title: HT1080−HA−SREBF2, HA, ChIP, rep 1

value: Cell line

value: Human Fibrosarcoma

value: Dox 1 ug/ml for 72 h


title: TCZ_SRBC7d_M25

status: Public on Apr 02 2025

type: SRA

city: Nijmegen

first: Franka

last: Buytenhuijs

state: Please select your county

address: Toernooiveld 200

country: Netherlands

institute: Radboud University

description: Library name: TCZ_SRBC7d_M25_v5364

library_source: transcriptomic

data_processing:
CDR3β identification, clonotype clustering and correction of sequencing errors were performed using MiTCR software.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Spleen T cell zone

extract_protocol:
Total RNA was extracted as described above and TCRβ-chain transcripts were amplified independently in a two-step reaction according to the manufacturer’s protocol (iRepertoire; patent no. 7,999,092).
The obtained TCRβ libraries were quantified using the PerfeCTa-NGS-Quantification Kit according to manufacturer’s protocol (Quantabio) and sequenced using the Illumina MiSeq Reagent Kit v2 300-cycle (150 paired-end read; Illumina), gaining an average of $\approx$1.8 × 10^6 reads per sample.

tag: tissue

value: Spleen T cell zone

tag: cell type

value: T cell

tag: genotype

value: WT

tag: treatment

value: 7 days after antigen challenge with SRBC


title: H12-Lonza-340-R3_S96

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

country: USA

institute: Texas A&M University

data_processing:
The gene count matrices were generated from single-end reads with 2 lanes per sample with 75 base pairs (bp).
Reads were quality trimmed using fastp (version 0.20.0 or 0.20.1) using the default settings with the exceptions of adapter trimming being excluded and the reads being trimmed to 50 bp (Chen et al., 2018).
The reads from the 2 lanes for each sample were combined to generate a single fastq file.
These files were used as input to the TempO-seq analysis pipeline (House et al., 2017) with the human S1500+ probe manifest file to generate a gene count matrix.
Transcripts with fewer than 25 mean counts across the entire sample space were removed as non-expressed except for the genes listed. For further analyses, a total of 2,582 genes were evaluated. The Bioconductor's DESeq2 package (Love et al., 2014) was utilized to perform differential expression analysis and generate the complete normalized count matrix for all experimental conditions.
Assembly: S1500+ Gene Set
Supplementary files format and content: normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: hash.csv file with meta data of the samples

organism: Homo sapiens

extract_protocol:
Cell lysates were prepared and cells were incubated for 10 minutes at room temperature after which the lysates were collected from each well. All lysates were stored at −80 °C until further processing. The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022)
TempO-seq libraries were prepared using the S1500+ targeted transcriptome panel (Mav et al., 2018) consisting of 2,982 transcripts according to the manufacturer’s instructions.

tag: cell line

value: vehicle


title: GV oocyte from day 8 fresh follicle, biol rep 2

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

description: Library name: F82

data_processing:
Galaxy version 24.2.rc1
RNA-seq reads were aligned to the whole mouse genome assembly-mm10 by HISAT2, quantified by featureCounts in Galaxy
Assembly: mm10
Supplementary files format and content: csv files includes raw counts for each sample

source_name: germ cell

extract_protocol:
RNA extraction and library preparation was done using SMART-Seq2 v4 Ultra Low Input RNA kit according to manufacture's instruction
RNA extraction and library preparation was done using SMART-Seq2 v4 Ultra Low Input RNA kit according to manufacture's instruction

value: germ cell

value: GV oocyte

value: Fresh


title: GC_SRBC4d_M24

description: Library name: GC_SRBC4d_M24_v5346

source_name: Spleen Germinal Center

value: Spleen Germinal Center

value: 4 days after antigen challenge with SRBC


title: SMAD2+/R114C*(RF10)_R2, ATACseq

city: Boston

first: Jon

last: Seidman

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: genomic

data_processing:
Libraries were sequenced (Illumina HiSeq 2000 or Illumina HiSeq 2500, paired end)  to a depth of 100 million reads per sample
All data was combined into a single fastq file
Reads were aligned to the hg38 reference genome using BWA-MEM.
Mitochondrial and duplicate reads were discarded using Samtools and Picard’s MarkDuplicates, respectively
Tagdirectories were created and combined for each genotype, and peaks were called using HOMER (v4.11), Heinz et al. 2008
Assembly: hg38
Supplementary files format and content: ATACseq combined peaks for each genotype

molecule: genomic DNA

growth_protocol: Induced pluripotent stem cells (iPSCs) were routinely generated by re-plating 6 non-adherent cell line cultures (typically 5 x 106 cells) on a matrigel coated plate in MTESR medium (Stemcell Technologies)

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2015; Corces et al., 2017).
ATACseq libraries were prepared for sequencing using standard Illumina protocols

value: Induced pluripotent stem cells

value: missense

value: untreated


title: SMAD2+/R114C*(RF10)_R1, ATACseq


title: GV oocyte from day 8 fresh follicle, biol rep 1

description: Library name: F81


title: BCZ_SRBC4d_M24

description: Library name: BCZ_SRBC4d_M24_v5346

source_name: Spleen B cell zone

value: Spleen B cell zone


title: H11-OAT-ciPTEC-R3_S89


title: CFA TMJ, scRNAseq

city: Los Angeles

first: Ziying

last: Lin

state: CA

address: 2250 Alcazar St. CSA Clinical Sciences Annex

institute: University of Southern California

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: TMJ

extract_protocol:
Freshly collected TMJ were dissected on ice-cold HBSS. Next, The TMJs were incubated in digestion buffer (α-MEM with 3 mg/ml collagenase type I and 4 mg/ml Dispase II) at 37 ℃ for 30 min. Single cell suspension was filtered through 70um filter.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: TMJ

tag: strain

tag: age

value: 8-10 weeks old

value: CFA


title: G9-OAT-Tert-R2_S71


title: SMAD2+/W274C*(RB1)_R2, ATACseq


title: SMAD2+/W274C*(RB1)_R1, ATACseq


title: GC_SRBC4d_M23

description: Library name: GC_SRBC4d_M23_v5348


title: PBS TMJ, scRNAseq

description: 10x Genomics

value: PBS


title: H10-OAT-HEK-R3_S80


title: G12-Lonza-340-R2_S95


title: TCZ_SRBC4d_M24

description: Library name: TCZ_SRBC4d_M24_v5346

value: Spleen T cell zone

value: T cell


title: BCZ_SRBC4d_M23

description: Library name: BCZ_SRBC4d_M23_v5348

value: WT


title: ChronicMEKi, Rep2

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

description: Library name: Sample_ChronicMEKi_2

library_source: other

data_processing:
FASTQ files were quality-checked using FastQC v0.12.0 and trimmed with Trim Galore v0.6.10 to remove adapter sequences and read ends with Phred scores below 15. STAR v2.7.0a was used to align the FASTQ files to the mm10 reference genome. The resulting SAM files were sorted using the sort function from Samtools v1.19.2 and indexed using the index function to generate BAM index files. Stranded bigWig files were generated using the bamCoverage function from deepTools v0.1.9. The BRGenomics package v1.6.0 was then used in R v4.1.2 to construct gene body and pause region count matrices, which were subsequently used to create pausing index tables with tidyverse v2.0.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text-file includes gene body read counts for each sample: GB_counts_table.txt
Supplementary files format and content: tab-delimited text-file includes raw isoform counts for each sample: PR_counts_table.txt

molecule: other

source_name: CD8 T-Cell

extract_protocol:
Nascent RNA was labeled in live cells and isolated using the Click-iT™ Nascent RNA Capture Kit (Thermo Fisher, Cat. No. C10365) following the manufacturer’s protocol. Briefly, 1 × 10⁶ Tcells were seeded in 500 µL of T-cell media per well in a 12-well plate. Actinomycin D (100 pM) was added to the negative control wells for 12 hours prior to labeling. Cells were then incubated with 0.2 mM 5-ethynyl uridine (5-EU) (Lumiprobe, #2439) at 37°C for 30 minutes to label newly synthesized RNA. After harvesting, cells were centrifuged at 250g for 5 minutes, and total RNA was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research, #R2050). For sequencing nascent RNA, the 5-EU-labeled nascent RNA was biotinylated through a click reaction with biotin-azide for 1 hour at room temperature, bound to Dynabeads MyOne Streptavidin T1 magnetic beads, and isolated for cDNA synthesis. Reverse transcription was performed using the SuperScript VILO kit (Thermo Fisher, Cat. No. 11754050). The resulting cDNA was purified and sequenced. For quantification in a limited number of cells, 5-EU-labeled nascent RNA was clicked to Alexa 488-azide and measured by flow cytometry.
RNA was isolated from T cells using the Direct-zol RNA Miniprep Kit (Zymo Research, #R2050) following the manufacturer’s instructions. RNA quantity and integrity were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer, respectively, before sequencing.  Core Nascent RNA-seq samples were sequenced using the Illumina NextSeq 500 platform, generating 100-base pair paired-end reads.  Library preparation and sequencing were performed by the MSK Integrated Genomics Operation.

value: CD8 T-Cell


title: ChronicMEKi, Rep3

description: Library name: Sample_ChronicMEKi_3


title: SMAD2+/W274C*(RG12)_R1, ATACseq


title: SMAD2+/R114C*(RA10)_R2, ATACseq


title: SMAD2+/W274C*(RG12)_R2, ATACseq


title: TCZ_SRBC4d_M23

description: Library name: TCZ_SRBC4d_M23_v5348


title: SMAD2+/P135*(RB9)_R2, ATACseq

value: heterozygous


title: G11-OAT-ciPTEC-R2_S87

value: vehicle


title: G10-OAT-HEK-R2_S79


title: Chronic, Rep3

description: Library name: Sample_Chronic_3


title: ChronicMEKi, Rep1

description: Library name: Sample_ChronicMEKi_1


title: SMAD2+/P135*(RB9)_R1, ATACseq


title: F9-OAT-Tert-R1_S70


title: GC_SRBC4d_M22

description: Library name: GC_SRBC4d_M22_v5344


title: BCZ_SRBC4d_M22

description: Library name: BCZ_SRBC4d_M22_v5344


title: Chronic, Rep2

description: Library name: Sample_Chronic_2


title: F12-Lonza-340-R1_S94


title: TCZ_SRBC4d_M22

description: Library name: TCZ_SRBC4d_M22_v5344


title: SMAD2+/P135*(RD11)_R2, ATACseq


title: F11-OAT-ciPTEC-R1_S86


title: GC_SRBC4d_M21

description: Library name: GC_SRBC4d_M21_v5354


title: SMAD2+/P135*(RD11)_R1, ATACseq


title: BCZ_SRBC4d_M21

description: Library name: BCZ_SRBC4d_M21_v5354


title: F10-OAT-HEK-R1_S78


title: Acute, Rep2

description: Library name: Sample_Acute_2


title: Wildtype_R2, ATACseq

value: Wildtype


title: Acute, Rep1

description: Library name: Sample_Acute_1


title: E9-Par-TERT-R3_S69

source_name: TERT

value: TERT


title: TCZ_SRBC4d_M21

description: Library name: TCZ_SRBC4d_M21_v5354

value: 4 days after antigen challenge with SRBC


title: E11-Par-ciPTEC-R3_S85

source_name: ciPTEC

value: ciPTEC


title: Wildtype_R1, ATACseq

value: Induced pluripotent stem cells


title: TSA-seq v1 LaminB in K562, 10 min reaction - condition 2 - no primary control, Bio rep 2, Tech rep 1

