title: crypt_f_26m_rep2 (total RNA-seq)

value: Small intestinal crypt

value: f


title: Intestinal stem cells, DMSO_ATAC_rep3

status: Public on Sep 05 2023

type: SRA

city: Beijing

first: Wei

last: Wu

address: Tsinghua Road, Medical Building

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
For bulk RNA-seq analysis, raw reads were trimmed for base call quality and for adapter sequences using Trim Galore! (v0.6.4_dev) and aligned to the mouse genome (Mus_musculus.GRCm38) using HISAT2 (v2-2.1.0), following quantified using HTSeq (v0.12.4) and differential expression analysis using DESeq2 (v1.24.0).
For ATAC-seq analysis, raw reads were trimmed for base call quality and for adapter sequences using Trim Galore! (v0.6.4_dev) and aligned to the mouse genome (Mus_musculus.GRCm38) using bowtie2 (v2.3.5.1). All mapped reads were shifted by +4 bp for the +strand and -5 bp for the -strand. Peaks were called for each sample using MACS2 (v 2.1.1.20160309) with parameters “-p 0.1 -nomodel -shift 100 -extsize 200 -B -SPMR”, and differential peaks were identified using DiffBind (v3.2.2). ChIPseeker (v1.28.3) was used to annotate accessible genomic regions.
For single cell RNA-seq analysis, the raw data were performed sample demultiplexing, barcode processing and single-cell 3′ gene counting with CellRanger software (v3.1.0) (10x Genomics). Mus_musculus GRCm38 genome with Ensemble transcriptome annotation was used as reference. Most subsequent analysis was performed with the Seurat R Package (v3.1.5). Cells with >1,200 UMIs and <7,000 UMIs were kept for downstream analysis. Cells with high percentage of mitochondrial reads (>15%) were considered as apoptotic and excluded as well. The cells were batch corrected using the Integrate function of Seurat.
Genome_build: Mus_musculus GRCm38
Supplementary_files_format_and_content: For bulk RNA-seq, raw gene counts of every gene and every sample were provided. In addition, differentially expressed gene list (including gene name, fold change, p value) generated using DESeq2 were in supplementary file.
Supplementary_files_format_and_content: For ATAC-seq, bigwig file were provided, scores represent signal intensity.
Supplementary_files_format_and_content: For single cell RNA-seq data, txt files for every sample were provided, the matrix containing gene counts of every gene in every barcoded single cells.

molecule: genomic DNA

organism: Mus musculus

source_name: intestinal stem cells sorted from organoids

growth_protocol: mouse intestinal organoids were cultured in ENR medium: Advanced DMEM/F12 (Thermo Scientific) supplemented with N2 (Thermo Scientific), B27 (Thermo Scientific), HEPES (Thermo Scientific), GlutaMax (Thermo Scientific), Penicillin/Streptomycin (Thermo Scientific), N-acetylcysteine (1.25 mM, Sigma Aldrich), EGF (50 ng/mL, Peprotech), Noggin (100 ng/mL, R&D), and R-spondin1 (500 ng/mL, made in-house).

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction.
cDNA library for bulk RNA seq was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). Sc-RNAseq library construction was prepared following standard 10x genomics protocols. The ATAC-seq libraries were prepared following Omni-ATAC protocol (Corces et al., 2017).

treatment_protocol: oranoids were treated with 0.05% DMSO or 25 μM Isx-9 for indicated period of time, starting at day 2 post passaging

tag: genotype

value: Lgr5-EGFP knock-in

tag: treatment

value: DMSO for 6 hours

tag: cell type


title: crypt_f_26m_rep1 (total RNA-seq)

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description: transcriptional profiling (RNA sequencing)

library_source: transcriptomic

data_processing:
Fastq files quality check was performed using FastQC v0.11.5.
The fastq files were mapped to the mm9 genome using TopHat v2.1.0 with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene is calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Htseq-count text file

molecule: total RNA

source_name: Small intestinal crypt

growth_protocol: Young (2 months old) and old (18-26 months old) male and female wild-type C57BL6/J mice were group housed and maintained in a specific pathogen-free animal facility in Fritz Lipmann Institute with 12 h of light/dark cycle and fed with a standard mouse chow.

extract_protocol:
Small intestinal crypts were isolated using the established protocol (Sato and Clevers, 2013) with minor modifications. Briefly, mouse small intestine was dissected, washed in cold PBS and opened longitudinally. Villi were removed by scraping with a coverslip. The villi-free intestinal pieces (2 cm) were washed four times in cold PBS and transferred to 5 mM EDTA/PBS, followed by two 30-min incubations at 4°C on a rotator. The tissue was transferred to fresh cold PBS and manually shaken for 30 sec. The crypt solution was filtered using a 70 µm cell strainer and centrifuged at 120xg for 5 min at 4°C.Isolated crypts were aliquoted, snap freezed in liquid nitrogen and stored at -80°C for further experiments. For RNA isolation, the crypts were immediately resuspended in Qiazol Lysis Reagent (Qiagen) and stored at -80°C.  Total RNA from crypts was isolated using QIAzol Lysis reagent (Qiagen) followed by isopropanol precipitation.
Total ribo-depleted RNA-seq library preparation was performed as described previously (Neri et al., Nature 2017) . In brief, 50 to 500 ng of total RNA were depleted of ribosomal RNA using the Ribo-Zero™ Gold Kit H/M/R Kit (illumina) following manufacturer’s instructions. Ribo-depleted RNA was resuspended in 17 μl of EFP buffer (illumina), heated to 94°C for 8 min, and used as input for first strand synthesis, using the TruSeq™ RNA Library Preparation Kit v2 (illumina) following manufacturer’s instructions.
Total RNA sequencing

tag: strain

tag: tissue

tag: gender

tag: age


title: Ctrl

first: Yuwei

last: Song

address: 38 Xueyuan Road

institute: Peking University

description:
10x Genomics
Homo_Ctrl-barcodes.tsv.gz
Homo_Ctrl-features.tsv.gz
Homo_Ctrl-matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (version 3.1) to demultiplex raw data and generate FASTQ files, and the resulting data were aligned and counted with Cell Ranger pipelines.
Assembly: mm10-2020-A; GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: skeletal muscle

extract_protocol:
Hindlimb gastrocnemius muscles were removed at 14 days after femoral artery ligation or sham operation (10 mice pre group). A single-cell suspension was prepared from hindlimb muscles by mechanical and enzymatic dissociation with minor modifications. Briefly, hindlimb muscles were dissected and minced into a fragmented muscle suspension. The muscle suspension was digested in Ham’s F10 containing 400 U/ml collagenase II (Worthington) and 11 U/ml dispase (Life Technologies) at 37 ℃ with reciprocal shaking (60 rpm/min) for 1 h. Detached cells were then filtered through a 40 μm cell strainer (BD Biosciences), and red cells were removed by lysis buffer. Subsequently, the remaining cells were washed with prewarmed (37 ℃) RPMI 1640 medium containing 10% FBS by centrifugation at 500 g for 5 min and suspended in PBS. Human muscle tissues were stored in prechilled PBS. A single-cell suspension was prepared from lower limb muscles by mechanical and enzymatic dissociation with minor modifications. Briefly, the muscle was cut into small fragments, and visible fat and connective tissue were removed. Then, the samples were transferred to low-glucose Dulbecco’s modified Eagle’s medium (LG-DMEM) containing 0.1% collagenase D and digested in a 37 °C water bath with agitation (60–70 rpm) for 60 min. Detached cells were then filtered through a 70 μm cell strainer (BD Biosciences), and red cells were removed with lysis buffer. Subsequently, the remaining cells were washed with prewarmed (37 ℃) LG-DMEM containing 10% FBS by centrifugation at 500 g for 5 min and suspended in PBS for further experiments. Cells were then stained with a LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit (1:1000) and Hoechst 33342 (Invitrogen, H3570, 1:1000) for 20 mins on ice. After being washed in PBS, cells were re-suspended in PBS. Single live cells (Hoechst+/Dead Cell Stain-) were sorted into PBS with 0.04% BSA using a BD FACS SymphonyS6 (BD Biosciences). In addition, we sorted tdTomato+ cells by the same method.
A Chromium Single Cell 3’ Reagent Kit v3 was used, and Standard 10X Chromium Single Cell 3’ v3 (10X Genomics GemCode Technology) protocols were followed for scRNA-seq. Briefly, single cells with specific 10X barcodes and unique molecular identifiers (UMIs) were generated by partitioning the cells into Gel Bead-in-Emulsions. A cDNA library was generated and sequenced with a Novaseq (S4) 6000 instrument (PE150).

value: muscle mononuclear single cells

value: skeletal muscle

tag: patient

value: A traffic accidents amputation patient

value: 70 years old


title: Intestinal stem cells, DMSO_ATAC_rep2

value: intestinal stem cells sorted from organoids


title: 24h post-infection (hpi) uninduced [UI σ28 KD 3]

city: Omaha

first: Scot

middle: P.

last: Ouellette

state: NE

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

country: USA

institute: University of Nebraska Medical Center

description: PolyA and rRNA depleted for both human and bacteria

data_processing:
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Chlamydia trachomatis 434/Bu by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Assembly: http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu_gca_000068585/Info/Index
Supplementary files format and content: excel file showing fold changes and statistical significance between strains and treatment conditions

organism: Chlamydia trachomatis L2/434/Bu

source_name: Infected McCoy cell line

growth_protocol: McCoy cells were infected with C. trachomatis L2 and induced or not at 4 or 14 hpi with aTc. Samples were collected at 24 or 18 hpi, respectively.

extract_protocol:
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove eukaryotic mRNA and both prokaryotic and eukaryotic rRNA using Oligotex, MicrobEnrich, MicrobExpress, and Ribozero.
Illumina Ribo-Zero plus Microbiome

treatment_protocol: Indicated above in the the first characteristics column.

value: C. trachomatis L2 434/Bu

tag: induction

value: Uninduced

tag: plasmid

value: pL12CRia (σ28)

tag: knockdown/overexpression

value: Knockdown - dCas12 mediated


title: APA-seq of SW480

city: Guangzhou

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

institute: The Sun YAT-SEN UNIVERSITY

data_processing:
Raw reads were trimmed, filtered, and mapped to the human genome (hg19) using Bowtie (version 0.12.5)
The reads were clustered into poly(A) sites as described previously (Fu et a., 2011; Fu et al., 2015).
Total read counts from each sample were normalized to eliminate bias introduced by unequal read counts, and poly(A) sites with five or more normalized reads were used for further analysis.
Assembly: hg19
Supplementary files format and content: Wig file

source_name: colorectal

growth_protocol: The HEK293T cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin-streptomycin at 37°C in a 5% CO2 humidified incubator. And the normal colorectal cell lines (NCM460) and colorectal cancer cell lines (SW480, RKO) were cultured in RPMI 1640 supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer’s recommendations
1 ug total RNA was used to prepare the IVT-SAPAS library according to the previous report (Fu et al., 2015)

treatment_protocol: The lentiviral vectors PCDH-Bsd-Flag-CPSF6, PCDH-Bsd-Flag-CPSF6_Mut1 and PCDH-puro-Myc-CLK2 were constructed for CPSF6, CPSF6_Mut1 and CLK2 expression, respectively. The HEK293T cells were used for the lentiviral production and supernatant was collected at 48h and 72h after transfection.

