title: K562_AHR_WT_FICZ

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

data_processing:
Briefly, raw reads were subjected to adapter removal (cutadapt 2.10) and mapped genome hg19 (bowtie2 2.4.1)(62) using --end-to-end --very-sensitive -–no-mixed -–no-discordant --phred33 -I 10 -X 700 parameters. Bigwig files were generated by bamCoverage(63) (version 3.3.0) and used for visualized in IGV(64) (version 2.8.6). Heatmaps were generated by deeptools(63) (version 3.3.0). SEACR (65) and MACS2 were used for peak calling from CUT&Run or ChIP-seq data, respectively. HOMER (66) was used for de novo motif analysis.
Assembly: hg19
Supplementary files format and content: bw
Library strategy: CUT&RUN

growth_protocol: Cells were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were washed twice with room temperature (RT) Wash Buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, Protease inhibitor cocktail (1:100)). After wash, cells were resuspended with RT Wash Buffer and incubated with activated Biomag Plus Concanavalin A (ConA) beads (BANGS LABORATORIES INC, BP531) for beads slurry. Cell-binding beads were incubated with freshly made antibody buffer (Wash Buffer, 0.01% Digitonin, 2mM EDTA) and primary antibody at 4°C overnight with rotation. The next day, beads were washed twice with ice-cold Digitonin Buffer (Wash Buffer with 0.01% Digitonin) and incubated with 2.5ul/sample CUTANA PAG-MNase (EpiCypher, 15-1116) to allow the binding of PAG-MNase.  After another 2 times washes with cold Digitonin Buffer, beads were incubated with 1ul/sample 100MM CaCl2 4°C on nutator for 2 hours to ensure efficient chromatin digestion. 33ul/sample Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 50ug/ml RNase A, 50ug/ml Glycogen) was added to stop MNase activity. DNA purifying was performed using the DNA Clean & Concentrate -5 kit (Zymo Research, D4014) as per manufacturer’s instructions. Briefly, 5 volumes of DNA Binding Buffer was added to each sample and washed twice with DNA Wash Buffer. Fragment DNA was eluted with 23ul/sample 0.1x TE Buffer and proceed to library preparation.
NEBNext Ultra II Library Prep kit was used for library preparation. CUT&RUN libraries were sequenced on the NovaSeq PE150 platform.

treatment_protocol: Cells were treated with FICZ(500nM) for 24hrs.

tag: agent

value: FICZ

value: Chronic myeloid leukemia cells

tag: chip antibody

value: anti-AHR(Proteintech, 17840-1-AP)


title: CD_TGF-b/SB431542_1

status: Public on Sep 01 2025

type: SRA

city: Bethesda

first: Youngjae

last: Bahn

state: Maryland

address: 10 Center Dr.

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
Single-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene. RPKM of each gene was calculated based on the length of the gene and the reads count mapped to that gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include transcript counts for each gene

molecule: total RNA

organism: Mus musculus

source_name: Primary preadipocytes

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA was further  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Primary preadipocytes

tag: genotype

value: WT

tag: treatment

value: Control Diet


title: MUT_24h_r1

city: Rehovot

first: Xun

last: Liang

address: Herzl 234

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description: Library name: TAD1_24h_TWEAK

data_processing:
Raw next-generation sequencing (NGS) data in the FASTQ format were analyzed using user-friendly transcriptome analysis pipeline (UTAP).
Briefly, reads were trimmed using “cutadapt” and mapped to the mouse reference genome (GRCm38/mm10) according to Gencode annotated genes using  STAR v2.7.10a .
UMI counting was done using HTSeq-count after marking duplicates in union mode. Differential gene expression analysis and normalization of the counts was performed using DESeq2 using the rld (log2 normalized) gene expression values
Assembly: mm10
Supplementary files format and content: Tab-delimited file includes raw counts for each sample
Supplementary files format and content: Tab-delimited file include processed counts for each sample

source_name: Skin

growth_protocol: Primary mouse dermal fibroblasts (MDF) were cultured in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 degree.

extract_protocol:
The RNA samples were prepared by  using either the RNeasy Mini Kit (QIAGEN) or the NucleoSpin RNA Mini Kit (MACHEREY-NAGEL). 50ng of total RNA was used for preparing sequencing library.
RNA libraries for RNA seq were prepared using a bulk version of the MARS-Seq procedure. Briefly, 50 ng of total RNA from each sample was barcoded during reverse transcription (RT) and then pooled. After cleanup with Agencourt AMPure XP beads (Beckman Coulter), the pooled samples underwent second-strand synthesis and were linearly amplified by T7 in-vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by adding Illumina sequences during ligation, RT, and PCR. Libraries were quantified using Qubit and TapeStation, as well as by qPCR for the ACTB gene.

treatment_protocol: 5th passage Primary MDF were treated or not with 100ng/ml TWEAK for 6 and 24 hours before collecting cell lysates

tag: tissue

value: Skin

tag: cell line

value: Primary cells

value: Dermal fibroblast

value: NIK X mut

value: 100ng/ml TWEAK for 24 hours


title: HFD_mock_1

value: Mock

value: High Fat Diet


title: Endometrial Cancer_ET19-86 [B02]

city: Chengdu

first: Xue

last: Xiao

state: Sichuan

address: 32# W. Sec 2, 1st Ring Rd

department: Department of Pathology

country: China

institute: Sichuan provincial people's hospital

data_processing:
The raw reads (raw sequencing FASTQ files) are selected for a DSP pipeline run
The raw reads are processed for high quality(if more than 50% base's Phred Q <=19), the adapters(for SE,if the adapter contamination length is greater than 5bp; for PE, if one read has adapter contamination, then both reads are removed) are removed, and the paired-end reads are merged
The reads are aligned to the DSP readout tag sequence identifier barcodes, then PCR duplicates are removed by matching on the Unique Molecular Index (UMI)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every Regions of Interest (ROIs)

organism: Homo sapiens

source_name: Endometrial Tumor

extract_protocol: After the GeoMx DSP system has completed collection, each GeoMx DSP aspirate in the collection plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. Following a pooling purification and quality control process, the final library is ready for sequencing on an Illumina NGS platform using a dualindex workflow.

value: Endometrial Tumor

tag: ec molecular_subtype

value: MMRd

tag: cd8+t cell_inifltration_status

value: TILs-high

tag: area of_analysis

value: Tumor area


title: MUT_0h_r1

description: Library name: TAD1_0h_TWEAK

value: Non-treated


title: CD_TGF-b_3


title: U937_FICZ_Replicate_2

library_source: genomic

molecule: genomic DNA

value: FICZ

value: Acute myeloid leukemia cells


title: MUT_6h_r2

description: Library name: TAD2_3h_TWEAK

value: 100ng/ml TWEAK for 6 hours


title: CD_TGF-b/SB431542_3

value: Primary preadipocytes

value: WT


title: CD_TGF-b_2

value: Control Diet


title: KO_6h_r2

description: Library name: KO2_3h_TWEAK

value: Skin

value: Primary cells

value: NIK knockout


title: CD_TGF-b_1


title: KO_24h_r2

description: Library name: KO2_24h_TWEAK

value: Dermal fibroblast

value: 100ng/ml TWEAK for 24 hours


title: shGpr151, DRG, Uninjured (IP) 2

city: Daegu

first: Eunsu

last: Jang

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

country: South Korea

institute: DGIST

description: Library name: shGpr151_CSDE1_ip_du_2

library_source: other

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

molecule: other

source_name: Dorsal root ganglion(DRG)

extract_protocol:
For CSDE1-IP sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-CSDE1 antibody, and the RNA from the immunoprecipitated product was extracted using RNeasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: Dorsal root ganglion(DRG)

value: Wild type

value: AAV-shGpr151, Uninjury


title: CD_mock_3

value: Mock


title: shGpr151, DRG, Injured (IP) 1

description: Library name: shGpr151_CSDE1_ip_dx_1

value: AAV-shGpr151, Injury


title: U937_FICZ_Replicate_1

value: anti-AHR(Proteintech, 17840-1-AP)


title: K562_EV_DMSO

value: DMSO

value: Chronic myeloid leukemia cells


title: shGpr151, DRG, Uninjured (IP) 3

description: Library name: shGpr151_CSDE1_ip_du_3


title: U937_DMSO_Replicate_1

value: Acute myeloid leukemia cells


title: KO_6h_r1

description: Library name: KO1_3h_TWEAK

value: 100ng/ml TWEAK for 6 hours


title: CD_mock_2

value: Primary preadipocytes

value: WT


title: shGpr151, DRG, Injured (IP) 2

description: Library name: shGpr151_CSDE1_ip_dx_2


title: Eca109 cell, Fn-3,48h

city: Guangzhou

first: Songhe

last: Guo

address: 132 Waihuan Road East, Guangzhou, China.

institute: Sun Yat-sen University

data_processing:
CLC. Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-qualty sequence using CLC genomic benchwork (parameter- Quality limt: 0. 05
Trimmed sequence reads were mapped to GrGM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
mm10
Assembly: Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited ted file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: MeRIP-seq

molecule: polyA RNA

extract_protocol:
a 50 μg RNA was obtained and ribosomal RNA was removed with the use of a RiboMinusTM Eukaryote Kit v2 (A15020, Invitrogen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Fn


title: shGpr151, DRG, Uninjured (IP) 1

description: Library name: shGpr151_CSDE1_ip_du_1


title: CD_mock_1

value: Control Diet


title: KO_24h_r1

description: Library name: KO1_24h_TWEAK

value: Skin

value: Primary cells

value: NIK knockout


title: shGpr151, DRG, Injured (Input) 3

description: Library name: shGpr151_input_dx_3

value: Dorsal root ganglion(DRG)


title: Eca109 cell, Fn-1,48h


title: shGpr151, DRG, Injured (Input) 2

description: Library name: shGpr151_input_dx_2

value: Wild type


title: U937_DMSO_Replicate_2


title: WT_CD47, replicate 1, snRNAseq

city: Hefei

first: Wenjie

last: Hu

address: No.81, Meishan Road

institute: Anhui Medical University

description: 10x Genomics

library_source: transcriptomic single cell

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

source_name: hippocampus

extract_protocol:
Freshly collected hippocampus tissue from WT and 5xFAD mice
R1 (read1primer sequence) were added to the molecules during GEM incubation.P5,P7,a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: hippocampus