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description: re-analysis of GSM3111188

data_processing:
TSA_Seq_v1_protocol: Chen et al. 2018 (doi:10.1083/jcb.201807108), TSA Seq v2 and modifications related to application of TSA-Seq to adherent cells, see Zhang et al. 2019 (doi: https://doi.org/10.1101/824433)
Assembly: GRCh38
Supplementary files format and content: File type: normalized counts (bw). Description: Bigwig file format
Library strategy: TSA-seq

source_name: blood cell

growth_protocol: H1-ESC (WA01), HFF-hTert-Clone 6 cells and HCT116 were obtained thorough the 4D Nucleome Consortium and were cultured according to the 4DN SOPs (https://www.4dnucleome.org/cell-lines.html). K562 cells were obtained from the ATCC and were cultured according to the ENCODE Consortium protocol (http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf).

extract_protocol:
Nucleolar and PCH TSA-Seq was performed using either Condition C (labeling with 1:3000 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) or Condition E (labeling with 1:300 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) with the following minor modification: 150ul of Dynabeads M-270 streptavidin (Invitrogen, catalog no. 65306) was used to purify the biotinylated DNA. LMNB1 TSA-seq was performed using Condition AI for HFFc6, H1, and K562 and Condition A for HCT116 cells.
POL1RE and MKI67IP TSA-Seq, raw sequencing reads were mapped to the Telomere-to-Telomere (version 1.1).

treatment_protocol: No Primary Control for Lamin B TSA-seq version 1 Reaction Condition 2 (PBS 50% sucrose) 10 minute Reaction on K562 cells replicate 2

value: blood cell

value: immortalized cell line

tag: biosample quantity

tag: donor sex

value: female

tag: donor lifestage

value: adult

tag: donor health_status

value: chronic myelogenous leukemia

tag: experiment url

tag: experiment replicate_info

value: Bio rep 2, Tech rep 1

tag: biosample url


title: E12-Lonza-405-R3_S93


title: GC_SRBC4d_M20

description: Library name: GC_SRBC4d_M20_v5356

value: Spleen Germinal Center


title: BCZ_SRBC4d_M20

description: Library name: BCZ_SRBC4d_M20_v5356

value: Spleen B cell zone

value: T cell


title: mouse_cortex_HyDrop_v2_C_beads_6

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
Library name: HYA__00c24b__20240117_Mouse_Cortex-c-ATAC
re-sequenced on Illumina NovaSeqX

library_source: genomic single cell

data_processing:
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed using trimgalore, corrected to a whitelist allowing 1 mismatch (in PUMATAC pipeline, nextflow version: nextflow-21.04.3), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
For all samples (mouse (in house generated and commercial), fly and barnyard cell lines): Reads were mapped to reference genomes using bwa-mem2 and fragemnet files were created with create_fragments_file by the (in PUMATAC pipeline, nextflow version: nextflow-21.04.3)
For mouse samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing the Otsu threshold in PUMATAC (nextflow version: nextflow-21.04.3) were included.
For Drosophila samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing  the trhshold of TSS_enrichment >2 and number of unique fragments > 800 in PUMATAC (nextflow version: nextflow-21.04.3) were included.
Assembly: For mouse samples: mm10, for hybrid samples in the barnyard: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary files format and content: For mouse and Drosophila samples: standard tab-separated fragments files, count matrix and metadata inforamtion for cell data (barcode) and region data in tsv format
Supplementary files format and content: For barnyard: standard tab separated fragment file

source_name: brain cortex

growth_protocol:
Barnyard cell culture: cultured in RPMI1640 (ThermoFisher 11875093) medium supplemented with 10% FBS (ThermoFisher 10270–106), 1% penicillin/streptomycin (Life Technologies 15140122), and 10 ug/mL insulin (Sigma Aldrich I9278) and passaged twice per week. Melanoma cell lines were derived by physical resection of primary cutaneous lesions. Mouse melanoma cells were cultured in DMEM (ThermoFisher 13345364) supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. All cell lines tested negative for mycoplasma prior to use.
Mouse: The mice were housed under standard housing conditions in a pathogen-free facility with a 14 hr light, 10 hr dark light cycle from 7 to 21 hr. Mice used in the study were 60 days old.
Drosophila: All flies were raised on a yeast-based medium and kept at 25 °C on a 12h/12h day/night light cycle. For embryo collection, flies were transferred to cages fixed to a plate with a normal yeast-based medium 24 hours before embryo collection. On the day of embryo collection, the plate was exchanged for a juice plate. The juice was prepped by adding 20 g agar and 22 g sucrose to 300 ml distilled water, boiling, and then mixing in 100 ml apple juice, 10 ml 95% ethanol, and 5 ml 100% glacial acetic acid. The flies laid eggs for four hours. Sixteen hours later, the embryos aged between 16 to 20 hours were collected from the juice plate with a small brush and transferred to a 70 µm nylon mesh filter.

extract_protocol:
Mouse: The nuclei were extracted from mouse cortex samples that were snap-frozen in liquid nitrogen and stored at -80 °C. We transferred ~1 cm3 of frozen mouse cortex to 500 μL of ice-cold homogenization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 0.1% IGEPAL CA-630, 1× complete protease inhibitor, and 1 mM DTT) in a Dounce Homogenizer. The tissue was left to thaw for 2 min before the tissue was homogenized with 10 strokes of the loose pestle and 5 strokes of the tight pestle. Before the end of a 5-minute incubation, the homogenate was filtered through a 70 μm cell strainer (Corning), and the homogenizer and strainer were washed with homogenization buffer to obtain a final volume of 1 mL. The filtrate was transferred to a 1.5 mL DNA LoBind tube (Eppendorf) and centrifuged at 500 xg for 5 minutes. The supernatant was discarded, and the pellet was topped up to 520 μL with wash buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 1× complete protease inhibitor, and 1 mM DTT) and resuspended. Next, we added 520 μL gradient medium (50% Optiprep, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 5 mM MgCl2, 75 mM sucrose, 1× complete protease inhibitor, and 1 mM DTT) and mixed the entire volume by gentle pipetting. In a 2 mL DNA LoBind tube we layered 790 μL Optiprep cushion (29% Optiprep, 31 mM Tris-HCl pH 8, 77.5 mM KCl, 15.5 mM MgCl2, 129.2 mM sucrose) at the bottom and 1040 μL of the sample on top, gently without disrupting the cushion. The tube was then centrifuged at 9000 xg for 20 minutes at 4 °C. After the centrifugation the debris on top was carefully removed with a 1 mL tip and the rest of the supernatant was also carefully removed until 50 μL was left in the tube. The pellet was gently resuspended before we mixed it with 50 μL 0.2× permeabilization buffer (20 mM Tris-HCl pH 7.5, 20 mM NaCl, 6 mM MgCl2, 0.2% Tween-20, 0.02% IGEPAL CA-630, 0.02% Digitonin, 2% BSA, and 2 mM DTT) and left the nuclei suspension for 2 minutes on ice before we stopped the permeabilization by mixing it with 1 mL of wash buffer 2 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA). The nuclei were pelleted by centrifugation at 500 xg for 5 minutes at 4 °C. The nuclei were resuspended in PBS with 0.04% BSA. For Drosophila, the nuclei were isolated by using an adapted protocol based on the nuclei isolation protocol for single-cell ATAC sequencing (10x Chromium CG000169-RevE).  Similar to mouse, for the barnyard, the cell lines were mixed to equal parts and a pellet of one million dissociated cells or fewer was incubated on ice in 200 μL of ATAC lysis buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 μM Pitstop in DMSO, 0.01% digitonin) for 5 minutes. 1 mL of ATAC nuclei wash buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm strainer (Flowmi).
Nuclei, resuspended in PBS (supplemented with 0.04% BSA), were tagmented for one hour at 37 °C in 15 μL ATAC reaction mix (10% DMF, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/µL Tn5, 70 µM Pitstop in DMSO, 0.1% Tween-20, 0,01% Digitonin). Tagmented nuclei were placed on ice and 95 µL of PCR mix (1.25× Phusion HF buffer, 15% Optiprep, 1.25 mM dNTPs, 75 mM DTT, 0.0625 U/µL Phusion HF polymerase, 0.0625 U/μL Deep Vent polymerase, 0.0125 U/μL ET SSB) was added. Next, 110 μL of nuclei mixed in PCR mix was co-encapsulated with 45 μL of HyDrop-ATACv2 beads in HFE-7500 Novac oil with EA-008 surfactant (RAN Biotech) using the Onyx microfluidics platform (Droplet Genomics). The resulting emulsion was split over two PCR tubes and was placed in a thermocycler with the following program: 72 °C – 15 mins, 98 °C – 3 mins, 12 cycles of 98 °C – 10 s; 55 °C – 30 s; 72 °C – 1 min; 72 °C – 5 mins, and finally the amplification products were cooled to 4 °C. To break the emulsion and remove excess oil, 125 μL of recovery agent (20% PFO in HFE) was added and the PCR tubes were inverted 10 times to mix before the oily phase was removed. Next, we added 180 μL GITC mix (5M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4), 10 μL Dynabeads, and 10 μL 2.4 M DTT to each of the aliquots, and mixed everything by pipetting up and down 10 times and incubating for 10 minutes. Dynabeads were pelleted on a magnet and washed twice with 80% ethanol. Elution was done in 50 μL of EB-DTT-Tween (24 mM DTT, 0.1% Tween-20 in EB (10 mM Tris-HCl pH 8.5)). Next, a 1.2× Ampure bead purification was performed according to manufacturer’s recommendations. Elution was done with 40 μL of EB-DTT (10 mM DTT in EB). The library was completed by amplifying the eluate in a total volume of 100 μL PCR mix (1× KAPA HiFi, 1 μM index i7 primer, 1 μM Universal P5 primer) with the following program: 95 °C – 3 mins, 12 cycles of 98 °C – 10 s; 63°C – 30 s; 72 °C – 1 min; 72 °C – 1 min, and finally a hold stage at 4 °C. The final libraries were subjected to 0.4×–1.2× doublesided Ampure purification and eluted in 20 μL elution buffer.

value: brain cortex

value: divers cells of brain cortex

value: C57B/6J background

tag: Sex

value: 60 days

tag: batch


title: RKO H3K4me3_2

city: Calgary

first: Ravinder

last: Bahia

state: Alberta

address: 3330 Hospital drive NW

department: Cell Biology and Anatomy

country: Canada

institute: University of Calgary

description: Library name: Sample19

data_processing:
The Partek Flow pipeline included the following steps: 1) convert alignments to unaligned reads
2) Filter out contaminants (rDNA, mtrDNA)
3) pre-alignment QA/QC
4) Aligned reads to human assembly GRCh38/hg38 using Bowtie 2
5) peak calling using MACS3 (default or broad setting), and annotation of peaks using Ensembl Transcripts release 91 (TSS region upstream and downstream limits set to 1000 bp)
Assembly: hg38
Supplementary files format and content: MACS3 (Broad setting) annotation (Hg 38 '-Ensembl transcripts release 91; TSS 1000 TTS 1000)
Supplementary files format and content: MACS3 (default setting) annotation (Hg 38 '-Ensembl transcripts release 91; TSS 1000 TTS  1000)

source_name: RKO

growth_protocol: The colorectal cancer cells (HCT 116, HT-29, RKO) were cultured using conditions recommended by ATCC. HCT 116 cells (CCL-247) and HT-29 cells (HTB-38) were cultured in McCoy's 5a medium supplemented with 10% FBS. RKO (CRL-2577) and CCD 841 CoN (CRL-1790) were cultured in Eagle's Minimum Essential Medium supplemented with 10% FBS.

