title: CUT&RUN_Mitotic_T105_HEK293T_H4K5ac_1

description: Library name: Sample 85

value: WT HEK293T


title: CUT&RUN_Mitotic_T80_HEK293T_H4K5ac_1

status: Public on Apr 22 2026

type: SRA

city: Orange

first: Matthew

middle: D

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

country: USA

institute: Yale University

description: Library name: Sample 81

library_source: genomic

data_processing:
TimeLapse-seq: Sequencing data was processed using the fastq2EZbakR pipeline (Vock et al., 2025).
TimeLapse-seq: Adapter sequences were trimmed using fastp and reads were aligned to a GRCh38 or combined dm6-GRCh38 genome using STAR. Tracks were normalized using DESeq2 (estimateSizeFactors) or Dm spike-ins with DESeq2 (estimateSizeFactors).
TimeLapse-seq: Final mutation counts and feature assignments were summarized in a cB output file.
ATAC-seq: Sequencing data was processed using the nf-core/atacseq pipeline (version 2.1.2) (Ewels et al., 2020).
ATAC-seq: Adapter sequences were trimmed using Cutadapt.
ATAC-seq: Reads were aligned to the human hg38 genome using the BWA aligner.
ATAC-seq: Duplicate reads and reads mapping to mitochondrial DNA were filtered out.
ATAC-seq: Peaks were called using MACS2 in narrow peak mode, and tracks were normalized using TMM normalization.
CUT&RUN: Reads were trimmed of adaptor sequences using fastp.
CUT&RUN: Reads were aligned to a combined E. coli-GRCh38 genome using bwa-mem2.
CUT&RUN: Aligned reads were processed using SAMtools. Tracks were normalized using TMM normalization or E.coli spike-ins.
CUT&RUN: Peaks were called using MACS2 with default parameters, in broad peak mode for H3K27me3, and in narrow peak mode for all other targets, with IgG samples used as controls.
ChIP-seq: For H3K27ac ChIP-seq samples, reads were trimmed of adaptor sequences using Cutadapt and aligned to the GRCh38 genome using Bowtie2 v2.2.9. Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, reads were processed using the nf-core/chipseq pipeline (version 2.0.0).
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, adapter sequences were trimmed using Trim Galore and reads were aligned to the GRCh38 genome using the BWA aligner.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, duplicate reads and reads mapping to blacklisted regions were filtered out. Counts Per Million (CPM) normalization was applied to create scaled bigWig files.
ChIP-seq: For all ChIP-seq samples, peaks were called using MACS2 with default parameters, using inputs as controls.
Assembly: GRCh38 and dm6
Supplementary files format and content: Normalized bigWig, TDF files, and MACS2 called-peak files.
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HEK-293T cells were cultured at 37°C in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin. S2 cells were cultured at 27°C in Schneider's Drosophila Medium with 10% heat-inactivated FBS and 1% Penicillin/Streptomycin. THP-1 cells were grown at 37°C as single cell suspensions in RPMI-1640 containing 10% FBS, 1% penicillin-streptomycin, and 0.05 mM 2-mercaptoethanol (BME).

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TimeLapse-seq, genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for TimeLapse-seq was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018. ATAC-seq was performed in HEK293T cells using the Active Motif ATAC-Seq Kit following the standard protocol. CUT&RUN was performed in HEK293T nuclei using the EpiCypher CUTANA ChIC/CUT&RUN Kit following the standard protocol. For Kacme, H4K5ac, and CTCF CUT&RUN samples, cells were crosslinked (0.1% formaldehyde, 1 min) prior to nuclei isolation. For ChIP-seq, 20-30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
TimeLapse-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413). ATAC-seq libraries were generated following the Active Motif ATAC-Seq Kit standard protocol. CUT&RUN library preparation was carried out with the EpiCypher CUTANA CUT&RUN Library Prep Kit. ChIP-seq libraries were prepared using standard Illumina protocols.

treatment_protocol: For transcriptional inhibition datasets, HEK293T cells were treated with 10 uM triptolide (MCE, HY-32735) for 1hr. KDM6A/B inhibition was performed by treating HEK293T cells with 5 uM GSK-J4 (MCE, HY-15648B) for either 6 or 24 hrs. THP-1 differentiation was carried out by treating cells with 40 ng/mL PMA (phorbol 12-myristate 13-acetate, Abcam, ab120297) for 48 hrs, followed by washing away non-adherent cells with PBS and incubating the adherent cells in fresh RPMI medium for an additional 24 hrs. Mitotic arrest and release were performed in HEK293T cells. For each sample, 2 million cells were seeded and allowed to adhere overnight. The following day, nocodazole (Sigma, M1404) was added to the media at a final concentration of 50 ng/mL, and cells were incubated for 16 hrs at 37 °C. Mitotic cells were harvested by manual shake-off.

tag: cell line

tag: genotype

tag: treatment

value: 80 min post-mitotic release

tag: antibody


title: CUT&RUN_Mitotic_T40_HEK293T_H4K5ac_2

description: Library name: Sample 79

value: 40 min post-mitotic release


title: Plastic_Day1_techRep3_bioRep1

city: Berlin

first: Rainer

last: Glauben

address: Hindenburgdamm 30

department: Klinik für Gastroenterologie, Infektiologie und Rheumatologie

country: Germany

institute: Charite CBF

description: Library name: AP1_3

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to the human reference genome (GRCh38, GENCODE v33) using HISAT2 v2.0.5 with default parameters. Gene-level counts were obtained using featureCounts v1.5.0-p3.
Assembly: GRCh38
Supplementary files format and content: txt document contains processed data for all samples combined
Supplementary files format and content: Combined raw data folder contains fq.gz files for each paired end sample

molecule: total RNA

source_name: Terminal ileum

growth_protocol: Organoids were cultured in organoid expansion medium consisting of WRN-conditioned medium produced from L-WRN cells (ATCC CRL-3276), supplemented with recombinant human EGF, SB202190, A83-01, Gastrin I, Nicotinamide, and Y-27632 during initial passages. Antibiotics were included during establishment to prevent contamination. Cultures were maintained at 37 °C and 5% CO₂, with medium exchange every other day and passaged weekly. Organoids at passages 5–6 were used for subsequent experiments.

extract_protocol:
Cells were lysed in QIAzol reagent and RNA was extracted using the Direct-zol RNA Microprep kit (Zymo Research). RNA integrity was assessed on an Agilent TapeStation (RNA ScreenTape assay, Software A.02.01 SR1), and samples with RNA integrity number (RIN) ≥ 8 were used for downstream analyses.
Libraries were prepared using the Illumina mRNA library preparation kit with poly-A enrichment from the recommended Novogene RNA input. Sequencing was performed on an Illumina platform using paired-end 150 bp reads, generating approximately 9 Gb of data per sample (~30 million reads per sample).

tag: tissue

value: Terminal ileum

value: Primary human intestinal organoids

tag: cell type

value: intestinal epithelial cells

value: healthy donor

tag: time


title: PPARG KO, 5 months FFD, repeat 2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 11
PPARG KO, 5 months FFD, repeat 2

data_processing:
Perform alignments with HISAT2 to the reference.
Assembly: mm10
Supplementary files format and content: TXT for count expression

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol (Sigma) method
Samples were submitted to Novogene for sequencing using Illumina NovaSeq platform.

value: liver

value: FFD

value: PPARG KO

tag: time point

value: 5 months


title: Plastic_Day1_techRep2_bioRep1

description: Library name: AP1_2


title: WT, 5 months FFD, repeat 2

description:
Library name: Sample 8
WT, 5 months FFD, repeat 2

value: WT


title: CUT&RUN_Mitotic_T40_HEK293T_H4K5ac_1

description: Library name: Sample 77


title: PPARG KO, 5 months FFD, repeat 1

description:
Library name: Sample 10
PPARG KO, 5 months FFD, repeat 1


title: PPARG KO, 2 months FFD, repeat 3

description:
Library name: Sample 6
PPARG KO, 2 months FFD, repeat 3

value: 2 months


title: PPARG KO, 2 months FFD, repeat 2

description:
Library name: Sample 5
PPARG KO, 2 months FFD, repeat 2


title: Scaffold_Day1_techRep1_bioRep1

description: Library name: AS1_1


title: Plastic_Day1_techRep1_bioRep1

description: Library name: AP1_1


title: CUT&RUN_Mitotic_T0_HEK293T_H4K5ac_2

description: Library name: Sample 75

value: 0 min post-mitotic release


title: PPARG KO, 2 months FFD, repeat 1

description:
Library name: Sample 4
PPARG KO, 2 months FFD, repeat 1


title: WT, 5 months FFD, repeat 1

description:
Library name: Sample 7
WT, 5 months FFD, repeat 1


title: CUT&RUN_Mitotic_T40_HEK293T_Kacme_1

description: Library name: Sample 76

value: Kacme


title: CUT&RUN_Mitotic_T80_HEK293T_Kacme_1

description: Library name: Sample 80


title: Scaffold_Day0_techRep3_bioRep1

description: Library name: AS0_3


title: CUT&RUN_Mitotic_T0_HEK293T_H4K5ac_1

description: Library name: Sample 73


title: CUT&RUN_Mitotic_T0_HEK293T_Kacme_2

description: Library name: Sample 74


title: Scaffold_Day0_techRep1_bioRep1

description: Library name: AS0_1


title: CUT&RUN_Mitotic_T0_HEK293T_Kacme_1

description: Library name: Sample 72


title: CUT&RUN_Mitotic_T0_HEK293T_IgG

description: Library name: Sample 71

value: IgG


title: CUT&RUN_Async_HEK293T_H4K5ac_2

description: Library name: Sample 70

value: Asynchronous


title: CUT&RUN_Async_HEK293T_H4K5ac_1

description: Library name: Sample 68

value: WT HEK293T


title: Plastic_Day0_techRep4_bioRep1

description: Library name: AP0_4


title: Scaffold_Day0_techRep2_bioRep1

description: Library name: AS0_2


title: WT, 2 months FFD, repeat 3

description:
Library name: Sample 3
WT, 2 months FFD, repeat 3


title: WT, 2 months FFD, repeat 2

description:
Library name: Sample 2
WT, 2 months FFD, repeat 2


title: CUT&RUN_Mitotic_T40_HEK293T_Kacme_2

description: Library name: Sample 78


title: CUT&RUN_Async_HEK293T_Kacme_2

description: Library name: Sample 69


title: Plastic_Day0_techRep3_bioRep1

description: Library name: AP0_3


title: CUT&RUN_Async_HEK293T_Kacme_1

description: Library name: Sample 67


title: ChIP-seq_HEK293T_Input

description: Library name: Sample 64

data_processing:
TimeLapse-seq: Sequencing data was processed using the fastq2EZbakR pipeline (Vock et al., 2025).
TimeLapse-seq: Adapter sequences were trimmed using fastp and reads were aligned to a GRCh38 or combined dm6-GRCh38 genome using STAR. Tracks were normalized using DESeq2 (estimateSizeFactors) or Dm spike-ins with DESeq2 (estimateSizeFactors).
TimeLapse-seq: Final mutation counts and feature assignments were summarized in a cB output file.
ATAC-seq: Sequencing data was processed using the nf-core/atacseq pipeline (version 2.1.2) (Ewels et al., 2020).
ATAC-seq: Adapter sequences were trimmed using Cutadapt.
ATAC-seq: Reads were aligned to the human hg38 genome using the BWA aligner.
ATAC-seq: Duplicate reads and reads mapping to mitochondrial DNA were filtered out.
ATAC-seq: Peaks were called using MACS2 in narrow peak mode, and tracks were normalized using TMM normalization.
CUT&RUN: Reads were trimmed of adaptor sequences using fastp.
CUT&RUN: Reads were aligned to a combined E. coli-GRCh38 genome using bwa-mem2.
CUT&RUN: Aligned reads were processed using SAMtools. Tracks were normalized using TMM normalization or E.coli spike-ins.
CUT&RUN: Peaks were called using MACS2 with default parameters, in broad peak mode for H3K27me3, and in narrow peak mode for all other targets, with IgG samples used as controls.
ChIP-seq: For H3K27ac ChIP-seq samples, reads were trimmed of adaptor sequences using Cutadapt and aligned to the GRCh38 genome using Bowtie2 v2.2.9. Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, reads were processed using the nf-core/chipseq pipeline (version 2.0.0).
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, adapter sequences were trimmed using Trim Galore and reads were aligned to the GRCh38 genome using the BWA aligner.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, duplicate reads and reads mapping to blacklisted regions were filtered out. Counts Per Million (CPM) normalization was applied to create scaled bigWig files.
ChIP-seq: For all ChIP-seq samples, peaks were called using MACS2 with default parameters, using inputs as controls.
Assembly: GRCh38 and dm6
Supplementary files format and content: Normalized bigWig, TDF files, and MACS2 called-peak files.

value: Untreated

value: Input


title: Plastic_Day0_techRep2_bioRep1

description: Library name: AP0_2

value: Terminal ileum


title: CUT&RUN_Async_HEK293T_IgG

description: Library name: Sample 65


title: IP_SMC3_STAG1_OE_rep2

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

description: Library name: Sample08

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag.
Samples were deduplicated using Picard, normalized and converted to bigWig files using bamCoverage with the --SPMR flag.
Assembly: mm9
Supplementary files format and content: bigWig including peak information for samples.