value: Microglia and neurons


title: KO_0h_r1

description: Library name: KO1_0h_TWEAK

value: Dermal fibroblast

value: Non-treated


title: Itga5-High_DM_3

value: Adipogenic differentiation


title: Eca109 cell, pbs-3,48h

value: pbs


title: shGpr151, DRG, Injured (Input) 1

description: Library name: shGpr151_input_dx_1

value: AAV-shGpr151, Injury


title: shGpr151, DRG, Uninjured (Input) 3

description: Library name: shGpr151_input_du_3

value: AAV-shGpr151, Uninjury


title: WT_mCherry, replicate 1, snRNAseq

description: 10x Genomics

value: AAV-mCherry


title: KO_0h_r2

description: Library name: KO2_0h_TWEAK


title: Eca109 cell, pbs-1,48h


title: KD.2

city: Basel

first: Edoardo

last: Sozzi

address: Klingelbergstrasse 48

country: Switzerland

institute: ETH Zurich

data_processing:
Raw base calls were demultiplexed and converted into sample specific fastq format files using default parameters of the bcl2fastq program provided by Illumina (v2.19).
Resulting fastq files were quantified using Salmon (v1.1).
Assembly: Gencode version 33
Supplementary files format and content: raw counts per sample in csv format

source_name: mESCs TBV2 129/SvP

extract_protocol:
To perform RNA extraction, we used Trizol (Thermo Fisher Scientific, Invitrogen; cat: 15596018). Total RNAs were reverse transcribed with the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific; cat:4368814).
Illumina TruSeq library preparation kit

value: mESCs TBV2 129/SvP

value: Gastruloids

tag: time

value: Gastruloid formation


title: DDX55_KO_CD4_ naive T_24h_RNA_2

city: 成都

first: ping

last: he

address: 17 Renmin South Road, Wuhou District, Chengdu

institute: sichuan university

description:
DDX55_WTandKO_NaiveCD15Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD15Tcell_TEExpression.txt

data_processing:
Raw fastq files were processed with fastp v0.12.4 to remove adaptor sequences, and the trimmed files were aligned to the mouse reference genome mm10 using STAR aligner v2.7.1a. Stranded mappings were counted with the summarize Overlaps function in the Genomic Alignments v1.26.0 R package using standard GTF files for annotated genes and the RepeatMasker GTF files curated by Huipeng Jiao et al80 for transposons (TEs).
Assembly: mm10
Supplementary files format and content: tab-delimited text files including genes and TEs counts

source_name: Spleen and pLN

extract_protocol:
Purified WT or Ddx55-KO naïve CD4+ T cells were stimulated with plate-bound anti-CD3(5 ug/ml) and anti-CD28(2.5 ug/ml) for 0, 8, and 24 hours followed by total RNA isolation with RNA-easy reagent (Vazyme, #R701) according to the manufacturer’s protocol.
RNA library preparation and high throughput sequencing were conducted by SeqHealth Technology Co., Ltd. (Wuhan, China). Stranded RNA sequencing libraries were prepared to eliminate duplication bias in the PCR and sequencing steps using the Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (DR08502, Wuhan Seqhealth Co., Ltd.) following the manufacturer’s instructions. The library products corresponding to 200-500 bp were enriched, quantified and finally sequenced on NovaSeq 6000 sequencer (Illumina) with the PE150 model.

value: Spleen and pLN

value: CD4+ naive T cell

value: DDX55 KO

value: anti-CD3/CD28 24h


title: KD.3


title: DDX55_KO_CD4_naive T_24h_RNA_1

description:
DDX55_WTandKO_NaiveCD14Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD14Tcell_TEExpression.txt


title: KD.1


title: shGpr151, DRG, Uninjured (Input) 1

description: Library name: shGpr151_input_du_1

value: Dorsal root ganglion(DRG)

value: Wild type


title: Ctrl.3

value: WT


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line H2228 (LUAD)

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Genetics and Gene Regulation

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: Library name: H2228_dRNA_ONT

data_processing:
Assembly: GRCh38
ONT datasets were basecalled with Dorado using rna004_130bps_sup@v5.1.0 for direct RNA and dna_r10.4.1_e8.2_400bps_sup@v5.0.0 for the cDNA datasets. Reads with mean quality scores <10 were discarded.
Reads were mapped to the reference genome GRCh38 and GENCODE v44 transcriptome using minimap2 (v2.28)
Transcript-level quantification was performed using Salmon (v1.10.2) for short-read datasets and Oarfish (v0.6.2) for long-read datasets, based on the GENCODE v44 transcriptome combined with spike-in sequences from SIRV Set 4 and Sequins.
•       Salmon uses an internal quasi-mapping approach.
•       Long-read datasets were first aligned to the transcriptome using minimap2 (v2.28), followed by quantification with Oarfish.
Supplementary files format and content:
Bulk RNA-seq count matrices follow the naming convention: <protocol>_bulk_<cell line>_matrix.tsv
Where <protocol> is one of:
•       dRNA – ONT direct RNA sequencing
•       ont – ONT PCR cDNA sequencing
•       pb – PacBio Kinnex
•       ill – Illumina

growth_protocol: Cells were maintained in RPMI 1640 medium supplemented with GlutaMAX™ (Thermo Fisher Scientific), 10% heat-inactivated fetal bovine serum (FBS; Gibco), and 1% penicillin-streptomycin (Thermo Fisher Scientific). Cultures were incubated at 37°C in a humidified atmosphere containing 5% CO2. Cells were routinely passaged at 70–80% confluency using standard culture procedures.

extract_protocol:
Total RNA was isolated from 1.5–2 M cells using TRIzol Reagent (Invitrogen) following the manufacturers guidelines.
llumina bulk RNA-Seq libraries we constructed using the Illumina Truseq v2 Stranded kit with polyA selection. Superscript III was used instead of SuperScript II, and the reverse transcription incubation step was accordingly adjusted to 50°C. Nanopore direct-RNA sequencing libraries were constructed using the ONT SQK-RNA004 kit, with the following modifications: input was increased to 2μg total RNA. RNA CS (calibrating strand) was omitted. NEB Induro Reverse Transcriptase was used in place of SuperScript III.
Nanopore direct-RNA sequencing libraries were constructed using the ONT SQK-RNA004 kit, with the following modifications: input was increased to 2μg total RNA. RNA CS (calibrating strand) was omitted. NEB Induro Reverse Transcriptase was used in place of SuperScript III.
Nanopore PCR-cDNA libraries were constructed using the ONT SQK-PCB114.24 kit, with the following modifications: reverse transcription was perormed for 90 minutes at 42°C, followed by 14 cycles of PCR with an extension time of 4 minutes.
Pacbio Bulk Kinnex libraries were prepared with the Iso-Seq express 2.0 kit and Kinnex PCR 8-fold kit

value: Epithelial

tag: Sex

value: Female

tag: disease stage

value: Lung Cancer


title: Wildtype, DRG, Injured (IP) 3

description: Library name: wild-type_CSDE1-IP_dx3

value: Wildtype

value: Injury


title: LUHMES, rs356182-KO (G/-) #1

city: Grand Rapids

first: Jordan

last: Prahl

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Following RNA sequencing, the fastq  files had their sequencing adapters trimmed and QC reports generated using the TrimGalore package (Version- 0.6.0).
The trimmed read files were aligned to the GRCh37-hg19 reference genome using STAR (Spliced Transcripts Aligned to a Reference, Version 2.7.8a).
STAR provided readPerGene.out files for each sample containing read counts for each gene. These read counts files were used to generate a master table containing read data for all samples.
Next, a differential gene expression (DGE) object was created, normalized to CPM, and filtered for low read counts using the EdgeR package (version- 3.32.1).
Finally, comparisons of sample groups were done using the Limma-voom method (version- limma-3.46.0).

source_name: LUHMES

growth_protocol: LUHMES cells, obtained from ATCC (CRL-2927), were cultured essentially as described by Scholz et al. (Scholz et al. 2011; Pierce et al. 2018); the cells were incubated in a humidified 37°C, 5% CO2 incubator in flasks pre-coated with 50 mg/mL poly-L-ornithine (Sigma, Cat # P3655) and 1 mg/mL fibronectin (Sigma, Cat # F114) in water. The coated flasks were incubated at 37°C overnight, rinsed with water, and allowed to dry before seeding cells. Cells were cultured in complete growth medium containing Advanced DMEM:F12 (Thermo Fisher, Cat # 12634-010) with 2mM L-glutamine (Thermo Fisher, Cat # 25030081), 1X N-2 supplement (Thermo Fisher, Cat # 17502-048), and 0.04 mg/mL bFGF (Stemgent, Cat # 03-0002). Cells were allowed to reach 80% confluency before passaging with 0.025% trypsin/EDTA.

extract_protocol:
RNA was isolated and purified using the QIAGEN QIAshredder (Cat. #: 79654) and RNeasy isolation kit (Cat. #: 74104).
Libraries were prepared by the Van Andel Research Institute Genomics Core from 1 μg of material using the KAPA Stranded mRNA-seq Kit (v4.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 250-300 bp. Prior to PCR amplification, cDNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA). The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).

treatment_protocol: Before differentiation, cells were seeded at 3.5×106 per T75 flask containing complete growth medium and incubated at 37 °C for 24 h (day -1). For induction of differentiation, culture medium was changed to freshly prepared DMEM:F12 with 2mM L-glutamine, 1X N-2, 1mM cAMP (Carbosynth, Cat # ND07996), 1 mg/mL tetracycline (Sigma, Cat # T7660), and 2 ng/mL glial cell line-derived neurotrophic factor (GDNF) (Sigma, Cat # G1777) (day 0). LUHMES cells were then grown in the differentiation media for 2 days before being passaged, again into differentiation media (day 2). Finally, cells were harvested on day 6 after the initial introduction of differentiation media (day 6).

value: LUHMES

value: Dopaminergic SNpc neuron

value: dopaminergic differentiation

value: Day 6


title: DDX55_KO_CD4_ naive T_8h_RNA_2

description:
DDX55_WTandKO_NaiveCD13Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD13Tcell_TEExpression.txt

value: anti-CD3/CD28 8h


title: DDX55_KO_CD4_naive T_8h_RNA_1

description:
DDX55_WTandKO_NaiveCD12Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD12Tcell_TEExpression.txt

value: Spleen and pLN


title: Ctrl.2

value: mESCs TBV2 129/SvP

value: Gastruloids

value: Gastruloid formation


title: Oxford Nanopore direct RNA-Seq of lung cancer cell line H1975 (LUAD)

description: Library name: H1975_dRNA_ONT


title: Wildtype, DRG, Injured (IP) 2

description: Library name: wild-type_CSDE1-IP_dx2

value: Dorsal root ganglion(DRG)


title: DDX55_KO_CD4_ naive T_0h_RNA_2

description:
DDX55_WTandKO_NaiveCD11Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD11Tcell_TEExpression.txt

value: CD4+ naive T cell

value: DDX55 KO

value: anti-CD3/CD28 0h


title: Ctrl.1

value: WT


title: LUHMES, rs356182-KO (A/-) #2


title: LUHMES, rs356182-KO (A/-) #3


title: Wildtype, DRG, Injured (IP) 1

description: Library name: wild-type_CSDE1-IP_dx1


title: shGpr151, DRG, Uninjured (Input) 2

description: Library name: shGpr151_input_du_2

value: Wild type

value: AAV-shGpr151, Uninjury


title: LUHMES, rs356182-KO (G/-) #3


title: epididymal white adipose tissue, wild type (WT) mice, 3

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 901 W State St

institute: Purdue University

description: Library name: WT3

data_processing:
Quality control for raw mRNA-seq data was conducted using FastQC v0.11.9.
Illumina adapter sequences and low-quality bases were trimmed with Trim Galore v0.6.0
High-quality paired-end reads were then mapped to the mouse genome using the STAR aligner v2.7.10a
Bam-filter in ngsutils v0.5.9 was utilized to retain only properly and uniquely mapped paired reads (MAPQ≥10)
Gene expression levels were summarized using FeatureCounts from the subread package v2.0.1
Assembly: GRCm38 version M25
Supplementary files format and content: xlsx file include CPM values for each sample

