LPS


title: shA1_LPS_R2


title: CID004707-1-reup

value: gut

tag: librarytype

value: UC

value: Post


title: CID004706-1-reup

value: Sigmoid

tag: age


title: CID004709-1-reup

tag: cellsloaded

value: CD


title: sh2_MED14_UT_R2

description: BMDM infected with Lentivirus expressing shRNA against MED14 and treated for 20minutes with Trichostatin A (TSA, cat. no. S1045, Selleck)

value: untreated


title: CID004716-1-reup

value: Rectum

tag: Sex


title: sh2_MED14_UT_R1


title: CID004704-1-reup

value: Pre

tag: ethnicity


title: sh2_MED14_TSA_R2

value: 15min NO + 20min TSA


title: CID004705-1-reup

tag: disease

value: No


title: sh2_MED14_TSA_R1

description: BMDM infected with Lentivirus expressing shRNA against MED14 and treated for 1h with lipopolysaccharide (LPS) from E. coli, serotype EH100(Ra) from Alexis (cat. no. ALX-581-010-L002) at 10 ng/mL


title: sh2_MED14_LPS_R2


title: sh2_MED14_LPS_R1


title: CID004701-1-reup

value: 3 prime v3.1

tag: disease duration

value: Yes


title: CID004702-1-reup

value: F


title: CID004712-1-reup

value: M

value: Caucasian


title: sh1_MED14_UT_R2

value: Mouse  Bone-Marrow derived Macrophages (BMDM)

tag: strain background


title: CID004700-1-reup

tag: patient


title: sh1_MED14_UT_R1


title: sh1_MED14_TSA_R2


title: sh1_MED14_TSA_R1


title: CID004698-1-reup

value: Inflamed

tag: inflammation score


title: CID004697-1-reup

value: gut

tag: site


title: CID004696-1-reup

value: UC

tag: match


title: sh1_MED14_LPS_R2

tag: treatment

value: 1h LPS


title: sh1_MED14_LPS_R1


title: Fat bodies, Control, rep3

city: Jerusalem, Kiryat Shemona

first: Neta

last: Herman

address: Kiryat Shemona

department: Gentics, Nutrition

country: Israel

institute: Hebrew University Of Jerusalem, Migal

data_processing:
To analyze the RNA sequencing data, we used the nf-core/rnaseq bioinformatics pipeline, version 3.14.025. The STAR–Salmon route was chosen for alignment and quantification.
Assembly: GCF_905115235.1_ _iHerIll2.2.curated.20191125.
Supplementary files format and content: csv file includes raw counts for each sample

molecule: polyA RNA

organism: Hermetia illucens

source_name: Fat bodies

growth_protocol: The larvae were reared on a sterile standard Gainesville diet for 10 days in rearing chamber (27 ± 1.0 °C, RH 70% ± 5%, and D/L 12/12 photoperiod) and then transferred into four treatment groups.

extract_protocol:
Four days after fungal treatment 5 larvae from each biological replication were dissected and the fat body was collected into Eppendorf on dry ice. RNA was then extracted using RNA extraction kit (Hybrid-RTM-GeneAll) and DNase removal performed using Clean-Up RNA concentrator Kit (A&A BIOTECHNOLOGY).
The libraries were then constructed using ++NEBNext Ultra II RNA Library Prep Kit and NEBNext Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: Eeach replicate comprising 50 larvae in 25 grams of standard Gainesville diet. The treatments were administered as follows: 1) Control (no fungi added) - 50 ml sterile water.  2) B. bassiana - commercial strain GHA-11.3% (RIMI). Fungal spore quantification was performed using a hemocytometer, and a concentration of 107 cells/ml was selected (10 ml of commercial strain and 40 ml of water) as previously described 16,17.  3) C. tropicalis-1 gram of yeast pellet in 50ml sterile water. 4) S. cerevisiae -1 gram of yeast pellet in 50ml sterile water.