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
20 million cells were crosslinked in 37o prewarmed culture medium with 1% formaldehyde for 10 min at RT.  Cells were then treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) for 10 min on ice, followed by treatment with nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) for 10 min at RT. Chromatin was subjected to sonication with Diagenode Bioruptor at 4o to achieve an average size of 200-300 bp (30 sec on, 30 sec off, 20 cycles with high energy input). Chromatin were then precleared with Dynabeads Protein A at 4o for 2 hours. 1/30 lysates were kept as input and the rest incubated with 2.5ug SMC3 antibody  or CTCF antibody overnight at 4o. IP samples were then captured by Dynabeads Protein A at 4o for at least 2 hours, followed by bead washing and elution. IP and Input DNA were then de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
Purified DNA was subjected to ChIP-Seq library preparation with the NEBNext Ultra II DNA Library Prep Kit for Illumina from New England Biolabs and sequenced via paired end 150-bp sequencing on a Illumina sequencing platform.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days.

value: v-Abl transformed pro-B cell line

value: Emu-Bcl2+, RAG1(D708A), full EF1alpha_STAG1

value: 3 uM STI-571 treated for 4 days


title: WT, 2 months FFD, repeat 1

description:
Library name: Sample 1
WT, 2 months FFD, repeat 1

value: liver


title: ChIP-seq_HEK293T_H3K27ac_2

description: Library name: Sample 63


title: IP_SMC3_STAG1_OE_rep1

description: Library name: Sample07


title: ChIP-seq_HEK293T_H3K27ac_1

description: Library name: Sample 62


title: Plastic_Day0_techRep1_bioRep1

description: Library name: AP0_1

value: Primary human intestinal organoids

value: intestinal epithelial cells

value: healthy donor


title: ChIP-seq_THP1_PMA_Input

description: Library name: Sample 61

value: WT THP-1

value: PMA (40 ng/mL), 72 h


title: ChIP-seq_THP1_DMSO_Input

description: Library name: Sample 60

value: DMSO, 72 h


title: TM004_F4

city: Göttingen

first: Lena-Christin

last: Conradi

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Göttingen

description: Library name: PDX_classical_F4

data_processing:
The raw reads were quality controlled using fastqc (RRID: SCR_014583) and checked for both microbial and mouse contamination using Kraken (RRID: SCR_005484) and fastq screen (RRID: SCR_000141). Reads assigned to mouse were removed before downstream alignment to the human reference genome. Next, the sequence reads were trimmed using trimmomatic (RRID: SCR_011848), mapped to the reference genome (Ensembl, genome assembly GRCh38.p13) using star (RRID: SCR_004463), and finally the features were quantified using htseq‐count (RRID: SCR_011867).
Assembly: genome assembly GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: subcutanous PDXs from primary PDAC tissue

extract_protocol:
RNA was isolated with Quick-RNA miniprep (Zymo Research, #R1055), according to the manufacturer's instructions.
Library preparation for RNA-Seq was performed on the STAR Hamilton NGS automation platform using the Illumina Stranded mRNA Prep Kit (Cat. No. 20040534) together with the Illumina RNA UD Indexes Set A, Ligation with 96 Indexes (Cat. No. 20091646), starting from 50 ng of total RNA.

tag: tissue type

value: classical PDX line generation F4

value: untreated


title: IP_SMC3_WT_rep5

description: Library name: Sample05

value: Emu-Bcl2+, RAG1(D708A)


title: IP_SMC3_WT_rep6

description: Library name: Sample06


title: ChIP-seq_THP1_DMSO_H4K5ac_2

description: Library name: Sample 57


title: IP_STAG1_STAG1_OE_rep2

description: Library name: Sample04


title: CUT&RUN_Async_HEK293T_H3K4me3

description: Library name: Sample 66

value: WT HEK293T

value: Asynchronous


title: ChIP-seq_THP1_DMSO_H4K5ac_1

description: Library name: Sample 56


title: ChIP-seq_THP1_PMA_H4K5ac_1

description: Library name: Sample 58


title: TM004_F2

description: Library name: PDX_classical_F2

value: subcutanous PDXs from primary PDAC tissue

value: classical PDX line generation F2


title: TM009

description: Library name: PDX_basal_F1

value: basal PDX line generation F1


title: ChIP-seq_THP1_PMA_H4Kacme_2

description: Library name: Sample 55


title: ChIP-seq_THP1_DMSO_H4Kacme_2

description: Library name: Sample 53


title: IP_STAG1_STAG1_OE_rep1

description: Library name: Sample03

value: v-Abl transformed pro-B cell line

value: Emu-Bcl2+, RAG1(D708A), full EF1alpha_STAG1


title: PLC/PRF/5_LAC2

city: Bunkyo-Ku

first: Masahiro

last: Yamane

state: Tokyo

country: Japan

institute: Institute science  Tokyo

description: Library name: PLC/PRF/5_LAC2

data_processing:
Sequence reads were checked by using FastQC.
Sequence reads were mapped to GRCm38/mm10 by using STAR.
Read count extraction was performed by using RSEM.
Normalization and differential expression analysis were performed by using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.

source_name: Liver

growth_protocol: Three human HCC cell lines, HLF (RRID: CVCL_2947), PLC/PRF/5 (RRID: CVCL_0485), and SNU475 (RRID: CVCL_0497), were purchased from the Japanese Collection of Research Bioresources Cell Bank (Osaka, Japan) and the American Type Culture Collection (Manassas, VA, USA). Authentication of these cell lines was confirmed by short tandem repeat DNA fingerprinting (BEX Co. Ltd., Tokyo, Japan).

extract_protocol:
Total RNA was extracted from cells by using TRIzol Reagent (Thermo Fisher Scientific). Contaminating DNA was removed by digestion with DNA-free DNA Removal Kit (Thermo Fisher Scientific). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).
RNA libraries for RNA-seq were prepared by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Cells were cultured with 20 mM lactate (lactic acid, Wako, Osaka, Japan) for 24 hours

value: Liver

value: Hepatocellular carcinoma cells

value: culture with lactate 20mM for 24hr


title: ChIP-seq_THP1_PMA_H4Kacme_1

description: Library name: Sample 54


title: ChIP-seq_THP1_DMSO_H4Kacme_1

description: Library name: Sample 52


title: IP_STAG1_WT_rep6

description: Library name: Sample02

value: 3 uM STI-571 treated for 4 days


title: PLC/PRF/5_LAC1

description: Library name: PLC/PRF/5_LAC1


title: IP_STAG1_WT_rep5

description: Library name: Sample01


title: ChIP-seq_THP1_PMA_Kacme_1

description: Library name: Sample 50

value: WT THP-1

value: Kacme


title: ChIP-seq_THP1_PMA_Kacme_2

description: Library name: Sample 51

value: PMA (40 ng/mL), 72 h


title: ChIP-seq_THP1_DMSO_Kacme_1

description: Library name: Sample 48

value: DMSO, 72 h


title: ChIP-seq_THP1_DMSO_Kacme_2

description: Library name: Sample 49


title: PLC/PRF/5_NM2

description: Library name: PLC/PRF/5_NM2

value: control


title: PLC/PRF/5_NM1

description: Library name: PLC/PRF/5_NM1


title: Wapl-AID2_CTCF-Nm_untreated_rep3

description: Library name: Sample 10

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same bait and prey coordinates and the same bait-prey junction sequence.
Assembly: mm9

extract_protocol:
DNA was lysed overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
Genomic DNA was extracted from G1 arrested cells. 2 to 4 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to illumina sequencing platforms with paired-end 300 bp or 150 bp sequencing.

treatment_protocol: RAG complementation and 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest.

value: Wapl-AID2, CTCF(Y226A/F228A), Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: CUT&RUN_24h_GSK-J4_HEK293T_H3K27me3_1

description: Library name: Sample 46

value: WT HEK293T

value: GSK-J4 (5 µM, 24 hr)


title: CUT&RUN_24h_GSK-J4_HEK293T_H3K27me3_2

description: Library name: Sample 47


title: Stag2KO_JH4_rep3

description: Library name: Sample 9

value: Stag2-/-, Emu-Bcl2+, RAG1(D708A)


title: SNU475_LAC1

description: Library name: SNU475_LAC1


title: CUT&RUN_6h_GSK-J4_HEK293T_H3K27me3_1

description: Library name: Sample 44

value: GSK-J4 (5 µM, 6 hr)


title: Stag2KO_JH4_rep2

description: Library name: Sample 8

value: v-Abl transformed pro-B cell line


title: SNU475_LAC2

description: Library name: SNU475_LAC2


title: CUT&RUN_Ctrl_HEK293T_H3K27me3_1

description: Library name: Sample 42

value: DMSO Control


title: Stag2KO_JH4_rep1

description: Library name: Sample 7


title: CUT&RUN_6h_GSK-J4_HEK293T_H3K27me3_2

description: Library name: Sample 45


title: CUT&RUN_Ctrl_HEK293T_H3K27me3_2

description: Library name: Sample 43


title: TimeLapse-seq_24h_GSK-J4_HEK293T_ns4U

description: Library name: Sample 39

tag: s4u feed


title: SNU475_NM1

description: Library name: SNU475_NM1

value: Liver


title: SNU475_NM2

description: Library name: SNU475_NM2

value: Hepatocellular carcinoma cells


title: Stag1KO_JH4_rep2

description: Library name: Sample 5

value: Stag1-/-, Emu-Bcl2+, RAG1(D708A)


title: HLF_LAC2

description: Library name: HLF_LAC2

value: HLF

value: culture with lactate 20mM for 24hr


title: AtInput

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description: Library name: AtInput

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Assembly: Arabidopsis TAIR10 genome (Ensemble Release 42)
Assembly: Marchantia polymnorpha MpTak1 5.1 version
Supplementary files format and content: Significant peaks of protein-DNA interactions in BED fromat generated by GEMv3.4

organism: Arabidopsis thaliana

source_name: 10 days-old seedlings

growth_protocol: Arabidopsis: 10 days-old seedlings grown in MS medium. Marchantia polymorpha: 21-d-old gemmalings grown in 0.5x GB5 medium

extract_protocol:
Genomic DNA extracted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a double i5/i7 index.