extract_protocol:
The crosslinked chromatin was digested with micrococcal nuclease to the extent that 70% of the chromatin was cleaved to mononucleosomes. Before performing the ChIP assay, the specificity of the anti-H3K4me3 antibody (Millipore Sigma 17-614 Lot# 2871690) was evaluated. ChIP assays with the anti-H3K4me3 antibody and a control rabbit IgG were done to produce input and ChIP fractions from the four cell lines to determine the enrichment of H3K4me3 mononucleosomes associated with the MCL1 exon 1, exon 2, exon 3, and intron 1.
ChIP libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina.
The libraries were sequenced at Genome Quebec using the Illumina HiSeq 4000 PE100 System at 25 million reads.

treatment_protocol: For H3K4me3 ChIP-seq, three colorectal cancer cell lines and normal colonic epithelial cells were crosslinked with 1% formaldehyde (F). The crosslinked chromatin was digested with micrococcal nuclease to the extent that 70% of the chromatin was cleaved to mononucleosomes.

value: RKO

value: Colon cancer cells

tag: chip antibodies


title: mouse_cortex_HyDrop_v2_C_beads_7

description:
Library name: HYA__177788__20240117_Mouse_Cortex-d-ATAC
re-sequenced on Illumina NovaSeqX

tag: tissue


title: TCZ_SRBC4d_M20

description: Library name: TCZ_SRBC4d_M20_v5356

value: Spleen T cell zone

tag: cell type

value: WT

value: 4 days after antigen challenge with SRBC


title: mouse_cortex_HyDrop_v2_C_beads_5

description:
Library name: HYA__87f862__20240117_Mouse_Cortex-b-ATAC
re-sequenced on Illumina NovaSeqX


title: TSA-seq v1 LaminB in K562, 10 min reaction - condition 2 - no primary control, Bio rep 1, Tech rep 1

description: re-analysis of GSM3111186

treatment_protocol: No Primary Control for Lamin B TSA-seq version 1 Reaction Condition 2 (PBS 50% sucrose) 10 minute Reaction on K562 cells replicate 1

value: blood cell

value: immortalized cell line

value: Bio rep 1, Tech rep 1


title: D9-Par-TERT-R2_S68

value: TERT

value: vehicle


title: Acute, Rep3

description: Library name: Sample_Acute_3

value: CD8 T-Cell


title: GC_SRBC4d_M19

description: Library name: GC_SRBC4d_M19_v5360

value: Spleen Germinal Center

tag: genotype


title: Chronic, Rep1

description: Library name: Sample_Chronic_1


title: RKO input

description: Library name: Sample15


title: mouse_cortex_HyDrop_v2_C_beads_4

description:
Library name: HYA__b606e2__20240117_Mouse_Cortex-a-ATAC
re-sequenced on Illumina NovaSeqX

value: female


title: BCZ_SRBC4d_M19

description: Library name: BCZ_SRBC4d_M19_v5360

value: Spleen B cell zone

value: T cell

tag: treatment


title: mouse_cortex_HyDrop_v2_E_beads_4

description:
Library name: HYA__67df33__20240105_Mouse_Cortex-d-ATAC
no resequencing

value: brain cortex

value: divers cells of brain cortex

value: C57B/6J background


title: HT29 H3K4me3_2

description: Library name: Sample13

tag: cell line

value: Colon cancer cells

value: anti-H3K4me3 antibody (Millipore Sigma 17-614 Lot# 2871690)


title: C666-1, BAY2

city: Huai'an

first: Xingchen

last: Dong

state: Jiangsu Province

address: No.1 Huanghe West Road

department: Department of Otorhinolaryngology

country: China

institute: Huai'an No.1 People's Hospital

description: Library name: BAY2

data_processing:
Raw data were quality controlled and filtered using fastp (v0.20.0)
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.1.0)
Gene expression levels were quantified using featureCounts (v2.0.0)
Differential expression analysis was performed using DESeq2 (v1.30.0), with genes having |log2FC|> 1.5 and padj<0.05 considered significantly differentially expressed
GO and KEGG enrichment analyses were performed using clusterProfiler (v3.18.0)
Assembly: GRCh38/hg38
Supplementary files format and content: Comma-delimited text files containing raw counts data for each sample

molecule: polyA RNA

source_name: nasopharyngeal carcinoma

growth_protocol: C666-1 cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum and 1% penicillin-streptomycin. All cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent. RNA concentration and purity were determined by spectrophotometry, and RNA integrity was detected using an Agilent 2100 Bioanalyzer, ensuring RIN values >8.0.
The NEBNext Ultra RNA Library Prep Kit for Illumina was used to construct mRNA libraries. Steps included mRNA enrichment, RNA fragmentation, cDNA first and second strand synthesis, end repair, adapter ligation, fragment selection, and PCR amplification.

treatment_protocol: C666-1 cells were treated with 2nM BAY2402234 dissolved in DMSO for 48 hours. The control group received an equal volume of DMSO (final concentration <0.1%).

value: nasopharyngeal carcinoma

value: nasopharyngeal carcinoma cells

value: WT

value: 2nM BAY2402234 dissolved in DMSO


title: D12-Lonza-405-R2_S92


title: TCZ_SRBC4d_M19

description: Library name: TCZ_SRBC4d_M19_v5360

value: Spleen T cell zone

value: 4 days after antigen challenge with SRBC


title: D11-Par-ciPTEC-R2_S84

value: ciPTEC

value: vehicle


title: D10-Par-HEK-R2_S76

source_name: HEK

value: HEK


title: E10-Par-HEK-R3_S77


title: HT29 input

description: Library name: Sample9


title: C12-Lonza-405-R1_S91


title: HT29 H3K4me3_1

description: Library name: Sample11


title: RKO H3K4me3_1

description: Library name: Sample17

value: RKO


title: BCZ_SRBC4d_M18

description: Library name: BCZ_SRBC4d_M18_v5352

value: Spleen B cell zone


title: GC_SRBC4d_M18

description: Library name: GC_SRBC4d_M18_v5352

value: Spleen Germinal Center

value: T cell


title: HCT116 H3K4me3

description: Library name: Sample7


title: HCT116 input

description: Library name: Sample5


title: Elastic, rep 1

first: Song

last: Li

state: California

address: 404 Westwood Plaza, Eng VI

institute: UCLA

description: Library name: Elastic 1

data_processing:
FASTQ files were trimmed with Trimmomatic after quality control checking. Pair-ended reads were then aligned to mouse reference genome (mm10) with Bowtie2. Mitochondrial reads and PCR duplicates were removed using SAMtools and Picard respectively. Peaks were called using MACS3 (q < 0.001), and only peaks outside the ENCODE blacklist regions were kept.
Assembly: mm10
Supplementary files format and content: bigwig file includes peak profiles of each sample

source_name: Ear

growth_protocol: Cells were expanded in mouse embryonic fibroblast (MEF) medium after isolation: DMEM (Gibco) with the addition of 10% fetal bovine serum (FBS, from Gibco) and 1% penicillin/streptomycin (Gibco), and used at passage 2.

extract_protocol:
1,000,000 cells were added to ATAC lysis buffer after thawing and centrifuged at 500 g in a pre-chilled centrifuge for 5 minutes. Supernatant was removed and the nuclei were resuspended in 50 µL of tagmentation reaction mix by pipetting up and down. The reactions were incubated at 37 °C for 30 minutes in a thermomixer with shaking at 1,000 rpm, and then cleaned up using the MiniElute reaction clean up kit (Qiagen).
Tagmented DNA was amplified with barcoded primers. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher), Tapestation High Sensitivity D1000 Assay (Agilent Technologies), and QuantStudio ® 5 System (Applied Biosystems). Equimolar pooling of libraries was performed based on QC values.

treatment_protocol: 1,000,000 fibroblasts seeded on elastic viscoelastic substrates were collected after 48 h and stored at -80 °C prior to sample processing.

value: Ear

value: Fibroblast


title: C11-Par-ciPTEC-R1_S83


title: Elastic, rep 2

description: Library name: Elastic 2


title: CCD H3K4me3

description: Library name: Sample3

source_name: CCD

value: CCD

value: normal colon epithelial cells


title: BCZ_SRBC4d_M17

description: Library name: BCZ_SRBC4d_M17_v5342


title: CCD input

description: Library name: Sample1


title: Niwa OCT-4 stable cell line 3

city: SEOUL

first: EUN JOO

last: LEE

state: MAPOGU

address: SOGANG R 1206

department: LIFE SCIENCE

country: South Korea

institute: SOGANG UNIVERSITY

description: Library name: OCT_4_3

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: stem cell

growth_protocol: EWS-OCT4, OCT4 Niwa stable cell lines and J1ESC cell line were cultured in ESC media with LIF.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: We treated 1ug/ml Doxycycline to down-regulate endogenous OCT-4 respectively in stable cell lines.

value: Niwa oct4


title: C10-Par-HEK-R1_S75


title: GC_SRBC4d_M17

description: Library name: GC_SRBC4d_M17_v5342


title: mouse_cortex_HyDrop_v2_E_beads_3

description:
Library name: HYA__21de27__20240105_Mouse_Cortex-c-ATAC
no resequencing

value: brain cortex

value: divers cells of brain cortex

tag: strain

value: C57B/6J background

value: female

value: 60 days


title: Niwa OCT-4 stable cell line 2

description: Library name: OCT_4_2


title: TSA-seq MKI67IP in H1 cells, condition2 - conditionE - anti-MKI67IP, Bio rep 2, Tech rep 1

treatment_protocol: MKI67IP TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on H1 cells replicate 2

value: stem cell

value: stem cell derived cell line

tag: antibody

value: anti-NIFK

tag: target

value: NIFK protein

value: male

value: embryonic

value: healthy

value: condition2 - conditionE - anti-MKI67IP

value: Bio rep 2, Tech rep 1


title: TSA-seq v2 Lamin B1 in H1, condition2 - conditionAI - anti-Lamin B1, Bio rep 2, Tech rep 1

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on H1 cells replicate 2

value: LMNB1 protein

tag: donor sex


title: Viscoelastic, rep 2

description: Library name: Viscoelastic 2

value: Ear

value: Fibroblast


title: TSA-seq v1 Lamin B1 in HCT116, condition2 - anti-Lamin B1, Bio rep 2, Tech rep 1

source_name: colon

treatment_protocol: Lamin B1 TSA-seq version 1 Reaction Condition 2 (PBS 50% Sucrose) 10 minute Reaction on HCT116 cells replicate 2

value: colon

value: immortalized cell line

tag: biosample quantity

tag: donor lifestage

value: adult

value: colon carcinoma

value: condition2 - anti-Lamin B1


title: Niwa OCT-4 stable cell line 1

description: Library name: OCT_4_1

value: Niwa oct4


title: Viscoelastic, rep 1

description: Library name: Viscoelastic 1


title: TSA-seq v1 Lamin B1 in HCT116, condition2 - anti-Lamin B1, Bio rep 1, Tech rep 1

treatment_protocol: Lamin B1 TSA-seq version 1 Reaction Condition 2 (PBS 50% Sucrose) 10 minute Reaction on HCT116 cells replicate 1

tag: donor health_status

tag: experiment url

value: Bio rep 1, Tech rep 1


title: TCZ_SRBC4d_M18

description: Library name: TCZ_SRBC4d_M18_v5352

source_name: Spleen T cell zone

value: Spleen T cell zone

value: T cell

value: WT

value: 4 days after antigen challenge with SRBC


title: TSA-seq MKI67IP in H1 cells, condition2 - conditionE - anti-MKI67IP, Bio rep 1, Tech rep 1

treatment_protocol: MKI67IP TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on H1 cells replicate 1

value: stem cell

value: stem cell derived cell line

value: anti-NIFK

value: NIFK protein

value: male

value: embryonic

value: healthy

tag: experiment replicate_info

tag: biosample url


title: MOUSE Embryonic stemcell 3

description: Library name: J1_ESC_3


title: TSA-seq v2 Lamin B1 in HFFc6, condition2 - conditionAI - anti-Lamin B1, Bio rep 2, Tech rep 2

source_name: skin fibroblast

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on HFFc6 cells replicate 2 library set2

value: skin fibroblast

value: immortalized cell line

value: LMNB1 protein

value: Bio rep 2, Tech rep 2


title: TSA-seq POL1RE in H1 cells, condition2 - conditionE - anti-POL1RE, Bio rep 2, Tech rep 1

treatment_protocol: pol1re TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on H1 cells replicate 2

value: POLR1E protein

value: condition2 - conditionE - anti-POL1RE

value: Bio rep 2, Tech rep 1


title: TSA-seq v2 Lamin B1 in HFFc6, condition2 - conditionAI - anti-Lamin B1, Bio rep 2, Tech rep 1

