title: Sox3_ChIP_St10.5_R1

city: Santa Ana

first: Clark

last: Hendrickson

state: CA

address: 17331 Grovemont

institute: University of California, Irvine

description: Library name: Sox3_ChIP_St10.5_R1

data_processing:
ChIP-seq peak calling and IDR: Reads were aligned to the X. tropicalis genome v10.0 using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 8, 9 or 10.5 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.001 but otherwise default options. Irreproducibility discovery rate (IDR) (Li et al., 2011) was used with a minimum P-value<0.05 cut-off.
Assembly: X. tropicalis genome v10.0 (Mitros et al., 2019)
Supplementary files format and content: Peaks retained after Irreproducibility Discovery Rate (IDR) analysis.  Histone modification regions ranked by read density and length.

organism: Xenopus tropicalis

source_name: Whole embryo

growth_protocol: Xenopus tropicalis females were injected with 10 units of Chorulon (Merck and Co.) 1-3 nights before embryo collection and 100 units of Chorulon on the day of embryo collection. Eggs were collected in a dish coated with 0.1% BSA in 1/9x MMR. The eggs are in vitro fertilized with sperm suspension in 0.1% BSA in 1/9x MMR. The embryos are dejellied with 3% cysteine in 1/9x MMR, pH 7.8, 10 minutes after fertilization and are then ready for manipulation. Embryos were staged using the Nieukwoop-Faber developmental table.

extract_protocol:
Fixed embryos were homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then centrifuged at 14,000rpm for 10 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 100-500bp. The resulting samples were centrifuged at 14,000 rpm for 30 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was pre-cleared by incubating with 20 mL Protein G-coated Dynabeads (Invitrogen) for 2 hours at 4°C with rotation. Meanwhile, another 20 mL Protein G Dynabeads were incubated in a tube rotator in 1 mg/mL torula RNA and 0.5% BSA in 1x PBS for 30 minutes at 4°C to block non-specific binding. This second 20 mL Protein G Dynabeads were then pre-bound with 2 mg anti-vegt antibody at 4°C for > 1 hour. The pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on a tube rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
ChIP-seq libraries were generated using Nextflex ChIP-seq kit (Bioo Scientific), or NEB E7645S DNA sequencing kit, then analyzed using an Agilent Bioanalyzer 2100, quantified using KAPA qPCR and sequenced using Illumina instruments.

treatment_protocol: Embryos were cross-linked in 1% formaldehyde in 1/9x MMR at room temperature for 50 minutes with gentle rocking where each microcentrifuge tube contains 200 embryos with 1mL of the formaldehyde solution. Crosslinking reactions were neutralized by the removal of the formaldehyde solution and incubation with 1ml 125mM glycine solution for 10 minutes on ice. Embryos were then washed twice with 400mL of cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche cOmplete protease inhibitor cocktail). Embryos were flash-frozen in liquid nitrogen and stored at -80°C.

value: Whole embryo

tag: cell line

value: Wild-type X. tropicalis

tag: cell type


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_23

status: Public on Sep 16 2025

type: SRA

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of Pex5 knockout KO, biological rep4

library_source: transcriptomic

data_processing:
Quality control of fastq files was performed by using fastqc  [1].
bbduk from bbtools [2] was used to remove adapters and low-quality tails from the reads, with the following parameters: k=13 ktrim=r useshortkmers=t mink=5 qtrim=rtrimq=10 minlength=20.
Then, trimmed and cleaned reads were aligned to the reference genome mm10 by using STAR [3], with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD.
Aligned reads were indexed with samtools [4].
Finally, number of reads mapping within genes was determined with htseq-count [5], run in intersection-nonempty mode.
[1] Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput SequenceData
[2] https://jgi.doe.gov/data-and-tools/software-tools/bbtools/
[3] Dobit, A. et al. (2013). STAR: ultrafast universal RNA-seq aligner
[4] Li, H. et al. (2009). The Sequence Alignment/Map format and SAMtools
[5] Putri, G. et al (2022). Analysing high-throughput sequencing data in Python withHTSeq 2.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: gastrocnemius muscle

growth_protocol: Mice were maintained on a 12-hour light/12-hour dark schedule and were fed standard rodent food chow and water ad libitum

extract_protocol:
Total RNA was extracted from gastrocnemius muscle using TRIzol reagent (Life Technologies) following manufacturer's protocol
the QuantSeq 3' mRNA-seq Library Prep kit (Lexogen) was employed for library construction following manufacturer's protocol

treatment_protocol: Muscle-specific Pex5 ablation was achieved by crossing Pex5 floxed mice  with a transgenic line expressing Cre recombinase (CRE) under the control of Myosin Light Chain 1 fast promoter. Gastrocnemius muscle from 9 months-old mice was collected.

tag: tissue

value: gastrocnemius muscle

tag: age

value: 9 months-old

tag: genotype


title: TSC37

type: genomic

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
minfi
normalized Average Beta (ssNoob)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Toddler Social Cognition

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAamp DNA Mini Kit (QIAGEN, Venlo, The Netherlands).

value: buccal epithelial

tag: gender

value: male

tag: days left at rt before the dna extraction

tag: group

value: typically developing

tag: nationality

value: Japanese


title: TSC31


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_18

description: Transcriptome profile of Pex5 knockout KO, biological rep2


title: TSC32


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_22

description: Transcriptome profile of Pex5 knockout KO, biological rep3


title: Sox3_ChIP_St9_R1

country: USA

description: Library name: Sox3_ChIP_St9_R1

library_source: genomic


title: gastrocnemius muscle from 18 months-old control mice, WT_068

description: Transcriptome profile of control WT, biological rep1

extract_protocol:
Total RNA was extracted  from gastrocnemius muscle using TRIzol reagent (Life Technologies) following manufacturer's protocol
the QuantSeq 3' mRNA-seq Library Prep kit (Lexogen) was employed for library construction following manufacturer's protocol

treatment_protocol: Muscle-specific Pex5 ablation was achieved by crossing Pex5 floxed mice  with a transgenic line expressing Cre recombinase (CRE) under the control of Myosin Light Chain 1 fast promoter. Gastrocnemius muscle from 18 months-old mice was collected.

value: 18 months-old

value: wild type


title: Heart, Naproxen, Experimental batch 1, Rep 06

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

description:
Library name: Heart_Naproxen_Exp1_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

data_processing:
FASTQ files from multiple lanes were merged for each sample using the unix 'cat' command.
Salmon (v1.9.0) was used to quantify transcript reads counts from the merged FASTQ files against v102 of the Ensembl mouse annotation. The Salmon index used for these analyses included transcript sequences from the ‘Mus_musculus.GRCm38.cdna.all.fa’ (all Ensembl transcripts, excluding non-coding RNAs) and ‘Mus_musculus.GRCm38.ncrna.fa’ (non-coding RNAs) FASTA files, both of which were downloaded from the Ensembl ftp site. The full DNA sequence from the primary genome assembly (GRCm38; also downloaded from Ensembl) was also included in the Salmon index as a decoy. Salmon was run to account for sequence, GC, and positional biases using the following command line parameters: "--seqBias --gcBias --posBias". Additionally, Salmon was run with the selective alignment mapping strategy ("--validateMappings") and the Inward Stranded Reverse LIBTYPE ("-l ISR").
Salmon transcript counts were imported into R (v4.2.2) and summarized to gene level quantifications with the tximeta package (v1.16.0).
Assembly: GRCm38
Supplementary files format and content: salmon_gene_quants.txt is a tab-delimited text file containing unnormalized salmon gene-level read counts for each gene in each sample (gene x sample format). The first two columns contain the Ensembl gene ID and common gene symbol for each gene in the table. The remaining columns contain gene counts for each sample in the study.

source_name: Heart

growth_protocol: Six-week-old C57BL/6 mice were obtained from the Jackson Laboratory and allowed to acclimatize for two weeks. Animals were kept in a 12-hour day/night cycle and had ad libitum access to food and water.

extract_protocol:
At the end of the treatment period, mice were sacrificed via CO2 asphyxiation and their whole heart and jejunum tissue were dissected, chopped into small pieces, and snap frozen in liquid nitrogen. Jejuna were flushed with PBS to remove fecal matter prior to chopping and freezing. RNA was extracted from whole heart or 30 mg of jejunum using the Promega Maxwell RSC simplyRNA Tissue Kit (AS1340).
Libraries for each sample were constructed from 400 ng of total RNA using either the Illumina TruSeq Stranded mRNA library prep kit (heart) or the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (jejunum). Jejuna RNA samples were processed with a ribo-depletion based library prep kit because they had RIN scores < 8.

treatment_protocol: Mice were randomly assigned to treatment groups (n=8 per group). For three weeks, mice from the "control" and "tryptophan" groups received normal chow, while mice in the "celecoxib", "naproxen", and "naproxen+tryptophan" groups received chow supplemented with either celecoxib (550 ppm for females) or naproxen (1323 ppm for females; 1610 ppm for males). During the third and final week of the dietary exposure, mice in the "tryptophan" and "naproxen+tryptophan" groups received i.p. (intraperitoneal) injections of 50 mg/kg of tryptophan in PBS (phosphate buffered saline), while mice in the "control", "celecoxib", and "naproxen" groups received i.p. injections of PBS. Injections were administered daily at noon. Mice from the first experimental batch (Exp1) did not receive any injections.

value: Heart

tag: strain

tag: treatment

value: Naproxen

tag: Sex

value: Male

value: 11 weeks

tag: experimental batch

tag: animal id

tag: dissection batch

tag: rrna removal_method

value: PolyA

tag: library prep_kit

tag: index barcode

value: AATCCGGA-AACTGTAG


title: Heart, Naproxen, Experimental batch 1, Rep 05

description:
Library name: Heart_Naproxen_Exp1_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: Illumina TruSeq Stranded mRNA library prep kit

value: GACCTGAA-CTCACCAA


title: TSC30

value: female


title: Heart, Naproxen, Experimental batch 1, Rep 04

description:
Library name: Heart_Naproxen_Exp1_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: TTGGACTC-CTGCTTCC


title: gastrocnemius muscle from 9 months-old Pex-KO mice, KO_17

description: Transcriptome profile of Pex5 knockout KO, biological rep1

value: gastrocnemius muscle

value: 9 months-old


title: TSC29

value: buccal epithelial

value: child maltreatment


title: Heart, Naproxen, Experimental batch 1, Rep 03

description:
Library name: Heart_Naproxen_Exp1_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: TTATAACC-TCGATATC


title: TSC28

value: typically developing

value: Japanese


title: gastrocnemius muscle from 9 months-old control mice, WT_34

description: Transcriptome profile of control WT, biological rep6

value: wild type


title: Sox3_ChIP_St8_R1

description: Library name: Sox3_ChIP_St8_R1

value: Whole embryo

tag: cell line

value: Wild-type X. tropicalis

tag: cell type


title: Foxi2_ChIP_St10.5_R2

description: Library name: Foxi2_ChIP_St10.5_R2

tag: tissue


title: Heart, Naproxen, Experimental batch 1, Rep 08

description:
Library name: Heart_Naproxen_Exp1_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Naproxen

value: Male

tag: age

value: 11 weeks

value: PolyA

value: TGGATCGA-TATCGCAC


title: Heart, Naproxen, Experimental batch 1, Rep 02

description:
Library name: Heart_Naproxen_Exp1_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: Illumina TruSeq Stranded mRNA library prep kit

value: CGGCGTGA-ACAGGCGC


title: TSC27

value: buccal epithelial

tag: gender

value: male


title: Heart, Naproxen, Experimental batch 1, Rep 01

description:
Library name: Heart_Naproxen_Exp1_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: GCTTGTCA-GTATGTTC


