title: KO_Ctrl_7

description: Library name: KO_Ctrl_7


title: Patient P001 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

status: Public on Jun 12 2026

type: SRA

city: New Haven

first: Darin

last: Dolezal

address: 310 Cedar Street

department: Pathology

country: USA

institute: Yale School of Medicine

description: Library name: P001_CRANI1_PLASMA_EPIC

library_source: genomic

data_processing:
Sequencing reads were processed to generate fragment-level methylation profiles.
Assembly: Sequencing libraries included lambda phage DNA as a spike-in control. Reads were processed relative to the human reference genome GRCh37 (hg19).
Supplementary files format and content: Differentially methylated fragments (DMFs) were quantified and aggregated into matrices for downstream analysis.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted from plasma and cerebrospinal fluid using standard protocols. Tumor genomic DNA was extracted from FFPE tissue sections.
Libraries were prepared using the PredicineEPIC platform for genome-wide methylation profiling.

tag: tissue

value: Human plasma

tag: cell type

value: Non-small cell lung carcinoma


title: Patient P003 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P003_CRANI1_PLASMA_EPIC


title: KO_Ctrl_6

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: Library name: KO_Ctrl_6

library_source: transcriptomic

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11) and the BCL files were demultiplexed into fastq files using bcl2fast2 v2.20.0.422. Data were then preprocessed using the Cumulus SMART-Seq2v2.6.1 workflow on Terra (https://terra.bio/). The workflow employs histat2 v2.1.0 to align read to mm10 mouse genome, and the RSEM v1.3.3 to calculate raw counts and TPM. The workflow computes the TPM-normalized count for each gene, defined as TPM_i / 10^6 * c rounded to the nearest integer, where TPM_i is the TPM for gene i, and c is the total number of reads achieved for the sample.
Assembly: mm10
Supplementary files format and content: comma-separated values (CSV) files include TPM-normalized count for every gene (rows)  in every sample (columns)

molecule: polyA RNA

organism: Mus musculus

source_name: in vitro; originally from spleen and dLN

extract_protocol:
For the CHD1 WT vs. cKO and GR WT vs. cKO experiments, EAE mice were euthanized and perfused intracardially with ice-cold PBS. The brain and spinal cord were finely minced using a razor blade and digested with 2.5 mg/ml collagenase D (Roche Diagnostics) at 37°C for 20 minutes. The digested tissue was then passed through a 70-μm strainer. Mononuclear cells were isolated by density gradient centrifugation using a Percoll (Amersham Biosciences) gradient of 37% and 70%. The mononuclear cells were collected from the interphase for further analysis. 2,000 CNS-infiltrating 2D2+ cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich). At the same time, draining lymph nodes (dLNs) cells were obtained by mechanically dispersing the organs through a 70-μm strainer. 2,000 2D2+ cells were sorted from dLN by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).  For the in vitro Dex treatment experiment, naive T cells from WT or IL-23R KO mice were differentiated into Th17Inf cells in vitro and treated with or without dexamethasone (Dex) for two days. 2,000 live Th17 cells were sorted by FACS into 5 μl of TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma-Aldrich).
Libraries were prepared using a modified SMART-Seq2 protocol, including RNA secondary structure denaturation at 72 °C for 3 min, reverse transcription with Maxima Reverse Transcriptase (Thermo Fischer Scientific) and whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix 2× (KAPA Biosystems) for 12 cycles. Whole-transcriptome amplification product quality was confirmed with a High Sensitivity DNA Chip run on a Bioanalyzer 2100 (Agilent, G2939BA) and quantified using a Qubit dsDNA HS Assay kit (Thermo Scientific). Libraries were prepared with a Nextera XT DNA Library Preparation kit (Illumina) and sequenced using a high-output V2 75 cycle kit (Illumina) on a NextSeq 500 sequencer (Illumina) with 2 × 38 paired-end reads.

value: T cell

tag: genotype


title: KO_Ctrl_5

description: Library name: KO_Ctrl_5

value: in vitro; originally from spleen and dLN


title: Patient P002 plasma cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P002_CRANI1_PLASMA_EPIC


title: Patient P101 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 2 of 3

description: Library name: P101_LMD2_CSF_EPIC

source_name: Human cerebrospingal fluid

value: Human cerebrospingal fluid


title: Patient P101 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 3 of 3

description: Library name: P101_LMD3_CSF_EPIC


title: WT_Ctrl_4

description: Library name: WT_Ctrl_4


title: WT_Ctrl_3

description: Library name: WT_Ctrl_3


title: Patient P101 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 1 of 3

description: Library name: P101_LMD1_CSF_EPIC


title: WT_Ctrl_2

description: Library name: WT_Ctrl_2


title: WT_Ctrl_1

description: Library name: WT_Ctrl_1


title: Patient P028 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P028_CRANI1_CSF_EPIC


title: Patient P029 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P029_CRANI1_CSF_EPIC


title: GR_cKO_CNS_7

description: Library name: GR_cKO_CNS_7

source_name: CNS

value: CNS

value: GR KO(C57/B6)


title: GR_cKO_CNS_9

description: Library name: GR_cKO_CNS_9


title: Patient P027 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P027_CRANI1_CSF_EPIC


title: Patient P026 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease

description: Library name: P026_LMD1_CSF_EPIC


title: GR_cKO_CNS_5

description: Library name: GR_cKO_CNS_5


title: GR_cKO_CNS_6

description: Library name: GR_cKO_CNS_6


title: Patient P023 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 2 of 2

description: Library name: P023_LMD2_CSF_EPIC


title: Patient P025 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P025_CRANI1_CSF_EPIC


title: GR_WT_CNS_4

description: Library name: GR_WT_CNS_4

value: GR WT (C57/B6)


title: Patient P023 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease 1 of 2

description: Library name: P023_LMD1_CSF_EPIC


title: Patient P022 CSF cfDNA PredicineEPIC methylation sequencing at leptomeningeal disease

description: Library name: P022_LMD1_CSF_EPIC


title: Patient P023 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P023_CRANI1_CSF_EPIC


title: GR_WT_CNS_1

description: Library name: GR_WT_CNS_1


title: GR_WT_CNS_2

description: Library name: GR_WT_CNS_2


title: GR_WT_CNS_3

description: Library name: GR_WT_CNS_3


title: Patient P021 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P021_CRANI1_CSF_EPIC


title: Spatial NT-seq of ECT30min-B2Slide2-SLAM

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

description: Mouse-4: ECS-30min, with in situ chemical conversion

data_processing:
The preprocessing of Spatial NT-seq data (obtained through the 10x Genomics Visium platform in this study) was first conducted using 'Space Ranger' (v2.0.0) from 10x Genomics. Initial steps involved read alignment, quality filtering, and the generation of count matrices of total RNAs for each spatially barcoded spot. Spatial NT-seq data were aligned to the mouse genome reference GRCm39 using 'Space Ranger', incorporating both intronic and exonic reads into mRNA count matrices for each spatial spot. Concurrently, histological H&E images were processed using 'Space Ranger' to identify locations covered by tissue sections by aligning pre-recorded spot locations with fiducial border spots in the histological H&E image.
Subsequent analysis of spatial NT-seq data followed a three-step ‘Dynast’ pipeline (v1.0.1; https://github.com/aristoteleo/dynast-release): 'dynast align', 'dynast consensus', and 'dynast count'. In the initial step, raw sequencing reads were mapped to the mouse genome GRCm39 using 'dynast align' with specific parameters in paired-end mode (i.e., "-x 10xv3"). Spatial spots were filtered using a barcode whitelist file generated from 'Space Ranger' to retain high-quality spots for downstream analyses. The second step involved constructing a consensus sequence for each transcript using 'dynast consensus,' pooling reads with the same UMI index and identifying the most frequent variant at each position. Finally, 'dynast count' was employed to quantify the levels of unspliced, spliced, newly-synthesized, and total RNA for each spatial spot.
Assembly: GRCm39
Supplementary files format and content: h5ad files: they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our sptial NT-seq experiment.
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_positions.csv.gz files: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: tissue_hires_image.png.gz files: hi-resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz files: low-resolution image of tissue
Library strategy: spatial NT-Seq

molecule: total RNA

source_name: Brain

growth_protocol: Experiments were conducted in accordance with the ethical guidelines of the National Institutes of Health and with the approval of the Institutional Animal Care and Use Committee of the University of Pennsylvania. Mice were group-housed in cages of three to five in a 12-hr light/dark cycle with food and water provided ad libitum.

extract_protocol:
The mice were labeled with 4-thiouridine (4sU) for 3 hours (adult mice in ECS experiments) or 4 hours (P7 pups), then whole brains were dissected and embedded in Optimal Cutting Temperature (OCT) Compound for spatial NT-seq analysis.
Most steps of spatial NT-seq library preparation were performed following the Visium user guide (10xGenomics, CG000239 Rev D), but adding an optimized in situ SLAM reaction before the “Tissue Permeabilization” step, replacing the original “Reverse Transcription Master Mix” with scNT-seq RT mix (with Maxima H Minuse Reverse Transcriptase, See below for details), and replacing the original “Second Strand Synthesis” reaction mixture with the optimized Bst 3.0 & random primer-based reaction mixture.
Spatial Transcriptomics (Spatial NT-seq)

treatment_protocol: Before the stimulation, both ECS-treated and control mice were subjected to a 3-hour labeling with intraperitoneal injections of 4-thiouridine (4sU) solution as described (1.2 mg 4sU per gram of body weight). For electroconvulsive stimulation, 8-week-old C57BL/6J male mice were administered with 1.0 s stimuli (total duration) consisting of 100-Hz, 18-mA, 0.3-ms pulses delivered usingwith an Ugo Basile ECT unit (Ugo Basile, Collegeville, model 57800) as previously described (Su et al., 2017). Control mice were similarly handled in parallel without the electrical current delivery.

value: Brain

tag: tissue region

value: Coronal Brain section

tag: age

tag: strain

tag: treatment

value: The mice were labeled with 4-thiouridine (4sU) for 3hr. Electroconvulsive stimulation at 30min before the mice were euthanized.


title: Spatial NT-seq of ECT30min-B2-SLAM


title: Patient P020 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P020_CRANI1_CSF_EPIC


title: Spatial NT-seq of ECT30min-B1-SLAM

description: Mouse-3: ECS-30min, with in situ chemical conversion


title: Patient P014 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P014_CRANI1_CSF_EPIC


title: Patient P019 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P019_CRANI1_CSF_EPIC


title: Spatial NT-seq of ECT30min-B1Slide2-SLAM


title: Patient P012 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P012_CRANI1_CSF_EPIC


title: Spatial NT-seq of ECT2hr-B2-SLAM

description: Mouse-6: ECS-120min, with in situ chemical conversion

value: The mice were labeled with 4-thiouridine (4sU) for 3hr. Electroconvulsive stimulation at 2 hours before the mice were euthanized.