value: Fat bodies

tag: agent

value: Control


title: Fat bodies, Control, rep2

tag: tissue


title: CID004703-1-reup

data_processing:
Cell Ranger v3.1.0 was used to align reads to reference (GRCh38-3.0.0) and generate feature- barcode matrices from the Chromium single-cell RNA-seq output.
Assembly: GRCh38-3.0.0
Supplementary files format and content: We have provided filtered matrices containing the outputs of the Cell Ranger pipeline in .h5 format for each sample as outlined above.

value: Sigmoid

tag: inflammation

tag: batch


title: Fat bodies, Control, rep4


title: Sertoli-like TM4 cells, mutated gdf6Y (del9), rep5

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422
The names of the RNA-seq reads were extended by their unique molecular identifier (UMI) with UMI-tools’ extract command version 1.1.1 (PMID: 28100584).
These name-modified reads were aligned to the mouse reference genome (GRCm39 with the Ensembl genome annotation release 107) using STAR 2.7.10a (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
PCR duplicates were removed from the alignment results using UMI-tools’s dedup command.
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 2.0.3 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677)
Assembly: GRCm39
Supplementary files format and content: csv file containing raw read counts per gene over all samples

source_name: Sertoli-like TM4 cells

growth_protocol: TM4 cells were cultivated in Dulbecco’s Modified Eagle Medium (DMEM; Gibco™ #41966 – high glucose, pyruvate) with 10 % FBS at 37°C and 5 % CO2.

extract_protocol:
To isolate RNA from transfected cells, the QIAGEN RNeasy Mini Kit was used. Cells were lysed directly in the wells using RT buffer containing ß-mercaptoethanol. Samples were further homogenized using QIAshredder (QIAGEN). DNase digestion was performed on-column using the RNase-Free DNase Set (QIAGEN) as suggested in the RNeasy Mini Kit protocol. The RNA was eluted in 50 µl DEPC-treated H2O.
Libraries were prepared from 300 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (New?England Biolabs). Deviating from the instruction, in order to avoid over-amplification of libraries in the final amplification step, qPCR was performed for each library priorily for determine the optimal cycle number (exponential phase) .

treatment_protocol: 0.5 x 106 TM4 cells per well were seeded into a 6-Well plate. 24 h later, the cells were transfected with 2.5 µg of plasmid DNA (gdf6Y: pcDgdf6Y, del9: pcDgdf6Ydel9, or EV: pcDNA3.1-HA) per well using Lipofectamine 3000 (Thermo Fisher Scientific) and incubated for 24 h at 37°C and 5 % CO2 before RNA isolation.

tag: cell line

value: Sertoli-like TM4 cells


title: Fat bodies, Control, rep1


title: Fat bodies, C. tropicalis, rep4

value: C. tropicalis


title: Sertoli-like TM4 cells, mutated gdf6Y (del9), rep4


title: Fat bodies, C. tropicalis, rep3


title: CID003682-1-reup

tag: librarytype

value: 3 prime V3

value: CD

value: Post

tag: age


title: CID003681-1-reup

tag: cellsloaded

tag: Sex

value: Yes


title: Sertoli-like TM4 cells, mutated gdf6Y (del9), rep3


title: Fat bodies, C. tropicalis, rep2


title: Sertoli-like TM4 cells, mutated gdf6Y (del9), rep2


title: Fat bodies, C. tropicalis, rep1


title: Fat bodies, S. cerevisiae, rep4

value: S. cerevisiae


title: CID003680-1-reup

tag: disease

value: F

tag: ethnicity


title: Sertoli-like TM4 cells, mutated gdf6Y (del9), rep1


title: CID003679-1-reup

tag: disease duration

value: Pre

value: Caucasian


title: Fat bodies, S. cerevisiae, rep3


title: CID003678-1-reup

tag: patient

value: Inflamed


title: Fat bodies, S. cerevisiae, rep1


title: Sertoli-like TM4 cells, gdf6Y, rep5


title: CID003683-1-reup

value: gut

value: Rectum

value: No

tag: inflammation score


title: Fat bodies, B. bassiana, rep4

value: Fat bodies

value: B. bassiana.


