title: SUM149_ML324_CTSL_HiChIP

data_processing:
ChIP-seq and ATAC-seq data processing were based on chips pipeline (Qiu et al., 2021; Taing et al., 2021). Peak calling was performed using MACS2 v2.1.2 with FDR<0.01 as the cutoff (Feng et al., 2012).
Reads were aligned to hg19 genome using BWA-MEM aligner (Li, 2013).
Seqplots (Stempor and Ahringer, 2016) was used to make the ChIP-Seq heatmaps and intensity plots using Bigwig files. DiffBind package was used for principle component analysis and peak set interaction based on Bed file (Stark and Brown, 2011). Genomic track visualization were conducted using WashU Epigenome Browser (Zhou and Wang, 2012). For motif enrichment analysis, fasta sequence files were extracted based on Bed files using BEDtools (Quinlan and Hall, 2010) and then input into MEME Suite AME module (Bailey et al., 2015) using HOCOMOCO full v11 database (Kulakovskiy et al., 2018) for calculation. E value below 10-5 is considered as a significant enrichment.
CTSL Hi-ChIP data were processed using the HiC-Pro pipeline (Servant et al., 2015). Briefly, reads were aligned to hg19 reference genome using Bowtie2 (Langmead and Salzberg, 2012). After restriction site detection and 2nd round of alignment was performed. Validated pairs were filtered and distributed to the whole genome binned in 500kb resolution. Inter- and intra-chromosomal interactions were visualized using HiTC package (Servant et al., 2012) after ICE normalization. Differential inter- and intra-chromosomal interaction sites were called using HiCCompare package (Stansfield et al., 2018) using the cutoff of interaction frequency (IF) >50 and padj<0.05.
Assembly: hg19
Supplementary files format and content: BED, Iced matrix

source_name: Human breast cancer cell line

growth_protocol: HCC1954, HCC70, HCC2157 and T47D cells were cultured in RPMI-1640 medium with 10% FBS and 100U/ml Penicillin-Streptomycin. SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin. MCF7 cells were cultured in DMEM medium with 10% FBS and 100U/ml Penicillin-Streptomycin.