value: 10 days-old seedlings

tag: protein

value: Arabidopsis Input sample


title: Stag1KO_JH4_rep3

description: Library name: Sample 6


title: Stag1KO_JH4_rep1

description: Library name: Sample 4


title: TimeLapse-seq_24h_GSK-J4_HEK293T_ys4U_2

description: Library name: Sample 41

value: 500 µM, 20 mins


title: HLF_LAC1

description: Library name: HLF_LAC1


title: TimeLapse-seq_24h_GSK-J4_HEK293T_ys4U_1

description: Library name: Sample 40


title: TimeLapse-seq_6h_GSK-J4_HEK293T_ys4U_2

description: Library name: Sample 38


title: HLF_NM2

description: Library name: HLF_NM2

value: control


title: TimeLapse-seq_6h_GSK-J4_HEK293T_ys4U_1

description: Library name: Sample 37


title: ME_3

type: genomic

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium Mouse Methylation BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (iScan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment (v2.20.0)
Average Beta

label: Cy3 and Cy5

source_name: Bone marrow

label_protocol: Standard Illumina Protocol

extract_protocol: FACS sorted cells were proceeded to DNA extraction.

value: Bone marrow

tag: strain

value: CD45.2+ bone marrow cells

value: CD45.2(+) MLL-ENL


title: AtPIF4 DAP-seq

description: Library name: AtPIF4 DAP-seq


title: WT_JH4_rep2

description: Library name: Sample 2

value: Emu-Bcl2+, RAG1(D708A)

value: RAG1 retrovirally complemented, 3 uM STI-571 treated for 4 days


title: ME_2


title: 3C_Stag2KO_CTCF-Nm_rep3

description: Library name: Sample 4

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively. Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used. We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality. To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, remove bait sequences shorter than 50nt and keep only 1 juction for duplicate junctions with the same bait and prey coordinates. Additionally, we filtered reads aligned to telomeric and satellite repeat regions to avoid potential PCR artifacts. We also removed bait region reads to minimize the impact of self-ligation on quantitative analysis.
Assembly: mm9
Supplementary files format and content: bedGraph including peak information for samples.

extract_protocol:
10 million cells were cross-linked with 2% formaldehyde at room temperature for 10 minutes, quenched by glycine (final 0.125M), and then lysed with cold cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, one tablet of protease inhibitor in 50 ml) on ice for 10 min. Nuclei were subjected to 0.3% SDS treatment (37 o, 1 hour) and 1.8% Triton X-100 treatment (37 o, 1 hour) successively, followed by overnight NalIII (700 units) digestion at 37 o .  DpnII was inactivated at 65 o for 20 min and samples were subjected to ligation under dilute condition with T4 DNA ligase (100 units). Ligated chromatin was de-crosslinked with Proteinase K (56 o, ON) and treated with RNaseA (37 o, 1 hour). DNA was purified via phenol/chloroform extraction and resuspended in 200ul 1XTE buffer.
10 ug of DNA were sonicated via Diagenode bioruptor (20 sec on, 1 min off, 2 cycles with low energy input) and subjected to linear amplification with a biotinylated primer (PCR with Phusion enzyme: 98o 2min, 1cycle; 95o 30sec, 58o 30sec, 72o 90sec, 80 cycles; 72o 2min, 1 cycle). Single-stranded PCR products were purified via Dynabeads MyOne streptavidin C1 beads and ligated to bridge adaptor (25o 1 hour, 22 o 3 hours, 16 o overnight). Adaptor-ligated Products were amplified via nested PCR with indexed locus-specific primers and adaptor primer (PCR with Phusion enzyme: 95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 15 cycles; 72o 6 min, 1 cycle). The PCR products were further tagged with P5-I5 and P7-I7 sequences (95o 5min, 1cycle; 95o 30sec, 60o 30sec, 72o 60sec, 12 cycles; 72o 6 min, 1 cycle), size-selected via gel extraction (500-1000 bp) and loaded to illumina sequencing platforms with paired-end sequencing.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days. For Wapl depeletion, 1 uM 5-Ph-IAA was added 4 hours prior to G1 arrest.

value: 3 uM STI-571 treated for 4 days


title: AtHY5 DAP-seq

description: Library name: AtHY5 DAP-seq


title: WT_JH4_rep3

description: Library name: Sample 3

value: v-Abl transformed pro-B cell line


title: TimeLapse-seq_6h_GSK-J4_HEK293T_ns4U

description: Library name: Sample 36

value: WT HEK293T

value: GSK-J4 (5 µM, 6 hr)


title: TimeLapse-seq_Ctrl_HEK293T_ys4U_1

description: Library name: Sample 34

value: DMSO Control


title: ChIP-seq_THP1_PMA_H4K5ac_2

description: Library name: Sample 59

value: WT THP-1

value: PMA (40 ng/mL), 72 h


title: WT_JH4_rep1

description: Library name: Sample 1


title: HLF_NM1

description: Library name: HLF_NM1

value: Liver

value: HLF

value: Hepatocellular carcinoma cells


title: WAPL_PDS5-AB_AID__SCC1-EGFP_+_aux_HeLa rep3

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: Library name: 234424

data_processing:
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.4
bowtie2 mapping against hg19 reference assembly
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with HOMER for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with  juicer tools pre command

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan)

extract_protocol:
Cells were cross-linked in falcon tube. The DNA was fragmented, biotynilated at both ends, and ligated at newly blunted ends together. Biotinylated DNA was captured and prepared for paired-end Illumina sequencing.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells


title: ME_1

value: Bone marrow


title: TimeLapse-seq_Ctrl_HEK293T_ns4U

description: Library name: Sample 33


title: TimeLapse-seq_Ctrl_HEK293T_ys4U_2

description: Library name: Sample 35

value: 500 µM, 20 mins


title: WAPL_PDS5-AB_AID__SCC1-EGFP_+_aux_HeLa rep2

description: Library name: 207257


title: CUT&RUN_HEK293T_Triptolide_Kacme_2

description: Library name: Sample 32

value: Triptolide (10 µM, 1 hr)

value: Kacme


title: MA9_3

value: CD45.2+ bone marrow cells


title: 3C_Stag2KO_rep6

description: Library name: Sample 3

value: Stag2-/-, Emu-Bcl2+, RAG1(D708A)

value: 3 uM STI-571 treated for 4 days


title: WAPL_PDS5-AB_AID__SCC1-EGFP_+_aux_HeLa rep1

description: Library name: 195059


title: 3C_CTCF-Nm_rep3

description: Library name: Sample 2

value: v-Abl transformed pro-B cell line


title: WAPL_CTCF_AID__SCC1-EGFP_+_aux_HeLa rep3

description: Library name: 234425


title: CUT&RUN_HEK293T_Triptolide_Kacme_1

description: Library name: Sample 31

value: WT HEK293T


title: MA9_2


title: TimeLapse-seq_Async_HEK293T_ys4U_3

description: Library name: Sample 30

value: Asynchronous


title: 3C_WT_rep6

description: Library name: Sample 1

value: Emu-Bcl2+, RAG1(D708A)


title: WAPL_CTCF_AID__SCC1-EGFP_+_aux_HeLa rep2

description: Library name: 221327


title: MA9_1


title: WAPL_CTCF_AID__SCC1-EGFP_+_aux_HeLa rep1

description: Library name: 189247


title: RAW264.7, WT,Stimulated, RepB

city: Madison

first: Jing

last: Fan

state: WI

address: 330 N. Orchard St.

institute: Morgridge Institute for Research

description:
Library name: WT_M1b
WT_M1b
RAW_gene_count.txt

data_processing:
Quality control was commenced with base recognition using CASAVA, followed by error rate assessment and GC content analysis.
The data were then subjected to stringent filtration, removing adapter contamination, reads with over 10% uncertain nucleotides, and reads where low-quality bases exceeded 50% of the sequence.
Post-filtration, the data were aligned to the mm10 mouse genome using the STAR software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: Murine bone marrow-derived macrophages were isolated from wildtype or iNOS KO C57BL/6J mice. Bone marrow cells were isolated and differentiated from 6–12-week-old males or females. WT or iNOS KO BMDMs and WT or Akr1a1 KO RAW cells were cultured in RPMI 1640 with 10% fetal bovine serum, 25mM HEPES, 2mM glutamine, 1% antibiotics (penicillin, streptomycin) at 37°C and 5% CO2. BMDM were cultured with 20 ng/mL M-CSF

extract_protocol:
For RNA collection, cells were washed twice with DPBS and then lysed with RNA STAT 60. Chloroform was used for phase separation. RNA was precipitated with isopropanol, washed with 75% ethanol, and solubilized in DEPC H2O.
mRNA library preparation was performed by Novogene using poly A enrichment

treatment_protocol: To stimulate BMDMs, cells were incubated with 50ng/mL LPS and 30ng/mL recombinant mouse IFNγ for 48 hours. To stimulated RAW264.7 cells, cells were incubated with 50ng/mL LPS and 10ng/mL recombinant mouse IFNγ for 48 hours. Stimuli then were removed, cells were washed with DPBS, and cell culture was continued in fresh media without stimuli for the remaining timecourse.