value: colorectal

tag: cell line

value: colorectal cancer

value: WT


title: 24h post-infection (hpi) uninduced [UI σ28 KD 2]


title: crypt_f_18m_rep4 (total RNA-seq)


title: APA-seq of RKO

value: RKO


title: crypt_f_18m_rep3 (total RNA-seq)

value: Small intestinal crypt


title: Intestinal stem cells, DMSO_ATAC_rep1


title: 24h post-infection (hpi) uninduced [UI σ54 KD 1]

value: pL12CRia (σ54)


title: APA-seq of NCM460


title: HEK_100K_m6A-CT1

city: Singapore

first: Kiyofumi

last: Hamashima

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology (IMCB)

data_processing:
Adapter sequences of paired-end raw reads were trimmed using Trim Galore with parameters -q 30.
Trimmed reads were aligned to the hg19 & mm9 genome assembly using STAR aligner version 2.7.2 with the following parameters: --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30  --outFilterMismatchNmax 3 --outFilterMultimapNmax 1.
Peaks were called using Macs2 with parameters -f BAM -B -q 0.01 --nomodel --extsize 100 --keep-dup all and called peaks with log-q-value > 10 were used in downstream analyses.
Assembly: hg19 and mm9
Supplementary files format and content: Bed files were narrowPeak files generated by Macs2.

extract_protocol: For bulk m6A-CT library preparation, E14, EPSC, MEF and HEK293T nuclei were isolated with the following conditions: 1 min on ice in 0.020 % Triton X-100 for E14, 0.015 % Triton X-100 for EPSC; 5 min on ice in 0.2 % NP-40 for MEF, 0.02 % NP-40 for HEK293T. Aliquots of nuclei (5,000–100,000 nuclei) were bound to pre-activated Concanavalin A (Con-A) Conjugated Paramagnetic Beads (EpiCypher, #21-1411) and used in assay. All wash steps were performed on a magnetic separation rack. Undirected cDNA/RNA hybrid tagmentation for INPUT RNA was carried out as described previously. Briefly, nuclei were resuspended in 50 μL Reverse Transcription & Tagmentation Buffer, and incubated for 1 hour at 37 °C. 2.5 μL pAG-Tn5 was then added and vortexed briefly, and incubated for 1 hour at 37 °C.  Antibody directed tagmentation for m6A-CT was carried out as  same as sc-m6A-CT using 1 μg anti-m6A antibody (Synaptic Systems, #202003). When tagmentation was done, 54.5 μL of 0.5 M EDTA, 1 μL of 20 mg/mL Proteinase K and 5.5 μL of 10% SDS were sequentially added to the sample and incubated at 58 °C for 1 hour. An equal amount of Phenol-chloroform-isoamyl alcohol 25:24:1 (PCI), pH 6.7 was added to each sample, and PCI extraction followed by ethanol precipitation were performed. To perform gap-filling, the purified RNA/DNA samples were mixed with 0.32 U/μL Bst 3.0 DNA Polymerase (New England Biolabs) and Q5 High-Fidelilty 2× PCR Master mix (New England Biolabs), and incubated for 5 min at 58 °C, 5 min at 72 °C, and then at 5 min at 80 °C to inactivate Bst 3.0. A qPCR cycle check can be performed at this stage using 1:100 templates. A successful experiment can be identified by comparing cycle threshold values to IgG-CT. A universal i5 and a uniquely barcoded i7 primer, and Q5 HiFi 2× PCR Master mix were used to amplify libraries with the following cycling conditions: 45 sec at 98 °C, followed by 14-21 cycles of 15 sec at 98 °C and 10 sec at 60 °C, with a final extension at 1 min at 72 °C. Post-PCR clean-up was performed by 0.5× right-side followed by 1.2× left-side SPRI beads (Beckman Counter) selection.

value: Human embryonic kidney

tag: antibody

value: m6A (Synaptic systems, #202003)

tag: replicate


title: Intestinal stem cells, ISX_RNA_rep2

value: Lgr5-EGFP knock-in

value: Isx-9 for 6 hours


title: 24h post-infection (hpi) uninduced [UI σ28 KD 1]


title: crypt_f_18m_rep2 (total RNA-seq)

value: f


title: 24h post-infection (hpi) induced [Induced NT 3]

value: 10 nM aTc @4hpi

value: pL12CRia (nt)


title: crypt_f_18m_rep1 (total RNA-seq)


title: APA-seq of RKO shCPSF6 CLK2

value: CPSF6 and CLK2 knockdown


title: 24h post-infection (hpi) induced [I σ28 KD 1]

value: C. trachomatis L2 434/Bu


title: 24h post-infection (hpi) induced [Induced NT 2]


title: APA-seq of RKO shCLK2

value: CLK2 knockdown


title: 24h post-infection (hpi) induced [Induced NT 1]

value: Knockdown - dCas12 mediated


title: Intestinal stem cells, ISX_RNA_rep1

value: intestinal stem cells sorted from organoids


title: Intestinal stem cells, DMSO_RNA_rep1

value: DMSO for 6 hours


title: APA-seq of RKO shCPSF6

value: colorectal

value: colorectal cancer

value: CPSF6 knockdown


title: 24h post-infection (hpi) uninduced [Uninduced NT KD 3]

value: Uninduced


title: Lgr5_f_Y_rep3 (total RNA-seq)

source_name: Lgr5 positive cells from small intestine (intestinal stem cells)

extract_protocol:
For the Lgr5-eGFP ISCs isolation, the villi-free intestinal pieces (2 cm) were incubated in 5mM EDTA/PBS on ice for 45 min. The tissue was then shaken vigorously for 1 min, the crypt solution was filtered through a 100 µm cell strainer and centrifuged at 300xg for 5 min at 4°C. The crypts were dissociated with the mixture of 18 ml TrypLE Express, 2 ml of 10X DNase I Buffer (100 mM Tris HCl pH 7.5, 25 mM MgCl2, 5 mM CaCl2) and 1 ml DNase I (10 mg/ml) for 30 min at 37°C with brief vortexing every 10 min. The single-cell suspension was then passed through a 20 µm cell strainer and centrifuged at 450xg for 5 minutes at 4°C. The pellet was resuspended in 3 ml FSM (2% FBS, 2.5 mM EDTA) containing 10 µM Y27632 and DAPI (1:1000). The single cell suspension was applied to FACS LSRII (BD Biosciences) and the Lgr5-eGFPHi ISCs were sorted for downstream analysis.
Total ribo-depleted RNA-seq library preparation was performed as described previously (Neri et al., Nature 2017) . In brief, 50 to 500 ng of total RNA were depleted of ribosomal RNA using the Ribo-Zero™ Gold Kit H/M/R Kit (illumina) following manufacturer’s instructions. Ribo-depleted RNA was resuspended in 17 μl of EFP buffer (illumina), heated to 94°C for 8 min, and used as input for first strand synthesis, using the TruSeq™ RNA Library Preparation Kit v2 (illumina) following manufacturer’s instructions.

tag: Sex

value: female

value: Young (2 months old)


title: ISX-treated Chgb-mCherry reporter organoids_scRNAseq

source_name: intestinal organoids

value: Chgb-mCherry knock-in

value: Isx-9 for 6 days

value: whole intestinal organoid


title: Lgr5_f_Y_rep2 (total RNA-seq)


title: APA-seq of RKO shNC

value: RKO

value: WT


title: DMSO-treated Chgb-mCherry reporter organoids_scRNAseq

value: DMSO for 6 days


title: 24h post-infection (hpi) uninduced [Uninduced NT KD 2]

value: C. trachomatis L2 434/Bu

value: pL12CRia (nt)


title: Lgr5_f_Y_rep1 (total RNA-seq)


title: APA-seq of HEK293T OE CPSF6 Mut

source_name: kidney

value: kidney

value: embryo kidney

value: CPSF6 mut overexpression


title: 24h post-infection (hpi) uninduced [Uninduced NT KD 1]

value: Knockdown - dCas12 mediated


title: Chgb-mCherry reporter organoids_scRNAseq


title: Lgr5_f_O_rep3 (total RNA-seq)

value: old (18-26 months old)


title: APA-seq of HEK293T OE CPSF6 WT

value: CPSF6 overexpression


title: WT intestinal organoids_scRNAseq

value: Wildtype


title: Lgr5_f_O_rep2 (total RNA-seq)

value: female


title: pear-derived microRNAs

city: Pamplona

first: Fermín

middle: Ignacio

last: Milagro Yoldi

state: Navarra

department: Department of Nutrition, Food Science and Physiology/Center for Nutrition Research

country: Spain

institute: University of Navarra

data_processing:
Adapter were removed from data using skewer.
Read with a size ranging from 15 to 30 bases were aligned to the reference genome with microRNA annotation from miRBase (maximum 2 mismatches in the seed area) using ShortStack.
Mapped tags were counted using htseq-count.
Reads were normalized with DESeq2.
Assembly: Prunus Persica (NCBIv2 and annotation NCBIv2.52 restricted to microRNAs)
Supplementary files format and content: text files that include raw counts for each sample
Supplementary files format and content: text file that includes normalized counts for each Sample

organism: Pyrus communis

source_name: edible portion

extract_protocol:
0.1 of fruits (apple, olive, orange, pear, tomato), 0.1 of vegetables (spinach) and 0.5 g of nuts (almond and nut) were ground in QIAzol Lysis Reagent for 1 min using Ultra-Turrax T25 Basic (Basic IKA- WerkeTotal RNA). Total RNA was isolated with miRNeasy Serum/Plasma Kit (Qiagen) according to manufacturer protocol.
Libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina kit

value: edible portion


title: APA-seq of HEK293T OE GFP

value: GFP overexpression


title: Lgr5_f_O_rep1 (total RNA-seq)


title: Intestinal stem cells, DMSO_RNA_rep2

value: Lgr5-EGFP knock-in

value: DMSO for 6 hours

value: intestinal stem cells sorted from organoids


title: SGD_rep1

status: Public on Sep 04 2023

city: Planegg-Martinsried

first: Axel

last: Imhof

address: Großhadernerstr. 9

institute: BioMedical center

data_processing:
The data processing of the MNase-seq data was done as described before (Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021; Chacin et al., 2023).
Sequencing reads were mapped to the S. cerevisiae SacCer3 (R64-1-1 build) using Bowtie2 (version 2.3.5.1) (Langmead, B. and Salzberg, S.L., 2012) and reads aligning to multiple sites were removed.
This was then imported into R Studio by using GenomicAlignments (Lawrence, M. et al., 2013).
The sequencing reads with a fragment length between 139 and 191 bp were selected and extended to 60 bp.
The coverage was calculated and aligned to a list of ACS sites (Soriano, I. et al., 2014).
The signal was normalized per ARS in a 2000 bp window centered at the ACS motif.
Assembly: SacCer3
Supplementary files format and content: bw (bigwig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