title: Foxi2_ChIP_St10.5_R1

description: Library name: Foxi2_ChIP_St10.5_R1


title: gastrocnemius muscle from 9 months-old control mice, WT_28

description: Transcriptome profile of control WT, biological rep4

value: gastrocnemius muscle

value: 9 months-old

tag: genotype


title: Foxi2_ChIP_St9_R2

description: Library name: Foxi2_ChIP_St9_R2


title: TSC26

value: female

tag: days left at rt before the dna extraction

tag: group

value: typically developing

value: Japanese


title: Sox3_ChIP_St9_R2

description: Library name: Sox3_ChIP_St9_R2

value: Whole embryo

value: Wild-type X. tropicalis


title: Heart, Control, Experimental batch 1, Rep 10

description:
Library name: Heart_Control_Exp1_10
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

tag: strain

value: Control

value: Male

value: TCTCTACT-GAACCGCG


title: Foxi2_ChIP_St9_R1

description: Library name: Foxi2_ChIP_St9_R1


title: TSC25

tag: nationality


title: Sox3_ChIP_St8_R2

description: Library name: Sox3_ChIP_St8_R2


title: Foxi2_ChIP_St8_R2

description: Library name: Foxi2_ChIP_St8_R2


title: gastrocnemius muscle from 9 months-old control mice, WT_14

description: Transcriptome profile of control WT, biological rep2

value: wild type


title: TSC24


title: gastrocnemius muscle from 9 months-old control mice, WT_12


title: Heart, Control, Experimental batch 1, Rep 09

description:
Library name: Heart_Control_Exp1_09
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: treatment

tag: Sex

value: 11 weeks

value: PolyA

value: Illumina TruSeq Stranded mRNA library prep kit

value: GGACTTGG-CGTCTGCG


title: gastrocnemius muscle from 3 months-old Pex-KO mice, KO_100

description: Transcriptome profile of Pex5 knockout KO, biological rep5

treatment_protocol: Muscle-specific Pex5 ablation was achieved by crossing Pex5 floxed mice  with a transgenic line expressing Cre recombinase (CRE) under the control of Myosin Light Chain 1 fast promoter. Gastrocnemius muscle from 3 months-old mice was collected.

value: 3 months-old


title: Foxi2_ChIP_St8_R1

description: Library name: Foxi2_ChIP_St8_R1


title: Heart, Control, Experimental batch 1, Rep 08

description:
Library name: Heart_Control_Exp1_08
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: experimental batch

tag: animal id

value: GGCTTAAG-GGTCACGA


title: Heart, Control, Experimental batch 1, Rep 07

description:
Library name: Heart_Control_Exp1_07
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: dissection batch

tag: rrna removal_method

value: ATGTAAGT-CATAGAGT


title: gastrocnemius muscle from 9 months-old control mice, WT_27

description: Transcriptome profile of control WT, biological rep3

value: gastrocnemius muscle

value: 9 months-old


title: TSC22

value: buccal epithelial

value: male

value: child maltreatment

value: Japanese


title: gastrocnemius muscle from 9 months-old control mice, WT_31

description: Transcriptome profile of control WT, biological rep5


title: TSC21


title: Heart, Control, Experimental batch 1, Rep 06

description:
Library name: Heart_Control_Exp1_06
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Control

tag: library prep_kit

tag: index barcode

value: CAAGCTAG-CGCTATGT


title: gastrocnemius muscle from 3 months-old Pex-KO mice, KO_96

description: Transcriptome profile of Pex5 knockout KO, biological rep3


title: Sox3_Cntrl_St10.5_R2

description: Library name: Sox3_Cntrl_St10.5_R2

data_processing:
RNA-seq gene expression calling: Reads were aligned using RSEM v.1.2.12 (Li and Dewey 2011) and Bowtie v2.2.7 (Langmead and Salzberg 2012) to the Xenopus tropicalis genome version v10.0 (Mitros et al., 2019; Xenbase FTP). Read counts were extracted from RSEM results output.
Assembly: Xenopus tropicalis V10.0 (Mitros et al. 2019)
Supplementary files format and content: Gene readcounts for treatment and control conditions.

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from embryos using TRIzol reagent (ThermoFisher). RNA pellets were resuspended in DEPC-treated water and precipitated overnight at 4C in 2.5M LiCl.
PolyA-selected mRNA transcripts were isolated using NEBNext PolyA mRNA Magnetic Isolation Module (NEB E7490S). RNA libraries were prepared using NEBNext Ultra II Library Preparation Kit (NEB E7770S), validated using an Agilent Bioanalyzer 2100, and sequenced on the Illumina Novaseq platform.

treatment_protocol: Foxi2 or Sox3 MO was microinjected into the animal hemisphere of 1-cell stage embryos and RNA was harvested at stage 9 and 10.5.

value: Whole embryo

tag: cell line

value: Wild-type X. tropicalis

tag: cell type

value: Morpholino


title: gastrocnemius muscle from 3 months-old Pex-KO mice, KO_99

description: Transcriptome profile of Pex5 knockout KO, biological rep4

tag: tissue

tag: age


title: Heart, Control, Experimental batch 1, Rep 05

description:
Library name: Heart_Control_Exp1_05
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

value: PolyA

value: Illumina TruSeq Stranded mRNA library prep kit

value: TAATACAG-GTGAATAT


title: Sox3_Cntrl_St10.5_R1

description: Library name: Sox3_Cntrl_St10.5_R1


title: TSC19

tag: gender

value: female


title: TSC20

tag: days left at rt before the dna extraction


title: Heart, Control, Experimental batch 1, Rep 04

description:
Library name: Heart_Control_Exp1_04
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: CCGCGGTT-CTAGCGCT


title: gastrocnemius muscle from 3 months-old Pex-KO mice, KO_94

description: Transcriptome profile of Pex5 knockout KO, biological rep2

value: gastrocnemius muscle

value: 3 months-old

tag: genotype


title: Sox3_MO_St10.5_R1

description: Library name: Sox3_MO_St10.5_R1


title: Sox3_MO_St10.5_R2

description: Library name: Sox3_MO_St10.5_R2


title: Heart, Control, Experimental batch 1, Rep 03

description:
Library name: Heart_Control_Exp1_03
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

tag: strain

value: AGTTCAGG-TCTGTTGG


title: TSC23

value: buccal epithelial

value: male

tag: group

value: child maltreatment

tag: nationality

value: Japanese


title: TSC18


title: gastrocnemius muscle from 3 months-old Pex-KO mice, KO_91

description: Transcriptome profile of Pex5 knockout KO, biological rep1


title: Sox3_Cntrl_St9_R2

description: Library name: Sox3_Cntrl_St9_R2

value: Whole embryo

tag: treatment


title: Heart, Control, Experimental batch 1, Rep 02

description:
Library name: Heart_Control_Exp1_02
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Heart

value: Control

tag: Sex

tag: experimental batch

value: ATCCACTG-ACGCACCT


title: gastrocnemius muscle from 3 months-old control mice, WT_101

description: Transcriptome profile of control WT, biological rep4

value: wild type


title: TSC17

value: typically developing


title: Heart, Control, Experimental batch 1, Rep 01

description:
Library name: Heart_Control_Exp1_01
Animal IDs are specific to each treatment and experimental batch (i.e. each experimental batch represented a distinct cohort of mice, even if they share animal IDs).

value: Female

value: 11 weeks

tag: animal id

tag: dissection batch

value: PolyA

value: Illumina TruSeq Stranded mRNA library prep kit

value: CCAAGTCT-TCATCCTT


title: Sox3_Cntrl_St9_R1

description: Library name: Sox3_Cntrl_St9_R1

value: Wild-type X. tropicalis

value: Morpholino


title: TSC16

value: buccal epithelial


title: gastrocnemius muscle from 3 months-old control mice, WT_98

value: gastrocnemius muscle

value: 3 months-old


title: Sox3_MO_St9_R2

description: Library name: Sox3_MO_St9_R2


title: gastrocnemius muscle from 3 months-old control mice, WT_86

description: Transcriptome profile of control WT, biological rep2


title: Glucocorticoid treated tumours, individually hashtagged and pooled [SZ26_02_HTO_S2]

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
Library name: SZ26_02_HTO_S2
10x Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were quality checked by Fragment Analyzer and quantified by qPCR using a KAPA Library Quantification Kit for Illumina (Roche). Paired-end sequencing was carried out on an Illumina NovaSeq 6000 with read lengths of 28+10+10+90 cycles. Mouse single cell RNA-Sequencing (scRNA-Seq) reads were aligned and quantified with CellRanger V.7.1.0 against the mm10-2020-A reference transcriptome, with introns included. Cite-Seq was used for ‘Cell Hashing’ to annotate cells with Hashtag Oligo (HTO) tags, enabling demultiplexing of data sets into separate samples. scRNA-Seq analysis was carried out in R 4.3.1 with Seurat V5.0.3, and Scater V1.30.1. Seurat was used to demultiplex the HTO tags and identify cells associated with one HTO sample tag (singlets). Singlets were then taken for quality control. Scater identified cells of low quality, defined as an outlier by 3 median absolute deviation from the median by quality control metrics. Quality metrics included counts, genes expressed, and percentage of mitochondrial genes per cell, and were identified by Seurat. Quality controlled and filtered singlets were taken for downstream analysis in Seurat. Library size normalization was carried out to account for sequencing depth using the NormalizeData function in the Seurat package, and 2000 highly variable genes were identified in each sample. Normalized gene counts were then scaled and Unified Manifold Approximation and Projection (UMAP) dimensionality reduction was used for visualization. Principal component analysis was completed with 50 principal components - all subsequent Seurat analyses used 50 principal components. Seurat’s Correlation Correction Analysis was used for integration, using default parameters. The resulting CCA reduction was used for clustering and UMAP generation. Cell clustering was performed by generating a shared nearest-neighbors graph, and input into a Louvain algorithm, with the resolution parameter set to 0.8. To visualize cells and clusters in a lower dimension, UMAPs were generated using default parameters. Cell-type specific markers were then identified using a Wilcoxon Rank-Sum test and used to annotate cells. The resulting filtered counts metadata information were loaded into Partek Flow software for further analysis.
Assembly: mm10
Supplementary files format and content: normalised_counts.csv.gz - library size-normalised count data, cells as column names and genes in rows.
Supplementary files format and content: meta.csv - cell meta data, including UMAP coordinates and cell type labels.

source_name: Ex-vivo tumour infiltrating immune cells

extract_protocol:
Tumors were collected into complete RPMI on ice, cut into small pieces and digested with Collagenase IV (200 U/ml, Worthington Biochemical) and DNase I (0.2 mg/ml, Roche) for 30 min at 37°C, vortexing once. The tumors were filtered through a 70µm cell strainer and pelleted. Cell pellets were resuspended in FACS buffer. Fc receptors were blocked with anti-CD16/CD32 (clone 93, eBioscience) 5 min before staining. Tumors were stained with Aqua LIVE/DEAD-405 nm (Invitrogen) and CD45-BV605 (Clone 30-F11) antibodies. Each tumor (n=5 per group) was stained with a TotalSeqTM HTO barcode (BioLegend) prior to sorting.  FACS buffer used in these experiments was EDTA and sodium azide free. Live CD45+ cells were sorted on a BD FACSAria III with a purity > 98%. Cells were counted using a hemocytometer after Trypan Blue exclusion. 17,100 (sample 1) or 3,500 (sample 2) live cells were loaded into a channel of a Chromium Next Gel Bead-in Emulsion (GEM) Chip G (10X Genomics, PN-1000120) and GEMs were generated on the Chromium X (10X Genomics).
Indexed sequencing libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10X Genomics, PN-1000268) according to BioLegend Totalseq-A protocol and 10x Genomics user guide, with 11 cycles of cDNA amplification and 15 cycles of sample index PCR.

