title: Brain_KO_NBH_1

description: Trem2-/- animal treated with NBH

value: KO

value: NBH


title: Brain_WT_ME7_2

status: Public on May 30 2025

type: RNA

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

description: WT animal treated with ME7

hyb_protocol: The miRNeasy mini kit was carried out according to manufacturer’s instructions with the final RNA elution repeated twice in 50µl RNase-free water. RNA concentration was quantified using the Thermo Scientific ND 1000 Nanodrop.

scan_protocol: Scanned images (DAT files) were transformed into intensities (CEL files) using the AGCC software (Affymetrix).

data_processing: Initial quality control was performed using arrayQualityMetrics package from Bioconductor. Intensities for 45141 probes were normalized using the RMA algorithm implemented in the affy package from Bioconductor. We filtered out probes without RMA normalized intensities greater than 4 in at least 2 samples. Probe to gene annotations were retrieved from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=ht_mg-430_pm_ap). RMA normalized intensities were aggregated to gene level using the mean, obtaining relative gene expression values for 12758 genes across 14 samples.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: brain

label_protocol: biotin

growth_protocol: Animals were maintained in standard 12-hour light- 12-hour dark cycles and given access to food and water ad libitum.

extract_protocol: RNA was extracted using the miRNeasy mini kit (Qiagen).

treatment_protocol: Animals of 7-13 weeks of age were inoculated intracerebrally with 20µl of a 1% (w/v) brain homogenate obtained from mice terminally infected with mouse-passaged ME7 scrapie prion strain.  Control mice were instead injected with normal brain homogenate (NBH). Female animals only at 90 days post-inoculation were used for microarray analysis.

tag: group

tag: genotype

value: WT

tag: treatment

tag: replicate

tag: Sex

value: female

tag: extraction


title: CAR19-DMSO-3

city: Charlestown

first: Michael

middle: C

last: Kann

state: MA

address: 149 13th Street

department: CCR

country: USA

institute: MGH

hyb_protocol: Nanostring nCounter protocol

scan_protocol: Nanostring nCounter protocol

data_processing: Nanostring nSolver

label: mCherry+ CAR

organism: Homo sapiens

source_name: Human CAR-T, antigen exposed 4 weeks.

label_protocol: Nanostring nCounter protocol

growth_protocol: CAR19+ cells exposed and replated at 1:1 ratio to CD19+ irradiated K562 every week for 4 weeks. CAR+ cells FACs sorted and total RNA extracted and run on Nanostring nCounter

extract_protocol: QIAGEN Rneasy, all samples run with same total mass of RNA

treatment_protocol: Treated every 48-72hr with 1uM lenalidomide or eq. DMSO control

tag: car

tag: agent

value: DMSO


title: mbdIL7-DMSO-1

value: CAR19 mbdIL7


title: X6986

type: SRA

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

library_source: transcriptomic

data_processing:
Raw read trimming with fastp
Transcript quantification with salmon
Normalization of expression levels with Salmon
Assembly: GRCm38
Supplementary files format and content: Tab-delimited tables containing abundance estimates, summarised at the gene level. Ensembl IDs

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
Total hippocampal RNA was extracted using TRI reagent kit (T9242, Sigma-Aldrich, MO,USA), followed by mRNA isolation
mRNA libraries were constructed with Illumina TruSeq™ RNA Sample Prep Kit v2 protocol. Standard quality checks for material degradation (Bioanalyzer, Agilent Technologies) and concentration (Qubit, Life Technologies) were done after library construction.

tag: tissue

value: Hippocampus

value: Saline


title: Brain_KO_ME7_3

description: Trem2-/- animal treated with ME7


title: Brain_KO_ME7_2

description: Trem2-/- animal treated with ME7


title: Cd100 rep3

city: Nanjing

first: Ling

last: Li

address: Zhongshanmenwai, Qianhuahoucun No.1

country: China

institute: nstitute of Botany, Jiangsu Province and Chinese Academy of Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality linit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC geomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost:3 length fraction: 0.8 similarity: 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
the clean reads were aligned to the centipedegrass genome using HISAT2
Assembly: GCF_000003195.3
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM for each Sample

organism: Eremochloa ophiuroides

source_name: root

growth_protocol: All plants were  relocated to polyethylene plastic pots containg red soil.

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

treatment_protocol: Plants were treated with Cd at 0, 50, 100, 200 mg/kg

value: root

value: Yuxi cultivar


title: X6967

value: TYR

value: NAP


title: MB125_3H_L7.D707

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

description: Library name: MB125_3H_L7.D707

data_processing:
For Experiment 1, basecall files were converted to FASTQ by bcl2fastq2, demultiplexed, quality trimmed, and filter using ea-utils (https://expressionanalysis.github.io/ea-utils/ ; last accessed 01-21-2020). Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed.
For Experiment 2, Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed, respectively in Partek Flow (v.8.0.19.0428; St. Louis, MO).
Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR (v.2.5.3a) with default settings in Partek Flow and strand specificity detection enabled for the paired-end reads from Experiment 1 but not for Experiment 2.
Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation.
Assembly: GRCz11/93 gene annotation
Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples
Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples

organism: Danio rerio

source_name: pooled heads collected anterior to swim bladder of larval zebrafish

extract_protocol:
Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis, LLC (Morrisville, NC, USA). Samples from experiment 2 underwent RNA extraction at US EPA (Durham, NC, USA) using Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit.
For Experiment 1, paired-end (50 base pair) total RNA-sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit for rRNA depletion (Illumina, San Diego, California, cat. No. RS-1222303) at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly, rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer (DNA 1000 kit #5067-1504) and qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA). Sample libraries were then normalized, randomly pooled, and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2, purified RNA from each sample (500 ng per sample) were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA (Durham, NC, USA). PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size (bp) was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library (μl x nM) was pooled from 16 randomized libraries to make the sequencing samples (total 2 pools of 16 libraries each) and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR (Single Read).

tag: strain

value: mixed wild type zebrafish line US EPA

tag: lifestage

value: larvae

tag: age

value: 10 days post fertilization

value: Conventionally colonized with microbes (control)

tag: experiment


title: Brain_KO_ME7_1

description: Trem2-/- animal treated with ME7


title: MB125_3G_L7.D705

description: Library name: MB125_3G_L7.D705

value: pooled heads collected anterior to swim bladder of larval zebrafish


title: CAR19-DMSO-2


title: Pooled cells from dpi0, dpi4, and dpi14

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description:
Sample_GOL1961_JCV_10X
single cell mRNA expression of dissociated CD44-sorted astrocytes from normal fetal brain tissue

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting
The gene/barcode matrix of RNA and UMI counts were imported into Seurat for all subsequent analysis
Genome_build: Mixed genome assembly of GRCh38 and JC polyomavirus, Ensembl release 95 and JC polyomavirus annotation
Supplementary_files_format_and_content: Gene counts (filtered_feature_bc_matrix) and antibody counts (umi_counts) are provided as a directory. This can then be read into Seurat with Read10X function.

source_name: primary fetal astrocytes

growth_protocol: All dissociates were maintained overnight in DMEM/F12/N1-based medium (Life Technologies) supplemented with 10 ng/ml FGF2

extract_protocol: Libraries were prepared using Chromium Single Cell v3 Reagent Kit (10x GENOMICS) according to the manufacturer’s protocols

treatment_protocol: Cortical tissues were minced and dissociated using papain (Worthington) and DNase (Sigma-Aldrich)

tag: cell sort marker

tag: developmental stage

value: fetal

tag: infection

value: JCV MAD1

tag: time

value: mixed sample (dpi0, dpi4, and dpi14)

value: brain

tag: cell type

value: primary fetal astrocytes


title: Cd100 rep2

tag: genotype


title: MB125_3F_L7.D706

description: Library name: MB125_3F_L7.D706

tag: treatment


title: Brain_WT_ME7_1

description: WT animal treated with ME7

tag: group

value: WT

tag: replicate

value: female


title: X6970

value: Hippocampus


title: CAR19-DMSO-1

value: DMSO


title: X6761


title: Slide 9, Xenium In Situ Spatial Gene Expression

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: The Xenium samples underwent several rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Baysor (v0.6.2) was used to re-segment cells with prior being default segmentations (cell_boundaries.parquet). Scanpy (v1.10.1) workflows were used for normalization to the median the downstream analysis.
The processed anndata object (processed_data.h5ad) contains cells after re-segmentation and integration. .X contains log-normalized counts.

label: Xenium Human Probe Set

source_name: 5 µm kidney section

label_protocol: Xenium Human Probe Set

extract_protocol: 5 μm sections were taken for Xenium.

value: kidney


title: Cd200 rep1

value: root

value: Yuxi cultivar


title: X2011

value: TYR

value: NAP


title: MB125_3C_L7.D704

description: Library name: MB125_3C_L7.D704

value: mixed wild type zebrafish line US EPA

value: larvae

value: 10 days post fertilization


title: Slide 7, Xenium In Situ Spatial Gene Expression


title: Cd50 rep2


title: Cd50 rep3


title: MB125_3A_L7.D702

description: Library name: MB125_3A_L7.D702

value: pooled heads collected anterior to swim bladder of larval zebrafish

value: Conventionally colonized with microbes (control)


title: MB125_3B_L7.D703

description: Library name: MB125_3B_L7.D703


title: X6724

value: Saline


title: Slide 6, Xenium In Situ Spatial Gene Expression


title: MB125_2H_L6.D701

description: Library name: MB125_2H_L6.D701

value: Conventionally re-colonized with microbes on day 1


title: CK rep3

value: CK


title: Cd50 rep1


title: X2008


title: MB125_2G_L6.D711

description: Library name: MB125_2G_L6.D711


title: Slide 4, Xenium In Situ Spatial Gene Expression


title: X6963

value: WT


title: X2007


title: Cd100 rep1


title: Slide 3, Xenium In Situ Spatial Gene Expression


title: MB125_2F_L6.D712

description: Library name: MB125_2F_L6.D712


title: MB125_2D_L6.D710

description: Library name: MB125_2D_L6.D710


title: MB125_2E_L6.D709

description: Library name: MB125_2E_L6.D709


title: X6957


title: CK rep1


title: X6723


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Cold24hrs_4

city: Hiroshima

first: Mitsunori

last: Miyazaki

state: Hiroshima

address: 1-2-3 Kasumi, Minami-Ku

department: Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima University

description: Library name: Cold_GM_D3_4

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 1%;  3) Remove low-quality reads (we define reads with bases with a quality score no more than 20 as the proportion of total bases in the reads that are greater than 40% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.  Software Information  SOAPnuke:  Version v2.3  Parameters -l 20 -q 0.4 -n 0.01  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke  References  [1]Cock P., et al.(2010). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6): 1767-1771.
Reference genome alignment Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) is software for mapping RNA-seq reads. . Compared with other software, HISAT has the advantages of high speed, high sensitivity and accuracy, and low memory consumption. HISAT's index based on Burrows-Wheeler transform and Ferragina-Manzini (FM) uses two types of indexes: whole genome indexes and partial genome indexes. See the HISAT alignment diagram for the details and statistics of genome mapping results.
First, HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software information:  Software Information  HISAT2:  Version：v2.0.4  Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF  Official Website：http://www.ccb.jhu.edu/software/hisat  References：  [1] Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357-360 (2015).
BCM_Maur_2.0
Assembly: Reference Genome Version：GCF_017639785.1_BCM_Maur_2.0
Supplementary files format and content: csv files include TPM,  Read Count, Normalized read count values for each Sample

organism: Mesocricetus auratus

source_name: skeletal muscle

growth_protocol: SCs were isolated according to the method of Yoshioka et al.17 Briefly, hindlimb skeletal muscles were dissected, minced with sterile surgical scissors, and digested in 0.2% type II collagenase solution at 37°C for 60 min. The tissue was gently homogenized using a 20-G syringe needle and filtered through a 40 µm nylon mesh strainer. The filtrate was centrifuged at 500 × g for 5 min and the pellet was resuspended in GM consisting of DMEM supplemented with 30% fetal bovine serum, 1% chick embryo extract, 10 ng/mL basic fibroblast growth factor, and 1× penicillin-streptomycin solution. The SCs were purified using a classical preplating method, followed by sequential replating to remove fibroblasts and enrich SCs. Purified SCs were plated onto Matrigel-coated culture dishes and maintained at 37°C in GM in a standard 5% CO2 incubator. The medium was changed every other day.