extract_protocol:
ChIP-seq: For histone modification ChIP-seq, 150 mm plates tissue culture plates were fixed in 1% formaldehyde (Electron Microscopy Sciences, 15714) containing fixing buffer (50 mM HEPESKOH pH7.5, 100 mM NaCl, 1 mM EDTA pH8 and 0.5 mM EGTA pH8) for 10 min at 37°C. For CTSL and GRHL2 ChIP-seq, 15 mM (ethylene glycol bis(succinimidyl succinate) (EGS) was diluted 1:10 in PBS and used to fix the cells for 30 min at RT, with the addition of 1% formaldehyde during the last 10 min. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M and further rocking the plates for 5 min. Cell monolayers were washed twice with ice-cold PBS and scrapped off the plate in 10 ml PBS, spun at 200g for 5 min, and flash frozen after removing the supernatant. Frozen pellets were resuspended in 1 ml of Cell Lysis Buffer (50 mM HEPES pH8, 140 mM NaCl, 1 mM EDTA pH8, 10 % glycerol, 0.5% NP-40, 0.25% Triton X-100 and PPI) and incubated for 10 min at 4°C with gentle rotation. Nuclei were then centrifuged at 1,700g for 5 min at 4°C. Pelleted nuclei were washed twice with 1 ml Wash Buffer (10 mM Tris-HCl pH8, 200 mM NaCl, 1mM EDTA pH8, 0.5 mM EGTA pH8 and PPI) and then resuspended in 1 ml of Shearing Buffer (10 mM Tris-HCl pH7.4, 1 mM EDTA pH8, 0.1% SDS, 1% Triton-X100, 0.1% Sodium Deoxycholate, 0.25% NLauroylsarcosine, 1 mM DTT and PPI) and sonicated in a Covaris E220 focused-ultrasonicator (peak intensity: 140, 5% duty cycle, 200 cycles per burst, 10-12 min) using 1 ml AFA fiber tubes. An equivalent of 5 x 106 cells was sonicated in each tube and used for each ChIP. Lysates were centrifuged for 15 min at 10,000g in a refrigerated centrifuge. Cleared supernatants were transferred to new tubes and NaCl was added to a final concentration of 150 mM. Samples were then incubated with Dynabeads Protein G (LifeTechnologies,10003D, 40 µl/ml of lysate) for 1 hour at 4°C, with constant rotation (pre-clearing). After magnetic separation of the beads, the appropriate primary antibody was added to each tube for an overnight immunoprecipitation, at 4°C, with gentle rotation. Antibody-bound cross-linked chromatin was precipitated with prewashed Dynabeads Protein G for 2 h at 4°C and with constant rotation. Beads were then washed sequentially with low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS), high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS), LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) and twice with 1X TE buffer. Each wash was performed for 5 min at 4°C with gentle rotation. DNA was eluted from the beads with 300 µl of 100 mM sodium bicarbonate and 1% SDS for 30 min at RT with constant shaking. Crosslinking was reversed overnight at 65°C and RNA and protein were then sequentially digested by adding 0.2 mg/ml RNase A for 30 min at 37°C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was extracted with 300 µl of phenol/chloroform/isoamyl-alcohol (Calbiochem, #516726) and centrifuged at 20,000g for 5 min at RT. DNA in the upper layer was then precipitated with 1 volume isopropanol, 1/3 volume of 2 M sodium perchlorate and 5 µl glycogen and centrifuged at 20,000g for 10 min at RT. Pelleted DNA was washed twice with 70% ethanol and resuspended in 20 µl low TE. For ATAC-seq: Fifty thousand cells were resuspended in 1ml of cold ATAC-seq resuspension buffer (RSB) (10mM Tris-HCl (pH 7.4), 10mM NaCl and 3mM MgCl2 in water). Cells were centrifuged at maximum speed for 10min in a prechilled (4 °C) fixed-angle centrifuge. After centrifugation, supernatant was carefully aspirated. Cell pellets were then resuspended in 50μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubated on ice for 3min. After lysis, 1ml of ATAC-seq RSB containing only 0.1% Tween-20 was added and the tubes were inverted to mix. Nuclei were then centrifuged for 5min at max speed in a prechilled fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50μl of transposition mix (25μl 2X TD buffer, 2.5μl transposase (100nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween20 and 5μl water46) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen MinElute columns.
ChIP-seq/Hi-ChIP: Libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) according to the manufacturer’s protocol. Library fragments were size-selected by PAGE within a 150kb and 700kb range. ATAC-seq: Libraries were amplified as previously described (Buenrostro et al., 2015).

treatment_protocol: Cells were seeded in 15 cm2 dishes. For treatements ,  0.1% DMSO, 0.1μg/ml doxycycline, 10 μM ML324 or 1 μM QC6352 were added the next day.

value: 10 microM ML324

tag: chip target

value: CTSL


title: dCas9-repressor MEF, induced, rep3

status: Public on Mar 23 2025

type: SRA

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: transcriptomic

data_processing:
counts.tsv
Assembly: mm10
Supplementary files format and content: counts.tsv

molecule: total RNA

organism: Mus musculus

source_name: MEF

growth_protocol: Cells were maintained in high glucose DMEM containing 10% tet-free FBS, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1x non-essential amino acids, 1 mM sodium pyruvate, and 400 mg/ml hygromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 10 ug of total RNA was further processed to remove the remaining DNA with TURBO DNase and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.
RNA-Seq, 150 bp paired-end

treatment_protocol: MEF dCas9-Activator cells were treated with 10 ng/ml doxycycline for 6 hrs, MEF dCas9-Repressor cells were treated with 100 ng/ml doxycycline for 24 hrs, and MEF dCas9-control cells were treated with 10 ng/ml doxycycline for 24 hrs.

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: inducible expression of dCas9-KM

