title: Priming, GFPplus, H3K27me3, rep3


title: Priming, GFPplus, H3K27me3, rep2

status: Public on Jan 20 2025

type: SRA

city: Oxford

first: Pawel

last: Mikulski

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
The raw reads (fastq) were downloaded from Basespace servers (Illumina) using basespace-cli and concatenated per sample using base unix. Read quality was assessed using Basespace (Illumina) and FastQC software.
The reads were mapped to hg38 genome with Bowtie2, adjusting trimming conditions dependent on the read quality.
SAM to BAM conversion, BAM sorting and indexing were performed with Samtools v1.1. Read duplicates were removed with Picard (MarkDuplicates command).
Sorted and duplicate-removed BAM files were subjected to read count, normalization (CPM) and conversion to bigwig format with Deeptools v2 (bamcoverage command).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: Cut&Run-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Hela Kyoto

growth_protocol: The cells were grown in Dulbecco's Modified Eagle Medium (DMEM) containing high glucose and pyruvate (ThermoFisher, 41966-029) supplemented with 10% NCS (newborn calf serum, ThermoFisher, 16010-159) and 1% Penicillin–Streptomycin (ThermoFisher, 15140-122) at 37°C, 5% CO2.

extract_protocol:
Cut&Run-seq was performed using CUTANA v3 kit (Epicypher) according to the manufacturer’s protocol and with mild crosslinking (1 min incubation with 1% formaldehyde at room temperature).
Sequencing libraries were performed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the published protocol (Nan Liu 2021. Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645). protocols.io https://dx.doi.org/10.17504/protocols.io.bagaibse). The samples were multiplexed with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (NEB). Size selection steps were performed with Ampure XP beads (Beckman Coulter) and adjusted for nucleosomal DNA fragment size (150bp, excluding adapters).

treatment_protocol: The cells were primed with 50 ng/ml IFNγ (Merck) or left untreated for 24 h, followed by IFNγ washout with DPBS (ThermoFisher) and trypsinization by TrypLE (ThermoFisher) to harvest cells. Cells were cultured with fresh medium for another 48 h unless stated otherwise. Next, naïve and primed cells were induced by IFNγ for 24 h. After 24 h, cells were trypsinized and harvested, and the pellets were processed for subsequent experiments.

tag: cell line

value: Hela Kyoto

tag: cell type

value: Cervical cancer

tag: cut&run antibody

value: H3K27me3 (Cell Signaling Technology, #9733)


title: A673-FLI-AID_CUTRUN-FLI_IAA_rep1

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

country: USA

institute: UT Southwestern Medical Center

data_processing:
The CUT&RUN reads were aligned to the hg38 human reference genome using the Bowtie2 aligner (Langmead, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks (Ramirez et al, 2014).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

growth_protocol: Cells were cultured in RPMI with 5% FBS and pen/strep.

extract_protocol:
CUT&RUN was performed with adjustments made for crosslinking. Briefly, 500,000 nuclei were cryopreserved in Wash150 (20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM NaButyrate, protease inhibitor cocktail (Roche), 0.5 mM Spermidine) + 10% DMSO then stored in liquid nitrogen until experiment. Nuclei were bound to CUTANA Concanavalin A Beads (Epicypher 21-1401) for 15 min, then incubated with 50 μL Wash150 + 0.1% BSA, 2 mM EDTA, and 1 μL primary antibody overnight at 4 °C. Nuclei were resuspended in 100 μL Wash150 + 1 μL secondary antibody at room temperature for 1 h. Nuclei were washed twice in 1 mL Wash150 (with no Spermidine), then resuspended in 200 μL Wash150 (no Spermidine) + 0.2% formaldehyde for 2 min and then quenched with 70.5μL 1M Tris-HCl (pH 8), final concentration of 150mM. Nuclei were washed once in 1 mL Wash350 (20 mM HEPES pH 7.5, 350 mM NaCl, 10 mM NaButyrate, 0.025% Digitonin, protease inhibitor cocktail (Roche), 0.5 mM Spermidine) then incubated in 47.5 μL Wash350 + 2.5 μL pAG-MNase (Epicypher 15-1016) for 1 h. Nuclei were washed twice in 1 mL Wash500 (20 mM HEPES pH 7.5, 500 mM NaCl, 10 mM NaButyrate, 0.025% Digitonin, protease inhibitor cocktail (Roche), 0.5 mM Spermidine), once in 1 mL WashLiCl (20 mM HEPES pH 7.5, 250 mM LiCl, 10 mM NaButyrate, 0.025% Digitonin, protease inhibitor cocktail (Roche), 0.5 mM Spermidine), twice in Wash150 (20 mM HEPES pH 7.5, 150 mM NaCl, 10 mM NaButyrate, 0.025% Digitonin, protease inhibitor cocktail (Roche), 0.5 mM Spermidine) then resuspended in 50 μL Wash150 + 10 mM CaCl2 and incubated for 1 h at 0°C (on aluminum block). Reaction stop and fragment purification is as previously described.
Library prep was performed using NEBNext® Ultra™ II for DNA Library Prep using the following protocol (https://www.protocols.io/view/library-prep-for-cut-amp-run-with-nebnext-ultra-ii-kxygxm7pkl8j/v2). The quality of the libraries was assessed using a D1000 ScreenTape on a 2200 TapeStation (Agilent) and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher). Libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina NextSeq 500 (paired-end, 50 base pair reads). Typical sequencing depth was at least 12 million reads per sample.

treatment_protocol: Cells were treated with DMSO or 300 nM 5-Ph-IAA for 24 hrs prior to being harvested for CUT&RUN.

tag: genotype

value: FLI-AID

tag: treatment

value: IAA

tag: antibody


title: Priming, GFPplus, H3K27me3, rep1


title: naïve mice, mPFC, rep1

city: Hangzhou

first: Liang

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

department: Medicine

country: China

institute: Zhejiang University

description: Library name: NC1

library_source: transcriptomic

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Mus musculus reference genome(ftp://ftp.ensembl.org/pub/release-103/gtf/mus_musculus/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm39
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: brain tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: tissue

value: brain tissue


title: A673-FLI-AID_CUTRUN-FLI_DMSO_rep3

value: DMSO


title: naïve mice, mPFC, rep2

description: Library name: NC2


title: A673-FLI-AID_CUTRUN-FLI_DMSO_rep2


title: CRS mice, NAc, rep3

description: Library name: CN3


title: A673_CUTRUN-FLI_rep2


title: A673_CUTRUN-FLI_rep3


title: A673-FLI-AID_CUTRUN-FLI_DMSO_rep1


title: CRS mice, NAc, rep2

description: Library name: CN2


title: A673_CUTRUN-FLI_rep1


title: CRS mice, NAc, rep1

description: Library name: CN1


title: Hela, Reinduction, timecourse-24h, H3K14ac, rep 2


title: naïve mice, NAc, rep3

description: Library name: NN3


title: Hela, Reinduction, timecourse-24h, H3K14ac, rep 1


title: Hela, Reinduction, timecourse-4h, H3K14ac, rep 2


title: Hela, Reinduction, timecourse-4h, H3K14ac, rep 1


title: CRS mice, mPFC, rep1

description: Library name: CC1


title: Hela, Primed2d, timecourse, H3K14ac, rep 2


title: naïve mice, NAc, rep1

description: Library name: NN1


title: Hela, Primed2d, timecourse, H3K14ac, rep 3


title: Hela, Primed2d, timecourse, H3K14ac, rep 1


title: Hela, Priming, timecourse-24h, H3K14ac, rep 2


title: CRS mice, VTA, rep3

description: Library name: CV3


title: Hela, Priming, timecourse-24h, H3K14ac, rep 1


title: Hela, Priming, timecourse-4h, H3K14ac, rep 2


title: CRS mice, VTA, rep2

description: Library name: CV2


title: Hela, Naive, timecourse,H3K14ac, rep 2


title: Hela, Naive, timecourse,H3K14ac, rep 1


title: naïve mice, VTA, rep3

description: Library name: NV3


title: Hela, Naive, timecourse,H3K14ac, rep 3


title: Hela, Priming, timecourse-4h, H3K14ac, rep 1


title: CRS mice, VTA, rep1

description: Library name: CV1


title: Hela, Reinduction, timecourse-24h, H3K27me3, rep 1


title: naïve mice, VTA, rep2

description: Library name: NV2


title: Hela, Reinduction, timecourse-4h, H3K27me3, rep 1


title: naïve mice, VTA, rep1

description: Library name: NV1


title: Hela, Primed2d, timecourse, H3K27me3, rep 2


title: CRS mice, vHippo, rep3

description: Library name: CH3


title: Hela, Priming, timecourse-24h, H3K27me3, rep 1


title: naïve mice, NAc, rep2

description: Library name: NN2


title: Hela, Primed2d, timecourse, H3K27me3, rep 3


title: CRS mice, vHippo, rep2

description: Library name: CH2


title: Hela, Priming, timecourse-4h, H3K27me3, rep 1


title: Hela, Priming, timecourse-24h, H3K27me3, rep 2


title: Hela, Naive, timecourse,H3K27me3, rep 3


title: Hela, Naive, timecourse,H3K27me3, rep 2


title: naïve mice, vHippo, rep3

description: Library name: NH3


title: Hela, Priming, timecourse-4h, H3K27me3, rep 2


title: Hela, Naive, timecourse,H3K27me3, rep 1


title: naïve mice, vHippo, rep2

description: Library name: NH2


title: Hela, Reinduction, H4K16ac, rep 2


title: Hela, Reinduction, timecourse-24h, H3K27me3, rep 2


title: Hela, Reinduction, H4K16ac, rep 1


title: Hela, Primed7d, H4K16ac, rep 3


title: Hela, Reinduction, timecourse-4h, H3K27me3, rep 2


title: naïve mice, vHippo, rep1

description: Library name: NH1


title: CRS mice with low FST scores, LHb, rep3

description: Library name: B_6


title: Hela, Primed7d, H4K16ac, rep 1


title: HAP1 cells, WT

city: Hinxton

first: Pierre

last: Murat

address: Wellcome Trust Genome Campus

institute: Wellcome Sanger Institute

description: Library name: HAP1_OTX2_WT

data_processing:
Transcript quantification was performed using Salmon and standard settings against a Salmon index constructed for the hg38 human reference genome. Further analysis was carried out with custom R scripts. Transcripts were aggregated to the gene level and TPMs calculated using tximport.
Assembly: hg38
Supplementary files format and content: TSV file reporting transcript count expressed in TPM

growth_protocol: HAP1 ∆MLH1 cells expressing a doxycycline-inducible prime editor were cultured in IMDM (Invitrogen) with 10% FBS (Invitrogen) and glutamine and penicillin-streptomycin (Invitrogen) at 37 °C and 5% CO2

extract_protocol:
RNA was extracted from 2–5 million flash-frozen cells using the RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared with the New England BioLabsNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs)