title: CID003677-1-reup

tag: site


title: CID004699-1-reup

value: 3 prime v3.1

value: UC

tag: match


title: Sertoli-like TM4 cells, gdf6Y, rep4

value: Sertoli-like TM4 cells

tag: treatment


title: Fat bodies, B. bassiana, rep3

tag: agent


title: CID003676-2-reup

tag: tissue

value: 3 prime V3

value: M


title: Sertoli-like TM4 cells, gdf6Y, rep2


title: Fat bodies, B. bassiana, rep2


title: Fat bodies, B. bassiana, rep1


title: Sertoli-like TM4 cells, gdf6Y, rep3


title: 6hr, DMSO, biorep2, RIBOSEQ

city: Trondheim

first: Felicity

middle: Jayne

last: Ashcroft

address: Hogskoleringen 5

department: Biology

country: Norway

institute: NTNU

data_processing:
EclipseBio pipeline v1
Unique molecular identifiers (UMIs) were pruned from read sequences using umitools (v1.1.1).
Next 3' adapters were trimmed from reads using cutadapt (v3.2).
Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome hg38 using STAR (v2.7.7a) and PCR duplicates were removed using umi_tools (v1.1.1).
Differentially expressed and occupied genes were identified using DESeq2
Assembly: UCSC version GRCh38 (hg38) / GENCODE Release 41 (GRCh38.p13)
Supplementary files format and content: deseq_results.tsv (results and statistics table for differential expression gene counts analysis)

source_name: CCRF-CEM

extract_protocol:
Eclipse Bio RNA extraction
250 ng of cytosolic RNA was used to build 3' RNA-Seq libraries, 10 ug RNA was used in the immunoprecipiation and Ribo-Seq analysis. RNA from both sources was fragmented and libraries egnerated from poly A tails

value: CCRF-CEM

tag: cell type

value: T-cell acute lymphoblastic leukemia

value: DMSO


title: CID003675-1-reup

extract_protocol:
Gut and synovial tissue samples and PBMCs were thawed into warm IMDM media with 10% FBS and washed. Gut samples were EDTA-treated pre-digestion with rotation for 15 min to remove dead/damaged epithelial cells, and then dissociated enzymatically with Liberase TM and DNase into a single-cell suspension with rotation. Thawed synovial samples were digested in Liberase TL and DNase in warm media for 30 min, with agitation. All cell samples were strained and washed twice with PBS with 0.4% bovine serum albumin (BSA). Live cells were counted using acridine orange/propidium iodide and ≤ 10,000 cells were loaded per 10X Chromium channel.
The GEX 3’ V3 protocol was followed.