value: Melanoma

value: Cell line generated from C57BL/6 Nras+LSL-G12D;Tyr::CreERT2+/o background; tumours grown in wild type C57BL/6 mice

value: Clobetasol propionate


title: Sox3_MO_St9_R1

description: Library name: Sox3_MO_St9_R1

value: Whole embryo


title: Glucocorticoid treated tumours, individually hashtagged and pooled [SZ26_02_10X_S2]

description:
Library name: SZ26_02_10X_S2
10x Genomics

value: Ex-vivo tumour infiltrating immune cells


title: gastrocnemius muscle from 3 months-old control mice, WT_84

description: Transcriptome profile of control WT, biological rep1

value: wild type


title: Control treated tumours, individually hashtagged and pooled [SZ26_01_HTO_S1]

description:
Library name: SZ26_01_HTO_S1
10x Genomics

value: Control


title: Foxi2_Cntrl_St10.5_R2

description: Library name: Foxi2_Cntrl_St10.5_R2


title: quantseq_AEBP2KO_D2_Rep3

city: Dublin 2

first: Adrian

middle: P.

last: Bracken

state: Co. Dublin

address: Smurfit institute of Genetics, Lincoln Place, Trinity College Dublin

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
ChIP-seq reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. PCR duplicate reads were removed by Picard.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a). Generally, normalization factor (a) was calculated by 1 divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, bigwigs were generated by BamCoverageat 10 bp resolution and RPGC normalization. ChIP-Rx bigwig files were generated by BamCoverage with Rx normalization factor.
QuantSeq: Reads were trimmed using BBDUK to remove the first 11 nucleotides from reads, polyA tails, TruSeq adapters, low quality nucleotides with a q below 10, and reads smaller than 20 nucleotides in length. Reads were aligned to the mm10 genome using the STAR aligner. Gene abundance was quantified using htseq-count and DESeq2 was utilised to identify differentially expressed genes.
Assembly: mm10

source_name: Epiblast-like cells (EpiLC)

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were split and media was changed every 2 days. For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium was changed daily.

extract_protocol: ChIP-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol. QuantSeq libraries were generated using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen; 015.24) in accordance with the manufacturer’s instructions.

treatment_protocol: No treatment/stimulations for this project.

value: EpiLC derived from AEBP2 knockout mouse embryonic stem cells (E14 background)


title: TSC14

value: male

value: typically developing

value: Japanese


title: TSC13

value: child maltreatment


title: Control treated tumours, individually hashtagged and pooled [SZ26_01_10X_S1]

description:
Library name: SZ26_01_10X_S1
10x Genomics


title: Foxi2_Cntrl_St10.5_R1

description: Library name: Foxi2_Cntrl_St10.5_R1

value: Wild-type X. tropicalis


title: TSC12


title: quantseq_AEBP2KO_D2_Rep2


title: Foxi2_MO_St10.5_R2

description: Library name: Foxi2_MO_St10.5_R2

value: Morpholino


title: TSC11

value: buccal epithelial

value: female


title: quantseq_AEBP2KO_D2_Rep1


title: Foxi2_MO_St10.5_R1

description: Library name: Foxi2_MO_St10.5_R1


title: quantseq_AEBP2KO_D0_Rep3

source_name: Mouse embryonic stem cells (this study)

value: AEBP2 knockout mouse embryonic stem cells (E14 background)


title: Whole brain, wildtype, rep 7

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Library name: WT_rep_7

data_processing:
Read trimming (trim_galore v0.6.10, cutadapt v3.4),
Genome alignment with STAR v2.7.10b
Gene-level read counting (summarizeOverlaps, mode = ’IntersectionNotEmpty’, package GenomicAlignments v1.28.0).
Normalization with DESeq2 v1.40.2
Assembly: GCRm39_109
Supplementary files format and content: tab-delimited file with normalized counts

source_name: whole brain

growth_protocol: All mice were treated in compliance with the institutional guidelines approved by the animal welfare and use committee of the government of Upper Bavaria. They were housed in standard cages in a specific pathogen-free facility, maintained on a 12-hour light/dark cycle, and given unrestricted access to food and water.

extract_protocol:
RNeasy Mini kit (Qiagen, Hilden, Germany) including Trizol treatment
Illumina® Stranded Total RNA Prep Ligation kit with Ribo-zero plus

treatment_protocol: No treatment

value: whole brain

value: 5 months


title: Whole brain, wildtype, rep 8

description: Library name: WT_rep_8


title: TSC10


title: Foxi2_Cntrl_St9_R3

description: Library name: Foxi2_Cntrl_St9_R3


title: Whole brain, wildtype, rep 6

description: Library name: WT_rep_6


title: TSC09


title: TSC15


title: Foxi2_Cntrl_St9_R2

description: Library name: Foxi2_Cntrl_St9_R2


title: quantseq_AEBP2KO_D0_Rep2


title: quantseq_AEBP2KO_D0_Rep1


title: TSC08


title: Whole brain, wildtype, rep 5

description: Library name: WT_rep_5


title: Foxi2_Cntrl_St9_R1

description: Library name: Foxi2_Cntrl_St9_R1


title: Whole brain, wildtype, rep 4

description: Library name: WT_rep_4


title: TSC07


title: quantseq_SKO_D2_Rep3

value: EpiLC derived from AEBP2S knockout mouse embryonic stem cells (E14 background)


title: Foxi2_MO_St9_R3

description: Library name: Foxi2_MO_St9_R3

value: Whole embryo


title: Whole brain, wildtype, rep 3

description: Library name: WT_rep_3


title: quantseq_SKO_D2_Rep2


title: Foxi2_MO_St9_R2

description: Library name: Foxi2_MO_St9_R2


title: quantseq_SKO_D2_Rep1


title: Whole brain, wildtype, rep 2

description: Library name: WT_rep_2


title: TSC05


title: Foxi2_MO_St9_R1

description: Library name: Foxi2_MO_St9_R1


title: Whole brain, wildtype, rep 1

description: Library name: WT_rep_1


title: quantseq_SKO_D0_Rep3

value: AEBP2S knockout mouse embryonic stem cells (E14 background)


title: TSC04


title: TSC03


title: Whole brain, Tecpr2 ki/ki, rep 8

description: Library name: Tecpr2_KI_rep_8

value: Tecpr2 L1152fs knock-in


title: Input_St10.5_Endo

description: Library name: Input_St10.5_Endo

data_processing:
ChIP-seq peak calling and IDR: Reads were aligned to the X. tropicalis genome v10.0 using Bowtie v2.2.7 (Langmead and Salzberg 2012) with default options and peaks were called against stage 8, 9 or 10.5 input DNA (Charney et al., 2017) using Macs v2.0.10 (Zhang et al., 2008) with the option –p 0.001 but otherwise default options. Irreproducibility discovery rate (IDR) was followed according to (Li et al., 2011) using a minimum P-value<0.05 cut-off.
Assembly: X. tropicalis genome v10.0 (Mitros et al., 2019)
Supplementary files format and content: Peaks retained after Irreproducibility Discovery Rate (IDR) analysis.  Histone modification regions retained and ranked by score and length.

source_name: Endoderm

value: Endoderm


title: quantseq_SKO_D0_Rep2


title: quantseq_SKO_D0_Rep1


title: Whole brain, Tecpr2 ki/ki, rep 7

description: Library name: Tecpr2_KI_rep_7


title: TSC01


title: Input_St10.5_Ecto

description: Library name: Input_St10.5_Ecto

source_name: Ectoderm

value: Ectoderm


title: quantseq_LKO_D2_Rep3

value: EpiLC derived from AEBP2L knockout mouse embryonic stem cells (E14 background)


title: P300_ChIP_St10.5_FSMO_Endo_Rep2

description: Library name: P300_ChIP_St10.5_FSMO_Endo_Rep2


title: Whole brain, Tecpr2 ki/ki, rep 5

description: Library name: Tecpr2_KI_rep_5


title: TSC06

value: typically developing


title: JAC20_BR

source_name: Judicial Autopsy Cases

extract_protocol: Brain DNA was extracted using the High Pure FFPET DNA Isolation Kit (Roche, Basel, Switzerland) from 10 mg block or six slices (12 um thickness, 3 cm2) until the total yield reached 250 ng. A modified pre-processing protocol, including five minutes ethanol wash twice, overnight PBS wash (50°C, 600 rpm), and overnight lysis (56°C, 600 rpm), was employed to improve efficiency (Nagai et al. 2016; Ohara et al. 2018).

value: brain (PFC)

value: male

value: Japanese


title: P300_ChIP_St10.5_FSMO_Endo_Rep1

description: Library name: P300_ChIP_St10.5_FSMO_Endo_Rep1

value: Wild-type X. tropicalis


title: quantseq_LKO_D2_Rep2


title: JAC11_BR


title: quantseq_LKO_D2_Rep1


title: Whole brain, Tecpr2 ki/ki, rep 3

description: Library name: Tecpr2_KI_rep_3


title: quantseq_LKO_D0_Rep3

value: AEBP2L knockout mouse embryonic stem cells (E14 background)


title: JAC07_BR

value: female

value: child maltreatment


title: JAC15_BR


title: Whole brain, Tecpr2 ki/ki, rep 2

description: Library name: Tecpr2_KI_rep_2

value: whole brain


title: quantseq_LKO_D0_Rep2


title: Input_St10.5

description: Library name: Input_St10.5

source_name: Whole Embryo

value: Whole Embryo


title: P300_ChIP_St10.5_WT_Endo_Rep1

description: Library name: P300_ChIP_St10.5_WT_Endo_Rep1


title: P300_ChIP_St10.5_FSMO_Ecto_Rep2

description: Library name: P300_ChIP_St10.5_FSMO_Ecto_Rep2


title: TSC02

value: buccal epithelial


title: Whole brain, Tecpr2 ki/ki, rep 6

description: Library name: Tecpr2_KI_rep_6

value: 5 months


title: quantseq_LKO_D0_Rep1


title: Lung_control_adult_mouse_Hashtag

city: Brussels

first: David

last: Vermijlen

state: non-US Resident

address: Boulevard de Triomphe, accès 2 (CP205/3)

department: Pharmacotherapy and Pharmaceutics

country: Belgium

institute: Université Libre de Bruxelles

description:
ALUgd_matrix.mtx.gz
ALUgd_features.tsv.gz

data_processing:
CellRanger (v7.1.0) software from 10x Genomics was used to demultiplex and map sequencing reads against GRCm39 and GRCh38 genomes. Count matrices were loaded into R using ´read10x’ function form Seurat R package. All downstream analyses were conducted using Seurat v5.0.0 in R v4.3.2. Low-quality and doublet cells were filtered out using the minimum cutoffs nFeature_RNA > = 200, % mitochondrial gene >5%. ‘Cellcyclescoring´ function from Seurat package was used to determine cell cycle phase of cells in the datasets (G1, G2 or S).  ScaleData function was used to normalize and stabilize variance in the datasets regressing out percent mitochondria genes, percent ribosomal genes, cell cycle scores, nFeatureRNA and TRDV TRGV genes. Principal component analysis (PCA) was subsequently performed using the RunPCA function with 30 principal components. To account for batch effects in integration of datasets, the Harmony algorithm was applied using the RunHarmony function. The Harmony embeddings were extracted using the Embeddings function. Dimensionality reduction was then carried out using the RunUMAP function, based on the top 10-20 Harmony components to generate a two-dimensional UMAP projection for visualization. The nearest-neighbor graph was constructed with the FindNeighbors function, and clustering was performed using the Louvain algorithm via the FindClusters function at a resolution of 0.5.
Assembly: GRCh38 & GRCm39
Supplementary files format and content: GEX: matrix.mtx features.tsv barcodes.tsv. matrix files include transcript count from each single-cell GEX library. barcodes tsv files includes the barcodes present in that single-cell GEX library and features tsv file includes the ID of the genes detected in that single-cell GEX library. TCR: filtered_contig_files include CDR3 junctions in csv and fasta format