value: WT


title: Hela, Primed2d, H4K16ac, rep 3


title: CRS mice with low FST scores, LHb, rep2

description: Library name: B_5


title: HAP1 cells, R4 and R5 domains deleted, clone 2

description: Library name: HAP1_OTX2_deltaR45_2

value: deletion


title: Hela, Primed2d, H4K16ac, rep 2


title: Hela, Primed2d, H4K16ac, rep 1


title: CRS mice with high FST scores, LHb, rep3

description: Library name: B_3


title: Hela, Priming, H4K16ac, rep 2


title: HAP1 cells, R4 and R5 domains deleted, clone 1

description: Library name: HAP1_OTX2_deltaR45_1


title: CRS mice, vHippo, rep1

description: Library name: CH1


title: Hela, Priming, H4K16ac, rep 1


title: Hela, Reinduction, H4K16ac, rep 3


title: 23768X26 porokeratosis

city: Salt Lake City

first: Doug

last: Grossman

state: Utah

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute

description: Library name: 57

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 106 and a reference database was created using STAR version 2.7.9a
A custom Perl script (smallRNA_pe_umi_extractor.pl) from https://github.com/HuntsmanCancerInstitute/UMIScripts was used to trim adapters and extract the Unique Molecular Index (UMI)
The trimmed reads were aligned to the reference database using STAR options optimized for shorter miRNA reads
A second Perl script (bam_umi_dedup.pl) removed PCR duplicates from the aligned BAM file
Mapped reads were assigned to miRNAs in miRbase release 22.1 using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited count matrix

molecule: total RNA

source_name: skin

extract_protocol:
Whole RNA was isolated using a RecoverAll kit (Thermo Fisher Scientific, AM1975), quantitated by ScreenTape Assay (Agilent), converted to cDNA  for sequencing.
Small RNA sequencing libraries were prepared from 10-100 ng of total RNA using the Qiagen QIAseq miRNA Library Kit

value: skin


title: CRS mice with high FST scores, LHb, rep2

description: Library name: B_2


title: 23768X25 porokeratosis

description: Library name: 56


title: Hela, Reinduction, H3K14ac, rep 3


title: Hela, Naive, H4K16ac, rep 1


title: CRS mice with high FST scores, LHb, rep1

description: Library name: B_1


title: Hela, Primed7d, H4K16ac, rep 2


title: Hela, Reinduction, H3K14ac, rep 2


title: naïve mice with high FST scores, LHb, rep3

description: Library name: A_6


title: naïve mice with high FST scores, LHb, rep2

description: Library name: A_5


title: 23768X24 verruca

description: Library name: 55


title: Hela, Primed7d, H3K14ac, rep 3


title: 23768X23 verruca

description: Library name: 54


title: Hela, Reinduction, H3K14ac, rep 1


title: Hela, Primed7d, H3K14ac, rep 2


title: naïve mice with high FST scores, LHb, rep1

description: Library name: A_4


title: Hela, Primed2d, H3K14ac, rep 3


title: Hela, Priming, H4K16ac, rep 3


title: 23768X21 sebaceous hyperplasia

description: Library name: 52


title: CRS mice with low FST scores, LHb, rep1

description: Library name: B_4


title: 23768X22 sebaceous adenoma

description: Library name: 53


title: Hela, Primed2d, H3K14ac, rep 2


title: Hela, Primed2d, H3K14ac, rep 1


title: Hela, Naive, H4K16ac, rep 3


title: 23768X20 atypical keratosis

description: Library name: 51


title: Hela, Naive, H4K16ac, rep 2


title: Hela, Priming, H3K14ac, rep 3


title: naïve mice with low FST scores, LHb, rep2

description: Library name: A_2


title: Hela, Priming, H3K14ac, rep 2


title: 23768X19 atypical keratosis

description: Library name: 50


title: Hela, Priming, H3K14ac, rep 1


title: Hela, Naive, H3K14ac, rep 2


title: 23768X18 seborrheic keratosis

description: Library name: 49


title: Nlrp3-/- BMDM without costimulation, replicate 3, RNA-seq

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: N3 C-3

data_processing:
DESeq2 Version 1.24.0
Assembly: GRCm39
Supplementary files format and content: xlsx inculdes FPKM

source_name: bone marrow-derived macrophages

extract_protocol:
Total RNA was extracted through Trizol reagent.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacture's protocols.

value: bone marrow-derived macrophages

value: without treatment


title: naïve mice with low FST scores, LHb, rep1

description: Library name: A_1


title: Hela, Naive, H3K14ac, rep 3


title: Hela, Primed7d, H3K14ac, rep 1


title: Hela, Naive, H3K14ac, rep 1


title: Hela, Reinduction, H3K4me1, rep 2


title: Hela, Reinduction, H3K4me1, rep 1


title: 23768X16 seborrheic keratosis

description: Library name: 47


title: 23768X17 seborrheic keratosis

description: Library name: 48


title: Hela, Primed7d, H3K4me1, rep 3


title: 23768X15 seborrheic keratosis

description: Library name: 46


title: naïve mice with low FST scores, LHb, rep3

description: Library name: A_3


title: Nlrp3-/- BMDM without costimulation, replicate 1, RNA-seq

description: Library name: N3 C-1


title: Nlrp3-/- BMDM with costimulation, replicate 3, RNA-seq

description: Library name: N3 AT-3

value: 4 hours of LPS preconditioning and subsequently 30 min of ATP stimulation


title: Hela, Primed2d, H3K4me1, rep 3


title: Hela, Primed2d, H3K4me1, rep 2


title: 23768X14 seborrheic keratosis

description: Library name: 45


title: Hela, Primed2d, H3K4me1, rep 1


title: Hela, Priming, H3K4me1, rep 3


title: 23768X13 seborrheic keratosis

description: Library name: 44


title: Hela, Priming, H3K4me1, rep 2


title: Hela, Primed7d, H3K4me1, rep 2


title: 23768X12 seborrheic keratosis

description: Library name: 43


title: Hela, Naive, H3K4me1, rep 3


title: 23768X11 seborrheic keratosis

description: Library name: 42


title: Hela, Naive, H3K4me1, rep 1


title: Hela, Reinduction, H3K4me3, rep 2


title: Hela, Naive, H3K4me1, rep 2


title: 23768X10 seborrheic keratosis

description: Library name: 41


title: Nlrp3-/- BMDM with costimulation, replicate 1, RNA-seq

description: Library name: N3 AT-1


title: wild type BMDM without costimulation, replicate 2, RNA-seq

description: Library name: WT C-2

value: wild-type


title: Hela, Reinduction, H3K4me3, rep 1


title: Nlrp3-/- BMDM without costimulation, replicate 2, RNA-seq

description: Library name: N3 C-2


title: Nlrp3-/- BMDM with costimulation, replicate 2, RNA-seq

description: Library name: N3 AT-2


title: Hela, Primed7d, H3K4me3, rep 3


title: Hela, Priming, H3K4me1, rep 1


title: 23768X8 seborrheic keratosis

description: Library name: 39


title: Hela, Primed7d, H3K4me3, rep 1


title: wild type BMDM without costimulation, replicate 1, RNA-seq

description: Library name: WT C-1


title: Hela, Primed2d, H3K4me3, rep 2


title: wild type BMDM with costimulation, replicate 3, RNA-seq

description: Library name: WT AT-3


title: wild type BMDM with costimulation, replicate 2, RNA-seq

description: Library name: WT AT-2


title: 23768X9 seborrheic keratosis

description: Library name: 40


title: 23768X7 seborrheic keratosis

description: Library name: 38


title: wild type BMDM with costimulation, replicate 1, RNA-seq

description: Library name: WT AT-1


title: Hela, Priming, H3K4me3, rep 3


title: Hela, Primed2d, H3K4me3, rep 1


title: Hela, Naive, H3K4me3, rep 2


title: Hela, Priming, H3K4me3, rep 2


title: GPR55 KO, KPCY55, tumor 6

city: Graz

first: Rudolf

last: Schicho

address: Neue Stiftingtalstraße 6

country: Austria

institute: Medical University of Graz

data_processing:
The raw data were aligned to GRCm39 using STAR 2.7.10b, after running FastQC 0.11.9.
Assembly: GRCm39
Supplementary files format and content: counts_table.txt, .txt file with raw count numbers of multiple samples

source_name: pancreatic tumor

extract_protocol:
RNA was extracted from tissue using Trizol (Life Technologies, #15596026). Samples were afterwards treated with the DNA-free™ DNA Removal Kit (Invitrogen, #10729525), and the concentration and quality of RNA was measured using Agilent Bioanalyzer 2100.
Poly-A selection was used as the RNA selection method for eukaryotic mRNA.

value: pancreatic tumor

value: mouse pancreatic adenocarcinoma cells overexpressing GPR55

value: GPR55 KO


title: 23768X5 seborrheic keratosis

description: Library name: 36


title: 23768X6 atypical keratosis

description: Library name: 37


title: GPR55 KO, KPCY55, tumor 5


title: D204-11

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

data_processing:
Quality and concentration were validated with TapeStation D1000 (Agilent Technologies). Samples were pooled in equimolar proportions, amplified by qPCR with specific primers and sequenced in a NextSeq High output 2x75 cycles run (Illumina).
Reads were mapped with STAR (version 2.5.9a) against the human reference from Ensembl (version GRCh38), and counts were obtained with HTSeq (version 0.9.1). MultiQC (version 1.9) was used for Quality Control assessment.
Assembly: GRCh38
Supplementary files format and content: log2(CPM)

source_name: NK cells

extract_protocol:
Total RNA was isolated using RNeasy® Micro Kit, 74004, Qiagen.
500ng of each sample were used to prepare NGS libraries with the NebNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) with PolyA capture.

treatment_protocol: Control and SMAD4 knock out human NK cells were cultured with rIL-2 (200 U/ml) or the combination of rIL-2 and TGFbeta (5 ng/ml). After 5 days, total RNA was extracted and sequenced. The experiment contain data from NK cells obtained from 3 different healthy individuals.

tag: patient

tag: condition

value: SMAD4 KO

value: Control

value: NK cells


title: D204-10

value: TGFB


title: GPR55 WT, KPCY55, tumor 6

value: GPR55 WT


title: 23768X3 actinic keratosis

description: Library name: 34


title: D204-9


title: GPR55 KO, KPCY55, tumor 4


title: D204-12


title: Hela, Naive, H3K4me3, rep 1

value: Hela Kyoto

value: Cervical cancer


title: Hela, Primed7d, H3K4me3, rep 2


title: D132-8


title: 23768X2 actinic keratosis

description: Library name: 33


title: D132-7


title: GPR55 KO, KPCY55, tumor 3


title: D132-5


title: 23768X1 actinic keratosis

description: Library name: 32


title: D132-6


title: GPR55 KO, KPCY55, tumor 2


title: Hela, Naive, H3K4me3, rep 3


title: 22488X16 invasive SCC

description: Library name: 31


title: 23768X4 actinic keratosis

description: Library name: 35


title: GPR55 KO, KPCY55, tumor 1


title: D111-3


title: D111-4


title: 22488X15 invasive SCC

description: Library name: 30


title: D111-2


title: D111-1


title: NALM6_RNA_SUMOi_rep2

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: NALM6 cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 1 U/µl penicillin and 1 µg/ml streptomycin. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.

treatment_protocol: NALM6 cells were treated either with vehicle (DMSO and EtOH), 10 nM of dexamethasone (Dex), 125 nM ML792 SAE inhibitor (SUMOi), or 10 nM Dex and 125 nM SUMOi for 24 h before extraction of RNA.