value: murine macrophage

value: wild-type


title: RAW264.7, WT, Stimulated, RepA

description:
Library name: WT_M1a
WT_M1a
RAW_gene_count.txt


title: WAPL_AID__SCC1-EGFP_+_aux_HeLa rep3

description: Library name: 214257


title: BN1_2


title: WAPL_AID__SCC1-EGFP_+_aux_HeLa rep2

description: Library name: 189246


title: TimeLapse-seq_Async_HEK293T_ys4U_1

description: Library name: Sample 28


title: BN1_1


title: TimeLapse-seq_Mitotic_T300_HEK293T_ys4U_3

description: Library name: Sample 26

value: 300 min post-mitotic release


title: TimeLapse-seq_Async_HEK293T_ys4U_2

description: Library name: Sample 29


title: WAPL_AID__SCC1-EGFP_+_aux_HeLa rep1

description: Library name: 189244


title: TimeLapse-seq_Async_HEK293T_ns4U

description: Library name: Sample 27


title: control_3


title: BN1_3


title: SCC1_EGFP_HeLa_+_aux_HeLa rep3

description: Library name: 234422


title: RAW264.7, Akr1a1 KO,Stimulated, RepB

description:
Library name: AkrKO_M1b
AkrKO_M1b
RAW_gene_count.txt

value: Akr1a1 knockout


title: RAW264.7, WT, Stimulated, RepB

description:
Library name: WT_M0b
WT_M0b
RAW_gene_count.txt

value: Unstimulated


title: control_2


title: TimeLapse-seq_Mitotic_T300_HEK293T_ys4U_2

description: Library name: Sample 25


title: RAW264.7, WT, Unstimulated, RepA

description:
Library name: WT_M0a
WT_M0a
RAW_gene_count.txt


title: TimeLapse-seq_Mitotic_T300_HEK293T_ns4U

description: Library name: Sample 23


title: RAW264.7, Akr1a1 KO, Stimulated, RepA

description:
Library name: AkrKO_M1a
AkrKO_M1a
RAW_gene_count.txt


title: RAW264.7, Akr1a1 KO, Stimulated, RepB

description:
Library name: AkrKO_M0b
AkrKO_M0b
RAW_gene_count.txt


title: SCC1_EGFP_HeLa_+_aux_HeLa rep1

description: Library name: 189243

value: HeLa Kyoto

value: human cervical cancer cells


title: control_1

value: Bone marrow


title: RAW264.7, Akr1a1 KO, Unstimulated, RepA

description:
Library name: AkrKO_M0a
AkrKO_M0a
RAW_gene_count.txt


title: SCC1_EGFP_HeLa_+_aux_HeLa rep2

description: Library name: 214256


title: PDS5-B_AID_+_aux_HeLa rep2

description: Library name: 195057


title: TimeLapse-seq_Mitotic_T105_HEK293T_ys4U_3

description: Library name: Sample 22

value: 105 min post-mitotic release

value: 500 µM, 20 mins


title: TimeLapse-seq_Mitotic_T300_HEK293T_ys4U_1

description: Library name: Sample 24


title: sorted_H3K27me3_DFP_FAS_rep2

city: Chengdu

first: Yiman

last: Peng

state: Sichuan

address: No.1, Keyuan 4th Road, Gaopeng Avenue, Chengdu, Sichuan, China

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University

country: China

institute: Sichuan University

description: Library name: sorted_H3K27me3_DFP_FAS_rep2

data_processing:
For samples containing E. coli λ sequences as spike-in controls. Reads were quality controlled using fastp and aligned to the mouse genome (mm10) and the E. coli λ spike-in sequence using Bowtie2. Sorted BAM files were generated with SAMtools. A scaling factor for each sample was calculated as 10,000 divided by the number of fragments mapped to the E. coli genome. Normalized bigWig files were generated using DeepTools with “--normalizeUsing None --binSize 50 --scaleFactor <scaling factor>”. Data normalization and difference comparison were performed using DESeq2. Peaks were called using MACS3 with “--broad --broad-cutoff 0.1 -q 0.05 -f BAMPE”.
Assembly: mm10, E. coli
Supplementary files format and content: bigWig, broadPeak
Library strategy: CUT&Tag

source_name: c-Kit +CD11b-Gr1- HSPC

growth_protocol: mouse cKit+ HSPCs and AML cells were cultured at 37 °C with 7.5% CO2 in BCM medium [45% IMDM + 45% DMEM + 10% FBS + 50 × 10-6 M β-mercaptoethanol + penicillin (100 U mL-1)/streptomycin (0.1 mg mL-1)] supplemented with 10% stem cell medium (SCM) including mIL-3 (10 ng mL-1, Cat# 403-ML; R&D Systems), mIL-6 (10 ng mL-1, Cat# 406-ML; R&D Systems), and mSCF (50 ng mL-1, Cat# 455-MC; R&D Systems)

extract_protocol: The CUT&Tag assay was performed using a NovoNGS CUT&Tag 2.0 High-Sensitivity kit (Novoprotein Scientific, N259-YH01-01A).

value: c-Kit +CD11b-Gr1- HSPC

value: WT


title: sorted_H3K27me3_DFP_FAS_rep1

description: Library name: sorted_H3K27me3_DFP_FAS_rep1


title: sorted_H3K27me3_IgG

description: Library name: sorted_H3K27me3_IgG


title: TimeLapse-seq_Mitotic_T105_HEK293T_ys4U_2

description: Library name: Sample 21


title: Spry4 G-KO  spermatogonia, BU+PD-D10, rep4

city: New York

first: Ying

state: NY

address: 1300 York Ave

department: Medicine

institute: Weill Cornell Medical College

description:
Library name: Spry4_GKO_BU10_PD_4
column name in FPKM_Spry4.csv: 453_A_Undiff_GCRT_Spry4KO_BU10_PD8_SP411_S224

data_processing:
Sequencing reads were de-multiplexed, checked for quality (FastQC), and trimmed/filtered when appropriate.
The resultant high quality reads were mapped (STAR  v2.7.10a) to the transcriptome sequence reference of the GENCODE mm10 GRCm39 version 107 build.
Gene counts and transcript abundance measures (FPKM values) were quantified using the R package edgeR (v4.0.14). Gene expression was reported as log2 transformed FPKM value.
Assembly: mm10
Supplementary files format and content: csv file includes FPKM values for each sample

molecule: polyA RNA

source_name: spermatogonia

extract_protocol:
Total RNA was extracted from fresh spermatogonia isolated by FACS using PicoPure RNA isolation kit (KIT0204, Applied Biosystems). Residual genomic DNA was removed by on-column DNA digestion (79254, Qiagen).
The stranded mRNA sequence libraries were generated using the KAPA mRNA HyperPrep Kit (Kapa Biosystems, KK8580).

treatment_protocol: Busulfan was administered to mice by IP injection (10 mg/kg). BU-treated cohorts were treated daily by IP injection starting from 3 days post-BU for 7 consecutive days with PD0325901 (2.5 mg/kg) or vehicle (10% DMSO/PBS).

value: spermatogonia

value: Spry4 germline-knockout

value: 10 days following Busulfan+PD treatment


title: Spry4 G-KO  spermatogonia, BU+PD-D10, rep3

description:
Library name: Spry4_GKO_BU10_PD_3
column name in FPKM_Spry4.csv: 450_A_Undiff_GCRT_Spry4KO_BU10_PD8_SP392_S221


title: TimeLapse-seq_Mitotic_T105_HEK293T_ys4U_1

description: Library name: Sample 20

value: WT HEK293T


title: PDS5-A_AID_+_aux_HeLa rep2

description: Library name: 195056


title: PDS5-AB_AID__SCC1-EGFP_+_aux_HeLa rep3

description: Library name: 234423


title: sorted_H3K27me3_DMSO_rep2

description: Library name: sorted_H3K27me3_DMSO_rep2


title: PDS5-A_AID_+_aux_HeLa rep1

description: Library name: 194494


title: Spry4 G-KO spermatogonia, BU-D10, rep4

description:
Library name: Spry4_GKO_BU10_4
column name in FPKM_Spry4.csv: 449_A_Undiff_GCRT_Spry4KO_BU10_SP390_S220

value: 10 days following Busulfan+DMSO treatment


title: sorted_H3K27me3_DMSO_rep1

description: Library name: sorted_H3K27me3_DMSO_rep1


title: TimeLapse-seq_Mitotic_T40_HEK293T_ys4U_3

description: Library name: Sample 18

value: 40 min post-mitotic release


title: Spry4 G-KO  spermatogonia, BU+PD-D10, rep2

description:
Library name: Spry4_GKO_BU10_PD_2
column name in FPKM_Spry4.csv: 444_A_Undiff_GCRT_Spry4KO_BU10_PD8_SP391_S215


title: TimeLapse-seq_Mitotic_T105_HEK293T_ns4U

description: Library name: Sample 19


title: sorted_H3K27me3_DFP_rep2

description: Library name: sorted_H3K27me3_DFP_rep2


title: TimeLapse-seq_Mitotic_T40_HEK293T_ys4U_2

description: Library name: Sample 17


title: PDS5-B_AID_+_aux_HeLa rep1

description: Library name: 194496


title: PDS5-AB_AID__SCC1-EGFP_+_aux_HeLa rep2

description: Library name: 207256


title: sorted_H3K27me3_DFP_rep1

description: Library name: sorted_H3K27me3_DFP_rep1


title: TimeLapse-seq_Mitotic_T40_HEK293T_ys4U_1

description: Library name: Sample 16


title: Spry4 G-KO spermatogonia, BU-D10, rep3

description:
Library name: Spry4_GKO_BU10_3
column name in FPKM_Spry4.csv: 448_A_Undiff_GCRT_Spry4KO_BU10_SP388_S219


title: Spry4 G-KO spermatogonia, BU-D10, rep2

description:
Library name: Spry4_GKO_BU10_2
column name in FPKM_Spry4.csv: 442_A_Undiff_GCRT_Spry4KO_BU10_SP387_S213


title: Spry4 G-KO  spermatogonia, BU+PD-D10, rep1

description:
Library name: Spry4_GKO_BU10_PD_1
column name in FPKM_Spry4.csv: 441_A_Undiff_GCRT_Spry4KO_BU10_PD8_SP318_S212


title: PDS5-AB_AID__SCC1-EGFP_+_aux_HeLa rep1

description: Library name: 195058


title: TimeLapse-seq_Mitotic_T40_HEK293T_ns4U

description: Library name: Sample 15


title: sorted_H3K27me3_shAbcb8_rep2

description: Library name: sorted_H3K27me3_shAbcb8_rep2


title: Spry4 G-KO spermatogonia, BU-D10, rep1

description:
Library name: Spry4_GKO_BU10_1
column name in FPKM_Spry4.csv: 440_A_Undiff_GCRT_Spry4KO_BU10_SP317_S211


title: sorted_H3K27me3_shAbcb8_rep3

description: Library name: sorted_H3K27me3_shAbcb8_rep3


title: sorted_H3K27me3_shAbcb8_rep1

description: Library name: sorted_H3K27me3_shAbcb8_rep1


title: NIPBL-FKBP_PDS5-AB_AID_HeLa rep2

description: Library name: 223216


title: NIPBL-FKBP_PDS5-AB_AID_HeLa rep3

description: Library name: 227431


title: TimeLapse-seq_Mitotic_T0_HEK293T_ys4U_1

description: Library name: Sample 12

value: 0 min post-mitotic release


title: TimeLapse-seq_Mitotic_T0_HEK293T_ys4U_3

description: Library name: Sample 14


title: sorted_H3K27me3_shRen_rep3

description: Library name: sorted_H3K27me3_shRen_rep3

value: shRen


title: WT spermatogonia, BU+PD-D10, rep2

description:
Library name: WT_BU10_PD_2
column name in FPKM_Spry4.csv: 446_A_Undiff_Spry4ff_BU10_PD8_SP397_S217


title: sorted_H3K27me3_shRen_rep2

description: Library name: sorted_H3K27me3_shRen_rep2


title: NIPBL-FKBP_PDS5-AB_AID_HeLa rep1

description: Library name: 221717


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_5h_HeLa rep2

description: Library name: 227432


title: WT spermatogonia, BU+PD-D10, rep4

description:
Library name: WT_BU10_PD_4
column name in FPKM_Spry4.csv: 454_A_Undiff_Spry4ff_BU10_PD8_SP416_S225


title: ATAC_Mitotic_T300_HEK293T_2

description: Library name: Sample 10

value: 300 min post-mitotic release


title: WT spermatogonia, BU+PD-D10, rep1

description:
Library name: WT_BU10_PD_1
column name in FPKM_Spry4.csv: 445_A_Undiff_Spry4ff_BU10_PD8_SP395_S216


title: WT spermatogonia, BU+PD-D10, rep3

description:
Library name: WT_BU10_PD_3
column name in FPKM_Spry4.csv: 452_A_Undiff_Spry4ff_BU10_PD8_SP409_S223


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_5h_+_aux_5h_HeLa rep2

description: Library name: 227435


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_5h_HeLa rep1

description: Library name: 221718


title: TimeLapse-seq_Mitotic_T0_HEK293T_ys4U_2

description: Library name: Sample 13


title: sorted_H3K27me3_shRen_rep1

description: Library name: sorted_H3K27me3_shRen_rep1


title: TimeLapse-seq_Mitotic_T0_HEK293T_ns4U

description: Library name: Sample 11


title: naive-2

first: Leonardo

middle: Daniel

last: Garma

address: Melchor Fernández Almagro 3

institute: Spanish National Cancer Research Center

description: Library name: naive-2

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina).
Assembly: hg38
Supplementary files format and content: Tab-separated values of raw counts for each sample

source_name: Splenocyte-derived cell cultures

extract_protocol:
After 48h in co-culture, 1x Brefeldin A (BioLegend, #420601) was added. Splenocytes were collected for FACS analysis and RNAseq analysis. RNA was extracted using RNAeasy Mini Plus Kit (Qiagen, #74134) and quantified in LabChip GX Touch Nucleic Acid Analyzer (PerkinElmer). RNA quality was determined by Agilent's 2100 Bioanalyzer Lab-Chip technology. Only samples with RNA Integrity Number (RIN)>7 was used for sequencing.
Total RNA samples (300ng; with average RIN/RQS 7.5, range 2.5-9.5) were converted into sequencing libraries using the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, in which random primers featuring a 6 nt long Unique Molecular Identifier tag are used {to be addressed for bias correction at data analysis}. Directional cDNA libraries, stranded in the sense orientation {--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq, --rna-strandness F in HISAT}, were completed by PCR and sequenced in a single read format on an NovaSeq X Illumina instrument.