extract_protocol:
Total RNA was extracted using the ISOGEN II and RNeasy Mini Kit.
Total RNA quantitation and quality checks for purity and integrity were performed using a 5300 Fragment Analyzer System. RNA libraries and transcriptome sequencing were performed by BGI (Guangdong, China). Briefly, the libraries were prepared with the Optimal Dual-mode mRNA Library Prep Kit based on the manufacturer’s recommended protocol.

treatment_protocol: To induce cold stress, SCs were precultured at 37°C for 48 h, followed by 24 h in GM supplemented with 100 mM HEPES (pH 7.4) at 37°C. HEPES was added to stabilize the pH during cold exposure and prevent temperature-dependent pH fluctuations. Sealed plastic containers containing a small amount of water were preequilibrated in a conventional refrigerator maintained at 4°C and monitored with a thermometer. The SC culture dishes were placed into these containers and stored at 4°C for 24h without medium change.

value: skeletal muscle

value: satellite cells

value: cultured at 37°C for 48 hours after plating, followed by 24-hour incubation in GM-HEPES at 37°C, and then exposed to 4°C for 24 hours


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Cold24hrs_3

description: Library name: Cold_GM_D3_3


title: MB125_2B_L6.D708

description: Library name: MB125_2B_L6.D708


title: MB125_1H_L6.D705

description: Library name: MB125_1H_L6.D705

value: Axenic


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Cold24hrs_2

description: Library name: Cold_GM_D3_2


title: X6982

value: Hippocampus


title: X2012


title: WT WGBS rep1

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Library name: WT WGBS rep1

library_source: genomic

data_processing:
Adapter sequences were removed using Trim_galore. Trimmed reads were aligned to the TAIR10 reference genome with BSMAP (v2.90), allowing up to two mismatches and retaining only the best alignment (-v 2 -w 1). Reads containing three or more consecutive CHH sites were classified as unconverted and excluded from further analysis. DNA methylation levels were calculated as the ratio of cytosine reads to the total reads at each cytosine position (#C / (#C + #T)). Biological replicates were merged into single BAM files using SAMtools (v1.9).
Assembly: TAIR10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: flower buds

growth_protocol: Plants were grown under long day conditions (16 hours light/8 hours dark) at 20°C.

extract_protocol:
DNA was extracted using DNeasy Plant Pro Kits
DNA were sheared for 2min, the Epitect Kit was used for bisulfite conversion, and the Ultralow Methyl Kit  was used for library preparation

value: flower buds

value: Columbia 0


title: CK rep2

value: root

value: Yuxi cultivar


title: X6734

value: TYR


title: WT WGBS rep2

description: Library name: WT WGBS rep2


title: hp3 x h2aw.7 WGBS rep2

description: Library name: hp3 x h2aw.7 WGBS rep2


title: X6959


title: h2aw.7 WGBS rep2

description: Library name: h2aw.7 WGBS rep2


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Normal Temperature_GMday3_4

description: Library name: Norm_GM_D3_4

value: cultured at 37°C for 6days


title: MB125_1D_L6.D703

description: Library name: MB125_1D_L6.D703

value: pooled heads collected anterior to swim bladder of larval zebrafish

value: mixed wild type zebrafish line US EPA

value: larvae

value: 10 days post fertilization


title: X6727

value: Saline


title: X6985


title: MB125_1G_L6.D707

description: Library name: MB125_1G_L6.D707


title: h2aw.7 WGBS rep1

description: Library name: h2aw.7 WGBS rep1


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Cold24hrs_1

description: Library name: Cold_GM_D3_1

value: WT


title: hp3 x h2aw.7 WGBS rep1

description: Library name: hp3 x h2aw.7 WGBS rep1


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Normal Temperature_GMday3_3

description: Library name: Norm_GM_D3_3

value: skeletal muscle

value: cultured at 37°C for 5days


title: MB125_1C_L6.D704

description: Library name: MB125_1C_L6.D704


title: X6992


title: hp3 WGBS rep1

description: Library name: hp3 WGBS rep1


title: hp3 WGBS rep2

description: Library name: hp3 WGBS rep2


title: MB125_1F_L6.D706

description: Library name: MB125_1F_L6.D706


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Normal Temperature_GMday3_2

description: Library name: Norm_GM_D3_2

value: satellite cells

value: cultured at 37°C for 4days


title: X6728

value: Hippocampus


title: MB125_1A_L6.D702

description: Library name: MB125_1A_L6.D702

value: Axenic


title: PMTC-056

status: Public on May 29 2025

type: genomic

city: Pittsburgh

first: CHANDAN K

last: SEN

state: PA

address: 221 Republic Street

institute: University of Pittsburgh

hyb_protocol: The Illumina Infinium MethylationEPIC array BeadChip (850K) was carried out by the Epigenomic  Services from Diagenode (Cat nr. G02090000).

data_processing:
The raw intensity data were assessed for quality using BeadArray Controls Reporter (Illumina).  The reference genome GRCh37/hg19 was used as the reference genome and obtained from the UCSC genome browser. Comparative analysis of the data was performed with the Biocionductor R package Chip Analysis Methylation Pipeline (ChAMP).
Probes with p-value > 0.01 or with < 3 beads in at least 5% of samples per probe were filtered. Also, non-CpG probes, SNP-related probes, multi-hit probes and probes located in chromosome X and Y were filtered. A total of 704,870 probes that passed the QC were included in our analyses. Then, the probe beta values per sample were calculated and checked for quality using the multidimensional scaling (MDS) plot and a density plot across the study groups. The beta value representing methylation degree was calculated (0 represents an unmethylated CpG site and 1 represents a fully methylated CpG site). Next, normalization of the obtained beta values was performed using BMIQ75. Differentially methylated probes (DMP) were identified using p-value < 0.001. DMPs were classified based on their genomic coordinates into different categories such as inside the gene body, inbetween genes, in untranslated regions or upstream regions.
processed value definition:  BMIQ75-normalized beta values

label: Cy3, Cy5

source_name: post-mortem whole skin

extract_protocol: genomic DNA was isolated using Qiagen QIAamp DNA kit. The DNA is deaminated with the EZ-96 DNA Methylation Kit (Zymo Research) according to Illumina’s  recommended deamination protocol.

value: post-mortem whole skin

tag: death type on hardy scale

value: Intermediate

tag: manner of death

value: Natural


title: PMTC-055

scan_protocol: The Illumina Infinium MethylationEPIC array BeadChip (850K) was carried out by the Epigenomic  Services from Diagenode (Cat nr. G02090000).


title: PMTC-054

label_protocol: The Illumina Infinium MethylationEPIC array BeadChip (850K) was carried out by the Epigenomic  Services from Diagenode (Cat nr. G02090000).

value: Fast


title: RNA-Seq of Mesocricetus auratus: Satellite cells_Normal Temperature_GMday3_1

description: Library name: Norm_GM_D3_1

value: cultured at 37°C for 3days


title: PMTC-052


title: PMTC-051

value: Homicide


title: PMTC-049


title: PMTC-050


title: PMTC-045

value: Accident


title: PMTC-048


title: PMTC-044


title: PMTC-047


title: PMTC-046


title: PMTC-040


title: PMTC-043

value: Slow


title: PMTC-039

value: Suicide


title: PMTC-042


title: PMTC-035

value: accidental


title: PMTC-036


title: PMTC-037


title: PMTC-034


title: PMTC-032


title: PMTC-031


title: PMTC-030


title: PMTC-026


title: PMTC-038


title: PMTC-024

value: Motor vehicle accident, head on collision


title: PMTC-025


title: PMTC-053


title: PMTC-020


title: PMTC-022


title: PMTC-023

value: Multiple blunt force trauma


title: PMTC-021


title: PMTC-017


title: PMTC-019


title: PMTC-016


title: PMTC-012


title: PMTC-014


title: PMTC-010

value: Unknown


title: PMTC-009


title: PMTC-027


title: PMTC-011


title: PMTC-041


title: PMTC-029


title: PMTC-006

value: suicide


title: PMTC-004


title: PMTC-003


title: PMTC-002


title: PMTC-018


title: PMTC-005

value: natural causes


title: PMTC-008


title: Brain_WT_ME7_4

description: WT animal treated with ME7

value: WT

tag: Sex

value: female

tag: extraction


title: Breast cancer organoid T_BB225

city: Zurich

first: Haithem

last: Dakhli

address: Ramistrasse 71

country: Switzerland

institute: University of Zurich

description:
Library name: Sample 3
10X Genomics

library_source: transcriptomic single cell

data_processing:
The analysis steps (demultiplexing, debarcoding, gene counting and aggregation) were performed using CellRanger v7.1.0
Assembly: GRCh38.p13
Supplementary files format and content: barcodes.tsv / features.tsv / matrix.mtx

source_name: Organoid generated from a breast cancer tissue

growth_protocol: Breast cancer organoids were embedded in Basal Membrane Extract type II at a density of 100.000 cells per 40uL of hydrogel and incubated for 20 minutes and put in an incubator for 20 minutes. Cells were then covered with complete organoid medium: Advanced DMEM-F12 medium containing 250 ng/mL R-Spondin 3, 5 nM Heregulin beta-1, 5 ng/mL FGF-7, 20 ng/mL FGF-10, 5 ng/mL EGF, 100 ng/mL Noggin, 500 nM A83-01, 5 μM Y-27632, 500 nM SB202190, 1X B27 supplement, 1.25 mM N-Acetylcystein, 5 mM Nicotinamide, 1X Glutamax, 10 mM HEPES, 100 U/mL Penicillin/Streptomycin, 50μg/mL primocin. Organoid were grown for 1-2 weeks with change of medium every 3-4 days.

extract_protocol:
The supernatant was discarded and 2 mL of TrypLE were used to disrupt the hydrogel structure. The suspension was then mixed by pipetting and checked under the microscope every 2 minutes until it reached a single-cell suspension state. The suspension was immediately diluted in 40 mL of cold PBS and filtered through a 35 µm sterile cell filter. The flowthrough was centrifugated at 300g for 5 minutes at 4 °C. Supernatant was discarded, the pellet was resuspended in 50 µL of cold PBS-0.02% BSA and subsequently sequenced.
Library was performed according to manufacturer's instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1, 10X Genomics). Cells were resuspended in a master mix to create GEMs, and retrotranscription from polyA RNA tails was performed, resulting in a barcoded cDNA. cDNA was amplified by PCR, cleaned and used for library construction.