value: Precursor B-cell acute lymphoblastic leukemia

tag: concentration

tag: time


title: 22488X13 invasive SCC

description: Library name: 28


title: GPR55 WT, KPCY55, tumor 5


title: GPR55 WT, KPCY55, tumor 3


title: NALM6_RNA_DexSUMOi_rep2

value: ML792 + Dex


title: 22488X14 invasive SCC

description: Library name: 29

value: skin


title: wild type BMDM without costimulation, replicate 3, RNA-seq

description: Library name: WT C-3

value: bone marrow-derived macrophages


title: NALM6_RNA_DexSUMOi_rep1


title: NALM6_RNA_Dex_rep1

value: Dex

value: 10 nM


title: GPR55 WT, KPCY55, tumor 4


title: GPR55 WT, KPCY55, tumor 2


title: NALM6_RNA_SUMOi_rep1


title: NALM6_RNA_Dex_rep2


title: 22488X10 SCC-in-situ

description: Library name: 25a


title: NALM6_RNA_CTRL_rep2

value: DMSO + EtOH

value: 0.01percent + 0.01percent


title: 22488X11 SCC-in-situ

description: Library name: 26


title: NALM6_input_SUMOi_rep1

data_processing:
Basecalls performed using CASAVA.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >4-fold over control sample and local background. Corresponding input sample was used as the control sample.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

growth_protocol: NALM6 cells were grown in RPMI medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
For ChIP-seq, after 1% formaldehyde crosslinking, cells were harvested, chromatin was sonicated to 100-300 bp fragments, and protein-DNA complexes were isolated with specified antibody.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit according to instructions.

treatment_protocol: NALM6 cells were treated either with vehicle (DMSO and EtOH), 10 nM of dexamethasone (Dex), 125 nM ML792 SAE inhibitor (SUMOi), or 10 nM Dex and 125 nM SUMOi for 24 h before the start of ChIPs.

tag: chip antibody


title: NALM6_input_DexSUMOi_rep1


title: Liver, Model3

city: Xi'an

first: Wenhui

last: Yan

state: Shaanxi

address: No. 76 Yanta West Road

institute: Xi'an Jiaotong  University

data_processing:
The filtered reads were mapped to the mouse genome reference sequence (GRCm39.dna.toplevel.fa Ensembl release103) using HISAT2. Gene expression levels were calculated by the fragments per kilobase of transcript per million mapped reads (FPKM) values. Genes were considered differentially expressed when ∣log2 (fold change)∣ > 1.5 and P-value < 0.05.
Assembly: release103
Supplementary files format and content: an excel spreadsheet includes read counts and fpkm values for each sample

source_name: liver

extract_protocol:
The total RNA was extracted using Trizol. RNA quality was verified using Agilent 2100 Bio-analyzer
RNA sequencing libraries were generated using Agilent High Sensitivity DNA Kit, and sequenced on an Illumina Novaseq 6000 platform.

value: liver

value: model


title: NALM6_input_Dex_rep1


title: NALM6_RNA_CTRL_rep1


title: NALM6_SUMO2_DexSUMOi_rep2

value: SUMO-2/3 (MBL International, M114-3)


title: NALM6_input_CTRL_rep1


title: NALM6_SUMO2_DexSUMOi_rep1


title: 22488X9 SCC-in-situ

description: Library name: 25


title: 22488X8 invasive SCC

description: Library name: 24


title: 22488X7 invasive SCC

description: Library name: 23


title: Liver, Model2


title: NALM6_SUMO2_SUMOi_rep2


title: Liver, Control3

value: control


title: sciATACseq_knockouts

city: Amsterdam

first: Elzo

last: de Wit

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Gastruloid pools at 120h from E14 WT, HM1 WT, HM1 CDX KO and HM1 MSGN1 KO cells. Samples can be deconvoluted using the Tn5 design and primers.tsv files.

library_source: genomic single cell

data_processing:
Fastq  files from single cell combinatorial indexing ATACseq were edited  such that the combination of i5, i7, P5 and P7 barcodes (further  referred to as ‘barcode’) from fastq comments were prepended with  the `BC:Z:` tag to allow transfer of barcodes to alignment files.
Edited fastq files were mapped to the mm10 reference genome with the bwa  program version 0.7.17-r118 using the command `bwa mem -MC`.
Mapped  reads were filtered with samtools version 1.10 using `samtools view  -h -b -q 10`.
Paired-end  alignments were further processed to apply the +4, -5 Tn5 shift to  proper pairs, deduplicated and matched to valid experimental  barcodes, and resulting fragments were written to tabix files, using  a custom R script. Fragments were considered duplicates when they  matched chromosome, start and end positions, strand of the first mate  and barcode.
Barcodes were considered to represent cells when at least 2.000 unique nuclear  fragments were represented by that barcode and the TSS score for that  barcode exceeded 4. TSS scores were calculated by taking 100  basepairs centred at the transcription start site of UCSC’s known  Genes ,  along with 1000 basepair upsteam and downstream flanks. The number of  overlapping fragments were determined for these TSSs and flanks, and  divided by the 100 and 1000 basepair widths of the regions. The TSS  score is then the ratio between the number for TSSs and the number  for flanks. The fragments of included cells were then used to call  peaks using MACS2 callpeak version 2.2.7.1 68  with the arguments `-g mm -f BED –nomodel –extsize 200 –shift  -100 –keep-duplicates=all`. A count matrix was constructed by  quantifying the number of overlapping fragments in each cell with the  Peaks.
Assembly: mm10
Supplementary files format and content: The ‘*.bed.gz’ files are gzipped, BED-formatted (tabix) files. These files list deduplicated fragments with valid barcodes. Their start- and end-locations represent the paired Tn5 insertion sites. The 4th column are the strands of the first mate. The 5th column contains the barcode. The 6th column gives the number of times a fragment was seen (1 + number of duplicates).
Supplementary files format and content: The `*.bed.gz.tbi` files are tabix indices for the `*.bed.gz` files.

source_name: gastruloid

growth_protocol: IB10-E14, HM1, HM1-ΔCDX, HM1-ΔMSGN1 were cultured in 2i-LIF medium with 50% DMEM/F12 (Gibco) and 50% Neurobasal media (Gibco) supplemented with 0.5x N2 (Gibco), 0.5x B27 + retinoic acid (Gibco), 0.05% BSA (Gibco), 3μM CHIR99021 (BioConnect), 1μM PD03259010 (BioConnect), 2mΜ Glutamine (Gibco), 1.5x10-4 M 1-thioglycerol (Sigma-Aldrich), 100U/ml LIF (Cell guidance systems) and 50U/ml penicillin-streptomycin (Gibco) on gelatin-coated 10cm petri dishes in a humidified incubator (5% CO2, 37ºC).

extract_protocol:
In brief, 2-5x105 cells were lysed for 3min in 500µL of RSB buffer (Tris-HCl pH 7.5 10mM, NaCl 10mM, MgCl2 3mM, NP40 0.1%, Tween-20 0.1%, digitonin 0.01%) in presence of cOmplete protease inhibitor cocktail (Roche). Next, cells were resuspended 3 times and washed in 10 mL of RSBT buffer (Tris-HCl pH 7.5 10mM, NaCl 10mM, MgCl2 3mM, Tween-20 0.1% and protease inhibitor cocktail) by inverting the tube 3 times and spinning at 500g for 10min at 4ºC.
Next, the buffer was removed and 2500 nuclei were resuspended in 7.6µL of cold PBS and pipetted in a well of a 96-well plate with 1µL of i7 and i5 transposons and 10.4μL of transposition mix containing 10μL of 2xTD buffer (20 mM Tris, 10 mM MgCl2, 20% dimethylformamide, pH adjusted to 7.6), 0.2µL digitonin 1% and 0.2µL Tween 10%. The tagmentation was carried at 55ºC for 30min, nuclei were pooled and stained with 3μM 4′,6-diamidino-2-phenylindole (DAPI). The reaction was stopped by incubation at 37ºC for 15 min with 20μL 40 mM EDTA supplemented with spermidine 1mM. Next, 25 nuclei were sorted into either one or four 96 well plates (see run details) containing 11µL of EB buffer (Qiagen) and 1μL of Proteinase K 10 mg/ml (Roche). Decrosslinking was carried overnight at 65ºC and PCR was performed by adding 25µL of KAPA HiFi HotStart ReadyMix (Roche), 5μL of P5 and P7 primers (see oligonucleotides list)., 1μL of BSA 10mg/mL and 2 μL H2O. The thermocycler was set up as follows: 72ºC for 3min, 98ºC for 30s, 21 cycles of 98ºC for 10s, 63ºC for 30s,72ºC for 1min and finally 72ºC for 5min. Next, all PCR reactions were pooled and 1mL of the solution was purified using DNA clean & concentrator 5 (Zymo Research) following manufacturer instructions. Next, the library was size selected by 1x and 0.55x selection steps using AMPure XP beads (Beckman Coulter), followed by purification with QIAquick PCR purification kit (Qiagen). Libraries were sequenced with a NextSeq 550 system (Illumina) using a customized protocol 62 (genomic DNA read 1 (cycles 1–51), index 1 (transposon i7, cycles 52–59, followed by 27 dark cycles, and PCR i7, cycles 60– 67), index 2 (PCR i5, cycles 68–75, followed by 21 dark cycles, and transposon i5, cycles 76–83), and genomic DNA read 2 (cycles 84–134).

treatment_protocol: Briefly, gastruloids were aggregated in differentiation medium (N2B27), which includes DMEM/F12 and Neurobasal medium supplemented with 0.5X N2, 0.5X B27 + Retinoic acid, 2mΜ Glutamine, β-mercaptoethanol and 50U/ml penicillin-streptomycin in U-bottom 96-well plates (Thermo Scientific) in a humidified incubator (5% CO2, 37ºC). Cells were dissociated in N2B27 medium using a serological pipette combined with a 200µL pipette tip. Next, 3.75x104 cells were transferred in N2B27 medium with final volume 5ml and 40µL of this suspension (~300 cells) was transferred to each well. For the chimeric gastruloid experiments, half of the total cell number was used from each line. Gastruloids were fixed with 4% formaldehyde (Sigma-Aldrich) at approximately 120 hours, washed with PBS once and stored in PBS at 4ºC.

value: gastruloid

value: embryonic stem cell derivatives

value: WT, CDX1/2/4  KO, MSGN1 KO

tag: time points

value: gastruloid protocol


title: 22488X12 SCC-in-situ

description: Library name: 27


title: NALM6_SUMO2_SUMOi_rep1


title: 22488X6 invasive SCC

description: Library name: 22


title: NALM6_SUMO2_Dex_rep2


title: Liver, Control2


title: Liver, Control1


title: GPR55 WT, KPCY55, tumor 1

value: pancreatic tumor

value: mouse pancreatic adenocarcinoma cells overexpressing GPR55

value: GPR55 WT


title: sciATACseq_timecourse-batch2

description: Gastruloid pools at 80, 88 and 120h from E14 mESC. Samples can be deconvoluted using the Tn5 design and primers.tsv files.

value: WT


title: 22488X5 invasive SCC

description: Library name: 21

value: skin


title: 22488X4 SCC-in-situ

description: Library name: 20


title: NALM6_SUMO2_Dex_rep1

value: Precursor B-cell acute lymphoblastic leukemia

value: Dex


title: sciATACseq_pilot

description: Gastruloid pool at 120h made from high-passage E14 mESC.