value: Splenocyte-derived cell cultures

value: Splenocyte

value: Naïve


title: WT spermatogonia, BU-D10, rep3

description:
Library name: WT_BU10_3
column name in FPKM_Spry4.csv: 451_A_Undiff_Spry4ff_BU10_SP404_S222


title: WT spermatogonia, BU-D10, rep4

description:
Library name: WT_BU10_4
column name in FPKM_Spry4.csv: 455_A_Undiff_Spry4ff_BU10_SP418_S226


title: NIPBL-FKBP_PDS5-AB_AID_+_dTAG_5h_+_aux_5h_HeLa rep1

description: Library name: 227434

value: HeLa Kyoto

value: human cervical cancer cells


title: naive-1

description: Library name: naive-1


title: NIPBL-FKBP_PDS5-AB_AID_+_aux_5h_HeLa rep2

description: Library name: 227433


title: ATAC_Mitotic_T105_HEK293T_1

description: Library name: Sample 7

value: 105 min post-mitotic release


title: ATAC_Mitotic_T105_HEK293T_2

description: Library name: Sample 8


title: ATAC_Mitotic_T300_HEK293T_1

description: Library name: Sample 9


title: WT spermatogonia, BU-D10, rep2

description:
Library name: WT_BU10_2
column name in FPKM_Spry4.csv: 447_A_Undiff_Spry4ff_BU10_SP401_S218


title: 3-spr-lavnx-OPNp

description: Library name: 3-spr-lavnx-OPNp

value: Exposed to RAW cells cultured under normoxia with SPP1, after media wash


title: ATAC_Mitotic_T40_HEK293T_2

description: Library name: Sample 6


title: WT spermatogonia, BU-D10, rep1

description:
Library name: WT_BU10_1
column name in FPKM_Spry4.csv: 443_A_Undiff_Spry4ff_BU10_SP389_S214

value: WT


title: 3-spr-lavnx-OPNn

description: Library name: 3-spr-lavnx-OPNn

value: Exposed to RAW cells cultured under normoxia without SPP1, after media wash


title: NIPBL-FKBP_PDS5-AB_AID_+_aux_5h_HeLa rep1

description: Library name: 221719


title: ATAC_Mitotic_T40_HEK293T_1

description: Library name: Sample 5


title: CTCF_AID_-_aux_HeLa rep4

description: Library name: 227438


title: CTCF_AID_-_aux_HeLa rep3

description: Library name: 227437


title: 3-spr-lavhx-OPNp

description: Library name: 3-spr-lavhx-OPNp

value: Exposed to RAW cells cultured under hypoxia with SPP1, after media wash


title: mESC, Spontaneous differentiation in EBs, D7

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description: Library name: 25L004482-ST

library_source: transcriptomic single cell

data_processing:
scRNAseq data generated using the BD Rhapsody platform were processed using the Seurat package in R. Low-quality cells and doublets were removed through standard quality control process. Subsequently, 2,000 highly variable genes were identified for downstream analysis. Harmony analysis was employed to remove batch effects. Cell clustering analysis was performed using FindClusters and FindNeighbors functions. Pearson correlation analysis was conducted to estimate the association between selected genes. PROGENy was used to assess pathway activities based on perturbation-derived gene signatures at the single-cell level and subsequently compared across cell populations or between different genes. Differential pathway activities were analyzed to depict signaling dynamics during cellular state transitions and the associations of individual genes with signaling pathways. Diffusion pseudotime (DPT) analysis was performed to infer cellular trajectories based on diffusion maps constructed from the normalized single-cell expression data. Epiblast cell population were specified as the root for pseudotime calculation, and cells were ordered along the inferred developmental trajectory. scTour was performed to construct cellular trajectories by learning latent temporal representations from the normalized single-cell expression data.
Assembly: GRCm38 was used as reference genome build within the BD Rhapsody Seven Bridges platform.
Supplementary files format and content: Processed data file format: Seurat Processed data file content: Matrix data

source_name: Mouse embryo (Blastocyst)

growth_protocol: Mouse embryonic stem cells (ESC) E14TG2α were cultured in Mouse ES Cell Basal Medium (ATCC, Manassas, Virginia, USA), 2-mercaptoethanol (Gibco™; 10 nM; Paisley, Scotland) and leukemia inhibitory factor (ESGRO®LIF; 1000 U/mL; Becton Dickinson, Heidelberg, Germany) supplemented with 10% FBS (Bio&SELL, Feucht, Germany) on 0.1% gelatin (InSCREENeX, Braunschweig, Germany) coated T25 flasks.

extract_protocol:
Single cell RNA sequencing was performed with the BD Rhapsody HT single cell analysis system (BD Biosciences, Heidelberg, Germany) using adapted protocols. Wildtype murine embryonic stem cells E14TG2α were harvested in four consecutive passages to form embryoid bodies for spontaneous differentiation in the absence of LIF for three, five, and seven days (D3, D5, D7) generating a total of n = 12 samples. EBs of each biological replicate were collected in separate reservoir tanks, transferred to 50 mL Falcon tubes, and sedimented via gravity before carefully removing supernatant. EBs were resuspended in 2 mL of TrypLE solution and incubated with constant mixing at 37°C for 1-2 minutes to generate single cell suspensions. Cells from each replicate and time point were separately centrifuged 5 min at 400 g, washed once with PBS with 1% FBS (FACS buffer). From here on, all steps were conducted on ice. Custom BDTM Single Cell Multiplexing Kit (#626545; anti-mouse MHC-calls I antibody, direct labelling) was used for sample tagging and pooled processing according to the manufacturer´s protocol. Labelled cells from four replicates (each 2,5 x 105 cells) were pooled for each individual time point to three samples (D3, D5, D7) and washed thrice in 2 mL of FACS buffer, centrifuged at 400 g for 5 min, and finally resuspended in 620 μL cold sample buffer. Staining cells with viability markers was achieved by adding 3.1 μL of 2 mM Calcein AM and 3.1 μL of 0.3 mM DRAQ7™ to the cell suspension in cold sample buffer (37°C in the dark, 5 min). Thereafter, 10 µL cells were counted using BD Rhapsody scanner 10 μL in an INCYTO™ disposable hemocytometer with the remaining cells kept on ice and protected from light. BD Rhapsody 8 lane cartridge were then primed, loaded with cells and, thereafter, with BD Rhapsody™ Enhanced Cell Capture Beads. After cell lysis and release of polyadenylated mRNAs, BD Rhapsody™ Enhanced Cell Capture Beads were retrieved, washed, and further processed for library preparation.
Library preparation: • Reverse transcription (BD RhapsodyTM cDNA kit #633773) • Library preparation using BD RhapsodyTM Whole Transcriptome Analysis Amplification kit (#633801), generating Illumina-compatible libraries.  cDNA library preparation and sequencing were performed by the group of Dr. Inti Alberto De La Rosa Velásquez of the Core Facility Genomics (Helmholtz Center Munich, Germany) on an Illumina NovaSeq X Plus sequencer in a 10B200 flow as paired-end reads.

treatment_protocol: Wildtype murine embryonic stem cells E14TG2α were harvested in four consecutive passages to form embryoid bodies (EBs) for spontaneous differentiation in the absence of LIF for three, five, and seven days (D3, D5, D7) generating a total of n = 12 samples. EBs of each biological replicate were collected in separate reservoir tanks, transferred to 50 mL Falcon tubes, and sedimented via gravity before carefully removing supernatant. EBs were resuspended in 2 mL of TrypLE solution and incubated with constant mixing at 37°C for 1-2 minutes to generate single cell suspensions.

value: Mouse embryo (Blastocyst)

value: Murine embryonic stem cell

value: E14TG2alpha mouse embryonic stem cells Culture in 3D as embryoid bodies Withdrawal of LIF to induce spontaneous differentiation Seven days in absence of LIF


title: ATAC_Mitotic_T0_HEK293T_2

description: Library name: Sample 4

value: WT HEK293T


title: mESC, Spontaneous differentiation in EBs, D3

description: Library name: 25L004480-ST

value: Murine embryonic stem cell line E14TG2a Genotype:Wild-type 129P2/Ola background with the HPRT mutation/6-TG resistance

value: E14TG2alpha mouse embryonic stem cells Culture in 3D as embryoid bodies Withdrawal of LIF to induce spontaneous differentiation Three days in absence of LIF


title: 3-spr-expnx-OPNp

description: Library name: 3-spr-expnx-OPNp

value: Exposed to RAW cells cultured under normoxia with SPP1


title: mESC, Spontaneous differentiation in EBs, D5

description: Library name: 25L004481-ST

value: E14TG2alpha mouse embryonic stem cells Culture in 3D as embryoid bodies Withdrawal of LIF to induce spontaneous differentiation Five days in absence of LIF


title: CTCF_AID_-_aux_HeLa rep2

description: Library name: 227436


title: ATAC_Mitotic_T0_HEK293T_1

description: Library name: Sample 3

value: 0 min post-mitotic release


title: CTCF_AID_+_aux_HeLa rep3

description: Library name: 231503


title: CUT&RUN_HEK293T_CTCF_2

description: Library name: Sample 2

data_processing:
TimeLapse-seq: Sequencing data was processed using the fastq2EZbakR pipeline (Vock et al., 2025).
TimeLapse-seq: Adapter sequences were trimmed using fastp and reads were aligned to a GRCh38 or combined dm6-GRCh38 genome using STAR. Tracks were normalized using DESeq2 (estimateSizeFactors) or Dm spike-ins with DESeq2 (estimateSizeFactors).
TimeLapse-seq: Final mutation counts and feature assignments were summarized in a cB output file.
ATAC-seq: Sequencing data was processed using the nf-core/atacseq pipeline (version 2.1.2) (Ewels et al., 2020).
ATAC-seq: Adapter sequences were trimmed using Cutadapt.
ATAC-seq: Reads were aligned to the human hg38 genome using the BWA aligner.
ATAC-seq: Duplicate reads and reads mapping to mitochondrial DNA were filtered out.
ATAC-seq: Peaks were called using MACS2 in narrow peak mode, and tracks were normalized using TMM normalization.
CUT&RUN: Reads were trimmed of adaptor sequences using fastp.
CUT&RUN: Reads were aligned to a combined E. coli-GRCh38 genome using bwa-mem2.
CUT&RUN: Aligned reads were processed using SAMtools. Tracks were normalized using TMM normalization or E.coli spike-ins.
CUT&RUN: Peaks were called using MACS2 with default parameters, in broad peak mode for H3K27me3, and in narrow peak mode for all other targets, with IgG samples used as controls.
ChIP-seq: For H3K27ac ChIP-seq samples, reads were trimmed of adaptor sequences using Cutadapt and aligned to the GRCh38 genome using Bowtie2 v2.2.9. Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, reads were processed using the nf-core/chipseq pipeline (version 2.0.0).
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, adapter sequences were trimmed using Trim Galore and reads were aligned to the GRCh38 genome using the BWA aligner.
ChIP-seq: For ChIP-seq samples collected in THP-1 cells, duplicate reads and reads mapping to blacklisted regions were filtered out. Counts Per Million (CPM) normalization was applied to create scaled bigWig files.
ChIP-seq: For all ChIP-seq samples, peaks were called using MACS2 with default parameters, using inputs as controls.
Assembly: GRCh38 and dm6
Supplementary files format and content: Normalized bigWig, TDF files, and MACS2 called-peak files.
Library strategy: CUT&Run