tag: tissue


title: Breast cancer organoid T_BB375

description:
Library name: Sample 4
10X Genomics

value: Organoid generated from a breast cancer tissue


title: Breast cancer organoid T_BB475

description:
Library name: Sample 6
10X Genomics

tag: cell line

value: breast cancer tissue


title: PMTC-001

value: post-mortem whole skin


title: Breast cancer organoid T_BB420

description:
Library name: Sample 5
10X Genomics


title: Breast cancer organoid T_BB171

description:
Library name: Sample 2
10X Genomics


title: Breast cancer organoid T_BB056

description:
Library name: Sample 1
10X Genomics


title: PBMC, CCC13 clinical form

city: Belo Horizonte

first: Thaiany

last: Goulart de Souza-Silva

address: Avenida Antônio Carlos

department: Morphology

country: Brazil

institute: Federal University of Minas Gerais

description: Library name: FR

data_processing:
Raw sequencing reads were processed using the BD Rhapsody Targeted Analysis Pipeline (version CWL-v1.2). The pipeline performed demultiplexing, read alignment to the human genome (GRCh38), UMI collapsing to remove PCR duplicates, and generation of gene-cell count matrices.
Assembly: GRCh38
Supplementary files format and content: .csv

source_name: Blood

extract_protocol:
RNA was extracted from single cells using the BD™ Single-Cell Multiplexing Kit (BD Biosciences), followed by cDNA synthesis and library preparation with the BD Rhapsody Express Single-Cell Analysis System. The BD Rhapsody cDNA kit (cat# 633663) and BD Target Amplification kit (cat# 633664) were used according to the manufacturer's protocols
cDNA libraries were constructed using the BD Rhapsody Express Single-Cell Analysis System (BD Biosciences), following the manufacturer’s instructions. The BD Rhapsody cDNA kit (cat# 633663) and BD Target Amplification kit (cat# 633664) were used for reverse transcription, cDNA synthesis, and amplification. Libraries incorporated sample barcodes and Unique Molecular Identifiers (UMIs) during cDNA synthesis to enable single-cell and molecule-level resolution.

value: Blood

value: Peripheral blood mononuclear cells

value: Wild type (human)

tag: batch


title: PBMC, CCC12 clinical form

description: Library name: BM


title: PMTC-033

value: Fast

value: Natural


title: PBMC, CCC11 clinical form

description: Library name: NMJ


title: PBMC, CCC10 clinical form

description: Library name: RRS


title: PBMC, IND3 clinical form

description: Library name: MLDM


title: PBMC, CCC9 clinical form

description: Library name: CJS


title: PBMC, CCC8 clinical form

description: Library name: NPS


title: PBMC, CCC7 clinical form

description: Library name: ARS


title: PBMC, CCC6 clinical form

description: Library name: JRS


title: PBMC, IND2 clinical form

description: Library name: MAC


title: PBMC, CCC5 clinical form

description: Library name: MMCS


title: PBMC, CCC4 clinical form

description: Library name: JSD


title: PBMC, IND1 clinical form

description: Library name: AMSM


title: PMTC-007

value: Intermediate


title: PBMC, CCC3 clinical form

description: Library name: MPS


title: PBMC, CCC1 clinical form

description: Library name: ACCL


title: H1048_PF_R2

city: Boston

first: Yixiang

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: H1048_PF_R2

data_processing:
Sequencing reads were mapped to the hg38 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.
Assembly: GrCh38
Supplementary files format and content: Supplementary files format and content: tab-delimited text file includes raw counts for each samples
Supplementary files format and content: Supplementary files format and content: tab-delimited text file includes FPKM values for each samples

source_name: NCI-H1048 cell line

growth_protocol: SCLC PDX tumor DFCI 393 originated from surgical biopsy at resistance from a patient that received prior chemotherapy and radiation. The surgical biopsy of DFCI 393 was implanted directly into the sub-renal capsule of NSG mice for expansion. Following initial implantation, all PDX tumors were expanded and passaged in NSG mice as subcutaneous tumors. Early passage NCI-H1048 cells from ATCC were grown in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS), P/S and Insulin-Transferrin-Selenium.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen #74106) including a DNase digestion step according to the manufacturer’s instructions and RNA sequencing was performed.
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell. Sequencing reads were mapped to the mm10 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.

treatment_protocol: The SCLC PDX DFCI393 tumors were treated with the orally bioavailable cyclin A/B RxL inhibitor CIRc-014 at 100 mg/kg PO TID or vehicle (30% PEG400, 20% Solutol HS15, 50% Phosal 53 MCT) three times a day for 4 days and tumors were collected 8 hours after the morning dose on the last day of treatment and snap frozen for RNA-seq. 6 independent tumors from 6 independent mice were used for CIRc-014 and 5 independent tumors from 5 independent mice were used for vehicle.  NCI-H1048 cells were plated  plated at 500,000 cells/mL density in presence of DMSO (vehicle), cyclin A/B RxL inhibitor (CIRc-004 or CIRc-014, 200nM), inactive enantiomer (CIRc-005, 200nM) or a Cdk2 inhibitor (PF-07104091, 500nM). 24 hours after treatment with drugs, cells were harvested for RNA. The NCI-H1048 cell line experiments were done in 2 biological replicates.

value: NCI-H1048 cell line

value: SCLC cells


title: H1048_PF_R1

description: Library name: H1048_PF_R1


title: H1048_14_R2

description: Library name: H1048_14_R2


title: H1048_14_R1

description: Library name: H1048_14_R1


title: PBMC, CCC2 clinical form

description: Library name: VPR


title: H1048_04_R2

description: Library name: H1048_04_R2


title: H1048_R2

description: Library name: H1048_R2

value: DMSO


title: H1048_05_R2

description: Library name: H1048_05_R2


title: DFCI393_340

description: Library name: DFCI393_340

source_name: SCLC PDX tumor

value: SCLC PDX tumor


title: DFCI393_334

description: Library name: DFCI393_334


title: DFCI393_325

description: Library name: DFCI393_325


title: DFCI393_321

description: Library name: DFCI393_321


title: DFCI393_320

description: Library name: DFCI393_320


title: H1048_04_R1

description: Library name: H1048_04_R1


title: H1048_R1

description: Library name: H1048_R1


title: DFCI393_346

description: Library name: DFCI393_346

value: Vehicle


title: DFCI393_331

description: Library name: DFCI393_331


title: DFCI393_309

description: Library name: DFCI393_309


title: DFCI393_305

description: Library name: DFCI393_305


title: DFCI393_323

description: Library name: DFCI393_323


title: T cells from Synovium tissue, GEX, AxSpA patient, rep 1

city: OXFORD

first: Feng

last: Liu

address: Green Templeton College, 43 Woodstock Road

institute: University of Oxford

description:
Library name: Sample3_GEX
Synovial T cells were isolated from fresh synovial tissue of an AxSpA patient via enzyme digestion followed by FACS enrichment of CD3+ cells.

data_processing:
The paired reads obtained were mapped to the hg38 reference genome to generate gene expression matrices using CellRanger.
Assembly: GRCh38 hg38
Supplementary files format and content: TAR file including seurat object

source_name: Synovium tissue

extract_protocol:
Synovial tissue was obtained from surgical procedures. Cells were isolated from fresh tissue through enzyme digestion using 100 µg/ml Liberase TL and 100 µg/ml DNase in RPMI. The isolated cells were either directly subjected to the Chromium Single Cell Gene Expression Chip (10X Genomics) assay or sorted into live CD3+ and CD3- populations using Fluorescence-activated Cell Sorting (FACS). For FACS, the single cell suspension was first incubated with Human TruStain FcX solution (Biolegend) to block Fc receptors and then stained with anti-CD3 (clone OKT3) and Fixable Viability Dye eFluor 780 (eBioscience/ThermoFisher).
Approximately 20,000 cells from each population were loaded onto a Chromium Next GEM Chip (10X Genomics), and scRNA-seq libraries were prepared according to the manufacturer’s instructions. For samples directly applied to library preparation without sorting, around 20,000 cells from each sample were loaded. The resulting DNA libraries were sequenced at >50,000 reads per cell on a NovaSeq 6000 using PE150 mode.

value: Synovium tissue

value: T cells

value: male

tag: age


title: Synovium tissue, AxSpA patient, rep 2

description:
Library name: Sample6_GEX
Synovial cells were isolated from fresh synovial tissue of an AxSpA patient via enzyme digestion

value: Synovial cells

value: female


title: T cells from Synovium tissue, TCR, AxSpA patient, rep 2

description:
Library name: Sample2_TCR
Synovial T cells were isolated from fresh synovial tissue of an AxSpA patient via enzyme digestion followed by FACS enrichment of CD3+ cells. T cell receptor library was used.


title: Synovium tissue, AxSpA patient, rep 1

description:
Library name: Sample5_GEX
Synovial cells were isolated from fresh synovial tissue of an AxSpA patient via enzyme digestion


title: DFCI393_316

description: Library name: DFCI393_316


title: HIPSCI_CNT_HIPSCI_yoch6_k27ac_r2

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

institute: University of Goettingen

description: Library name: yoch6_k27ac_r2

data_processing:
For visualisation of Cut&Tag signal across HipSci donor lines, initial quality check of paired-end reads was performed by FastQC v0.11.5.
Nextera Transposase adapter and low-quality bases were eliminated using Cutadapt v1.17
Reads were mapped to the hg38 reference using bowtie2 v2.3.4.2, mapped pairs with mapping quality <30 were removed.
Replicates were removed using GATK Picard MarkDuplicates.
Genome browser tracks in bigwig format were generated using deepTools bamCoverage (options: binsize = 10, RPGC normalization)
Assembly: GRCh38
Supplementary files format and content: bigwig coverage files
Library strategy: CUT&Tag