title: sciATACseq_timecourse-batch1

description: Gastruloid pools at 72, 96 and 120h (+ matrigel at 96h) from E14 mESC. Samples can be deconvoluted using the Tn5 design and primers.tsv files.

value: gastruloid protocol + matrigel after 96 hours


title: FN14KO bleomycin D14 scRNAseq

first: pei

last: wu

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcodes processing counting and aggregation were made using the Cell ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: zip  file includes matrix files for each sample

source_name: lung

extract_protocol:
CD45+ cells from 4 mice each group (WT saline, WT bleomycin, Fn14 KO Saline, Fn14 KO Bleomycin) were sorted by FACS
Library was performed according to the manufacture's instructions(single cell 3' v3 protocol, 10x Genomics）

value: lung

tag: strain

value: Immune cells

value: 1.7mg/kg bleomycin


title: 22488X3 SCC-in-situ

description: Library name: 19


title: NALM6_SUMO2_CTRL_rep1

value: DMSO + EtOH

value: 0.01percent + 0.01percent

value: SUMO-2/3 (MBL International, M114-3)


title: 22488X2 SCC-in-situ

description: Library name: 18


title: Liver, Model1

value: liver

value: model


title: WT_E14_mESCs

description: Wildtype mouse embryonic stem cells

data_processing:
Fastq files were aligned to the mm10 reference genome using the bwa mem software version 0.7.17-r1188 with the `-M` argument.
Alignments were filtered to exclude low quality alignments with samtools version 1.10 using the command `samtools view -h -b -q 10`.
Duplicated alignments were removed using the `MarkDuplicates` command from Picard tools version 2.12.0 with the argument `REMOVE_DUPLICATES=true`.
Properly paired reads of primary alignments were converted to fragments with a +4/-5 shift of 5’ ends of positive and negative strand reads using a custom R script.
Bigwig files were build from the fragments files pooled by condition, by scaling coverage to the sum of length of the standard chromosomes using a custom R script.
Assembly: mm10
Supplementary files format and content: The `.bw` file is in the BigWig file format and contains scaled coverage.

source_name: Embryo

growth_protocol: IB10-E14 mESCs were cultured in 2i-LIF medium with 50%  DMEM/F12 (Gibco) and 50% Neurobasal media (Gibco) supplemented with  0.5x N2 (Gibco), 0.5x B27 + retinoic acid (Gibco), 0.05% BSA (Gibco),  3μM CHIR99021 (BioConnect), 1μM PD03259010 (BioConnect), 2mΜ  Glutamine (Gibco), 1.5x10-4 M 1-thioglycerol (Sigma-Aldrich), 100U/ml  LIF (Cell guidance systems) and 50U/ml penicillin-streptomycin  (Gibco) on gelatin-coated 10cm petri dishes in a humidified incubator  (5% CO2, 37ºC).

extract_protocol:
In brief, 50,000 mESCs were collected in cold PBS and lysed with a 2x lysis buffer (Tris-HCl pH7.5 1M, NaCl 5M, MgCl2 1M, 10% IGEPAL).
Next, cells were pelleted and incubated with 2xTD buffer and 2 uL transposon mix. Next, PCR amplification was carried twice by KAPA HiFi HotStart ReadyMix using P5 and P7 indexed primers (see oligonucleotide list). Fragments between 200 and 700 bp were purified using AMPure XP beads. Quality control was performed by Bioanalyzer High Sensitivity DNA analysis (Agilent).

value: Embryo

value: Embryonic Stem Cell


title: WT bleomycin D14 scRNAseq

description: 10X Genomics


title: 22488X1 SCC-in-situ

description: Library name: 17


title: ME49-DD-BFD1-Ty-Shield_R3

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

description:
Library name: Sample 18
reverse stranded

data_processing:
Illumina: The quality of the raw sequencing reads was assessed using FastQC (www.bioinformatics. babraham.ac.uk/projects/fastqc/) and MultiQC. For the expression data quantification and normalization, the FASTQ reads were aligned to the ToxoDB-65 build of the T. gondii ME49 genome using Subread version 2.0.1 with the following options ‘subread-align -d 50 -D 600 --sortReadsByCoordinates’. Read counts for each gene were calculated using featureCounts from the Subread package. Transcripts were quantified and normalized using TPMCalculator.
Assembly: Toxoplasma gondii ME49 strain (ToxoDB-65, ME49 genome).
Supplementary files format and content: xlsx format. The Processed data table includes subread raw count values and TPMCalculator normalized counts of T. gondii transcripts for each sample.

organism: Toxoplasma gondii

source_name: HFF and ME49 parasites

growth_protocol: Toxoplasma gondii strains were maintained by serial passage in Human foreskin fibroblast (HFF) monolayer under tachyzoite growth conditions in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
Cells were harvested and total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

treatment_protocol: HFF cells were grown to confluence and infected with Toxoplasma strains.Transcriptome profiles in each strain left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours or Shield for 48 hours.

value: Human fibroblasts infected by T. gondii

value: ME49 ku80 DD-BFD1-Ty

value: Shield treated for 48h

tag: batch


title: NALM6_GR_DexSUMOi_rep1

value: ML792 + Dex

value: GR (Santa Cruz Biotechnology, sc-1003)


title: ME49-DD-BFD1-Ty-Shield_R2

description:
Library name: Sample 17
reverse stranded


title: WT bleomycin D7 scRNAseq

description: 10X Genomics

value: WT


title: 21038X16 nodular BCC

description: Library name: 16

value: skin


title: 21038X15 nodular BCC

description: Library name: 15


title: NALM6_GR_SUMOi_rep2

value: Precursor B-cell acute lymphoblastic leukemia


title: FN14KO Saline scRNAseq

description: 10X Genomics

value: lung

value: Immune cells

value: Saline


title: NALM6_GR_SUMOi_rep1


title: 21038X14 nodular BCC

description: Library name: 14


title: ME49-DD-BFD1-Ty-UT_R3

description:
Library name: Sample 15
reverse stranded

value: untreated sample


title: WT Saline scRNAseq

description: 10X Genomics


title: lung primary fibroblasts 100ng/ml TWEAK stimulation 48 hours repeat2

data_processing:
The raw paired end reads were trimmed and quality controlled by Skewer with default parameters
STAR software was used to compare the preprocessed sequecnces with the reference genome sequences of sequenced species
STringTie was used to count the original sequence of known genes
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample

growth_protocol: lung mouse primary fibroblasts were maintained in DMEM supplemented with10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5%CO2 at 37 °C

extract_protocol:
RNA was harvested using Direct-zolTM RNA MicroPrep（Zymo research), 2ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Kit following manufacture's protocols

value: primary mouse lung fibroblasts

value: fibroblasts


title: NALM6_SUMO2_CTRL_rep2

value: DMSO + EtOH

value: 0.01percent + 0.01percent

value: SUMO-2/3 (MBL International, M114-3)


title: NALM6_GR_Dex_rep1

value: Dex

value: 10 nM


title: 21038X13 nodular BCC

description: Library name: 13


title: ME49-DD-BFD1-Ty-UT_R2

description:
Library name: Sample 14
reverse stranded

value: Human fibroblasts infected by T. gondii

value: ME49 ku80 DD-BFD1-Ty


title: NALM6_GR_Dex_rep2

value: GR (Santa Cruz Biotechnology, sc-1003)


title: ME49-DD-BFD1-Ty-UT_R1

description:
Library name: Sample 13
reverse stranded


title: lung primary fibroblasts 30ng/ml TWEAK stimulation 48 hours repeat2

value: WT


title: 21038X11 nodular BCC

description: Library name: 11

value: skin


title: NALM6_GR_CTRL_rep2

value: Precursor B-cell acute lymphoblastic leukemia


title: NALM6_GR_DexSUMOi_rep2

value: ML792 + Dex


title: NALM6_GR_CTRL_rep1


title: 21038X12 nodular BCC

description: Library name: 12


title: FN14KO bleomycin D7 scRNAseq

description: 10X Genomics

value: lung

value: Immune cells

value: 1.7mg/kg bleomycin


title: Pru-MORC-KD-BFD1-KO-IAA_R3

description:
Library name: Sample 12
reverse stranded

source_name: HFF and Prugniaud parasites

value: Pru ku80 MORC-mAID, Dbfd6

value: IAA treated for 24h


title: Pru-MORC-KD-BFD1-KO-IAA_R2

description:
Library name: Sample 11
reverse stranded

value: Pru ku80 MORC-mAID, Dbfd5


title: 21038X10 nodular BCC

description: Library name: 10


title: ME49-DD-BFD1-Ty-Shield_R1

description:
Library name: Sample 16
reverse stranded

value: Shield treated for 48h


title: lung primary fibroblasts 30ng/ml TWEAK stimulation 48 hours repeat1

value: primary mouse lung fibroblasts

value: fibroblasts


title: NALM6_ATAC_DexSUMOi_rep2

data_processing:
Basecalls performed using CASAVA.
The reads were aligned to human reference genome version hg38 by using Bowtie2 software version 2.3.4.1. with end-to-end sensitive mode allowing no mismatches.
Peaks were called using HOMER program version 4.10. using findPeaks with style factor, FDR<0.01, >25 tags, >6-fold over local background. ENCODE hg38 blacklist peaks were filtered out from the peak list.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.

extract_protocol:
For ATAC-seq, 100 000 isolated nuclei were treated with 2.5 µl Tn5 Transposase loaded with sequencing adapters.
ATAC-seq libraries were prepared with loaded Diagenode Tagmentase (#C01070012) according to instructions.

treatment_protocol: NALM6 cells were treated either with vehicle (DMSO and EtOH), 10 nM of dexamethasone (Dex), 125 nM ML792 SAE inhibitor (SUMOi), or 10 nM Dex and 125 nM SUMOi for 24 h before the start of nuclei extraction for tagmentation.