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on HFFc6 cells replicate 2 library set1


title: TCZ_SRBC3d_M16

description: Library name: TCZ_SRBC3d_M16_v4619

value: Spleen T cell zone

value: T cell

value: 3 days after antigen challenge with SRBC


title: TSA-seq POL1RE in H1 cells, condition2 - conditionE - anti-POL1RE, Bio rep 1, Tech rep 1

treatment_protocol: pol1re TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on H1 cells replicate 1

value: stem cell

value: Bio rep 1, Tech rep 1


title: TCZ_SRBC3d_M14

description: Library name: TCZ_SRBC3d_M14_v4611

value: WT


title: MOUSE Embryonic stemcell 2

description: Library name: J1_ESC_2


title: MOUSE Embryonic stemcell 1

description: Library name: J1_ESC_1


title: Niwa EWS-OCT-4 stable cell line 3

description: Library name: EWS_OCT_4_3

value: Niwa ews oct4


title: BCZ_SRBC3d_M13

description: Library name: BCZ_SRBC3d_M13_v4631

value: Spleen B cell zone


title: TSA-seq v2 Lamin B1 in H1, condition2 - conditionAI - anti-Lamin B1, Bio rep 1, Tech rep 1

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on H1 cells replicate 1

value: stem cell derived cell line

value: male

value: embryonic


title: TSA-seq MKI67IP in  HCT116 cells, condition2 - conditionC or conditionE - anti-MKI67IP, Bio rep 2, Tech rep 1

treatment_protocol: MKI67IP TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on HCT116 cells replicate 2

value: colon

value: immortalized cell line

value: anti-NIFK

value: NIFK protein

value: adult

value: colon carcinoma


title: Niwa EWS-OCT-4 stable cell line 2

description: Library name: EWS_OCT_4_2


title: TSA-seq MKI67IP in  HCT116 cells, condition2 - conditionC or conditionE - anti-MKI67IP, Bio rep 1, Tech rep 1

treatment_protocol: MKI67IP TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition C (1:3000 tyramide-biotin, 30 minute reaction) on HCT116 cells replicate 1


title: TCZ_SRBC3d_M13

description: Library name: TCZ_SRBC3d_M13_v4631

value: Spleen T cell zone


title: TCZ_SRBC4d_M17

description: Library name: TCZ_SRBC4d_M17_v5342

value: T cell

value: 4 days after antigen challenge with SRBC


title: TSA-seq CENPB in HCT116 cells, condition2 - conditionC or conditionE - anti-CENPB, Bio rep 2, Tech rep 1

treatment_protocol: CENPB TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on HCT116 cells replicate 2

value: anti-CENP-B

value: CENPB protein

value: Bio rep 2, Tech rep 1


title: BCZ_SRBC3d_M12

description: Library name: BCZ_SRBC3d_M12_v4627

value: WT

value: 3 days after antigen challenge with SRBC


title: Niwa EWS-OCT-4 stable cell line 1

description: Library name: EWS_OCT_4_1

value: Niwa ews oct4


title: A594,MYC+M2-3,RNA

city: Nanjing

first: Xuming

last: Song

state: Jiangsu

address: Baiziting 42

institute: Jiangsu Institute of Cancer Research

data_processing:
Sequencing data were quality controlled using "fastqc" software and rRNA sequencing was removed using "SortMeRNA".
Aligning to Genome with STAR-aligner and Summarizing Gene Counts with featureCounts.
Generating analysis report with multiQC.
Assembly: hg19
Supplementary files format and content: Csv files with FPKM data.

source_name: LUAD cell line

growth_protocol: Cancer cells were maintained in DMEM (KeyGEN BioTech) supplemented with 10% Fetal Bovine Serum (Corning) and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the classical Trizol method.
RNA library perpared by TruePrep RNA Library Prep Kit for Illumina.

treatment_protocol: c-Myc-expression vector (pcDNA3-cmyc, Addgene, #16011, RR_ID:Addgene_16011) and pcDNA3 empty vector (Keris Biotechnology Co.) were transfected by Lipo3000, which was performed using the manufacturer's standard plasmid transfection method. Noncontact cocultures of A549 cells and M2-like macrophages were performed for 72 hours with the use of 3μm Insert Systems (Corning).

value: LUAD cell line

value: LUAD


title: A594,MYC+M2-2,RNA


title: A594,MYC+M2-1,RNA


title: TSA-seq CENPB in HCT116 cells, condition2 - conditionC or conditionE - anti-CENPB, Bio rep 1, Tech rep 1

treatment_protocol: CENPB TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition C (1:3000 tyramide-biotin, 30 minute reaction) on HCT116 cells replicate 1

value: colon

value: male

value: Bio rep 1, Tech rep 1


title: SCDi, TUMOR CELLS

first: Alessandro

last: Sammarco

institute: Massachusetts General Hospital

description:
Library name: Sample4
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes)
Assembly: Mouse mm10 (mm10-2020-A)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
For scRNAseq, 3 mice per experimental group were pooled into 1 sample prior to FACS-sorting to account for inter-animal variability. Each brain pool was sorted into 2 cell populations: tumor cells (DAPI-/CD45-/GFP+) and immune cells (DAPI-/CD45+/GFP-). Within 30 minutes after sorting, 3’ scRNA-seq libraries were generated using a 10X Genomics Chromium controller. Libraries were then sequenced on a NovaSeq 6000 platform using a NovaSeq S2 flow cell (Illumina). Data analysis was performed in R studio (v1.3.1073) using Seurat (v4.1.1).
Library preparation was performed according to the manufacturer’s instructions (Chromium™ Single Cell 3’ v3 Protocol, 10X Genomics). Briefly, cells were resuspended in the master mix and loaded with partitioning oil and gel beads into the chip to generate the gel-bead-in-emulsion (GEM). The poly-A RNA from the cell lysate in every single GEM was retrotranscripted to cDNA, which contains an illumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriate-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added, but the transcript read was only single-end.

value: brain

value: tumor cells

value: SCDi


title: TSA-seq DDX18 in HCT116 cells, condition2 - conditionC - anti-DDX18, Bio rep 1, Tech rep 1

treatment_protocol: DDX18 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition C (1:3000 tyramide-biotin, 30 minute reaction) on HCT116 cells replicate 1

value: immortalized cell line

value: DDX18 protein

value: adult

value: colon carcinoma

value: condition2 - conditionC - anti-DDX18


title: BCZ_SRBC3d_M11

description: Library name: BCZ_SRBC3d_M11_v4603

source_name: Spleen B cell zone

value: Spleen B cell zone

value: T cell


title: TCZ_SRBC3d_M12

description: Library name: TCZ_SRBC3d_M12_v4627

value: Spleen T cell zone

value: WT

value: 3 days after antigen challenge with SRBC


title: TCZ_SRBC3d_M15

description: Library name: TCZ_SRBC3d_M15_v4601


title: TSA-seq v2 Lamin B1 in HFFc6, condition2 - conditionAI - anti-Lamin B1, Bio rep 1, Tech rep 1

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on HFFc6 cells replicate 1

value: skin fibroblast

value: LMNB1 protein


title: TSA-seq Nucleolin in HCT116 cells, condition2 - conditionC - anti-Nucleolin, Bio rep 1, Tech rep 1

treatment_protocol: Nucleolin TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition C (1:3000 tyramide-biotin, 30 minute reaction) on HCT116 cells replicate 1

value: colon

value: anti-NCL

value: NCL protein

value: male


title: A594,EV+M2-3,RNA

value: LUAD cell line

value: LUAD


title: TCZ_SRBC3d_M11

description: Library name: TCZ_SRBC3d_M11_v4603


title: CTRL, TUMOR CELLS

description:
Library name: Sample2
10X Genomics

value: brain

value: tumor cells

value: Vehicle


title: A594,EV+M2-2,RNA


title: SCDi, CD45 CELLS

description:
Library name: Sample3
10X Genomics

value: immune cells

value: SCDi


title: TSA-seq MKI67IP in k562 cells, condition2 - conditionE - anti-MKI67IP, Bio rep 2, Tech rep 1

treatment_protocol: MKI67IP TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on K562 cells replicate 2

value: blood cell

value: immortalized cell line

value: anti-NIFK

value: NIFK protein

value: female

value: adult

value: chronic myelogenous leukemia

value: condition2 - conditionE - anti-MKI67IP

value: Bio rep 2, Tech rep 1


title: A594,EV+M2-1,RNA


title: CTRL, CD45 CELLS

description:
Library name: Sample1
10X Genomics


title: BCZ_SRBC3d_M10

description: Library name: BCZ_SRBC3d_M10_v4617

value: Spleen B cell zone

value: T cell

value: WT

value: 3 days after antigen challenge with SRBC


title: TSA-seq MKI67IP in k562 cells, condition2 - conditionE - anti-MKI67IP, Bio rep 1, Tech rep 1

treatment_protocol: MKI67IP TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on K562 cells replicate 1

value: Bio rep 1, Tech rep 1


title: BCZ_SRBC3d_M14

description: Library name: BCZ_SRBC3d_M14_v4611


title: C9-Par-TERT-R1_S67

value: TERT

value: vehicle


title: TCZ_SRBC3d_M10

description: Library name: TCZ_SRBC3d_M10_v4617

value: Spleen T cell zone


title: A549,MYC+Veh-3,RNA

value: LUAD cell line

value: LUAD

value: MYC+Veh


title: Liver, Ketogenic Diet, Clstn3 LKO, rep4

first: Yajing

last: Gao

address: 675 Charles E Young Dr S

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

description:
Library name: KO-D
2x50

data_processing:
Raw fastq data was processed in UCLA Hoffman2 cluster.
Adapter and quality trimming of raw FASTQ files was performed using Trimmomatic. FastQC was used to perform quality control of the FASTQ files before and after trimming.
Trimmed FASTQ files were aligned to GRCm38/mm10 using STAR package.
HTSeq-count was used to extract gene counts.
Gene expression analysis was performed using DESeq2 package implemented in R.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: xlsx file containing compiled normalized counts from DESeq analysis

source_name: Liver

growth_protocol: At age 10 weeks, male littermate control and Clstn3 LKO mice were put on 4 weeks of Ketogenic diet.