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was extracted from cells or tissues using Trizol Reagent according to the manufacturer's instructions.
A complementary DNA library was then constructed using mRNA enriched by anti-polyA beads, and sequencing was performed according to the Illumina HiSeq standard protocol.

value: epididymal white adipose tissue

value: wild type (WT)


title: LUHMES, rs356182-KO (A/-) #1

value: LUHMES

value: Dopaminergic SNpc neuron


title: DDX55_KO_CD4_naive T_0h_RNA_1

description:
DDX55_WTandKO_NaiveCD10Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD10Tcell_TEExpression.txt


title: Wildtype, DRG, Uninjured (IP) 3

description: Library name: wild-type_CSDE1-IP_du3

value: Wildtype

value: Uninjury


title: WT_CD4_ naive T_24h_RNA_2

description:
DDX55_WTandKO_NaiveCD9Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD9Tcell_TEExpression.txt

value: Spleen and pLN

value: anti-CD3/CD28 24h


title: LUHMES, wildtype #3

value: dopaminergic differentiation

value: Day 6


title: epididymal white adipose tissue, wild type (WT) mice, 2

description: Library name: WT2


title: WT_CD4_naive T_24h_RNA_1

description:
DDX55_WTandKO_NaiveCD8Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD8Tcell_TEExpression.txt


title: Wildtype, DRG, Uninjured (IP) 2

description: Library name: wild-type_CSDE1-IP_du2

value: Dorsal root ganglion(DRG)


title: epididymal white adipose tissue, wild type (WT) mice, 1

description: Library name: WT1


title: Wildtype, DRG, Uninjured (IP) 1

description: Library name: wild-type_CSDE1-IP_du1


title: LUHMES, rs356182-KO (G/-) #2


title: WT_CD4_ naive T_8h_RNA_2

description:
DDX55_WTandKO_NaiveCD7Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD7Tcell_TEExpression.txt

value: CD4+ naive T cell

value: anti-CD3/CD28 8h


title: LUHMES, wildtype #1


title: epididymal white adipose tissue, Prmt5 knockout (KO) mice, 3

description: Library name: KO3

value: Prmt5 knockout (KO)


title: WT_CD4_ naive T_0h_RNA_2

description:
DDX55_WTandKO_NaiveCD5Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD5Tcell_TEExpression.txt

value: WT

value: anti-CD3/CD28 0h


title: RiboTag, AAV-shCsde1 (IP) 1

description: Library name: RiboTag_ip_shCsde1_1

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts
Library strategy: Ribo-Seq

source_name: Cultured adult dorsal root ganglion neurons

extract_protocol:
For RiboTag sequencing, lysate from the freshly collected DRGs were immunoprecipitated with an anti-HA antibody, and the RNA from the immunoprecipitated product was extracted using RNeasy mini kit(Qiagen, 74104).
Libraries were prepared following the instrcutions from the manufacture. (cDNA-PCR barcoding kit(SQK-PCB112.24))

value: Preconditioned


title: WT_CD4_naive T_8h_RNA_1

description:
DDX55_WTandKO_NaiveCD6Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD6Tcell_TEExpression.txt


title: RiboTag, AAV-shCsde1 (IP) 3

description: Library name: RiboTag_ip_shCsde1_3

value: Cultured adult dorsal root ganglion neurons


title: RiboTag, AAV-Control (IP) 3

description: Library name: RiboTag_ip_Control_3


title: WT_CD4_naive T_0h_RNA_1

description:
DDX55_WTandKO_NaiveCD4Tcell_GeneExpression.txt
DDX55_WTandKO_NaiveCD4Tcell_TEExpression.txt


title: Calvaria-KO-3

city: Madison

first: Samantha

last: Weaver

state: WI

address: 2015 Linden Drive

institute: University of Wisconsin-Madison

description: Library name: KO3

data_processing:
The samples were sequencing using a 2 x 150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control software.
Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: mm10
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: Calvaria

extract_protocol:
Calvaria were isolated from 2- to 3-day-old female WT (n=4) and Girk3-/- (n=4) mice. The calvaria were isolated, washed with PBS, then snap frozen. Calvaria were homogenized in 1 mL Trizol, then total RNA was extracted using the Zymo Direct-zol RNA Miniprep Kit.
RNA Sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina per the manufacturer’s instructions (NEB, Ipswich, MA).

value: Calvaria

tag: strain

value: Female

value: Girk3 knockout

tag: age

value: 2- to 3-day-old


title: RiboTag, AAV-shCsde1 (IP) 2

description: Library name: RiboTag_ip_shCsde1_2


title: epididymal white adipose tissue, Prmt5 knockout (KO) mice, 2

description: Library name: KO2

value: epididymal white adipose tissue


title: Calvaria-KO-4

description: Library name: KO4


title: WT_CD4_Naive_HA_CUT&Tag_2

data_processing:
CUT&Tag data processing and analysis were performed following a previously described protocol. Reads were trimmed of adaptor sequences using fastp v0.12.4, and aligned to the mouse mm10 and E. coli genomes using Bowtie2 v2.5.0 with the parameters --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700. Unmapped reads, and low mapping quality reads (MAPQ < 2) were removed using SAMtools v1.15.1. Pol II peaks were called using MACS3 v3.0.0b1 using default parameters and a q value cut-off of 0.05. H3K9me3 peaks were detected by using the ‘broad’ option of MACS3 v 3.0.0b1. To detect real R-loop domains, RNase-treated WT samples were used as a control to perform the peak calling with MACS3 v3.0.0b1(--broad --broad-cut-off 0.1) and peak annotation was performed with the R package ChIPseeker v1.30.3. Peaks that overlapped between replicates were then retained and merged to obtain a consensus peak set for each CUT&Tag target.
Assembly: mm10
Supplementary files format and content: bed files including peak region for each CUT&Tag target
Library strategy: CUT&Tag

extract_protocol:
5 × 105cells were washed twice with cell wash buffer, then incubated with activated concanavalin A-coated magnetic beads at room temperature for 10 min. Then, 0.5-1 ug of primary antibodies that specifically bind to R-loops (S9.6 anti–DNA-RNA hybrid antibody, Millipore, MABE1095), H3K9me3-histone modification (Abcam, ab8898),DDX55 (this paper), HA-tag (CST, 3724) or RNA polymerase II (CST, 2629) were added and incubated with the bead-bound cells by rotating for 2 hours at room temperature. For the R-loop CUT&Tag assay, 20 U of RNase H (NEB, M0297S) was added to the control groups during the antibody incubation stage. Then, 0.5 ul of mouse anti-rabbit IgG antibody or rabbit anti-mouse IgG antibody was added and incubated for another hour. After washing, bead-bound cells were mixed with pA/G-Tn5 transposome mix (2.5 μM) and rotated at room temperature for 1 hour. Spike-in DNA were added and bead-bound cells were then digested with proteinase K at 55°C for 1 hour.
The purified tagmentation products were subjected to DNA sequencing library preparation with Hieff NGS® Tagment Index Kit for Illumina (Cat#12416ES). The library products corresponding to 200-1000 bp were enriched, quantified and sequenced on NovaSeq 6000 sequencer (Illumina) with the PE150 model.

value: Spleen and pLN


title: WT_0h_r4

description: Library name: WT4_0h_TWEAK

value: Skin

value: Primary cells

value: Dermal fibroblast

value: Wild-type

value: Non-treated


title: RiboTag, AAV-Control (IP) 1

description: Library name: RiboTag_ip_Control_1


title: Calvaria-KO-2

description: Library name: KO2


title: e5'UTR, primary DRG neuron, Injured (Input) 2

description: Library name: eDRG_input_e5UTR_2

source_name: Primary DRG neuron

value: Primary DRG neuron

value: Wild type


title: Calvaria-KO-1

description: Library name: KO1


title: WT_CD4_Naive_HA_CUT&Tag_1

value: CD4+ naive T cell

value: WT


title: RiboTag, AAV-shCsde1 (Input) 3

description: Library name: RiboTag_TCL_shCsde1_3

value: Preconditioned


title: WT_24h_r4

description: Library name: WT4_24h_TWEAK

value: 100ng/ml TWEAK for 24 hours


title: WT_CD4_Naive_IgG_CUT&Tag

description: IgG.bw


title: epididymal white adipose tissue, Prmt5 knockout (KO) mice, 1

description: Library name: KO1

value: Prmt5 knockout (KO)


title: DDX55_KO_CD4_Naive_DDX55_CUT&Tag_2

description:
DDX55_KO.bw
DDX55_merge.bed

value: DDX55 KO


title: RiboTag, AAV-Control (IP) 2

description: Library name: RiboTag_ip_Control_2

value: Cultured adult dorsal root ganglion neurons


title: Calvaria-WT-4

description: Library name: WT4

value: Calvaria

value: Female

value: 2- to 3-day-old


title: Calvaria-WT-3

description: Library name: WT3


title: RiboTag, AAV-shCsde1 (Input) 2

description: Library name: RiboTag_TCL_shCsde1_2


title: sh_u1_2

type: RNA

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The Affymetrix Human Genome U133 Plus 2.0 Array were processed in R using the packages 'oligo'  and  'affy'. The data was RMA normalized.

label: biotin

label_protocol: standard Affymetrix protocol

growth_protocol: BE(2)C cells were grown in RPMI supplemented with 10% FBS media as described in the methods section.

extract_protocol: Trizol reagent RNA extraction using glycogen as a carrier was used as per the manufacturer protocol.

treatment_protocol: BE(2)C cells were infected with lentiviral preps, then selected for infection by puromycin treatment.