title: lung primary fibroblasts 10ng/ml TWEAK stimulation 48 hours repeat2


title: Pru-MORC-KD-BFD1-KO-IAA_R1

description:
Library name: Sample 10
reverse stranded

value: Pru ku80 MORC-mAID, Dbfd4


title: 21038X9 nodular BCC

description: Library name: 9


title: NALM6_ATAC_DexSUMOi_rep1


title: lung primary fibroblasts 10ng/ml TWEAK stimulation 48 hours repeat1


title: Pru-MORC-KD-BFD1-KO-UT_R3

description:
Library name: Sample 09
reverse stranded

value: Human fibroblasts infected by T. gondii

value: Pru ku80 MORC-mAID, Dbfd3

value: untreated sample


title: 21038X8 superficial BCC

description: Library name: 8


title: NALM6_ATAC_SUMOi_rep2


title: lung primary fibroblasts untreated 48 hours repeat2

value: WT

value: untreated


title: Pru-MORC-KD-BFD1-KO-UT_R2

description:
Library name: Sample 08
reverse stranded

value: Pru ku80 MORC-mAID, Dbfd2


title: lung primary fibroblasts 100ng/ml TWEAK stimulation 48 hours repeat1


title: 21038X7 superficial BCC

description: Library name: 7

value: skin


title: NALM6_ATAC_SUMOi_rep1

value: Precursor B-cell acute lymphoblastic leukemia


title: lung primary fibroblasts untreated 48 hours repeat1

value: lung


title: 21038X6 superficial BCC

description: Library name: 6


title: NALM6_ATAC_Dex_rep2

value: Dex

value: 10 nM


title: Pru-MORC-KD-BFD1-KO-UT_R1

description:
Library name: Sample 07
reverse stranded

value: Pru ku80 MORC-mAID, Dbfd1


title: Pru-MORC-KD-IAA_R3

description:
Library name: Sample 06
reverse stranded

value: Pru ku80 MORC-mAID

value: IAA treated for 24h


title: NALM6_ATAC_Dex_rep1


title: Pru-MORC-KD-IAA_R2

description:
Library name: Sample 05
reverse stranded


title: 21038X5 superficial BCC

description: Library name: 5


title: Liver tumor tissue, TCM treatment, 3 months, rep3

city: DaLian

first: aiguo

last: Wang

address: DaLian

institute: Dalian Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM37/mm9 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Liver tumor tissue

growth_protocol: 22℃, 37RH%, feeding feed and water

extract_protocol:
RNA was harvested using mir VanaTM miRNA Isolation kit (Cat# AM1561, Ambion). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Ras-Tg and DEN-induced mice with and without TCM treatment

value: Liver tumor tissue

value: TCM treatment


title: NALM6_ATAC_CTRL_rep2

value: DMSO + EtOH

value: 0.01percent + 0.01percent


title: 21038X4 superficial BCC

description: Library name: 4


title: Liver tumor tissue, TCM treatment, 3 months, rep2


title: 21038X3 superficial BCC

description: Library name: 3


title: Pru-MORC-KD-IAA_R1

description:
Library name: Sample 04
reverse stranded

value: Human fibroblasts infected by T. gondii


title: NALM6_ATAC_CTRL_rep1


title: Pru-MORC-KD-UT_R3

description:
Library name: Sample 03
reverse stranded

value: untreated sample


title: 21038X2 superficial BCC

description: Library name: 2


title: Liver tumor tissue, TCM treatment, 3 months, rep1


title: Pru-MORC-KD-UT_R2

description:
Library name: Sample 02
reverse stranded


title: Liver peri-tumor tissue, TCM treatment, 3 months, rep4

source_name: Liver peri-tumor tissue

value: Liver peri-tumor tissue


title: 21038X1 superficial BCC

description: Library name: 1


title: Pru-MORC-KD-UT_R1

description:
Library name: Sample 01
reverse stranded


title: Liver peri-tumor tissue, TCM treatment, 3 months, rep3


title: HEK293_3U_3_75

city: Taipei City

first: Chien-Ling

last: Lin

address: No. 128, Sec. 2, Academia Road, Nangang District

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv

data_processing:
0-3 random nucleotides were attached at the end of the amplicons to ensure the balanced fluorescence detection on the NextSeq platform.
SH-SY5Y raw fastq files were first remove duplicate by nubeam-dedup
Deduplicated SH-SY5Y fastq then remove adapter by trimmomaic
HEK293T raw paired-end fastq files were first trim adapter by trimmomatic
Trimmed HEK293T fastq files then extract UMI barcode by "UMI-tools extract”
Both SH-SY5Y and HEK293T fastq were aligned to lab synthetic UTR genome by hisat2
Alignment result then pipe into “samtools view” to filter high quality (q=60) alignment result
Filtered alignment result furthur pipe into “samtools sort”, save as bam file, then index by “samtools index"
HEK293T bam files deplicated alignment result removed by “UMI-tools dedup"
Raw count matrix table were generated by “bedtools multicov"
Supplementary files format and content: Raw count matrix table include sample (cell line) and batches from same UTR experiment
Library strategy: Amplicon-seq

source_name: Human embryonic kidney cells

growth_protocol: The HEK293T and SH-SY5Y cells were grown in 12-well plates including Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum at the day before the transfection.

extract_protocol:
Harvest cells at different time-points after the transfection (HEK293T:30 min, 75 min, 120 min; SH-SY5Y: 20 min, 40 min, 60 min) and the cells were washed with PBS.  The RNA extraction was according to the instruction of Direct-zol™ RNA MiniPrep Plus kit (Zymo Research). The cDNA was prepared from 2 μg total RNA using SuperScript®IV reverse transcriptase (Thermo Fisher Scientific) with random hexamer, following the manufacturer’s protocol.
Standard Illumina library construction protocol
Amplicon sequencing; The PCR amplicons were subject to Illumina NextSeq 150 paired-end (HEK293T) or single-end (SH-SY5Y) sequencing

treatment_protocol: The HEK293T and SH-SY5Y cells cultured in 12-well plate were transfected with 500ng of the RNA library by using Lipofectamine™ 3000 Reagent.

value: embryonic kidney


title: HEK293_3U_3_30

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: BMP4_YS_human_EB_Day15

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

description:
Library name: Sample6
10x Genomics

data_processing:
Illumina sequencing reads were aligned to the human mRNA reference genome (GRCh38) using the 10x Genomics CellRanger pipeline (version 3.0.2) with default parameters.
Assembly: GRCh38
Supplementary files format and content: tar compressed  files include filtered_gene_bc_matrices after running CellRanger pipeline

source_name: embryonic

growth_protocol: BMP4 induced human gastruloids were cultured in a 96-well U-shaped ultra-low plate with mTeSR medium. Small molecule compounds  inducing differentiation were added according to the treatment protocol. Samples were collected on day 2,day 4,day 6, day8, day10 and day 15 of differentiation.

extract_protocol:
On Days 2, 4, 6, 8, 10, and 15, embryoids were dissociated into single cells using Accutase for 15-30 minutes at 37°C. The cells were collected in 1.5 mL Eppendorf tubes, treated with 10% BSA/DPBS, and centrifuged at 180 g for 3 minutes. The samples were then washed twice with 1% BSA/DPBS and filtered through a 40 μm cell strainer. Cell density and viability were assessed using a CountStar (IC1000).
Libraries were prepared using Single Cell 3′Library & gel Bead kit v3 (10x Genomics, Cat# PN-1000268) according to the manufacturer’s protocol for 10000 cell recovery.

value: embryonic

value: human embryonic stem cells

value: stem cell


title: Liver tumor tissue, TCM treatment, 3 months, rep4


title: Liver peri-tumor tissue, TCM treatment, 3 months, rep2


title: H

description:
Library name: Sample 9
reverse stranded

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 17 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 17, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma Type I GT1 strain (ToxoDB-52, GT1 genome) as reference template.
The ArrayStar module (version 17, DNASTAR. Madison, WI, USA) was used for variant detection and statistical analysis of uniquely mapped paired-end reads using the default parameters.
Variant calls were filtered to select variants in coding regions with the following criteria: variant depth ≥ 30, Qcall ≥ 60, and absence in the parental wild-type strain. SNVs, insertions and deletions present in regulatory or intergenic regions were filtered out as they are unlikely to contribute to drug resistance.
For the RNA-seq transcipts expression data quantification, fastq reads were aligned with Subread package and raw counts were generated with featureCounts (v2.0.1).
Assembly: Toxoplasma GT1 strain (ToxoDB-52, GT1 genome).
Supplementary files format and content: xlsx format. The Processed data table includes RNA-Seq report, raw counts values of T. gondii transcripts for each sample. Variants detected in each strain when compared to the GT1 reference genome are also provided.

source_name: HFF and RH parasites

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
18 hours post-infection, cells were harvested and total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

value: HFF and RH parasites

value: Human fibroblasts infected by T. gondii RH strain

value: mutagenized, drug-resistant parasites


title: HEK293_3U_2_120

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: BMP4_YS_human_EB_Day8

description:
Library name: Sample4
10x Genomics


title: Liver peri-tumor tissue, TCM treatment, 3 months, rep1


title: HEK293_3U_2_75

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: G

description:
Library name: Sample 8
reverse stranded


title: F

description:
Library name: Sample 7
reverse stranded


title: BMP4_YS_human_EB_Day10

description:
Library name: Sample5
10x Genomics


title: Liver tumor tissue, control, 3 months, rep3

value: control


title: Liver tumor tissue, control, 3 months, rep4


title: HEK293_3U_2_30

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: HEK293_3U_3_120

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: HEK293_3U_1_120

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: E

description:
Library name: Sample 6
reverse stranded


title: BMP4_YS_human_EB_Day6

description:
Library name: Sample3
10x Genomics


title: D

description:
Library name: Sample 5
reverse stranded


title: BMP4_YS_human_EB_Day2

description:
Library name: Sample1
10x Genomics


title: BMP4_YS_human_EB_Day4

description:
Library name: Sample2
10x Genomics


title: Liver tumor tissue, control, 3 months, rep1


title: Liver tumor tissue, control, 3 months, rep2


title: CUT-CGA-TMZ_rep2

city: Wenzhou

first: LIjun

last: Chen

state: Other

address: Wenzhou Medical University, Wenzhou City, Zhejiang Rrovince,China

institute: Wen Zhou Medical University

data_processing:
We aligned paired-end RNA-seq reads of H9 to the hg38 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed.   For quantitative analysis, we normalized the read counts by computing the number of RPKMs using BAM files with FeatureCounts.
We aligned paired-end CUT&Tag reads of H3K27ac to the hg38 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed. Next, we pooled the biological replicates for each stage and performed downstream analysis. For peak calling, we converted sequence alignments in BAM format into BEDPE records using the BEDTools function bamtobed. CUT&Tag peaks were called on merged replicates and normalized to input using MACS2 v2.2.7.1 software. Peak annotation was performed using the R package ChIPseeker with the default parameters. Peak comparisons and overlaps were evaluated using the BEDTools suite for autosomal chromosomes. For quantitative analysis, we normalized the read counts by computing the number of RPKMs using merged replicate BAM files with the bamCoverage tool in deepTools software.
Assembly: hg38
Supplementary files format and content: txt
Supplementary files format and content: bw
Library strategy: CUT&Tag

growth_protocol: The regulatory mechanism of chlorogenic acid on fatty acid metabolism in human embryonic stem cells

extract_protocol:
Cells were washed two times in 0.5% BSA-PBS solution.  cDNA was amplified using the Single Cell Full Length mRNA-Amplification Kit(N712, Vazyme) according to the manufacturer’s instructions.
Cells were incubated in 50 µL antibody buffer; 0.5 μg antibody was added and the mixture was incubated at 4℃ overnight. After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 1 µL pG/A-Tnp and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer. We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h.The reaction was stopped with 5 μl Proteinase K、100 μl Buffer L/B, and extraction with DNA Extract beads.
Library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) according to the manufacturer’s instructions.
CUT&Tag was performed using the Hyperactive Universal CUT & Tag Assay Kit for Illumina (TD903, Vazyme).Cells were incubated in 50 µL antibody buffer;  0.5 μg antibody was added and the mixture was incubated at 4℃ overnight.After washing twice with dig-wash buffer, 50 µL dig-wash buffer with 0.2 µg secondary antibody was added and the mixture was incubated at room temperature for 1 h. After washing twice with 100 µL dig-wash buffer, 2 µL pA/G-Tnp and 49 µL dig-300 buffer were added, and the samples were incubated at room temperature for 1 h. Next, the samples were washed twice with 100 µL dig-wash buffer.We subsequently added 200 µL tagmentation buffer and incubated the samples at 37°C for 1 h. The reaction was stopped with 5 μl Proteinase K、100 μl Buffer L/B; After extraction with DNA Extract beads PCR was performed to amplify the libraries under the following conditions: 72°C for 3 min, 98°C for 30 s, 17 cycles of 98°C for 10 s and 60°C for 5 s, and a final extension at 72°C for 1 min with a hold at 4°C.