extract_protocol:
RNA was harvested in trizol using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA library preparations and sequencing reactions were conducted at UCLA Technology Center for Genomics & Bioinformatics (TCGB). RNA sequencing libraries were prepared using the Illumina Stranded mRNA (polyA) kit with 1ug RNA input.

treatment_protocol: After 4 weeks on diet, 14 week old males mice were euthanized following a 6 hour fast with isoflurane and secondary cardiac puncture. Liver was immediately extracted and flash frozen.

value: Liver

value: Albumin Cre+ Clstn3 f/f

value: Ketogenic Diet


title: Liver, Ketogenic Diet, Clstn3 LKO, rep3

description:
Library name: KO-C
2x50


title: TSA-seq POL1RE in k562 cells, condition2 - conditionE - anti-POL1RE, Bio rep 2, Tech rep 1

treatment_protocol: pol1re TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on K562 cells replicate 2

value: blood cell

value: immortalized cell line

value: POLR1E protein

value: female

value: adult

value: chronic myelogenous leukemia

value: condition2 - conditionE - anti-POL1RE


title: BCZ_SRBC3d_M9

description: Library name: BCZ_SRBC3d_M9_v4615

value: Spleen B cell zone

value: T cell

value: WT

value: 3 days after antigen challenge with SRBC


title: A549,MYC+Veh-2,RNA

value: LUAD cell line


title: TSA-seq POL1RE in k562 cells, condition2 - conditionE - anti-POL1RE, Bio rep 1, Tech rep 1

treatment_protocol: pol1re TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on K562 cells replicate 1

value: Bio rep 1, Tech rep 1


title: TCZ_SRBC3d_M9

description: Library name: TCZ_SRBC3d_M9_v4615

value: Spleen T cell zone


title: TSA-seq CENPB in k562 cells, condition2 - conditionE - anti-CENPB, Bio rep 2, Tech rep 1

treatment_protocol: cenpb TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on K562 cells replicate 2

value: anti-CENP-B

value: CENPB protein

value: condition2 - conditionE - anti-CENPB

value: Bio rep 2, Tech rep 1


title: A549,MYC+Veh-1,RNA

value: LUAD

value: MYC+Veh


title: BCZ_PBS_M8

description: Library name: BCZ_PBS_M8_v4585

value: not applicable


title: Liver, Ketogenic Diet, Clstn3 LKO, rep2

description:
Library name: KO-B
2x50

value: Liver

value: Albumin Cre+ Clstn3 f/f

value: Ketogenic Diet


title: TSA-seq CENPB in k562 cells, condition2 - conditionE - anti-CENPB, Bio rep 1, Tech rep 1

treatment_protocol: cenpb TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on K562 cells replicate 1

value: blood cell

value: immortalized cell line

value: female

value: adult

value: chronic myelogenous leukemia


title: A594,EV+Veh-3,RNA

value: LUAD cell line

value: EV+Veh


title: TCZ_PBS_M8

description: Library name: TCZ_PBS_M8_v4585

value: Spleen T cell zone

value: T cell

value: WT


title: Liver, Ketogenic Diet, Clstn3 LKO, rep1

description:
Library name: KO-A
2x50


title: Liver, Ketogenic Diet, Control, rep3

description:
Library name: WT-C
2x50

value: Albumin Cre- Clstn3 f/f


title: A594,EV+Veh-2,RNA

value: LUAD


title: BCZ_PBS_M7

description: Library name: BCZ_PBS_M7_v5322

value: Spleen B cell zone


title: Liver, Ketogenic Diet, Control, rep4

description:
Library name: WT-D
2x50


title: TSA-seq POL1RE in HFFc6 cells, condition2 - conditionE - anti-POL1RE, Bio rep 1, Tech rep 1

treatment_protocol: pol1re TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on Hffc6 cells replicate 1

value: skin fibroblast

value: POLR1E protein

value: male

value: condition2 - conditionE - anti-POL1RE

value: Bio rep 1, Tech rep 1


title: TSA-seq POL1RE in HFFc6 cells, condition2 - conditionE - anti-POL1RE, Bio rep 2, Tech rep 1

treatment_protocol: pol1re TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on Hffc6 cells replicate 2

value: immortalized cell line

value: Bio rep 2, Tech rep 1


title: A594,EV+Veh-1,RNA


title: Patient 3,Acunar-tissue,RNA

source_name: LUAD Tissue

value: LUAD Tissue

value: Tissue

value: Acinar-subtype


title: TSA-seq CENPB in HFFc6 cells, condition2 - conditionE - anti-CENPB, Bio rep 1, Tech rep 1

treatment_protocol: cenpb TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on Hffc6 cells replicate 1

value: anti-CENP-B

value: CENPB protein

value: condition2 - conditionE - anti-CENPB


title: Liver, Ketogenic Diet, Control, rep2

description:
Library name: WT-B
2x50

value: Liver

value: Ketogenic Diet


title: TCZ_PBS_M7

description: Library name: TCZ_PBS_M7_v5322

value: Spleen T cell zone

value: T cell

value: WT

value: not applicable


title: BCZ_PBS_M6

description: Library name: BCZ_PBS_M6_v4597

value: Spleen B cell zone


title: Liver, Ketogenic Diet, Control, rep1

description:
Library name: WT-A
2x50

value: Albumin Cre- Clstn3 f/f


title: TSA-seq CENPB in HFFc6 cells, condition2 - conditionE - anti-CENPB, Bio rep 2, Tech rep 1

treatment_protocol: cenpb TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition E (1:300 tyramide-biotin, 30 minute reaction) on Hffc6 cells replicate 2

value: skin fibroblast

value: male


title: TCZ_PBS_M6

description: Library name: TCZ_PBS_M6_v4597


title: Patient 2,Acrinar-tissue,RNA

value: LUAD


title: P+Fer-1

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

description:
Library name: Sample 2
10X Genomics

data_processing:
The raw sequencing reads were processed and aligned to the GRCm39 mouse genome using CellRanger (v7.0.0).
Downstream analyses were conducted in R (v4.4.1) using Seurat (v5.1.0). Quality control filtering retained cells with more than 200 detected genes, less than 20% mitochondrial gene expression, and excluded cells with abnormally high unique molecular identifier (UMI) counts to remove low-quality cells.
DoubletFinder package (v2.0.4) in R were used to remove doublets. The data were normalized with SCTransform, and highly variable genes were identified to enhance downstream analysis. To mitigate batch effects across samples, Seurat objects were integrated using canonical correlation analysis (CCA).
Cells were clustered using the Louvain algorithm, with a clustering resolution set to 0.5 to define distinct cell populations. Cell types were then annotated with the scType tool, utilizing a custom marker gene list optimized for mouse brain and cancer cell types.
CellChat package (v2.1.2) in R was utilized to infer intercellular communication patterns among these annotated cell types.
Assembly: Mus musculus, GRCm38 (mm10)
Supplementary files format and content: Count matrix produced by Cell Ranger in MTX format

source_name: Brain

extract_protocol:
Cells were resuspended in PBS (without Ca or Mg) with 0.04% BSA and freshly processed. Cell viability was assessed with Cellometer Auto 2000 (Nexcelom) using a AOPI staining. Samples with viability ≥ 80% were loaded in the Chromium X instrument (10X Genomics) to capture approximately 10 x 103 targeted cells using Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 Dual Index form 10X Genomics (cat# 1000268).
scRNA-seq libraries were generated according to the manufacturer’s instructions. QC (quality control) analysis was performed prior to sequencing with 2100 Bioanalyzer and 2200 TapeStation (Agilent, Santa Clara, CA, USA). Library concentration was assessed prior to sequencing using Qubit Fluorometer (Thermo Fisher). Sequence was performed with Novaseq6000 System Illumina (Illumina Inc. San Diego, CA) platform following 10X Genomics guideline; read lengths U28|I10|I10|Y90 and sequencing depth 40,000 paired-end reads per cell.

treatment_protocol: oncolytic HSV with or without Ferrostatin-1

value: Brain

value: murine glioma cells

value: oncolytic HSV1 + Ferrostatin-1


title: Patient 3,MP-tissue,RNA

treatment_protocol: c-Myc-expression vector (pcDNA3-cmyc, Addgene, #16011, RR_ID:Addgene_16011) and pcDNA3 empty vector (Keris Biotechnology Co.) were transfected by Lipo3000, which was performed using the manufacturer's standard plasmid transfection method. Noncontact cocultures of A549 cells and M2-like macrophages were performed for 72 hours with the use of 3μm Insert Systems (Corning).

value: LUAD Tissue

value: Tissue

value: MP-subtype


title: P

description:
Library name: Sample 1
10X Genomics

value: oncolytic HSV1


title: TSA-seq v2 Lamin B1 in k562, condition2 - conditionAI - anti-Lamin B1, Bio rep 1, Tech rep 1

source_name: blood cell

treatment_protocol: Lamin B1 TSA-seq version 2 Reaction Condition 2 (PBS 50% Sucrose) Enhancement Condition AI (1:10000 tyramide-biotin, 20 minute reaction) on k562 cells replicate 1

value: blood cell

value: immortalized cell line

value: LMNB1 protein

value: female

value: adult

value: chronic myelogenous leukemia

value: Bio rep 1, Tech rep 1


title: TCZ_PBS_M5

description: Library name: TCZ_PBS_M5_v5334

value: Spleen T cell zone

value: T cell

value: WT

value: not applicable


title: BCZ_PBS_M4

description: Library name: BCZ_PBS_M4_v4593

value: Spleen B cell zone


title: Allogeneic treated Wnt-C59 + belumosudil rep 4

city: Düsseldorf

first: Alexandru-Emil

last: Matei

address: Merowingerpl. 1A

country: Germany

institute: Hiller Research Center, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University

description: Library name: sample 15

data_processing:
Raw sequencing reads for all samples were assessed for quality using FastQC on the Galaxy platform. This step identified adaptor sequences and low-quality bases. Adaptor sequences and low-quality bases were removed from all samples using Trim Galore on the Galaxy platform with default parameters. Trimmed reads from all samples were aligned to the reference genome GRCm39 using HISAT2 on the Galaxy platform. Default settings were applied for the alignment, and no samples were removed during this step. Gene-level read counts for all samples were generated using featureCounts on the Galaxy platform. The GTF annotation file from the reference genome GRCm39 was used for feature quantification.
Assembly: GRCm39
Supplementary files format and content: Txt file included raw counts for each samples

source_name: Skin

extract_protocol:
Total RNA was extracted using Nucleospin RNA kits (Macherey-Nagel) according to the manufacturer’s instructions.
Total RNA was sent to Novogene Co., Ltd. (Cambridge, UK) for library preparation and sequencing. The libraries were constructed using Novogene's standard protocols for RNA sequencing. Details of the library construction procedure can be provided by the service provider upon request.

value: Skin

value: Wnt-C59 (5 mg/kg daily, orally) and belumosudil (150 mg/kg daily, orally) was administered daily from day 21 to day 49 post-alloBMT


title: H1975-OR/tet-MUC1shRNA_DOX+ Rep3

city: Brookline

first: Naoki

last: Haratake

address: 44 Washington St. #1001,

institute: Dana-Farber Cancer Institute

description:
Sample 6
H1975_RT_DOX_3

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: STAR_Gene_TPM.csv

source_name: lung

growth_protocol: H1975-OR cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were cultured in RPMI1640 medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA).