value: CD

tag: inflammation

value: Post

value: Yes

tag: batch


title: 6hr, DMSO, biorep1, RIBOSEQ

tag: cell line


title: 6hr, AVX420, biorep1, RIBOSEQ


title: CID003673-1-reup

tag: librarytype

value: Pre

tag: age

value: Caucasian


title: Sertoli-like TM4 cells, gdf6Y, rep1


title: CID003674-1-reup

value: gut

tag: cellsloaded

value: Inflamed

tag: Sex


title: 1hr, AVX420, biorep2, RIBOSEQ


title: Sertoli-like TM4 cells, empty vector (EV), rep6

value: EV


title: 1hr, Torin1, biorep2, RIBOSEQ


title: 1hr, DMSO,biorep2, RIBOSEQ


title: CID003672-1-reup

tag: disease

tag: ethnicity


title: Fat bodies, S. cerevisiae, rep2

value: Fat bodies

value: S. cerevisiae


title: Sertoli-like TM4 cells, empty vector (EV), rep5


title: 1hr, AVX420, biorep1, RIBOSEQ


title: 1hr, Torin1, biorep1, RIBOSEQ


title: Sertoli-like TM4 cells, empty vector (EV), rep4


title: 1hr, DMSO,biorep1, RIBOSEQ


title: CID003670-1-reup

value: UC

tag: disease duration

tag: patient

value: Sigmoid

value: F

value: No


title: 16hr, AVX420, biorep2, RNASEQ

value: CCRF-CEM


title: 16hr, DMSO, biorep2, RNASEQ

value: T-cell acute lymphoblastic leukemia


title: Sertoli-like TM4 cells, empty vector (EV), rep3

value: Sertoli-like TM4 cells


title: 16hr, AVX420, biorep1, RNASEQ


title: CID003671-1-reup

value: 3 prime V3

value: CD

tag: site

value: M

tag: inflammation score


title: 6hr, AVX420, biorep2, RIBOSEQ

tag: treatment


title: 16hr, DMSO, biorep1, RNASEQ

value: DMSO


title: Sertoli-like TM4 cells, empty vector (EV), rep2


title: 6hr, DMSO, biorep2, RNASEQ


title: CID003667-1-reup

value: Pre

value: Caucasian

tag: match

value: Yes


title: 6hr, AVX420, biorep2, RNASEQ


title: CID003669-1-reup

tag: tissue

value: gut

value: Inflamed

value: Post


title: Sertoli-like TM4 cells, empty vector (EV), rep1

value: EV


title: CID003665-1-reup

value: UC


title: 1hr, AVX420, biorep2, RNASEQ

tag: cell type


title: Elastase-expt2-rep2

city: Columbus

first: Yan

last: Hu

state: OH

address: 575 Children’s Crossroad, RB3 6th Floor WB6271

department: Pediatrics

institute: Nationwide Children's Hospital

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
cell_metadata.csv.gz

data_processing:
FASTQ files were processed and aligned to the mm10 reference genome using the cell ranger count pipeline (10X Genomics). The mm10 genome was supplemented with eGFP-SV40 and tdtomato-SV40 transgene sequences. Gene expression data were analyzed using the Seurat R package. Cells from the first experiment were filtered to only include those with >500 UMI counts, <60,000 UMI counts, >1500 genes detected, and <12.5% mitochondrial counts. Cells from the second experiment were filtered to include those with >500 UMI counts, <20,000 UMI counts, >200 genes detected, < 5000 genes detected and < 3 Mean Absolute Deviations and < 20% mitochondrial counts. UMI counts were normalized by the total counts for the cell, multiplied by a scale factor (10,000), and log-transformed (NormalizeData). Normalized counts were scaled and centered (ScaleData) using the top 3,000 variable features (FindVariableFeatures). The scaled data were used for PCA (RunPCA), and the first 20 principal components were used for clustering (FindNeighbors, FindClusters) and to calculate uniform manifold approximation and projection (RunUMAP). The two experiments were integrated using Harmony, with the theta parameter set to 1. Cell types were annotated using clustifyr with a murine lung regeration single cell dataset as the reference. Differentially expressed genes were identified for each cluster using the R package presto (github.com/immunogenomics/presto). Gene set enrichment analysis was performed using the R package clusterProfiler.
Assembly: mm10
Supplementary files format and content: cell_metadata.csv.gz: Cell level metadata containing cell type assignments in .csv format
Supplementary files format and content: barcodes.tsv.gz,features.tsv.gz,matrix.mtx.gz: UMI count matrix in marketMatrix format.

extract_protocol:
At day 21 after PPE or saline treatment, lung lobes were inflated and submerged with dispase  at room temperature for 45min. The digested lung lobes were further homogenized in DMEM/F12 with PenStrep and DNAseI. The single cell suspension was sequentially filtered through 70µm and 40µm cell strainers on top of 50ml tubes, followed by centrifuge at 300g for 10min at 15°C. Epithelial cells were enriched with anti-mouse CD326  and MACS LS column. Cells were stained with APC anti-mouse Epcam and DAPI to FACS sort for Epcam+/DAPI-/tdTomato+ cells for single cell capture with 10x Chromium system.
Single cell libraries were generated using the 10x genomics chromium 3' end library prepartion kit.

treatment_protocol: Both male and female Scgb1a1-CreERTM;Rosa-tdTomato mice at age of 8 to 10 weeks old were subject to intraperitoneal injections of tamoxifen (200mg/kg bodyweight; Sigma, T5648) in corn oil (Sigma, C8267) every 2 days for 3 doses. One week after the last does of tamoxifen, mice were treated with a single dose of porcine pancreatic elastase (PPE, n=3) (40U/kg body weight in 80ul volume; Sigma, 45124) or saline (n=2) via oropharyngeal injections.