title: HEK293_3U_1_75

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: HEK293_3U_1_30

description:
3U stands for 3' UTR.
HEK_U3_Raw.csv


title: Liver peri-tumor tissue, control, 3 months, rep4


title: B

description:
Library name: Sample 3
reverse stranded


title: CUT-CGA-TMZ_rep1


title: HEK293_5U_3_120

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: Liver peri-tumor tissue, control, 3 months, rep3


title: A

description:
Library name: Sample 2
reverse stranded


title: CUT-CGA_rep2


title: HEK293_5U_3_75

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: Liver peri-tumor tissue, control, 3 months, rep1


title: CUT-Vehide_rep2


title: C2C12 WFS1 knockout, WFS1-FlagTag expressing proliferating myoblasts, WFS1 ChIP, 36 cycles

city: Vienna

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

department: Center for Medical Biochemistry

institute: Max Perutz Labs, Medical University of Vienna

data_processing:
Fastq reads were mapped using NextGenMap version0.5.5 using default options.
Mapped reads with a quality score below 10 were removed using samtools view.
Log2ratios of ChIP vs Input were generated using deepTools bamCompare --scaleFactorsMethod SES.
The bed files contain peaks which were called with MACS2 using the settings -q 0.05 -m 5 50 --keep-dup 1.
Assembly: Mus musculus genome assembly GRCm38 (mm10)
Supplementary files format and content: Processed files are in bigwig format and they contain log2ratios of ChIP/Input.
Supplementary files format and content: Bed files include peaks.

growth_protocol: DMEM supplemented with 15% fetal calf serum, 100 U/ml penicillin and 100 μg/ml streptomycin; cultured at 37°C and 5% CO2

extract_protocol:
Cells were subjected to dual crosslinkin using 2mM DSG and 1% v/v formaldehyde. Fixation was quenched and followed by washing and cell lysis. Chromatin was sonicated using the Bioruptor PICO sonicator by Diagenode.
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina and unique NEB adaptors. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: WFS1 knockout was generated using CRISPR/Cas9 and three WFS1-targeting sgRNAs, a Flag-tagged WFS1 coding sequence was introduced in knockout cells for stable FlagTag WFS1 expression

value: myoblast

value: WFS1 knockout; WFS1-FlagTag overexpression

value: WFS1 antibody (ProteinTech, #26995-1-AP)


title: WT

description:
Library name: Sample 1
reverse stranded

value: wild-type parasites


title: Hi-C_5toA_rep2

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

institute: Institut Pasteur

description: Library name: PL01

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: GCF_000146045.2 for S. cerevisiae , J01347.1 for the 2µ plasmid , GCA_000011445 for mycoides /  GCF_000004695.1 for D. discoideum / GCA_900074765.1 for L. fermentati / GCA_030580015.1 for L. waltii
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

tag: background

value: S. cerevisiae


title: C2C12 WFS1 knockout, WFS1-FlagTag expressing proliferating myoblasts, WFS1 ChIP, 30 cycles


title: Hi-C_H4_mutant_17_20

description: Library name: FG0147

value: RSGY 1155


title: HEK293_5U_3_30

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: C

description:
Library name: Sample 4
reverse stranded


title: HEK293_5U_2_30

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: C2C12 wildtype proliferating myoblasts, WFS1 ChIP, 36 cycles

value: wildtype


title: HEK293_5U_2_75

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: CUT-CGA_rep1


title: MDA231-LM2-TAF7-shRNA-3-3

city: Wuhan

first: 婉君

last: 张

state: Hubei

address: hongshan street

department: College of Life Science and Technology

institute: huazhong university of science and technology

data_processing:
Fastp(v 0.23.2) is used to control the quality of Raw Data, and Clean Data is obtained. Subsequent analysis is based on Clean Data
Use STAR(v 2.7.10a) to compare the Clean Data obtained after data quality control to the reference genome and sort it, and finally obtain the BAM format comparison result file .
Use Qualimap2(v2.2.2) to evaluate the quality of the comparison results of each sample
STAR was used to count the number of all genes compared to the reference genome annotation, and TPM (Transcripts Per Million) was used to standardize the gene count  as a measure of gene expression.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: MDA 231-LM2/shTAF7-3

growth_protocol: MDA MB-231 cells, MDA MB-231/shTAF7 cells, MDA 231-LM2 and MDA 231-LM2/shTAF7 cells 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 harvested using trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
After the RNA sample is tested as qualified, the preparation of the entire library is completed through mRNA enrichment, fragmentation, cDNA one strand synthesis, two strand synthesis, end repair, adding A tail, adding sequencing connector, purification, PCR amplification and other steps.

value: breast cancer cells

value: TAF7 knockdown


title: HEK293_5U_1_120

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv

value: embryonic kidney


title: CGA-TMZ_rep1

data_processing:
We aligned paired-end RNA-seq reads of H9 to the hg38 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed.   For quantitative analysis, we normalized the read counts by computing the number of RPKMs using BAM files with FeatureCounts.
We aligned paired-end CUT&Tag reads of H3K27ac to the hg38 reference genome using Bowtie2 v2.5.0 software. Unmapped and non-uniquely mapped reads were removed. Next, we pooled the biological replicates for each stage and performed downstream analysis. For peak calling, we converted sequence alignments in BAM format into BEDPE records using the BEDTools function bamtobed. CUT&Tag peaks were called on merged replicates and normalized to input using MACS2 v2.2.7.1 software. Peak annotation was performed using the R package ChIPseeker with the default parameters. Peak comparisons and overlaps were evaluated using the BEDTools suite for autosomal chromosomes. For quantitative analysis, we normalized the read counts by computing the number of RPKMs using merged replicate BAM files with the bamCoverage tool in deepTools software.
Assembly: hg38
Supplementary files format and content: txt
Supplementary files format and content: bw


title: MDA231-LM2-TAF7-shRNA-3-2

source_name: MDA 231-LM2/shTAF7-2


title: C2C12 wildtype proliferating myoblasts, WFS1 ChIP, 30 cycles


title: Liver peri-tumor tissue, control, 3 months, rep2

value: Liver peri-tumor tissue


title: CUT-Vehide_rep1


title: CGA_rep2


title: Hi-C_H4_mutant_15_17

description: Library name: FG0146

value: RSGY 1154


title: CGA-TMZ_rep2


title: HEK293_5U_1_75

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: HEK293_5U_2_120

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: MDA231-LM2-Ctrl-shRNA-3

source_name: MDA 231-LM2/shNC-3

value: WT


title: CGA_rep1


title: MDA231-LM2-Ctrl-shRNA-2

source_name: MDA 231-LM2/shNC-2


title: MDA-MB-231-TAF7-shRNA-3-3

source_name: MDA MB-231shTAF7-3


title: SH-SY5Y_3U_60_3

description:
3U stands for 3' UTR.
SH_U3_Raw.csv

source_name: neuroblastoma cells

value: neuroblastoma


title: C2C12 wildtype proliferating myoblasts, Input, 36 cycles


title: Vehide_rep2


title: C2C12 WFS1 knockout, WFS1-FlagTag expressing proliferating myoblasts, Input, 30 cycles


title: IL16-treated Th1 cells, rep2

city: Hangzhou

first: Peng

last: Xiao

address: No.3 East Qingchun Road

institute: Zhejiang University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCm39 using HISAT2
Read count extraction and normalization were performed using featureCounts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Peritoneal macrophage

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Peritoneal macrophage


title: SH-SY5Y_3U_60_2

description:
3U stands for 3' UTR.
SH_U3_Raw.csv


title: C2C12 wildtype proliferating myoblasts, Input, 30 cycles


title: KIs-Day3,Biol rep2

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations, and gene annotations.
Assembly: Hg38
Supplementary files format and content: BED-formatted feature tracks

source_name: blood

growth_protocol: After transduction with CD19-directed CAR via retroviral vector, cells were expanded in culture medium in the presence of IL-7 and IL-15

extract_protocol:
Cryopreserved cells were processed by a vendor, Active Motif, via thawing, pelleting and washing with cold PBS before tagmentation via the ActiveMotif ATAC-Seq kit.  Tagmented DNA was purified using MinElute PCR kit (Qiagen) before PCR amplification and purification with Agencourt AMPure SPRI beads (Beckman Coulter).
Resulting DNA was quantified using the iSeq (Illumina) and sequenced with PE42 on the NovaSeq 6000 sequencer (Illumina)

treatment_protocol: Naive cells were collected , then either DMSO (0.75µM) or KIs (0.75µM) were added to the culture medium with subsequent samples collected at Day3 post adding DMSO or Inhibitors. Samples were washed, collected, frozen at -80 until all the samples were collected.

value: blood

value: Mononuclear cells

value: T cell

value: 0.75µM KIs


title: MDA-MB-231-Ctrl-shRNA-2

source_name: MDA MB-231shNC-2


title: HEK293_5U_1_30

description:
5U stands for 5' UTR.
HEK_U5_Raw.csv


title: SH-SY5Y_3U_60_1

description:
3U stands for 3' UTR.
SH_U3_Raw.csv


title: KIs-Day3,Biol rep1


title: -Leucine 4 - GCN2 Inhibitor

city: Clermont-Ferrand

first: Aurore

last: Dougé

state: France

address: 28 place Henri Dunant

department: Oncology

institute: University Hospital

data_processing:
Libraries were sequenced on an Illumina Hiseq4000 sequencer as single end 50 bases reads.
Reads were preprocessed to remove the adapter, polyA, and low-quality sequences (Phred quality score below 20).
After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8 and reads mapping to rRNA sequences were removed for further analysis.
Assembly: Reads were mapped onto the hg38 assembly of the Homo sapiens genome using STAR version 2.5.3a. Gene expression quantification was performed using htseq-count version 0.6.1p1, with annotations from Ensembl version 99 and “union” mode. Only non-ambiguously assigned reads have been retained for further analyses.
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Primary T cells

growth_protocol: Activated human T cells were incubated in 10% FBS-RPMI medium supplemented with IL-2 at 37°C and 5% CO2 for 7 days of expansion.

extract_protocol:
mRNA of each sample was extracted with a NucleoSpin RNA kit (Macherey Nagel) according to the manufacturer's instructions. mRNA quality was validated by Nanodrop analysis. mRNA samples were stored at -80°C until gene expression analysis.
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions.

treatment_protocol: At day 8 post activation, Dulbecco’s Modified Eagle’s Medium (DMEM) (with 10% of dialyzed calf serum) lacking leucine was used (GENAXXON bioscience). A control medium was simultaneously reconstituted by adding all nine EAAs. RPMI-cultured human T cells were collected and washed in PBS with centrifugation at room temperature at 300xg for 5 min. Cells were then resuspended either in reconstituted DMEM control or in DMEM lacking leucine, at a density of 1x106 cells/mL. DMEM was freshly supplemented with IL-2 (50 IU/mL). GCN2 inhibitor (TAP20) was generously provided by Merck KGaA. The compound was resuspended in DMSO and used at a final concentration of 2.5 µM. Cells were cultured in DMEM Control or DMEM lacking leucine +/- GCN2 inhibitor for 6 hours (quadruplicate) and were then collected for mRNA extraction.