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).

value: lung

value: Lung Cancer

value: MUC1-C shRNA silencing

value: DOX


title: Allogeneic treated Wnt-C59 + belumosudil rep 3

description: Library name: sample 14


title: Patient 2,MP-tissue,RNA

value: LUAD Tissue

value: Tissue

value: LUAD

value: MP-subtype


title: H1975-OR/tet-MUC1shRNA_DOX+ Rep2

description:
Sample 5
H1975_RT_DOX_2


title: Patient 1,MP-tissue,RNA


title: TCZ_PBS_M4

first: Franka

last: Buytenhuijs

address: Toernooiveld 200

institute: Radboud University

description: Library name: TCZ_PBS_M4_v4593

data_processing:
CDR3β identification, clonotype clustering and correction of sequencing errors were performed using MiTCR software.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted as described above and TCRβ-chain transcripts were amplified independently in a two-step reaction according to the manufacturer’s protocol (iRepertoire; patent no. 7,999,092).
The obtained TCRβ libraries were quantified using the PerfeCTa-NGS-Quantification Kit according to manufacturer’s protocol (Quantabio) and sequenced using the Illumina MiSeq Reagent Kit v2 300-cycle (150 paired-end read; Illumina), gaining an average of $\approx$1.8 × 10^6 reads per sample.


title: Allogeneic treated Wnt-C59 + belumosudil rep 2

description: Library name: sample 13


title: H1975-OR/tet-MUC1shRNA_DOX+ Rep1

description:
Sample 4
H1975_RT_DOX_1


title: Allogeneic treated Wnt-C59 + belumosudil rep 1

description: Library name: sample 12


title: LNCaP R2, replicate 2, scRNAseq

city: Tianjin

first: Yu

last: Zhao

state: Tianjin

address: 238 Baidi Road

department: Institute of Radiation Medicine

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: 10x Genomics

data_processing:
Reads with mismatched barcode, UMI containing mono-oligo-chain, unknown bases (N), low quality (Q <10), or UMI count < m*10% barcode will be filtered by 10X Genomics Cell Ranger software (version 3.1.0). The clean reads were then mapped to the human genome (hg38).
Seurat software (version 3.1.1) was used for downstream analysis. Cells that have unique feature counts over 8,000 or less than 200 and the mitochondrial gene percent over 30% were filtered for secondary quality control.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: LNCaP

growth_protocol: LNCaP cells were obtained from American Type Culture Collection (ATCC). The cells were maintained in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS) (Gibco) and 1% l-glutamine (Solarbio) and kept at 37˚C with 95% air and 5% CO2. The cells were divided into two groups and seeded at a density of 1×105/cm2 24 hours prior to treatment.

extract_protocol:
The cells were digested with 0.25% (w/v) trypsin (Gibco) and collected by centrifugation for subsequent analysis. Samples with ≥90% living cells were analyzed.The concentrationof cellular suspensions wasadjustedto1 × 104cellsper μL using PBS containing 0.04% bovine serum albumin (BSA) (Thermo Fisher Scientific).
The experiment was performed according to the manufacture of Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, PN-1000121). The cDNA was digested into 200-300 bp fragments by PCR at first. Before PCR proceeded, the thermal cycler was pre-cooled at 4°C. 10 µl purified cDNA sample, 5 µl Fragmentation Buffer, 10 µl Fragmentation Enzyme, and 25 µl Buffer EB were mixed and then processed in a program having 10 cycles of 32°C for 5 min, 65°C for 30 min, and hold at 4˚C. SPRIselect Reagent Kit (0.6X SPRI and 0.8X SPRI) were used to do double sided size selection of post fragmentation, end-repair, and A-tailing. Then, a PCR reaction was set up to perform adaptor ligation with a system of 50 µl sample, 20 µl Ligation Buffer, 10 µl DNA Ligase, and 20 µl Adaptor Oligos. The thermal cycler was 20°C for 15 min and hold at 4°C. 0.8X SPRI was used to do adaptor ligation selection. A PCR reaction with a mix containing 30 µl sample, 10 µl SI Primer, and 50 µl AmpMix was used to add sample index. The mix was incubated in a thermal cycler with the following protocol: 98°C for 45 sec; 5 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min; hold at 4°C. 0.6X SPRI and 0.8X SPRI were used to do double sided size selection. Finally, fragments containing R1, R2, P5, P7, and sample index were produced. The insert size of the library was examined using Agilent 2100. The effective concentration of the library was examined by preliminary quantitative Q-PCR performed by Qubit3.0 to accurately quantify.

treatment_protocol: exposed to 0 Gy and 2 Gy of ionizing radiation

value: LNCaP

value: Human prostate cancer cell

value: exposed to 2 Gy of ionizing radiation


title: H1975-OR/tet-MUC1shRNA_DOX- Rep3

description: Sample 3

value: control

value: DMSO


title: Allogeneic treated Wnt-C59 rep 4

description: Library name: sample 11

value: Wnt-C59 monotherapy (5 mg/kg daily, orally) was administered daily from day 21 to day 49 post-alloBMT


title: TCZ_PBS_M3

description: Library name: TCZ_PBS_M3_v4599

value: Spleen T cell zone

value: T cell

value: WT

value: not applicable


title: Patient 1,Acinar-tissue,RNA

value: Acinar-subtype


title: LNCaP R2, replicate 1, scRNAseq

description: 10x Genomics


title: TSA-seq v2 Lamin B1 in k562, condition2 - conditionAI - anti-Lamin B1, Bio rep 2, Tech rep 1

value: blood cell

value: immortalized cell line

value: LMNB1 protein

value: female

value: adult

value: chronic myelogenous leukemia

value: Bio rep 2, Tech rep 1


title: Allogeneic treated Wnt-C59 rep 3

description: Library name: sample 10

value: Skin


title: BCZ_PBS_M2

description: Library name: BCZ_PBS_M2_v5324

value: Spleen B cell zone


title: BCZ_PBS_M5

description: Library name: BCZ_PBS_M5_v5334


title: H1975-OR/tet-MUC1shRNA_DOX- Rep2

description: Sample 2

value: lung

value: Lung Cancer

value: control


title: TCZ_PBS_M2

description: Library name: TCZ_PBS_M2_v5324

value: Spleen T cell zone


title: H1975-OR/tet-MUC1shRNA_DOX- Rep1

description: Sample 1

value: DMSO


title: BS-seq sequencing data

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

institute: wuhan university

data_processing:
For initial quality control of the raw sequencing data in FASTQ format, we utilized FastQC software (version 0.11.8). To trim low-quality bases and remove adaptor sequences, we employed Cutadapt (version 3.5) in conjunction with Trimmomatic (version 0.39). Bismark (version 0.24.0) was then used to align the deaminase-treated or bisulfite-treated reads to the human reference genome (GRCh38.p13), with indexing facilitated by Bowtie2.41 Quantification of methylation at each cytosine site involved tallying the number of 'C' bases as 5mC sites (denoted as NC) and the number of 'T' bases as unmodified cytosine sites (denoted as NT). We defined sequencing depth as N = NC + NT and computed the coverage of samples using both Bismark and Samtools (version 1.9).
Methylated sites were statistically determined using a binomial test that factored in the counts of methylated cytosines (mC), the total count of cytosines (mC + umC), and the non-conversion rate of the bisulfite treatment. Sites were deemed methylated if they had an FDR-corrected p-value less than 0.05. For the calculation of methylation levels across the genome, we partitioned the sequence into bins of 10 kb. The methylation level (ML) for each bin or individual cytosine site was calculated as the proportion of methylated 'C' reads, defined by the formula: ML(C) = reads(mC) / (reads(mC) + reads(C)). Lastly, we identified differentially methylated regions (DMRs) using DSS software (version 2.12.0), which allowed for the analysis of methylation variation between different sample groups or conditions.
Assembly: GRCh38.p13
Supplementary files format and content: 5mC signals from NTD-seq(TXT)
Supplementary files format and content: 5mC signals from BS-seq(TXT)
Supplementary files format and content: column headers are: Chromosome, location, strand, C reads, T reads, methylation rate, site type, P value (last column was provided by sequencing company and not used in the analysis).

source_name: Sequencing data for 5mC from HEK293T by BS-seq

extract_protocol:
Genomic DNA of HEk293T was extracted using Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA)
NTD-seq：The genomic DNA from HEK293T cells was isolated using the Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) following the manufacturer's protocol. Unmodified genomic DNA from lambda bacteriophage (Sangon Biotech, Shanghai, China) was added to the genomic DNA as a spike-in control (0.1% of spike-in DNA was added). The mixture was then sheared to an average size of 200-400 bp using a JY92-II N Ultrasonic Homogenizer (Scientz Biotechnology Co., Ltd, China). The fragmented DNA mixture was end-repaired and adenylated using the Hieff NGS Ultima Endprep Mix kit (Yeasen Biotechnology Co., Ltd, Shanghai). Subsequently, DNAm-adaptors (Table S5) were ligated to both ends of the repaired DNA using the Hieff NGS Ultima DNA Ligation Module kit (Yeasen, Shanghai, China), and the resulting DNA was purified using 0.9× KAPA Pure beads (Roche). Additionally, L-5mC-dsDNA was added as a spike-in to evaluate the deamination rates of C and 5mC (0.1% of L-5mC-dsDNA was added). The DNA mixture was then oxidized by nTET and purified using 0.9× KAPA Pure beads. Subsequently, the resulting DNA was denatured and deaminated using A3Am protein. The deaminated DNA was amplified by PCR with 6 cycles using 1 U of EpiMark Hot Start Taq DNA polymerase (New England Biolabs), 0.2 mM of dNTP, 0.4 μM of pre-P5 primer, and 0.4 μM of pre-P7 primer. Following purification using 0.9× KAPA Pure beads, the DNA products were amplified by PCR with 8 cycles using 1 U of Q5 Hot Start High-Fidelity DNA polymerase (New England Biolabs), 0.2 mM of dNTP, 0.4 μM of P5-index primer, and 0.4 μM of P7-index primer. The PCR products were purified with 0.9× KAPA Pure beads and examined using 2% agarose gel electrophoresis. The library quality was assessed on the Agilent Bioanalyzer 2100 system and then sequenced on an Illumina NovaSeq 6000 platform (Novogene Co., Ltd, Nanjing, China).
BS-seq：The genomic DNA from HEK293T cells was isolated using the Tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) following the manufacturer's protocol. Unmodified genomic DNA from lambda bacteriophage (Sangon Biotech, Shanghai, China) was added to the genomic DNA as a spike-in control (0.1% of spike-in DNA was added). The mixture was then sheared to an average size of 200-400 bp using a JY92-II N Ultrasonic Homogenizer (Scientz Biotechnology Co., Ltd, China). Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragments. The library kit (Accel-NGS Methyl-Seq DNA Library Kit(Swift, USA) adds a low complexity polynucleotide tail with an average length of 8 bases to the 3’ end of each fragment during the addition of the first NGS adapter molecule. If these tails are not trimmed bioinformatically from the sequencing data, it is normal and expected to observe them at the beginning of Read 2 (R2). When read length is close to fragment size, the tail may also be observed toward the end of Read 1 (R1) data. Therebefore, it’s highly recommended to trim 10 bases from the beginning of both R1 and R2 to eliminate any artifactual cytosine methylation introduced as a result of filling inoverhangs during end repair steps of conventional dsDNA library preparation and low quality bases due to bisulfite treatment. Subsequently, library qualitywas assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). Pair-end sequencing of sample was performed on an Illumina NovaSeq 6000 platform (Illumina, USA).