tag: treatment

value: 100 ng/ml doxycycline, 24 hr


title: dCas9-repressor MEF, induced, rep2


title: SUM149_Control_CTSL_HiChIP

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: DMSO


title: SUM149_sh20_shKDM4C_ATACseq

value: 1 ug/ml Doxycycline


title: dCas9-repressor MEF, induced, rep1


title: SUM149_sh20_Control_ATACseq


title: SUM149_sh20_QC6352_ATACseq

value: 1 microM QC6352


title: dCas9-repressor MEF, uninduced, rep2

value: untreated


title: dCas9-repressor MEF, uninduced, rep1


title: dCas9-repressor MEF, uninduced, rep3


title: dCas9-control MEF, induced, rep3

value: inducible expression of dCas9-control

value: 10 ng/ml doxycycline, 24 hr


title: SUM149_sh17_ML324_ATACseq


title: SUM149_sh17_shKDM4C_ATACseq


title: SUM149_sh17_QC6352_ATACseq


title: dCas9-control MEF, induced, rep2


title: dCas9-control MEF, induced, rep1


title: HCC1954_sh20_QC6352_ATACseq


title: HCC1954_sh20_ML324_ATACseq


title: HCC1954_sh20_Control_ATACseq


title: dCas9-control MEF, uninduced, rep1


title: dCas9-control MEF, uninduced, rep3


title: SUM149_sh17_Control_ATACseq


title: HCC1954_sh20_shKDM4C_ATACseq


title: HCC1954_sh17_ML324_ATACseq


title: spleen, live allo + costimulation blockade, rep1

city: Chicago

first: Samantha

middle: L

last: Schroth

state: IL

address: 320 E Superior St

institute: Northwestern University Feinberg School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
spleens were collagenase D and DNAse I digested and subjected to independent CD45+ and pan DC magnetic enrichment and re-pooled at a 1:1 ratio per condition
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, single cells from splenic cell suspenion were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: spleen

value: Live allo (BALB/c) splenic cell + antiCD40L infusion


title: Barcode Amplicon Sample 1.

first: Songlei

last: Liu

address: 77 Avenue Louis Pasteur

institute: Harvard University

description:
Library name: Sample 1
PCR from cDNA

data_processing:
The demultiplexing, bacod processing, gene couting and aggregation were made using the cell Ranger software cellranger-6.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: TF (pBAN-TF-BC) and Super PiggyBac (SPB) Transposase (System Biosciences, PB210PA-1) expression vectors were mixed at a mass ration of 4:1 and transfected into hiPSCs using P3 Primary Cell 4D-Nucleofector X Kit L (Lonza, V4XP-3024) on a 4D-Nucleofector X Unit (Lonza, AAF-1002X) following manufacturer’s instructions. For the pooled TF screen, 600,000 cells were transfected with 5 µg of DNA and seeded into one well of a 6-well plate. Program CB150 was used for the nucleofections. 48 hours after nucleofection, 1 µg/mL of puromycin (Gibco, A1113803) or 50 µg/mL of zeocin (Gibco, R25001) was added to the culture for the selection of TF-integrated cells. Cells were passaged again when reaching 80% confluency.

extract_protocol:
Cells were harvested by first washing with PBS (- calcium, - magnesium) followed by dissociating cultures into single cell suspensions with Accutase (StemCell Technologies, 07920) for 10 minutes at 37°C, cultures were then quenched with DMEM/F12 (Gibco, 11320033) and subsequently centrifuged at 300g for 3 minutes. The cell pellet was rinsed with PBS (- calcium, - magnesium) and centrifuged again at 300g for 3 minutes prior to library prep and resuspended in PBS-/- supplemented with 0.04% w/v BSA.
scRNA-seq experiments were performed using 10x Genomics Chromium Single Cell 3' Reagent Kits v3 or v3.1 following the manufacturer’s instruction. 5000 single cells were calculated as targeted input for each sample. For the first iteration, 10% of stem cells were spiked in as undifferentiated control. For the second iteration, 5% stem cells and 5% MG3.1-SFC were spiked in as undifferentiated and initial differentiation control. The only modification made to the protocol was at the Sample Index PCR step, where 5 µL of the PCR mix was taken out and mixed with 0.5 µL 1000X SYBR Gold (Invitrogen, S11494) for a qPCR reaction. The optimal amplification cycle was determined as the cycle just before half maximum of the total signal. Final libraries were sequenced on NextSeq 500 or NovaSeq with a goal of at least 30,000 reads per cell.

treatment_protocol: For induction of TF expression, cells were seeded into mTeSR Plus media containing 0.5 µg/mL doxycycline (Sigma-Aldrich, D3072) and 10 µM Y-27632 ROCK inhibitor and were changed into media only containing doxycycline after 24 hours. Dox treatment was continued for 4 days.

value: iPSC


title: HCC1954_sh17_shKDM4C_ATACseq


title: Barcode Amplicon Sample 2.