value: Primary cells

value: T cells

value: DMEM without leucine + GCN2 Inhibitor (6h)


title: SH-SY5Y_3U_40_3

description:
3U stands for 3' UTR.
SH_U3_Raw.csv


title: IL16-treated Th1 cells, rep1


title: DMSO-Day3,Biol rep1

value: 0.75µM DMSO


title: PBS-treated Th1 cells, rep2

value: PBS


title: SH-SY5Y_3U_40_2

description:
3U stands for 3' UTR.
SH_U3_Raw.csv


title: PBS-treated Th1 cells, rep1


title: SH-SY5Y_3U_40_1

description:
3U stands for 3' UTR.
SH_U3_Raw.csv


title: C2C12 WFS1 knockout, WFS1-FlagTag expressing proliferating myoblasts, Input, 36 cycles

value: myoblast

value: WFS1 knockout; WFS1-FlagTag overexpression


title: MDA-MB-231-TAF7-shRNA-3-2

source_name: MDA MB-231shTAF7-2

value: breast cancer cells

value: TAF7 knockdown


title: -Leucine 3 - GCN2 Inhibitor


title: Vehide_rep1


title: Naive cells,Biol rep2


title: MDA-MB-231-Ctrl-shRNA-3

source_name: MDA MB-231shNC-3


title: SH-SY5Y_3U_20_2

description:
3U stands for 3' UTR.
SH_U3_Raw.csv


title: -Leucine 2 - GCN2 Inhibitor


title: Phaseolus vulgaris 4004, pod,20DAF,2

first: Yunxiu

last: Liu

address: No. 258 Xueyuan Street, Xiasha Higher Education Park

institute: China Jiliang University

data_processing:
The joint sequence in reads was removed, and the reads without inserted fragments were removed due to the joint self-connection and other reasons.
The bases with low quality (mass value less than 20) at the end of the sequence (3 'end) are pruned away. If there are still bases with mass value less than 10 in the remaining sequence, the whole sequence is eliminated, otherwise it is retained.
reads containing more than 10% N were removed.
Discard sequences less than 75bp in length after adapter removal and mass pruning.
Assembly: 3885

organism: Phaseolus vulgaris

source_name: Pod

extract_protocol:
RNA was obtained using the TRIzol® Reagent kit. 1μg total RNA was used to construct sequencing library RNA-seq.
RNA libraries for RNA-seq were prepared using SMARTER mRNA--Seq Library Prep Kit following manufacturer's protocols.

value: Pod

tag: developmental stage


title: SH-SY5Y_3U_20_3

description:
3U stands for 3' UTR.
SH_U3_Raw.csv

tag: cell line


title: Naive cells,Biol rep1

tag: cell type


title: -Leucine 1 - GCN2 Inhibitor

value: WT


title: Phaseolus vulgaris 4004, pod,20DAF,3


title: Control 4 - GCN2 Inhibitor

value: Control DMEM + GCN2 Inhibitor (6h)


title: SH-SY5Y_3U_20_1

description:
3U stands for 3' UTR.
SH_U3_Raw.csv

value: neuroblastoma


title: normal breast tissue, patient 932398

description: GEXSCOPE

data_processing:
Raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 to trim poly-A tail and adapter sequences.
Barcodes and UMIs were extracted from R1 reads and corrected.Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the GRCh38 (hg38) transcriptome using STAR(v2.6.1b).
Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1).Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
The demltiplexing,barcoded processing, gene counting and aggregation were made using CeleScope software V 1.14.0 (https://github.com/singleron-RD/CeleScope/)
Assembly: hg38
Supplementary files format and content: expression matrix file using RNA raw count

source_name: normal breast tissue

extract_protocol:
Fresh breast cancer tissues and the corresponding normal tissues were stored in the sCelLive® Tissue Preservation Solution (Singleron Biotechnologies, Nanjing, China) on ice immediately after surgery. Tissues were then washed with Hanks Balanced Salt Solution (HBSS) for 3 times, minced into small fragments, and digested in sCelLive® Tissue Dissociation Solution (Singleron Biotechnologies) at 37 °C for 15 minutes. The dissociated tissues were filtered through 40 μm cell strainers. The red blood cells were removed by GEXSCOPE® red blood cell lysis buﬀer (Singleron Biotechnologies) at room temperature for 6 minutes. The single cell suspensions in PBS were loaded into microfluidic devices.
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix®Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron).

value: normal breast tissue

tag: individual

value: patient 932398


title: DMSO-Day3,Biol rep2

value: blood

value: Mononuclear cells

value: T cell


title: SH-SY5Y_5U_60_3

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: Phaseolus vulgaris 4004, grain,20DAF,3

source_name: Grain

value: Grain


title: normal breast tissue, patient 931881

description: GEXSCOPE

value: patient 931881


title: Phaseolus vulgaris 4004, grain,20DAF,2


title: normal breast tissue, patient 930137

description: GEXSCOPE

value: patient 930137


title: SH-SY5Y_5U_60_1

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: Phaseolus vulgaris 4004, grain,20DAF,1


title: Control 2 - GCN2 Inhibitor

value: Primary cells

value: T cells

tag: genotype


title: Control 1 - GCN2 Inhibitor

tag: treatment


title: normal breast tissue, patient 929677

description: GEXSCOPE

value: patient 929677


title: -Leucine 4 - DMSO

value: DMEM without leucine (6h)


title: normal breast tissue, patient 929267

description: GEXSCOPE

value: patient 929267


title: SH-SY5Y_5U_40_2

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: breast cancer tissue, patient 932398

description: GEXSCOPE

source_name: breast cancer tissue

value: breast cancer tissue


title: SH-SY5Y_5U_40_1

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: SH-SY5Y_5U_40_3

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: Phaseolus vulgaris 4004, pod,15DAF,1

value: Pod


title: Phaseolus vulgaris 4004, pod,20DAF,1


title: normal breast tissue, patient 932058

description: GEXSCOPE

value: patient 932058


title: -Leucine 3 - DMSO

value: WT


title: -Leucine 2 - DMSO


title: SH-SY5Y_5U_20_3

description:
5U stands for 5' UTR.
SH_U5_Raw.csv

value: neuroblastoma


title: Phaseolus vulgaris 4004, grain,15DAF,3


title: breast cancer tissue, patient 932058

description: GEXSCOPE


title: -Leucine 1 - DMSO


title: SH-SY5Y_5U_20_2

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: breast cancer tissue, patient 931881

description: GEXSCOPE


title: Control 3 - GCN2 Inhibitor

value: Control DMEM + GCN2 Inhibitor (6h)


title: Phaseolus vulgaris 4004, grain,15DAF,2


title: Control 4 - DMSO

value: Control DMEM (6h)


title: SH-SY5Y_5U_60_2

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: Phaseolus vulgaris 4004, grain,15DAF,1


title: breast cancer tissue, patient 929677

description: GEXSCOPE


title: Phaseolus vulgaris 4004, pod,15DAF,3


title: HUCCT1-H3K9me3

first: Fei

last: Xiong

address: Jiefang Road No.1095

institute: Huazhong University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with useful quality. Clean data (clean reads) were obtained after quality control, adapter trimming, quality filtering and per-read quality cutting.
Bowtie2 software was used to compare Clean Reads with the reference genome for analysis; DeepTools' computeMatrix module was used to analyze the Reads distribution in the upstream and downstream 3kb regions of transcription start sites (TSS).
MACS2 software was used to complete Peak detection in genome-wide range, and CHIPseeker software R package was used to analyze and calculate the distribution of Peak in each functional area.
MACS2 software is used to compare the Peaks of different experimental groups in two groups, so as to obtain the Peaks difference between different experimental groups. For a candidate difference peaks region, it is required to be enriched in at least one sample, and its likelihood ratio (log10 Likelihood ratio) is used to determine whether there is a difference.
Assembly: GRCh38
Supplementary files format and content: txt, narrowPeak
Library strategy: CUT&Tag

source_name: Intrahepatic cholangiocarcinoma

growth_protocol: HUCCT1 cells were cultured in RPMI-1640 medium. All cell culture media were supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
CUT & Tag assay was performed with the Hyperactive Universal CUT&Tag Assay Kit (Vazyme). 1×106 TFK-1 cells were harvested and their nuclei were extracted. The extracted nuclei were immobilized with activated concanavalin A‐coated magnetic beads and reacted with anti-Flag antibodies (1:50) in 100 μL DIG buffer overnight at 4℃. After being washed, the bound antibodies were reacted with secondary antibodies (1:50) for 1 h at room temperature and incubated with 100 μl Hyperactive pA/G-Transposon adapter complex (0.04 μM) for 1 h at room temperature. The precipitated immunocomplex was diluted in Trueprep Tagment Buffer L and after proteinase K digestion, the DNA fragments were extracted and stored at -80 ℃.
A DNA library was constructed using the TruePrep Index Kit V2 (Vazyme). The DNA fragments were mixed with N5XX and N7XX and amplified by PCR at 72 ℃ for 3 min, 95 ℃ for 3 min, and subsequent 10 cycles of 98 ℃ for 10 sec and 60 ℃ for 5 sec, 72 ℃ for 1 min and hold at 4 ℃. The library was extracted by VAHTS DNA Clean Beads (Vazyme). Average insert size of the molecules sequenced in H2 sample is 1095. Average insert size of the molecules sequenced in H3 sample is 645. Average insert size of the molecules sequenced in H4 sample is 757. Average insert size of the molecules sequenced in H5 sample is 792. Average insert size of the molecules sequenced in H6 sample is 1187. The specific gene sequences with paired ends were analyzed with DNA sequencing in an Illumina HiSeq 2000 platform (Illumina)

treatment_protocol: No special treatment was applied to HUCCT1 cells.