value: human BE(2)C cells

tag: genotype/variation

value: shRNA LIN28B


title: DDX55_KO_CD4_Naive_DDX55_CUT&Tag_1

description:
DDX55_KO.bw
DDX55_merge.bed

value: Spleen and pLN


title: sh_u1_3


title: sh_4_3


title: sh_4_2


title: RiboTag, AAV-shCsde1 (Input) 1

description: Library name: RiboTag_TCL_shCsde1_1


title: WT_CD4_Naive_DDX55_CUT&Tag_2

description:
DDX55_WT.bw
DDX55_merge.bed


title: RiboTag, AAV-shControl (Input) 3

description: Library name: RiboTag_TCL_Control_3


title: sh_u1_1


title: Calvaria-WT-1

description: Library name: WT1


title: WT_CD4_Naive_DDX55_CUT&Tag_1

description:
DDX55_WT.bw
DDX55_merge.bed


title: Calvaria-WT-2

description: Library name: WT2


title: RiboTag, AAV-shControl (Input) 2

description: Library name: RiboTag_TCL_Control_2


title: sh_1_2


title: sh_4_1


title: sh_1_3


title: DDX55_KO_CD4_Naive_Rloop_RNaseH_CUT&Tag_2

description:
Rloop_KO_RNaseH.bw
DDX55_Rloop_merge.bed

value: RNase H


title: IKKβ knockout, 4-NQO, pair 5

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

description: Library name: MPT16_7979

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: esophagus

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
Directional mRNA libraries were prepared using NEBNext Kits per the manufacturer’s instructions

treatment_protocol: Mice were treated with 4-nitroquinoline (4-NQO) in there drinking water (100ug/ml) or 2% propylene glycol (vehicle) for 1-month

value: esophagus

value: mucosal cells

value: Cre+, IKKb L/L

value: 4-NQO 1-month


title: RiboTag, AAV-shControl (Input) 1

description: Library name: RiboTag_TCL_Control_1


title: DDX55_KO_CD4_Naive_Rloop_RNaseH_CUT&Tag_1

value: CD4+ naive T cell


title: control, 4-NQO, pair 5

description: Library name: MPT15_7977

value: IKKb +/L


title: WT_CD4_Naive_Rloop_RNaseH_CUT&Tag_2

description:
Rloop_WT_RNaseH.bw
DDX55_Rloop_merge.bed

value: WT


title: RiboTag, DRG, Injured (IP) 3

description: Library name: RiboTag_IP_dx_3

value: Dorsal root ganglion(DRG)

value: Injury


title: IKKβ knockout, 4-NQO, pair 4

description: Library name: MPT14_7685


title: sh_scr_3

value: shRNA control


title: sh_scr_2


title: sh_1_1


title: control, 4-NQO, pair 4

description: Library name: MPT13_7684

value: IKKb L/L


title: WT_CD4_Naive_Rloop_RNaseH_CUT&Tag_1


title: RiboTag, DRG, Injured (IP) 1

description: Library name: RiboTag_IP_dx_1


title: DDX55_KO_CD4_Naive_Rloop_CUT&Tag_2

description:
Rloop_KO.bw
DDX55_Rloop_merge.bed

value: DDX55 KO


title: LUHMES, wildtype #2

value: LUHMES

value: Dopaminergic SNpc neuron

value: dopaminergic differentiation

value: Day 6


title: IKKβ knockout, vehicle, pair 3

description: Library name: MPT12_3604

value: Vehicle 1-month


title: CD4+t CELLS, RA (ATPLOW)-1,CONTROL

city: Rochester

first: Yanyan

last: Zheng

state: Minnesota

address: 839 16th ST SW, Apt421

institute: Mayo Clinic

description: A

data_processing:
The procedure of raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
CLC genomics workbench v11.0.1
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). D
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: pbmc

extract_protocol:
rna was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: pbmc

value: cd3+cd28+ stimulated cd4+t

tag: disease

value: RA (ATPlow)

value: ra

value: vehicle


title: control, vehicle, pair 3

description: Library name: MPT11_3602

value: esophagus

value: mucosal cells

value: IKKb +/L


title: RiboTag, DRG, Uninjured (IP) 2

description: Library name: RiboTag_IP_du_2

value: Dorsal root ganglion(DRG)

value: Uninjury


title: RiboTag, DRG, Uninjured (IP) 3

description: Library name: RiboTag_IP_du_3


title: WT_CD4_Naive_Rloop_CUT&Tag_2

description:
Rloop_WT.bw
DDX55_Rloop_merge.bed

value: Spleen and pLN

value: CD4+ naive T cell

value: WT


title: control, 4-NQO, pair 3

description: Library name: MPT10_3607

value: 4-NQO 1-month


title: 279850_R_B18_wt

city: London

first: Rushad

last: Pavri

address: Guy's Campus, Great Maze Pond, SE1 9RT

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King’s College London

description: Library name: 279850_R_B18_wt

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Assembly: Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Supplementary files format and content: NCBI hg38
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

source_name: Ramos

growth_protocol: see Methods

extract_protocol:
cells were harvested and genomic.DNA prepared by PCI extraction and EtOH precipitation
2 rounds of PCRs were used to add adapter sequences and dual barcoding for paired-end sequencing on Illumina platform

treatment_protocol: see Methods

value: Ramos

value: Burkitt's Lymphoma


title: sh_scr_1

value: human BE(2)C cells

value: shRNA control


title: ctrl_3

value: Empty vector control


title: DDX55_KO_CD4_Naive_Rloop_CUT&Tag_1

description:
Rloop_KO.bw
DDX55_Rloop_merge.bed

value: DDX55 KO


title: WT_CD4_Naive_Rloop_CUT&Tag_1

description:
Rloop_WT.bw
DDX55_Rloop_merge.bed


title: RiboTag, DRG, Uninjured (IP) 1

description: Library name: RiboTag_IP_du_1


title: 279838_R_B18_wt

description: Library name: 279838_R_B18_wt


title: RiboTag, DRG, Injured (IP) 2

description: Library name: RiboTag_IP_dx_2

value: Injury


title: ctrl_1


title: RiboTag, DRG, Injured (Input) 3

description: Library name: RiboTag_input_dx_3


title: DDX55_KO_CD4_Naive_PolII_CUT&Tag_2

description:
PolII_KO.bw
DDX55_PolII_merge.bed


title: 279837_R_B18_wt

description: Library name: 279837_R_B18_wt


title: RiboTag, DRG, Injured (Input) 2

description: Library name: RiboTag_input_dx_2


title: IKKβ knockout, 4-NQO, pair 3

description: Library name: MPT09_3603

value: Cre+, IKKb L/L


title: DDX55_KO_CD4_Naive_PolII_CUT&Tag_1

description:
PolII_KO.bw
DDX55_PolII_merge.bed


title: ctrl_2


title: IKKβ knockout, 4-NQO, pair 2

description: Library name: MPT08_3600

value: esophagus


title: control, 4-NQO, pair 2

description: Library name: MPT07_3598

value: mucosal cells


title: 279851_R_B18_wt

description: Library name: 279851_R_B18_wt


title: WT_CD4_Naive_PolII_CUT&Tag_2

description:
PolII_WT.bw
DDX55_PolII_merge.bed


title: IKKβ knockout, vehicle, pair 2

description: Library name: MPT06_3599

value: Vehicle 1-month


title: WT_CD4_Naive_PolII_CUT&Tag_1

description:
PolII_WT.bw
DDX55_PolII_merge.bed


title: 242063_R_B18_wt

description: Library name: 242063_R_B18_wt


title: control, vehicle, pair 2

description: Library name: MPT05_3594

value: IKKb L/L


title: RiboTag, DRG, Uninjured (Input) 2

description: Library name: RiboTag_input_du_2

value: Dorsal root ganglion(DRG)

value: Uninjury


title: 242034_R_B18_wt

description: Library name: 242034_R_B18_wt


title: DDX55_KO_CD4_Naive_H3K9me3_CUT&Tag_2

description:
H3K9me3_KO.bw
DDX55_H3K9me3_merge.bed

value: Spleen and pLN

value: CD4+ naive T cell


title: IKKβ knockout, vehicle, pair 1

description: Library name: MPT04_3596


title: 242033_R_B18_wt

description: Library name: 242033_R_B18_wt


title: DDX55_KO_CD4_Naive_H3K9me3_CUT&Tag_1

description:
H3K9me3_KO.bw
DDX55_H3K9me3_merge.bed


title: control, vehicle, pair 1

description: Library name: MPT03_3595

value: IKKb +/L


title: RiboTag, DRG, Uninjured (Input) 1

description: Library name: RiboTag_input_du_1


title: WT_CD4_Naive_H3K9me3_CUT&Tag_2

description:
H3K9me3_WT.bw
DDX55_H3K9me3_merge.bed

value: WT


title: 227405_R_B18_wt

description: Library name: 227405_R_B18_wt

value: Ramos

value: Burkitt's Lymphoma


title: de2f1b mutant biol rep 4

city: Montréal

first: Nam Sung

last: Moon

state: Quebec

address: 1205 Docteur Penfield Avenue, N3/17

department: Biology

country: Canada

institute: McGill University

description:
Library name: de2f1b mutant biol rep 4
bb1

data_processing:
The quality of the raw reads was assessed with FASTQC v0.11.8. After examining the quality of the raw reads, no trimming was deemed necessary.. The reads were aligned to the fly reference genome with STAR v2.7.6a with mean of 87 % of reads uniquely mapped. The raw counts were calculated with FeatureCounts v1.6.0 based on the fly reference genome (release 102). Differential expression was performed using DESeq2 R package. DEGs heatmap was drawn based on z-score of normalized count.
Assembly: BDGP6
Supplementary files format and content: csv file for normalized count with DESEQ2 : mutant_1b_vs_ctl_counts_normalized_relative_to_library_size.csv

organism: Drosophila melanogaster

source_name: Salivary gland

extract_protocol:
Total RNA was extracted  from salivary glands from third instar larvae of the appropriate genotype using the RNeasy Mini Kit (Qiagen). DNase treatment was performed.
RNA librairies were prepared following Illumina protocols.