organism: Saccharomyces cerevisiae

source_name: genomic DNA plasmid pool

extract_protocol:
The reactions with reconstituted chromatin were incubated with 100 U MNase (Sigma-Aldrich) and 1.5 mM CaCl2 for 5 min at 30 °C. The digest was stopped by the addition of 10 mM EDTA and 0.5 % SDS. This was followed by a proteinase K treatment for 1 h at 37 °C and ethanol precipitation. The purified DNA was run in 1.5 % agarose gels for 1.5 h at 110 V constant in 1X TAE, the mononucleosomal DNA was cut out and purified using the PureLink Quick Gel Extraction kit (Invitrogen).
The sequencing libraries of the vitro reconstituted chromatin samples were prepared as previously described (Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021, Chacin et al., 2023) by using 10-30 ng mononucleosomal DNA. The amplified DNA was run in a 1.5 % agarose gel, cut out, purified and the concentration was measured with the Qubit dsDNA HS Assay Kit (Fisher Scientific). The libraries were diluted to 10 nM, pooled according to the sequencing reads (~ 5 million reads/sample), and quantified using the 4150 TapeStation System (Agilent). The pool was sequenced on an Illumina NextSeq1000 in 60 bp paired-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

treatment_protocol: In vitro remodeling assay The assay was done as previously described (Chacin et al., 2023, Oberbeckmann, E., Niebauer, V. et al., 2021; Oberbeckmann, E., Krietenstein, N. et al., 2021). For a 100 µL remodeling reaction, the following concentrations of chromatin factors were used: 30 nM ORC, 20 nM INO80. The foldamer was titrated against a constant DNA concentration of 0.8 µg and the following amounts (w:w ratio) of foldamer were used: 0.8 µg (1:1), 1.6 µg (1:2), 3.2 µg (1:4), and 6.4 µg (1:8). The reactions were started by the addition of the SGD chromatin, incubated for 2 h at 30 °C and stopped by addition of 0.2 U apyrase (NEB), incubated at 30 °C for 20 min.

tag: chromatin

value: Salt gradient dialysis (SGD) -  in vitro reconstituted

tag: histone type

value: Drosophila melanogaster embryos

tag: orc

value: WT ORC

tag: remodeler

value: WT INO80

tag: dna

value: foldamer ratio:1:0


title: SGD_rep2

value: WT INO81


title: INO80_ORC_rep2

value: WT INO83


title: INO80_ORC_foldamer_14_rep2

value: WT INO89

value: foldamer ratio:1:4


title: INO80_ORC_foldamer_18_rep1

value: WT INO90

value: foldamer ratio:1:8


title: INO80_ORC_foldamer_12_rep1

value: WT INO86

value: foldamer ratio:1:2


title: INO80_ORC_foldamer_11_rep1

value: WT INO84

value: foldamer ratio:1:1


title: Primary human myoblasts, 776 µM metformin, 48 h, rep10

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

data_processing:
BGI provided cleaned, adapter-free paired-end data.
Reads were aligned to the GRCh38.103 genome with STAR v2.7.9a.
Gene-level read counts were calculated with summarizeOverlaps, mode = ’Union’, package GenomicAlignments v1.30.0.
Ensembl gene IDs were annotated based on the Ensembl database using Biomart (genome version GRCh38.p13).
Linear normalized counts were obtained by DESeq2 (v1.32.0), after removing low expressed genes across all samples (>60 sum of total counts).
Assembly: GRCh38.103
Supplementary files format and content: *.txt: Linear normalized counts obtained by DESeq2 v1.32.0.

source_name: Primary myoblasts

growth_protocol: Primary human myoblasts were obtained from muscle biopsies collected within a recently published study at the pre-intervention timepoint. Myoblast isolation and enrichment is described in. Cell culture plates were prepared with a non-gelling thin-layer GelTrex™ (Thermo Fisher Scientific, Schwerte, Germany) coating. Myoblasts were seeded with 10,000 cells/well of a 6-well plate, 100,000 cells/10cm dish or 150,000 cells/15cm dish and grown in cloning media (α-MEM:Ham’s F-12 (1:1), 20% FBS, 1% Chicken Extract, 1% Glutamine, 1% Pen.-Strep., 0.2% Amphotericin B) until 90% confluence was reached. Then, cells were fused into myotubes (day of differentiation 0; D0) by providing fusion media (α-MEM, 1% Glutamine, 1% Pen-Strep, 0.2% Amphotericin B, BSA-coupled fatty acids: 50 µM palmitate, 50 µM oleate, 100 µM carnitine). Medium was changed every second day during the whole time of culturing.

extract_protocol:
RNeasy Mini Kit (Qiagen, Hilden, Germany) after cells have been washed with 1 mL cold DPBS.
DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing protocol.

treatment_protocol: 48 hours before harvest (D3) metformin treatment was performed by refreshing fusion media containing metformin hydrochloride (Cayman Chemical, Ann Arbor, MI, USA) in the concentrations as stated. Harvest and analysis were performed at D5.

tag: cell type

value: Primary myoblasts

tag: treatment

value: 776 uM metformin

tag: time


title: INO80_ORC_foldamer_11_rep2

value: Salt gradient dialysis (SGD) -  in vitro reconstituted

value: WT INO85


title: HIBEpic-NEW  rep 1

city: lanzhou

first: Jing

middle: Jin

last: Hu

state: 甘肃省

address: 1 West Donggang Road, The first Hospital of Lanzhou University, Lanzhou, China

institute: Lanzhou University

data_processing:
Sequencing data quality control
Use HISAT software to quickly and accurately compare Clean Reads with the Homo_sapiens.GRCh38
Library quality evaluation，Alternative splicing analysis，Gene structure optimization.
Using StringTie through maximum flow algorithm and FPKM for standardization as an indicator to measure transcript or gene expression levels.
Perform differential analysis using DESeq2 software; Use Fold Change ≥ 2 and FDR<0.01 as the screening criteria.
Assembly: HISAT
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

source_name: Human Intrahepatic Biliary Epithelial Cell

growth_protocol: ICC-X1-PCGF4H and ICC-X2-PCGF4L, HIBEpic cell lines were maintained (37°C, 90 % humidity, 5% CO2) in RPMI-1640 medium (Gibico, USA), supplemented with 10% FBS (ABW, Uruguay)

extract_protocol:
RNA was harvested using TRIZOL
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit

tag: tissue

value: WT


title: INO80_ORC_foldamer_14_rep1

value: Drosophila melanogaster embryos

value: WT ORC

value: WT INO88


title: Primary human myoblasts, 776 µM metformin, 48 h, rep6


title: Primary human myoblasts, 776 µM metformin, 48 h, rep3


title: Primary human myoblasts, 776 µM metformin, 48 h, rep9


title: Primary human myoblasts, 776 µM metformin, 48 h, rep4


title: HIBEpic-NEW  rep 2

value: Human Intrahepatic Biliary Epithelial Cell


title: Primary human myoblasts, 776 µM metformin, 48 h, rep1


title: Primary human myoblasts, 388 µM metformin, 48 h, rep10

value: 388 uM metformin


title: Primary human myoblasts, 776 µM metformin, 48 h, rep8


title: Primary human myoblasts, 388 µM metformin, 48 h, rep9


title: INO80_ORC_foldamer_12_rep2

value: WT INO87


title: INO80_ORC_foldamer_18_rep2

value: WT INO91


title: Primary human myoblasts, 776 µM metformin, 48 h, rep7


title: Primary human myoblasts, 776 µM metformin, 48 h, rep5


title: Primary human myoblasts, 388 µM metformin, 48 h, rep8


title: INO80_ORC_rep1

value: WT INO82

value: foldamer ratio:1:0


title: Primary human myoblasts, 388 µM metformin, 48 h, rep6


title: Primary human myoblasts, 388 µM metformin, 48 h, rep4


title: Primary human myoblasts, 776 µM metformin, 48 h, rep2


title: KO, PA/OA (-)

city: Sendai

first: Can

last: Jiang

state: Miyagi

address: 2-1 Seiryomachi, Aobaku

department: Investigative Pathology

country: Japan

institute: Tohoku University

data_processing:
FastQC v0.11.7
Trimmomatic 0.38 performed trimming depending on various parameters on illumina paired-end
HISAT2 version 2.1.0, Bowtie2 2.3.4.1was used for mapping next-generation sequencing reads to genomes.
StringTie version 2.1.3b was used to assemble the RNA-Seq alignments into potential transcripts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM, count, TPM values for each Sample

source_name: Mouse liver

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

extract_protocol:
RNA was extracted from primary hepatocytes treated with or without a mixture of PA and OA after incubating for 24 hours, using the RNeasy Mini Kit (74104; QIAGEN) and RNase-Free DNase Set (79254; QIAGEN). 0.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Reference Guide (1000000040499 v00).

treatment_protocol: After primary hepatocytes were cultured for 3 hours, lipid accumulation was induced by palmitic acid (Sigma) and oleic acid (Sigma) mixture (0.5 mM/1 mM) for 24 hours.

value: Mouse liver

value: Primary hepatocyte

tag: genotype

value: Dusp6 knockout

value: No treatment


title: KO, PA/OA (+)

value: Palmitic and oleic acids mixture


title: WT, PA/OA (+)


title: Primary human myoblasts, 388 µM metformin, 48 h, rep1

value: Primary myoblasts


title: WT, PA/OA (-)


title: Primary human myoblasts, 78 µM metformin, 48 h, rep8

value: 78 uM metformin


title: Primary human myoblasts, 78 µM metformin, 48 h, rep7


title: Primary human myoblasts, 78 µM metformin, 48 h, rep10


title: WT_REP5

city: Newark

first: Dahui

last: Wang

state: NJ

address: 73 Warren st

department: Biological Science

institute: Rutgers University, Newark

description:
WT9_4993
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv

data_processing:
The raw sequence files were aligned with hg19
The aligned reads were then filtered based on alignment score (>=80), quality(>=10), and match count(<=1)
The filtered reads were normalized and quantified using Deseq
Assembly: mm10
Supplementary files format and content: comma spread file includes raw counts for each sample
Supplementary files format and content: comma spread file includes Deseq normalized value for each sample

source_name: ileum

extract_protocol:
RNA was harvest using RNeasy Plus Micro Kit from Qiagen (Cat No. 74034) from mouse ileum
RNA library construct through Ion Total RNA-seq Kit v2 from Life Technologies(Cat#4479789)

value: ileum

value: VilinCre


title: WT_REP3

description:
WT7_4991
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: WT_REP2

description:
WT4_4985
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: Primary human myoblasts, 78 µM metformin, 48 h, rep9


title: TET3KO_REP4

description:
KO4_4988
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv

value: TET3F/F, VilinCre


title: Primary human myoblasts, 78 µM metformin, 48 h, rep6


title: Primary human myoblasts, 78 µM metformin, 48 h, rep5


title: Primary human myoblasts, 78 µM metformin, 48 h, rep3


title: WT_REP1

description:
WT1_4979
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: TET3KO_REP3

description:
KO3_4984
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: TET3KO_REP5

description:
KO5_4989
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: Primary human myoblasts, 78 µM metformin, 48 h, rep4


title: Primary human myoblasts, 78 µM metformin, 48 h, rep2


title: TET3KO_REP2

description:
KO2_4983
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: Primary human myoblasts, 388 µM metformin, 48 h, rep7