description:
Library name: Sample 2
PCR from cDNA


title: Barcode Amplicon Sample 2

description:
Library name: Sample 2
PCR from cDNA

data_processing:
The demultiplexing, bacod processing, gene couting and aggregation were made using the cell Ranger software v3.0.2
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files


title: SUM149_sh20_ML324_ATACseq


title: HCC1954_sh17_QC6352_ATACseq


title: SUM149_GFP_H3_ML324_GFP_H3_ChIPseq

value: GFP


title: SUM149_GFP_H3_ML324_Ct_H3_ChIPseq

value: C-terminus H3


title: SUM149_GFP_H3_Control_GFP_H3_ChIPseq


title: Barcode Amplicon Sample 1

description:
Library name: Sample 1
PCR from cDNA


title: iNK cells,control,3

city: Beijing

first: Cai

last: Runze

address: Xueyuan Rd.,Haidian District

country: China

institute: Peking University Health Science Center

description: Library name: sample12

data_processing:
Fastqc v0.11.9
Htseq-count v2.0.2
Samtools v1.16.1
STAR v2.7.10
Trim Galore v0.6.10
Assembly: ensembl_92_homo_sapiens_grch38_toplevel
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: NK cells

extract_protocol:
Lyse the sample in TRIzol or lysis buffer, add chloroform (if using TRIzol), and centrifuge to separate phases.Transfer the RNA-containing aqueous phase, precipitate RNA with isopropanol, wash with ethanol, and resuspend in RNase-free water.
Convert extracted RNA into cDNA, fragment it, add adapters, and amplify to create a sequencing-ready library.

value: NK cells


title: iNK cells,control,2

description: Library name: sample11


title: iNK cells,control,1

description: Library name: sample10


title: HCC1954_sh17_Control_ATACseq


title: iNK cells,OE226,3

description: Library name: sample9


title: SUM149_GFP_H3_Control_Ct_H3_ChIPseq


title: iNK cells,OE226,2

description: Library name: sample8


title: dCas9-control MEF, uninduced, rep2


title: iNK cells,OE226,1

description: Library name: sample7


title: YT cells,control,3

description: Library name: sample6


title: SUM149_V5_H3_ML324_Ct_H3_ChIPseq

value: 10 microM ML324


title: SUM149_V5_H3_ML324_V5_H3_ChIPseq


title: SUM149_V5_H3_Control_V5_H3_ChIPseq


title: YT cells,control,2

description: Library name: sample5


title: SUM149_V5_H3_Control_Ct_H3_ChIPseq


title: SUM149_sgScramble_Control_CTSL_ChIPseq

value: CTSL


title: YT cells,control,1

description: Library name: sample4


title: SUM149_sgGRHL2_Control_CTSL_ChIPseq


title: YT cells,OE226,3

description: Library name: sample3


title: YT cells,OE226,2

description: Library name: sample2


title: SUM149_ML324_KDM4C_ChIPseq


title: SUM149_ML324_KDM4B_ChIPseq


title: YT cells,OE226,1

description: Library name: sample1


title: SUM149_ML324_KDM4A_ChIPseq


title: SUM149_Control_KDM4C_ChIPseq


title: SUM149_Control_KDM4B_ChIPseq


title: SUM149_Control_KDM4A_ChIPseq


title: HCC1954_Parental_Control_GRHL2_ChIPseq


title: 1080 3

city: Vancouver

first: Stuart

last: Turvey

state: BC

address: 938 W 28th Ave

country: Canada

institute: BCCHRI

description:
Library name: 1080 3
F131581_10803_AGATGAGG-AGAGACTC.bam

data_processing:
Sequencing was done on rRNA depleted RNA libraries using PE150 Illumina NovaSeq Sequencing, targeting 100M individual reads (50M read pairs/clusters) per sample
Sequenced reads were aligned to a reference sequence using Spliced Transcripts Alignment to a Reference aligner. E1 Assembly and expression were estimated using Cufflinks E2 through bioinformatics apps on Illumina BaseSpace.
Expression data was normalized to reads between samples using the edgeR package in R (R Foundation). Normalized counts were filtered to remove low counts using the filterByExpr function in edge. Principal component analysis (PCA) was done on log2 (normalized counts+0.25) in R using the PCA function. Differential expression analysis was accomplished using Limma. Differentially expressed genes were defined as those with adjusted p-value less than 0.05.
Assembly: hg38
Supplementary files format and content: .txt - rawcounts
Supplementary files format and content: .txt - filtered and normalized counts

source_name: T cells

growth_protocol: T cells were isolated from PBMCs of a healthy control.