value: Intrahepatic cholangiocarcinoma

value: Intrahepatic cholangiocarcinoma cell


title: Control 3 - DMSO


title: Phaseolus vulgaris 4004, pod,15DAF,2


title: Control 2 - DMSO


title: Phaseolus vulgaris 4004, pod,10DAF,5


title: HUCCT1-H3K9ac


title: breast cancer tissue, patient 929267

description: GEXSCOPE


title: Control 1 - DMSO


title: Phaseolus vulgaris 4004, pod,10DAF,4


title: Phaseolus vulgaris 4004, pod,10DAF,3


title: CI5

city: Suita

first: Shugo

last: Sasaki

state: Osaka

address: 2-2 Yamadaoka, Suita-shi

department: Metabolic Medicine

country: Japan

institute: Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 (Illumina) with NovaSeq Reagent Kits v1.5 (150bp × 2 paired-end). Fastq files from each sample were analyzed using the cloud platform, RaNA-seq [Prieto C, Barrios D. Bioinformatics 2020]. Gene enrichment analyses were performed using the online tools, Enrichr, Kyoto Encyclopedia of Gene and Genomes (KEGG) and Gene Ontology [Kuleshov MV, et al. Nucleic Acids Res 2016, Kanehisa M, Goto S. Nucleic Acids Res 2000, Ashburner M, et al. Nat Genet 2000].
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: Matrix table with TPM values for every gene and every sample

source_name: iPSC-derived β-like cell spheroid

growth_protocol: iPSCs were differentiated using the modified version of the protocol published by Nair et al. [Nair GG, et al. Nat Cell Biol 2019]. Before the differentiation, ~80% confluent iPSC cultures were dissociated into single cells using Accutase (#12679-54, nacalai tesque), and seeded 6.0×106 cells per well in 6-well suspension plate in 5.5 mL StemFit with 10 µM Y-27632. The plates were incubated at 37℃ with 5% carbon dioxide on an orbital shaker at 100 rpm to form a 3D structure. After 24 hours, the cells were washed with PBS, deposited by gravity, and resuspended in Day 1 medium. Thereafter, the medium was changed every day with removing 4.5 mL (5 mL until Day 3) of medium and adding 5 mL (5.5 mL until Day 22) of fresh medium. The content of medium are as follows: Day 1: RPMI (#05176-25, nakalai tesque) containing 1:100 Glutamax (#04260-64, nakalai tesque), 0.2% FBS, 1:5000 ITS (#090-06741, FUJIFILM Wako Pure Chemical Corporation), 100 ng/mL ActivinA (#QK-035, Qkine), 3 μM CHIR99021 (#038-23101, FUJIFILM Wako Pure Chemical Corporation), and 1 μM JNJ-42041935 (#400093, Calbiochem). Day 2: RPMI containing 1:100 Glutamax, 0.2% FBS, 1:2000 ITS, 100 ng/mL ActivinA, and 1 μM JNJ-42041935. Day 3: RPMI containing 1:100 Glutamax, 0.2% FBS, 1:1000 ITS, 25 ng/mL KGF (#QK-046, Qkine), and 2.5 μM TGF-β1 Ⅳ (#039-24111, FUJIFILM Wako Pure Chemical Corporation). Day 4-5: RPMI containing 1:100 Glutamax, 0.4% FBS, 1:1000 ITS, and 25 ng/mL KGF. Day 6-7: DMEM with 25 mM glucose (#08488-55, nakalai tesque) containing 1:100 Glutamax, 1:100 B27 (#17504044, Thermo Fisher Scientific), 3 nM TTNPB (#T3757, Sigma Aldrich), and 0.5 mM Vitamin C (#13571-56, nakalai tesque). Day 8: DMEM with 25 mM glucose containing 1:100 Glutamax, 1:100 B27, 3 nM TTNPB, 0.5 mM Vitamin C, and 50 ng/mL EGF (#236-EG-200, R&D systems). Day 9-10: DMEM with 25 mM glucose containing 1:100 Glutamax, 1:100 B27, 0.5 mM Vitamin C, and 50 ng/mL EGF, 50 ng/mL KGF. Day 11-15: DMEM with 25 mM glucose containing 1:100 Glutamax, 1:100 ITS, 1:100 NEAA (#06344-56, nakalai tesque), 1 mM pyruvate (#06977-34, nakalai tesque), 10 μg/mL Heparin sulphate (#H3149-10KU, Sigma Aldrich), 1 mM N-acetyl cysteine (#A7250-5G, Sigma Aldrich), 10 μM zinc sulphate (#Z0251-100G, Sigma Aldrich), 1.75 μL 2-mercaptoethanol (#ES-007-E, Merck Millipore), 1% BSA (#A3803-100G, Sigma Aldrich), 10 μM Repsox (#S7223, selleck), 2 μM T3 (#038-25541, FUJIFILM Wako Pure Chemical Corporation), 0.5 μM LDN-193189 (#SML0559-5MG, Sigma Aldrich), and 1 μM DBZ (#S2711, Selleck). Day 16-22: CMRL (#11530037, Thermo Fisher Scientific) containing 1:100 Glutamax, 1:100 ITS, 1:100 NEAA, 1 mM pyruvate, 10 μg/mL Heparin, 1 mM N-acetyl cysteine, 10 μM zinc sulphate, 1.75 μL 2-mercaptoethanol, 1% BSA, 1:100 HEPES (#17557-94, nakalai tesque), 10 μM Repsox, 2 μM T3, and 0.155 mM Vitamin C.

extract_protocol:
From the differentiated spheroids, RNA was extracted using TRIzol Reagent (#10296028, Thermo Fisher Scientific) and purified using isopropanol and 75% ethanol. RNA samples were depleted DNase using TURBO DNA-freeTM Kit (#AM1907, Thermo Fisher Scientific), and purified to mRNA by Poly-A selection using NEBTNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs). Only RNA samples with RIN > 6 were used to generate libraries.
Following purification of first-strand cDNA, libraries were PCR amplified in accordance with their input RNA amount and purified using NEBNext Ultra II Directional RNA Library Prep Kit (#E7760, New England Biolabs).

treatment_protocol: For the experiments, 1 mM metformin (#PHR1084, Merk), 1mM imeglimin (provided by Sumitomo Pharma Co., Ltd.), 10 ng/mL TNF-α (#570106, Biolegend), and 10 ng/mL IFN-γ (#570206, Biolegend) were added on Day 16-22.

value: Human iPSC line derived from healthy individual

value: Cytokine and imeglimin


title: ChAP DNA associated with mutant tRF - replicate 4

city: San Marcos

first: Hong-Gu

last: Kang

address: 601 University Dr

institute: Texas State University

data_processing:
Pair-end reads were adapter-trimmed (forward: GATCGGAAGAGCACACGTCTGAACT, reverse: GATCGGAAGAGCGTCGTGTA) and quality-trimmed (3:25) via cutadapt (v2.10) and trimmomatic (v0.36), respectively.
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2 (v2.2.9) with the options ‘--no-unal, --no-discordant, --end-to-end, --no-mixed’. Only unique alignments aligned to the nuclear genome were retained.
Peaks were identified by MACS2 with default parameters, and filtered with p-value ≤ 0.05 using aligned reads for tRF31Asp2 and tRF31Asp2_mSS as IP and control, respectively.
Reproducible peaks found in a minimum of two independent biological replicates were merged as primary peaks.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files contain aignment information; pair-end reads were merged after alignment
Supplementary_files_format_and_content: bw files from bed files are intended for a genome browser
Supplementary_files_format_and_content: narrowPeak files contain peak position information; note that WT_tRF and Mut_tRF was used as sample and control, respectively, thus, this pair gives one narrowPeak file

organism: Arabidopsis thaliana

source_name: 3.5 wk-old leaves

growth_protocol: Plants were grown in soil at 22°C, 60% relative humidity, and in a 16 h light period.

extract_protocol:
Collected tissues were crosslinked with 1% formaldehyde at room temperature for 15 min and ground with liquid N2. Nuclei isolated as described above were lysed in the lysis buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and 25 U/ml RNase Inhibitor) and sonicated (Diagenode, Bioruptor Pico) for the 10 cycles of 30 sec on/off interval. Biotin-bound DNA was affinity-purified from nuclear lysate using Dynabeads M-280 streptavidin (ThermoFisher) at 4°C for overnight.
DNAs were recovered and used for the ChAP-seq library using NEBNext Ultra II DNA Library Prep kit (NEB).
ChAP(Chromatin-affinity precipitation)-seq

treatment_protocol: Renatured nucleotides were syringe-infiltrated into the abaxial side of the leaves.

tag: ecotype

value: treated with mutant tRF RNA for 1 hr


title: HUCCT1-H3K4me3

tag: tissue


title: Phaseolus vulgaris 4004, grain,10DAF,3

value: Grain


title: CI2


title: HUCCT1-H3K27me3


title: ChAP DNA associated with wildtype tRF - replicate 4

value: treated with wildtype tRF RNA for 1 hr


title: ChAP DNA associated with mutant tRF - replicate 3


title: CM5

value: Cytokine and metformin


title: HUCCT1-IgG

value: Normal rabbit IgG (A7016, Beyotime)


title: HUCCT1-H3K27ac


title: SH-SY5Y_5U_20_1

description:
5U stands for 5' UTR.
SH_U5_Raw.csv


title: breast cancer tissue, patient 930137

description: GEXSCOPE

value: patient 930137


title: Phaseolus vulgaris 4004, grain,10DAF,1


title: ChAP DNA associated with wildtype tRF - replicate 3


title: HUCCT1-HP1α

extract_protocol:
CUT & Tag assay was performed with the Hyperactive Universal CUT&Tag Assay Kit (Vazyme). 1×106 TFK-1 cells were harvested and their nuclei were extracted. The extracted nuclei were immobilized with activated concanavalin A‐coated magnetic beads and reacted with anti-Flag antibodies (1:50) in 100 μL DIG buffer overnight at 4℃. After being washed, the bound antibodies were reacted with secondary antibodies (1:50) for 1 h at room temperature and incubated with 100 μl Hyperactive pA/G-Transposon adapter complex (0.04 μM) for 1 h at room temperature. The precipitated immunocomplex was diluted in Trueprep Tagment Buffer L and after proteinase K digestion, the DNA fragments were extracted and stored at -80 ℃.
A DNA library was constructed using the TruePrep Index Kit V2 (Vazyme). The DNA fragments were mixed with N5XX and N7XX and amplified by PCR at 72 ℃ for 3 min, 95 ℃ for 3 min, and subsequent 10 cycles of 98 ℃ for 10 sec and 60 ℃ for 5 sec, 72 ℃ for 1 min and hold at 4 ℃. The library was extracted by VAHTS DNA Clean Beads (Vazyme). Average insert size of the molecules sequenced in A2 sample is 499. The specific gene sequences with paired ends were analyzed with DNA sequencing in an Illumina HiSeq 2000 platform (Illumina).

treatment_protocol: HUCCT1 cells were transfected with HP1α overexpression vector or normal control vector.

value: HA (51064-2-AP, Proteintech)

value: HP1a overexpression


title: Formalehyde treated, FA4

city: Talas

first: Ghulam Asghar

last: Sajid

state: Kayseri

address: Yenidoğan, Turhan Baytop Sokak No:1

department: Animal Science Department

country: Turkey

institute: Erciyes University

description:
Library name: Sample 8
Column name in raw reads.txt = FA4

data_processing:
Preprocessed with FastQC; cleaned using HTStream; alignment to chicken genome using Salmon; DESeq2 for normalization and differential expression analysis.
Assembly: Chicken reference genome from Ensembl (https://www.ensembl.org/Gallus_gallus/Info/Index).
Supplementary files format and content: Tab-delimited text file contains raw reads of all samples

organism: Gallus gallus

source_name: Embryo liver tissue

growth_protocol: Tinted breed chick embryos incubated at 37.8°C with 58-63% relative humidity.

extract_protocol:
Total RNA isolated using Nucleogene RNA extraction kit (Nucleogene, Istanbul, Türkiye).
Prepared using TruSeq RNA Sample Preparation Kit v2 Guide (Illumina, San Diego, CA, USA).

treatment_protocol: Formaldehyde (FA) gas fumigation using 35 mL formalin + 17.5 g KMnO4 for FA concentration of 6 g/m³ for 25 minutes.

value: Embryo liver tissue

value: liver cells

value: chicken tinted

value: formaledehyde


title: CM2


title: ChAP DNA associated with mutant tRF - replicate 2