value: lung

value: PPE


title: 1hr, DMSO,biorep2, RNASEQ

value: CCRF-CEM


title: Saline-expt2-rep2

value: Saline


title: CID003386-1-reup

tag: inflammation


title: CID003385-1-reup

value: No

tag: batch


title: 1hr, AVX420, biorep1, RNASEQ

tag: cell line

value: T-cell acute lymphoblastic leukemia


title: 1hr, DMSO,biorep1, RNASEQ


title: Saline-expt1-rep1


title: CID003384-1-reup

tag: librarytype

value: 3 prime V3

value: CD


title: 1hr, Torin1, biorep1, RNASEQ


title: Elastase-expt2-rep1


title: CID003383-1-reup

value: Rectum

tag: age

value: M


title: CLL3 CD45+ and CD45-

city: Boston

first: Antonio

last: Ferreira

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB-652

institute: Brigham and Women’s Hospital

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 and aligned to the GRCh38 transcriptome with STAR aligner.
Assembly: GRCh38
Supplementary files format and content: Tab-separaed value file and matrix files

source_name: Lymph node

extract_protocol:
Fresh samples were cut with a scalpel into 1mm3 fragments, viably frozen, and stored at -80°C in Cryostor® CS10. Samples involved by reactive processes, FL, or CLL were selected for downstream analyses. LN samples were thawed and digested with proteases at 37o C for up to 1 hr. Debris/cell clumps were removed by filtration through mesh with 100 μm pores and red cells were lysed. After staining with DAPI to exclude dead cells, CD45+ and CD45- cells were isolated by cell sorting and subjected immediately to scRNA-seq.
Encapsulation and cDNA library generation (10X Genomics Single Cell 3′Kit V3.1) from sorted cells were per the manufacturer’s protocol. cDNA libraries were sequenced to an average of 41,764 reads per cell using an Illumina Nextseq 500.

value: Lymph node

tag: sample type

value: CLL/SLL

value: CD45+ and/or CD45-


title: CLL2 CD45+


title: CID003666-1-reup

value: gut

tag: cellsloaded

value: Inflamed

value: Pre

tag: Sex

value: F

value: Caucasian


title: 6hr, AVX420, biorep1, RNASEQ


title: FL 3 CD45+ and CD45-

value: FL, grade 2-3A, follicular growth pattern


title: 6hr, DMSO, biorep1, RNASEQ

value: CCRF-CEM

value: DMSO


title: CID003382-1-reup

tag: disease

value: Post

tag: ethnicity

value: Yes


title: FL 2 CD45+

value: FL, grade 1-2 of 3, follicular growth pattern


title: CID003380-1-reup

value: 3 prime V3

value: CD

tag: disease duration

tag: patient


title: Hypothalamus in normal mouse #3

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

data_processing:
Adapter sequences, low-quality bases, and reads with excessive ambiguity were removed utilizing TrimGalore (v0.6.6).
Alignments of trimmed reads to the Mus musculus reference genome (GRCm38) were performed using the STAR aligner (v2.7.9a).
Transcript abundance was quantified as both read count and transcripts per million (TPM) for each gene using RSEM (v1.3.3).
Assembly: Mus musculus reference genome (GRCm38)
Supplementary files format and content: Tab-delimited text file includes expected_count,  TPM,     FPKM for each sample

source_name: Hypothalamus

growth_protocol: CT-26 murine colon carcinoma cell line (CRL-2638) was purchased from the American Type Culture Collection in Manassas, VA, USA. The cells were cultured in Dulbecco's Modified Eagle Medium containing 4.5 g/L glucose (DMEM), supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) and 100 IU penicillin/100 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated from gasrocnemius muscle and hypothalamus of CT-26 tumor-bearing cachectic mice (n = 3) and healthy controls (n = 3) using TRIzol reagent (Cat# 15596026, Invitrogen).
mRNA sequencing libraries were constructed using the the MGIEasy RNA Directional Library Prep Kit and sequenced on the MGISEQ-2000 system with 100 bp paired-end reads.