source_name: lung

extract_protocol:
Mouse lung cells from individual subjects (8 fetal (Day 0) and 8 adults (10weeks old)) were stained with barcoded hashing antibodies TotalSeq-C 5′ chemistry, following the recommendations of the manufacturer (Biolegend), prior to staining for FACS sorting. Human lung cells from 6 fetal lungs samples (18-23 weeks old) were individually hashed with MULTI-Seq lipid barcodes as previously described (McGinnis Nat Methods 2019) followed by staining for FACS sorting. For all samples, CD3+ γδTCR+ cells were sorted on FACS Aria III cell sorter (BD Biosciences).
Libraries for sc RNA and TCR sequencing were generated from 1.5-2*104 FACS-pool sorted γδ T cells using the Chromium Single Cell 5’ Library Gel Bead and Construction kit as well as Chromium Single Cell V(D)J Enrichment Kit (10x Genomics, CA, USA) according to the user guidelines (v2 Chemistry, Single Cell V(D)J protocol number CG000330). Single-cell TCR & gene expression libraries were generated according to Chromium Single Cell V(D)J protocol (10x Genomics). 2μL of cDNA amplified and purified from GEMs (“Gel bead in Emulsion” droplets) were used to amplify γδTCR CDR3 sequences. Custom primers specific for TRDC and TRGC constant gene segments were designed for this purpose. In brief, for the first step in the enrichment of CDR3 sequences the custom outer primer sets followed by second target enrichment (inner) primer sets. The remaining volume of cDNA was used for construction of gene expression library according to 10X Genomics protocol instructions. Agilent Bioanalyzer High Sensitivity DNA chips were used to check quality control read-outs of sc RNA-seq and sc TCR-seq libraries using a Bioanalyzer 2100 machine (Agilent Technologies). Indexed libraries were pooled and sequenced on Illumina NovaSeq 6000 from BRIGHTcore (Brussels Interuniversity Genomics High Throughput core) platform.

value: lung

value: Gamma delta T cell

value: 10 wk old


title: JAC06_BR


title: quantseq_WT_D2_Rep3

value: EpiLC derived from WT mouse embryonic stem cells (E14 background)


title: P300_ChIP_St10.5_FSMO_Ecto_Rep1

description: Library name: P300_ChIP_St10.5_FSMO_Ecto_Rep1

value: Ectoderm


title: Lung_control_adult_mouse_gdTCR

description:
ALUgd_filtered_contig_annotations.csv
ALUgd_filtered_contig.fasta


title: JAC23_BR

value: typically developing


title: Whole brain, Tecpr2 ki/ki, rep 1

description: Library name: Tecpr2_KI_rep_1

value: Tecpr2 L1152fs knock-in


title: P300_ChIP_St10.5_WT_Ecto_Rep2

description: Library name: P300_ChIP_St10.5_WT_Ecto_Rep2


title: Whole brain, Tecpr2 ki/ki, rep 4

description: Library name: Tecpr2_KI_rep_4


title: JAC01_BR

value: brain (PFC)


title: P300_ChIP_St10.5_WT_Endo_Rep2

description: Library name: P300_ChIP_St10.5_WT_Endo_Rep2

value: Endoderm


title: quantseq_WT_D2_Rep2


title: P300_ChIP_St10.5_WT_Ecto_Rep1

description: Library name: P300_ChIP_St10.5_WT_Ecto_Rep1

value: Wild-type X. tropicalis


title: JAC13_BR

value: Japanese


title: Lung_control_adult_mouse_GEX

description:
ALUgd_matrix.mtx.gz
ALUgd_features.tsv.gz
ALUgd_barcodes.tsv.gz


title: quantseq_WT_D2_Rep1


title: Lung_control_neonate_mouse_Hashtag

description:
NLUgd_matrix.mtx.gz
NLUgd_features.tsv.gz

value: Day 0 old


title: quantseq_WT_D0_Rep3

value: WT mouse embryonic stem cells (E14 background)


title: WT_St10.5_snRNAseq_SubLib2

description: Library name: WT_St10.5_snRNAseq_SubLib2

data_processing:
Parse Biosciences' in-house alignment software (dnanexus.com) command "Parse Batch Analysis v1.1.4" was used with the default commands against the UCB_Xtro_10.0 (GCA_000004195.4) Ensembl reference. The unfiltered Parse output containing "all_genes.csv", "cell_metadata.csv" and "DGE.mtx" were first amalgamated into a .h5Seurat object using the R software "Seurat", "Matrix", "SeuratDisk", "Reticulate" and the command "CreateSeuratObject". The .h5Seurat object was converted into an .h5ad file using the "Convert" command with the option "dest = "h5ad"". The unfiltered.h5ad file was analyzed in python using scanpy v1.9.6 (Wolf et al. 2018) , pandas v2.1.4 (McKinney et al. 2010), where the nuclear data was log transformed, normalized and highly variable genes were annotated. Doublets were predicted using Scrublet (Wolock et al. 2019), then manually inspected, confirmed and removed based on illogical ectopic co-expression of germ-layer specific markers and outlier read counts. Leiden (Traag et al. 2019) was used to predict de novo cluster formation, visualized via Uniform Manifold Approximation Projection (UMAP) (McInnes et al. 2018). Scanpy was used to calculate differential gene expression analysis of known marker genes between de novo clusters which were assigned to their germ-layer identity. Accordingly, clusters were merged based on co-expression of known marker genes from stage specific in-situ hybridization experiments curated through xenbase.org.
Assembly: UCB_Xtro_10.0
Supplementary files format and content: Raw Parse alignment output's contain alignment matrix (snRNAseq_St105_DGE.mtx), genes (snRNAseq_St105_all_genes.csv) and metadata (snRNAseq_St105_cell_metadata.csv). Raw alignments converted to python compatible snRNAseq_St105_unfiltered.h5ad, and analyzed annotations to snRNAseq_St105_Processed-Annotated.h5ad

extract_protocol:
Nuclei were isolated from stage 10.5 embryos using previously published discontinuous sucrose gradient protocols followed by a separate centrifugation through 80% glycerol. 200 embryos were homogenized in a 250mM sucrose solution containing glycerol and snap frozen in liquid nitrogen. Homogenates were later thawed on ice, brought to ~2.2M sucrose and centrifuged through a 2.4M sucrose layer at 130,000g for 2 hours at 4oC using a Beckman SW55Ti rotor, followed by a 3400xg centrifugation for 10 min at 4oC through an 80% glycerol cushion containing 0.2 U/ml RNAse and 5mg/ml protease inhibitors. Nuclei were finally resuspended in "nuclear" PBS with 0.5% BSA and 0.2 U/ml RNase inhibitor. DAPI stained nuclei were counted with hemocytometer, then fixed using Parse Bioscience Evercode Fixation Kit (SB1003). Nuclei in DMSO were slow-frozen to -80C overnight.
A bar-coded snRNAseq library was prepared using the Parse WT Mini Kit (ECW01010)

value: Whole embryo


title: WT_St10.5_snRNAseq_SubLib1

description: Library name: WT_St10.5_snRNAseq_SubLib1


title: JAC12_BR

value: male


title: JAC16_BR

value: child maltreatment


title: Lung_control_neonate_mouse_gdTCR

description:
NLUgd_filtered_contig_annotations.csv
NLUgd_filtered_contig.fasta


title: H3K27me3_ChIP_Endo_St10.5_R2

description: Library name: H3K27me3_ChIP_Endo_St10.5_R2


title: quantseq_WT_D0_Rep2


title: Lung_control_neonate_mouse_GEX

description:
NLUgd_matrix.mtx.gz
NLUgd_features.tsv.gz
NLUgd_barcodes.tsv.gz


title: quantseq_WT_D0_Rep1


title: JAC14_BR


title: H3K27me3_ChIP_Endo_St10.5_R1

description: Library name: H3K27me3_ChIP_Endo_St10.5_R1


title: HNF4G KPC Liver mets rep 2

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

description:
HNF4G hichip
kpc_hnf4g_liver_mets.interact.bed.gz

data_processing:
Paired-end fastq files were processed using HiC-Pro (version 3.1.0) (Servant et al., 2015) pipeline with default settings using mm10 reference genome and MboI restriction map.
Hichipper pipeline (Lareau et al., 2018) was further used to map valid read pairs to ChIP regions of interest and generate interaction loops.
All significant interactions were recorded in various formats including UCSC-compatible bed interact files which can be visualized in the genomic browser.
Assembly: GRCm38
Supplementary files format and content: bed/text
Library strategy: HiChIP-Seq

source_name: mouse pancreatic cancer cells

growth_protocol: KPC mouse cells were grown in DMEM 10% FBS

extract_protocol:
Hi-ChIP protocol was performed .Maxwell R Mumbach et al. 2016 from Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits Mentioned in materials and methods. Antibody-HNF4G-HPA005438
DNA was prepared for Illumina sequencing on the Nova seq 6000

treatment_protocol: mostly untreated or CRISPR pertubation

value: mouse pancreatic cancer cells

value: liver metastasis cell line

value: pancreatic cancer cells

value: WT

value: Untreated

tag: antibody


title: JAC03_BR


title: JAC25_BR

value: female


title: H3K27me3_ChIP_Ecto_St10.5_R1

description: Library name: H3K27me3_ChIP_Ecto_St10.5_R1

value: Ectoderm


title: HNF4G KPC Liver mets rep 1


title: rescues_AL_SUZ12

description: 10% human NT2 cells was used for spike-in chromatin.

value: AEBP2 KO + AEBP2L rescue mouse embryonic stem cells (E14 background)

value: SUZ12 (Cell Signaling, D39F6)


title: rescues_AS_SUZ12

value: AEBP2 KO + AEBP2S rescue mouse embryonic stem cells (E14 background)


title: H3K27me3_ChIP_Ecto_St10.5_R2

description: Library name: H3K27me3_ChIP_Ecto_St10.5_R2

value: Wild-type X. tropicalis


title: HNF4G KPC tumour rep 2

description:
HNF4G hichip
kpc_hnf4g_tumour.interact.bed.gz

value: tumour


title: rescues_AEBP2KO_SUZ12

value: AEBP2 KO mouse embryonic stem cells (E14 background)


title: rescues_AS_AEBP2

value: AEBP2 (Cell Signaling, D7C6X)


title: JAC09_BR

value: brain (PFC)

value: typically developing

value: Japanese


title: jc8530_kpc_liver_mets

description: KPC liver mets

data_processing:
STAR, version 2.6.1a, was used to align reads against human hg38 or mouse mm10 reference genome.
The read counting was performed using featureCounts v2.0.4.
For normalized measurement of mRNA expression the read counts were converted into RPKM values.
Differential gene expression analysis was performed using DESeq2 workflow.
Assembly: GRCh38,GRCm38
Supplementary files format and content: text

source_name: KPC liver mets-Rep 4

growth_protocol: Mouse cells were grown in DMEM 10% FBS, Sodium pyruvate. HPAF-II cells were grown in MEM media.  The cells were injected into NSG mice and tumours were monitored using ultra sound. The mice were killed at an humane endpoint and tumours were extracted and processed for RNA seq

extract_protocol:
Maxwell® RSC simplyRNA Cells Kit
RNAseq libraries were prepared using Illumina’s TruSeq mRNA Stranded Sample prep kit.