title: Patient P011 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P011_CRANI1_CSF_EPIC


title: Patient P010 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P010_CRANI1_CSF_EPIC


title: Patient P009 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P009_CRANI1_CSF_EPIC


title: Spatial NT-seq of ECT2hr-B2Slide2-SLAM


title: Spatial NT-seq of ECT2hr-B1-SLAM

description: Mouse-5: ECS-120min, with in situ chemical conversion


title: Spatial NT-seq of ECT2hr-B1Slide2-SLAM


title: Patient P008 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P008_CRANI1_CSF_EPIC


title: Patient P007 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P007_CRANI1_CSF_EPIC


title: Patient P006 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P006_CRANI1_CSF_EPIC


title: Spatial NT-seq of Ctrl-B2-SLAM

description: Mouse-2: No ECS, with in situ chemical conversion

value: The mice were labeled with 4-thiouridine (4sU) for 4hr


title: Spatial NT-seq of Ctrl-B2Slide2-NTC

description: Mouse-2: No ECS, without in situ chemical conversion


title: Patient P004 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy 2 of 2

description: Library name: P004_CRANI2_CSF_EPIC


title: Spatial NT-seq of Ctrl-B2Slide2-SLAM


title: Spatial NT-seq of Ctrl-B2-NTC


title: Patient P002 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P002_CRANI1_CSF_EPIC


title: Patient P001 CSF cfDNA PredicineEPIC methylation sequencing at craniotomy

description: Library name: P001_CRANI1_CSF_EPIC


title: Patient P100 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P100_CRANI1_TUMOR_EPIC

source_name: Human brain metastasis tissue

value: Human brain metastasis tissue


title: Spatial NT-seq of Ctrl-B1Slide2-SLAM

description: Mouse-1: No ECS, with in situ chemical conversion


title: Patient P099 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P099_CRANI1_TUMOR_EPIC


title: Patient P098 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P098_CRANI1_TUMOR_EPIC


title: Spatial NT-seq of Ctrl-B1-SLAM


title: Spatial NT-seq of Ctrl-B1-NTC

description: Mouse-1: No ECS, without in situ chemical conversion


title: Patient P097 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P097_CRANI1_TUMOR_EPIC


title: Spatial NT-seq of Ctrl-B1Slide2-NTC


title: Spatial NT-seq of P7 mouse brain-4 (Control, no SLAM)

description: Four coronal mouse brain sections from a 4sU-labeled wild-type mouse (P7)


title: Patient P096 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P096_CRANI1_TUMOR_EPIC


title: Spatial NT-seq of P7 mouse brain-3 (Control, no SLAM)


title: Spatial NT-seq of P7 mouse brain-2 (in situ SLAM)


title: Patient P095 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P095_CRANI1_TUMOR_EPIC


title: Spatial NT-seq of P7 mouse brain-1 (in situ SLAM)


title: Patient P094 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P094_CRANI1_TUMOR_EPIC


title: Patient P093 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P093_CRANI1_TUMOR_EPIC


title: Patient P092 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P092_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-KD 5-Ph-IAA 12h ESCs Replicate 2, Hi-C

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

data_processing:
Read pairs were individually mapped to the mouse genome (mm9) using the 4dn-hic pipeline (https://github.com/4dn-dcic/docker-4dn-hic). After read mapping, After mapping, the aligned reads were further processed to remove duplicates (https://github.com/mirnylab/pairtools) and obtain a set of filtered reads defined as valid pairs.
Valid pairs were binned into contact matrices at resolutions of 200 kb and then normalized using the cooler (Abdennur and Mirny, 2020). The bias-corrected contact heatmaps were used to generate the A/B compartment profiles (200-kb bins) in each chromosome and saddle plots using cooltools (https://github.com/open2c/cooltools).
Assembly: mm9
Supplementary files format and content: .cool
Supplementary files format and content: bigWig

growth_protocol: C57BL/6N mESCs were grown in serum free medium NDiff 227 (Cellartis, Y40002), 1 μM PD0325901 (Wako, 162-25291) and 3 μM CHIR99021 (Wako, 034-23103), 0.1 mM 2-mercaptoethanol and 1000 U/ml mLIF on iMatrix-511 (Matrixome, 892012) coated dishes.

extract_protocol:
Hi-C experiments were performed as previously reported with some modifications (Kadota et al., 2020). Cells were fixed with 1% formaldehyde for 10 min at room temperature. Glycine was added to 0.125 M final concentration and incubated for 5 min at room temperature. Tubes were placed on ice for 15 min. Cells were washed in ice-cold PBS by centrifuging at 400 g at 4°C. Then, 1–2 x 10^6 fixed cell pellets were used for the following steps. Cell pellets were resuspended in 400 µl of lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40) with 1x protease inhibitor cocktail (Roche, 11873580001), transferred to 1.5 ml Protein LoBind Tubes (Eppendorf) and incubated on ice for 20 min. The samples were spun down for 5 min at 1000 g at 4℃. After removing the supernatants carefully, pellets were resuspended in 250 µl of 1x NEBuffer 2 with 0.3% SDS and incubated for 1 h at 37°C in the Thermomixer C3 at 1100 rpm (Eppendorf). Then, 28 µl of 20% Triton X-100 were added to 2% final concentration and the samples were incubated for 1 h at 37°C. Next, 100 U of DpnIII (NEB, R0543S) was added and the samples were incubated overnight at 37°C in the Thermomixer C3 at 1100 rpm. The next day, after the inactivation of enzyme activity with 65˚C for 20 min, the samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 100 µl of “Biotin fill-in mix” (1 x NEBuffer 2, 15 µM each of dCTP, dGTP, dTTP and 15 µM of Biotin-14-dATP (Invitrogen, 19524-016), 15 U of Klenow (NEB, M0210S), 1% Triton X-100) and incubated for 45 min at 25°C. After spinning down for 5 min at 4°C and removing the supernatants carefully, the pellets were resuspended in 100 µl of “Ligation Mix” (1x T4 DNA ligase buffer (NEB), 6 µl of T4 DNA ligase (1 U/µl, Invitrogen, 15224-025), 1% Triton X-100) and incubated 6 hours at 16°C. The sample volumes were brought up to ~100 µl by adding 10 mM Tris-HCl (pH 8.0) / 5 mM EDTA and RNaseA-treated for 30 min at 37°C by adding 5 µl of 10 mg/ml RNaseA. Reverse-crosslinking and proteinase K treatment were performed overnight at 65°C by adding "Reverse-crosslink Mix" (1.5% SDS, 375 mM NaCl, 1 mg/ml Proteinase K). The next day, 5 µl of 20 mg/ml Proteinase K was added and incubated for 2 h at 55°C. Samples were then extracted twice with phenol/chloroform and once with chloroform. After this, 500 µl of 2-propanol was added. The samples were incubated for 10 min and spun down for 30 min at 20,000 g at 4°C for DNA precipitation. After 70% EtOH washes (add 1 ml, cfg for 5 min at 20,000 g at 4°C), the DNA pellets were resuspended in 30 µl of EB (QIAGEN, 19086).
For generating next-generation sequencing libraries, 1-2 µg of Hi-C DNA was used per library. To remove biotin from unligated ends, Hi-C DNA was mixed with 50 µl of “T4 DNA pol mix” (1x NEBuffer 2.1, 100 µM dATP, 100 µM dGTP, 2.5 U of T4 DNA polymerase (NEB, M0203S)) and incubated for 30 min at 37°C. The sample volumes were brought up to ~130 µl by adding TE buffer. DNA samples were sheared (300–500 bp) using the following settings in Covaris S220 (Duty Factor: 5.0, Peak incident power: 175 W, Cycles per burst: 200, Treatment time: 120 sec) using microTUBE with snap cap (Covaris, 520045). After DNA shearing, DNA size selection was performed using AMPure XP beads (Beckman Coulter). Using the size-selected DNA samples, biotin pull-down and sequencing library preparations were performed using 30 µl of Dynabeads M-280 Streptavidin (Invitrogen, 11206D) and a part of KAPA LTP kit (KAPA BIOSYSTEMS, KK8232) following the kit’s protocol. For library amplification, KAPA Real-Time Amplification Kits (KAPA BIOSYSTEMS, KK2701) were used to determine the optimal PCR cycles (5–8 cycles) and the final PCR products were purified by AMPure XP beads.

treatment_protocol: (1) Nocodazole treatment: nocodazole was added to the culture medium at a final concentration of 1 µM for 7-10 hours, then G2/M cell population was sorted by cell sorter based on the relative levels of Propidium iodide. (2) Thymidine treatment: after nocodazole treatment, cells were released to G1 phase with thymidine at a final concentration of 2.5 mM for certain time, then G1 population was sorted. (3) 5-Ph-IAA treatment: after nocodazole treatment, cells were released to G1 phase with 5-Ph-IAA at a final concentration of 1 µM for certain time, then G1 population was sorted.

tag: cell line

value: embryonic stem cells

tag: genetic modification

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: 5-Ph-IAA treatment 12h, G1 sort


title: scNT-seq of P12UPRT-Ctx with DMSO injections (negative control for 4tU injections)

description: Drop-seq / scNT-seq

data_processing:
The preprocessing (read alignment, quality filtering and generation of count matrices) of scNT-seq2 datasets was performed using Dynast (v1.0.1; https://github.com/aristoteleo/dynast-release) with platform-specific modifications. Analysis of each scNT-seq2 dataset followed a three-step ‘Dynast’ pipeline: 'dynast align', 'dynast consensus', and 'dynast count'. In the initial step, raw sequencing reads were mapped to the mouse genome GRCm39 using 'dynast align' with specific parameters in paired-end mode (i.e., "--strand forward -x dropseq"). Cells were filtered with the parameter “-soloCellFilter TopCells” from 'STARsolo' to only retain high quality cells (generating a cell-barcode white list) for all downstream analyses. The second step involved constructing a consensus sequence for each transcript using 'dynast consensus' pooling reads with the same UMI index and taking the most frequent variant at each position. Finally, 'dynast count' was employed to quantify the levels of unspliced, spliced, newly-synthesized, and total RNA for each spatial spot.
Assembly: GRCm39
Supplementary files format and content: h5ad.gz files: they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scNT-seq experiments.
Library strategy: scNT-seq