source_name: hiPSC

extract_protocol:
CUT&Tag libraries were generated according to the EpiCypher protocol (Kaya-Okur et al., 2019) with minor modifications. As described for ATAC-seq, hiPSCs were harvested with accutase (StemCell Technologies; 07922). After resuspension in 1X DPBS (Life Technologies; 14190144), 2 x 10⁵ cells per CUT&Tag reaction underwent centrifugation at 300 x g for 3 min at RT. Cells were then lysed in 100μl of cold Nuclear Extraction (NE) Buffer (20mM HEPES–KOH, pH 7.9, 10mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5mM Spermidine (Sigma-Aldrich; 05292), 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor (Roche; 11836170001)) per CUT&Tag reaction for 10 min on ice. The nuclei were then centrifuged for 3 min at 600 x g at RT before resuspension in cold NE Buffer to achieve a final concentration of 1.2 x 10⁶ nuclei/ml.  For each CUT&Tag reaction, 11μl of concanavalin A (ConA) beads (EpiCypher; 21-1401) were washed twice on a magnetic stand with 100 μl of Bead Activation (BA) Buffer (20mM HEPES, pH 7.9, 10mM KCl, 1mM CaCl₂, 1mM MnCl₂). The beads were then resuspended in 11μl of BA Buffer, and 10μl beads were aliquoted into a 0.2ml tube. Each tube of activated ConA beads was then incubated with 100μl of nuclei for 10 min at RT. The supernatant was then removed with a magnet and the beads were resuspended in 50μl of cold Antibody150 Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2mM EDTA) containing a 1:50 dilution of rabbit primary antibody (anti-H3K4me1 (Active Motif; 39298) or anti-H3K27ac (Abcam; ab4729)) and incubated overnight at 4°C on a rocker.  The following day, the supernatant was discarded with a magnet and the beads were incubated in 50μl of Digitonin150 Buffer (20mM HEPES, pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin) containing 0.5μg of anti-rabbit secondary antibody (Epicypher; 13-0047) for 1 hour at RT. The beads were then washed twice on a magnet with Digitonin150 Buffer, then incubated in 50μl of Digitonin300 Buffer (20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1x cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin), and 1.25μl of CUTANA pAG-TN5 (EpiCypher; 15-1017) for 1 hour at RT. The beads were then washed twice with a magnet by resuspension in Digitonin300 Buffer, then incubated in 50μl of chilled Tagmentation Buffer (Digitonin 300 Buffer, 10mM MgCl₂) for 1 hour at 37°C.  The supernatant was then discarded with a magnet and the beads were washed once with 50μl RT TAPS Buffer (10mM TAPS, pH 8.5, 0.2mM EDTA). The supernatant was again removed with the magnet and the beads were resuspended in 5μl of RT SDS Release Buffer (10mM TAPS, pH 8.5, 0.1% SDS) and vortexed on maximum speed for 10 sec followed by a brief centrifugation. The beads were then incubated for 1 hour at 58°C before the addition of 15μl of RT SDS Quench Buffer (0.67% Triton-X 100 in Molecular grade H₂O), vortexing at maximum speed for 10 sec, and a brief centrifugation.
For library amplification, samples were combined with 2μl of 5µM i5 primer, 2μl of 5µM i7 primer and 25μl of CUTANA High Fidelity PCR mix (EpiCypher; 15-1018). The following PCR programme was then used for all libraries: 58°C for 5 min, 72°C for 5 min, and 98°C for 45 sec. This was followed by 11 cycles for anti-H3K27ac and 13 cycles for anti-H3K4me1 of [98°C for 15 sec and 60°C for 10 sec], before a final extension at 72°C for 1 min.  Libraries then underwent two 1X AMPure XP bead (Beckman Coulter; A63881) cleanups. Following QC on a Bioanalyzer, libraries were multiplexed and sequenced (paired-end 150 bp) using a NovaSeq 6000 instrument (Illumina).

value: hiPSC


title: T cells from Synovium tissue, GEX, AxSpA patient, rep 2

description:
Library name: Sample4_GEX
Synovial T cells were isolated from fresh synovial tissue of an AxSpA patient via enzyme digestion followed by FACS enrichment of CD3+ cells.


title: HIPSCI_CNT_HIPSCI_wibj2_k4me1_r2_L1_2

description: Library name: wibj2_k4me1_r2_L1_2


title: HIPSCI_CNT_HIPSCI_yoch6_k4me1_r2

description: Library name: yoch6_k4me1_r2


title: T cells from Synovium tissue, TCR, AxSpA patient, rep 1

description:
Library name: Sample1_TCR
Synovial T cells were isolated from fresh synovial tissue of an AxSpA patient via enzyme digestion followed by FACS enrichment of CD3+ cells. T cell receptor library was used.


title: HIPSCI_CNT_HIPSCI_yoch6_k4me1_r1

description: Library name: yoch6_k4me1_r1


title: HIPSCI_CNT_HIPSCI_yoch6_k27ac_r1

description: Library name: yoch6_k27ac_r1


title: HIPSCI_CNT_HIPSCI_wibj2_k4me1_r2_L1_1

description: Library name: wibj2_k4me1_r2_L1_1


title: HIPSCI_CNT_HIPSCI_wibj2_k4me1_r1_L1_1

description: Library name: wibj2_k4me1_r1_L1_1


title: H1048_05_R1

description: Library name: H1048_05_R1


title: HIPSCI_CNT_HIPSCI_wibj2_k27ac_r1_L1_2

description: Library name: wibj2_k27ac_r1_L1_2


title: HIPSCI_CNT_HIPSCI_wibj2_k4me1_r1_L1_2

description: Library name: wibj2_k4me1_r1_L1_2


title: HIPSCI_CNT_HIPSCI_wibj2_k27ac_r2_L1_2

description: Library name: wibj2_k27ac_r2_L1_2


title: HIPSCI_CNT_HIPSCI_sojd3_k4me1_r1

description: Library name: sojd3_k4me1_r1


title: HIPSCI_CNT_HIPSCI_wibj2_k27ac_r1_L1_1

description: Library name: wibj2_k27ac_r1_L1_1


title: HIPSCI_CNT_HIPSCI_sojd3_k4me1_r2

description: Library name: sojd3_k4me1_r2


title: HIPSCI_CNT_HIPSCI_sojd3_k27ac_r2

description: Library name: sojd3_k27ac_r2


title: HIPSCI_CNT_HIPSCI_qolg1_k4me1_r2

description: Library name: qolg1_k4me1_r2


title: HIPSCI_CNT_HIPSCI_sojd3_k27ac_r1

description: Library name: sojd3_k27ac_r1


title: HIPSCI_CNT_HIPSCI_qolg1_k27ac_r1

description: Library name: qolg1_k27ac_r1


title: HIPSCI_CNT_HIPSCI_qolg1_k27ac_r2

description: Library name: qolg1_k27ac_r2


title: HIPSCI_CNT_HIPSCI_podx1_k4me1_r2

description: Library name: podx1_k4me1_r2


title: HIPSCI_CNT_HIPSCI_letw5_k4me1_r2

description: Library name: letw5_k4me1_r2


title: HIPSCI_CNT_HIPSCI_podx1_k4me1_r1

description: Library name: podx1_k4me1_r1


title: HIPSCI_CNT_HIPSCI_letw5_k27ac_r2

description: Library name: letw5_k27ac_r2


title: HIPSCI_CNT_HIPSCI_kucg2_k4me1_r2

description: Library name: kucg2_k4me1_r2


title: HIPSCI_CNT_HIPSCI_letw5_k27ac_r1_L1_5

description: Library name: letw5_k27ac_r1_L5


title: HIPSCI_CNT_HIPSCI_letw5_k27ac_r1_L1_1

description: Library name: letw5_k27ac_r1_L1


title: HIPSCI_CNT_HIPSCI_podx1_k27ac_r1

description: Library name: podx1_k27ac_r1


title: HIPSCI_CNT_HIPSCI_wibj2_k27ac_r2_L1_1

description: Library name: wibj2_k27ac_r2_L1_1


title: HIPSCI_CNT_HIPSCI_kucg2_k27ac_r1

description: Library name: kucg2_k27ac_r1


title: HIPSCI_CNT_HIPSCI_kucg2_k4me1_r1

description: Library name: kucg2_k4me1_r1


title: HIPSCI_CNT_HIPSCI_kolf3_k4me1_r1

description: Library name: kolf3_k4me1_r1


title: HIPSCI_CNT_HIPSCI_kolf2_k4me1_r1

description: Library name: kolf2_k4me1_r1


title: HIPSCI_CNT_HIPSCI_kolf2_k4me1_r2

description: Library name: kolf2_k4me1_r2


title: HIPSCI_CNT_HIPSCI_kucg2_k27ac_r2

description: Library name: kucg2_k27ac_r2


title: HIPSCI_CNT_HIPSCI_kolf2_k27ac_r1

description: Library name: kolf2_k27ac_r1


title: HIPSCI_CNT_HIPSCI_bima1_k4me1_r1

description: Library name: bima1_k4me1_r1


title: HIPSCI_CNT_HIPSCI_kolf3_k27ac_r1

description: Library name: kolf3_k27ac_r1


title: HIPSCI_CNT_HIPSCI_qolg1_k4me1_r1

description: Library name: qolg1_k4me1_r1


title: HIPSCI_CNT_HIPSCI_bima1_k4me1_r2

description: Library name: bima1_k4me1_r2


title: HIPSCI_CNT_HIPSCI_letw5_k4me1_r1

description: Library name: letw5_k4me1_r1


title: HIPSCI_CNT_HIPSCI_bima1_k27ac_r2

description: Library name: bima1_k27ac_r2


title: HIPSCI_CNT_HIPSCI_bima1_k27ac_r1

description: Library name: bima1_k27ac_r1


title: HASMC, H2A.Z, rep2 (Cut&Tag)

city: Xiamen

first: Wei

last: Shen

state: Fujian

address: 2999 Jinshan Rd, Huli District

institute: Xiamen University

description:
Library name: HASMC_H2A.Z_rep2, CUTnTag
human aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to GRCh38.p14 genome downloaded from ensembl by bowtie2
duplicated reads were further removed by picard
bigwig files were generated by deeptools
Assembly: GRCh38.p14
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: aortic smooth muscle cell

extract_protocol:
cells lysed and nucleus were incubated with tn5 transposase to retrieve the accessible DNA
library was contructed by using CUT&TAG 3.0 High-Sensitivity Kit for Illumina (Novoprotein N259-YH01) or TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD502)

value: aortic smooth muscle cell

value: WT


title: MM13_KI67minus_rep2

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

description: Library name: Sample2

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg38 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg38 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each condition (KI67 positive vs KI67 negative)
Assembly: hg38
Supplementary files format and content: raw HT counts  tab delimited file
Supplementary files format and content: A tab delimited file with raw read counts for  each sample

source_name: metastasis of cutaneous melanoma

growth_protocol: MM13 PDXs cells were  fixed using PFA 1% and stained for KI67-647 antibody. Samples were sorted at 4C for KI67 expression and sub-populations collected.

extract_protocol:
RNA extraction was immediately performed using the RNeasy FFPE RNA extraction kit (Qiagen) according to manufacturer’s instructions.
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA

value: metastasis of cutaneous melanoma

value: melanoma


title: MM13_KI67minus_rep1

description: Library name: Sample1


title: MM13_KI67plus_rep3

description: Library name: Sample4


title: HIPSCI_CNT_HIPSCI_kolf3_k4me1_r2

description: Library name: kolf3_k4me1_r2


title: HIPSCI_CNT_HIPSCI_podx1_k27ac_r2

description: Library name: podx1_k27ac_r2


title: HASMC (ATAC-Seq)

description:
Library name: HASMC, ATAC-Seq
human aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to GRCh38.p14 genome downloaded from ensembl by bowtie2
duplicated reads were further removed by picard
bigwig files were generated by deeptools
Assembly: GRCh38.p14
Supplementary files format and content: bigwig


title: HASMC, H2A.Z, rep1 (Cut&Tag)

description:
Library name: HASMC_H2A.Z_rep1, CUTnTag
human aortic smooth muscle cell


title: HIPSCI_CNT_HIPSCI_kolf2_k27ac_r2

description: Library name: kolf2_k27ac_r2


title: HASMC, H2A.Z, rep3 (Cut&Tag)

description:
Library name: HASMC_H2A.Z_rep3, CUTnTag
human aortic smooth muscle cell


title: HASMC2_rep3

description:
Library name: HASMC2_rep3
human aortic smooth muscle cell

data_processing:
raw reads was cleaned by fastp with default parameters
cleaned reads were mapped to GRCh38.p14 or Rn7 genome downloaded from ensembl by STAR
Raw counts were generated by using htseq-count with default parameters
Assembly: GRCh38.p14, Rn7
Supplementary files format and content: raw counts

extract_protocol:
The mRNA were purified, fragmented and amplified for RNA-Seq
Library was constructed by using Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (Yeasen, 12301ES96)


title: HASMC2_rep1

description:
Library name: HASMC2_rep1
human aortic smooth muscle cell


title: HASMC2_cholesterol_rep3

description:
Library name: HASMC2_cholesterol_rep3
human aortic smooth muscle cell