title: Primary human myoblasts, 388 µM metformin, 48 h, rep3


title: Primary human myoblasts, 388 µM metformin, 48 h, rep2


title: Primary human myoblasts, 78 µM metformin, 48 h, rep1


title: WT_REP4

description:
WT8_4992
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: Primary human myoblasts, 39 µM metformin, 48 h, rep10

value: 39 uM metformin


title: rv0158Comp_H2O23

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

data_processing:
A custom (. gff) annotation file was made for the reference genome sequence (.fna) for the wild type strain Mtb H37Rv (accession number: NC_000962.3) downloaded from the NCBI website ("https://www.ncbi.nlm.nih.gov/nuccore/448814763").
Raw reads from sequencing were obtained as .fastq files. Raw read quality was checked using the FastQC software (version v0.11.5.)
BWA (version0.7.12-r1039) was used to index the reference genome.
Reads with raw read quality ≥ 20 were aligned using BWA aln -q option. The format of the annotation file (.gff) was changed to .bed using an in-house python
SAMTOOLS (version 0.1.19-96b5f2294a) was used to filter out multiply mapped reads
BEDTOOLS (version 2.25.0) was used to calculate the reads count per gene using the annotation file (.bed)
The format of the annotation file (.gff) was changed to .bed using an in-house python script.
Genome_build: accession number: NC_000962.3
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene

organism: Mycobacterium tuberculosis H37Rv

source_name: bacteria

growth_protocol: All Mtb strains were grown to early log phase (optical density =0.6) at 37 degree celsius at 180 rpm in a shaker incubator

extract_protocol:
25 mL GTC buffer (5 M guanidium thiocyanate, 0.5% sarcosyl, 0.5% Tween-80, 1% β mercaptoethanol (freshly added)) was added to 10 mL of bacterial culture, mixed, and cells were immediately harvested. Total RNA was extracted using MP Biomedicals™ FastRNA™ Pro Blue Kit (MP Biomedical, cat. No.- 116025050) and QIAGEN Rneasy Kit (Cat. No.- 74136)24. DNA contamination was removed from the isolated RNA using a TURBO DNA-free Kit (Invitrogen, Cat. No. -AM1907). Ribosomal RNA (16s and 23s rRNA) was depleted from these RNA samples using MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, cat. No.- AM1905).
rRNA depleted RNA (≈ 15 ng per sample) was fragmented and then used to prepare library using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat. No.-E7765s) and NEBNext Multiplex oligos for Illumina (New England Biolabs, Cat. No.-E7335s), according to the manufacturer’s protocol. RNA libraries were sequenced using standard Illumina protocols

treatment_protocol: For H2O2 (hydrogen peroxide )- treatment, Mtb strains were grown as mentioned above and then 5 mM H2O2 was added to all the strains for 2 hours, before total RNA was isolated.

tag: treatment condition

value: treated with 5 mM H2O2 for 2 hours

tag: growth phase of cells

value: mid log phase (OD= 0.6)

value: Rv0158 complemented strain under KO background with H2O2 treatment


title: TET3KO_REP1

description:
KO1_4982
PrimeBio_Raw_reads.csv
PrimeBio_DEseq_nomralized_reads.csv


title: Primary human myoblasts, 39 µM metformin, 48 h, rep8


title: rv0158Comp_H2O21


title: Primary human myoblasts, 388 µM metformin, 48 h, rep5

value: 388 uM metformin


title: Primary human myoblasts, 39 µM metformin, 48 h, rep6


title: Primary human myoblasts, 39 µM metformin, 48 h, rep3


title: Primary human myoblasts, 39 µM metformin, 48 h, rep7


title: Primary human myoblasts, 39 µM metformin, 48 h, rep2


title: WT_H2O23

value: WT Mtb H37Rv with H2O2 treatment


title: Primary human myoblasts, 39 µM metformin, 48 h, rep9


title: Primary human myoblasts, 39 µM metformin, 48 h, rep5


title: WT_H2O21


title: rv0158KO_H2O21

value: Rv0158 KO strain with H2O2 treatment


title: Primary human myoblasts, 39 µM metformin, 48 h, rep4


title: Primary human myoblasts, 16 µM metformin, 48 h, rep10

value: 16 uM metformin


title: rv0158Comp_U2

value: untreated

value: Rv0158 complemented strain under KO background


title: rv0158Comp_U1


title: rv0158KO_U1

value: Rv0158 KO strain


title: Primary human myoblasts, 16 µM metformin, 48 h, rep9


title: WT_U1

value: WT Mtb H37Rv


title: Primary human myoblasts, 39 µM metformin, 48 h, rep1

value: Primary myoblasts


title: rv0158KO_U2


title: WT_U3


title: Primary human myoblasts, 16 µM metformin, 48 h, rep8


title: rv0158KO_H2O22


title: Primary human myoblasts, 16 µM metformin, 48 h, rep5


title: Primary human myoblasts, 16 µM metformin, 48 h, rep6


title: Primary human myoblasts, 16 µM metformin, 48 h, rep7


title: Primary human myoblasts, 16 µM metformin, 48 h, rep4


title: alx-3(RNAi) Intact rep 3

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Adapter sequences were removed using trimmomatic (v0.39)
Trimmed sequence reads were then aligned to a previously described planarian transcriptome (NCBI Bio Project PRJNA215411) with the program Salmon (v1.4.0)
R package DESeq2 (v 1.30.1) was used to analyze differences in gene expression between control(RNAi) and alx-3(RNAi) (adj. p <0.05)
Assembly: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary files format and content: Excel, normalized_reads.xlsx contains normalized abundance measurments (generated using DESeq2 output). deseq_results.xlsx contains significant diffential expression (analysis performed with DeSeq2)

organism: Schmidtea mediterranea

source_name: Whole animal

growth_protocol: Asexual populations of Schmidtea mediterranea (strain CIW4) were maintained as previously described (Sánchez Alvarado, Newmark, Robb, & Juste, 2002). Planarians were kept at 18°C in milliQ water supplemented with 0.21g/L Instant Ocean, 0.1 mM KCl, 0.1 mM MgSO4, 0.12 mM NaHCO3. Animals were fed calf liver paste approximately once per week.

extract_protocol:
RNA was extracted using Trizol reaagent and RNA quality was analyzed on a bioanalyzer
Samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.

treatment_protocol: In all homeostatic experiments and regeneration experiments, RNAi food was fed to 7-day starved worms every third day for a total of 9 feedings. Amputations were performed 4 days after the 9th feed and animals were allowed to regenerate for the specified amount of time.

value: Whole animal

value: Asexual CIW4

value: 9 RNAi feeds

value: Intact


title: alx-3(RNAi) Intact rep 2


title: alx-3(RNAi) Intact rep 1


title: contol(RNAi) Intact rep 3


title: contol(RNAi) Intact rep 1


title: alx-3(RNAi) 72HPA rep 3

source_name: Tail fragment

value: Tail fragment

value: 72 hours


title: alx-3(RNAi) 72HPA rep 2


title: Primary human myoblasts, 16 µM metformin, 48 h, rep3


title: Primary human myoblasts, 16 µM metformin, 48 h, rep2


title: contol(RNAi) Intact rep 2


title: Primary human myoblasts, 16 µM metformin, 48 h, rep1


title: Primary human myoblasts, 0 µM metformin, 48 h, rep10

value: 0 uM metformin


title: contol(RNAi) 72HPA rep 2


title: alx-3(RNAi) 72HPA rep 1


title: Primary human myoblasts, 0 µM metformin, 48 h, rep9


title: contol(RNAi) 72HPA rep 3


title: contol(RNAi) 72HPA rep 1


title: Primary human myoblasts, 0 µM metformin, 48 h, rep7


title: Primary human myoblasts, 0 µM metformin, 48 h, rep8


title: alx-3(RNAi) 48HPA rep 2

value: 48 hours


title: Primary human myoblasts, 0 µM metformin, 48 h, rep6


title: Primary human myoblasts, 0 µM metformin, 48 h, rep4


title: Primary human myoblasts, 0 µM metformin, 48 h, rep5


title: alx-3(RNAi) 48HPA rep 3


title: alx-3(RNAi) 48HPA rep 1


title: Primary human myoblasts, 0 µM metformin, 48 h, rep3


title: contol(RNAi) 48HPA rep 2


title: Primary human myoblasts, 0 µM metformin, 48 h, rep2


title: Primary human myoblasts, 0 µM metformin, 48 h, rep1


title: alx-3(RNAi) 24HPA rep 1

value: 24 hours


title: contol(RNAi) 24HPA rep 3


title: alx-3(RNAi) 24HPA rep 2


title: contol(RNAi) 24HPA rep 2


title: alx-3(RNAi) 24HPA rep 3


title: contol(RNAi) 48HPA rep 1


title: alx-3(RNAi) 6HPA rep 2

value: 6 hours


title: alx-3(RNAi) 6HPA rep 1


title: contol(RNAi) 24HPA rep 1


title: contol(RNAi) 6HPA rep 2


title: alx-3(RNAi) 6HPA rep 3


title: contol(RNAi) 6HPA rep 3


title: contol(RNAi) 48HPA rep 3


title: contol(RNAi) 6HPA rep 1


title: alx-3(RNAi) 0.5HPA rep 2

value: 0.5 hours


title: alx-3(RNAi) 0.5HPA rep 3


title: CRMM1-2-CUT&Tag-rep2.Input

city: Shanghai

first: Xiang

last: Gu

address: Zhizaoju Road

institute: shanghai ninth people hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
GO and pathway enrichment analyses were performed.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: 92.1 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. CRMM1 cells were maintained in F12K supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: Ocular melanoma cells

value: input


title: contol(RNAi) 0.5HPA rep 3


title: CRMM1-2-CUT&Tag-rep2.IP


title: CRMM1-2-CUT&Tag-rep1.IP


title: contol(RNAi) 0.5HPA rep 2


title: contol(RNAi) 0.5HPA rep 1


title: genomic DNA from leptomeninges 4

type: genomic

city: Warsaw

first: Szymon

middle: Piotr

last: Baluszek

state: mazowieckie

address: Wilhelma Konrada Roentgena 5

department: Department of Molecular and Translational Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

description: leptomeninges

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

source_name: leptomeninges 4

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from FFPE tissue using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE [Thermo Fisher Scientific, Waltham, Massachusetts, USA]