source_name: Cortex

extract_protocol:
For embryonic cortex samples (E16.5), brain dissection was performed in cold DPBS solution under microscope. Tissue samples were kept in cold buffers and on ice at all times. Cerebral cortex from two embryos were pooled and resuspended in 0.5 mL DPBS+0.01% BSA supplemented with transcription inhibitor (30 μM Actinomycin D (Sigma, A9415)). Tissue was then dissociated by pipetting (about 20 times with P1000 tip, then two times with P200 on top of P1000 tip) and filtering through a 40 μm cell strainer. Cells were pelleted at 300 g, 5 min, and resuspended in 0.5 mL DPBS+ 0.01% BSA (without transcription inhibitor). After counting the cell with Countess II system, the cells were split to two 1.5 mL LoBind tubes (Eppendorf) and fixed with 80% methanol. For cortex samples from P7-P12, mice were sacrificed by cervical dislocation and cortical dissected was performed on ice-cold platform. Tissue samples were cut to small pieces with blade and kept in cold DPBS+0.01% BSA supplemented with transcription inhibitor (30 μM ActD) until all samples were collected. The pieces were dissociated using the Worthington Papain kit, with 30-60 min enzymatic digestion, following the user guide with minor changes. Specifically, transcription inhibitor (15 μM ActD) was supplemented in the Papain-DNase-EBSS digestion solution and the albumin-ovomucoid inhibitor solution (density gradient). Cells were pelleted at 100 g, 6 min, and resuspended in 0.5 mL DPBS+ 0.01% BSA (without transcription inhibitor). After counting the cell with Countess II system, the cells were split to two 1.5 mL LoBind tubes (Eppendorf) and fixed with 80% methanol. For P7 heart samples, whole heart was dissected and kept in cold HBSS buffer until all samples were collected. The tissue was cut to small pieces with scissors and enzymatically dissociated using Pierce Primary Cardiomyocyte Isolation Kit (Thermo Scientific, cat# 88281), with 30 min enzymatic digestion, following the user guide. Cells were resuspended in 0.5 mL DPBS+ 0.01% BSA and filtering filtered through a 100 μm cell strainer before being fixed with 80% methanol. For P7 kidney samples, the kidney was dissected and kept in cold HBSS buffer until all samples were collected. The tissue was minced to small pieces with blade and digested with 1 mL Liberase TM mixture (0.2 mg/ml CaCl2, 5 μM MgCl2, 0.1% BSA, and 0.1 mg/ml Liberase TM in HBSS) for 30 min at 37 °C . After digestion, the enzyme solution was removed and the tissue was washed once with 0.5 mL DPBS+ 0.01% BSA buffer, then resuspended in 0.5 mL complete DMEM (DMEM+15%FBS). The samples were further dissociated by pipetting up and down with P1000 and filtering through a 100 μm cell strainer, then red blood cells were removed with ACK lysing buffer (Quality Biological Inc., cat# 118-156-101) following the user guide. Cells were pelleted at 300 g, 5 min, and resuspended in 1 mL DPBS+ 0.01% BSA before filtering through a 40 μm cell strainer. After counting the cell with Countess II system, the cells were split to two 1.5 mL LoBind tubes (Eppendorf) and fixed with 80% methanol.
Drop-seq was performed as previously described, with default settings. Specifically, the single cell suspension was diluted to a concentration of 100 cells/μL in DPBS containing 0.01% BSA. Approximately 1.5 mL of diluted single cell suspension was loaded for each scNT-Seq run. The single-nucleus suspension was then co-encapsulated with barcoded beads (ChemGenes) using an Aquapel-coated PDMS microfluidic device (uFluidix) connected to syringe pumps (KD Scientific) via polyethylene tubing with an inner diameter of 0.38 mm (Scientific Commodities). Barcoded beads were resuspended in lysis buffer (200 mM Tris-HCl pH8.0, 20 mM EDTA, 6% Ficoll PM-400 (GE Healthcare/Fisher Scientific), 0.2% Sarkosyl (Sigma-Aldrich), and 50 mM DTT (Fermentas; freshly made on the day of run) at a concentration of 120 beads/μL. The flow rates for cells and beads were set to 3,200 μL/hour, while QX200 droplet generation oil (Bio-rad) was run at 12,500 μL/hour. Droplet breakage with Perfluoro-1-octanol (Sigma-Aldrich). After droplet breakage, the beads were treated with TimeLapse chemistry to convert 4sU to cytidine-analog5. Briefly, 50,000-100,000 beads were washed once with 450 μL washing buffer (1 mM EDTA, 100 mM sodium acetate (pH 5.2)), then the beads were resuspended with a mixture of TFEA (600 mM), EDTA (1 mM) and sodium acetate (pH 5.2, 100 mM) in water. A solution of 192 mM NaIO4 was then added (final concentration: 10 mM) and incubated at 45°C for 1 hr with rotation. The beads were washed once with 1 mL TE, then incubated in 0.5 mL 1 X Reducing Buffer (10 mM DTT, 100 mM NaCl, 10 mM Tris pH 7.4, 1 mM EDTA) at 37°C for 30 min with rotation, followed by washing once with 0.3 mL 2X RT-buffer. Reverse transcription and exonuclease I treatment were performed, as previously described, with minor modifications 4. Specifically, up to 120,000 beads, 200 μL of reverse transcription (RT) mix (1x Maxima RT buffer (ThermoFisher), 4% Ficoll PM-400, 1 mM dNTPs (Clontech), 1 U/μL RNase inhibitor, 2.5 μM Template Switch Oligo (TSO: AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG ) 4, and 10 U/ μL Maxima H Minus Reverse Transcriptase (ThermoFisher)) were added. The RT reaction was incubated at room temperature for 30 minutes, followed by incubation at 42°C for 120 minutes.  After exonuclease I treatment, an optimized second strand synthesis reaction was applied to improve library complexity. Specifically, pooled beads were washed once with TE-SDS buffer and twice with TE-TW buffer to remove the exonuclease I reaction mixture. The beads were resuspended in 500 μl of 0.1 M NaOH and incubated for 5 min at room temperature with rotation, and 500 μl of 0.2 M Tris-HCl (pH 7.5) was then added to neutralize the solution. The beads were washed once with TE-TW buffer and once with 10 mM Tris-HCl (pH 8.0). For the 2nd SS reactionTo synthesize 2nd strand cDNA, the beads were resuspended in 200 μl of Bst3-based reaction mixture (1× Isothermal Amplification Buffer II (NEB), 6 mM MgSO4, 4% Ficoll PM-400, 1.4 mM dNTPs (Clontech), 10 μM Template Switch Oligo-random primer (TSO-N3G2N4B: AAGCAGTGGTATCAACGCAGAGTGA (N1:25252525)(N1)(N1)GG(N1)(N1)(N1)(N1)(N2: 00333433); N1 represents a mixture of A, T, C and G at a 25:25:25:25 ratio, N2 represents a mixture of A, T, C and G at a 0:33:34:33 ratio), and 0.4 U/μl Bst 3.0 DNA polymerase (NEB, M0374)). The reaction was incubated on ice for 2 min for primer annealing, followed by incubation at 60 °C for 15 min with rotation. The reaction was stopped by washing the beads once with TE-SDS buffer and twice with TE-TW buffer.  The downstream steps (cDNA amplification, Tn5-based tagmentation, and indexing PCR) were performed as previously described. To determine an optimal number of PCR cycles for amplification of cDNA, an aliquot of 6,000 beads (corresponding to ~100 nuclei) was amplified by PCR in a volume of 50 μL (25 μL of 2x KAPA HiFi hotstart readymix (KAPA biosystems), 0.4 μL of 100 μM TSO-PCR primer (AAGCAGTGGTATCAACGCAGAGT 4, 24.6 μL of nuclease-free water) with the following thermal cycling parameter (95°C for 3 min; 4 cycles of 98°C for 20 sec, 65°C for 45 sec, 72°C for 3 min; 9 cycles of 98°C for 20 sec, 67°C for 45 sec, 72°C for 3 min; 72°C for 5 min, hold at 4°C). After two rounds of purification with 0.6x SPRISelect beads (Beckman Coulter), amplified cDNA was eluted with 10 μL of water. 10% of amplified cDNA was used to perform real-time PCR analysis (1 μL of purified cDNA, 0.2 μL of 25 μM TSO-PCR primer, 5 μL of 2x KAPA FAST qPCR readymix, and 3.8 μL of water) to determine the additional number of PCR cycles needed for optimal cDNA amplification (Applied Biosystems QuantStudio 7 Flex). We then prepared PCR reactions per total number of barcoded beads collected for each sNucDrop-Seq run, adding 6,000 beads per PCR tube, and ran the aforementioned program to enrich the cDNA for 4 + 10 to 12 cycles. We then tagmented cDNA using the Nextera XT DNA sample preparation kit (Illumina, cat# FC-131-1096), starting with 550 pg of cDNA pooled in equal amounts, from all PCR reactions for a given run. Following cDNA tagmentation, we further amplified the library with 12 enrichment cycles using the Illumina Nextera XT i7 primers along with the P5-TSO hybrid primer (AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C).
scRNA-seq (scNT-seq)

treatment_protocol: Mice were injected intraperitoneally with 4sU solution or saline solution (negative control).

value: Cortex

value: Primary cells from the tissue

value: Postnatal day 12

value: Mice were injected with DMSO&Corn oil solution


title: scNT-seq of P12UPRT-Ctx with Saline injections (negative control for 4sU injections)

description: Drop-seq / scNT-seq

value: Mice were injected with saline


title: scNT-seq of P12UPRT-Ctx with 4sU injections

description: Drop-seq / scNT-seq

value: Mice were labeled 4 hours with 0.8 mg 4sU per gram of body weight (i.p. injections)


title: Patient P091 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P091_CRANI1_TUMOR_EPIC

value: Non-small cell lung carcinoma


title: Gins4-mAID G1-KD 5-Ph-IAA 12h ESCs Replicate 1, Hi-C


title: scNT-seq of P7Ctx-50mg

description: Drop-seq / scNT-seq

value: Postnatal day 7

value: Mice were labeled 4 hours with 0.4 mg 4sU per gram of body weight (i.p. injections)


title: scNT-seq of P7Ctx-100mg

description: Drop-seq / scNT-seq


title: Patient P090 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P090_CRANI1_TUMOR_EPIC


title: scNT-seq of P12UPRT-Ctx with 4tU injections

description: Drop-seq / scNT-seq

value: Mice were labeled 4 hours with 0.4 mg 4tU per gram of body weight (i.p. injections)


title: Gins4-mAID Asy G1-sorted ESCs Replicate 1, Hi-C

description: Library name: Sample234

data_processing:
Read pairs were individually mapped to the mouse genome (mm9) using the 4dn-hic pipeline (https://github.com/4dn-dcic/docker-4dn-hic). After mapping, the aligned reads were further processed to remove duplicates (https://github.com/mirnylab/pairtools) and obtain a set of filtered reads defined as valid pairs.
Valid pairs were binned into contact matrices at resolutions of 200 kb and then normalized using the cooler (Abdennur and Mirny, 2020). The bias-corrected contact heatmaps were used to generate the A/B compartment profiles (200-kb bins) in each chromosome and saddle plots using cooltools (https://github.com/open2c/cooltools).
Assembly: mm9
Supplementary files format and content: .cool
Supplementary files format and content: bigWig

extract_protocol:
Hi-C experiments were performed as previously reported with some modifications (Kadota et al., 2020). Cells were fixed with 1% formaldehyde for 10 min at room temperature. Glycine was added to 0.125 M final concentration and incubated for 5 min at room temperature. Tubes were placed on ice for 15 min. Cells were washed in ice-cold PBS by centrifuging at 400 g at 4°C. Then, 1–2 x 10^6 fixed cell pellets were used for the following steps. Cell pellets were resuspended in 400 µl of lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40) with 1x protease inhibitor cocktail (Roche, 11873580001), transferred to 1.5 ml Protein LoBind Tubes (Eppendorf) and incubated on ice for 20 min. The samples were spun down for 5 min at 1000 g at 4℃. After removing the supernatants carefully, pellets were resuspended in 250 µl of 1x NEBuffer 2 with 0.3% SDS and incubated for 1 h at 37°C in the Thermomixer C3 at 1100 rpm (Eppendorf). Then, 28 µl of 20% Triton X-100 were added to 2% final concentration and the samples were incubated for 1 h at 37°C. Next, 100 U of DpnIII (NEB, R0543S) was added and the samples were incubated overnight at 37°C in the Thermomixer C3 at 1100 rpm. The next day, after the inactivation of enzyme activity with 65˚C for 20 min, the samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 100 µl of “Biotin fill-in mix” (1 x NEBuffer 2, 15 µM each of dCTP, dGTP, dTTP and 15 µM of Biotin-14-dATP (Invitrogen, 19524-016), 15 U of Klenow (NEB, M0210S), 1% Triton X-100) and incubated for 45 min at 25°C. After spinning down for 5 min at 4°C and removing the supernatants carefully, the pellets were resuspended in 100 µl of “Ligation Mix” (1x T4 DNA ligase buffer (NEB), 6 µl of T4 DNA ligase (1 U/µl, Invitrogen, 15224-025), 1% Triton X-100) and incubated 6 hours at 16°C. The sample volumes were brought up to ~100 µl by adding 10 mM Tris-HCl (pH 8.0) / 5 mM EDTA and RNaseA-treated for 30 min at 37°C by adding 5 µl of 10 mg/ml RNaseA. Reverse-crosslinking and proteinase K treatment were performed overnight at 65°C by adding ""Reverse-crosslink Mix"" (1.5% SDS, 375 mM NaCl, 1 mg/ml Proteinase K). The next day, 5 µl of 20 mg/ml Proteinase K was added and incubated for 2 h at 55°C. Samples were then extracted twice with phenol/chloroform and once with chloroform. After this, 500 µl of 2-propanol was added. The samples were incubated for 10 min and spun down for 30 min at 20,000 g at 4°C for DNA precipitation. After 70% EtOH washes (add 1 ml, cfg for 5 min at 20,000 g at 4°C), the DNA pellets were resuspended in 30 µl of EB (QIAGEN, 19086).
For generating next-generation sequencing libraries, 1-2 µg of Hi-C DNA was used per library. To remove biotin from unligated ends, Hi-C DNA was mixed with 50 µl of “T4 DNA pol mix” (1x NEBuffer 2.1, 100 µM dATP, 100 µM dGTP, 2.5 U of T4 DNA polymerase (NEB, M0203S)) and incubated for 30 min at 37°C. The sample volumes were brought up to ~130 µl by adding TE buffer. DNA samples were sheared (300–500 bp) using the following settings in Covaris S220 (Duty Factor: 5.0, Peak incident power: 175 W, Cycles per burst: 200, Treatment time: 120 sec) using microTUBE with snap cap (Covaris, 520045). After DNA shearing, DNA size selection was performed using AMPure XP beads (Beckman Coulter). Using the size-selected DNA samples, biotin pull-down and sequencing library preparations were performed using 30 µl of Dynabeads M-280 Streptavidin (Invitrogen, 11206D) and a part of KAPA LTP kit (KAPA BIOSYSTEMS, KK8232) following the kit’s protocol. For library amplification, KAPA Real-Time Amplification Kits (KAPA BIOSYSTEMS, KK2701) were used to determine the optimal PCR cycles (5–8 cycles) and the final PCR products were purified by AMPure XP beads.