treatment_protocol: To induce cachexia, CT-26 cells (2×106 cells/mouse) were subcutaneously injected into the abdominal region of 7-week-old male BALB/c mice. By day 10 post-tumor injection, tumor-bearing mice showed a 7−10% decrease in body weight compared to healthy mice. On day 25 post-tumor injection, mice were euthanized using CO2 inhalation, and tumors, epididymal fat, and hind-limb were removed and weighed. Hind-limb muscle and hypothalamus samples were snap-frozen on dry ice and stored at -80°C for RNA sequencing.

value: Hypothalamus

value: male

tag: strain

value: BALB/c

value: No tumor injection


title: Gastrocnemius in normal mouse #2

source_name: Gastrocnemius

value: Gastrocnemius

tag: treatment


title: Gastrocnemius in normal mouse #3


title: CID003381-1-reup

value: gut

tag: site

value: Inflamed

tag: match

tag: inflammation score


title: FL 2 CD45-

tag: tissue

value: Lymph node

tag: cell type

value: CD45+ and/or CD45-


title: CLL2 CD45-

value: CLL/SLL


title: CLL1 CD45-


title: Hypothalamus in normal mouse #2


title: Reactive 3 CD45+ and CD45-

value: Nonspecific reactive hyperplasia


title: CID003379-1-reup

tag: inflammation

value: Pre

value: F

value: Caucasian

tag: batch


title: Hypothalamus in normal mouse #1

tag: age


title: 1hr, Torin1, biorep2, RNASEQ

tag: cell line

value: CCRF-CEM

value: T-cell acute lymphoblastic leukemia


title: Gastrocnemius in normal mouse #1


title: Reactive 2 CD45-

tag: sample type

value: Nonspecific reactive hyperplasia (Toxoplasmosis)


title: CID003378-1-reup

tag: librarytype

value: 3 prime V3

tag: cellsloaded

value: CD

value: Rectum

tag: Sex

value: Yes


title: CLL1 CD45+


title: Edaravone treated, biol rep 3, Hour 48

city: Ottawa

first: Arezu

last: Jahani-Asl

state: Ontario

address: 451 Smyth Road

department: Department of Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
RNA-seq reads were mapped to the human genome assembly (hg38) using HISAT2.
The number of aligned reads per gene was obtained with HTSeq and gene annotations were retrieved from GENCODE (Basic gene annotation, release #38).
Genes with an average read counts smaller than 10 were filtered out. Differential expression analysis was performed with DESeq2, p-values were corrected by independent hypothesis weighting. Genes with an adjusted p-value smaller than 0.1 were considered statistically differentially expressed.
Assembly: hg38
Supplementary files format and content: tab gene count files (HTSeq output).
Supplementary files format and content: CSV of gene names, adj. P-values, and LFC (DESeq output).

extract_protocol:
Total RNAs were isolated from cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Libraries for poly (A)+ RNA were prepared according to the Illumina protocol

treatment_protocol: BTSC73 were treated with vehicle control or Edaravone for 48 hours.

value: Brain tumour stem cells

value: Edaravone (Sigma, # M70800)


title: Reactive 2 CD45+


title: FL 1 CD45-

value: FL, grade 1-2 of 3, follicular growth pattern


title: Reactive 1 CD45-

value: Lymph node


title: CID003377-1-reup

value: gut

tag: disease

tag: disease duration

value: Inflamed

value: Post

tag: ethnicity


title: Hypothalamus in cachectic mouse #3

value: Hypothalamus

value: male

tag: strain

value: BALB/c

tag: treatment

value: CT-26 cell injection


title: Edaravone treated, biol rep 2, Hour 48


title: FL 1 CD45+

value: CD45+ and/or CD45-


title: Control, biol rep 2, Hour 48

value: vehicle control (DMSO 0.1%)