value: Salivary gland


title: 242064_R_B18_wt

description: Library name: 242064_R_B18_wt


title: IKKβ knockout, 4-NQO, pair 1

description: Library name: MPT02_6930

value: 4-NQO 1-month


title: control, 4-NQO, pair 1

description: Library name: MPT01_6928


title: DDX55_KO_ CD4 naive T_ATAC_2

description:
ATAC_KO_0h.bw
DDX55_ATAC_merge.bed

data_processing:
ATAC-seq low-quality reads and adaptor contaminations were removed using fastp v0.12.4. Trimmed reads were aligned to the mouse reference genome mm10 using Bowtie2 v2.5.08 with the parameters --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700. Unmapped reads, and low mapping quality reads (MAPQ < 2) were removed using SAMtools v1.15.1. Peaks were called using MACS3 v3.0.0b1 with option ‘-q 0.05’.
Assembly: mm10
Supplementary files format and content: bed files including peak region for ATAC-seq

extract_protocol:
The purified naïve CD4+cells from WT and Ddx55-KO mice were washed twice with ice-cold PBS and cell pellets were lysed in 50 μl ice-cold lysis buffer (10 mM Tris-HCl, pH 7.5; 10 mM NaCl, 3 mM MgCl2, 0.08% NP40 substitute, 0.01% digitonin ) for 30 min and immediately subjected to DNA fragmentation
DNA library preparation using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-503) following the manufacturer’s instructions. The library products corresponding to 250-450 bp were enriched, quantified, and finally sequenced on NovaSeq 6000 sequencer (Illumina) with the PE150 model.

value: DDX55 KO


title: WT_CD4_Naive_H3K9me3_CUT&Tag_1

description:
H3K9me3_WT.bw
DDX55_H3K9me3_merge.bed


title: 227404_R_B18_wt

description: Library name: 227404_R_B18_wt


title: MINO_IgG

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: Library name: sample28

data_processing:
Sequencing reads were aligned to hg38 reference genome using Bowtie v2.4.4 with the parameter (-sensitive --no-unal -p 20 -x). Peak calling was performed by MACS2 v1.4.2 with default parameters. BigWig files and analysis of read density in peak regions were generated using deeptools v3.5.1. Read density of specific genomic regions were displayed using Integrative Genomics Viewer (IGV) v2.17.2.
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&Run

source_name: B lymphocytes

growth_protocol: 10% FBS in RPMI1640 media

extract_protocol:
MINO cells expressing wildtype or mutant SMARCA4 or treated with FHD-286 were analyzed by ATAC-seq and Cut&Run. CCMCL1 cells expressing cas9-sgROSA or cas9-sgBRG1 were analyzed by ATAC-seq. JEKO cells ectopically expressing MEF2B were analyzed by Cut&Run analysis.
For ATAC-seq, 55,000 cells flash-frozen in 10% DMSO were lysed, permeabilized, and tagmented using the Omni ATAC-seq protocol followed by 12 cycles of barcoding PCR. Gel-purified libraries were sequenced on the Element Biosciences AVITI to obtain approximately 10M paired-end reads. For Cut&Run, 50,000 MCL cells were harvested and fixed with 0.1% formaldehyde for 5 min and further processed by Epicypher ChIC system. All the recovered DNA was used for dual indexed library preparation and sequenced for 10M paired end reads per sample.

treatment_protocol: Actively growing MCL cells with specified genotypes were harvested.

value: B lymphocytes

value: MINO

value: mantle cell lymphoma

value: expressing wildtype BRG1

tag: batch


title: RiboTag, DRG, Injured (Input) 1

description: Library name: RiboTag_input_dx_1

data_processing:
Basecalls were performed on the fast5 files generated from MinION output.
The sequence reads were trimmed for adaptor or barcoding sequence using qcat(score=0).
All replicates were collected and shuffled, and split into three fastq files using Seqkit.
The sequence reads were mapped to GRCm39/mm39 using minimap2 and quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Tab separated value(tsv.) file for raw counts

value: Injury


title: de2f1b mutant biol rep 1

description:
Library name: de2f1b mutant biol rep 1
b1


title: de2f1b mutant biol rep 3

description:
Library name: de2f1b mutant biol rep 3
b2


title: 242052_R_B18_cdr3_tgct

description: Library name: 242052_R_B18_cdr3_tgct


title: MINO BRG WT_BRG1

description: Library name: sample27


title: w1118 biol rep 4

description:
Library name: w1118 biol rep 4
a4


title: DDX55_KO_ CD4 naive T_ATAC_1

description:
ATAC_KO_0h.bw
DDX55_ATAC_merge.bed


title: WT CD4_ naive T_ATAC_2

description:
ATAC_WT_0h.bw
DDX55_ATAC_merge.bed


title: w1118 biol rep 1

description:
Library name: w1118 biol rep 1
a1


title: WT CD4_naive T_ATAC_1

description:
ATAC_WT_0h.bw
DDX55_ATAC_merge.bed


title: 242051_R_B18_cdr3_tgct

description: Library name: 242051_R_B18_cdr3_tgct


title: MINO BRG WT_H3K27Ac

description: Library name: sample25


title: 242022_R_B18_cdr3_tgct

description: Library name: 242022_R_B18_cdr3_tgct


title: 227406_R_B18_wt

description: Library name: 227406_R_B18_wt


title: sh_u1_3 [miRNA]

data_processing: The Affymetrix GeneChip miRNA 3.0 arrays were processed in R as follows. First, we re-annotaed the probes we loaded raw .CEL files using the ‘oligo’ and ‘affy’ packages. Second, we empirically defined a background level of expression as 5.41 by determining two standard deviations above the mean probe intensity of all probes mapping to Zea mays. We excluded all non-human probes and probes mapping to un-annotated genes, leaving 1,724 probes for further analysis. We further restricted downstream analysis to the 542 probes were detected (i.e. mean expression in the group > the background defined above) in at least one experimental group. We used the mirFocus database (http://mirfocus.org/index.php) to annotate miRNAs as clustered or singletons. Data was quantile normalized.

value: human BE(2)C cells

value: shRNA LIN28B


title: de2f1b mutant biol rep 2

description:
Library name: de2f1b mutant biol rep 2
ss1


title: CM degron dTAG HA

description: Library name: sample24

value: expressing FOXO1-FKBP12(F36V) with dTAG treatment


title: 242021_R_B18_cdr3_tgct

description: Library name: 242021_R_B18_cdr3_tgct


title: RiboTag, DRG, Uninjured (Input) 3

description: Library name: RiboTag_input_du_3

value: Dorsal root ganglion(DRG)

value: Uninjury


title: mESC, 33kpa, 72h

city: Mumbai

first: Shamik

last: Sen

state: Maharashtra

address: Powai

department: Biosciences and Bioengineering

country: India

institute: IIT Bombay

data_processing:
Raw FASTQ files were mapped to Mus_musculus.GRCm39.cdna reference cDNA transcriptome using Kallisto (v0.45.0) for estimating transcript abundance. Data annotation was carried out using AnnotationHub and genes exhibiting a Counts Per Million (CPM) value of less than 1 in at least three samples were excluded from further analysis. The resulting filtered count matrix was then normalized by Trimmed Mean of M-values (TMM) method using edgeR package
Differential Gene Expression was carried out using PyDESeq2 package
Gene Ontology Analysis was performed using gprofiler2 package
Assembly: Mus_musculus.GRCm39.cdna
Supplementary files format and content: A comma-separated values (CSV) file containing TPM normalized gene-level count matrix. Each row in the matrix represents a distinct gene, while each column corresponds to a sample. The values within the matrix indicate the abundance of each gene in the respective sample.

source_name: embryo, blastocyst

growth_protocol: mESCs were maintained in KO DMEM supplemented with 10% KO FBS, L-glumatine and non-essential amino acid, in presence of LIF cultured on 0.1% gelatin coated dishes. Cells were grown in a de humidified incubator with 5 % CO2.

extract_protocol:
Total RNA was isolated using TRIzol (Ambion) according to instructions from the manufacturer to generate libraries from a total of 1µg RNA for each sample.
Ribo-Zero Plus stranded library preparation kit (Illumina) was used to generate libraries

treatment_protocol: mESCs were cultured on fibronectin (FN) coated polyacrylamide (PA) hydrogels of varying stiffnesses (0.6 kPa, 4 kPa, 33 kPa) without LIF to induce differentiation. 2 uM Etoposide was added to one condition to induce DNA damage in absence of LIF on 0.6 kPa PA gel.

value: embryo, blastocyst

value: embryonic stem cells

value: no LIF

tag: substrate stiffness

value: 33 kPa

value: 72 hrs


title: mESC, 0.6kPa, Etoposide

tag: cell type

value: WT

value: 0.6 kPa

value: 24 hrs


title: mESC, 33kPa, 24h

tag: genotype


title: CM degron dTAG PAX5

description: Library name: sample22

value: B lymphocytes

tag: treatment


title: CM degron no dTAG HA

description: Library name: sample23

tag: tissue

value: mantle cell lymphoma

value: expressing FOXO1-FKBP12(F36V)


title: 227403_R_B18_wt

description: Library name: 227403_R_B18_wt

value: Ramos

tag: cell line

value: Burkitt's Lymphoma


title: 227344_R_B18_cdr3_tgct

description: Library name: 227344_R_B18_cdr3_tgct


title: MINO BRG T910M_H3K27Ac

description: Library name: sample26

value: MINO

value: expressing T910M BRG1


title: sh_u1_1 [miRNA]

value: human BE(2)C cells

value: shRNA LIN28B


title: CM degron no dTAG PAX5

description: Library name: sample21


title: 227343_R_B18_cdr3_tgct

description: Library name: 227343_R_B18_cdr3_tgct


title: JEKO MEF2B HA

description: Library name: sample20

value: expressing MEF2B-HA


title: mESC, 33kPa, 6h

value: embryo, blastocyst

value: embryonic stem cells

value: 6 hrs


title: 227333_R_B18_cdr3_tgct

description: Library name: 227333_R_B18_cdr3_tgct


title: mESC, 4kPa, 72h

value: no LIF

value: 4 kPa

value: 72 hrs


title: sh_4_3 [miRNA]


title: JEKO parent HA

description: Library name: sample19

value: non-expressor


title: 242054_R_B18_cdr3_tgca

description: Library name: 242054_R_B18_cdr3_tgca


title: 227334_R_B18_cdr3_tgct

description: Library name: 227334_R_B18_cdr3_tgct


title: mESC, 4kPa, 24h

value: WT

value: 24 hrs


title: sh_4_2 [miRNA]


title: sh_4_1 [miRNA]


title: sh_1_3 [miRNA]


title: sh_u1_2 [miRNA]


title: UPN1  degron 8h dTAC_ATAC (2)

description:
Library name: sample18
UPN_FOXO1degron_8h_dedup.bw

data_processing:
Sequencing reads were aligned to hg38 reference genome using Bowtie v2.4.4 with the parameter (-sensitive --no-unal -p 20 -x). Peak calling was performed by MACS2 v1.4.2 with default parameters. BigWig files and analysis of read density in peak regions were generated using deeptools v3.5.1. Read density of specific genomic regions were displayed using Integrative Genomics Viewer (IGV) v2.17.2.
Assembly: hg38
Supplementary files format and content: BigWig