treatment_protocol: (1) Nocodazole treatment: nocodazole was added to the culture medium at a final concentration of 50 ng/ml for 7-10 hours, then G2/M cell population was sorted by cell sorter based on the relative levels of Propidium iodide. (2) Thymidine treatment: after nocodazole treatment, cells were released to G1 phase with thymidine at a final concentration of 2.5 mM for certain time, then G1 population was sorted. (3) 5-Ph-IAA treatment: after nocodazole treatment, cells were released to G1 phase with 5-Ph-IAA at a final concentration of 1 µM for certain time, then G1 population was sorted. (4) INK-128 treatment: INK-128 (MedChemExpress, HY-13328) was added to the culture medium at a final concentration of 1 µM for more than 50 hours, then G1 cell population was sorted. (5) 5-Ph-IAA removed: after nocodazole treatment, cells were released into G1 phase with 5-Ph-IAA at a final concentration of 1 µM for 15 hours. The medium was then replaced with normal culture medium after washing the cells twice with 1xPBS. Early S cell population was sorted after 6 hours.

value: G1 sort


title: scNT-seq of P7Ctx-Saline (Control for P7 dosage experiment)

description: Drop-seq / scNT-seq

value: Mice were injected with saliine


title: scNT-seq of P7Ctx-150mg

description: Drop-seq / scNT-seq

value: Mice were labeled 4 hours with 1.2 mg 4sU per gram of body weight (i.p. injections)


title: Gins4-mAID G1-KD 5-Ph-IAA 9h ESCs Replicate 2, Hi-C

value: 5-Ph-IAA treatment 9h, G1 sort


title: scNT-seq of P7Ctx-Saline (Control for P7 time-course experiment)

description: Drop-seq / scNT-seq


title: Patient P089 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P089_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue


title: Patient P088 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P088_CRANI1_TUMOR_EPIC


title: scNT-seq of P7Ctx-2hr (rep-2)

description: Drop-seq / scNT-seq

value: Mice were labeled 2 hours with 0.8 mg 4sU per gram of body weight (i.p. injections)


title: Gins4-mAID G1-KD 5-Ph-IAA 9h ESCs Replicate 1, Hi-C

value: embryonic stem cells

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: scNT-seq of P7Ctx-2hr (rep-1)

description: Drop-seq / scNT-seq

value: Cortex

value: Primary cells from the tissue


title: scNT-seq of P7Ctx-4hr (rep-1)

description: Drop-seq / scNT-seq


title: Patient P087 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P087_CRANI1_TUMOR_EPIC


title: scNT-seq of P7Ctx-4hr (rep-2)

description: Drop-seq / scNT-seq


title: Gins4-mAID G1-KD 5-Ph-IAA 6h ESCs Replicate 2, Hi-C

value: 5-Ph-IAA treatment 6h, G1 sort


title: scNT-seq of E16Ctx-4hr (rep-4)

description: Drop-seq / scNT-seq

value: Embryonic day 16.5

value: Pregnant females were labeled 4hours with 0.8 mg 4sU per gram of body weight (i.p. injections) before embyonic cortical tissues were collected.


title: scNT-seq of E16Ctx-Saline (negative control)

description: Drop-seq / scNT-seq

value: Pregnant females were injected with saline before embryonic cortical tissues were collected.


title: Gins4-mAID G1-KD 5-Ph-IAA 6h ESCs Replicate 1, Hi-C


title: Patient P086 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P086_CRANI1_TUMOR_EPIC

value: Non-small cell lung carcinoma


title: scNT-seq of E16Ctx-4hr (rep-3)

description: Drop-seq / scNT-seq


title: scNT-seq of E16Ctx-4hr (rep-2)

description: Drop-seq / scNT-seq


title: Gins4-mAID G1-KD 5-Ph-IAA 3h ESCs Replicate 2, Hi-C

value: 5-Ph-IAA treatment 3h, G1 sort


title: Patient P085 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P085_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-KD 5-Ph-IAA 3h ESCs Replicate 1, Hi-C


title: scNT-seq of E16Ctx-4hr (rep-1)

description: Drop-seq / scNT-seq


title: Patient P084 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P084_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-Control Thymidine 12h ESCs Replicate 2, Hi-C

value: Thymidine treatment 12h, G1 sort


title: CD103N

city: Guangzhou

first: Ren

last: Mao

address: 58 Zhongshan Road 2nd, Guangzhou

country: China

institute: The First Affiliated Hospital, Sun Yat-Sen University

description:
Library name: sample7
10× Genomics

library_source: transcriptomic single cell

data_processing:
Human mesenteric tissue single-nucleus RNA-seq data were processed using Cell Ranger software (v3.1.0; 10x Genomics). Raw sequencing reads were converted to FASTQ files, aligned to the human reference genome, and quantified to generate gene-barcode expression matrices for each sample. Low-quality barcodes and UMIs were filtered out. Reads uniquely mapped to the transcriptome and intersecting exonic regions were counted. UMI sequences were corrected for sequencing errors, and valid cell/nucleus barcodes were identified for downstream matrix generation. Cell-by-gene count matrices were generated by UMI counting and cell barcode calling. The filtered feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, are provided as processed data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Normal mesenteric adipose tissue in Crohn's disease

extract_protocol:
The samples were chopped on ice into 1-2 mm³ pieces, transferred to cryovials, snap-frozen in liquid nitrogen for 5 minutes, and then stored in an ultra-low temperature freezer and liquid nitrogen.. Then transfer the tissue from the cryovial to a Dounce homogenizer and add 500 μl of pre-chilled lysis buffer to thaw. Use a small and a tight pestle to press the tissue 15-20 times and 5-10 times, respectively, to create a homogenate. Add 700 μl of nuclear wash buffer, mix, and filter through a 70 μm cell strainer. Add 1 ml of 50% iodixanol to the filtrate, mix gently, and layer onto a gradient solution of 30% and 33% iodixanol. Centrifuge at 10,000×g for 20 minutes at 4°C. Extract the white nuclear layer at the interface, add nuclear wash buffer, mix, and centrifuge at 500×g for 8 minutes at 4°C. Transfer the supernatant, resuspend the nuclei, and repeat the wash. Filter through a 40 μm filter, centrifuge, resuspend the nuclei, and adjust the concentration to 700-1200 nuclei/μl using a microscope.
Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Libraries were generated and equenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.


title: K562_BCOR

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

description: Library name: Exp289_UMCG_ChIP_9_K562_BCOR_mAID_BCOR

data_processing:
Quality of the sequenced raw read files was evaluated using FastQC tools. Next, the reads were aligned to the hg38 reference genome using Burrows-Wheeler Aligner (BWA) with default settings. Aligned reads were further processed using SAMtools. Then the generated aligned reads were sorted, indexed and prepared in two different files containing reads that aligned to human chromosomes and a file containing reads that aligned to mouse chromosomes using SAMtools. Spike-in normalization factors were calculated per sample. Using BEDtools genomecov, the total number of overlapping fragments at each position in the genome were determined and scaled according to the spike-in normalization factor. The resulting BedGraph files were converted to BigWig files using UCSC bedGraphToBigWig. Ngs.plot was used to generate average plots of read count per reference million (RRPM) mapped reads, and heatmaps, representing a -/+ 5 Kb region around the transcription start site (TSS) or gene body. Peak calling was performed on the BAM files using MACS3. Tracks were visualized using the Integrative Genomics Viewer.The Burrows-Wheeler Aligner (BWA) was used to align these reads to the hg38 reference genome. Then the generated aligned reads were sorted, indexed and prepared in two different files containing reads that aligned to human chromosomes and a file containing reads that aligned to mouse chromosomes with SAMtools and normalization factors were calculated per file. Using BEDtools, the total number of overlapping fragments at each position in the genome were found. The resulting BedGraph files were converted to BigWig files and visualized using the Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were cross-linked using PBS including 1% formaldehyde for 10 minutes. Cross-linked samples were quenched using 125 mM glycine, followed by a PBS wash and snap freezing SDS buffer (100 mM NaCl, 0.5% SDS, 5 mM EDTA, 50 mM Tris-HCl (pH 8.0), protease inhibitors (CLAP and 0.1 mM PMSF), and 0.2% NaN3. Next, cross-linked samples were IP buffer containing: 2x SDS buffer and 1 x Triton Dilution buffer (5% Triton X-100, 5 mM EDTA, 100 mM Tris-HCl (pH 8.6), 100 mM NaCl, 0.2% NaN3, 1 x CLAP, 0.1 mM PMSF). Sonication was performed using a Bioruptor (Diagenode) or PIXUL® Multi-Sample Sonicator (Active Motif). Then, the samples were precleared using 1 mg pre-equilibrated Dynabeads Protein G (Invitrogen) for 20 minutes and subsequently ChIP reactions were conducted in 1 ml IP buffer and incubated overnight at 4 °C with 5% mouse spike-in control chromatin and 2 µg of either of the following antibodies: anti-GFP (ab290, Abcam), IgG (I8141, Sigma), anti-KDM2B (09-846, Merck), anti-H2AK119ub (D27C4, Cell Signaling Technology), anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (C15410196, Diagenode), anti-H3K27me3 (C15410069, Diagenode) and anti-H3K36me3 (C15410192, Diagenode). Next, ChIP reactions were incubated for 3h with 25 ml pre-equilibrated Dynabeads Protein G (invitrogen) at 4°C and subsequently washed with Mixed Micelle Wash buffer (150 mM NaCl, 20 mM Tris-HCl (pH 8.1), 5 mM EDTA, 5.2% sucrose, 1% Triton X-100, 0.2% SDS, 0.2% NaN3, 3 washes), buffer 500 (50 mM Hepes-KOH (pH 7.5), 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% NaN3; 2 washes), LiCl Wash buffer (250 mM LiCl, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.2% NaN3; 2 washes) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA; 1 wash). Finally, chromatin was eluted from the beads using Elution Buffer (0.1 M NaHCO3, 0.1% SDS) and reverse cross-linked overnight at 65 degrees. Finally, 2 ml RNase A (10mg/ml; ThermoFisher) was added and samples were incubated for 2 hours at 37 degrees followed by addition of 2 ml Proteinase K (20mg/ml; ThermoFisher) and incubation for 2 hours at 55 degrees. Finally, the DNA was extracted using a PCR purification kit (Qiagen). The purified DNA samples were analyzed by sequencing.
ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Roche Sequencing and Life Sciences) following the manufacturer’s instructions. The resulting DNA fragment libraries were subjected to a sequencing on an Illumina NextSeq500 and generated the paired-end reads FASTQ files, using the manufacturer’s instructions.

tag: chip antibody

value: anti-BCOR (12107-1-AP, Proteintech)

value: Untreated


title: K562_BCOR_8h5phIAA_H3K4me3_2

description: Library name: 48248_Exp289_UMCG_ChIP_29_4D_Z12

value: anti-H3K4me3 (C15410003, Diagenode)


title: K562_BCOR_8h5phIAA_H3K4me3_1

description: Library name: 48243_Exp289_UMCG_ChIP_24_3D_Z46


title: Patient P083 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P083_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-Control Thymidine 12h ESCs Replicate 1, Hi-C


title: WiDr GSK715 RNA-seq replicate 3

city: Nanjing

first: Mu

last: Xu

address: No.32, Gongqingtuan Road,

department: Nanjing First Hospital

institute: Nanjing Medical University

description:
Library name: WiDr_GSK715_3
Total RNA from WiDr cells treated with 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h was subjected to poly(A)-enriched library construction and paired-end sequencing. Processed data file(s): widr_gene_count_matrix.tsv.gz.