title: Edaravone treated, biol rep 1, Hour 48


title: CID003376-1-reup

value: 3 prime V3

tag: patient

tag: site

value: F

value: Caucasian

tag: match


title: Gastrocnemius in cachectic mouse #3

tag: tissue

value: Gastrocnemius


title: CID003375-1-reup

value: CD

tag: inflammation

value: Yes

tag: inflammation score


title: Hypothalamus in cachectic mouse #2

tag: age


title: CID003374-1-reup

value: Rectum

tag: batch


title: Gastrocnemius in cachectic mouse #2


title: Hypothalamus in cachectic mouse #1


title: CID003373-1-reup

value: UC

value: Pre

value: M


title: B73/Mo17 mixed, seedling, frozen

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
FASTQ files from demultiplexed BCLs were processed with cellranger
Assembly: Zea mays AGPv5
Supplementary files format and content: maize_seedling_snRNA_seq_raw_counts.rds; matrix with 3' read counts overlapping genes by barcode
Supplementary files format and content: maize_seedling_snRNA_seq_metadata.txt; metadata for barcodes found in the raw counts matrix

organism: Zea mays

source_name: Seedling

extract_protocol:
Nuclei were isolated identically to the protocol used here: https://doi.org/10.1016/j.cell.2021.04.014
10x Genomics 3' snRNA-seq version 3.1 per manufactures instructions

value: Seedling

tag: genotype

value: B73/Mo17 mixed

value: fozen


title: B73, seedling, fresh

value: fresh


title: Gastrocnemius in cachectic mouse #1

value: male

value: BALB/c

value: CT-26 cell injection


title: CID003372-1-reup

city: Oxford

first: Tom

last: Thomas

institute: University of Oxford

value: gut

tag: librarytype

value: 3 prime V3

value: Inflamed


title: maize_seedlings_pool39_scATAC

data_processing:
FASTQ files from demultiplexed BCLs were processed with chromap and a custom barcode whitelist (depending on the Novaseq chemistry).
Chromap output BAM files were used as input for soup_or_cell to genotype cell barcodes.
Barcodes corresponding to the same genotype were aggregated in total (Merged_Genotype) or by cell type.
Chromatin accessibility scores for accessible chromatin regions were scored as counts per million and then inverse normal transformed.
Cis chromatin accessibility QTL were identified using tensorQTL
Assembly: Zea mays AGPv5
Supplementary files format and content: All_contexts.pass_FDR.cis_caQTL.rds: R data.frame object containing the results of caQTL mapping. The original matrix has been filtered to retain only caQTL meeting significance thresholds.
Supplementary files format and content: normalized_chromatin_accessibility_and_covariate_matrices.tar.gz: A directory containing the bed formatted matrices of inverse normal transformed chromatin accessibility scores across all ACRs and genotypes. One matrix per cell type. This directory includes the same number of matrices, but for covariates.
Supplementary files format and content: All_pools.socObj.raw.rds: an R object containing a sparse matrix with 500bp genome tiles as rows and cell barcodes as columns. 1 corresponds to at least 1 Tn5 insertion within the genomic window.

source_name: seedling

extract_protocol:
See doi.org/10.1016/j.xpro.2021.100737
10x Genomics scATAC-seq per manufactures instructions

value: seedling


title: CID003370-1-reup

tag: cellsloaded

value: Caucasian


title: B73/Mo17 mixed, seedling, fresh


title: maize_seedlings_pool37_scATAC


title: Control_24 [N33]

city: Shanghai

first: Zhang

last: Weijia

address: Dongan Road 131

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality
Trimmed sequence reads were mapped to GRCh38
Read count extraction and normalization
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Aorta

extract_protocol:
RNA of aortic tissues was harvested using TRIzol. RNA concentration was measured using Agilent 2100  Bioanalyzer. A total of 1.5 μg RNA per sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit.

value: Aorta

tag: tissue type

value: Control

tag: subject status


title: CID003369-1-reup

address: Old Road Campus, Roosevelt Dr, Headington

source_name: gut

tag: disease

value: UC

tag: disease duration

value: Post

tag: Sex

value: Yes


title: CID003371-2-reup

tag: treatment

value: Pre

value: M

tag: ethnicity