tag: histology

value: leptomeninges


title: genomic DNA from leptomeninges 3

description: leptomeninges

source_name: leptomeninges 3


title: genomic DNA from leptomeninges 1

description: leptomeninges

source_name: leptomeninges 1


title: CRMM1-2-CUT&Tag-rep1.Input

tag: cell line


title: genomic DNA from meningioma 19

description: menigothelial meningioma

source_name: meningioma 19

tag: grade

value: menigothelial meningioma

tag: nf2 mutant status


title: genomic DNA from meningioma 7

description: fibrous meningioma

source_name: meningioma 7

value: fibrous meningioma


title: genomic DNA from meningioma 17

description: menigothelial meningioma

source_name: meningioma 17


title: genomic DNA from leptomeninges 2

description: leptomeninges

source_name: leptomeninges 2


title: genomic DNA from meningioma 6

description: menigothelial meningioma

source_name: meningioma 6


title: 92.1-2-CUT&Tag-rep2.Input

tag: antibody


title: genomic DNA from meningioma 16

description: anaplastic meningioma

source_name: meningioma 16

value: anaplastic meningioma


title: 92.1-2-CUT&Tag-rep1.IP


title: genomic DNA from leptomeninges 5

description: leptomeninges

source_name: leptomeninges 5


title: genomic DNA from meningioma 13

description: fibrous meningioma

source_name: meningioma 13


title: alx-3(RNAi) 0.5HPA rep 1


title: genomic DNA from meningioma 3

description: fibrous meningioma

source_name: meningioma 3


title: genomic DNA from meningioma 4

description: anaplastic meningioma

source_name: meningioma 4


title: genomic DNA from meningioma 21

description: menigothelial meningioma

source_name: meningioma 21


title: genomic DNA from meningioma 9

description: atypical meningioma

source_name: meningioma 9

value: atypical meningioma


title: genomic DNA from meningioma 18

description: fibrous meningioma

source_name: meningioma 18


title: genomic DNA from meningioma 2

description: menigothelial meningioma

source_name: meningioma 2


title: genomic DNA from meningioma 10

description: atypical meningioma

source_name: meningioma 10


title: CRMM1-1-ChIP-Seq-rep1.IP

data_processing:
Basecalls performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie version 1.1.2.
The locations of the mapped CHIP-seq reads were extended to 150bp to represent sequence fragments.
Peaks were called using PeaksFind version 2.2 with the significance cut-off q-value <=0.01.
GO and pathway enrichment analyses were performed.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde and sonicated for 8 min. Sonicated chromatin fragments (150 μl) were diluted 10-fold, and Protein G agarose (60 μl) (Millipore, USA) was added and shaken at 4 °C for 2 h. Then, the mixture was briefly centrifuged at 1000 rpm for 5 min at 4 °C. Anti-H3K18la (PTM-1406) was added to the supernatant and incubated overnight at 4 °C. Protein A and protein G magnetic beads (60 μl) (Millipore, USA) were retained in the supernatant for 6 h to pull down the protein at 4 °C. The DNA was released from the bound chromatin after cross-linking reversal and proteinase K treatment, precipitated, and diluted in 100 μ l of 0.2 M. glycine.
Purified DNA fragments were constructed and added to ChIP-seq libraries, amplified, and sequenced on an HiSeq 2500 platform (Illumina).


title: two serial sections of mutant OB (same mouse as M2)

city: Jerusalem

first: Tamar

last: Licht

address: Hadassah ein karem

department: Medical Neurobiology

country: Israel

institute: Hebrew University

description: fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data was prepared using 10XGenomics Space ranger
sequences were aligned to genome using Space ranger
gene expression levels of coding genes were quantified using Space ranger
visium slide serial number V10T10-310
Assembly: GRCm39_Ens106
Supplementary files format and content: barcodes.tsv: a list of barcodes
Supplementary files format and content: features.tsv: list of genes IDs
Supplementary files format and content: matrix.mtx: gene expression count data in MTX format

source_name: olfactory bulb

extract_protocol:
olfactory bulbs were dissected, embedded in OCT and liquid nitrogen-isobutane  (see visium protocol for fresh frozen tissue preparation https://www.10xgenomics.com/support/spatial-gene-expression-fresh-frozen  10 micrometer coronal slices were mounted on visium slide
spatial transcriptome sequencing were prepared with 10X Visium spatial gene expression slides and reagent kits according to instructions CG000239
Spatial transcriptomics

treatment_protocol: A transgenic soluble form of VEGFR1 was used to block VEGF during development using a brain-specific, tetracycline regulated (camk2a-tTa) manner (see PMID: 25689256). Mouse was sacrificed at 5 months.

value: olfactory bulb

value: mutant

value: vegf blockade at e13.5


title: genomic DNA from meningioma 8

description: atypical meningioma

source_name: meningioma 8


title: 92.1-2-CUT&Tag-rep1.Input


title: 92.1-2-CUT&Tag-rep2.IP


title: genomic DNA from meningioma 14

description: anaplastic meningioma

source_name: meningioma 14


title: genomic DNA from meningioma 22

description: anaplastic meningioma

source_name: meningioma 22


title: genomic DNA from meningioma 20

description: anaplastic meningioma

source_name: meningioma 20


title: 92.1-1-ChIP-Seq-rep1.Input


title: 395, nephrectomy (PCR-cDNAseq)

city: York

first: Joshua

last: Lee

address: University Road

department: Hull York Medical School

country: United Kingdom

institute: University of York

data_processing:
RNAseq reads with a minimum MinKNOW read quality threshold of Q>7 were orientated by pychopper (version 2.5.0), filtered for the presence of 5' and 3' sequencing adpators and trimmed by cutadapt (version 4.1). mapped to hg38 with minimap2 (version 2.24) using the recommended parameters for Oxford Nanopore Technologies long-read sequencing (-ax splice -uf -k14). Samtools (version 1.16) was used to filter out low mapping quality alignments (MAPQ < 10). Reads per gene were counted using featureCounts (version 2.0.0) with long-read counting mode (-L).
Assembly: hg38
Supplementary files format and content: Tab-delimited count matrix files containing sequence read counts mapped to the reference genome

source_name: Kidney

extract_protocol:
Nephractomy samples were first homogenised in QIAzol using stainless steel beads and TissueLyser LT (Qiagen). Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) with an additional Dnase I digestion (QIAGEN) according to manufacturer's instruction.
200ng  of total RNA

value: Kidney


title: GW3965_4

city: Urbana

first: Erik

last: Nelson

state: IL

address: 523 Burrill, 407 South Goodwin Ave

institute: University of Illinois at Urbana-Champaign

data_processing:
Raw reads were mapped to indexed GRCm39/mm39 using STAR aligner.
FeatureCounts from Subread package was used for summarizing mapped read counts at the gene level
The output file from featureCounts were further processed using R pachages including filtering (cpm>=1 & gene should be detected across all replicates in one group) and normalized followed by differentially expressed gene analysis.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab delimited text file containing raw read counts that successfully assigned to target genome for each sample
Supplementary files format and content: Tab delimited text file containing a summary of successfully assigned to target genome for each sample

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow derived cells were colllected from C57BL/6 female mice. Cells were cultured in complete DMEM F12 media supplemented with 20ng/mL of recombinant murine M-DSF. On day 3, 5mL of fresh complete media was added; on day 7, media was replaced, and macrophages were differentiated.

extract_protocol:
Treated cells were washed with PBS and frozen in -80 immediately.
RNA was isolated using Qiagen RNeasy Mini Kit
At leat 4ug of total RNA was used for the construction of sequencing libraries
The RNAseq libraries were prepared with Kapa Hyper Stranded mRNA library kit (Roche) . Read 1 aligns to the ANTISENSE strand.

treatment_protocol: Mature macrophages were harvested and seeded at cell densitty of 700k cells/well in 6-well plate. 5 biological replicates were included for each treatment group. 5 treatment groups were DMSO, DSHN, GW3965 and DSHN+GW3965. Cells were incubated with treatment for 24hrs.

value: Bone marrow derived macrophage


title: GW3965_3


title: 382, nephrectomy (PCR-cDNAseq)


title: two serial section of mutant olfactory bulb (same mouse as M1)


title: CRMM1-1-ChIP-Seq-rep2.Input


title: genomic DNA from meningioma 11

description: atypical meningioma

source_name: meningioma 11


title: 318, nephrectomy (PCR-cDNAseq)


title: 314, nephrectomy (PCR-cDNAseq)


title: CRMM1-1-ChIP-Seq-rep1.Input


title: CRMM1-1-ChIP-Seq-rep2.IP


title: 254, nephrectomy (PCR-cDNAseq)


title: genomic DNA from meningioma 1

description: atypical meningioma

source_name: meningioma 1


title: 92.1-1-ChIP-Seq-rep2.Input


title: genomic DNA from meningioma 15

description: atypical meningioma

source_name: meningioma 15


title: ICC-X1-1-PCGF4H rep 2

source_name: Intrahepatic Cholangiocarcinoma

value: Intrahepatic Cholangiocarcinoma

value: WT


title: GW3965_5


title: 171, nephrectomy (PCR-cDNAseq)


title: one slice of control olfactory bulb (same mouse as C1)

value: control


title: 92.1-1-ChIP-Seq-rep2.IP


title: genomic DNA from meningioma 12

description: atypical meningioma

source_name: meningioma 12


title: genomic DNA from meningioma 5

description: atypical meningioma

source_name: meningioma 5


title: two serial sections of control OB (same mouse as C2)


title: RCC4, IFNg + TNF treated, biol rep 3, DRS

data_processing:
RNAseq reads with a minimum MinKNOW read quality threshold of Q<7 were mapped to hg38 with minimap2 (version 2.24) using the recommended parameters for Oxford Nanopore Technologies direct RNA sequencing (-ax splice -uf -k14). Samtools (version 1.16) was used to filter out low mapping quality alignments (MAPQ < 10). Reads per gene were counted using featureCounts (version 2.0.0) with long-read counting mode (-L).
Assembly: hg38
Supplementary files format and content: Tab-delimited count matrix files containing raw read counts mapped to the reference genome

molecule: polyA RNA

growth_protocol: RCC4 cells were maintained at 37C in a humidified atmosphere of 5% CO2 and grown in complete Dulbecco’s Modified Eagle’s Medium (DMEM). Complete DMEM media was prepared by using DMEM, supplemented with 10% foetal bovine serum (FCS), 1% 200 mM L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
Cells were first washed with ice-cold PBS (Gibco), followed by lysis with Qiazol (Qiagen). Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) with an additional Dnase I digestion (QIAGEN) according to manufacturer's instruction. Poly(A)+ RNA molecules were enriched from total RNA with the Dynabeads mRNA purification kit (Thermo Fisher).
Sequencing libraries were generated using the SQK-RNA002 sequencing kit using 500ng of polyA enriched RNA following manufacturer's protocol

treatment_protocol: RCC4 cells were treated with pro-inflammatory cytokines IFN-γ (1000U/mL)  and TNF (25 ng/mL) for 24 hours before harvested for RNA extraction. 3 flasks of T75s were used for each biological replicate

value: Renal cell carcinoma epithelial cell

value: IFNg + TNF


title: RCC4, IFNg + TNF treated, biol rep 1, DRS


title: 329, nephrectomy (PCR-cDNAseq)


title: ICC-X2-1-PCGF4L rep 2


title: GW3965_1


title: 92.1-1-ChIP-Seq-rep1.IP

value: Ocular melanoma cells


title: 320, nephrectomy (PCR-cDNAseq)


title: RCC4, untreated, biol rep 3, DRS

value: Untreated


title: 273, nephrectomy (PCR-cDNAseq)


title: Caco2BBE1, 3hr infected Biological INPUT_REP_1

data_processing:
library strategy: 5hmeDIP-seq
differential hydroxymethylation coverage was calculated by using the Bioconductor package MEDIPS
Differential HydroxyMethylation Region(DHMR) are identified with MEDIPS with 500bp window size bin for the whole genome (v.1.48.0, BSgenome = "BSgenome.Hsapiens.UCSC.hg38", extend = 200, uniq = 1, window_size = 500, paired = TRUE, p.value = 0.001, adj = F, ratio = NULL, bg.counts = NULL, CNV = F)
Assignment of DHMRs to genes was done using the Bioconductor package annotatr.  (genome = hg38, annotations = c ("hg38_cpgs", "hg38_basicgenes","hg38_enhancers_fantom"), minoverlap = 1L, ignore.strand = TRUE)
DHMRs are assigned to exons, CpG islands, and enhancers through annotatr. Promoter regions were annotated as as ±1 kb around transcription start sitesusing the Bioconductor package ChIPSeeker.(v. 1.32.1, tssRegion = c (-1000,1000), TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene)
Assembly: hg38
Supplementary files format and content: tax deliminated file with FPKM value for each sample

growth_protocol: Caco2BBE1 was growth and maintained in DMEM(signma D5671) with 20% FBS, sodium pyruvate and L-gulatmin and antibotics. Cell is maintained in a 37 degree incubator with 5% CO2.