data_processing:
Short-read RNA-seq: Adapters and low-quality reads were removed with Cutadapt. Clean reads were aligned to GRCh38 using HISAT2, and transcript abundance was quantified as FPKM using StringTie. Differential expression analysis was performed with DESeq2 (adjusted P < 0.05, |log2FC| >= 1).
ONT full-length cDNA sequencing: Raw pod5/fast5 signals were base-called with Dorado (--no-trim) to generate FASTQ reads. Reads passing the basecalling quality filter (Q >= 10) were retained as clean reads. Full-length cDNA reads were identified, oriented and trimmed using Pychopper (-Q 7 -z 50), followed by additional filtering with NanoFilt (-q 7 -l 50). Filtered full-length reads were aligned to GRCh38 using minimap2 (-ax splice -uf -k14). Consensus transcript sets were constructed using Pinfish, and transcript reconstruction and merging were performed with StringTie. Transcript abundance was quantified as TPM using Salmon. Differentially expressed transcripts and genes were identified using DESeq2 (P < 0.05 and |log2FoldChange| > 2). Poly(A) sites were identified, clustered and annotated using QuantifyPoly(A) to analyze 3'-end heterogeneity.
Processed matrices prepared for GEO: hct116_gene_count_matrix.tsv.gz; widr_gene_count_matrix.tsv.gz; ont_widr_gene_counts_matrix.tsv.gz; ont_widr_full_length_stats.tsv.gz.
Assembly: GRCh38
Supplementary files format and content: hct116_gene_count_matrix.tsv.gz and widr_gene_count_matrix.tsv.gz are gzip-compressed tab-delimited gene-level count matrices for short-read RNA-seq samples.
Supplementary files format and content: ont_widr_gene_counts_matrix.tsv.gz is a gzip-compressed tab-delimited gene-level count matrix for ONT full-length cDNA sequencing samples; ont_widr_full_length_stats.tsv.gz contains full-length read summary statistics.

source_name: colon

growth_protocol: HCT116 and WiDr cells were cultured under standard mammalian cell culture conditions before treatment.

extract_protocol:
Total RNA was extracted from treated cells and assessed for quality before library construction.
Total RNA from WiDr and HCT-116 cells treated with DMSO, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor) for 96 h was subjected to poly(A)-enriched library construction by Lianchuan Biotechnology (Hangzhou) and paired-end sequencing on an Illumina NovaSeq 6000. WiDr cells treated with DMSO or 5 uM GSK715 (GSK3368715, PRMT1 inhibitor) for 96 h were subjected to Oxford Nanopore Technologies (ONT) full-length cDNA sequencing on a PromethION platform by Benagen (Wuhan).

treatment_protocol: Cells were treated for 96 h with DMSO vehicle control, 5 uM GSK715 (GSK3368715, PRMT1 inhibitor), or 10 uM GSK025 (GSK3235025, PRMT5 inhibitor), as applicable.

value: colon

value: WiDr

value: colorectal carcinoma cell line

tag: batch

value: short-read RNA-seq


title: K562_BCOR_8hDMSO_H3K4me3_2

description: Library name: 48238_Exp289_UMCG_ChIP_19_2D_Z38

value: DMSO


title: Patient P082 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P082_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue


title: Gins4-mAID G1-Control Thymidine 9h ESCs Replicate 2, Hi-C

value: embryonic stem cells

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: Thymidine treatment 9h, G1 sort


title: K562_BCOR_8hDMSO_H3K4me3_1

description: Library name: 48233_Exp289_UMCG_ChIP_14_1D_Z33


title: Patient P081 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P081_CRANI1_TUMOR_EPIC


title: K562_BCOR_8h5phIAA_H3K27ac_1

description: Library name: 48242_Exp289_UMCG_ChIP_23_3C_Z45

value: anti-H3K27ac (C15410196, Diagenode)


title: K562_BCOR_8h5phIAA_H3K27ac_2

description: Library name: 48247_Exp289_UMCG_ChIP_28_4C_Z11


title: Patient P080 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P080_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-Control Thymidine 9h ESCs Replicate 1, Hi-C


title: K562_BCOR_8hDMSO_H3K27ac_2

description: Library name: 48237_Exp289_UMCG_ChIP_18_2C_Z37


title: K562_BCOR_8hDMSO_H3K27ac_1

description: Library name: 48232_Exp289_UMCG_ChIP_13_1C_Z32


title: Gins4-mAID G1-Control Thymidine 6h ESCs Replicate 2, Hi-C

value: Thymidine treatment 6h, G1 sort


title: K562_BCOR_8h5phIAA_H3K27me3_2

description: Library name: 48246_Exp289_UMCG_ChIP_27_4B_Z10

value: anti-H3K27me3 (C15410069, Diagenode)


title: Patient P079 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P079_CRANI1_TUMOR_EPIC

value: Non-small cell lung carcinoma


title: Gins4-mAID G1-Control Thymidine 6h ESCs Replicate 1, Hi-C


title: K562_BCOR_8h5phIAA_H3K27me3_1

description: Library name: 48241_Exp289_UMCG_ChIP_22_3B_Z44


title: K562_BCOR_8hDMSO_H3K27me3_2

description: Library name: 48236_Exp289_UMCG_ChIP_17_2B_Z36


title: Patient P078 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P078_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-Control Thymidine 3h ESCs Replicate 2, Hi-C

value: Thymidine treatment 3h, G1 sort


title: K562_BCOR_8hDMSO_H3K27me3_1

description: Library name: 48231_Exp289_UMCG_ChIP_12_1B_Z31


title: K562_BCOR_8h5phIAA_H2AK119ub_1

description: Library name: 48240_Exp289_UMCG_ChIP_21_3A_Z43

value: anti-H2AK119ub (D27C4, Cell Signaling Technology


title: Gins4-mAID G1-Control Thymidine 3h ESCs Replicate 1, Hi-C


title: K562_BCOR_8h5phIAA_H2AK119ub_2

description: Library name: 48245_Exp289_UMCG_ChIP_26_4A_Z48


title: K562_BCOR_8hDMSO_H2AK119ub_2

description: Library name: 48235_Exp289_UMCG_ChIP_16_2A_Z35


title: Patient P076 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P076_CRANI1_TUMOR_EPIC


title: K562_BCOR_8hDMSO_H2AK119ub_1

description: Library name: 48230_Exp289_UMCG_ChIP_11_1A_Z30


title: Patient P077 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P077_CRANI1_TUMOR_EPIC


title: Gins4-mAID Metaphase Nocodazole 10h 5-Ph-IAA 4h ESCs Replicate 1, Hi-C

value: Nocodazole treatment, G2/M sort


title: GBM034_Edge

first: Allegra

middle: A

last: Petti

state: Massachusetts

address: 185 Cambridge St.

department: Department of Neurosurgery

institute: Massachusetts General Hospital

description:
Library name: GBM034_Edge_scRNA
10x Genomics single cell RNA-seq of GBM Sample GBM034_Edge

data_processing:
Downstream processing steps, including filtering, doublet removal, normalization, scaling, identification of variable genes, dimensionality reduction, clustering, and cell typing were performed using a WDL pipeline we developed for tailored analysis of GBM scRNA-seq data (https://dockstore.org/organizations/PettilabMGH).
Briefly, doublets were identified using multiple tools, including “doubletCells”,“cxds”, “bcds”, “hybrid”, “scDblFinder” and “DoubletFinder”. Cells predicted to be doublets by a majority of these were removed from the data. Next, cells were retained for further analysis if they met the following filtering criteria: mitochondrial gene percentage < 5%, nCount (UMIs/cell) < 93rd percentile, and nFeature (unique genes/cell) > 700. Data was then log-normalized, scaled, and corrected for cell cycle gene expression using functions from Seurat V4.
The optimal number of Principal components (PCs) for graph-based clustering77 and UMAP layout was determined based on the Jackstraw test and statistical significance after Bonferoni correction. Cell types were then determined using a combination of reference-based (SingleR) and marker-based (scSorter) tools. To this end, cells were first partitioned into CD45+ (immune) and CD45- (non-immune) clusters based on PTPRC expression. Immune cells were further classified by training these tools on the single-cell Brain immune atlas and the immune component of the STAB atlas (adult samples only).Non-immune cells were further classified by training these tools on a combination of published GBM data and the non-immune component of STAB. Putative tumor cells were further classified based on the cell states in Neftel et al using a marker-based prediction method called scSorter. The malignant status of putative tumor cells was further confirmed using copy number variant (CNV) predictions obtained using CONICSmat.
Assembly: GRCh38
Supplementary files format and content: Filtered feature matrices output from cellranger 5.0

source_name: Brain tumor section (IDH wildtype Glioblastoma)

extract_protocol:
We used the 10x Genomics 3’ v2 and 5’ v2 Chromium Gene Expression Solution to generate high-quality scRNA-seq data for 11 GBM samples from nine patients, three of whom also contributed Visium data. Because the size of tumor samples was often limiting, we could not obtain scRNA-seq samples from every patient analyzed using Visium. Sequencing reads were demultiplexed, aligned, and counted using the Cellranger 5.0 pipeline
Sequencing reads were demultiplexed, aligned, and counted using the Cellranger 5.0 pipeline


title: Patient P075 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P075_CRANI1_TUMOR_EPIC


title: GBM034_Core

description:
Library name: GBM034_Core_scRNA
10x Genomics single cell RNA-seq of GBM Sample GBM034_Core

value: Brain tumor section (IDH wildtype Glioblastoma)


title: Gins4-mAID Metaphase Nocodazole 10h ESCs Replicate 1, Hi-C


title: Healthy+IL-17A neutrophil 1

city: Kunming

first: xiang

middle: wen

last: lan

address: 300 Bailong Temple, Panlong District, Kunming, Yunnan 650224, China

institute: Southwest Forestry University

description: Library name: B_1

data_processing:
Raw reads were filtered using Trimmomatic to remove low-quality bases and adapter sequences.
Assembly: Homo sapiens reference genome build GRCh38 (NCBI assembly: GCA_000001405.29).
Supplementary files format and content: The processed data file 1_genes_fpkm_expression.txt contains gene-level FPKM values for all samples, formatted as a tab-delimited text matrix. The first column contains Ensembl gene IDs, and subsequent columns correspond to each sample’s FPKM expression values.

source_name: Vaginal lavage fluid-derived neutrophils

extract_protocol:
Total RNA was extracted from neutrophils using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and purity were assessed using Agilent 2100 Bioanalyzer and NanoDrop spectrophotometry, with RIN values ≥ 7.0 used for library construction.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina. Briefly, mRNA was purified from total RNA, fragmented, and reverse-transcribed into cDNA. Adapters were ligated to the cDNA fragments, followed by PCR amplification. Library quality was validated using qPCR and Agilent 2100 before sequencing.