title: HIPSCI_CNT_HIPSCI_kolf3_k27ac_r2

description: Library name: kolf3_k27ac_r2


title: HASMC2_cholesterol_rep2

description:
Library name: HASMC2_cholesterol_rep2
human aortic smooth muscle cell


title: HASMC2_cholesterol_rep1

description:
Library name: HASMC2_cholesterol_rep1
human aortic smooth muscle cell


title: HASMC1_rep3

description:
Library name: HASMC1_rep3
human aortic smooth muscle cell


title: HASMC1_cholesterol_rep2

description:
Library name: HASMC1_cholesterol_rep2
human aortic smooth muscle cell

value: cholesterol


title: HASMC2_rep2

description:
Library name: HASMC2_rep2
human aortic smooth muscle cell


title: MM13_KI67plus_rep2

description: Library name: Sample3


title: HASMC1_cholesterol_rep3

description:
Library name: HASMC1_cholesterol_rep3
human aortic smooth muscle cell


title: Ad-CTR+PDGF-BB3

city: Jinan

first: lei

last: wang

address: 07 Wenhua xi road, Jinan, Shandong

institute: Qilu hospital Shandong University

description:
Library name: Sample 6
TRL_PDGF3

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCh38.108
Supplementary files format and content: FPKM, counts

source_name: HASMC

growth_protocol: HASMCs were maintained in Smooth Muscle Cell Medium (SMCM) containing 2% FBS, 1% penicillin/streptomycin solution and  1% smooth muscle cell growth supplement at at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from the arteries and cells via an RNApure Tissue & Cell Kit (CW0581M; CWBIO, Taizhou, China) according to the manufacturer’s instructions. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HASMCs were transfected with control or ZFP36 adenovirus in complete growth medium for 12 hours, and then cultured in SMCM witout FBS for 24 hours followed by PDGF-BB treatment (20ng/ml, Proteintech) for another 24 hours.

value: HASMC

value: smooth muscle cell

value: Transfected with Ad-CTR and treated with PDGF-BB


title: Ad-CTR+PDGF-BB1

description:
Library name: Sample 4
TRL_PDGF1


title: HASMC1_cholesterol_rep1

description:
Library name: HASMC1_cholesterol_rep1
human aortic smooth muscle cell


title: Ad-CTR+PDGF-BB2

description:
Library name: Sample 5
TRL_PDGF2


title: Ad-ZFP36+PDGF-BB2

description:
Library name: Sample 2
Ad_TTP_PDGF2

value: Transfected with Ad-ZFP36 and treated with PDGF-BB


title: Ad-ZFP36+PDGF-BB1

description:
Library name: Sample 1
Ad_TTP_PDGF1


title: Ad-ZFP36+PDGF-BB3

description:
Library name: Sample 3
Ad_TTP_PDGF3


title: Human aortic media

description:
Library name: Aorta
human aortic smooth muscle cell

library_source: genomic single cell

data_processing:
sequencing data was processed by cellranger-atac and sequencing data were merged during this step. Both the pre-bullt genome reference and self-build genome reference (ensembl assembly 112) were used.
processed files was further analyzed by r packages of Signac and Suerat
Assembly: cellranger's pre-built genome reference and self-build genome reference (ensembl assembly 112)
Supplementary files format and content: h5 files

source_name: aortic media

extract_protocol:
The isolated human aorta media was dounced, lysed and washed to retrieve cell nuclei for scATAC-Seq.
Received cell nuclei were then proceeded to construct a scATAC-Seq v2 library by using Chromium Next GEM Single Cell ATAC Reagent Kits v2 (10x Genomics 1000390), and 20 GB sequencing data were generated to trace chromatin accessibility at single cell level.

value: aortic media

value: vascular smooth muscel cells


title: Donor 4 replicate 2 Mock

city: Roma

first: Giuseppe

middle: Rubens

last: Pascucci

state: RM

address: Viale Regina Elena, 291

department: Center for Life Nano Science

institute: Istituto Italiano di Tecnologia

description: Library name: s4 rep2 Mock

data_processing:
The sequencing quality of each sample was assessed with FASTQC v.0.11.9.
RNA-seq reads were independently aligned against the Ensamble hg19 reference transcriptome and quantified using Kallisto v.0.46.2 with the -b 60 parameter and Sleuth v.0.30.0
Assembly: hg19
Supplementary files format and content: TPM_Transcripts_Level_Sleuth_s4_Mock-INF.txt

source_name: Liver

growth_protocol: PHHs were prepared using the protocol described in Le Cluyse & Alexandre (2010) with minor modifications. Liver samples are first perfused in Solution I (NaCl 58,44 M, KCl 74,56 M, Na2HPO4, 2H2O 177,99 M, Hepes 0,6%, EGTA 0,5 mM; pH7,4) and then in Solution II (NaCl 58,44 M, KCl 74,56 M, Na2HPO4, 2H2O 177,99 M, Hepes 0,6%, CaCl2 110 M) containing 0,4 mg/ml of collagenase from Clostridium histolyticum (Sigma-Aldrich, #C5138). Cells are seeded at 2,5x10^5 cells per cm² on collagen type IV (Corning, #354236) pretreated plates and cultured overnight in William’s medium (Life Technologies, #22551-089) supplemented with 10% Fetal Clone II (GE Healthcare), 1% penicillin/streptomycin (Invitrogen, #15140122), 1% Glutamax X100 (Invitrogen, #35050038), 5 µg/ml Insulin (Sigma–Aldrich, #I9278) and 5×10-7 M hydrocortisone (Upjohn Laboratories). PHHs are then extensively washed in serum-free medium, kept in serum-free medium for 24 hours to counter-select the growth of contaminating fibroblast and endothelial cells, and then plated in complete William’s medium. PHHs were treated with 2% of DMSO (Sigma–Aldrich, #D2650) for 24 hours before infection and then incubated for 16 h with an HBV inoculum produced in HepAD38 cells at a multiplicity of infection of 250 vge (virus genome equivalents) per cell, in presence of 4% PEG-8000 (Polyethylene glycol, Sigma–Aldrich, #1546605).

extract_protocol:
Total cellular RNA was extracted with the Extract-All reagent (Eurobio, #GEXEXT040U) following the manufacturer’s protocol. Extracted RNA was treated for 1 h at 37 °C with RNAse-free DNase I (Invitrogen, #AM2222), which was subsequently inactivated at 70 °C for 20 min. RNA reverse transcription was performed using the Superscript® IV RT kit (Invitrogen, #18090010), according to manufacturer's instructions.
mRNA libraries were prepared using the TruSeq® Stranded RNA HT (w/Ribo-Zero™) kit to increases the depth of sequencing. Each library was pair-end and was sequenced using 75x2 cycles on a NextSeq 500 Illumina platform for s1, s2 and s3 samples, while 100x2 cycles on a NovaSeq 6000 Illumina platform for s4 samples

treatment_protocol: The HBV inoculum used in this study was prepared from HepAD38 cells as previously described (Ladner et al., 1997). HepAD38 is an HepG2-derived stable cell line Carrying a 1.3 HBV transgene (genotype D, serotype ayw) under the control of a tet-off promoter. HepAD38 cells were cultured in HYPERFlask® (Corning, #10020) coated with type IV collagen (Corning, #354236) in 550 ml of complete DMEM-F12 medium supplemented with 10% decomplemented FBS (Gibco, #10270-106), 1% penicillin/streptomycin (Invitrogen, #15140122) and 1% sodium-pyruvate (Invitrogen, #11360039). Supernatants (550 ml/flask) were harvested twice a week for at 3-4 months, clarified first through 0.45 μm and then 0.22 µm filters (Millipore, #10785534) and precipitated overnight at 4 °C with 8% PEG-8000 (Sigma–Aldrich, #1546605), The precipitates were centrifuged at 3500 g for 1 hour and the pellets resuspended in Opti-MEM (Invitrogen, #31985070) to achieve a 50 to 100 fold concentration. After DNA extraction (QIAmp Ultrasens Virus kit, Qiagen) the HBV inoculum was tittered by qPCR using serial dilutions of an HBV plasmid to build a standard curve. Primers are detailed in Supplementary Figure 1. All viral preparations were tested for the presence of endotoxins (Lonza Verviers, Belgium). IFN2a treatment (Roferon-A, Roche) on MOCK-infected PHH was administered post infection (1000 UI/ml) and renewed every 48h until the desired time points (1000 UI/ml).

value: Liver

value: Primary Human Hepatocytes (PHHs)

value: Control sample


title: Donor 4 replicate 3 Mock-IFN

description: Library name: s4 rep3 Mock-IFN

value: IFN treated


title: Donor 4 replicate 3 Mock

description: Library name: s4 rep3 Mock


title: HASMC_rep3

description:
Library name: HASMC_rep3
human aortic smooth muscle cell

extract_protocol:
cells lysed and nucleus were incubated with tn5 transposase to retrieve the accessible DNA
library was contructed by using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD502)


title: HASMC_rep1

description:
Library name: HASMC_rep1
human aortic smooth muscle cell


title: HASMC_rep2

description:
Library name: HASMC_rep2
human aortic smooth muscle cell


title: Donor 4 replicate 1 Mock

description: Library name: s4 rep1 Mock


title: replicate 1 of BG4 CUT&Tag in HeLa, add PDS

city: Changsha

first: Ke-wei

last: Zheng

address: Lushan Road (S), Yuelu District

department: School of Medical Sciences

institute: Hunan University

description: Library name: HeLa_BG4_CUT_Tag_PDS_rep 1

data_processing:
CUT&Tag reads were aligned with bowtie2 (Galaxy Version 2.5.0+galaxy0) using default parameters. Normalized (RPKM, reads per kilobase per million) coverage tracks were generated using deepTools bamcoverage (Galaxy Version 3.5.1.0.0) with parameters -binSize 50 –ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: cervical cancer tissue

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin (P/S)

extract_protocol:
CUT&Tag was constructed as described (Zheng et al., 2024). The bead-bound cells were resuspended in 100 uL dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1 uL protease inhibitors) containing 1/50 DNA G-quadruplex (BG4) antibody (MABE917, sigma) and followed by anti-FLAG M2 antibody (F1804, sigma) and secondary antibodies.
To amplify libraries, 21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high-fidelity 2× master mix. The libraries were purified with 1.2× volume of Ampure XP beads (Beckman Counter), and libraries were eluted in 30 µL 10 mM Tris-HCl (pH 8.0).

treatment_protocol: HeLa cells were treated with 5 µM PyBI or 5 µM PDS for 24 hours.