treatment_protocol: No treatment was performed on these cells. Lentiviral over expression and CRISPR KO's  were generated and this has been indicated in the descriptions.

value: pancreatic adenocarcinoma

value: KPC cell line

value: KPC


title: H3K27ac_ChIP_Ecto_St10.5

description: Library name: H3K27ac_ChIP_Ecto_St10.5


title: H3K27ac_ChIP_Endo_St10.5

description: Library name: H3K27ac_ChIP_Endo_St10.5

value: Endoderm


title: HNF4G KPC tumour rep 1

value: mouse pancreatic cancer cells

value: pancreatic cancer cells

value: WT

value: Untreated


title: JAC05_BR

value: female

value: child maltreatment


title: JAC02_BR


title: P300_ChIP_Ecto_St10.5

description: Library name: P300_ChIP_Ecto_St10.5

value: Ectoderm

value: Wild-type X. tropicalis


title: jc8528_kpc_liver_mets

description: KPC liver mets

source_name: KPC liver mets-Rep 3


title: rescues_AEBP2KO_AEBP2

value: AEBP2 KO mouse embryonic stem cells (E14 background)


title: jc8529_kpc_tumour

description: KPC tumour

source_name: KPC tumour- Rep 4


title: JAC08_BR

value: male


title: Sox3_ChIP_St10.5_R2

description: Library name: Sox3_ChIP_St10.5_R2

source_name: Whole embryo

value: Whole embryo


title: FHs 74 Int cells,AGE-HS,4 hours,biol rep 3

city: Krems

first: Sabine

last: Geiselhart

address: Dr.-Karl-Dorrek-Straße 30

country: Austria

institute: Karl Landsteiner University of Health Sciences

description: Library name: SG01024

data_processing:
FASTQ format reads were produced using the Illumina bcl2fastq command line tool (v2.19.1.403). Reads were then trimmed and filtered with cutadapt version 2.8 to remove polyA tails, reads with N’s, and bases with a quality of less than 30 from the 3’ ends. After this procedure, 2.2 million reads remained on average. FASTQ reads were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted the raw reads per gene.
The data analysis was performed in RStudio Server version 2024.4.1.748. First, we kept only those genes which code for proteins. Genes with Ensembl gene IDs were annotated to Entrez gene IDs by keeping one Entrez gene ID by choosing the gene with the highest overall count. Annotation was performed with packages biomaRt version v2.60.0 and AnnotationDbi version 1.66.0 with annotation database org.Hs.eg.db version 3.19.1. Finally, we removed genes with total reads equal to zero. Differential expression analysis was performed using DESeq2 version 1.44.0 and Wald test. P-values were adjusted using the Benjamini & Hochberg method. Reported log2 fold changes (LFC) were obtained by shrinkage with lfcShrink function from DESeq2 ashr version 2.2.63.
Assembly: Human reference genome version GRCh38 with Gencode annotations
Supplementary files format and content: raw_gene_counts_GeneSymbols_GeneTypes.tsv: File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner; Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)
Supplementary files format and content: vst_transf_counts_GeneSymbols_GeneTypes.tsv:  File containing variance-stabilizing-transformed count data generated by DESeq2 function vst . Columns: GeneType, GeneSymbol, Ensembl Gene ID, sampleIDs with vst transformed counts

source_name: FHs 74 Int

growth_protocol: FHs 74 Int cells were maintained  in HybriCare medium supplemented with 10% FBS, anitibiotics and 30 ng/ml epidermal growht factor in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) including DNase I digestion
Sequencing libraries were prepared from total RNA samples at the Core Facility Genomics, Medical University of Vienna, with the QuantSeq FWD using the UDI V2 protocol (Lexogen). Eleven PCR cycles were performed for library preparation, determined by qPCR according to manual. Libraries underwent quality control on a Bioanalyzer 2100 (Agilent) with a High Sensitivity DNA Kit to confirm correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). The pooled libraries were sequenced on a NextSeq500 instrument (Illumina) in 1x75bp single-end mode, generating approximately 3.8 million reads per sample.

treatment_protocol: Cells were starved for two hours and then treated with the respective compounds for one or four hours

value: FHs 74 Int

value: small intestinal epithelial cells

value: AGE-HS

tag: time

value: 4 hours


title: jc8527_kpc_tumour

description: KPC tumour

source_name: KPC tumour- Rep 3

value: pancreatic adenocarcinoma

tag: cell line

value: KPC cell line

value: KPC


title: FHs 74 Int cells,AGE-HS,4 hours,biol rep 2

description: Library name: SG01023

tag: cell type


title: JAC26_BR

tag: tissue

value: brain (PFC)

value: typically developing

value: Japanese


title: JAC22_BR

value: female

tag: age


title: jc8526_kpc_liver_mets

description: KPC liver mets

source_name: KPC liver mets-Rep 2

value: WT


title: JAC21_BR

tag: gender

value: child maltreatment


title: FHs 74 Int cells,AGE-HS,4 hours,biol rep 1

description: Library name: SG01022


title: jc8525_kpc_tumour

description: KPC tumour

source_name: KPC tumour- Rep 2


title: FHs 74 Int cells,HS,4 hours,biol rep 3

description: Library name: SG01021

value: HS


title: JAC10_BR


title: rescues_AL_AEBP2

value: AEBP2 KO + AEBP2L rescue mouse embryonic stem cells (E14 background)

value: AEBP2 (Cell Signaling, D7C6X)


title: JAC04_BR

value: male


title: jc8524_kpc_liver_mets

description: KPC liver mets

source_name: KPC liver mets-Rep 1


title: P300_ChIP_Endo_St10.5

description: Library name: P300_ChIP_Endo_St10.5

value: Endoderm

value: Wild-type X. tropicalis


title: FHs 74 Int cells,HS,4 hours,biol rep 2

description: Library name: SG01020

value: FHs 74 Int

value: small intestinal epithelial cells


title: jc8523_kpc_tumour

description: KPC tumour

source_name: KPC tumour- Rep 1

value: pancreatic adenocarcinoma


title: FHs 74 Int cells,HS,4 hours,biol rep 1

description: Library name: SG01019

value: 4 hours


title: JAC24_BR


title: FOXA1 KPC Liver mets Rep 2

description: FOXA1 hichip

source_name: liver metastasis cell line

extract_protocol:
Hi-ChIP protocol was performed .Maxwell R Mumbach et al. 2016 from Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits Mentioned in materials and methods. Antibody FOXA1- ab5089
DNA was prepared for Illumina sequencing on the Nova seq 6000

value: liver metastasis cell line

value: mouse pancreatic cancer cells

value: Untreated


title: FHs 74 Int cells,S100A12,4 hours,biol rep 3

description: Library name: SG01018


title: JAC18_BR

value: brain (PFC)

value: Japanese


title: FHs 74 Int cells,S100A12,4 hours,biol rep 2

description: Library name: SG01017

value: WT


title: FOXA1 KPC tumour Rep 2

description: FOXA1 hichip

source_name: tumour

value: tumour


title: FOXA1 KPC Liver mets  Rep 1

description: FOXA1 hichip


title: JAC21_BL

extract_protocol: DNA was extracted from whole blood samples using the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Venlo, Netherlands).

value: whole blood

value: female

value: child maltreatment


title: FHs 74 Int cells,S100A12,4 hours,biol rep 1

description: Library name: SG01016


title: FOXA1 KPC tumour Rep 1

description: FOXA1 hichip


title: FHs 74 Int cells,control, 4 hours,biol rep 3

description: Library name: SG01015


title: Healthy Controls, S38

type: RNA

city: Karachi

first: Asghar

last: Nasir

state: Sindh

address: Stadium Road

department: Pathology and Laboratory Medicine

country: Pakistan

institute: Aga Khan University

hyb_protocol: Clariom S Array Type gene expression, Affymetrix

scan_protocol: GeneChipTM Scanner 3000 7G

data_processing: CEL files were analysed using the TCAS Transcriptome Analysis Software Suite (version 2) using the Summarization Method: Gene Level - SST-RMA Pos vs Neg AUC Threshold: 0.7 against Genome Version: hg38 (Homosapiens)

label: biotin

source_name: blood

growth_protocol: RNA was extracted from whole blood collected in Plasma/EDTA tube.

extract_protocol: Qiagen RNA Blood Mini Kit (Qiagen, GmbH, Germany)

treatment_protocol: no treatment

value: blood

value: male

tag: ltbi

value: LTBi-positive

tag: diabetes

value: No


title: Healthy Controls, S36

label_protocol: Clariom S Array Type gene expression, Affymetrix


title: FHs 74 Int cells,control, 4 hours,biol rep 2

description: Library name: SG01014

value: FHs 74 Int

value: small intestinal epithelial cells

tag: genotype


title: Healthy Controls, S37


title: JAC15_BL

source_name: Judicial Autopsy Cases

tag: group

value: typically developing


title: jc6641_KPC_mets_input_untreated

description:
input
KPC mets
METS input

data_processing:
Reads were mapped to hg38 or mm10 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences. Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Assembly: GRCh38,GRCm38
Supplementary files format and content: bed/text

growth_protocol: HPAF-II & ASPC-1 cells were grown in MEM & RPMI High 10% FBS, Sodium pyruvate. KPC mouse cells were grown in DMEM 10% FBS

extract_protocol:
ChIP-Seq was performed at described in Ross-Innes CS et al. Nature. 2012. Antibodies used are specified above FOXA1-ab5089, HNF4G-atlas HPA005438, PRMT1-atlas HPA069769,H3K27Ac-ab4729,flag-sigma-F1804,GATA6-RD-AF1700
DNA was prepared for Illumina sequencing on the Nova Seq 6000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: untreated or CRISPR pertubation

value: Pancreatic adenocarcinoma

value: untreated


title: Healthy Controls, S34


title: Healthy Controls, S33


title: JAC08_BL

tag: nationality


title: Healthy Controls, S35


title: jc6640_KPC_tumour_input_untreated

description:
input
KPC tumour
KPC input

tag: treatment


title: Healthy Controls, S32


title: JAC22_BL


title: Healthy Controls, S31


title: JAC14_BL


title: FHs 74 Int cells,AGE-HS,1 hour,biol rep 3

description: Library name: SG01012

value: AGE-HS

value: 1 hour


title: jc6633_KPC_mets_HNF4G_untreated

description:
HNF4G-KPC mets-Rep 1
KPC mets
HNF4G METS


title: Healthy Controls, S29


title: JAC07_BL

value: Japanese


title: FHs 74 Int cells,AGE-HS,1 hour,biol rep 2

description: Library name: SG01011

value: WT


title: Healthy Controls, S30


title: JAC16_BL


title: jc6614_KPC_tumour_FOXA1_untreated

description:
FOXA1-KPC tumour-Rep 1
KPC tumour
FOXA1 KPC


title: JAC13_BL


title: Healthy Controls, S28


title: KPC Liver mets rep 4

description: KPC Liver mets

data_processing:
Reads were mapped to hg38 or mm10 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library.
The peaks were called with MACS2, version 2.1.1.20160309, using following parameters:  -g hs -f BAM --nomodel --shift -100 --extsize 200.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Assembly: GRCh38,GRCm38
Supplementary files format and content: bed/text

source_name: liver mets

growth_protocol: HPAF-II cells were grown in MEM 10% FBS, Sodium pyruvate. KPC cells were grown in DMEM +10% FCS

extract_protocol:
Omni ATAC-seq protocol was performed from Corces et al., 2017, Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits.
DNA was prepared for Illumina sequencing on the NovaSeq 6000.