value: Neutrophils

value: IL-17A treated


title: Patient P074 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P074_CRANI1_TUMOR_EPIC


title: WU-1226-edgeCD45neg

description:
Library name: WU-1226-edgeCD45neg_scRNA
10x Genomics single cell RNA-seq of GBM Sample WU-1226-edgeCD45neg


title: Gins4-mAID S-KD 5-Ph-IAA 15h ESCs Replicate 2, Hi-C

value: 5-Ph-IAA treatment, S sort


title: WU-1226-coreCD45neg

description:
Library name: WU-1226-coreCD45neg_scRNA
10x Genomics single cell RNA-seq of GBM Sample WU-1226-coreCD45neg


title: WU-1225-edge

description:
Library name: WU-1225-edge_scRNA
10x Genomics single cell RNA-seq of GBM Sample WU-1225-edge


title: B189

description:
Library name: B189_scRNA
10x Genomics single cell RNA-seq of GBM Sample B189 replicate 1


title: WU-1225-core

description:
Library name: WU-1225-core_scRNA
10x Genomics single cell RNA-seq of GBM Sample WU-1225-core


title: Gins4-mAID S-KD 5-Ph-IAA 15h ESCs Replicate 1, Hi-C


title: B183_3

description:
Library name: B183_3_scRNA
10x Genomics single cell RNA-seq of GBM Sample B183 replicate 3


title: Patient P072 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P072_CRANI1_TUMOR_EPIC


title: Patient P073 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P073_CRANI1_TUMOR_EPIC


title: B183_2

description:
Library name: B183_2_scRNA
10x Genomics single cell RNA-seq of GBM Sample B183 replicate 2


title: Gins4-mAID G1-KD 5-Ph-IAA 15h ESCs Replicate 2, Hi-C

value: 5-Ph-IAA treatment 15h, G1 sort


title: B183_1

description:
Library name: B183_1_scRNA
10x Genomics single cell RNA-seq of GBM Sample B183 replicate 1


title: Patient P071 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P071_CRANI1_TUMOR_EPIC


title: Gins4-mAID G1-KD 5-Ph-IAA 15h ESCs Replicate 1, Hi-C


title: B178_3

description:
Library name: B178_3_scRNA
10x Genomics single cell RNA-seq of GBM Sample B178 replicate 3


title: Patient P070 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P070_CRANI1_TUMOR_EPIC


title: B178_2

description:
Library name: B178_2_scRNA
10x Genomics single cell RNA-seq of GBM Sample B178 replicate 2


title: B178_1

description:
Library name: B178_1_scRNA
10x Genomics single cell RNA-seq of GBM Sample B178 replicate 1


title: Gins4-mAID S-Control ESCs Replicate 2, Hi-C

value: S srot


title: Patient P069 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P069_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue


title: Gins4-mAID S-Control ESCs Replicate 1, Hi-C

value: embryonic stem cells


title: HepG2 sEVs, shSYNCRIP biol rep 3

city: Rome

first: Luca

last: Quattrocchi

state: Lazio

address: Viale Regina Elena 324

country: Italy

institute: Sapienza University of Rome

description: Library name: Sample 6

data_processing:
Low-quality reads and reads outside the expected length range for microRNAs (16-26 nucleotides) were filtered out using Cutadapt
MiRDeep2 (mapper.pl and quantifier.pl modules) was used to parse the samples in a collapsed multifasta, align the reads to the reference and generate raw counts
Raw counts filtering and normalization were performed using the R packages dplyr and edgeR
Assembly: Homo Sapiens: GRCh38, miRbase v22.1
Supplementary files format and content: tab-delimited file contains raw counts for each sample

source_name: Liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with exosome-free FBS, L-Glu and antibiotics in humified atmosphere with 5% CO2 at 37°C for 72 hours

extract_protocol:
miRNAs were extracted using miRNeasy Mini Kit and Rneasy MinElute Cleanup Kit (QIAGEN)
miRNA libraries were prepared using NEXFLEX Small RNA-Seq Kit v4 (PerkinElmer), following manufacturer's protocol

treatment_protocol: sEVs pellet was collected after differential centrifugation at 2000g, 20000g, 100000g plus final wash at 100000g

value: Liver

value: HepatoCellular Carcinoma


title: HepG2 sEVs, shSYNCRIP biol rep 4

description: Library name: Sample 7


title: HepG2 sEVs, shSYNCRIP biol rep 2

description: Library name: Sample 5


title: HepG2 sEVs, shSYNCRIP biol rep 1

description: Library name: Sample 4


title: Gins4-mAID G1-Control Thymidine 15h ESCs Replicate 2, Hi-C

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4

value: Thymidine treatment 15h, G1 sort


title: Patient P068 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P068_CRANI1_TUMOR_EPIC


title: Patient P067 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P067_CRANI1_TUMOR_EPIC


title: HepG2 sEVs, shCTR biol rep 3

description: Library name: Sample 3


title: Gins4-mAID G1-Control Thymidine 15h ESCs Replicate 1, Hi-C


title: HepG2 sEVs, shCTR biol rep 2

description: Library name: Sample 2


title: Patient P066 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P066_CRANI1_TUMOR_EPIC


title: HepG2 sEVs, shCTR biol rep 1

description: Library name: Sample 1


title: Gins4-mAID 5-Ph-IAA Asynchronous ESCs Replicate 2, Hi-C


title: Patient P065 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P065_CRANI1_TUMOR_EPIC


title: KDM2B(DCxxC)-GFP

description: Library name: GFP3_Z19_S14

data_processing:
Quality of the sequenced raw read files was evaluated using FastQC tools. The Burrows-Wheeler Aligner (BWA) was used to align these reads to the hg38 reference genome. Then the generated aligned reads were sorted, indexed and prepared in two different files containing reads that aligned to human chromosomes and a file containing reads that aligned to mouse chromosomes with SAMtools and normalization factors were calculated per file. Using BEDtools, the total number of overlapping fragments at each position in the genome were found. The resulting BedGraph files were converted to BigWig files and visualized using the Integrative Genomics Viewer.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were cross-linked using PBS including 1% formaldehyde for 10 minutes. Cross-linked samples were quenched using 125 mM glycine, followed by a PBS wash and snap freezing SDS buffer (100 mM NaCl, 0.5% SDS, 5 mM EDTA, 50 mM Tris-HCl (pH 8.0), protease inhibitors (CLAP and 0.1 mM PMSF), and 0.2% NaN3. Next, cross-linked samples were IP buffer containing: 2x SDS buffer and 1 x Triton Dilution buffer (5% Triton X-100, 5 mM EDTA, 100 mM Tris-HCl (pH 8.6), 100 mM NaCl, 0.2% NaN3, 1 x CLAP, 0.1 mM PMSF). Sonication was performed using a Bioruptor (Diagenode) or PIXUL® Multi-Sample Sonicator (Active Motif). Then, the samples were precleared using 1 mg pre-equilibrated Dynabeads Protein G (Invitrogen) for 20 minutes and subsequently ChIP reactions were conducted in 1 ml IP buffer and incubated overnight at 4 °C with 2 µg of either of the following antibodies: anti-GFP (ab290, Abcam), IgG (I8141, Sigma), anti-KDM2B (09-846, Merck), anti-H2AK119ub (D27C4, Cell Signaling Technology), anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (C15410196, Diagenode), anti-H3K27me3 (C15410069, Diagenode) and anti-H3K36me3 (C15410192, Diagenode). Next, ChIP reactions were incubated for 3h with 25 ml pre-equilibrated Dynabeads Protein G (invitrogen) at 4°C and subsequently washed with Mixed Micelle Wash buffer (150 mM NaCl, 20 mM Tris-HCl (pH 8.1), 5 mM EDTA, 5.2% sucrose, 1% Triton X-100, 0.2% SDS, 0.2% NaN3, 3 washes), buffer 500 (50 mM Hepes-KOH (pH 7.5), 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% NaN3; 2 washes), LiCl Wash buffer (250 mM LiCl, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 0.2% NaN3; 2 washes) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA; 1 wash). Finally, chromatin was eluted from the beads using Elution Buffer (0.1 M NaHCO3, 0.1% SDS) and reverse cross-linked overnight at 65 degrees. Finally, 2 ml RNase A (10mg/ml; ThermoFisher) was added and samples were incubated for 2 hours at 37 degrees followed by addition of 2 ml Proteinase K (20mg/ml; ThermoFisher) and incubation for 2 hours at 55 degrees. Finally, the DNA was extracted using a PCR purification kit (Qiagen). The purified DNA samples were analyzed by sequencing.
ChIP-seq libraries were prepared with the KAPA Hyper Prep Kit (Roche Sequencing and Life Sciences) following the manufacturer’s instructions. The resulting DNA fragment libraries were subjected to a sequencing on an Illumina NextSeq500 and generated the paired-end reads FASTQ files, using the manufacturer’s instructions.

value: anti-GFP (ab290, Abcam

value: Untreated


title: KDM2Bsf-GFP

description: Library name: GFP2_Z18_S12


title: Patient P064 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P064_CRANI1_TUMOR_EPIC

value: Non-small cell lung carcinoma


title: KDM2Blf-GFP

description: Library name: GFP1_Z17_S19


title: Gins4-mAID 5-Ph-IAA Asynchronous ESCs Replicate 1, Hi-C


title: 43948_12_K562_5_ph_IAA_GSK343_A92

description: Library name: 43948_12_K562_5_ph_IAA_GSK343_A92

data_processing:
Single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.
Assembly: hg38
Supplementary files format and content: RNAseqcount text file which includes expression values for each sample fo each gene

extract_protocol:
For RNA sequencing total RNA was extracted from cells, using the RNeasy Mini Kit from Qiagen (Venlo, The Netherlands) according to the manufacturer’s recommendations.
RNA samples were qualified by automated gel electrophoresis on the 2200 TapeStation System (Agilent Technologies). Using KAPA RNA HyperPrep kit with riboErase (HMR) from Roche Sequencing and Life Sciences, cDNAs were synthesized from fragmented RNA and the sequences library were generated, according to the manufacturer’s recommendations. These libraries were then sequenced on an Illumina NextSeq500 using standard settings and the single-end reads obtained from treated cells were analyzed with Strand Avadis NGS (v3.0) software (Strand Life Sciences Pvt. Ltd). The STAR aligner was used in two-pass mode with default settings to map the obtained paired-end reads from treated cells to the hg38 reference genome. Using the DESeq2 package, the data was normalized and differentially expressed genes (DEGs) were found. Genes with an adjusted p-value < 0.05 and log2FoldChanges > < 0.585 were found to be differentially expressed and were used in further analysis.


title: Gins4-mAID Control Asynchronous ESCs Replicate 2, Hi-C


title: Patient P063 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P063_CRANI1_TUMOR_EPIC


title: Gins4-mAID Control Asynchronous ESCs Replicate 1, Hi-C


title: 43947_11_K562_5_ph_IAA_GSK343_A91

description: Library name: 43947_11_K562_5_ph_IAA_GSK343_A91


title: 43946_10_K562_5_ph_IAA_GSK343_A90

description: Library name: 43946_10_K562_5_ph_IAA_GSK343_A90


title: 43945_9_K562_GSK343_A87

description: Library name: 43945_9_K562_GSK343_A87


title: Patient P062 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P062_CRANI1_TUMOR_EPIC


title: 43944_8_K562_GSK343_A79

description: Library name: 43944_8_K562_GSK343_A79


title: mAID-Mcm6 5-Ph-IAA Asynchronous ESCs Replicate 2, Hi-C

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at N-terminus of Mcm6


title: 43943_7_K562_GSK343_A78

description: Library name: 43943_7_K562_GSK343_A78


title: 43942_6_K562_5_ph_IAA_A77

description: Library name: 43942_6_K562_5_ph_IAA_A77


title: Patient P061 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P061_CRANI1_TUMOR_EPIC


title: Patient P060 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P060_CRANI1_TUMOR_EPIC


title: mAID-Mcm6 5-Ph-IAA Asynchronous ESCs Replicate 1, Hi-C


title: 43940_4_K562_5_ph_IAA_A75

description: Library name: 43940_4_K562_5_ph_IAA_A75


title: mAID-Mcm6 Control Asynchronous ESCs Replicate 2, Hi-C


title: 43941_5_K562_5_ph_IAA_A76

description: Library name: 43941_5_K562_5_ph_IAA_A76


title: 43939_3_K562_DMSO_A74

description: Library name: 43939_3_K562_DMSO_A74

value: DMSO


title: Patient P059 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P059_CRANI1_TUMOR_EPIC


title: mAID-Mcm6 Control Asynchronous ESCs Replicate 1, Hi-C


title: 43937_1_K562_DMSO_A72

description: Library name: 43937_1_K562_DMSO_A72


title: 43938_2_K562_DMSO_A73

description: Library name: 43938_2_K562_DMSO_A73


title: Patient P058 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P058_CRANI1_TUMOR_EPIC