value: cervical cancer tissue

value: HeLa

value: add PDS


title: Donor 4 replicate 2 Mock-IFN

description: Library name: s4 rep2 Mock-IFN


title: replicate 1 of BG4 CUT&Tag in HeLa, add PyBI

description: Library name: HeLa_BG4_CUT_Tag_PyBI_rep 1

value: add PyBI


title: Donor 4 replicate 1 Mock-IFN

description: Library name: s4 rep1 Mock-IFN


title: replicate 2 of BG4 CUT&Tag in HeLa, add PDS

description: Library name: HeLa_BG4_CUT_Tag_PDS_rep 2


title: replicate 2 of BG4 CUT&Tag in HeLa, untreated

description: Library name: HeLa_BG4_CUT_Tag_Untreated_rep 2

value: untreated


title: replicate 2 of BG4 CUT&Tag in HeLa, add PyBI

description: Library name: HeLa_BG4_CUT_Tag_PyBI_rep 2


title: HASMC1_rep1

description:
Library name: HASMC1_rep1
human aortic smooth muscle cell

value: aortic smooth muscle cell

value: WT


title: HONE1, KO, rep2

city: Guangzhou

first: Xiaoyu

last: Liang

address: 651 Dongfengdongroad, Guangzhou, Guangdong

institute: Sun Yat-sen University Cancer

description:
Library name: Sample 4
Column name in FPKM_all_samples.xls : KO_2 FPKM

data_processing:
RNAseq libraries were loaded on the cBot (automated cluster generation system) (Illumina), and sequenced using the Illumina NovaSeq 6000 platform. Sequencing reads were mapped to the human (hg38) reference genome with HiSat2 (version 2.1.0).
FPKM (Fragments Per Kilobase of exon modelper Million mapped fragments) was used to calculate relative transcript level of genes.
Subsequently, genes which did not have at least 10 reads were discarded. Differential expression analysis was conducted by the Bioconductor packages edgeR (version 3.12) and limma (version 3.12).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: xls files include FPKM values for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent kit.
RNA sequencing libraries were prepared based on the standard Illumina instruction.

value: Nasopharyngeal carcinoma cell line

value: PROCR  knockout

value: radiation


title: HASMC1_rep2

description:
Library name: HASMC1_rep2
human aortic smooth muscle cell


title: replicate 1 of BG4 CUT&Tag in HeLa, untreated

description: Library name: HeLa_BG4_CUT_Tag_Untreated_rep 1


title: HONE1, WT, rep1

description:
Library name: Sample 1
Column name in FPKM_all_samples.xls : WT_1 FPKM


title: HONE1, WT, rep2

description:
Library name: Sample 2
Column name in FPKM_all_samples.xls : WT_2 FPKM


title: RJ-A87

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

data_processing:
Reads were aligned using the STAR software . Aligned reads were counted using HTSeq framework
Assembly: hg38
Supplementary files format and content: raw counts

source_name: Bone marrow

extract_protocol:
Total RNA was isolated and purified using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, 80004). The quantity and integrity of RNA was assessed using the Agilent 2100 bioanalyzer.
Total RNA-seq libraries were prepared using the KAPA RNA HyperPrep kit (Roche, 07962312001)

value: Bone marrow

value: Male

tag: disease

value: Adult T-ALL


title: RJ-A86


title: RJ-A84

value: Female


title: RJ-A82


title: RJ-A80


title: RJ-A79


title: RJ-A78


title: RJ-A77


title: RJ-A76


title: RJ-A73


title: RJ-A71


title: RJ-A72


title: RJ-A74


title: HONE1, KO, rep1

description:
Library name: Sample 3
Column name in FPKM_all_samples.xls : KO_1 FPKM


title: RJ-A66


title: RJ-A67


title: RJ-A68


title: RJ-A64


title: RJ-A62


title: RJ-A69


title: LJR-220107-220126


title: RJ-A65


title: LJR-211231-2109566


title: LJR-211110-2107968


title: LJR-211022-2107359


title: LJR-211011-2106959


title: LJR-210922-2106545


title: LJR-210917-2106492


title: LJR-211203-2108656


title: LJR-211025-2107462


title: RJ-A70


title: RJ-A63


title: LJR-211206-2108750


title: RJ-A83


title: LJR-220107-220129


title: LJR-210825-2105790


title: LJR-210611-2103735


title: LJR-211201-2108585


title: LJR-210714-2104593


title: LJR-210915-2106396


title: LJR-210917-2106393


title: LJR-210428-2102697


title: LJR-210428-2102643


title: LJR-210421-2102460


title: LJR-210922-2106547


title: LJR-210906-2106127


title: LJR-210906-2106126


title: LJR-210804-2105253


title: LJR-210818-2105618


title: LJR-211115-2108106


title: LJR-210827-2105869


title: LJR-210416-2102353


title: LJR-210723-2104864


title: LJR-210402-2102029


title: LJR-201123-2006207


title: LJR-2012011-2006396


title: LJR-210625-2104105


title: LJR-201202-2006391


title: LJR-210616-2103785


title: LJR-2012011-2006699


title: LJR-210127-2100576


title: LJR-201023-2005500


title: LJR-201012-2005162


title: LJR-201127-2006326


title: LJR-201009-2005127


title: LJR-210208-2100822


title: LJR-200311-2000851


title: LJR-200327-2001038


title: LJR-210326-2101863


title: LJR-200819-2004127


title: LJR-190916-1905038


title: LJR-200921-2004847


title: LJR-190724-1903968


title: LJR-190719-1903873


title: LJR-210329-2101938


title: LJR-201016-2005309


title: 543_ATRX_3

city: Houston

first: Sharvari

last: Dharmaiah

state: TX

address: 2130 W. Holcombe Blvd.

institute: MD Anderson Cancer Center

data_processing:
The raw fastq files were subjected to FASTQC analysis for quality control analysis, followed by allignment to the human hg19 genome using Bowtie2 (version 2.4.5).
BAM files were filtered and coverage plots were generated after normalizing to IgG.
For peak calling, MACS2 callpeak (version 2.2.7.1) was used from BAM files with default parameters.
DiffBind (version 2.10.0) was used to compute differentially bound H3.3 sites in  samples.
Gene annotations were performed using BED files subjected to GREAT (version 4) analysis with Basal plus extension parameters ( Proximal: 5kb upstream, 1kb downstream, plus distal up to 1000kb), followed by pathway prediction analysis using Enrichr.
Peak annotation and visualization were performed using the PAVIS annotation tool.
Assembly: hg19
Supplementary files format and content: BED
Supplementary files format and content: BAM
Library strategy: CUT&Tag

growth_protocol: Patient-derived glioma stem cells (GSCs) were grown and maintained in DMEM (Dulbecco's Modified Eagle Medium)/F-12 media (Gibco), B-27™ Supplement (Gibco), 20 ng/mL EGF, 10 ng/mL FGF, and 2 µg/mL heparin (Stemcell Technologies)

extract_protocol:
GSC DNA was extracted using the CUT&Tag-IT Assay Kit (Active Motif, #53160) following manufacturer's protocols.
Library pool was constructed using i7 and i5 indexing primers (following PCR conditions) following manufacturer's protocols (Active Motif, #53160)

treatment_protocol: Cells were untreated

value: Glioma stem cell

value: ATRX wildtype

tag: cut&tag antibody

value: ATRX (Cell Signaling, #10321)

tag: run format


title: LJR-190708-1903626


title: LJR-190522-1902653


title: LJR-210412-2102230


title: 543_ATRX_2


title: 543_ATRX_1


title: clone-271, wt, bmp4 23d, rep1

city: Uppsala

first: Bengt

last: Westermark

address: Dag Hammarskjölds väg 20

country: Sweden

institute: Uppsala University

description: Sen#6_C271_BMP4_DMSO_day 23

data_processing:
Nextflow (v 22.04.0) nf-core/rnaseq using reference genome  Ensembl GRCh37
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes tpm for all samples

source_name: Glioblastoma cell line

growth_protocol: Cells were grown adherently on laminin (Sigma-Aldrich)-coated Primaria cell culture dishes (BD Biosciences) in serum-free neural stem cell media (Neurobasal and DMEM/F12 media (1:1) supplemented with N2, B27 w/o retinoic acid (Thermo Fisher Scientific), EGF (10 ng/ml) and bFGF (10 ng/ml) (Peprotech)). For cell detachment, TrypLE Select or TrypLE Express (Thermo Fisher Scientific) was used.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (Qiagen)
llumina Stranded mRNA Library Prep