treatment_protocol: Untreated or CRISPR pertubation

value: KPC Liver met cell line

value: Pancreatic cancer cells


title: FHs 74 Int cells,control, 4 hours,biol rep 1

description: Library name: SG01013

value: 4 hours


title: FHs 74 Int cells,HS,1 hour,biol rep 3

description: Library name: SG01009

value: HS


title: FHs 74 Int cells,HS,1 hour,biol rep 2

description: Library name: SG01008


title: KPC Liver mets rep 3

description: KPC Liver mets


title: Healthy Controls, S26

value: blood

value: female


title: KPC Liver mets rep 2

description: KPC Liver mets


title: JAC05_BL

value: whole blood

value: child maltreatment


title: jc6632_KPC_tumour_HNF4G_untreated

description:
HNF4G-KPC tumour-Rep 1
KPC tumour
HNF4G KPC


title: JAC04_BL

value: male


title: FHs 74 Int cells,S100A12,1 hour,biol rep 3

description: Library name: SG01006

value: FHs 74 Int

value: small intestinal epithelial cells


title: Healthy Controls, S25

value: LTBi-positive

value: No


title: FHs 74 Int cells,AGE-HS,1 hour,biol rep 1

description: Library name: SG01010

value: AGE-HS


title: JAC11_BL

value: typically developing


title: Healthy Controls, S27


title: KPC tumour rep 3

description: KPC tumour

value: Pancreatic adenocarcinoma

value: KPC tumour cell line

value: untreated


title: Healthy Controls, S23


title: FHs 74 Int cells,S100A12,1 hour,biol rep 1

description: Library name: SG01004

value: WT

value: 1 hour


title: DM, S22

value: Yes


title: KPC tumour rep 4

description: KPC tumour

value: Pancreatic cancer cells


title: DM, S21

value: blood


title: JAC12_BL

value: whole blood

value: Japanese


title: JAC06_BL

value: female

value: child maltreatment


title: KPC tumour rep 2

description: KPC tumour


title: JAC10_BL


title: FHs 74 Int cells,control,1 hour,biol rep 3

description: Library name: SG01003

value: FHs 74 Int

value: small intestinal epithelial cells


title: KPC tumour rep 1

description: KPC tumour


title: KPC Liver mets rep 1

description: KPC Liver mets

value: KPC Liver met cell line


title: FHs 74 Int cells,control,1 hour,biol rep 2

description: Library name: SG01002


title: JAC02_BL


title: SCI_d28

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

country: China

institute: The first affiliated hospital of nanjing medaical university

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1 contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCm38
Supplementary files format and content: tar archives include barcodes.tsv, genes.tsv, and matrix.mtx files.

source_name: spinal cord

extract_protocol:
The spinal cord of indicated groups were collected, and the tissue dissociation solution was used to form single-cell suspension, and immune cells were sorted by flow cytometry.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a NovaSeq 6000 platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

value: spinal cord

value: immune cells

value: 8-10 weeks

tag: strain

tag: condition

value: spinal cord injury

tag: timepoint

value: day 28 post injury


title: JAC09_BL

value: typically developing


title: FHs 74 Int cells,HS,1 hour,biol rep 1

description: Library name: SG01007

value: WT

value: HS

value: 1 hour


title: DM, S20

value: blood

value: LTBi-positive

value: Yes


title: DM, S19

value: female


title: Healthy Controls, S24

value: No


title: DM, S18

value: LTBi-Negative


title: FHs 74 Int cells, control, 1 hour,biol rep 1

description: Library name: SG01001

value: FHs 74 Int

value: small intestinal epithelial cells


title: FHs 74 Int cells,S100A12,1 hour,biol rep 2

description: Library name: SG01005


title: SCI_d7

value: spinal cord

value: day 7 post injury


title: SCI_d14

value: immune cells

value: 8-10 weeks

value: day 14 post injury


title: JAC01_BL

value: whole blood

value: child maltreatment

value: Japanese


title: JAC03_BL

value: male


title: SCI_d3

value: spinal cord injury

value: day 3 post injury


title: SCI_d1

value: day 1 post injury


title: MCF10A  cells, SUVASO2M_2, repeat2

city: yangzhou

first: Yu

last: Shiyi

state: Jiangsu

address: hanjiang district jiangyangzhonglu136, Hanjiang district, Jiangyangzhonglu 136

institute: yangzhou university

description:
Library name: MCF10A_SUVASO2M_2, RNAseq
MCF710A_SUVASO2M vs CtrASOM_all_counts.xlsx

data_processing:
Raw data were filtered with SOAPnuke (v1.5.6).
The clean data were mapped to the human genome (hg38) using Hisat2 (v 2.2.1; parameter: default) to generate SAM files.
After that, the SAM files were processed with SAMtools (v 1.21; parameter: default) and the featureCounts (v2.1.1; parameter: default) were used to calculate counts for each sample.
Finally, the DEGs (p < 0.05, |LogFC| > 1) were calculated with the DESeq2 (v 1.48.1; parameter: default).
The gene enrichment analysis was performed with GSEA (v4.4.0; Database: HALLMARK.v2025.1) and REACTOME (v88; parameter: default).
Assembly: hg38
Supplementary files format and content: Process the counts files of the treatment group compared to the control group, in xlsx format.

source_name: breast cancer

growth_protocol: MCF7-ABER and MCF7-PALR cells were maintained in Phenored-free RPMI1640 (Procellsystem, cat.PM150120), supplemented with 10% Charcoal Stripped FBS (VivaCell, cat.C3830-0500). MCF10A cells were maintained in MCF10A Cell Complete Medium (Procellsystem, cat.CM-0525),

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Thermo Fisher, 15596026CN). The library was constructed and sequenced on the DNBSEQ-G400 platform.
The library was constructed and sequenced on the DNBSEQ-G400 platform.

treatment_protocol: MCF7-ABER cell were transfected with pcDNA3 or RAD21. And MCF7-ABER, MCF7-PALR and MCF10A cells were treated with CtrASOM or SUVASO2M

value: breast cancer

value: breast cancer cells

value: WT

tag: batch


title: MCF10A  cells, SUVASO2M_1, repeat1

description:
Library name: MCF10A_SUVASO2M_1, RNAseq
MCF710A_SUVASO2M vs CtrASOM_all_counts.xlsx


title: DM, S17

value: blood

value: LTBi-Negative

value: Yes


title: Uninjured

value: spinal cord

value: uninjured


title: MCF10A  cells, CtrASOM_2, repeat2

description:
Library name: MCF10A_CtrASOM_2, RNAseq
MCF710A_SUVASO2M vs CtrASOM_all_counts.xlsx

value: CtrASOM


title: MCF10A  cells, CtrASOM_1, repeat1

description:
Library name: MCF10A_CtrASOM_1, RNAseq
MCF710A_SUVASO2M vs CtrASOM_all_counts.xlsx


title: DM, S16

value: female


title: MCF7-ABER  cells, SUVASO2M_2, H3K9me3, repeat2

description: Library name: SUVASO2M_2, CUT_Tag

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.1; parameters: Default), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Alignment to the human reference genome (hg38) was performed using Bowtie2 (v2.2.6; parameters: Default)
Sambamba (version 0.7.1; parameters: -r -t 4 -l 7) is used for sam/bam format conversion and PCR duplicate reads removal.
Peaks were called using macs2 (version 2.2.7.1; parameters:-f BAM -B --shift -100 --extsize 200 --nomodel --keep-dup all -p 0.01 --SPM) .
Bigwig files were produced for each sample using deeptools（version 2.4.1; parameters: --binSize 10 --normalizeUsing RPKM --scaleFactor 1)
Assembly: hg38
Supplementary files format and content: bw; broadpeak
Library strategy: CUT&Tag

growth_protocol: Phenored-free RPMI1640, 10% Charcoal Stripped FBS

extract_protocol:
MCF7-ABER cells were collected from cultures.The cells were then incubated with ConA Beads Pro (Vazyme, China, cat. TD904) for 10 minutes at room temperature to facilitate cell attachment. Following incubation, a 1:50 dilution of the primary antibody against H3K9ME3 protein (Active Motif, cat. 39062) was added to the cells. The mixture was gently vortexed and subjected to a brief centrifugation to ensure even distribution of the antibody. The cells were then incubated with the primary antibody overnight at 4°C to allow for specific protein binding. The following day, the appropriate secondary antibody was added at a 1:100 dilution, and the cells were incubated on a rotating platform at room temperature for 60 minutes. After incubation, the cells were washed twice using a magnetic rack to remove any unbound secondary antibodies present in the supernatant.then, the cells were resuspended, and a 1:50 dilution of pA/G-Tnp Pro (Vazyme, China, cat. TD904) was added to the cell suspension. The mixture was gently mixed and centrifuged to promote binding. The binding reaction with pA/G-Tnp Pro was carried out at room temperature for 1 hour on a rotating platform. To eliminate any unbound pA/G-Tnp Pro, the cells were washed twice using a magnetic rack. The cells were then resuspended and incubated at 37°C for 1 hour to activate the transposase enzymatic activity. To halt the tagmentation reaction, 10% SDS was added, and the sample was incubated at 55°C for 10 minutes. Last, The tagmented DNA was recovered using DNA Extract Beads Pro (Vazyme, China, cat. TD904)
CUT&Tag library preparation was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, China, cat.TD904) according to the manufacturer instructions.

treatment_protocol: cells were treated with CtrASOM or SUVASO2M


title: MCF7-PALR  cells, SUVASO2M_2, repeat2

description:
Library name: MCF7-PALR_SUVASO2M_2, RNAseq
MCF7-PALR_SUVASO2M vs CtrASOM_all_counts.xlsx


title: BT-549_CAT_rep4

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

description: Gene expression of LSBE treated BT-549 cells

hyb_protocol: The probes were hybridized for 17 h at 65oC on Agilent SurePrint G3 Human GE 8x60k arrays

scan_protocol: The slides were scanned with Agilent G2505C Microarray Scanner at 5 µm resolution

data_processing: Microarray images were processed with Agilent Feature Extraction software v. 11.5.1.1.

source_name: triple-negative breast cancer cell line, LSBE treated

label_protocol: Microarray probes labeled with Cy3 were synthesized from 200 ng of total RNA with Low Input Quick Amp Labeling Kit and checked for quality and quantity with NanoDrop ND-1000 (Thermo Fischer Scientific)

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 0.02% insulin, 1% penicillin–streptomycin and 1% glutamine.

extract_protocol: Total RNA was extracted using the phenol-chloroform method following cell lysis with TriReagent solution

treatment_protocol: After 24 hours of cell plating, the culture medium was removed and replaced with 3 mL of fresh medium containing 12 µM (IC50) of LSBE, respectively, fresh culture medium. Cells were incubated with LSBE treatment and fresh culture medium for 24 hours at 37ºC in a 5% CO2 incubator and humidified atmosphere.

value: LSBE treatment


title: DM, S15

value: LTBi-positive


title: MCF7-PALR  cells, SUVASO2M_1, repeat1

description:
Library name: MCF7-PALR_SUVASO2M_1, RNAseq
MCF7-PALR_SUVASO2M vs CtrASOM_all_counts.xlsx


title: MCF7-ABER  cells, SUVASO2M_1, H3K9me3, repeat1

description: Library name: SUVASO2M_1, CUT_Tag


title: MCF7-ABER  cells, CtrASOM_2, H3K9me3, repeat2

description: Library name: CtrASOM_2, CUT_Tag


title: MCF7-PALR  cells, CtrASOM_2, repeat2

description:
Library name: MCF7-PALR_CtrASOM_2, RNAseq
MCF7-PALR_SUVASO2M vs CtrASOM_all_counts.xlsx


title: BT-549_CAT_rep3


title: DM, S12


title: DM, S13


title: MCF7-ABER cells, CtrASOM_1, H3K9me3, repeat1

description: Library name: CtrASOM_1, CUT_Tag


title: LP040011

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

institute: Medical University Vienna

description:
Library name: Sample12
Column name in raw_counts_All_THP1 Samples.tsv: LP040011

data_processing:
Reads in FASTQ format were generated using the Illumina bcl2fastq command-line tool (v2.19.1.403) and the Lexogen idemux tool for optimal demultiplexing of long, unique, dual indices. Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N's, and trim bases with a quality of less than 30 from the 3' ends of the reads. On average, 5 million reads were left after this procedure. Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using the STAR aligner version 2.6.1a in 2-pass mode. STAR counted raw reads per gene. Differential gene expression was calculated using DESeq2 version 1.22.2.
Assembly: Reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode
Supplementary files format and content: raw_counts_All_U937 Samples.tsv and raw_counts_All_THP1 Samples.tsv contain a matrix with raw gene counts, gene symbols and gene types for each sample, respectively.