title: 41486_30_dCxxC_5_Ph_IAA_A39

description: Library name: 41486_30_dCxxC_5_Ph_IAA_A39


title: 41485_29_dCxxC_5_Ph_IAA_A38

description: Library name: 41485_29_dCxxC_5_Ph_IAA_A38


title: Patient P057 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P057_CRANI1_TUMOR_EPIC


title: 41484_28_dCxxC_5_Ph_IAA_A37

description: Library name: 41484_28_dCxxC_5_Ph_IAA_A37


title: 41483_27_dCxxC_DMSO_A36

description: Library name: 41483_27_dCxxC_DMSO_A36


title: 41482_26_dCxxC_DMSO_A35

description: Library name: 41482_26_dCxxC_DMSO_A35


title: Patient P056 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P056_CRANI1_TUMOR_EPIC


title: Gins4-mAID 5-Ph-IAA-removal 6h ESCs Replicate 2, BrdU-IP Early

description: DEP_01_149_04_w200ks40k_TagDensity.bedGraph

data_processing:
Two-step adapter trimming was performed to first remove the Illumina adapter and the SEQXE adapter.
Trimmed fastq files were aligned to mm9 genome.
Duplicated reads were filtered out.
Reads per million (rpm) normalization were calculated for early- and late-S-phase BrdU-IP samples in sliding windows of 200-kb at 40-kb intervals and a nonoverlapping 200-kb bins for Robust scaling analysis, respectively.
The ratio of early-S-phase to total read counts [(early-S reads)/(early-S reads + late-S reads)] was calculated for each bin, and their distribution was converted to fit within a ±1 scale. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Assembly: mm9
Supplementary files format and content: bedGraph
Library strategy: BrdU-IP Repli-seq

extract_protocol:
We followed the BrdU-IP-based protocol as described (Ryba et al., 2011). 75% ethanol fixed cells were stained with Propidium iodide (Nacalai tesque, 29037), then early-S phase and late-S phase cell population (at least 10,000 cells/fraction) were sorted by a Sony SH800 cell sorter (ultra-purity mode). For nocodazole/5-Ph-IAA removal experiments, only early-S phase cells were collected. Extracted DNA was sonicated by a Bioruptor BR2012A (Sonic Bio). BrdU-incorporated DNA was immunoprecipitated using anti-BrdU antibody (BD Biosciences Pharmingen, #555627).
BrdU-immunoprecipitated DNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed from early- and late-replicating DNA after WGA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions

treatment_protocol: (1) Transfection of gRNA-carrying vector was performed with Lipofectamine LTX&PLUS (ThermoFisher, 15338100) according to the manufacturer’s instructions. Cells were collected 4 days after transfection. (2) 5-Ph-IAA treatment: 5-Ph-IAA solution was added at a final concentration of 1 µM to the medium. (3) Nocodazole removal: after 15 hours of 50 ng/ml nocodazole treatment, the medium containintg nocodazole was replaced with normal culture medium. (4) 5-Ph-IAA removal: after 15 hours of 1 µM 5-Ph-IAA treatment, the medium containing 5-Ph-IAA was replaced with normal culture medium.

value: 5-Ph-IAA removal 6h


title: 41481_25_dCxxC_DMSO_A34

description: Library name: 41481_25_dCxxC_DMSO_A34


title: Patient P055 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P055_CRANI1_TUMOR_EPIC


title: 41480_24_dLRRS_5_Ph_IAA_A33

description: Library name: 41480_24_dLRRS_5_Ph_IAA_A33


title: 41479_23_dLRRS_5_Ph_IAA_A32

description: Library name: 41479_23_dLRRS_5_Ph_IAA_A32


title: Patient P054 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P054_CRANI1_TUMOR_EPIC


title: 41478_22_dLRRS_5_Ph_IAA_A31

description: Library name: 41478_22_dLRRS_5_Ph_IAA_A31


title: 41477_21_dLRRS_DMSO_A10

description: Library name: 41477_21_dLRRS_DMSO_A10


title: Patient P053 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P053_CRANI1_TUMOR_EPIC


title: 41476_20_dLRRS_DMSO_A29

description: Library name: 41476_20_dLRRS_DMSO_A29


title: 41474_18_SF_5_Ph_IAA_A27

description: Library name: 41474_18_SF_5_Ph_IAA_A27


title: Gins4-mAID 5-Ph-IAA-removal 4h ESCs Replicate 1, BrdU-IP Early

description: DEP_01_142_66_w200ks40k_TagDensity.bedGraph

value: 5-Ph-IAA removal 4h


title: 41475_19_dLRRS_DMSO_A28

description: Library name: 41475_19_dLRRS_DMSO_A28


title: Gins4-mAID Nocodazole-removal 8h ESCs Replicate 2, BrdU-IP Early

description: DEP_01_149_05_w200ks40k_TagDensity.bedGraph

value: Nocodazole removal 8h


title: 41473_17_SF_5_Ph_IAA_A26

description: Library name: 41473_17_SF_5_Ph_IAA_A26


title: Patient P051 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P051_CRANI1_TUMOR_EPIC


title: 41472_16_SF_5_Ph_IAA_A25

description: Library name: 41472_16_SF_5_Ph_IAA_A25


title: Patient P050 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P050_CRANI1_TUMOR_EPIC


title: Gins4-mAID Nocodazole-removal 6h ESCs Replicate 2, BrdU-IP Early

description: DEP_01_149_03_w200ks40k_TagDensity.bedGraph

value: Nocodazole removal 6h


title: 41468_12_LF_5_Ph_IAA_A21

description: Library name: 41468_12_LF_5_Ph_IAA_A21


title: Patient P049 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P049_CRANI1_TUMOR_EPIC


title: Patient P048 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P048_CRANI1_TUMOR_EPIC


title: 41466_10_LF_5_Ph_IAA_A19

description: Library name: 41466_10_LF_5_Ph_IAA_A19


title: 41465_9_LF_DMSO_A18

description: Library name: 41465_9_LF_DMSO_A18


title: 41464_8_LF_DMSO_A17

description: Library name: 41464_8_LF_DMSO_A17


title: Patient P047 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P047_CRANI1_TUMOR_EPIC


title: Gins4-mAID Nocodazole-removal 4h ESCs Replicate 1, BrdU-IP Early

description: DEP_01_142_65_w200ks40k_TagDensity.bedGraph

value: Nocodazole removal 4h


title: 41463_7_LF_DMSO_A16

description: Library name: 41463_7_LF_DMSO_A16


title: K562_EZH2

description: Library name: Exp289_UMCG_ChIP_10_K562_BCOR_mAID_EZH2

value: anti-EZH2 (D2C9, Cell Signaling Technology)


title: Patient P046 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P046_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue


title: Gins4-mAID 5-Ph-IAA ESCs Replicate 2, BrdU-IP Late

description: 210614_03_EGR101_Gins4-AID16_24h_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph

value: embryonic stem cells

value: 5-Ph-IAA treatment


title: 41462_6_EV_5_Ph_IAA_A15

description: Library name: 41462_6_EV_5_Ph_IAA_A15


title: Patient P045 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P045_CRANI1_TUMOR_EPIC


title: Gins4-mAID 5-Ph-IAA-removal 8h ESCs Replicate 2, BrdU-IP Early

description: DEP_01_149_06_w200ks40k_TagDensity.bedGraph

value: 5-Ph-IAA removal 8h


title: 41460_4_EV_5_Ph_IAA_A13

description: Library name: 41460_4_EV_5_Ph_IAA_A13


title: Gins4-mAID 5-Ph-IAA ESCs Replicate 2, BrdU-IP Early

value: OsTIR1 (F74G) knockin at Rosa26 locus, mAID knockin at C-terminus of Gins4


title: Gins4-mAID 5-Ph-IAA-removal 8h ESCs Replicate 1, BrdU-IP Early

description: DEP_01_142_70_w200ks40k_TagDensity.bedGraph


title: 41459_3_EV_DMSO_A12

description: Library name: 41459_3_EV_DMSO_A12


title: Patient P044 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P044_CRANI1_TUMOR_EPIC


title: 41458_2_EV_DMSO_A11

description: Library name: 41458_2_EV_DMSO_A11


title: Gins4-mAID 5-Ph-IAA-removal 6h ESCs Replicate 1, BrdU-IP Early

description: DEP_01_142_68_w200ks40k_TagDensity.bedGraph


title: Gins4-mAID 5-Ph-IAA-removal 4h ESCs Replicate 2, BrdU-IP Early

description: DEP_01_149_02_w200ks40k_TagDensity.bedGraph


title: Gins4-mAID 5-Ph-IAA ESCs Replicate 1, BrdU-IP Late

description: 02_GINS4_AID_IAA_DEP_01_073_17_IP_w200ks40k_Percent_q0.05.bedGraph


title: 41457_1_EV_DMSO_A10

description: Library name: 41457_1_EV_DMSO_A10


title: Patient P043 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P043_CRANI1_TUMOR_EPIC


title: 72H_1_K562_KDM2BB_72h5phIAA_A40_S19

description: Library name: 72H_1_K562_KDM2BB_72h5phIAA_A40_S19


title: Gins4-mAID 5-Ph-IAA ESCs Replicate 1, BrdU-IP Early


title: 72H_1_K562_KDM2BB_72h5phIAA_A39_S18

description: Library name: 72H_1_K562_KDM2BB_72h5phIAA_A39_S18


title: Patient P052 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P052_CRANI1_TUMOR_EPIC


title: Gins4-mAID Nocodazole-removal 8h ESCs Replicate 1, BrdU-IP Early

description: DEP_01_142_69_w200ks40k_TagDensity.bedGraph


title: 41471_15_SF_DMSO_A24

description: Library name: 41471_15_SF_DMSO_A24


title: Patient P042 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P042_CRANI1_TUMOR_EPIC


title: 72H_1_K562_KDM2BB_72h5phIAA_A38_S17

description: Library name: 72H_1_K562_KDM2BB_72h5phIAA_A38_S17


title: Gins4-mAID Control ESCs Replicate 2, BrdU-IP Late

description: 210614_01_EGR101_Gins4-AID16_0h_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph


title: 24H_1_K562_KDM2BB_24h5phIAA_A37_S16

description: Library name: 24H_1_K562_KDM2BB_24h5phIAA_A37_S16


title: Patient P041 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P041_CRANI1_TUMOR_EPIC


title: Gins4-mAID Control ESCs Replicate 2, BrdU-IP Early


title: 24H_1_K562_KDM2BB_24h5phIAA_A36_S15

description: Library name: 24H_1_K562_KDM2BB_24h5phIAA_A36_S15


title: 24H_1_K562_KDM2BB_24h5phIAA_A35_S14

description: Library name: 24H_1_K562_KDM2BB_24h5phIAA_A35_S14


title: Patient P040 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P040_CRANI1_TUMOR_EPIC


title: 41469_13_SF_DMSO_A22

description: Library name: 41469_13_SF_DMSO_A22


title: 41470_14_SF_DMSO_A23

description: Library name: 41470_14_SF_DMSO_A23


title: Gins4-mAID Nocodazole-removal 6h ESCs Replicate 1, BrdU-IP Early

description: DEP_01_142_67_w200ks40k_TagDensity.bedGraph


title: 8H_1_K562_KDM2BB_8h5phIAA_A34_S13

description: Library name: 8H_1_K562_KDM2BB_8h5phIAA_A34_S13


title: 41467_11_LF_5_Ph_IAA_A20

description: Library name: 41467_11_LF_5_Ph_IAA_A20


title: Gins4-mAID Control ESCs Replicate 1, BrdU-IP Late

description: 01_GINS4_AID_noIAA_DEP_01_073_13_IP_w200ks40k_Percent_q0.05.bedGraph


title: Patient P039 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P039_CRANI1_TUMOR_EPIC