value: cell line

value: Human Embryonic Kidney


title: LNCaP Control, replicate 2, scRNAseq

description: 10x Genomics

value: LNCaP

value: Human prostate cancer cell

value: exposed to 0 Gy of ionizing radiation


title: LNCaP Control, replicate 3, scRNAseq

description: 10x Genomics


title: Allogeneic treated Wnt-C59 rep 2

description: Library name: sample 9

value: Wnt-C59 monotherapy (5 mg/kg daily, orally) was administered daily from day 21 to day 49 post-alloBMT


title: NTD-seq sequencing data

data_processing:
For initial quality control of the raw sequencing data in FASTQ format, we utilized FastQC software (version 0.11.8). To trim low-quality bases and remove adaptor sequences, we employed Cutadapt (version 3.5) in conjunction with Trimmomatic (version 0.39). Bismark (version 0.24.0) was then used to align the deaminase-treated or bisulfite-treated reads to the human reference genome (GRCh38.p13), with indexing facilitated by Bowtie2.41 Quantification of methylation at each cytosine site involved tallying the number of 'C' bases as 5mC sites (denoted as NC) and the number of 'T' bases as unmodified cytosine sites (denoted as NT). We defined sequencing depth as N = NC + NT and computed the coverage of samples using both Bismark and Samtools (version 1.9).
Methylated sites were statistically determined using a binomial test that factored in the counts of methylated cytosines (mC), the total count of cytosines (mC + umC), and the non-conversion rate of the bisulfite treatment. Sites were deemed methylated if they had an FDR-corrected p-value less than 0.05. For the calculation of methylation levels across the genome, we partitioned the sequence into bins of 10 kb. The methylation level (ML) for each bin or individual cytosine site was calculated as the proportion of methylated 'C' reads, defined by the formula: ML(C) = reads(mC) / (reads(mC) + reads(C)). Lastly, we identified differentially methylated regions (DMRs) using DSS software (version 2.12.0), which allowed for the analysis of methylation variation between different sample groups or conditions.
Assembly: GRCh38.p13
Supplementary files format and content: 5mC signals from NTD-seq(TXT)
Supplementary files format and content: 5mC signals from BS-seq(TXT)
Supplementary files format and content: column headers are: Chromosome, location, strand, C reads, T reads, methylation rate, site type, P value (last column was provided by sequencing company and not used in the analysis).
Library strategy: NTD-seq

source_name: Sequencing data for 5mC from HEK293T by NTD-seq


title: LNCaP Control, replicate 1, scRNAseq

description: 10x Genomics


title: BCZ_PBS_M1

description: Library name: BCZ_PBS_M1_v5332

value: T cell

value: WT

value: not applicable


title: TCZ_PBS_M1

description: Library name: TCZ_PBS_M1_v5332


title: Murine blood leukocytes, freshly isolated from three 6-month-old C57BL/6NHsd mice

city: St. Louis

first: Polina

middle: V

last: Lishko

state: Missouri

address: 425 S. Euclid ave

department: Cell Biology and Physiology

institute: Washington University in St. Louis, School of Medicine

description: Library name: Murine peripheral blood leukocytes (sample #5)

data_processing:
Bioinformatic support was provided by Centrillion Biosciences Inc. (Palo Alto, CA).
Assembly: GRCm39
Supplementary files format and content: Excel format with combined reads for sperm (well #4) and leukocytes (well #5)
Supplementary files format and content: Addtionally, corresponding *BAM files are provided for each sample

source_name: freshly isolated blood leukocytes

extract_protocol:
Total RNA was extracted from murine epididymal spermatozoa isolated from three 6-month-old C57BL/6NHsd male mice. Sperm population was purified by gradient centrifugation using ISolateTM (Irvine Scientific, CA) density gradient. 80% and 40% ISolateTM gradients were prepared with HS solution. Sperm purification was carried out by overlaying epidydimal sperm suspension on top of 40% gradient, and centrifuged for 30 min at 300g. Pure sperm cells were collected at the bottom and visually examined for purity and contamination under phase-contrast microscope. Only 100% pure sperm samples were used for the RNA extraction. To exclude potential contamination with leukocytes, comparison of both transcriptomes was used to determine sperm specific transcripts. Peripheral blood leukocytes (Pbl) were obtained from three 6-month-old C57BL/6NHsd male mice postmortem using heart puncture. Total amount of blood collected was 2 mL. Total RNA was extracted from cells using Qiagen RNeasy kit, and converted to cDNA followed by fragmentation to 200 bp. Total RNA obtained from murine Pbl was 55.2 µg and total RNA obtained from murine sperm was 14.73 µg; both RNA isolations have purity above A260/A280 = 2,1.
DNA fragments with appropriate lengths (e.g., 200 bp) were purified using gel electrophoresis and sequencing libraries were prepared with poly(A)+-enriched RNA using Illumina mRNA-Seq Sample Prep Kit according to the manufacturer’s instructions. Illumina Single Read Cluster Generation Kit v2 (Lot 4941271) was used for cluster generation. Final libraries concentrations were: mouse sperm: 49.1 ng/mcL; mouse leukocytes: 41.4 ng/mcL. The final libraries were assessed using Bioanalyzer to check fragment size, concentration, and purity. Sperm library (well #4) and pbl library (well #5) were loaded onto a single-read flow cell, where they underwent bridge amplification to form clonal clusters. Libraries were sequenced on the Illumina Genome Analyzer II using a 36-cycle Run v3 sequencing kit (Lot 4935209) by standard protocols. Sequences were aligned to mouse genome GRCm39. Bioinformatics support was provided by Centrillion Biosciences Inc. (Palo Alto, CA).

value: blood leukocytes

tag: batch

value: flow cell, well # 5 October 2, 2009


title: hicCne2

city: Nantong

first: Tian

last: Xia

address: Xisi Road 20, Nantong, Jiangsu Province

department: Institute of Otolaryngology-Head and Neck Surgery

institute: Affiliated Hospital of Nantong University

data_processing:
Capture Hi-C processing FASTQ files (paired-end Illumina data) were processed with the HiC-Pro v2.11.1 using Bowtie2 v2.3.5.1 for mapping short reads to the reference genome mm10/hg19. After the mapping, filtering and deduplication steps of the HiC-Pro pipeline, normalized matrices were generated at 500 kb, 200 kb, 40 kb and 10 kb resolutions.
FitHiC v2.0.7 software was used to screen for significant chromatin interactions. Assigning statistical confidence estimates to mid-range intra-chromosomal contacts by jointly modeling the random polymer looping effect and previously observed technical biases.
HiCPlotter can draw maps of all chromosomes with different resolutions. The “all.validpair” files generated after HiC-Pro processing were converted into “hic” file, which can be visualized by juicebox. A/B compartments was visualized by cworld::dekker scripts. TAD Compare was used to identify differential TAD boundaries and show TAD boundaries change between two datasets.
Assembly: hg38
Supplementary files format and content: hicCne2.allValidPairs.hic

extract_protocol:
Chromatin was isolated from samples using a high-throughput chromatin isolation (HIC) protocol.
Formaldehyde is used to fix cells, followed by DNA digestion with the DpnII enzyme, which recognizes the GATC sequence to create 5'-overhangs. Then, dNTPs and biotin-14-dATP are utilized to fill in the 5'-overhangs, converting them into blunt ends. During this step, blunt ends are ligated, introducing a new restriction enzyme site (ClaI) into the DNA, which can be used to assess the efficiency of the filling-in reaction. After ligation, the cross-links are reversed to remove proteins from the DNA. The DNA is then cut into fragments of 200 to 300 base pairs, suitable for paired-end sequencing. Finally, streptavidin magnetic beads are employed to enrich the ligation products, and sequencing adapters are added in preparation for subsequent sequencing analysis.

value: nasopharyngeal carcinoma cells


title: Allogeneic rep 3

description: Library name: sample 7

value: Skin

value: Oral gavage of 0.4% methylcellulose was administered daily from day 21 to day 49 post-alloBMT


title: 90_WT_7p

city: Strasbourg

first: Salim

last: Megat

state: Alsace

address: 1 rue Eugène Boeckel

country: France

institute: Center for Research in Biomedicine of Strasbourg (CRBS)

description: Library name: CNRX137

data_processing:
Raw counts were imported into R.4.3.1 and batch effects were removed on raw counts using the Combat-Seq method 62. Combat-seq uses a negative binomial regression method that retain the integer nature or raw counts. Batch-corrected counts were then processed following the the ARMOR workflow 63. The ARMOR workflow uses the edgeR-QL framework which provides more accurate type I error rate control, as it accounts for the uncertainty of the dispersion estimates. After visual inspection of sample clustering using PCA and definition of DEG contrast, differential expression was performed between presymptomatic and symptomatic Sod1G86R mice compared to controls for both cell types. Significance was fixed at FDR<0.05
Assembly: mm10
Supplementary files format and content: normalized_counts

extract_protocol:
RNA was extracted with Trizol (Invotrogen)
Full length cDNA was obtained using the SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Clontech, CA) according to the manufacturer’s instructions

value: Brain

value: corticospinal neuron

value: wild type genotype


title: Allogeneic rep 2

description: Library name: sample 6


title: LNCaP R2, replicate 3, scRNAseq

description: 10x Genomics

value: exposed to 2 Gy of ionizing radiation


title: Allogeneic rep 1

description: Library name: sample 5


title: BCZ_PBS_M3

city: Nijmegen

description: Library name: BCZ_PBS_M3_v4599

value: Spleen B cell zone


title: Allogeneic treated Wnt-C59 rep 1

description: Library name: sample 8


title: NP69

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences. Sequencing reads were aligned to the human genome build hg38 (mouse genome mm10) using bowtie2 (v2.3.5.1) using default parameters. Regions of enrichment of H3K27ac were calculated using MACS2 (v2.1.2) using parameters -m 5 50. MACS peaks of H3K27ac were used as constituent enhancers for super-enhancer identification.
Enhancers were stitched and super-enhancers were identified using ROSE (https://bitbucket.org/young_computation/rose) as described previously. Briefly, this algorithm stitches constituent enhancers together if they are within a certain distance and ranks the enhancers by their input-subtracted signal of H3K27ac .
The genes that were associated with super-enhancers were analyzed using clusterProfiler R package (v3.6.0). Super-enhancers peaks were chosen for the motif analysis using meme (v5.1.1).
Assembly: hg38
Supplementary files format and content: CNE2-H3k27ac_peaks.bed,NP69_peaks.bed,merged_peaks.bed
Supplementary files format and content: CNE2-H3k27ac.bw,NP69.bw
Library strategy: CUT&Tag

extract_protocol:
Protein-DNA interactions were mapped using the CUT&Tag method, employing H3k27ac/specific antibody to target [protein/histone of interest] in the samples
The specific antibody (anti-H3K27ac) binds in situ to the chromatin-associated protein and is subsequently anchored to the A-Tn5 transposition fusion protein. Upon activation of the Tn5 transposable enzyme, it fragments the chromatin selectively bound to the target protein, efficiently generating high-resolution, low-background fragment libraries.

value: normal nasopharyngeal epithelial cells


title: CNE2


title: 90_WT_9p

description: Library name: CNRX143


title: shOgdh_Mouse_6

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: Library name: shOgdh_Mouse_6

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (2.0.6).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: Murine crypts

growth_protocol: All animal experiments in this study were performed in accordance with protocols approved by the Memorial Sloan Kettering Institutional Animal Care and Use Committee (approval number: 11-06-012). The mice were housed with a 12 h light/dark cycle between 8:00 and 20:00 in a temperature-controlled room (22 ± 1°C) with free access to water and food. Both male and female mice were used in equal proportions for all experiments. .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Cag-rtTA3 mediating shRenilla and shOgdh expression was activated by feeding mice with a doxycycline hyclate diet (200 mg/kg) at adult stage. After 3 days on Dox, crypts were isolated as described in the materials and method section.