value: Glioblastoma cell line

value: wt

value: bmp4 23d


title: clone-271, wt, bmp4 33d, rep1

description: Sen#6_C271_BMP4_day 33

value: bmp4 33d


title: clone-271, wt, ctrl 33d, rep1

description: Sen#6_C271_CTL_day 33

value: ctrl 33d


title: clone-271, wt, bmp4 13d, rep1

description: Sen#6_C271_BMP4_day 13

value: bmp4 13d


title: clone-475, wt, bmp4 38d, rep1

description: Sen#5_C475_BMP4_DMSO_day 38

value: bmp4 38d


title: clone-271, wt, navitoclax 13d, rep1

description: Sen#6_C271_CTL+ABT_day 13

value: navitoclax 13d


title: clone-271, wt, ctrl 13d, rep1

description: Sen#6_C271_CTL_day 13

value: ctrl 13d


title: LJR-200904-2004480


title: clone-475, wt, ctrl 28d, rep2

description: Sen#5_C475_CTL_DMSO_day 28

value: ctrl 28d


title: clone-475, wt, ctrl 38d, rep1

description: Sen#5_C475_CTL_DMSO_day 38

value: ctrl 38d


title: clone-475, wt, bmp4 and navitoclax 18d, rep1

description: Sen#5_C475_BMP4+ABT_day 18

value: bmp4 and navitoclax 18d


title: clone-271, wt, ctrl 7d, rep1

description: Sen#6_C271_CTL_day 7

value: ctrl 7d


title: clone-475, wt, bmp4 12d, rep1

description: Sen#5_C475_BMP4_day 12

value: bmp4 12d


title: clone-475, wt, ctrl 18d, rep1

description: Sen#5_C475_CTL_DMSO_day 18

value: ctrl 18d


title: clone-475, siCtrl, ctrl 12d, rep1

value: siCtrl

value: ctrl 12d


title: clone-475, wt, navitoclax 18d, rep1

description: Sen#5_C475_CTL+ABT_day 18

value: Glioblastoma cell line

value: navitoclax 18d


title: clone-475, wt, bmp4 18d, rep1

description: Sen#5_C475_BMP4_DMSO_day 18

value: wt

value: bmp4 18d


title: clone-475, siSmad4, bmp4 12d, rep1


title: clone-475, wt, bmp4 7d, rep1

description: Sen#5_C475_BMP4_day 7

value: bmp4 7d


title: clone-475, p21-ko, ctrl 14d, rep3

value: ctrl 14d


title: clone-475, siSmad4, ctrl 12d, rep1


title: clone-271, wt, bmp4 7d, rep1

description: Sen#6_C271_BMP4_day 7


title: clone-271, wt, bmp4 and navitoclax 13d, rep1

description: Sen#6_C271_BMP4+ABT_day 13

value: bmp4 and navitoclax 13d


title: clone-475, wt, bmp4-release 21d, rep21

value: bmp4-release 21d


title: clone-475, siCtrl, bmp4 12d, rep1


title: clone-475, wt, bmp4 14d, rep3

value: bmp4 14d


title: clone-475, p21-ko, bmp4 14d, rep3


title: clone-475, wt, ctrl 28d, rep1

value: ctrl 28d


title: clone-475, wt, ctrl 31d, rep2

value: ctrl 31d


title: clone-475, wt, ctrl 14d, rep3


title: clone-475, wt, bmp4 28d, rep2

description: Sen#5_C475_BMP4_DMSO_day 28

value: bmp4 28d


title: clone-475, wt, bmp4-release 21d, rep1


title: clone-475, wt, 10gy 3d, rep1

value: 10gy 3d


title: clone-475, wt, palbociclib 9d, rep1

value: palbociclib 9d


title: clone-475, wt, 4gy 7d, rep1

value: 4gy 7d


title: clone-475, wt, bmp4 14d, rep2


title: clone-475, wt, ctrl 12d, rep1

description: Sen#5_C475_CTL_day 12


title: clone-475, wt, ctrl 14d, rep4


title: clone-475, wt, bmp4 28d, rep1


title: clone-271, wt, palbociclib 9d, rep1


title: clone-475, wt, ctrl 7d, rep1

description: Sen#5_C475_CTL_day 7

value: ctrl 7d


title: u3065mg, siSmad4, ctrl 12d, rep1

value: ctrl 12d


title: clone-271, wt, 4 gy 7d, rep1

value: Glioblastoma cell line

value: 4 gy 7d


title: clone-271, wt, ctrl 14d, rep1

value: wt


title: u3065mg, siCtrl, ctrl 12d, rep1

value: siCtrl


title: clone-271, wt, bmp4 14d, rep1


title: u3065mg, siSmad4, bmp4 12d, rep1

value: bmp4 12d


title: u3065mg, siCtrl, bmp4 12d, rep1


title: u3065mg, p21-ko, ctrl 14d, rep3

value: ctrl 14d


title: u3065mg, p21-ko, ctrl 14d, rep1


title: u3065mg, p21-ko, ctrl 14d, rep2


title: u3065mg, wt, ctrl 14d, rep3


title: u3065mg, p21-ko, bmp4 14d, rep1


title: u3065mg, wt, ctrl 14d, rep2


title: u3065mg, wt, palbociclib 9d, rep1


title: u3065mg, p21-ko, bmp4 14d, rep3


title: u3065mg, p21-ko, bmp4 14d, rep2


title: u3065mg, wt, bmp4 14d, rep3


title: clone-475, wt, bmp4 31d, rep1

value: bmp4 31d


title: clone-475, wt, navitoclax 20d, rep2

value: navitoclax 20d


title: u3065mg, wt, bmp4 14d, rep2

value: bmp4 14d


title: u3065mg, wt, ctrl 14d, rep1


title: u3065mg, wt, ctrl 13d, rep1

value: ctrl 13d


title: u3065mg, wt, bmp4 14d, rep1


title: u3065mg, wt, bmp4 13d, rep1

value: bmp4 13d


title: clone-475, wt, navitoclax 20d, rep1


title: clone-271, wt, bmp4 and navitoclax 20d, rep1

value: bmp4 and navitoclax 20d


title: clone-475, wt, ctrl 20d, rep2

value: ctrl 20d


title: clone-271, wt, navitoclax 20d, rep1


title: clone-271,wt, bmp4 20d, rep1

value: bmp4 20d


title: clone-271, wt, ctrl 20d, rep1


title: clone-475, wt, ctrl 14d, rep2


title: clone-475, wt, ctrl 20d, rep1


title: MOLM13_OE_RUNX1CNDel_Rep3

city: Farmington

first: Harshpreet

last: Chandok

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

data_processing:
Reads were mapped to the transcriptome annotations assembly with RSEM v1.2.4, modified to utilize Bowtiw v1.0.0 with the '-v 2' option
Reminaing unaligned reads were mapped to the genome and a database of possible splice junctions with TopHat v2.0.8b. The resulting alignments generated by TopHat were combined with the RSEM outputs. Reads that spanned splice junctions had to have at least a 6nt overhang.
Assembly: hg38
Supplementary files format and content: Processed Data contains normalized counts as well as differential expression analysis

source_name: Cell line

growth_protocol: MOLM13 cells were maintained in RPMI-1640 media suppleented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin in a humidified incubator at 5%CO2 at 37ºC

extract_protocol:
Total RNA was extracted with the Rneasy Plus Mini Kit (Qiagen) and QIAshredder folloiwng the manufacturer's protocol.
Poly(A) mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module using ~1µg of total RNA as input following the manufacturer's protocol. The NEXTflex Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) was used to generate cDNA libraries utilizing the NEXTflex RNA-Seq barcodes accoridng to the manufacturer's protocol. Libraries were sequenced using a Nova-Seq X with 150bp paired end reads.

treatment_protocol: All cDNA constructs were cloned into a lentiviral fector (EF1α-IRES-Puromycin-T2A-ZsGreen) and spin infections were performed at 32ºC at 1500 RCF for 60min with 5µg/mL polybrene and lentiviral supernatants. Cells were collected 3 days after transduction and processed for RNA isolation and library preparation.

value: Cell line

value: Acute Myeloid Leukemia

value: RUNX1C_NDel OE

value: Lentiviral infection and overexpression


title: clone-475, p21-ko, ctrl 14d, rep2

value: Glioblastoma cell line


title: clone-475, wt, bmp4 14 d, rep2

value: wt

value: bmp4 14 d


title: clone-475, p21-ko, bmp4 14d, rep1


title: clone-475, p21-ko, ctrl 14d, rep1


title: clone-475, wt, bmp4 14d, rep1


title: MOLM13_OE_RUNX1A_Rep3

value: RUNX1A OE


title: MOLM13_OE_RUNX1A_Rep2


title: MOLM13_OE_RUNX1C_Rep2

value: RUNX1C OE


title: MOLM13_OE_RUNX1C_Rep3


title: MOLM13_OE_RUNX1B_Rep1

value: RUNX1B OE


title: clone-475, wt, ctrl 14d, rep1

value: ctrl 14d


title: MOLM13_OE_Ctrl_Rep1

value: WT


title: HPAd, Adipocyte differentiation medium (ADM) with adrenaline, Day 2, triplicate sample 3

city: San Diego

first: Hung

last: Chan

state: CA

address: 9452 Medical Center Drive,ACTRI Bldg, L1W420

institute: UCSD

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to STAR using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: mm10 for mouse; hg38 for human
Supplementary files format and content: tab-delimited text files with raw counts values for each sample

source_name: cell line

extract_protocol:
ThermoFisher PureLink RNA Kit Illumina stranded mRNA or Illumina total RNA prep (ribodepletion)
transcriptomic

value: cell line

value: HPAd

value: Human Preadipocytes

value: wildtype

value: Adipocyte differentiation medium + adrenaline


title: MOLM13_OE_RUNX1B_Rep2

value: Cell line


title: MOLM13_OE_RUNX1B_Rep3

value: Acute Myeloid Leukemia


title: MOLM13_OE_RUNX1C_Rep1


title: clone-475, p21-ko, bmp4 14d, rep2

value: bmp4 14d


title: HPAd, Adipocyte differentiation medium (ADM), Day 2, triplicate, sample 3

value: Adipocyte differentiation medium


title: HPAd, Adipocyte differentiation medium (ADM) with adrenaline, Day 2, triplicate sample 1


title: MOLM13_OE_RUNX1A_Rep1

value: Lentiviral infection and overexpression


title: HPAd, Adipocyte differentiation medium (ADM), Day 2, triplicate, sample 2


title: MOLM13_OE_RUNX1CNDel_Rep1

value: RUNX1C_NDel OE


title: MOLM13_OE_Ctrl_Rep3


title: MOLM13_OE_RUNX1CNDel_Rep2


title: HPAd, Adipocyte differentiation medium (ADM), Day 2, triplicate sample 1


title: MOLM13_OE_Ctrl_Rep2


title: HPAd, Control, Day 2, triplicate sample 3

value: Control


title: HPAd, Adreanline, Day 2 triplicate sample 1

value: adrenaline


title: HPAd, Adipocyte differentiation medium (ADM) with adrenaline, Day 2, triplicate sample 2


title: HPAd, Adreanline, Day 2, triplicate sample 3


title: HPAd, Control, Day 2, triplicate sample 1


title: HPAd, Control, Day 2, triplicate sample 2


title: HPAd, Adreanline, Day 2, triplicate sample 2


title: IgG control of CUT&Tag in HeLa

source_name: Cervical cancer tissue

extract_protocol:
CUT&Tag was constructed as described (Zheng et al., 2024). The bead-bound cells were resuspended in 100 μL dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1 μL protease inhibitors) containing 100 nM G4P or 18 μg/mL recombinant anti-RAD51 antibody (ab133534, Abcam) or 10 μg/mL anti-53BP1 antibody (4937S, CST).     CUT&Tag detection DNA break was constructed as described (Zheng et al., 2024) with some modifications. The cell bound magnetic beads were first permeated with 100 μL dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES-KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1 μL protease inhibitors) for 30 min, and then the supernatant was discarded and added to 100 μL TdT buffer (200 mM potassium cacodylate, 25 mM Tris, 0.01% (v/v) Triton X-100, 1 mM CoCl2 (pH 7.2)) containing 5 μM biotin-11-dUTP and 5 U TdT to label the intracellular DNA break site for 1h. The bead-bound cells were resuspended in 100 μL dig-wash buffer containing 10 μg/mL recombinant anti-Biotin antibody (ab201341, Abcam).
To amplify libraries, 21 μL DNA was mixed with a universal i5 and a uniquely barcoded i7 primer, and amplified with NEB Q5 high-fidelity 2× master mix. The libraries were purified with 1.2× volume of Ampure XP beads (Beckman Counter), and libraries were eluted in 30 µL 10 mM Tris-HCl (pH 8.0).

value: Cervical cancer tissue

value: HeLa

value: untreated

value: control group


title: Replicate 1 of 53BP1 CUT&Tag in HeLa, add PyBI

value: add PyBI

value: experiment group


title: Replicate 2 of 53BP1 CUT&Tag in HeLa, untreated


title: Replicate 1 of 53BP1 CUT&Tag in HeLa, untreated


title: Replicate 2 of 53BP1 CUT&Tag in HeLa, add PyBI


title: Replicate 2 of RAD51 CUT&Tag in HeLa, untreated


title: Replicate 2 of G4P CUT&Tag in HeLa, untreated


title: Replicate 1 of G4P CUT&Tag in HeLa, untreated


title: Replicate 1 of RAD51 CUT&Tag in HeLa, add PyBI


title: Replicate 2 of RAD51 CUT&Tag in HeLa, add PyBI


title: Replicate 1 of RAD51 CUT&Tag in HeLa, untreated


title: Si-NC-2

city: Nanjing

first: Mingyu

last: Pan

state: Jiangsu

address: Long Mian 639 Nanjing

institute: China Pharmaceutical University

description: control HeLa cells  stimulated with HTDNA

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads.
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome.
The gene alignment and FPKM were calculated using featureCounts v1.6.2 / StringTie v1.3.4d.
DESeq2 v1.22.1 / edgeR v3.24.3 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression.
Assembly: GRCm39.104
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Uterus; Cervix

extract_protocol:
HeLa cells were collected, the total RNA was extracted using Trizol reagent (Invitrogen, 15596018) and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Uterus; Cervix

value: epithelial cell

value: human

value: si-NC


title: Si-SESN1-2

description: SESN1 knockdown HeLa cells stimulated with HTDNA


title: Replicate 1 of G4P CUT&Tag in HeLa, add PyBI


title: Replicate 2 of G4P CUT&Tag in HeLa, add PyBI


title: HEK293_1

city: Suwon

first: Gwang

last: Lee

state: Yeongtong-gu

address: 206 Worldcup-ro

department: Department of Physiology and Department of Biomedical Sciences

country: South Korea

institute: Ajou University

data_processing:
Preprocessing: cutadapt version 2.8
Alignment: STAR version 2.7.1a
Abundance estimation: RSEM version 1.3.1, featureCounts version 2.0.0, HTSeq-count version 0.11.2, Cufflinks version 2.2.1
Assembly: GRCh38.p13
Supplementary files format and content: The processed data file (genes.expression.xlsx) contains the information of genes and the values of the read count, RPKM, and TPM of 4 samples.