title: 8H_1_K562_KDM2BB_8h5phIAA_A32_S4

description: Library name: 8H_1_K562_KDM2BB_8h5phIAA_A32_S4


title: Gins4-mAID Control ESCs Replicate 1, BrdU-IP Early


title: 2H_1_K562_KDM2BB_2h5phIAA_A30_S5

description: Library name: 2H_1_K562_KDM2BB_2h5phIAA_A30_S5


title: 2H_1_K562_KDM2BB_2h5phIAA_A29_S2

description: Library name: 2H_1_K562_KDM2BB_2h5phIAA_A29_S2


title: Patient P038 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P038_CRANI1_TUMOR_EPIC


title: 8H_1_K562_KDM2BB_8h5phIAA_A33_S12

description: Library name: 8H_1_K562_KDM2BB_8h5phIAA_A33_S12


title: Gins4-mAID Nocodazole-removal 4h ESCs Replicate 2, BrdU-IP Early

description: DEP_01_149_01_w200ks40k_TagDensity.bedGraph


title: mAID-Mcm6 5-Ph-IAA ESCs Replicate 2, BrdU-IP Late

description: DEP_01_163_7_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph


title: Patient P037 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy 2 of 2

description: Library name: P037_CRANI2_TUMOR_EPIC


title: 2H_1_K562_KDM2BB_2h5phIAA_A31_S7

description: Library name: 2H_1_K562_KDM2BB_2h5phIAA_A31_S7


title: UNT_1_K562_KDM2BB_Untreated_A28_S6

description: Library name: UNT_1_K562_KDM2BB_Untreated_A28_S6


title: UNT_1_K562_KDM2BB_Untreated_A27_S3

description: Library name: UNT_1_K562_KDM2BB_Untreated_A27_S3


title: mAID-Mcm6 5-Ph-IAA ESCs Replicate 2, BrdU-IP Early


title: Patient P037 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy 1 of 2

description: Library name: P037_CRANI1_TUMOR_EPIC


title: mAID-Mcm6 5-Ph-IAA ESCs Replicate 1, BrdU-IP Late

description: 04_DEP_01_117_7_Mcm6_IAA_IP_w200ks40k_Percent_q0.05.bedGraph


title: UNT_1_K562_KDM2B_Untreated_A26_S1

description: Library name: UNT_1_K562_KDM2B_Untreated_A26_S1


title: Patient P036 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P036_CRANI1_TUMOR_EPIC


title: Z1_K562BCO_72h5phIAA_A37_S13

description: Library name: Z1_K562BCO_72h5phIAA_A37_S13


title: Patient P035 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P035_CRANI1_TUMOR_EPIC


title: mAID-Mcm6 Control ESCs Replicate 2, BrdU-IP Late

description: DEP_01_163_5_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph


title: Patient P034 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P034_CRANI1_TUMOR_EPIC


title: Y1_K562BCO_24h5phIAA_A34_S11

description: Library name: Y1_K562BCO_24h5phIAA_A34_S11


title: X3_K562BCO_8h5phIAA_A33_S3

description: Library name: X3_K562BCO_8h5phIAA_A33_S3


title: Patient P033 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P033_CRANI1_TUMOR_EPIC


title: mAID-Mcm6 Control ESCs Replicate 2, BrdU-IP Early


title: Y2_K562BCO_24h5phIAA_A35_S6

description: Library name: Y2_K562BCO_24h5phIAA_A35_S6


title: X2_K562BCO_8h5phIAA_A32_S7

description: Library name: X2_K562BCO_8h5phIAA_A32_S7


title: X1_K562BCO_8h5phIAA_A31_S16

description: Library name: X1_K562BCO_8h5phIAA_A31_S16


title: mAID-Mcm6 Control ESCs Replicate 1, BrdU-IP Late

description: 03_DEP_01_117_5_Mcm6_noIAA_IP_w200ks40k_Percent_q0.05.bedGraph


title: W3_K562BCO_2h5phIAA_A30_S12

description: Library name: W3_K562BCO_2h5phIAA_A30_S12


title: mAID-Mcm6 Control ESCs Replicate 1, BrdU-IP Early


title: W2_K562BCO_2h5phIAA_A29_S4

description: Library name: W2_K562BCO_2h5phIAA_A29_S4


title: W1_K562BCO_2h5phIAA_A28_S8

description: Library name: W1_K562BCO_2h5phIAA_A28_S8


title: Rex1-EmGFPd2 Rfc2 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_085_19_Rfc2_167_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
14_Rfc2_mean_w200ks40k.bedGraph

value: EmGFPd2 knockin at Rex1 locus, Cas9 knockin at Rosa26 locus

value: pU6-Rfc2-gRNA#2-CBA-PuroR transfection


title: V2_K562BCO_Untreated_A26_S9

description: Library name: V2_K562BCO_Untreated_A26_S9

value: Untreated


title: V3_K562BCO_Untreated_A27_S10

description: Library name: V3_K562BCO_Untreated_A27_S10


title: Rex1-EmGFPd2 Rfc2 gRNA#2 mESCs, BrdU-IP Early


title: Patient P030 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P030_CRANI1_TUMOR_EPIC

value: Non-small cell lung carcinoma


title: V1_K562BCO_Untreated_A25_S5

description: Library name: V1_K562BCO_Untreated_A25_S5


title: Patient P029 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P029_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Rfc2 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_085_17_Rfc2_165_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
14_Rfc2_mean_w200ks40k.bedGraph

value: pU6-Rfc2-gRNA#1-CBA-PuroR transfection


title: KO_Dex_2

description: Library name: KD11

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11) and the BCL files were demultiplexed into fastq files using bcl2fast2 v2.20.0.422.
Bulk ATAC-seq data were preprocessed using the ATAC-seq Pipeline (v1.2.0) on Via Foundry (https://www.gcp.viafoundry.com/). Specifically, read quality filtering (phred >= 33) and adaptors trimming were performed using Trimmomatic v0.39, trimmed reads were then aligned to the mm10 mouse genome using Bowtie2 v2.3.5, and duplicated reads were marked and removed by Picard v2.18.27. BAM files were sorted and indexed using Samtools v1.3.
Data were further cleaned up by filtering out the reads that meet any of the following criteria using deepTools v3.5.6: (1) mapped to chrM (mitochondria), chr*_random, chrUn, and chrY (because cells are derived from female mice); (2) mapped to blacklist regions (https://github.com/Boyle-Lab/Blacklist); (3) with low mapping quality (MAPQ < 30); (4) fragment length < 50bp. Peak calling was then performed for all samples together using Genrich v0.6.1 (joint ATAC-seq mode). Peaks were then quantified using featureCounts v2.1.1 from the Subread package.
Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv) files include read counts for every peak (rows)  in every sample (columns)
Supplementary files format and content: BigWig (.bw) files contain the normalized, genome-wide chromatin accessibility signal (read depth) for each sample.

extract_protocol:
6,000 cells were sorted by FACS into PBS buffer supplemented with 0.5% BSA.
For library preparation, cells were lysed and tagmented with 9.5uL lysis and transposition mix buffer (10mM TAPS-NaOH pH 8.5, 5mM MgCl2, 10% DMF, 0.02% digitonin) and 0.5uL Tn5 transposase (Diagenode) at 37 °C for 30 min. Tagmentation was terminated by the direct addition of 10 µL stop buffer (100 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.4% SDS, 40 µg/mL proteinase K), followed by incubation at 55 °C overnight. Subsequently, 5 µL of 25% Tween-20 was added directly to the reaction. Libraries were amplified by PCR for 16 cycles under the following conditions: 72 °C for 5 min; 98 °C for 3 min; followed by cycling at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min; with a final extension at 72 °C for 5 min. PCR products were purified using a two-step SPRI beads cleanup (1.5× followed by 0.6×). Library concentration was measured using the Qubit dsDNA HS Assay Kit (Invitrogen), and fragment size distribution was assessed using an Agilent FA5400 Fragment Analyzer. Final libraries were sequenced on an Illumina NextSeq™ 1000/2000 platform using a P2 XLEAP-SBS™ Reagent Kit (100 cycles; Cat. No. 20100987).

value: in vitro; originally from spleen and dLN

value: T cell

value: GR cKO (C57/B6)

value: Dex


title: Patient P028 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P028_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Rfc2 gRNA#1 mESCs, BrdU-IP Early


title: KO_Dex_1

description: Library name: KD10


title: KO_Ctrl_3

description: Library name: KC9

value: control


title: Rex1-EmGFPd2 Haus1 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_085_13_Haus1_163_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
08_Haus1_mean_w200ks40k.bedGraph

value: pU6-Haus1-gRNA#2-CBA-PuroR transfection


title: Patient P026 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P026_CRANI1_TUMOR_EPIC


title: WT_Dex_3

description: Library name: WD6


title: Rex1-EmGFPd2 Haus1 gRNA#2 mESCs, BrdU-IP Early


title: WT_Dex_1

description: Library name: WD4


title: Patient P025 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P025_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Haus1 gRNA#1 mESCs, BrdU-IP Late

description:
DEP_01_085_11_Haus1_161_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
08_Haus1_mean_w200ks40k.bedGraph

value: pU6-Haus1-gRNA#1-CBA-PuroR transfection


title: Patient P024 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P024_CRANI1_TUMOR_EPIC

value: Human brain metastasis tissue


title: WT_Ctrl_2

description: Library name: WC2


title: Rex1-EmGFPd2 Haus1 gRNA#1 mESCs, BrdU-IP Early

value: embryonic stem cells


title: WT_Ctrl_1

description: Library name: WC1


title: Patient P023 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P023_CRANI1_TUMOR_EPIC


title: Rex1-EmGFPd2 Pfn1 gRNA#2 mESCs, BrdU-IP Late

description:
DEP_01_085_09_Pfn1_155_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.bedGraph
11_Pfn1_mean_w200ks40k.bedGraph

value: pU6-Pfn1-gRNA#2-CBA-PuroR transfection


title: Patient P022 brain metastasis tissue PredicineEPIC methylation sequencing at craniotomy

description: Library name: P022_CRANI1_TUMOR_EPIC


title: E110_rep1

city: Xianyang City

first: Guanghui

last: Tan

address: No.22, Xinong Road, Yangling Demonstration Zone, Yangling District, Xianyang City

institute: Northwest A&F University

description: Library name: C5_3_TP_rep1

data_processing:
Raw sequencing data were demultiplexed and processed with Cell Ranger (v7.1.0) against the ARS-UCD2.0 bovine reference genome.
Assembly: Bovine reference genome ARS-UCD2.0 (Ensembl release) was used for read alignment and downstream analyses.
Supplementary files format and content: Processed expression matrices are provided in Matrix Market format (MTX) along with barcodes and feature annotation files. Additional processed data are provided as Seurat R objects (RDS format) containing metadata, normalized counts, dimensionality reduction coordinates, and cell type annotations.

organism: Bos taurus

source_name: placenta

growth_protocol: All experimental animals were healthy Holstein heifers (Bos taurus) with normal estrous cycles. Estrus synchronization was performed by hormone treatment, followed by embryo transfer on day 7 after estrus as previously described (Moraes et al., 2018). Pregnant animals were humanely euthanized at different gestational stages (E60, E85, E110, E180, E240, and E280) for placenta collection.

extract_protocol:
Frozen placental tissues were minced into 2 mm pieces and homogenized in EZ lysis buffer supplemented with protease and RNase inhibitors using a Dounce homogenizer. The nuclear fraction was isolated by filtration and centrifugation steps, stained with 7-AAD, and sorted by FACS to remove debris and doublets. Nuclei were resuspended at 700–1200 nuclei/μl in PBS + 0.07% BSA + RNase inhibitor before loading.
Single-nucleus suspensions were processed using the Chromium Single Cell 3' v3 Reagent Kit (10x Genomics) according to the manufacturer’s instructions. Libraries were quality checked and sequenced on an Illumina NovaSeq 6000 platform (paired-end 150 bp).

value: placenta

tag: characteristics [gestation_stage]


title: E280_rep3

description: Library name: TP_C4_2_rep3


title: Rex1-EmGFPd2 Pfn1 gRNA#2 mESCs, BrdU-IP Early


title: E280_rep2

description: Library name: TP_C4_2_rep2