extract_protocol:
Caco2 cells are harvets after 3 hours, the genomic DNA is then isolated, purified with the Chromatin IP DNA purification kit (Active motif). Purified DNA is then sonicated and hydroxymethylated fragment is captured with hMeDIP kit (active motif), using the manufecture protocol.
Library prepartion is done by novogene. Briefly, The DNA fragments are repaired, dA-tailed. The DNA fragments with A tail are ligated to sequencing adaptors.  The final DNA library is obtained by size selection and PCR amplification.

treatment_protocol: salmonella typhimurium is collected after 4 hours growth in 37 degree. 10^8 CFU salmonella typhimurium is added to media and incubate with Caco2 for 3 hours. Afterward, the cell is incubate for 45 mintues in DMEM with gentamicin before collection.

value: enterocyte

value: salmonella typhimurium infection


title: 260, nephrectomy (PCR-cDNAseq)


title: 395, nephrectomy

data_processing:
RNAseq reads with a minimum MinKNOW read quality threshold of Q>7  were mapped to hg38 with minimap2 (version 2.24) using the recommended parameters for Oxford Nanopore Technologies direct RNA sequencing (-ax splice -uf -k14). Samtools (version 1.16) was used to filter out low mapping quality alignments (MAPQ < 10). Reads per gene were counted using featureCounts (version 2.0.0) with long-read counting mode (-L).
Assembly: hg38
Supplementary files format and content: Tab-delimited count matrix files containing sequence read counts mapped to the reference genome

extract_protocol:
Nephractomy samples were first homogenised in QIAzol using stainless steel beads and TissueLyser LT (Qiagen). Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) with an additional Dnase I digestion (QIAGEN) according to manufacturer's instruction.
2 μg of total RNA


title: DSHNplusGW_5

value: DSHNplusGW


title: Caco2BBE1, 3hr infected Biological REP_3

tag: chip antibody

value: anti-5hmc(Active motif Cat#39999)


title: RCC4, untreated, biol rep 2, DRS


title: GW3965_2


title: 243, nephrectomy (PCR-cDNAseq)


title: 382, nephrectomy


title: ICC-X1-1-PCGF4H  rep 1


title: 329, nephrectomy


title: 135, nephrectomy (PCR-cDNAseq)


title: Caco2BBE1, 3hr infected Biological REP_2


title: ICC-X2-1-PCGF4L rep 1


title: Caco2BBE1, 3hr infected Biological INPUT_REP_2


title: 318, nephrectomy


title: DSHN_4

value: DSHN


title: DSHNplusGW_3


title: DSHNplusGW_4


title: DSHN_2


title: 314, nephrectomy


title: Caco2BBE1, 3hr infected Biological INPUT_REP_3


title: 320, nephrectomy


title: 260, nephrectomy


title: DSHNplusGW_1


title: RCC4, IFNg + TNF treated, biol rep 2, DRS


title: 254, nephrectomy


title: RCC4, untreated, biol rep 1, DRS


title: DSHN_1


title: DSHN_5


title: DSHNplusGW_2


title: Caco2BBE1, Uninfected Biological INPUT_REP_1


title: DSHN_3


title: 135, nephrectomy


title: Caco2BBE1, Uninfected Biological REP_3


title: 273, nephrectomy


title: Caco2BBE1, 3hr infected Biological REP_1


title: Caco2BBE1, Uninfected Biological REP_2


title: Caco2BBE1, Uninfected Biological INPUT_REP_3


title: 243, nephrectomy


title: Caco2BBE1, Uninfected Biological INPUT_REP_2


title: 171, nephrectomy


title: flag-SS18-SSX1-S181A-D182K-E184R-EDDE deletion

city: Beijing

first: Kezhang

last: He

address: Shuangqing Road

institute: Tsinghua University

data_processing:
The raw reads were performed quality control using Fastp, then aligned to hg19 genome by hisat2. Peak calling was performed with macs2 and deeptools. Plots were generated with the IGV software.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: HEK293T cells (ATCC) were cultured in DMEM (Invitrogen) supplemented with 10% FBS (Invitrogen), and 1% penicillin/streptomycin (Invitrogen) at 37°C with 5% CO2 incubation.

extract_protocol:
The chromatin immunoprecipitation (ChIP) assay was performed with SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell signaling technology, #9005) following the manufacturer’s instructions.
DNA library were prepared with NEBNext® UltraTM II DNA Library Prep Kit (NEB, USA, Catalog #: E7645L).

value: DYKDDDDK Tag (D6W5B) Rabbit mAb #14793


title: DMSO_4

value: DMSO


title: DMSO_3


title: Caco2BBE1, Uninfected Biological REP_1


title: Control05_reanalyzed

type: RNA

city: Sacramento

first: JAEHWAN

last: KIM

state: CA

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

description:
Control skin from a healthy volunteer
GSM2066664

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label: biotin

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit (Qiagen) according to the manufacturer’s protocol.

tag: disease state

value: Control

value: skin

tag: lesional (ls) vs. normal

value: Normal

value: Pretreatment

value: Baseline


title: Control08_reanalyzed

description:
Control skin from a healthy volunteer
GSM2066667


title: flag-SS18-SSX1-R167A


title: DMSO_1

value: Bone marrow derived macrophage


title: Control04_reanalyzed

description:
Control skin from a healthy volunteer
GSM2066663


title: DMSO_5


title: Beta-glucan_treated 4

city: Philadelphia

first: Max

middle: M

last: Wattenberg

state: PENNSYLVANIA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Data were then processed using the Cellranger pipeline (10x genomics) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome with the include introns parameter and creation of feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: Barcode, features and matrix Cell Ranger pipeline outputs

source_name: Liver

extract_protocol:
Tissues were processed in RPMI supplemented with 10% fetal bovine serum, 83 μg/ml gentamicin, and 1% GlutaMAX, henceforth referred to as RPMI complete media, digested in RPMI containing collagenase and DNase, and washed with RPMI complete media. After passage through a 40μm strainer, a single cell suspension was achieved. Dead cells were removed using the Dead Cell Removal Kit (STEMCELL Technologies). CD45+ cells were then isolated with the CD45+ isolation kit (STEMCELL Technologies). To increase the recovery of Kupffer cells, the flow through from the CD45+ isolation kit was then layered over Ficoll Plaque Plus (Millipore Sigma) and spun at 2200 rpm for 20 minutes. Cells from the buffy coat were then combined with the CD45+ cells and passed through a 35μm strainer to ensure a single cell suspension.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3.1 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run. Sequencing for each library targeted 20,000 mean reads per cell.

treatment_protocol: Mice were treated with beta-glucan (1.2mg/kg) intravenous on days -2, 5 and 12. On day 0 intra-portal injection of PDA.8572-YFP tumor cells was performed. On day 14 necropsy was performed and livers were processed for scRNAseq.

value: Liver

value: KPC derived mouse pancreatic ductal adenocarcinoma

value: WT

value: Beta-glucan (1.2mg IV x3)


title: Beta-glucan_treated 2


title: Psoriasis61

description: Psoriasis lesional skin before treatment

value: Psoriasis

value: LS


title: Control03_reanalyzed

description:
Control skin from a healthy volunteer
GSM2066662


title: flag-SS18-SSX1-R169A


title: Control02

description: Control skin from a healthy volunteer


title: DMSO_2


title: Beta-glucan_treated 1


title: control untreated_2

value: untreated


title: control untreated_1


title: flag-SS18-SSX1-7 acidic aa deletions


title: flag-SS18-SSX1-S181A-D182K-E184R


title: control untreated_4


title: c-TBI

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 10%;    Cell Gene Number < 10000;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Hippocampus

growth_protocol: C57BL/6J mice aged between 7-10 weeks (n=3/group) were selected for the study, and were provided with free access to food and water under standard conditions (12-hour light/dark cycle, temperature: 22-25°C, relative humidity: 40-60%) for at least one week prior to the experiments.

extract_protocol:
After 48 hours of injury, 4% isoflurane was used for anesthesia, followed by 1-2% isoflurane for maintenance anesthesia.  The mouse brain tissue from the hippocampal region was micro-dissected (n=3/group) after cardiac perfusion of 20-25 ml of PSB treated with hypothermia until the mouse liver turned pale.  The brain tissues were washed in pre-chilled PBS to remove any residual blood and placed in liquid nitrogen for rapid freezing before being transferred to -80°C for subsequent experiments. The frozen hippocampus was treated with NLB buffer (X-100 (Sigma-Aldrich, St Louis, MO, USA), 0.2 U/μL RNase Inhibitor (Takara, Kyoto, Japan), 250 mM sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton, 0.1 mM EDTA) for purification of nuclei using density gradient centrifugation with sucrose solutions of varying concentrations.   Initially, the lysate was diluted in 3 mL sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM MgAc, 0.1 mM EDTA, 1 mM DTT) and filtered through a 40 μm filter.   The filtered lysate was then centrifuged at 3200 × g for 10 minutes at 4°C.   The pellet was resuspended in sucrose buffer and incubated on ice for 2 minutes.   Subsequently, 12.5 mL of density sucrose buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM MgAc, 1 mM DTT) was layered under the sample.   The mixture was centrifuged at 3200 × g for 20 minutes, and the supernatant was discarded immediately.   The nuclei present on the side of the tubes were resuspended in 100 μL of PBS containing 0.04% BSA and 0.2 U/μL RNase Inhibitor (Takara, Kyoto, Japan).   Finally, the concentration of nuclei was adjusted to 1000 nuclei/μL suitable for snRNA-seq.
Single-cell RNA sequencing (scRNA-seq) was performed using 10X Genomics Chromium platform. Related operations including Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all carried out following the manufacturer’s protocol. Clustering analysis, proportion analysis, RNA velocity, myeloid trajectory analysis lymphoid trajectory analysis was performed.150-base-pair paired-end reads was applied.

treatment_protocol: In this experiment, C57BL/6J mice aged 7-10 weeks were randomly assigned to either a bTBI or a sham-operated group, with 3 mice in each group. They were housed in a room with a 12-hour light-dark cycle and controlled temperature. Prior to surgery, the mice were anesthetized with intraperitoneal injection of pentobarbital (5 mg/100 g ip) and immobilized to prevent movement. In the bTBI group, a compressed gas-driven BST-I bio-shock tube was used to expose the mice to a 5.0 MPa blast shock wave, created by rupturing an aluminum sheet with high-pressure compressed gas, to simulate open-field conditions and construct the bTBI injury model. In contrast, the sham-operated group was anesthetized and placed near the blast chamber, but was not exposed to the blast shock wave. After the blast shock, all mice were returned to a 12-hour light-dark cycle, temperature-controlled room for housing after they regained consciousness.