value: Untreated

value: CTCF


title: KO surface library

city: La Jolla

first: Ananda

middle: W

last: Goldrath

state: CA

address: 9500 Gilman Drive

department: Molecular Biology

institute: University of California, San Diego

description: Library name: KO surface library

library_source: other

data_processing:
Gene expression and TotalSeq-C antibody (surface protein panel and hashtags) counts were obtained using CellRanger (v7.1.0, 10x Genomics) with default parameters. Reads were aligned to the mm10 (2020) reference transcriptome and the DNA barcode for the TotalSeq-C panel. Samples were demultiplexed using hashtag oligo (HTO) counts and the HashSolo algorithm, and doublets (cells positive for multiple hashtags) were excluded. Surface protein expression was normalized using the DSB method to remove ambient background and technical noise. Cells were filtered if they met any of the following criteria: expression of two isotype control antibodies, fewer than 150 RNA UMI counts, or >5% mitochondrial gene expression. RNA counts were normalized to 10,000 transcripts per cell using normalize_total() and log-transformed with log1p in Scanpy. Highly variable genes were selected using the Seurat v3 method with batch correction, and expression data were scaled to unit variance (max value = 10) prior to integration. To jointly model RNA and protein data, we applied totalVI from the scvi-tools framework90. RNA and protein modalities from 2 conditions (Control and KO) were concatenated using MuData, and totalVI was trained to a shared latent space accounting for batch effects and noise.
Assembly: mm10
Supplementary files format and content: mtx files storing feature counts per cell before (raw) and after (filtered) Cellranger filtering. Barcode mappings to antibody identities are stored in feature_reference.csv files.
Library strategy: CITE-seq

molecule: protein

source_name: Spleen, Liver, IEL

extract_protocol:
We first sorted 5x10^4 P14 T cells from the IEL, liver, and spleen of 4 pooled mice per group (control vs NEURL3 KO, control vs RNF149 KO, and control vs WSB1 KO) into DMEM supplemented with 2% bovine growth serum and 10 mM HEPES. Due to the number of groups, all control samples were pooled together and all KO samples were pooled together. Following the first sort, hash-tagged cells were pooled incubated with antibody-derived tags (ADT, TotalSeq-C Mouse Universal Cocktail, V1.0) and washed thoroughly. For the second sort, all stained cells from the pooled tissues were sorted as well as 5x10^4 CD8+ T cells from a naive spleen were also sorted to allow for batch correction with totalVI.
scRNA-seq was performed using 10X Genomics 5’v2 with feature barcoding for cell surface protein and immune receptor mapping following the manufacturer’s instructions. After cDNA amplification, the smaller fragments containing the TotalSeq-C–derived cDNA were purified and saved for feature barcode library construction. The larger fragments containing transcript-derived cDNA were saved for gene expression library construction. For both cDNA portions, the library size was measured with an Agilent Bioanalyzer D5000 high-sensitivity DNA assay and quantified using a Qubit 2.0 fluorometer. Transcript-derived cDNA was processed into RNA libraries. After enzymatic fragmentation and size selection, purified cDNA was ligated to an Illumina R2 sequence and indexed with unique Dual Index TT set A index sequences with an index PCR. TotalSeq-C–derived cDNA was processed into feature barcode libraries. The cDNA was indexed with unique Dual Index TN set A index sequences with an index PCR. The two libraries were pooled together on the basis of molarity with relative proportions of 40% GEX (RNA) and 10% surface (feature barcode) for each control and KO pooled samples. This pool was then sequenced on an Illumina NovaSeq X Plus 10B. The sequencing configuration followed 10X Genomics specifications.

value: Spleen, Liver, IEL

value: P14 T cell

value: KO

value: LCMV Armstrong


title: Control surface library

description: Library name: Control surface library

value: Control


title: 3-spr-lavhx-OPNn

description: Library name: 3-spr-lavhx-OPNn

value: Splenocyte-derived cell cultures

value: Splenocyte

value: WT

value: Exposed to RAW cells cultured under hypoxia without SPP1, after media wash


title: CUT&RUN_HEK293T_CTCF_1

description: Library name: Sample 1

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For TimeLapse-seq, genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for TimeLapse-seq was treated with oxidative-nucleophilic-aromatic-substitution chemistry as described in Schofield et al. Nature Methods 2018. ATAC-seq was performed in HEK293T cells using the Active Motif ATAC-Seq Kit following the standard protocol. CUT&RUN was performed in HEK293T nuclei using the EpiCypher CUTANA ChIC/CUT&RUN Kit following the standard protocol. For Kacme, H4K5ac, and CTCF CUT&RUN samples, cells were crosslinked (0.1% formaldehyde, 1 min) prior to nuclei isolation. For ChIP-seq, 20-30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
TimeLapse-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413). ATAC-seq libraries were generated following the Active Motif ATAC-Seq Kit standard protocol. CUT&RUN library preparation was carried out with the EpiCypher CUTANA CUT&RUN Library Prep Kit. ChIP-seq libraries were prepared using standard Illumina protocols.

value: WT HEK293T


title: CTCF_AID_-_aux_HeLa rep1

description: Library name: 221470

value: HeLa Kyoto

value: human cervical cancer cells


title: 3-spr-exphx-OPNn

description: Library name: 3-spr-exphx-OPNn

value: Exposed to RAW cells cultured under hypoxia without SPP1


title: 3-spr-exphx-OPNp

description: Library name: 3-spr-exphx-OPNp

value: Exposed to RAW cells cultured under hypoxia with SPP1


title: 3-spr-expnx-OPNn

description: Library name: 3-spr-expnx-OPNn

value: Exposed to RAW cells cultured under normoxia without SPP1


title: CEL replicate 3

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

institute: University of Louisville

description:
Library name: CELA54903
A549 cells treated with 1 µM CEL_Replicate 3

data_processing:
Raw sequences were checked for quality values using in-house Perl scripts developed by Novogene.
The sequences were directly aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.5)
Differential gene expression analysis was conducted with the DESeq2 R package (v1.20.0)
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited file includes normalized counts for each sample

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Universal Mini Kit
ABclonal’s Fast RNA-seq Lib Prep Kit V2 (Catalog #RK20306) for Illumina was used for library prep

value: Lung cancer

value: CEL


title: KO GEX library

description: Library name: KO GEX library

value: Spleen, Liver, IEL


title: 3-spm-expnx-OPNp

description: Library name: 3-spm-expnx-OPNp

value: Exposed to cell culture media of RAW cells cultured under normoxia with SPP1


title: CEL replicate 2

description:
Library name: CELA54902
A549 cells treated with 1 µM CEL_Replicate 2


title: Control GEX library

description: Library name: Control GEX library

value: P14 T cell


title: CTCF_AID_+_aux_HeLa rep2

description: Library name: 231502


title: SCC1 ChIP in control_+_aux

description:
Library name: SCC1_ChIP_in_control_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

data_processing:
Basecalling software: Illumina RTA
Aligment against hg19 reference assembly: bowtie version 1.2.2 , reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq  peak calling using MACS2  version 2.2.5
pile-up and heat map generation and plotting with deeptools version 3.5.4
Assembly: hg19
Supplementary files format and content: bigWig files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper, they can be used for visualization in IGV and Juicebox browsers

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with respective antibody; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols.


title: 3-spm-expnx-OPNn

description: Library name: 3-spm-expnx-OPNn

value: Exposed to cell culture media of RAW cells cultured under normoxia without SPP1


title: CEL replicate 1

description:
Library name: CELA54901
A549 cells treated with 1 µM CEL_Replicate 1


title: Vehicle A549 replicate 3

description:
Library name: UntA54903
Untreated A549 cells served as control_Replicate 3

value: Vehicle


title: 3-spm-exphx-OPNp

description: Library name: 3-spm-exphx-OPNp

value: Splenocyte-derived cell cultures

value: Exposed to cell culture media of RAW cells cultured under hypoxia with SPP1


title: SCC1 ChIP in WAPL_PDS5-AB_AID_+_aux

description:
Library name: SCC1_ChIP_in_WAPL_PDS5-AB_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: Gastruloid with 2.5 days of differentiation, Sp5/8 double knock out mutant

city: Frederick

first: Francisco

last: Pereira Lobo

state: Maryland

address: 1050 Boyles St

institute: National Cancer Institute

description: Library name: Gastruloid_D2_5_Sp5_Sp8_DM

data_processing:
We processed our data by sequentially: 1) mapping reads in the reference genome using STARSolo as provided by the STAR aligner (v. 2.7.9a); 2)  using CellBender (v. 0.3.0) to remove ambient gene expression and empty droplets from the unprocessed raw count read matrix; 3) using Seurat (v. 5.1.0) to generate merged, harmony-integrated processed seurat objects.
Assembly: mm10 - 2020-A
Supplementary files format and content: Format: R data file (.rds). Content: processed Seurat object.

source_name: Gastruloid

growth_protocol: Gastruloid protocol was initiated as described previously (Beccari, L et al, 2018). About 300 ES cells from Wild type (WT) R1 and Sp5/8dko were plated on 96 well ultra- low attachment dishes in serum free N2B27 media.

extract_protocol:
Gastruloids were treated with 0.5ml of TrypLE Express dissociation reagent (Life Technologies) in a 15ml conical tube at 37 °C for 5 minutes. After the initial incubation, the cell suspension was gently pipetted up and down four times and incubated for an additional 1 minute at 37 °C. To quench, 1 mL of heat-inactivated FBS was added, and the suspension was triturated gently three times to mix. Cells were pelleted by centrifugation at 900 rpm for 5 minutes at 12 °C in a tabletop centrifuge. The pellet was washed once with 1 mL of cold PBS containing 0.04% bovine serum albumin (BSA), followed by centrifugation under the same conditions. After removing the supernatant, approximately 50 µL was left to avoid disturbing the pellet. Cells were then resuspended in 500 µL of cold PBS with 0.04% BSA and filtered through a 40-μm Flowmi tip strainer (ThermoFisher Scientific, 136800040) into a pre-chilled 15 mL conical tube. A typical recovery volume was ~495 µL. Cell concentration and viability were determined, and remaining cells were kept on ice for immediate downstream processing.
Two 10x genomics Single cell 3’ki V3.1 libraries were sequenced on two NovaSeq X plus runs. Bothe samples have sequencing yields of more than 406 million read per sample. The sequencing run was setup as 28 cycles+90 cycles non-symmetric run. Demultiplexing was done allowing 1 mismatch in the barcodes. Sequencing quality is good, over 97.5% of bases in the barcode regions have Q30 or above and at least 97.6% of bases in the read have Q30 or above. More than 98.2% of bases in the UMI have Q30 or above. The analysis was performed with the Cell Ranger 8.0.1 software using the default parameters. For day 2.5 Wildtype (WT) and Sp5/8dko, the number of cells captured are 9,238 and 11,190; mean reads per cell are 50,959 and 50,334, median genes per cell are 5,333 and 5,398; total number of genes are 25,523 and 25,786 respectively. Cells with extremely low number of UMI counts were filtered out.