source_name: [HEK293 cell line] [control] [rep1]

growth_protocol: Cells were cultured in Dulbecco’s modified essential medium (DMEM; HyClone, USA), supplemented with 10% fetal bovine serum (FBS; Corning, USA), 100 units/ml of penicillin, and 100 μg/ml of streptomycin (Thermo Fisher Scientific, USA) at 37℃ and 5% CO2 in a humidified incubator.

extract_protocol:
1 μg of total RNA was isolated using TruSeq Stranded Total RNA Library Prep Kit (Illumina).
The libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina). mRNAs were fragmented and synthesized as double-stranded cDNA through random hexamer priming. Following the end repair, A-tailing, and adapter ligation, cDNA libraries were amplified with PCR.
The quality of cDNA libraries was evaluated with Agilent 2100 BioAnalyzer (Agilent Technologies). The quantification of cDNA libraries was conducted using KAPA library quantification kit (Kapa Biosystems). Following cluster amplification, RNA-seq progressed as paired-end (2×150bp) using Illumina Novaseq6000 (Illumina).

value: kidney; Embryo

value: HEK293 cell line

value: human embryonic kidney

value: WT

value: non-treated


title: Si-NC-1


title: Si-SESN1-1


title: HEK293_2

source_name: [HEK293 cell line] [control] [rep2]


title: Synph-293_2

source_name: [HEK293 cell line] [synphilin-1 overexpression] [rep2]

value: synphilin-1 overexpression


title: Synph-293_1

source_name: [HEK293 cell line] [synphilin-1 overexpression] [rep1]


title: Tb_input_1

city: Chicago

first: Tao

address: 929E 57th street

institute: The University of Chicago

data_processing:
The raw reads are aligned by BWA/MEM (0.7.17-r1188) and the product was transformed into bam file and sorted with samtools (v1.6)
Duplications of reads are removed by picard (v2.27.4) and then the bam file was transformed into bed file with a python script SAMtoBED provided by KAS-seq pipeline.
Then the bed file was sorted with bedSort (v377) and peaks were called by macs2 (v2.2.7.1). When calling the peaks, the 4 replicates of thrombin-seq pulldown samples were compared to the 4 thrombin-seq input samples respectively, while the and KAS-seq pulldown sample was compared to the thrombin-seq input sample 1.
For the called peaks of the 4 replicates, the peaks aligned to chromosomes were retained. Overlap of peaks were identified by bedtools (v2.30.0)
Assembly: GRCh38.p13
Supplementary files format and content: The processed files are the bed files generated by MACS2 which contains the quantification data of the peaks called.

source_name: HL-60 cell line

growth_protocol: dHL60 cells were cultured and induced for NETosis in 10 cm dishes at the cell density of 1 x 10^6 cells/ml in serum-free RPMI 1640 medium with 500 nM PMA for 4h

extract_protocol:
The cell culture media was replaced with serum-free RPMI 1640 medium supplemented with 1 μM biotinylated alpha thrombin. After another 1h incubation, the supernatant was carefully removed and washed twice with PBS gently. The NET layer was fixed by cross-linking solution (1% vol/vol formaldehyde in PBS). After 10 min incubation at room temperature, the fixation was stopped by adding glycine to a final concentration of 0.12 M. Gently mix by rotating slowly for 10 min at room temperature. Wash the cells twice with cold PBS and add 10 ml of cold PBS. Scape the cells with cell lifter and collect the cell containing PBS into falcon tube and process the same treatment for NET isolation, which is centrifuge at 1,500 rpm for 15 min to remove cell bodies and then transfer to 1.5 ml tubes and centrifuge at 17,500 rpm for 30 min at 4 C. Resuspend the DNA pellet in cold buffer TE and do DNA sonication. DNA was fragmented by using Novaris sonication system under low power mode (intensity at 3, 15 cycles, 30s on and 60s off) at 2 C. Always keep the DNA on ice.
To enrich thrombin bound DNAs, streptavidin Dynabeads C1 was applied for pull-down experiments. Firstly, save 500 ng DNA as sequencing inputs. Dilute 1 μg DNA into 100 μl 1x PBS. Prepare 50 μl Dynabeads by washing with 500 μl 1x PBS for 3 times and blocked with 1% BSA and 10 μg/ml yeast tRNA (Thermofisher AM7119) in PBS for 30 min at 37 ℃ in the thermomixer under rotation 1,200 rpm. After blocking, mix 100 μl DNA with 100 μl beads solution and incubate at 37 C for 30 min with 1,200 rpm shaking. To wash the beads, cold washing buffer (1x PBS and 0.1% Tween-20) was prepared. The beads were washed with 400 μl washing buffer three times 37 C for 10 min with 1,400 rpm shaking. Then the DNA was eluted from the beads by adding 95 μl buffer TE and 5 μl Proteinase K and incubated under 1,200 rpm shaking for 1h at 37 C, then for another 2 h at 65 C. The DNA was purified with Qiaquick DNA purification columns and eluted in 20 μl nuclease free water. DNA concentration was measured via Qubit. 15 ng DNA from input and pull-down enriched samples were sent to Genomic Sequencing and Analysis Center at UT Austin for library preparation and sequencing.

value: HL-60 cell line

value: input


title: Tb_input_4


title: Tb_input_3


title: Tb_input_2


title: MM13 lymphonode axillary metastasis GFPnegative M5

data_processing:
After demultiplexing and barcode processing gene counting and aggregation was performed using  Cell Ranger Software v7.0.0
Assembly: GRCH38
Supplementary files format and content: Tab separated files and matrix files

source_name: melanoma PDX lymph node axillary metastasis

extract_protocol:
Frozen vital pieces of primary and metastatic melanoma MM13 and MM27 H2B-GFP collected from NSG mice were defrost and mechanically and enzymatically digest with collagenase typeIII in a shaking incubator at 37C for the time necessary to reach single cell suspension. Digestion was stopped with medium supplemented with 10% serum and washed with PBS.  Sorting was performed using fluorescence-associated cell sorters (Aria and Melody, BD Bioscience) to isolate GFP positive and GFP negative populations from primary tumors after DAPI staining for live cells and from mice metastatic organs after labeling with human CD298-PE and DAPI for human melanoma and live cells. Sorted cell populations were resuspended in PBS-0.04%BSA for Chromium Next GEM Single Cell protocol.
Library was prepared with   10x Chromium  protocol according manufacturer recpommendation(10X Genomics 3′ v3 Single Cell Gene Expression Solution).Briefly, cell suspension was loaded onto each channels of the 10x Chromium Single Cell Chip tand single cells were then captured in GEMs. Captured polyA-mRNAs were reverse transcribed into cDNAs and amplified to generate amplified full-length cDNA tagged with CB and UMI (PCR1).

value: melanoma


title: MM13 lymphonode axillary metastasis GFP positive M5

value: melanoma PDX lymph node axillary metastasis


title: MM13 lymphonode axillary metastasis GFPnegative M4


title: Tb_pulldown_4

value: pulldown


title: Tb_pulldown_3


title: MM13 lymphonode axillary metastasis GFPpositive M4


title: Tb_pulldown_2


title: MM13 lymphonode axillary metastasis GFPnegative M2


title: MM13 lymphonode mesenteric metastasis GFPpositive  M4

source_name: melanoma PDX lymph node mesenteric metastasis


title: Tb_pulldown_1


title: MM13 lymphonode axillary metastasis GFPpositive M2


title: MM13 primary tumor GFP negative M5

source_name: melanoma PDX primary

value: melanoma PDX primary


title: MM13 primary  tumor  GFP, positive M5


title: MM13 lymphonode mesenteric metastasis GFPnegative M4

value: melanoma PDX lymph node mesenteric metastasis


title: MM13 primary  tumor GFP positive M4


title: MM13 primary tumor GFP negative M2


title: KAS

data_processing:
The raw reads are aligned by BWA/MEM (0.7.17-r1188) and the product was transformed into bam file and sorted with samtools (v1.6)
Duplications of reads are removed by picard (v2.27.4) and then the bam file was transformed into bed file with a python script SAMtoBED provided by KAS-seq pipeline.
Then the bed file was sorted with bedSort (v377) and peaks were called by macs2 (v2.2.7.1). When calling the peaks, the 4 replicates of thrombin-seq pulldown samples were compared to the 4 thrombin-seq input samples respectively, while the and KAS-seq pulldown sample was compared to the thrombin-seq input sample 1.
For the called peaks of the 4 replicates, the peaks aligned to chromosomes were retained. Overlap of peaks were identified by bedtools (v2.30.0)
Assembly: GRCh38.p13
Supplementary files format and content: The processed files are the bed files generated by MACS2 which contains the quantification data of the peaks called.
Library strategy: DNA-seq

extract_protocol: N3-Kethoxal was purchased from APExBIO Inc. Cells were cultured and induced for NETosis as described above. In a well of a 6-well plate, after NETosis induction for 4h, we replaced the cell culture media with serum-free RPMI 1640 supplemented with 5mM N3-Kethoxal and incubated for 10 min in the cell culture incubator. After 3 times of gentle washing with DPBS, the NET was isolated as described above without proteinase K heat-inactivation. The DNA pellet was eluted in 130 μl TE buffer and fractionated with Novaris sonication system, 15 cycles, intensity at 3, 30s on/30s off. After sonication, the DNA lengths were checked with agarose gel. 5 ug fractionated DNA were diluted into 100 μl labeling buffer (1x PBS, 0.5mM DBCO-PEG4-Biotin, 30 mM Boric acid), and incubated for 2h in the thermomixer at 37 ℃ with 1,200 rpm shaking. 5 μl RNase A/T1 was added into the reaction and incubated for another 30 min. Purify the DNA with Qiaquick purification columns and eluted the DNA into 40 ul water. Dilute the DNA into 100ul 1x PBS by adding water and 10x PBS. Save 5 μl as the sequencing input sample. Use the rest 95 μl DNA to enrich biotin-tagged ssDNAs. ssDNA pull down was achieved by using Dynabeads Streptavidin C1 according to the manufacture’s protocol. 20 μl beads were washed 3 times in PBS in thermomixer at room temperature for 15 min each time. Then the beads were blocked with PBS supplemented with 1% BSA and 10 μg/ml yeast tRNA (Thermofisher AM7119) for 30 min at 37 C with shaking. Then, the DNA was mixed with blocked Dynabeads in a final volume 200 μl and incubated for 30 min at room temperature with shaking. The beads were washed three times with 400 μl PBST (PBS supplemented with 0.1% Twenn-20). The bound DNA was eluted by heating the beads to 95 ℃ for 10 min. Then the DNA was quantified with Qubit dsDNA HS kit and send to Genomic Sequencing and Analysis Center at UT Austin for library preparation and sequencing.


title: MM13 primary  tumor GFP positive M2


title: LN229 control-3

city: Harbin

first: Xiangqi

last: Meng

address: No. 157, Baojian Road

institute: Harbin Medical University

data_processing:
Quality control-The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome-Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level-featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include transcript expression for each sample

source_name: glioblastoma cell line

extract_protocol:
Total RNA was isolated using TRIzol reagent (Cat. 15596018, Invitrogen, USA) according to the manufacturer’s instructions. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

value: glioblastoma cell line

value: glioblastoma