value: Hippocampus

tag: strain

tag: age


title: Psoriasis56


title: Psoriasis57

description: Psoriasis lesional skin 12 weeks after IL17A blockade

value: Posttreatment


title: Psoriasis54


title: flag-SS18-SSX1-Y177A

value: DYKDDDDK Tag (D6W5B) Rabbit mAb #14793


title: Psoriasis52


title: Psoriasis58


title: Psoriasis59


title: Psoriasis53


title: Control06_reanalyzed

description:
Control skin from a healthy volunteer
GSM2066665


title: flag-SS18-SSX1-L168A


title: Control01

description: Control skin from a healthy volunteer


title: flag-SS18-SSX1-W164A


title: Psoriasis50

description: Psoriasis lesional skin 24 weeks after IL17A blockade


title: Control07_reanalyzed

description:
Control skin from a healthy volunteer
GSM2066666


title: flag-SS18-SSX1


title: Psoriasis49


title: 4108_PRMT5_LI_IEC_Het

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: Ribosome depleted RNA

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM19 annotation
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
Assembly: mm10
Supplementary files format and content: Excel files include normalized Deseq count for each gene per sample

source_name: Colon epithelium

growth_protocol: All mice were raised in Specific Pathogen Free (SPF) facility on normal diet. 8-12 week old animals were used for experiments.

extract_protocol:
RNA were isolated using Qiagen Rneasy mini kit (74106)
Ribosome-depleted RNAs were used to generate the cDNA libraries using the KAPA Hyper Prep Kit (KR0961) according to the manufacturer's instructions. Briefly, DNA was end-repaired and A-tailed to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-ligation clean was used to remove the extra adapters. Then the adapter-ligated DNA was PCR amplified with Illumina primers for 8 cycles, followed with post-amplification clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq S4 following the manufacturer's protocols.

treatment_protocol: No treatment. Steady state mice were harvest at around 8-week old.

value: Colon epithelium

value: PRMT5 Het

value: Steady state


title: flag-SS18-add 8aas


title: Psoriasis60

value: skin


title: b-TBI


title: Psoriasis55


title: 3692_PRMT5_LI_IEC_Het

description: Ribosome depleted RNA


title: Psoriasis51

value: Pretreatment


title: RING1B

value: RING1B (D22F2) XP® Rabbit mAb #5694


title: 4107_PRMT5_LI_IEC_WT

description: Ribosome depleted RNA

value: PRMT5 WT


title: Psoriasis47


title: Input


title: H2AK119Ub

value: Ubiquityl-Histone H2A (Lys119) (D27C4) XP® Rabbit mAb #8240


title: flag-SS18


title: SS18

value: SS18 (D6I4Z) Rabbit mAb #21792


title: 24h LPS-treated primary microglia replicate 3

city: Groningen

first: Alejandro

last: Marmolejo

state: Groningen

address: Antonius Deusinglaan 2

country: Netherlands

institute: University of Groningen

data_processing:
GenomeScan delivers the alignment (BAM with index), feature counts, and differential expression analysis using the RNA-Seq pipeline that was developed in-house and described in standard operating procedure SOP 70 (RNA-Seq Analysis). The workflow includes library prep QC (INS 74), raw data quality control (INS 92), UMI processing (INS 78), adapter trimming (INS 88), alignment of short reads (INS 61), feature counting and differential expression (INS 79).
The reads were mapped to the reference sequence using a short read aligner based on Burrows—Wheeler Transform (Tophat v2.0.14) with default settings. The aligner is a splice-aware mapper that detects splice junctions and incorporates them to help align the entire read. The statistics of mapping the reads to the reference genome are shown in Fig. 4 and Table 5. Samples are comparable is there is uniformity of the mapping result for each sample.
BAM files were generated as a result of this step. The alignment files (BAM files sorted on coordinates and indexed with the samtools v2.0.14 package) containing the mapping information are provided in the Mapping folder.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0. The hit counts were summarised and reported using the gene_id feature inthe annotation file. Only unique reads that fall within exon regions were counted.  The counts were savedto count files, which serve as input for downstream RNA-Seq differential expression analysis
Assembly: GRCm38.p6; GRCh38.p13
Supplementary files format and content: tab-delimited count files include count values for each Sample

source_name: Primary microglial culture

extract_protocol:
Isolation of RNA was performed using the Nucleospin® RNA isolation Kit (Macherey-Nagel). The samples were stored at -80°C until they were sent for transcriptomic analysis.
The quality of the samples, the construction and the sequencing of the RNA-libraries were performed by GenomeScan Bv. Data obtained from the transcriptomic analysis: quality control data, raw count files, FPKMs, RPMs and CPMs.

value: Primary microglial culture

tag: cell type

value: Mouse microglia

value: WT

value: LPS


title: Psoriasis48

value: Psoriasis

value: LS

tag: treatment

value: Baseline


title: 3691_PRMT5_LI_IEC_WT

description: Ribosome depleted RNA


title: 4h LPS-treated primary microglia replicate 3

tag: time


title: 24h LPS-treated primary microglia replicate 2


title: Psoriasis39

tag: tissue


title: Psoriasis46


title: Psoriasis35


title: Psoriasis34


title: Psoriasis33

value: Posttreatment


title: Control primary microglia replicate 3

tag: genotype

value: Untreated


title: Psoriasis37


title: 4h LPS-treated primary microglia replicate 2


title: HT1080 tumor_676

city: Zürich

first: Markus

middle: S

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

country: Switzerland

institute: ETH Zürich

data_processing:
Reads were mapped to a combined reference genome containing hg38 and mm10 with STAR v2.7.2b and the argument twopassMode Basic.
Counts per gene were generated with featureCounts v1.6.4 with arguments -t exon and -g gene_id
Assembly: hg38, mm10
Supplementary files format and content: count data for all samples against hg38 and mm10 Ensembl genes

source_name: xenograft subcutaneous tumor

growth_protocol: HT1080, SMG7KO and RESCUE cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
To extract total RNA from the tumor samples, the tissue was first lysed and homogenized by dual centrifugation at 2500 rpm, -5 °C for 4 minutes using the ZentriMix 380R (Hettich) and RNA was purified using the GeneElute™ Mammalian Total RNA Midiprep Kit (Sigma Aldrich) following the manufacturer’s instructions, including the in-column DNAse digestion step.
Libraries were prepared with the Illumina TruSeq Stranded Total RNA library kit, including rRNA depletion.

treatment_protocol: Two million cells were inyected subcutaneously into one flank of NOD scid gamma (NSG) mice. When tumors reached a volume of 1500 mm3, or when mice had to be sacrificed because of their health conditions, tumors were extracted and snap frozen.

value: xenograft subcutaneous tumor

value: fibrosarcoma

tag: host

value: NOD scid gamma (NSG) mice


title: Psoriasis44

value: skin

value: Pretreatment


title: Psoriasis42


title: Psoriasis45


title: HT1080 tumor_675


title: Psoriasis40


title: Psoriasis41


title: Control primary microglia replicate 2


title: Psoriasis38


title: RESCUE tumor_921

value: SMG7KO + SMG7 RESCUE


title: 24h LPS-treated primary microglia replicate 1


title: Psoriasis36


title: Psoriasis43


title: Psoriasis31


title: 4h LPS-treated primary microglia replicate 1


title: HT1080 tumor_674


title: RESCUE tumor_904


title: SMG7KO tumor_658


title: Control primary microglia replicate 1


title: Psoriasis32


title: 24h LPS-treated human iMGL replicate 4

source_name: iPSC-derived microglia like cells from Control 8.2 Cell Line

value: Human microglia-like cells


title: Psoriasis30


title: Psoriasis27


title: 4h LPS-treated human iMGL replicate 4

value: iPSC-derived microglia like cells from Control 8.2 Cell Line


title: SMG7KO tumor_657


title: BG_7

data_processing:
Data were processed using the Cellranger pipeline (10x genomics) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome with the include introns parameter and creation of feature-barcode matrices.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mice were euthanized and then the lung and liver were perfused with PBS through the portal vein, inferior vena cava and the heart. Successful perfusion was achieved by complete blanching of the organ. Livers were removed and rinsed in RPMI supplemented with 10% fetal bovine serum, 83 μg/ml gentamicin, and 1% GlutaMAX, henceforth referred to as RPMI complete media. Tissues were minced with dissecting scissors in RPMI complete media, digested in RPMI containing collagenase and DNase, and washed with RPMI complete media. After passage through a 40μm strainer, a single cell suspension was achieved. Dead cells were removed using the Dead Cell Removal Kit (STEMCELL Technologies). CD45+ cells were then isolated with the CD45+ isolation kit (STEMCELL Technologies). To increase the recovery of Kupffer cells, the flow through from the CD45+ isolation kit was then layered over Ficoll Plaque Plus (Millipore Sigma) and spun at 2200 rpm for 20 minutes. Cells from the buffy coat were then combined with the CD45+ cells and passed through a 35μm strainer to ensure a single cell suspension.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3.1 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run. Sequencing for each library targeted 20,000 mean reads per cell.

treatment_protocol: β-glucan (Imprime PGG/Odetiglucan, Hibercell, 1.2mg) was suspended in 100mL PBS and administered intravenously (IV) to mice.

value: Liver

value: Leukocytes

tag: Sex

value: Female

value: 9 weeks

value: Beta-glucan


title: BG_6


title: Control human iMGL replicate 4

value: WT


title: BG_8


title: 24h LPS-treated human iMGL replicate 3

value: LPS


title: Control_4

value: Control


title: 4h LPS-treated human iMGL replicate 3


title: Psoriasis28

value: Psoriasis

value: LS

value: Posttreatment


title: Psoriasis29

value: Baseline


title: BG_5


title: Control_2


title: 24h LPS-treated human iMGL replicate 2


title: Control_3


title: Control human iMGL replicate 3

value: Untreated


title: Control_1


title: Psoriasis26

value: skin


title: Control human iMGL replicate 2


title: Psoriasis24


title: 4h LPS-treated human iMGL replicate 2


title: DB, replicate 1, scRNAseq

city: Shenzhen

first: Lin

state: Guangdong

address: Liuxian

institute: Sustech Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Bone marrow

growth_protocol: Mice were housed in ventilated cages (23 °C) and maintained in a pathogen-free, accredited facility on a 12-hour light/dark cycle.