source_name: Human monocytic cell line from an acute monocytic leukemia

growth_protocol: The human cell lines THP-1 and U937 were maintained in RPMI 1640 medium (Gibco Life Technologies, CA, USA)

extract_protocol:
Total RNA was isolated with the ExtractMe total RNA kit (Blirt S.A., Gdańsk, Poland).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq 3' FWD protocol version 2 with unique dual indices (Lexogen GmbH, Vienna, Austria). Fifteen PCR cycles were used for library preparation, as determined by quantitative PCR (qPCR) according to the library preparation manual.

treatment_protocol: The human cell lines THP-1 and U937 were incubated for 24 hours without or with 300 µg/mL of enamel derivative matrix (EMD; Straumann AG, Basel, Switzerland).

value: monocytes

value: treat with EMD


title: MCF7-PALR  cells, CtrASOM_1, repeat1

description:
Library name: MCF7-PALR_CtrASOM_1, RNAseq
MCF7-PALR_SUVASO2M vs CtrASOM_all_counts.xlsx


title: DM, S14


title: BT-549_CAT_rep1


title: LP04007

description:
Library name: Sample11
Column name in raw_counts_All_THP1 Samples.tsv: LP04007

value: Human monocytic cell line from an acute monocytic leukemia


title: DM, S11


title: HASMC, YAP, Ad.TAX1BP3_rep 2

city: Guangzhou

first: yulong

last: zhong

state: Guangdong Province

address: 1838 Guangzhou Avenue North

department: physiology

institute: Southern Medical University

data_processing:
Sequencing reads were trimmed by cutadapt (v 4.3) to get high quality reads. High quality reads were aligned to the human reference genome hg19 using Bowtie2 (v 2.2.5) with the parameter of "-X 2000". The mapped reads were sorted using Samtools (v 1.13), retaining any reads with a MAPQ less than 30. Duplicated reads were removed by Picard (v 2.7). Peaks were called by MACS2 (v 2.2.7.1).  Bigwig files were generated from bam files using deeptools (v 3.5.1) bamCoverage. All samples were normalized to 1 million reads with binsize as 50-bp by "--scaleFactor --binSize 50" parameters.
Assembly: hg19
Supplementary files format and content: The processed files were bigwig files and bed files.

source_name: HASMC

growth_protocol: HASMCs were cultured in primary smooth muscle cell low serum culture system (PriMed-iCell-004, Bioscience Inc) according to the vender's protocol and maintained in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
In summary, the fixed cells underwent three times washing with 0.1% BSA/PBS. The cells were then resuspended in 80 µl of Antibody Buffer (a mixture of 4 µl 0.5 M EDTA and 1 ml 0.01% Digitonin-Wash Buffer (Dig-Wash Buffer), supplemented with cocktail, 10 mM sodium butyrate, and 0.05% Triton X-100) that contained 1.6 µg of the primary antibody. This mixture was incubated at 4°C for 4 hours on a rotator with 16 rpm. The cells were subsequently washed twice with 180 µl of Dig-Wash Buffer. The secondary antibody (used at a 1:500 ratio) was incubated under the same conditions, except for a shorter duration of 10 minutes. After two times washing with Dig-Wash Buffer, the cells were suspended in 80 µl of Dig-Wash Buffer (containing 0.05% Triton-X, cocktail, and 10 mM sodium butyrate) that also contained 0.83 µM PAT-MEA/B. This was done at 4°C for 1 hour. The free PAT-MEA/B were then dislodged with 180 µl Dig-Wash Buffer containing 0.05% Triton X-100 three times at 5 min each time. The reaction was activated by suspending the cells with 10 µl Reaction Buffer (10 mM TAPS-NaOH pH 8.3, 5 mM MgCl2, 10% DMF, 300 mM NaCl, 0.05% Triton-X, 0.01% Digtonin and supplemented with cocktail, 10 mM sodium butyrate), followed by gently flicking and incubating at 37°C for 1 h in an Eppendorf ThermoMixer with 300 rpm. The reaction was gently mixed once after 30 min incubation and was halted by adding 10 µl of 40 mM EDTA, followed by further incubation at 4°C for 10 min. The samples were then washed with 0.1% BSA/PBS and finally resuspended in 5 µl of Lysis Buffer (0.1 mg/ml Proteinase K, 10 mM Tris-HCl pH 8.5, and 0.05% SDS), and lysed at 55°C for 3 hours in a PCR cycler. Finally, 1.8% Triton X-100 with 5 mM PMSF was added to the cell lysate and incubated at room temperature for 10 minutes to inactivate the proteinase K. This was followed by a 5-minute incubation at 55°C to quench the SDS in the reaction.
After PCR enrichment using 2x KAPA master mix,fragments larger than 1 kb were first eliminated using 0.4x AMPure beads, after which the library was purified using the Zymo DNA Clean and Concentrator-5 Kit.

treatment_protocol: The HASMCs were infected with VEC or Ad-TAX1BP3 adenovirus for 48 hours, and then in situ ChIP-seq was performed.

tag: chip antibody

value: YAP (senta #sc-101199)

value: HASMC

value: Human primary aortic smooth muscle cell

value: overexpression TAX1BP3


title: BT-549_ctr_rep2

description: Gene expression of untreated BT-549 cells

source_name: triple-negative breast cancer cell line, untreated

value: untreated


title: BT-549_ctr_rep4


title: MCF7-ABER  cells, SUVASO2M_2, repeat2

description:
Library name: MCF7-ABER_SUVASO2M_2, RNAseq
MCF7-ABER_SUVASO2M vs CtrASOM_all_counts.xlsx

value: breast cancer

value: breast cancer cells

value: WT


title: DM, S9

value: blood

value: LTBi-Negative

value: Yes


title: BT-549_ctr_rep1


title: BT-549_CAT_rep2


title: HASMC, YAP, Ad.TAX1BP3_rep 1


title: MCF7-ABER  cells, SUVASO2M_1, repeat1

description:
Library name: MCF7-ABER_SUVASO2M_1, RNAseq
MCF7-ABER_SUVASO2M vs CtrASOM_all_counts.xlsx


title: DM, S10

value: male


title: HASMC, YAP, VEC_rep 2


title: MCF7-ABER  cells, CtrASOM_2, repeat2

description:
Library name: MCF7-ABER_CtrASOM_2, RNAseq
MCF7-ABER_SUVASO2M vs CtrASOM_all_counts.xlsx

value: CtrASOM


title: LP04005

description:
Library name: Sample8
Column name in raw_counts_All_THP1 Samples.tsv: LP04005


title: MCF7-ABER  cells, CtrASOM_1, repeat1

description:
Library name: MCF7-ABER_CtrASOM_1, RNAseq
MCF7-ABER_SUVASO2M vs CtrASOM_all_counts.xlsx


title: LP04001

description:
Library name: Sample7
Column name in raw_counts_All_THP1 Samples.tsv: LP04001


title: NK-92 Cas9-BFP clone1, Brunello pDNA library

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

institute: St. Anna Children's Cancer Research Institute

description: Library name: Brunello_pDNA_library

data_processing:
De-multiplexed next generation sequencing data were processed in accordance with the Brunello protocol. Deconvolution of the sequencing files was performed using PoolQ v 3.2.11 (Broad Institute, Inc.) considering the start of the construct barcode search prefix between 10-40 with a sequence of CGAAACACCG and the sample barcode starting at index 0.
Assembly: "broadgpp-brunello_for_poolq.csv", "broadgpp-brunello-library-contents.txt"
Supplementary files format and content: "poolq_with_sort_counts.txt": Tab delimited file containing a PoolQ output count matrix with the samples as columns and the constructs as rows
Library strategy: CRISPR Screen

source_name: NK-92 Cas9-BFP clone1

extract_protocol:
gDNA was isolated using QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol with following modifications. Cell pellets were thawn on ice and resuspend in PBS as 5 million cells per 200µl per reaction. After lysis, samples were incubated for 18 hours at 56°C for decrosslinking
Concentration and DNA purity was assessed using Nanodrop and was further PCR amplified in accordance to Doench et. al., using the Nextera P7 primer indexing strategy. Each sample was PCR amplified in parallel reactions with 5µg gDNA/ 100ng pDNA per 50µl reaction each containing: 0.75µl ExTaq Polymerase (Clontech), 5µl 10x reaction buffer, 4µl dNTPs, 2.5µl 10µM staggered P5 forward primer mix, 5µl 5µM P7 indexing primer topped up with HPLC water for total 50µl. Primers were ordered as 20nmole Ultramer DNA Oligo, standard desalting, lab ready (normalized to 100µM in IDTE pH 8.0) stocks from IDT (see table below). PCR was done as follows: 1min 95°C, 25 cycles for gDNA and 15 cycles for pDNA of 30sec 95°C, 30sec 53°C, 30sec 72°C, and 10min 72°C final elongation. Target sequence amplification of 351-359bp (dependent on the P5 staggered primer) was measured by agarose gel electrophoresis. PCR reactions from one sample were pooled and cleaned up with 0.65 – 1X AMPure XP double size selection. Samples were eluted in 10mM Tris-HCl pH 8.0, concentration was determined by Qubit dsDNA HS and BR Assay (Invitrogen) and pooled at equimolar levels. The library pool was purified with 0.8X AMPure XP size selection, adjusted to 4nM and 50bp single end sequenced on HiSeq3000/4000 for approximately 66 million reads per sample total.