treatment_protocol: After 2 days of growth, aggregates were treated with 3uM CHIR and 12h later samples were pooled and washed with PBS+2% heat-inactivated fetal bovine serum (FBS) to remove residual medium.

value: Gastruloid

value: R1 ESCs

value: ESC

value: Double Mutant Sp5/8

value: Mutant


title: CTCF_AID_+_aux_HeLa rep1

description: Library name: 221471

value: HeLa Kyoto

value: human cervical cancer cells


title: CR_2_REPLICATE_4

city: Milano

first: Raul

last: Pirona

address: Via Alfonso Corti 12

country: Italy

institute: IBBA-CNR

description:
Library name: Unknown_BJ191-S09-001T0012
C4
Cr 2 FASTQ REPLICATE 4

data_processing:
Fastp
Salmon
DESEq2
Assembly: Tomato SL4, ITAG 4.1
Supplementary files format and content: counts.csv

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Seedling were transferred in 10 cm pots with potting soil and grown in a greenhouse plants were exposed to temperatures between 14 and 21 °C and to light intensities between 170 and 210 µmol m-² s-1

extract_protocol:
RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany).
150 paired end mRNA stranded

treatment_protocol: Water deficit conditions were imposed at growth stage 4th primary apical side shoot visible (24 BBCH-scale) by suspending irrigation for 14 days.

value: leaf

value: water stress


title: CR_2_REPLICATE_3

description:
Library name: Unknown_BJ191-S09-001T0011
C3
Cr 2 FASTQ REPLICATE 3


title: Gastruloid with 2.5 days of differentiation, wild type

description: Library name: Gastruloid_D2_5_WT

value: WT

value: Control


title: Vehicle A549 replicate 2

description:
Library name: UntA54902
Untreated A549 cells served as control_Replicate 2

value: Lung cancer


title: FT246 si1

city: Los Angeles

first: Michelle

last: Jones

address: 8700 Beverly Blvd

department: Bioinformatics and Functional Genomics

institute: Cedars Sinai

description:
Library name: Sample8
column name in raw counts: FT246si1

data_processing:
Data processed with Dragen 4.3.6 using Hash Table Version 10.  gencode.v46.chr_patch_hapl_scaff.annotation.gtf was used for gene identification
Assembly: hg38
Supplementary files format and content: comma separated text file includes raw counts for each sample

growth_protocol: Kuramochi cells purchased from JCRB and CaOv3 cells purchased from ATCC were grown and maintained in RPMI 1640 (Thermo Fisher) and supplemented with 10% FBS (Thermo Fisher) and 100 U/mL Penicillin-Streptomycin (Gibco). FT246 and FT282 were donated by Cedars Sinai and maintained in DMEM F12 50/50 (Corning) supplemented with 10% FBS (Thermo Fisher), 2mM L-Glutamine (Thermo Fisher), and 100 U/mL Penicillin-Streptomycin (Gibco).

extract_protocol:
RNA was harvested using a Zymo Quick-RNA mini prep and 1ug of RNA was used in library prep
RNA libraries were prepared using NEBNext Poly(A) mRNA Megnetic Isolation Module to purify the mRNA and IDT xGen Broad-Range RNA Library Prep Kit for library prep

treatment_protocol: Cells were transfected with 25nM siRNA incubated with .33ul lipofectamine per mL of serum free media

value: Fallopian tube secretory epithelial cell

value: MDC1 knockdown

value: growth


title: FT246 siCTL

description:
Library name: Sample7
column name in raw counts: FT246SCR


title: CR_1_REPLICATE_4

description:
Library name: Unknown_BJ191-S09-001T0008
B4
Cr 1 FASTQ REPLICATE 4


title: CR_2_REPLICATE_1

description:
Library name: Unknown_BJ191-S09-001T0009
C1
Cr 2 FASTQ REPLICATE 1


title: SCC1 ChIP in WAPL_CTCF_AID_+_aux

description:
Library name: SCC1_ChIP_in_WAPL_CTCF_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: Vehicle A549 replicate 1

description:
Library name: UntA54901
Untreated A549 cells served as control_Replicate 1

value: Vehicle


title: CR_2_REPLICATE_2

description:
Library name: Unknown_BJ191-S09-001T0010
C2
Cr 2 FASTQ REPLICATE 2


title: CR_1_REPLICATE_2

description:
Library name: Unknown_BJ191-S09-001T0006
B2
Cr 1 FASTQ REPLICATE 2


title: CR_1_REPLICATE_3

description:
Library name: Unknown_BJ191-S09-001T0007
B3
Cr 1 FASTQ REPLICATE 3


title: Kuramochi si1

description:
Library name: Sample4
column name in raw counts: Kuramochisi1

source_name: Kuramochi

value: Kuramochi

value: epithelial ovarian cancer


title: SCC1 ChIP in WAPL_AID_+_aux

description:
Library name: SCC1_ChIP_in_WAPL_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: SCC1 ChIP in PDS5-AB_AID_5h_aux

description:
Library name: SCC1_ChIP_in_PDS5-AB_AID_5h_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: 2-spr-lavnx-OPNn

description: Library name: 2-spr-lavnx-OPNn

value: Splenocyte-derived cell cultures

value: Splenocyte

value: Exposed to RAW cells cultured under normoxia without SPP1, after media wash


title: SCC1 ChIP in CTCF_AID_-aux

description:
Library name: SCC1_ChIP_in_CTCF_AID_-aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: 2-spr-exphx-OPNp

description: Library name: 2-spr-exphx-OPNp

value: Exposed to RAW cells cultured under hypoxia with SPP1


title: SCC1 ChIP in PDS5-AB_AID_+_aux

description:
Library name: SCC1_ChIP_in_PDS5-AB_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

value: HeLa Kyoto


title: SCC1 ChIP in CTCF_AID_+_aux

description:
Library name: SCC1_ChIP_in_CTCF_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

value: human cervical cancer cells


title: SCC1 ChIP in control

description:
Library name: SCC1_ChIP_in_control
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: 2-spr-lavhx-OPNp

description: Library name: 2-spr-lavhx-OPNp

value: Exposed to RAW cells cultured under hypoxia with SPP1, after media wash


title: CR_1_REPLICATE_1

description:
Library name: Unknown_BJ191-S09-001T0005
B1
Cr 1 FASTQ REPLICATE 1

value: leaf

value: water stress


title: WT_REPLICATE_4

description:
Library name: Unknown_BJ191-S09-001T0004
A4
WT FASTQ REPLICATE 4

value: WT


title: FT282 si1

description:
Library name: Sample6
column name in raw counts: FT282si1


title: Kuramochi siCTL

description:
Library name: Sample3
column name in raw counts: KuramochiSCR


title: 2-spr-expnx-OPNn

description: Library name: 2-spr-expnx-OPNn

value: Exposed to RAW cells cultured under normoxia without SPP1


title: FT282 siCTL

description:
Library name: Sample5
column name in raw counts: FT282SCR

value: Fallopian tube secretory epithelial cell


title: CaOv3 si1

description:
Library name: Sample2
column name in raw counts: CaOv3si1

value: MDC1 knockdown


title: 2-spr-lavhx-OPNn

description: Library name: 2-spr-lavhx-OPNn

value: Exposed to RAW cells cultured under hypoxia without SPP1, after media wash


title: CTCF-ChIP in control_+_aux

description:
Library name: CTCF_ChIP_in_control_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: 2-spr-expnx-OPNp

description: Library name: 2-spr-expnx-OPNp

value: Exposed to RAW cells cultured under normoxia with SPP1


title: 2-spr-lavnx-OPNp

description: Library name: 2-spr-lavnx-OPNp

value: Exposed to RAW cells cultured under normoxia with SPP1, after media wash


title: SCC1 ChIP in NIPBL_1h_dTAG_PDS5-AB_AID_5h_aux

description:
Library name: SCC1_ChIP_in_NIPBL_1h_dTAG_PDS5-AB_AID_5h_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: 2-spr-exphx-OPNn

description: Library name: 2-spr-exphx-OPNn

value: Exposed to RAW cells cultured under hypoxia without SPP1


title: CaOv3 siCTL

description:
Library name: Sample1
column name in raw counts: CaOv3SCR

value: epithelial ovarian cancer

value: growth


title: CTCF-ChIP in WAPL_PDS5-AB_AID_+_aux

description:
Library name: CTCF_ChIP_in_WAPL_PDS5-AB_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: WT_REPLICATE_3

description:
Library name: Unknown_BJ191-S09-001T0003
A3
WT FASTQ REPLICATE 3


title: 2-spm-expnx-OPNp

description: Library name: 2-spm-expnx-OPNp

value: Splenocyte-derived cell cultures

value: Splenocyte

value: Exposed to cell culture media of RAW cells cultured under normoxia with SPP1


title: LAC3

description: Library name: LAC3

data_processing:
Step1:Quality Control The quality of the raw paired-end sequence reads was assessed with FastQC (Version 0.11.7).
Step2:Trimming Low quality ($<20$) bases and adapter sequences were trimmed by Trimmomatic (Version 0.38) with the following parameters: ILLUMINACLIP: adapter.fa:2:30:10, LEADING:20, TRAILING:20, SLIDINGWINDOW:4:15, and MINLEN:362
Step 3: Mapping The trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (Version 2.3.4.2). Resultant SAM files were converted into BAM files with Samtools (Version 1.9).
Step 4: Deduplication Picard (Version 2.18.11) was used to remove duplicate reads using the MarkDuplicates tool.
Step 5: Peak Calling Peak calling was performed using MACS2 (Version 2.2.6) with the input samples as controls. The parameters were set to "--nomodel -q 0.01". Step 6: Quantification The number of uniquely mapped reads in the merged peak regions was estimated with featureCounts (Version 1.6.3).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.
Supplementary files format and content: BAM format:  Contains read alignment data mapped to the hg38 reference genome using Bowtie2.     Duplicate reads were removed using Picard MarkDuplicates.     Files are sorted and indexed.    BigWig (.bw) format:  Contains signal intensity data (coverage) across the genome.     Normalized using RPKM (Reads Per Kilobase per Million mapped reads) with a bin size of 5 bp.   narrowPeak format:  Contains genomic coordinates of protein-enriched regions (peaks) identified by MACS2.     Peak calling was performed with a q-value threshold of 0.01.  Includes peak locations, signal values, and statistical significance (p-value and q-value).  TXT format (Annotation):  Contains peak-to-gene annotations, including genomic region classification (e.g., Promoter, Exon, Intron) and nearest gene symbols within 1 Mbp.

growth_protocol: human HCC cell lines, PLC/PRF/5 (RRID: CVCL_0485) was purchased from the Japanese Collection of Research Bioresources Cell Bank (Osaka, Japan) and the American Type Culture Collection (Manassas, VA, USA). Authentication of these cell lines was confirmed by short tandem repeat DNA fingerprinting (BEX Co. Ltd., Tokyo, Japan).