extract_protocol:
Bone marrow from three mice in each group aged 7 months was harvested from the femur and tibia for the single-cell sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Mice in the T2D group were treated with a high-fat diet (HFD, D12492, Research Diets) and a single dose of intraperitoneal injection of streptozotocin (STZ, 100 mg/kg, S0130, Sigma) to establish a type 2 diabetes model

value: Bone marrow cell

value: Bone marrow

value: 7 months old


title: Psoriasis23


title: Psoriasis16

value: Pretreatment


title: Psoriasis11


title: Psoriasis13


title: WT, replicate 1, scRNAseq

description: 10x Genomics

value: control


title: Psoriasis21

description: Psoriasis lesional skin 32 weeks after IL17A blockade


title: Psoriasis18


title: Psoriasis12


title: Arabidopsis tRNA TRM1A/B-3

city: Strasbourg

first: Philippe

last: Giegé

address: 12 rue du general Zimmer

country: France

institute: IBMP-CNRS

data_processing:
cutadapt, 4.1, -a GATATCGTCAAGATCGGAAGAGC -q25;
cutadapt, 4.1, -u2;
cutadapt, 4.1, -g  CTTGACGATATC -m 25;
mimseq, 1.1.7, --species Atha --cluster-id 0.95 --threads 15 --min-cov 0.0005 --max-multi 4 --remap---remap-mismatches 0.075;
Assembly: ncbi genome build tair10.1 GCF_000001735.4
Supplementary files format and content: csv file containing differential expression levels (log2 fold change) of tRNAs in TRM1A/B vs WT
Supplementary files format and content: csv file containing differential misincorporations (log odds ratio) of each tRNA at each position in TRM1A/B vs WT
Library strategy: Mim-tRNAseq

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Plants were grown at 22°C with day/night cycles as follows: light for 16h and in the dark for 8h

extract_protocol:
tRNAs were enriched from the soluble fraction of a LiCl precipitation, and then deacylated and dephosphorylated.
Libraries were constructed accordingto a protocol derived from Behrens et al. 2021. An RNA adaptor was ligated at the 3’ end of tRNAs. After purification with Zymo oligo D4060 (Zymo research), the adaptor-ligated-tRNAs were retro-transcribed with TGIRT III (Clinisciences), and the cDNA were purified. With Zymo oligo. The cDNA was then circularized using CircLigase (Euromedex) and submitted to Illumina indexing by amplification, using Illumina adapters. The DNA was purified with Zymo columns D4013. After quality control and quantification on Bioanalyzer (Agilent), the libraries were pooled with 35 ng per sample. This pool of samples was finally size-purified on a 6% polyacrylamide gel, quality was verified with a Bioanlyzer (Agilent) and quantified with a Qubit device (Thermo).

value: leaf tissue

tag: ecotype

value: TRM1A/B knock out


title: Psoriasis17


title: Psoriasis09


title: Psoriasis25


title: Psoriasis22


title: Psoriasis14


title: Psoriasis07


title: Psoriasis19


title: Psoriasis08


title: Psoriasis06


title: Psoriasis15


title: 24h LPS-treated human iMGL replicate 1

tag: cell line

value: iPSC-derived microglia like cells from Control 8.2 Cell Line

value: Human microglia-like cells


title: Arabidopsis tRNA TRM1A/B-1


title: Psoriasis05


title: Psoriasis10


title: Psoriasis20


title: Arabidopsis tRNA WT-3

value: WT


title: Psoriasis01


title: Psoriasis03


title: Psoriasis04


title: Psoriasis02


title: 4h LPS-treated human iMGL replicate 1

value: LPS


title: Arabidopsis tRNA WT-2


title: Control human iMGL replicate 1


title: GlucoBAT [Muscle-V5_9]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

data_processing:
fastp v0.20 used for read trimming
STAR v2.7.4a used for read mapping
Rsubread v2.2.4 used for gene expression quantification
R package edgeR v3..34 used for differential gene expression analysis
R package clusterProfiler v4.0 used for gene set enrichment analysis
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw counts

source_name: Muscle (M. vastus lateralis)

extract_protocol:
RNA was harvested using Trizol reagent
Smartseq II was applied to generate full length cDNA, Illumina DNA Prep Kit was used for the construction of sequencing libraries

value: Muscle (M. vastus lateralis)

tag: subject

value: Placebo

tag: day of_visit


title: VMCUB1_KM_MSC18_1

city: Duesseldorf

first: Michèle

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

institute: Heinrich Heine University, Medical Faculty

data_processing:
Illumina bcl2fastq v2.17.1.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq)and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to hg38 whole genome using CLC Genomics Workbench v20.0.3 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v20.0.3 with standard parameters. Multi-group comparisons were calculated using the Empirical Analysis of DGE (version 1.1, cutoff = 5) after grouping of samples (three biological replicates each) according to their respective experimental condition. The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 1.5 fold.
Assembly: hg38
Supplementary files format and content: The excel file includes RPKM values for each sample

growth_protocol: MSC and FB were cultivated in Dulbecco’s Modified Eagle’s Medium (DMEM; 4.5g/L glucose) with 2mM α-glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 10% fetal bovine serum (FBS) (Biochrom, Berlin, Germany). Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2. UC were cultured in DMEM (4.5 g/L glucose) with GlutaMAX-Supplement, 10 % FBS, 100 U/ml penicillin, 100 µg/ml streptomycin at 37 °C in a humidified atmosphere at 5 % CO2.

extract_protocol:
Rneasy Mini Kit, Qiagen, according to manufacturer with optional DNAse treatment
Libraries were prepared according to Vazyme instructions accompanying the VAHTS™ Universal V6 RNA-Seq Library Prep Kit for Illumina. Briefly, 300 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.

treatment_protocol: MSC and FB were used to generate conditioned media. MSC and FB were seeded in T175 cm2 cell culture flasks in 35 ml standard cell culture medium. MSC were plated in a seeding density of 9 x 105 and FB in a cell concentration of 7 x 105. After 72 h media from six different donors in cell culture passages 3 – 8 were collected and sterile filtrated (0.2 µm). The conditioned media (CM) was aliquoted and frozen at - 80 °C until pooling on a parity basis and usage. CM of 6 different donors was pooled prior to application to UC cell lines.UC cells were treated with conditined media for 72h.

value: urothelial carcinoma cell line

value: cond. medium mesenchymal stem cells


title: GlucoBAT [Muscle-V5_7]

value: Prednisone


title: VMCUB1_KM_MSC18_3


title: VMCUB1_KM_MSC18_2


title: Arabidopsis tRNA TRM1A/B-2


title: Arabidopsis tRNA WT-1


title: VMCUB1_KM_Fibro10_2

value: cond. medium fibroblasts


title: GlucoBAT [Muscle-V5_6]


title: VMCUB1_KM_Fibro10_1


title: A549-siMALAT1

city: Cheongju-si

first: Wanyeon

last: Kim

state: Chungbuk

address: Taeseongtabyeonro 250, Gangnaemyeon, Heungdeokgu

department: Biology Education

country: South Korea

institute: Korea National University of Education

description: Transcriptome profiling analysis after down-regulation MALAT1 in NSCLC cell lines (H460, H1299, A549)

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to hg19 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Trizol was added to the prepared mammalian cells, reacted for 5 minutes, and then chloroform was added and reacted for 3 minutes. After centrifugation at 4℃ and 1,3000 rpm for 15 minutes, the supernatant was transferred to a new tube. After adding isopropanol and reacting for 10 minutes, centrifugation was performed at 4℃ and 1,3000 rpm for 10 minutes. After discarding the supernatant, add 80% ethanol, centrifuge at 4℃ and 1,3000 rpm for 5 minutes, and discard the supernatant. After air drying for 5 minutes, add sterilized tertiary distilled water and store it.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NSCLC

value: MALAT1 knockdown

value: siMALAT1 transfection


title: H1299-cont

value: tumor

value: non


title: VMCUB1_KM_Fibro10_3


title: A549-cont


title: H460-siMALAT1


title: WT_24

data_processing:
Raw reads were mapped to indexed GRCm39/mm39 using STAR aligner.
FeatureCounts from Subread package was used for summarizing mapped read counts at the gene level
The output file from featureCounts were further processed using R pachages including filtering (cpm>=1 & gene should be detected across all replicates in one group) and normalized followed by differentially expressed gene analysis.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab delimited text file containing raw read counts that successfully assigned to target genome for each sample
Supplementary files format and content: Tab delimited text file containing a summary of successfully assigned to target genome for each sample

source_name: Mammary tumor

growth_protocol: Tumors were collected once the tumor volumn reached 2000mm^3

extract_protocol:
Tumors were frozen in -80 until RNA isolation
Frozen tumor mass were dissociated using homogenizer
RNA was isolated using PureLink RNA Mini Kit from Invitrogen
At leat 3ug of total RNA was used for the construction of sequencing libraries
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand.

value: Mammary tumor

tag: model

value: MMTV-PyMT

value: SHP WT


title: WT_23


title: H1299-siMALAT1


title: H460-cont


title: GlucoBAT [Muscle-V5_5]


title: VMCUB1_DMEM_2

value: DMEM control


title: WT_22


title: GlucoBAT [Muscle-V5_3]


title: VMCUB1_DMEM_3


title: WT_20


title: VMCUB1_DMEM_1


title: GlucoBAT [Muscle-V5_15]


title: WT_18


title: GlucoBAT [Muscle-V5_4]


title: WT_17


title: WT_15


title: WT_16


title: GlucoBAT [Muscle-V5_13]


title: GlucoBAT [Muscle-V5_14]


title: BFTC_KM_MSC18_3


title: GlucoBAT [Muscle-V5_12]


title: WT_14


title: BFTC_KM_MSC18_2


title: BFTC_KM_Fibro10_3


title: KO_11

value: SHP KO


title: WT_13


title: GlucoBAT [Muscle-V5_10]


title: KO_12


title: GlucoBAT [Muscle-V5_11]


title: BFTC_KM_MSC18_1


title: BFTC_KM_Fibro10_1


title: KO_7


title: KO_8


title: BFTC_KM_Fibro10_2


title: GlucoBAT [Muscle-V2_9]


title: KO_10


title: WT_19


title: KO_6


title: BFTC_DMEM_3


title: GlucoBAT [Muscle-V2_7]


title: WT_21


title: KO_5


title: GlucoBAT [Muscle-V2_6]


title: KO_2


title: BFTC_DMEM_1


title: GlucoBAT [Muscle-V2_5]


title: KO_9


title: KO_3


title: GlucoBAT [Muscle-V2_3]


title: MYC overexpressing U266 sample 3

city: Lille

first: Lama

last: Hasan Bou Issa

address: 1 Rue du Professeur Calmette

institute: Canther

data_processing:
We used Bcbio_nextgen to process the RNA data
cutadapt was used to trim adapters
trimmed reads were aligned to Human reference genome (GRCh37) with tophat2
Assembly: GRCh37
Supplementary files format and content: tsv format
Supplementary files format and content: transcript information

growth_protocol: Cells were cultures in 90% RPMI-1640 + 10% FBS+ 1% penicilin/streptomycin

extract_protocol:
Total RNA was isolated from U266/Control and U266/MYC cells using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
A starting amount of 500 ng of RNA was used to prepare poly-A enriched, single barcoded libraries using the NEBNext® Ultra™ RNA Library Prep Kit. Quality control of the libraries was evaluated by Bioanalyzer analysis with High Sensitivity chips. Sequencing was performed on a HiSeq 4000 ,

value: myeloma; plasmacytoma

value: MYC overexpressing


title: MYC overexpressing U266 sample 2


title: Control U266 cell line sample 3

value: control


title: MYC overexpressing U266 sample 1


title: BFTC_DMEM_2

value: urothelial carcinoma cell line


title: GlucoBAT [Muscle-V2_15]

value: Muscle (M. vastus lateralis)