value: Mix

value: Murine crypts

tag: time

value: TetO. shOgdh; Cag-rtTA

value: doxycycline


title: Syngeneic rep 4

description: Library name: sample 4

tag: tissue


title: 90_WT_3p

description: Library name: CNRX63

tag: cell type


title: shOgdh_Mouse_5

description: Library name: shOgdh_Mouse_5

tag: genotype


title: HUDEP-2 cells, WT, Pol-II

city: Guangzhou

first: Xiuqin

last: Bao

address: No. 1838, Guangzhou avenue north, baiyun district, Guangzhou

institute: Southern Medical University

data_processing:
All clean reads passed quality control with FASTQC and were mapped onto hg19 with bowtie2.
After removal of duplicates with picard, the bam data were ranked, and an index was created with samtools.
We used MACS2 to generate peak calls with input as the control and set a 200-bp bandwidth in the shiftingmodel to denote the peak with p < 0.01.
Assembly: hg19
Supplementary files format and content: tdf files were generated using the MACS

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Human umbilical cord blood-derived erythroid progenitor

tag: chip antibody

value: POI-II


title: 60_WT_7p

description: Library name: CNRX133


title: Syngeneic rep 3

description: Library name: sample 3

tag: treatment


title: HUDEP-2 cells, WT, H3K27ME3

tag: cell line


title: Syngeneic rep 2

description: Library name: sample 2


title: 60_WT_3p

description: Library name: CNRX87


title: shOgdh_Mouse_4

description: Library name: shOgdh_Mouse_4

tag: strain


title: shOgdh_Mouse_3

description: Library name: shOgdh_Mouse_3


title: 60_WT_2p

description: Library name: CNRX69


title: HUDEP-2 cells, WT, H3K4ME3


title: 90_WT_6p

description: Library name: CNRX117


title: Syngeneic rep 1

description: Library name: sample 1


title: HUDEP-2 cells, WT, input

value: input


title: shOgdh_Mouse_1

description: Library name: shOgdh_Mouse_1


title: 30_WT_5p

description: Library name: CNRX103


title: Murine epididymal sperm, freshly isolated from three 6-month-old C57BL/6NHsd mice

description: Library name: Murine epididymal sperm (sample #4)

source_name: freshly isolated sperm cell

value: epididymal sperm

value: sperm

value: flow cell, well # 4 October 2,2009


title: WT_veh_1_H3K4me3_BC

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

data_processing:
CUT&Tag FASTQ files were first processed by removing the adapter ‘CTGTCTCTTATACACATCT’ using the Cutadapt software (version 4.5) and then aligned to the mouse genome (version mm10) by Bowtie2 (version 2.5.1). Duplicated fragments were marked and removed by Picard (version 3.1.1). Signals were generated by deepTools's bamCoverage function (version 3.5.4) to convert BAM files into bigWig files using RPGC normalization excluding Chromosome M.
Assembly: mm10
Supplementary files format and content: bigWig files of CUT&Tag signals
Library strategy: CUT&Tag

source_name: Fetal Liver

extract_protocol:
DNA was purified by spin columns (Cell Signaling 14209S) for GATA2 and PU.1 samples and by phenol-chloroform extraction and ethanol precipitation for H3K4me3 samples.
1.31 ul of DNA was used in a 25-ul PCR reaction to determine the number of cycles for library prepration.

value: Fetal Liver

value: myelo-erythoid progenitor

value: wild type

value: vehicle

tag: antibody


title: 30_WT_4p

description: Library name: CNRX83

value: Brain

value: corticospinal neuron

value: wild type genotype


title: HUDEP-2 cells, 4-17, H3K27ME3


title: WT_combo_1_H3K4me3_BD

value: IFNg and Pam3CSK4


title: WT_combo_2_H3K4me3_CJ


title: 30_WT_3p

description: Library name: CNRX77


title: HUDEP-2 cells, 4-17, H3K27AC


title: HUDEP-2 cells, WT, H3K27AC


title: shRen_Mouse_4

city: New York

description: Library name: shRen_Mouse_4

value: Mix

value: Murine crypts

value: TetO. shRen; Cag-rtTA


title: 30_WT_1p

description: Library name: CNRX57


title: HUDEP-2 cells, 4-17, H3K4ME3

value: Human umbilical cord blood-derived erythroid progenitor


title: shOgdh_Mouse_2

description: Library name: shOgdh_Mouse_2

value: TetO. shOgdh; Cag-rtTA

value: doxycycline


title: WT_veh_2_H3K4me3_CI


title: 105_WT_9p

description: Library name: CNRX97


title: shRen_Mouse_3

description: Library name: shRen_Mouse_3


title: 60_WT_1p

description: Library name: CNRX67


title: shRen_Mouse_2

description: Library name: shRen_Mouse_2


title: KO_veh_1_H3K4me3_BE


title: HUDEP-2 cells, 4-17, input

value: input


title: KO_combo_1_H3K4me3_BF


title: shFTO, IP, rep2

first: dan

middle: hu

last: liu

state: hubei

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

description: shFTO.IP.bw

data_processing:
Raw sequencing files were filtered using Fastp, and then aligned against the human reference genome (GRCh38/hg38) using STAR.
Performing peak differential analysis using exomePeak2
Assembly: hg38
Supplementary files format and content: bigWig(except for Input sample)

extract_protocol:
Total RNA was extracted using Trizol reagent  following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >8.0. The poly(A) mRNA was purified from the total RNA using the Dynabeads mRNA purification kit (Invitrogen).mRNA was subjected to incubated for 2 h at 4℃ with m6A-specific antibody (Abcam).
RNA libraries were then constructed using the NEB Next Ultra Directional RNA Library Prep Kit (NEB)
m6A-seq

value: T-cell acute lymphoblastic leukemia

value: FTO knockdown

tag: rip antibody


title: shRen_Mouse_6

description: Library name: shRen_Mouse_6


title: 105_WT_13p

description: Library name: CNRX125


title: shFTO, IP, rep1

description: shFTO.IP.bw


title: 105_WT_12p

description: Library name: CNRX107


title: Organoids_ISC_Ren_3d_3

description: Library name: ISC_Ren_3d_3

source_name: Organoids

treatment_protocol: Crypts were isolated from mice with the described phenotype and cultured in ENR-CV media for six days before adding DM-αKG or doxycycline. Organoids were then maintained under the indicated treatment for three days.

tag: mouse strain

value: Organoids


title: shRen_Mouse_5

description: Library name: shRen_Mouse_5


title: DKO_veh_2_H3K4me3_DA

value: Fetal Liver

value: myelo-erythoid progenitor


title: 105_WT_11p

description: Library name: CNRX101


title: shFTO, input, rep2


title: KO_veh_2_H3K4me3_CK

value: vehicle


title: 90_WT_9m

description: Library name: CNRX144

value: Brain


title: Organoids_ISC_Ren_3d_1

description: Library name: ISC_Ren_3d_1


title: shFTO, input, rep1


title: shControl, IP, rep2

description: shControl.IP.bw

value: WT


title: DKO_combo_2_H3K4me3_DB


title: shRen_Mouse_1

description: Library name: shRen_Mouse_1


title: Organoids_ISC_3d_aKG_3

description: Library name: ISC_3d_aKG_3

value: 600 mg/ Kg DM-aKG


title: KO_combo_2_H3K4me3_CL

value: IFNg and Pam3CSK4


title: Organoids_ISC_3d_aKG_2

description: Library name: ISC_3d_aKG_2

value: Mix


title: DKO_combo_1_H3K4me3_BH


title: 90_WT_3m

description: Library name: CNRX64

value: wild type genotype


title: 90_WT_6m

description: Library name: CNRX118


title: shControl, IP, rep1

description: shControl.IP.bw


title: 90_WT_7m

description: Library name: CNRX138


title: WT_veh_GATA2_Rep3

value: wild type

value: GATA2 (in house)


title: WT_veh_GATA2_Rep2


title: shControl, input, rep1


title: 60_WT_1m

description: Library name: CNRX68


title: Organoids_ISC_3d_2081_2

description: Library name: ISC_3d_2081_2

value: TetO. shOgdh; Cag-rtTA


title: shControl, input, rep2


title: 30_WT_5m

description: Library name: CNRX104


title: WT_veh_GATA2_Rep4


title: Organoids_ISC_Ren_3d_2

description: Library name: ISC_Ren_3d_2

value: TetO. shRen; Cag-rtTA

value: doxycycline


title: DKO_veh_1_H3K4me3_BG


title: Organoids_ISC_3d_2081_3

description: Library name: ISC_3d_2081_3


title: WT_veh_GATA2_Rep1


title: Organoids_ISC_3d_aKG_1

description: Library name: ISC_3d_aKG_1


title: KOPTK1, shFTO, rep2

description:
RNAseq_shFTO_shControl_KOPTK1_reads_counts.txt
KOPTK1_shFTO_RNAseq.bw

data_processing:
Raw sequencing files were filtered using Fastp, and then aligned against the human reference genome (GRCh38/hg38) using STAR.
Filtered reads were processed using samtools, and differential analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: bigwig files for shFTO and its corresponding shControl
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >8.0. The poly (A) mRNA was purified from the total RNA using the Dynabeads mRNA purification kit (Invitrogen).
RNA libraries were then constructed using the NEB Next Ultra Directional RNA Library Prep Kit (NEB)

value: T-cell acute lymphoblastic leukemia


title: KOPTK1, shFTO, rep3

value: FTO knockdown


title: KOPTK1, shFTO, rep1


title: 30_WT_4m

description: Library name: CNRX84


title: WT_combo_GATA2_Rep4


title: Organoids_ISC_3d_346_3

description: Library name: ISC_3d_346_3

value: Organoids


title: 30_WT_3m

description: Library name: CNRX78


title: WT_combo_GATA2_Rep3

value: Fetal Liver


title: 60_WT_2m

description: Library name: CNRX70


title: KOPTK1, shControl for shFTO, rep2

description:
RNAseq_shFTO_shControl_KOPTK1_reads_counts.txt
KOPTK1_shControl_RNAseq.bw


title: KOPTK1, shControl for shFTO, rep3


title: WT_combo_GATA2_Rep2

value: myelo-erythoid progenitor


title: Organoids_ISC_3d_346_1

description: Library name: ISC_3d_346_1


title: Organoids_ISC_3d_346_2

description: Library name: ISC_3d_346_2


title: KOPTK1, shControl for shFTO, rep1


title: 30_WT_1m

description: Library name: CNRX58


title: 105_WT_9m

description: Library name: CNRX98


title: WT_combo_GATA2_Rep1


title: IntestCrypts_aKG_Day10_R1_Mouse_4

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_4

treatment_protocol: DM-aKG supplementation, mice were injected (intraperitoneally) once daily with 600 mg/kg of DM-aKG (349631-5G, Sigma-Aldrich) dissolved in PBS. For the vehicle control, mice were injected with PBS.

value: Murine crypts


title: 105_WT_13m

description: Library name: CNRX126

value: Brain


title: KO_veh_GATA2_Rep4

value: vehicle


title: 105_WT_12m

description: Library name: CNRX108


title: IntestCrypts_aKG_Day10_R1_Mouse_2

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_2

value: 600 mg/ Kg DM-aKG


title: IntestCrypts_aKG_Day10_R1_Mouse_3

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_3