value: B lymphocytes

value: mantle cell lymphoma

value: expressing FOXO1-FKBP12(F36V)


title: 242053_R_B18_cdr3_tgca

description: Library name: 242053_R_B18_cdr3_tgca

value: Ramos

value: Burkitt's Lymphoma


title: UPN1  degron 8h dTAC_ATAC (1)

description:
Library name: sample17
UPN_FOXO1degron_8h_dedup.bw


title: UPN1  degron 2h dTAC_ATAC (2)

description:
Library name: sample16
UPN_FOXO1degron_2h_dedup.bw

value: expressing FOXO1-FKBP12(F36V) with 8h dTAG treatment


title: mESC, 4kPa, 6h


title: mESC, 0.6kPa, 72h

value: 0.6 kPa


title: 242024_R_B18_cdr3_tgca

description: Library name: 242024_R_B18_cdr3_tgca


title: 242023_R_B18_cdr3_tgca

description: Library name: 242023_R_B18_cdr3_tgca


title: mESC, 4kPa, 3h

value: 3 hrs


title: sh_1_2 [miRNA]

value: human BE(2)C cells

value: shRNA LIN28B


title: mESC, 0.6kPa, 24h

value: embryo, blastocyst

value: embryonic stem cells


title: UPN1  degron 2h dTAC_ATAC (1)

description:
Library name: sample15
UPN_FOXO1degron_2h_dedup.bw


title: mESC, 33kPa, 3h

value: no LIF

value: 33 kPa


title: sh_scr_3 [miRNA]

value: shRNA control


title: 227345_R_B18_cdr3_tgca

description: Library name: 227345_R_B18_cdr3_tgca


title: sh_1_1 [miRNA]


title: sh_scr_2 [miRNA]


title: UPN1 degron no dTAG_ATAC (1)

description:
Library name: sample13
UPN_FOXO1degron_0h_dedup.bw


title: mESC, 0.6kPa, 3h

value: WT


title: 227336_R_B18_cdr3_tgca

description: Library name: 227336_R_B18_cdr3_tgca


title: mESC, 0.6kPa, 6h

value: 6 hrs


title: CCMCL1 degron 8h dTAC_ATAC (2)

description:
Library name: sample12
CM_FOXO1degron_8h_dedup.bw

value: B lymphocytes


title: 227335_R_B18_cdr3_tgca

description: Library name: 227335_R_B18_cdr3_tgca


title: sh_scr_1 [miRNA]


title: mESC, LIF, S3

value: pluripotent/+LIF

value: not relevant, 2


title: ctrl_3 [miRNA]

value: Empty vector control


title: CCMCL1 degron 8h dTAC_ATAC (1)

description:
Library name: sample11
CM_FOXO1degron_8h_dedup.bw

value: mantle cell lymphoma


title: 242058_R_B18_cdr3_agcc

description: Library name: 242058_R_B18_cdr3_agcc

value: Ramos

value: Burkitt's Lymphoma


title: mESC, LIF, S2

value: not relevant, 1


title: mESC, LIF, S1

value: not relevant, 0


title: 242057_R_B18_cdr3_agcc

description: Library name: 242057_R_B18_cdr3_agcc


title: 227346_R_B18_cdr3_tgca

description: Library name: 227346_R_B18_cdr3_tgca


title: CCMCL1 degron no dTAG_ATAC (2)

description:
Library name: sample8
CM_FOXO1degron_0h_dedup.bw

value: expressing FOXO1-FKBP12(F36V)


title: ctrl_1 [miRNA]

value: human BE(2)C cells


title: 242028_R_B18_cdr3_agcc

description: Library name: 242028_R_B18_cdr3_agcc


title: ctrl_2 [miRNA]


title: CCMCL1 degron 2h dTAC_ATAC (2)

description:
Library name: sample10
CM_FOXO1degron_2h_dedup.bw


title: Spleen, WT, replicate 1, scRNAseq

city: Zwijnaarde

first: Sophie

last: Janssens

address: Technologiepark 71

department: Inflammation Research Center

country: Belgium

institute: VIB/UGhent

description: BD Rhapsody

data_processing:
The BD Rhapsody Sequence Analysis Pipeline (BD; version 1.9.1) was used to map the FASTQ files to the mouse reference genome (mm10-2020-A). Single-cell analysis was performed using RStudio (R version 4.0.5) starting from RSEC_MolsPerCell.csv (data table containing molecules per gene per cell based on RSEC (recursive substitution error correction)).
Pre-processing of the RNA UMI matrix was done according to the workflow proposed by the Marioni lab (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112579/). Outliers were identified based on 3 metrics: number of expressed genes, library size and mitochondrial proportion. Cells 5 MADs (Median Absolute Deviation) away from the median value were filtered out for the number of expressed genes and library size, 5 MADs was used as an upper limit for the mitochondrial proportion.
The subsequent count matrix was used to create a Seurat Object with the Seurat R package (v4.0.5). Count normalization, detecting highly variable genes and scaling was performed with the SCTransform function with default parameters. Finding clusters and creating UMAP plots was done using the Seurat pipeline. Clustering was performed using the first 35 principal components and a resolution of 1.
Assembly: mm10
Supplementary files format and content: BD Rhapsody unfiltered data table of gene counts in sparse format: NVA8_BD1_cDNA_Expression_Data_Unfiltered.st.gz
Supplementary files format and content: BD Rhapsody filtered data table containing molecules per gene per cell based on RSEC error correction: NVA8_BD1_cDNA_RSEC_MolsPerCell.csv
Supplementary files format and content: Seurat object: seuratObj_NVA8_BD1_paper.rds

source_name: Spleen

extract_protocol:
Single-cell suspension of splenocytes was obtained by enzymatic digestion. Cell sorting was performed on FACSymphony S6 sorter (BD Biosciences). To sort different immune cells spiked in equal numbers, the total single-cell suspension was enriched prior to staining and cell sorting by depletion of CD3e+ and CD19+ cells using biotin-labeled monoclonal antibodies and MagniSort Streptavidin Negative Selection Beads (Thermo Fisher Scientific; MSNB-6002-74). CD3e+ and CD19+ cells were sorted from a not enriched fraction of the sample. 1985 T cells (CD3e+), B cells (CD19+), Basophils (CD200R3+, Fcer1+, CD45dim), ILCs (CD3e-, CD127+, CD90.2+), Macrophages (F4/80+, CD64+), NKT cells (CD3e+, CD161+), NK cells (CD3e- CD161+), cDC1s (CD11c+, MHCII+, XCR1+), cDC2s (CD11c+, MHCII+, CD172a+), neutrophils (CD11b+ Ly6G+), monocytes (CD11b+, Ly6G-, Ly6C+), eosinophils (CD11b+ SiglecF+) , pDCs (CD11b- Bst2+ Ly6C+) and 205 Mast cells (Fcer1+, CD117+, CD11c-) were sorted, centrifuged and resuspended in Rhapsody buffer.
The sorted single-cell suspension was resuspended at an estimated final concentration of 2000 cells/µl and loaded on a BD Rhapsody cartridge with a targeted capture of 15000 cells. Reverse transcription, cDNA amplification and library construction were performed following the manufacturer’s instructions (23-24117(02)). Libraries were sequenced on a NovaSeq6000 flow cell (Illumina).

value: Spleen

value: Total splenocytes


title: CCMCL1 degron 2h dTAC_ATAC (1)

description:
Library name: sample9
CM_FOXO1degron_2h_dedup.bw

value: expressing FOXO1-FKBP12(F36V) with 2h dTAG treatment


title: UPN1 degron no dTAG_ATAC (2)

description:
Library name: sample14
UPN_FOXO1degron_0h_dedup.bw


title: Heart, CFZ, EA, rep2

city: Nanjing

first: Yuxuan

last: Chen

state: Jiangsu

address: 138 Xianlin Rd

institute: Nanjing University of Chinese Medicine

description:
M_E2
genes_fpkm_expression.txt

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Mus musculus（ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially removes a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 builds a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
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.
Assembly: Mus musculus.GRCm38
Supplementary files format and content: Tab-delimited text file includes FPKM and count values for each Sample.

source_name: heart, intraperitoneal injection with Carfilzomib (8 mg/kg), electroacupuncture at PC6 acupoint

extract_protocol:
Hearts were removed and flash frozen on liquid nitrogen. Total RNA was extracted using Trizol reagent (thermofisher) following the manufacturer's procedure. The total RNA quantity and purity were analyzed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: heart

tag: weight

value: 7-8 weeks

value: wide type

value: Carfilzomib, electroacupuncture at PC6 acupoint


title: 242027_R_B18_cdr3_agcc

description: Library name: 242027_R_B18_cdr3_agcc


title: 227350_R_B18_cdr3_agcc

description: Library name: 227350_R_B18_cdr3_agcc


title: Heart, CFZ, EA, rep1

description:
M_E1
genes_fpkm_expression.txt


title: CCMCL1 sgBRG1_ATAC

description: Library name: sample6

value: B lymphocytes

value: expressing sgBRG1


title: Heart, CFZ, rep2

description:
mod2
genes_fpkm_expression.txt

source_name: heart, intraperitoneal injection with Carfilzomib (8 mg/kg)

value: Carfilzomib


title: CCMCL1 sgROSA_ATAC

description: Library name: sample5

value: mantle cell lymphoma

value: expressing sgROSA


title: Heart, CFZ, rep1

description:
mod1
genes_fpkm_expression.txt


title: Heart, Control, rep2

description:
con2
genes_fpkm_expression.txt

source_name: heart, intraperitoneal injection with 10% DMSO

value: DMSO


title: 227339_R_B18_cdr3_agcc

description: Library name: 227339_R_B18_cdr3_agcc

value: Ramos

value: Burkitt's Lymphoma


title: MINO FHD_ATAC

description: Library name: sample3

value: MINO

value: FHD-286 for 24 h


title: MINO control_ATAC

description: Library name: sample4

value: no treatment


title: Liver - Control - Rep6

city: Toulouse

first: LAILA

last: LAKHAL

address: 180 chemin de Tournefeuille

department: SA

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 12 out of 15 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 33989 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 31357 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Polycarbonate cages Type S , 20-24°C, 12h Light/dark cycle, Ad libitum food and water, Stainless steel hut.