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were conducted using a SimpleChIP® Plus Sonication Chromatin IP Kit (CST) and ChIP-IT Express (Active motif) according to the manufacturer’s protocol.
ChIP-seq reads underwent quality control (FastQC), trimming (Trimmomatifc), alignment (Bowtie2), and duplicate removal (Picard). Normalized coverage tracks were generated from BAM files. These tracks, along with called peaks, were visualized using the Integrative Genomics Viewer (IGV) to produce figures illustrating signal

value: Liver

value: Hepatocellular carcinoma cells

value: culture with lactate 20mM for 24hr

tag: chip antibody

value: H4K5la (PTM-1407RM)


title: WT_REPLICATE_2

description:
Library name: Unknown_BJ191-S09-001T0002
A2
WT FASTQ REPLICATE 2

value: leaf

value: WT

value: water stress


title: CTCF-ChIP in WAPL_CTCF_AID_+_aux

description:
Library name: CTCF_ChIP_in_WAPL_CTCF_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

value: HeLa Kyoto

value: human cervical cancer cells


title: CTCF-ChIP in WAPL_AID_+_aux

description:
Library name: CTCF_ChIP_in_WAPL_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: LAC2

description: Library name: LAC2


title: 2-spm-expnx-OPNn

description: Library name: 2-spm-expnx-OPNn

value: Exposed to cell culture media of RAW cells cultured under normoxia without SPP1


title: NM3

description: Library name: NM3

value: control


title: CTCF-ChIP in PDS5-AB_AID_+_aux

description:
Library name: CTCF_ChIP_in_PDS5-AB_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: WT_REPLICATE_1

description:
Library name: Unknown_BJ191-S09-001T0001
A1
WT FASTQ REPLICATE 1


title: 1-spr-lavnx-OPNp

description: Library name: 1-spr-lavnx-OPNp

value: Exposed to RAW cells cultured under normoxia with SPP1, after media wash


title: CTCF-ChIP in CTCF_AID_+_aux

description:
Library name: CTCF_ChIP_in_CTCF_AID_+_aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes


title: 2-spm-exphx-OPNn

description: Library name: 2-spm-exphx-OPNn

value: Exposed to cell culture media of RAW cells cultured under hypoxia without SPP1


title: 2-spm-exphx-OPNp

description: Library name: 2-spm-exphx-OPNp

value: Exposed to cell culture media of RAW cells cultured under hypoxia with SPP1


title: 7814749_surgery (BC360 9.15.2023)

type: RNA

city: Oklahoma City

first: Suresh

last: Niture

state: OK

address: 800 NE 10th St, Department Of Radiation Oncology

institute: Department of Radiation Oncology, Stephenson Cancer Center, Oklahoma Unive

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 19

hyb_protocol: Panel standard is a DNA oligo blend containing all BC360 and IO 360 probe target sequences, that is run on each cartridge within the experiment for normalization of non-PAM50 genes; while reference sample is an RNA oligo blend containing PAM50 probe target sequences for PAM50 genes.

scan_protocol: nCounter technology provides a robust method for multiplexing up to 800 gene expression targets using direct detection technology. The simple, efficient workflow requires just 15 minutes hands-on time for most panels using an automated benchtop processing system and produces highly reproducible data, requiring no amplification or technical replicates in less than 24 hours. This workflow rapidly accelerates biomarker validation and biomarker development, providing gene expression data you can count on.

data_processing:
nCounter Analysis System and nSolver Analysis Software
Housekeeper Normalization for non-TIS and non-PAM50 Genes
Genes are normalized using a ratio of the expression value to the geometric mean of all housekeeping genes on the panel.
Housekeeper Normalization for TIS Genes
Genes in the TIS signature are normalized using a ratio of the expression value to the geometric mean of the housekeeper genes used only for the TIS signature.
Housekeeper Normalization for PAM50 Genes
Genes in the PAM50 signature are normalized using a ratio of the expression value to the geometric mean of the housekeeper genes used only for the PAM50 signature.
Panel Standard Normalization for non-PAM50 Genes
Genes not in the PAM50 signature are additionally normalized using a ratio of the housekeeper-normalized data and a panel standard run on the same cartridge as the observed data. In the absence of a panel standard column, values from panel standard run on the same codeset lot as the observed data may be substituted. If a cartridge is missing a panel standard run, the average of all panel standards present is substituted for that cartridge.
Reference Sample Normalization for PAM50 genes
Genes in the PAM50 signature are additionally normalized using a ratio of the housekeeper-normalized data and a reference sample run on the same codeset lot from a NanoString archive is used.
Final Adjustments
The housekeeper-normalized and panel standard-normalized data is Log(2) transformed. A constant of 8 is added to TIS so that it is on the same scale as investigational use only (IUO) TIS, making scores comparable across research use only (RUO) and IUO assays. Other non-TIS signatures are also adjusted with constants to express values in a similar range.
Differential Expression Analysis
Grouping Variable
Differential expression is fit on a per gene or per signature basis using a linear model for analyses without a blocking factor. The statistical model uses the expression value or signature score as the dependent variable and fits a grouping variable as a fixed effect to test for differences in the levels of that grouping variable.
Expression(gene or signature)= μ+Group+ε
P-values are adjusted within each analysis, gene or signature, and on the grouping variable level difference t-test using the Benjamini and Yekutieli False Discovery Rate (FDR) adjustment to account for correlations amongst the tests. All models are fit using the limma package in R.

label: Photocleavable oligonucleotide

source_name: primary breast cancer

label_protocol: The nanoString (nCounter Run) technology was used, and two approaches were applied for tumor analysis: 1) The nCounter® Breast Cancer 360™ panel and 2) PanCancer IO 360 panel.  Breast Cancer 360™ data analysis report provides a unique 360° view of gene expression for the breast tumor microenvironment and immune response, and PanCancer IO 360 panel provides a unique 360 ° view of gene expression for the tumor, microenvironment, and immune response. 19 BC samples passed all QCs, which include 5 Pre-RT (biopsy), and 14 post-RT (surgery). Three samples failed housekeeping geomean QC and were excluded from the analysis. Two-panel standards were used for normalization.  In IO 360 panel, 20 samples passed all QCs. 2 samples failed housekeeping geomean QC and were excluded from the analysis. One panel standard was used for normalization.

growth_protocol: Breast Cancer Patients were recruited at Myco College of Medicine, Jacksonville, FL. The study was conducted through a protocol approved by the Myco College of Medicine Institutional Review Board (IRB)

extract_protocol: Paraffin-embedded tissue biopsy samples from 20 BC patients (5 biopsy and  15 post RT surgical) were used to extract total RNA. We used whole sections of biopsy and surgical tissue for RNA extraction. RNA samples were isolated using the RNeasy Plus Universal Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. The quality and concentration of RNA were estimated using the NanoDrop ND-1000 spectrophotometer. Further analysis of RNA integrity was performed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer.

treatment_protocol: n this cohort study, we isolated 20 tumor tissues from 20 breast cancer patients, of which 5 tumors were collected during diagnosis and biopsy.  These patients were treated with standard radiation therapy (RT), and treatment included a total of 30 Gy radiation in three weeks.

tag: tissues

value: primary breast cancer

tag: race

value: Not Hispanic or Latino

tag: histology

value: Grade I

tag: Sex

value: Female

tag: Stage

tag: age


title: 1-spr-lavhx-OPNp

description: Library name: 1-spr-lavhx-OPNp

value: Splenocyte-derived cell cultures

value: Splenocyte

tag: genotype

tag: treatment

value: Exposed to RAW cells cultured under hypoxia with SPP1, after media wash


title: GM05386_TGFb_rep2

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Département de microbiologie et infectiologie

country: Canada

institute: Université de Sherbrooke

description: Library name: 48h_TGFb_rep2

data_processing:
Sequence reads were trimmed using Trimmomatic (V0.39) and the following parameters: ILLUMINACLIP:adapters.fa:2:30:10, LEADING:20, TRAILING:20, and MINLEN:45. The quality of the reads was assessed using FastQC (V0.11.9).
The transcriptome of the human genome GRCh38 was created using gffread (cufflinks V2.2.1) with the Ensembl annotation and genome files (V109).
Kallisto (V0.48.0) was used to align the reads to the transcriptome and to quantify the transcripts. The transcript abundance was combined to obtain the gene level quantification.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM vlues for each sample

source_name: fibroblasts

growth_protocol: GM 05386 primary skin fibroblasts (Coriell Institute for Medical Research) were maintained in Alpha Modification of Eagle’s medium (AMEM) supplemented with 20 mL of 10% heat activated FBS (VWR, CA76327-086), 5 mL of 5% L-glutamine (Wisent, 609-065-EL), 5 mL of 5% penicillin-streptomycin (VWR, CA45000-652), 800 uL of amphotericin B (Wisent, 450-105-QL), 5 mL of 5% sodium pyruvate (Wisent, 600-110-EL), 25 uL of 40ug/mL of fibroblast growth factor β (FGFβ) (Wisent, 511-126-QU), and 125 uL of 0.2% heparin (Sigma, H3393-50KU). The cells were passage twice a week with a seeding cell volume of 1 X 106 cells. Prior to cell seeding, the T-75 flasks used for its passages are always coated with 5 mL of 1ug/mL fibronectin (Sigma-Aldrich, F1141) diluted in PBS (with Ca & Mg) (Corning #21-030-CV) overnight at 4°C or 4 hours in 37oC incubator to aid adhesion and proliferation of the cells, followed by aspiration and washing of the flask with 5 mL of PBS w/o Ca & Mg.

extract_protocol:
RNA extraction was performed using a hybrid trizol-column protocol. Briefly, the upper aqueous phase after chloroform phase separation was then transferred and diluted with an equal volume of 70% ethanol, followed by transfer to a RNeasy mini spin column (Qiagen, 74104) as the manufacturer`s recommendation. RNA extracts were DNAse treated using the RNAse free DNAse set (Qiagen, 79254), and their quality checked by Agilent Bioanalyzer for the RNA integrity (RIN value). Library preparation and sequencing was performed by Genome Québec
Libraries were generated from 20 ng of total RNA as following: mRNA enrichment and cDNA synthesis was achieved with theNEBNext Single Cell Low Input RNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the KAPA Library Quantification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument.

treatment_protocol: Primary skin fibroblast (GM05386) cells of 5 to 10 passage numbers were used for this experiment. The cells were seeded in 6-well per 1 mL of complete media (for RNA-Seq analysis) and 96-well per 200 uL of complete media (for qRT-PCR analysis) plates and kept for 3 days until it reaches 70 to 80% confluency. Afterwards, the supernatant was aspirated and fresh media without FBS was added followed by the addition of a 1 ug/mL TGF-β (Abeomics, 32-1763-10) stock to reach a final concentration of 10 ng/mL. Cells were kept in an incubator and harvested after 2 days.

tag: tissue

value: fibroblasts

tag: cell line

value: fibroblast

value: normal

value: TGFβ

tag: batch


title: InputLAC

description: Library name: InputLAC

value: Liver

tag: cell type

value: Hepatocellular carcinoma cells

value: culture with lactate 20mM for 24hr


title: InputNM

description: Library name: InputNM

value: control


title: 12701592_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 17


title: GM05386_TGFb_rep3

description: Library name: 48h_TGFb_rep3


title: CTCF-ChIP in CTCF_AID_-aux

description:
Library name: CTCF_ChIP_in_CTCF_AID_-aux
5% MEF (mouse embryonic fibroblast) cells added for calibration purposes

value: HeLa Kyoto

value: human cervical cancer cells


title: 1-spr-lavhx-OPNn

description: Library name: 1-spr-lavhx-OPNn

value: WT

value: Exposed to RAW cells cultured under hypoxia without SPP1, after media wash


title: NM2

description: Library name: NM2

value: H4K5la (PTM-1407RM)


title: 1-spr-expnx-OPNp

description: Library name: 1-spr-expnx-OPNp

value: Exposed to RAW cells cultured under normoxia with SPP1


title: 3-spm-exphx-OPNn

description: Library name: 3-spm-exphx-OPNn

value: Splenocyte-derived cell cultures

value: Exposed to cell culture media of RAW cells cultured under hypoxia without SPP1


title: GM05386_noTGFb_rep3

description: Library name: 48h_rep3

value: untreated


title: 7953417_surgery (BC360 9.15.2023)

description:
Total tumor RNA
BC360 9.15.2023
SAMPLE 15

value: primary breast cancer

value: Not Hispanic or Latino

value: Grade I

value: Female