value: NK-92 Cas9-BFP clone1


title: MCF7-ABER  cells, RAD21_2, repeat2

description:
Library name: MCF7-ABER_RAD21_2, RNAseq
MCF7-ABER_RAD21 vs pcDNA3_all_counts.xlsx

value: RAD21 overexpression


title: MCF7-ABER  cells, RAD21_1, repeat1

description:
Library name: MCF7-ABER_RAD21_1, RNAseq
MCF7-ABER_RAD21 vs pcDNA3_all_counts.xlsx


title: LP050011

description:
Library name: Sample6
Column name in raw_counts_All_U937 Samples.tsv: LP050011

source_name: Human monocytic cell line from histiocytic lymphoma

value: monocytes

value: treat with EMD


title: NK-92 Cas9-BFP clone1, CD107a hi sort1

description: Library name: CD107a_hi_sort1


title: MCF7-ABER cells, pcDNA3_2, repeat2

description:
Library name: MCF7-ABER_pcDNA3_2, RNAseq
MCF7-ABER_RAD21 vs pcDNA3_all_counts.xlsx


title: LP04003

description:
Library name: Sample10
Column name in raw_counts_All_THP1 Samples.tsv: LP04003

value: Human monocytic cell line from an acute monocytic leukemia


title: NK-92 Cas9-BFP clone1, CD107a hi sort2

description: Library name: CD107a_hi_sort2


title: xgenomic_9

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

description: Library name: genomic_9

data_processing:
Read trimming (trimmomatic – for short reads, and porechop + nanofilt – for long reads
short read alignment (using hisat2 on RNA-seq reads, and bowtie2 – for ChIP-seq reads)
counting of exon-spanning reads with featureCounts (for RNA-seq)
calling enriched genomic regions with MACS2 (for ChIP-seq)
de novo genomic assembly with Flye (for long Nanopore reads)
Supplementary files format and content: featureCounts expression matrix (RNA-seq), MACS2-called peaks in broad mode (ChIP-seq)

organism: Drosophila virilis

source_name: ovary

extract_protocol:
Females of the 101 and 1051.47 strains were collected for DNA extraction and aged for 10-15 days. Genomic DNA was isolated from thirty pairs of ovaries using high-salt denaturing buffer containing 100 mM Tris-HCl (pH = 8), 10 mM EDTA (pH = 8), 350 mM NaCl, 2% SDS, and 7 M Urea following phenol-chloroform extraction. Before sequencing, we performed a size selection of high molecular weight DNA by depleting short DNA fragments below 10 kb using the Short Read Eliminator Kit (Circulomics, USA)
The preparation of DNA libraries for sequencing was carried out using the 1D ligation SQK-LSK109 kit (Oxford Nanopore Technologies (ONT), UK), by the recommended protocol from ONT. Sequencing was performed on a flow cell FLO-MIN-106D r9.4 (ONT, UK). The result was an average of 9.5 billion bases sequenced, with a median length of sequenced fragments from 20 to 40 kb for different libraries.

value: ovary


title: LP04009

description:
Library name: Sample9
Column name in raw_counts_All_THP1 Samples.tsv: LP04009


title: LP05007

description:
Library name: Sample5
Column name in raw_counts_All_U937 Samples.tsv: LP05007

value: Human monocytic cell line from histiocytic lymphoma


title: NK-92 Cas9-BFP clone1, CD107a neg sort1

description: Library name: CD107a_neg_sort1


title: LP05003

description:
Library name: Sample4
Column name in raw_counts_All_U937 Samples.tsv: LP05003


title: BT-549_ctr_rep3


title: xgenomic_160

description: Library name: genomic_160


title: MCF7-ABER cells, pcDNA3_1, repeat1

description:
Library name: MCF7-ABER_pcDNA3_1, RNAseq
MCF7-ABER_RAD21 vs pcDNA3_all_counts.xlsx


title: DM, S7


title: HASMC, YAP, VEC_rep 1

value: YAP (senta #sc-101199)

value: HASMC

value: Human primary aortic smooth muscle cell


title: NK-92 Cas9-BFP clone1, CD107a neg sort2

description: Library name: CD107a_neg_sort2


title: LP05009

description:
Library name: Sample3
Column name in raw_counts_All_U937 Samples.tsv: LP05009

value: untreated


title: DM, S6

value: LTBi-positive


title: DM, S4

value: blood

value: female


title: DM, S8

value: LTBi-Negative

value: Yes


title: DM, S5

value: male


title: DM, S3


title: DM, S2


title: guide_minus

city: Shinjuku-ku

first: Akisa

last: Nemoto

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

data_processing:
Sequences were produced using a DNBSEQ instrument (BGI).
Gene expression count matrices were generated using Cellranger (v7.0.1) with GRCh38 reference (GENCODE v32/Ensembl 98) and were analyzed using Seurat (v4.3.0). We excluded cells with more than 10,000 or less than 1,000 detected genes, those with less than 2,000 UMI counts, and those with a mitochondrial content higher than 20%. Gene expression was then normalized using a global-scaling normalization method (normalization.method = ‘‘LogNormalize’’, scale.factor = 10,000), and the 2,000 most variable genes were selected (selection.method = ‘‘vst’’). gRNA(+) and (–) datasets were integrated using an anchor-based integrated strategy. ‘FindIntegrationAnchors’ and ‘IntegrateData’ functions used the anchor object to integrate both datasets with the default parameter. The top 10 principal components were utilized for visualization with UMAP and clustering (‘FindNeighbors’ and ‘FindClusters’ functions with a resolution of 0.3). Based on the expression of known markers, we grouped together clusters that were originally separate.
Assembly: GRCh38
Supplementary files format and content: matrix exchange format for sparse matrices of gene count data for each sample

extract_protocol:
Hypothalamic organoids at d63-66 were dissociated into a single-cell suspension using Papain Dissociation System kit (Worthington Biochemical). The dissociated cells were resuspended in ice-cold PBS containing 0.04% BSA (Miltenyi Biotec). 10,000 cells were loaded onto a Chromium Single Cell 3′ Chip (10x Genomics) and processed through the Chromium controller to generate single-cell gel beads in emulsion.
The libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics).

value: Hypothalamic organoids

tag: differentiation day

value: guideRNA(-), dCas9-Suntag-TET1(+)


title: xgenomic_1051

description: Library name: genomic_1051


title: NK-92 Cas9-BFP clone1, DAY17 puro selected cells

description: Library name: DAY17_puro_selected_cells

tag: cell line

value: NK-92 Cas9-BFP clone1


title: LP05005

description:
Library name: Sample2
Column name in raw_counts_All_U937 Samples.tsv: LP05005

tag: cell type

value: monocytes


title: xgenomic_101N

description: Library name: genomic_101N

tag: tissue


title: C18

status: Public on Sep 15 2025

city: Beijing

first: Ziqin

last: Feng

address: Beijing xicheng district northern cabinet number five

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sciences

description: Library name: Sample 10

data_processing:
The fastp software was used to process the raw reads in fastq format, and clean reads were obtained after removing low-quality reads for subsequent data analysis. The HISAT2 software was used for reference genome alignment and gene expression quantification (FPKM), and the read counts (counts) for each gene were obtained using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme, Nanjing, China) according to the manufacturer’s
The libraries were constructed using VAHTS Universal V5 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: PBMC

tag: Sex

value: After BSSGHY treatment


title: C14

description: Library name: Sample 9


title: NK-92 Cas9-BFP clone1, DAY9 puro selected cells

description: Library name: DAY9_puro_selected_cells


title: C04

description: Library name: Sample 7


title: A14

description: Library name: Sample 4

value: Before BSSGHY treatment


title: C2

description: Library name: Sample 6


title: guide_plus

value: guideRNA(+), dCas9-Suntag-TET1(+)


title: A10

description: Library name: Sample 3


title: A04

description: Library name: Sample 2


title: A18

description: Library name: Sample 5


title: A2

description: Library name: Sample 1


title: DM, S1

tag: age

tag: gender


title: Patient 1881, intermediate-risk, no tumor progression

city: Saint Louis

first: Christopher

middle: A.

last: Maher

state: Missouri

address: Division of Oncology

institute: Washington University School of Medicine in Saint Louis: Washington University in St Louis School of Medicine

description: Library name: N1881

data_processing:
Raw reads were trimmed using TrimmGalore (v0.6.10). To remove methylation bias and remove low-quality sequences, an additional 10 bp of the 5’ ends of each read was removed. Duplicated reads were removed to reduce PCR bias. Then, they were aligned to the human genome reference (hg38) using Bismark (v0.24.0), with methylation calls derived by comparing cytosines at converted (T) versus protected (C) positions.
Assembly: hg38
Supplementary files format and content: csv contains differentially methylated region data
Library strategy: EM-seq

source_name: Prostate Cancer

extract_protocol:
Genomic DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) and quantified by Qubit 4.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Sample integrity and absence of degradation were verified via spike-in controls of Lambda DNA (Thermo Fisher Scientific, Waltham, MA, USA) and pUC19 plasmid (New England Biolabs, Ipswich, MA, USA).
EM-seq libraries were prepared by an enzymatic conversion approach2. Briefly, 50–100 ng of input DNA was treated with TET2 enzyme (New England Biolabs, Ipswich, MA, USA) to oxidize 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) to 5-carboxylcytosine. Oxidized residues were protected via glucosylation with β-glucosyltransferase (β-GT; New England Biolabs, Ipswich, MA, USA). Unmodified cytosines were deaminated to uracil using APOBEC3A (Zymo Research, Irvine, CA, USA), while glucosylated 5-carboxylcytosines remained intact. Converted DNA was purified using AMPure XP beads (Beckman Coulter, Brea, CA, USA), enzymatically fragmented to ~300 bp (Covaris S2 sonicator; Covaris, Woburn, MA, USA), and processed for library preparation using the Illumina DNA Prep Kit (Illumina, San Diego, CA, USA). Libraries underwent end repair, adapter ligation by IDT for Illumina UD Indexes (Integrated DNA Technologies, Coralville, IA, USA), and PCR amplification by KAPA HiFi HotStart ReadyMix (Roche, Basel, Switzerland). Library quality and size distribution were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), followed by paired-end sequencing (2 × 150 bp) on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

value: Prostate Cancer

tag: clinical t_stage

tag: surgical t_stage

tag: gleason score1

tag: gleason score2

tag: gleason score

tag: recurrence

tag: psa recurrence

tag: death

tag: lymp nodes_mets

tag: tumor progression

tag: risk

value: intermediate-risk


title: Patient 1920, high-risk, tumor progression

description: Library name: N1920

value: high-risk


title: Patient 1796, high-risk, tumor progression

description: Library name: N1796


title: Patient 1674, intermediate-risk, tumor progression

description: Library name: N1674


title: Patient 1822, intermediate-risk, tumor progression

description: Library name: N1822


title: Patient 1679, high-risk, tumor progression

description: Library name: N1679


title: Patient 1516, intermediate-risk, tumor progression

description: Library name: N1516


title: Patient 1511, intermediate-risk, no tumor progression

description: Library name: N1511


title: Patient 1501, high-risk, tumor progression

description: Library name: N1501


title: Patient 1530, intermediate-risk, tumor progression

description: Library name: N1530


title: Patient 1573, intermediate-risk, tumor progression

description: Library name: N1573


title: Patient 1764, intermediate-risk, no tumor progression

description: Library name: N1764


title: Patient 1445, high-risk, tumor progression

description: Library name: N1445


title: LP05001

description:
Library name: Sample1
Column name in raw_counts_All_U937 Samples.tsv: LP05001

value: Human monocytic cell line from histiocytic lymphoma

tag: cell line

tag: treatment

value: untreated


title: C10

description: Library name: Sample 8

tag: tissue

value: female


title: Patient 1404, intermediate-risk, tumor progression

description: Library name: N1404


title: Patient 1439, high-risk, tumor progression

description: Library name: N1439


title: Patient 1364, intermediate-risk, tumor progression

description: Library name: N1364


title: Patient 1349, intermediate-risk, tumor progression

description: Library name: N1349


title: Patient 1361, intermediate-risk, tumor progression

description: Library name: N1361


title: Patient 1437, intermediate-risk, no tumor progression

description: Library name: N1437


title: Patient 1343, high-risk, no tumor progression

description: Library name: N1343


title: Patient 1344, high-risk, tumor progression

description: Library name: N1344


title: Patient 1383, intermediate-risk, tumor progression

description: Library name: N1383


title: Patient 1340, high-risk, no tumor progression

description: Library name: N1340


title: Patient 1267, intermediate-risk, tumor progression

description: Library name: N1267


title: Patient 1292, intermediate-risk, tumor progression

description: Library name: N1292


title: Patient 1247, low-risk, no tumor progression

description: Library name: N1247

value: low-risk


title: Patient 1250, high-risk, tumor progression

description: Library name: N1250


title: Patient 1213, intermediate-risk, no tumor progression

description: Library name: N1213


title: Patient 1320, intermediate-risk, no tumor progression

description: Library name: N1320


title: Patient 1208, intermediate-risk, tumor progression

description: Library name: N1208