extract_protocol: RNA extraction was done with Tri reagent following the method of (Chomczynski and Sacchi, 1987)

treatment_protocol: Snap frozen in liquid nitrogen

tag: condition

value: Control

value: male


title: 242060_R_B18_cdr3_agca

description: Library name: 242060_R_B18_cdr3_agca


title: CCMCL1 degron no dTAG_ATAC (1)

description:
Library name: sample7
CM_FOXO1degron_0h_dedup.bw

value: expressing FOXO1-FKBP12(F36V)


title: Liver - Control - Rep5


title: Liver - Pesticides_TBT - Rep2


title: Heart, Control, rep1

description:
con1
genes_fpkm_expression.txt

value: heart

value: 7-8 weeks


title: Liver - Pesticides - Rep3

value: Pesticides


title: Liver - Pesticides_TBT - Rep3


title: 242059_R_B18_cdr3_agca

description: Library name: 242059_R_B18_cdr3_agca


title: Liver - Control - Rep3


title: Liver - Pesticides_TBT - Rep1


title: MINO BRG T910M_ATAC

description: Library name: sample2

value: B lymphocytes

value: expressing T910M BRG1


title: MINO BRG WT_ATAC

description: Library name: sample1

value: expressing wildtype BRG1


title: 227349_R_B18_cdr3_agcc

description: Library name: 227349_R_B18_cdr3_agcc


title: 242030_R_B18_cdr3_agca

description: Library name: 242030_R_B18_cdr3_agca


title: Gal3-treatment, replicate 1, snRNAseq

city: Shenzhen

first: Zilong

last: Wang

address: XueyuanDadao

institute: Southern University of Science and Technology

description: GEXSCOPE® Single Nucleus RNA-seq Kit

data_processing:
The barcode processing, unique molecular identifiers filtering, gene counting and sample mapping to the reference GRCm38 were made using the CeleScope (v1.14.0) pipeline (https://github.com/singleron-RD/CeleScope).
Assembly: mm10
Supplementary files format and content: Matrix files

molecule: nuclear RNA

source_name: Spinal dorsal horn

extract_protocol:
Frozen SDH tissue from C57BL/6J wild-type mice was washed in pre-cooled PBSE (PBS buffer containing 2 mM EGTA). GEXSCOPE® Nucleus Separation Solution (Singleron Biotechnologies) was used to isolate the single nucleus, referring to the manufacturer's product manual. The isolated nuclei were re-suspended in PBSE to 106 nuclei per 400 μl and then filtered through a 40 μm cell strainer. Finally, the nuclei were counted by Trypan blue. DAPI (1:1,000) (TermoFisher Scientific, D1306) was used to stain the nuclei enriched in PBSE, which were defined as DAPI-positive singlets.
Single nucleus suspension (3×105-4×105 nuclei/ml) with PBS was loaded onto a microfluidic chip (GEXSCOPE® Single Nucleus RNA-seq Kit, Singleron Biotechnologies). Subsequently, the snRNA-seq libraries were constructed based on the manufacturer’s instructions (Singleron Biotechnologies). The resulting snRNA-seq libraries were pooled for sequencing on the Illumina novaseq 6000 with 150 bp paired-end reads.

value: Spinal dorsal horn

value: wild-type

value: 6-8 weeks old

value: 6-days intrathecal injection (drug injections were performed once every day)


title: 227340_R_B18_cdr3_agcc

description: Library name: 227340_R_B18_cdr3_agcc

value: Ramos

value: Burkitt's Lymphoma


title: JEKO1-MEF2B HA

description: Library name: JPWCM01_02

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC hg38reference genome using tophat v2.0.11.
Transcript abundances was estimated with Salmon. Salmon outputs normalized expression values, including TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: hg38
Supplementary files format and content: excel file including gene id, gene symbol, FPKM or TPM value of each gene in each sample

growth_protocol: MCL cells were grown in 10% FBS in RPMI1640 media.

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mantle cell lymphoma

value: expressing MEF2B-HA


title: vehicle control, replicate 1, snRNAseq

description: GEXSCOPE® Single Nucleus RNA-seq Kit


title: JEKO1

description: Library name: JPWCM01_01

value: non-expressor


title: Liver - Pesticides_TBT - Rep4

value: male


title: 227352_R_B18_cdr3_agca

description: Library name: 227352_R_B18_cdr3_agca


title: Liver - Control - Rep2

value: Control


title: DNFB, replicate 1, scRNA-Seq

description: GEXSCOPE® Single Cell RNA Library Kits

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: mm10
Supplementary files format and content: matrix files

extract_protocol:
Fresh mouse cervical spinal cord tissues were stored in Tissue Preservation Solution (Singleron Biotechnologies, Nanjing, China) and placed on ice. After samples were washed 3 times with HBSS, GEXSCOPE™ Tissue Dissociation Solution (Singleton Biotechnologies)Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS. was added to each sample. Subsequently, the tissue was finely cut into small pieces with scissors and then digested at 37°C for 8 min to dissociate the tissue into single cells.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Novaseq6000 platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

value: wild type

value: 9-10 weeks old

value: DNFB model treated with i.t. vehicle during days 5-11 (drug injections were performed once every day)


title: Liver - Pesticides - Rep2

value: Pesticides


title: primary MCL cells (Pt#6)

description: Library name: 25021R-01-06

value: B lymphocytes

value: primary MCL

value: no treatment


title: 227351_R_B18_cdr3_agca

description: Library name: 227351_R_B18_cdr3_agca


title: Naïve, replicate 1, scRNA-Seq

description: GEXSCOPE® Single Cell RNA Library Kits

value: Spinal dorsal horn

value: naive


title: 227342_R_B18_cdr3_agca

description: Library name: 227342_R_B18_cdr3_agca


title: Liver - Pesticides - Rep5


title: bCatKras_NASH2

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

institute: VIB-KU Leuven

description: The liver nuclei were isolated following the protocol described by Slyper et al. (2020) with NST buffer. A piece of 150 mg flash frozen liver big lobe was sectioned on dry ice and transferred to a Dounce homogenizer containing 1 mL of ice-cold NST buffer (146mM NaCl, 1mM CaCl2, 21mM MgCl2, 10mM Tris-HCl (pH 7.5), 0.01% BSA, 0.2% Nonidet P40 and 5μl RNasin Plus RNase Inhibitor (Promega) and incubated for 5 minutes. The tissue was then homogenized with 5 strokes of pestle A and 10 strokes of pestle B until a homogeneous nuclei suspension was achieved and incubated for 5 minutes on ice. The resulting homogenate was filtered through a 70-μm cell strainer (Corning) while keeping on ice. The strainer was washed with 1mL of NST  buffer and then with 3 mL of ST buffer (146mM NaCl, 1mM CaCl2, 21mM MgCl2, 10mM Tris-HCl (pH 7.5)). Next, the sample was transferred to a 15mL Falcon tube and centrifuged at 500g for 5 minutes at 4°C. After gently removing the supernatant, the pellet was resuspended in 1.5mL ST buffer, transferred to 2 mL Eppendorf tube and incubated on ice for 5 minutes. Nuclei were then washed twice in Resuspension Buffer (1x PBS, 1% BSA and 7.5μl RNasin Plus RNase Inhibitor (Promega)) and finally resuspended in 500 μL Resuspension Buffer. Prior to FACS, nuclei were filtered through a 40 μm cell strainer on ice and sorted GFP+ nuclei were collected in Resuspension Buffer.

data_processing:
The fastq files were processed with cellranger (v 7.1.0) count function. Reads were aligned to a pre-mRNA Mus musculus GRCm39 reference genome including introns.
Assembly: GRCm39
Supplementary files format and content: Compressed folder of the filtered feature bs matrix CellRanger output with barcodes.tsv, features.tsv and matrix.mtx files.

extract_protocol: Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and Chromium Single Cell 3’ Reagent v3 Kits (10x Genomics) according to the manufacturer’s protocol.

value: Liver

value: Tumor cell

tag: diet

value: NASH-inducing diet

tag: time on_nash_diet

value: 6 weeks


title: primary MCL cells (Pt#5)

description: Library name: 25021R-01-05

value: mantle cell lymphoma


title: 242029_R_B18_cdr3_agca

description: Library name: 242029_R_B18_cdr3_agca

value: Ramos

value: Burkitt's Lymphoma


title: primary MCL cells (Pt#4)

description: Library name: 25021R-01-04


title: 227341_R_B18_cdr3_agca

description: Library name: 227341_R_B18_cdr3_agca


title: 242056_R_B18_cdr3_aact

description: Library name: 242056_R_B18_cdr3_aact


title: Jurkat cell Neg CRISPRa-seq replicate 2

city: Guangzhou

first: Mulin Jun

last: Li

state: Guangdong

address: No. 9 Jinsui Road, Guangzhou

institute: Guangzhou Women and Children's Medical Center

data_processing:
Two replicates of both the sorted group (the top 10% of Jurkat cells expressing CD28) and the unsorted group were sequenced and underwent quality control using MAGeCK-VISPR.
We extracted the sgRNA sequences from the original 150-bp reads, and the abundance of guides was determined using the MAGeCK “count” module based on the extracted sgRNAs.
We utilized the non-targeting control guides to estimate the size factor for normalization and assessed significant enrichment at the enhancer level according to the MAGeCK-test algorithm.
Finally, significant hits were identified with a false discovery rate (FDR) of less than 0.05.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-separated values files
Library strategy: CRISPRa screening

source_name: Jurkat cell

growth_protocol: Jurkat (Clone E6-1) cell line (ATCC, CRL-9855) was cultured in Iscove’s Modified Eagle’s Medium (IMDM; Thermo Fisher Scientific, 31980030) containing 10% FBS and Penicillin and Streptomycin. All cell lines were authenticated by Short Tandem Repeat (STR) and tested no mycoplasma contamination utilizing the Quantiative PCR mycoplasma detection kit (Sigma-Aldrich, MP0040A).

extract_protocol:
We generated the Jurkat-dCas9-VP64 cell line that stably expressing the Lenti-dCas9-VP64-blast (Addgene, 61425) transgene, as described below. The lentiviral library was titered using the Lenti-PacTM HIV qRT-PCR Titration Kit (GeneCopoeia, LT005). Jurkat-dCas9-VP64 cells were infected with lentiviral gRNA library by resuspending the cells at a concentration of 2 × 10^6 cells per ml in fresh media containing the titered lentivirus and 2 µg/ml polybrene (Millipore, TR-1003). The cells were spin-infected for 1.5 hours at 1,200 × g and 4°C, followed by resuspension in fresh media at a concentration of 0.5 × 10^6 cells per ml. To limit the number of cells expressing multiple gRNAs, a low multiplicity of infection (MOI) of 0.25 was employed to ensure that only 10−20% of the cells were infected. After 24 hours, 1 µg/ml puromycin (ApeXbio, B7587) was added to select for effectively infected Jurkat-VP64 cells and to eliminate uninfected cells. The number of initially infected cells was at least 200 times the number of gRNAs in the library, and this ratio was maintained throughout the experiment. Seven days post-infection, cells were sorted based on CD28 expression. Briefly, the cells were resuspended in sterile sort buffer (PBS + 2% FBS) containing FITC anti-human CD28 antibody (Biolegend, 302906) at a 1:25 dilution. The cells were stained for 30 minutes on ice, washed twice with sort buffer, and passed through a 70-µm mesh (BD, 352350). The top 10% of Jurkat cells expressing CD28 were sorted according to their CD28 expression levels according to the previous study15. The total number of cells collected was at least 200 times the number of gRNAs in the library. Additionally, unsorted cells, also at least 200 times the number of gRNAs in the library, were collected at this time. Duplicate infections and sorts were performed for each library. The collected cells were centrifuged at 1,500 × g for 5 minutes, and the cell pellets were stored at -80°C until genomic DNA was extracted. Genomic DNA samples were extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102) for PCR amplification (Vazyme, N616).
The amplified products were subjected to library construction using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions, followed by next-generation sequencing on a HiSeq X Ten platform.

treatment_protocol: Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

value: Jurkat cell

value: Cells derived from human T cells

value: resting


title: bCatKras_ND

value: normal diet

value: 0 weeks


title: bCatKras_NASH


title: primary MCL cells (Pt#1)

description: Library name: 25021R-01-01

value: B lymphocytes


title: DNFB-AM1241, replicate 1, scRNA-Seq

description: GEXSCOPE® Single Cell RNA Library Kits

value: wild type

tag: Sex

value: male

value: 9-10 weeks old

value: DNFB model treated with i.t. 10 ug AM1241 during days 5-11 (drug injections were performed once every day)


title: Liver - Control - Rep4

value: Control


title: 242055_R_B18_cdr3_aact

description: Library name: 242055_R_B18_cdr3_aact


title: primary MCL cells (Pt#2)

description: Library name: 25021R-01-02

value: primary MCL

value: no treatment


title: NASH_w6_3

description: Mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50mg/kg). Livers were perfused for 5min with 40ml of perfusion medium SC-1 to remove the blood and for rapid destruction of intercellular junctions, followed by perfusion with 40ml of SC-2 medium containing 10mg collagenase for 5min to break up the supporting extracellular matrix. Each lobe was dissected off, and the tissue was disrupted inside of a beaker containing 50ml of SC-2 with 20mg collagenase (Roche) and 1ml DNase I (Sigma) followed by rotating incubation for 20min at 37°C. Cells were then filtered through a 100μm strainer and centrifuged at 50g for 2min at room temperature. Hepatocytes were washed once with 1X PBS and centrifuged again at 50g for 2min. Pellet was resuspend with 2ml of 1X PBS containing 0.04% BSA, filtered through a 70µm strainer and FACS sorted. 500,000 sorted cells were collected and lysed for RNA extraction.

data_processing:
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt with parameters -q 20,20 --minmum-length 40, -a AGATCGGAAGAG, -a "A{100}".
Trimmed sequence reads were mapped to the mouse genome GRCm39 using STAR v2.7.1a (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted immediately using the RNAeasy mini spin kit (Qiagen) and stored at -80°C.
Library preparation was performed according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen).

value: Liver

value: Hepatocyte

value: NASH-inducing diet

value: 6 weeks


title: 242026_R_B18_cdr3_aact

description: Library name: 242026_R_B18_cdr3_aact

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Assembly: Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Supplementary files format and content: NCBI hg38
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

value: Ramos

value: Burkitt's Lymphoma


title: UPN1-FOXO1-degron cells, dTAG47 treated

description: Library name: UPN_deg_dTAG

value: mantle cell lymphoma

value: dTAG47 treated


title: 242025_R_B18_cdr3_aact

description: Library name: 242025_R_B18_cdr3_aact


title: NASH_w6_1


title: Liver - Control - Rep1


title: UPN1-FOXO1-degron cells, no treatment

description: Library name: UPN_deg


title: Jurkat cell CD28 CRISPRa-seq replicate 1

value: Jurkat cell

value: Cells derived from human T cells

value: resting


title: 227348_R_B18_cdr3_aact

description: Library name: 227348_R_B18_cdr3_aact


title: Liver - Pesticides - Rep4

value: Pesticides

value: male


title: primary MCL cells (Pt#3)

description: Library name: 25021R-01-03

value: B lymphocytes


title: Jurkat cell stimulated ChIP-seq CTCF rep1

data_processing:
For data analysis, sequences with adaptors and low quality were trimmed for all 150-bp paired-end reads.
The clean reads were mapped against the human reference genome (GRCh37/hg19) using BWA (v0.7.17).
All samples were processed separately, and unique mapped reads were retained.
Peaks were called using MACS2 (v2.1.1) with IgG as the control.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig

extract_protocol:
1 × 10^7 Jurkat cells were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) in 10% FBS/phosphate-buffered saline (PBS) for 9 minutes at room temperature and subsequently quenched with 0.125 M glycine (Sigma-Aldrich, 50046). The cells were then collected and lysed twice using ice-cold lysis buffer, which consisted of 20 mM Tris-HCl (pH 7.5) (Thermo Fisher Scientific, 15567027), 2 mM EDTA (Thermo Fisher Scientific, 15575020), 1% Triton X-100 (Sigma-Aldrich, T8787), 0.1% SDS (Thermo Fisher Scientific, 15525017), 0.1% sodium deoxycholate (Sigma-Aldrich, D6750), and 1× protease inhibitors (Thermo Fisher Scientific, 78425) for 15 minutes with slow rotation at 4°C. The nuclear lysates were sonicated to obtain DNA fragments ranging from 200 to 500 bp using a Biorupter system (Diagenode, B01060001) at high energy, with a working time of 30 seconds and a resting time of 30 seconds, for a total of 30 cycles, until the solutions became clear. After removing insoluble debris, the lysates were incubated separately with specific antibodies against Rabbit IgG (1:100, Cell Signaling Technology, 7074), CTCF (1:100, Abcam, ab128873), ZNF384 (1:100, Novus Biologicals, NBP3-30592), H3K27me3 (1:100, Cell Signaling Technology, 9733), Rpb1 NTD (1:100, Cell Signaling Technology, 14958), H3K4me1 (1:100, Cell Signaling Technology, 5326), H3K4me3 (1:100, Cell Signaling Technology, 9751), or H3K27ac (1:100, Abcam, ab4729), and then purified using protein A-agarose beads (Millipore, 16-157). The beads were washed four times with TE buffer (10 mM Tris-HCl pH 8.0 [Thermo Fisher Scientific, 15568025] and 1 mM EDTA), TSE I buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), TSE II buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), and Buffer III (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.25 M LiCl [Sigma-Aldrich, L4408], and 1% sodium deoxycholate) before elution (20 mM Tris-HCl pH 7.5, 5 mM EDTA, 50 mM NaCl, and 1% SDS), reverse cross-linking, and subsequent DNA extraction.
ChIP-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions and were sequenced on a HiSeq X Ten platform (Illumina).

tag: chip antibody

value: CTCF antibody (Abcam, #ab128873)

value: anti-CD3/CD28 stimulated


title: NASH_w5_3

tag: strain

value: 5 weeks


title: Liver - Pesticides - Rep1


title: Jurkat cell stimulated ChIP-seq RNA PoII rep1

value: Rpb1 NTD antibody (CST, #14958)


title: NASH_w5_2

value: Liver

value: Hepatocyte


title: CCMCL1-FOXO1-degron cells, FHD-286 treated

description: Library name: CM_deg_FHD

value: FHD-286 for 24 h


title: CCMCL1-FOXO1-degron cells, dTAG47 treated

description: Library name: CM_deg_dTAG


title: Jurkat cell stimulated ChIP-seq H3K27me3 rep1

value: H3K27me3 antibody (CST, #9733)


title: NASH_w5_1

value: NASH-inducing diet


title: 227338_R_B18_cdr3_aact

description: Library name: 227338_R_B18_cdr3_aact

value: Ramos

value: Burkitt's Lymphoma


title: Jurkat cell stimulated ChIP-seq H3K4me3 rep1

value: Jurkat cell

value: H3K4me3 antibody (CST, #9751)


title: 227337_R_B18_cdr3_aact

description: Library name: 227337_R_B18_cdr3_aact


title: CCMCL1-FOXO1-degron cells, no treatment

description: Library name: CM_deg

value: mantle cell lymphoma

value: no treatment


title: Jurkat cell CD28 CRISPRa-seq replicate 2

value: Cells derived from human T cells

value: resting


title: NASH_w4_3

value: 4 weeks


title: MINO parent cells treated with FHD-286

description: Library name: MINO

value: B lymphocytes

value: MINO


title: NASH_w6_2

value: 6 weeks


title: Jurkat cell stimulated ChIP-seq H3K4me1 rep1

value: H3K4me1 antibody (CST, #5236)

value: anti-CD3/CD28 stimulated


title: MINO expressing wild type BRG1

description: Library name: MINO_FHD

value: BRG1 wild type


title: NASH_w4_2

value: Liver

value: Hepatocyte


title: NASH_w4_1

value: NASH-inducing diet


title: 279871_R_B18_all_tgct_T2

description: Library name: 279871_R_B18_all_tgct_T2

value: Ramos

value: Burkitt's Lymphoma


title: Jurkat cell stimulatedChIP-seq H3K27ac rep1

value: Jurkat cell

value: H3K27ac antibody (Abcam, #ab4729)


title: 279872_R_B18_all_tgct_T2

description: Library name: 279872_R_B18_all_tgct_T2


title: Jurkat cell stimulated ChIP-seq Input rep1


title: MINO expressing BRG1-T910M mutant

description: Library name: MINO_BRG_WT

value: mantle cell lymphoma

value: BRG1 T910M

value: expressing T910M BRG1


title: 279870_R_B18_all_tgct_T2

description: Library name: 279870_R_B18_all_tgct_T2


title: NASH_w3_3

value: 3 weeks


title: NASH_w3_4


title: Jurkat cell resting ChIP-seq CTCF rep1

value: Cells derived from human T cells

value: CTCF antibody (Abcam, #ab128873)

value: resting


title: 227347_R_B18_cdr3_aact

description: Library name: 227347_R_B18_cdr3_aact


title: MINO parent cells

description: Library name: MINO_BRG_T910M

value: B lymphocytes

value: MINO

value: wild type

value: expressing wildtype BRG1


title: Jurkat cell resting ChIP-seq RNA PoII rep1

value: Rpb1 NTD antibody (CST, #14958)


title: 279855_R_B18_all_tgct_T2

description: Library name: 279855_R_B18_all_tgct_T2


title: NASH_w3_2

value: Liver

value: Hepatocyte

value: NASH-inducing diet


title: 279854_R_B18_all_tgct_T2

description: Library name: 279854_R_B18_all_tgct_T2

value: Ramos

value: Burkitt's Lymphoma


title: NASH_w3_1