extract_protocol:
Following sorting, the volume of Buffer RLT Plus was adjusted so that there was exactly 350 ml of Buffer RLT Plus to 100 ml of sorted sample volume.
RNA isolation was done according to the RNeasy Plus Mini Kit instructions (Qiagen).

treatment_protocol: To investigate the global transcriptome of the transduced HC primary T cells stably expressing EV, WT, or p.K360N variant. Cells were sorted based on GFP expression using BD FACS Aria (BD Biosciences) cell sorter directly into 500 ml of cold Buffer RLT Plus (Qiagen) supplemented with 2-Mercaptoethanol according to the Qiagen RNeasy Plus Mini Kit instructions.

value: T cells


title: 1080 2

description:
Library name: 1080 2
F131580_10802_GATGAGAC-CCGAAGAT.bam


title: scRNAseq 1

description: Library name: scRNAseq 1

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed using the BD Rhapsody Targeted Analysis Pipeline and Seven Bridges (www.sevenbridges.com) according to manufacturer’s recommendations. The R package Seurat was utilized for all downstream analysis. Scaling and clustering were performed on each pool of samples independently. Dimensionality reduction using PCA was done on the most variable genes, and UMAP was based on the first 20 PCs.
Cell identities were annotated manually, or via cell surface antibody sequencing (Ab-seq), to first identify major cell types (T cells, B cells, NK cells and Monocytes) and then defining subtypes (CD4+ T cells, CD8+ T cells, Double Positive T cells, and their subsequent Naïve and Memory subgroups). For differential gene expression analyses, we utilized the Seurat implementation of negative binomial test, assuming an underlying negative binomial distribution in RNA-Seq data while leveraging the UMI counts to remove technical noise.
Assembly: Homo Sapiens (GRCh38)
Supplementary files format and content: barcodes.tsv - cell barcodes; features.tsv - feature names; matrix.mtx - processed counts

source_name: PBMC

extract_protocol:
The BD Rhapsody Single Cell platform was used for extraction and library construction, which included the Rhapsody Enhanced Cartridge Reagent Kit (BD), the BD Rhapsody Cartridge Kit (BD), the Rhapsody cDNA Kit (BD), the Rhapsody WTA Amplification Kit (BD), the Human Single-Cell Multiplexing Kit (BD), used according to manufacturer’s recommendations and protocols. Cells from each donor werelabelled with sample tags and a panel of BD® AbSeq Ab-oligos (BD), washed with stain buffer, and pooled together in cold sample buffer to obtain ~60,000 cells in 620 ul for each of the pooled unstimulated and stimulated samples. Two nanowell cartridges were primed and subsequently loaded with the pooled samples.
Libraries for whole transcriptome and AbSeq analysis were prepared by following the BD Rhapsody System (TCR/BCR Full Length, mRNA WTA, BD® AbSeq, and Sample Tag Library Preparation) Protocol. Quality control was performed using Agilent DNA High Sensitivity Kit (Agilent Technologies) and the Agilent 2100 Bioanalyzer (Agilent Technologies) on the intermediate and final sequencing libraries, including estimating the concentration of each sample, measuring the average fragment size of the libraries, and following sequencing recommendations. Libraries were diluted to 350-650 picomolar range per sample and sequenced using Illumina NovaSeq 150bp PE sequencing targeting 8,000M individual reads (4,000M read-pairs) with PhiX spike-in of 20%.

treatment_protocol: Whole transcriptome analysis (WTA) was conducted on peripheral blood mononuclear cells (PBMCs) from the patient and three age-matched healthy controls. Briefly, thawed PBMCs were rested overnight and then stimulated with ImmunoCult™ Human CD3/CD28 T Cell Activator (STEMCELL Technologies) or left untreated for 16 hours.

value: PBMC


title: scRNAseq 2

description: Library name: scRNAseq 3


title: 1080 1

description:
Library name: 1080 1
F131579_10801_ATAGCGGT-TATCGCGA.bam


title: WT3

description:
Library name: WT3
F131578_WT3_AACAACCG-AACGTAGC.bam


title: HCC1954_Parental_Control_INPUT_ChIPseq

value: Input


title: SUM149_Parental_ML324_GRHL2_ChIPseq


title: WT1

description:
Library name: WT1
F131576_WT1_ATACTCCG-AACGCCTT.bam


title: SUM149_Parental_Control_GRHL2_ChIPseq

value: DMSO


title: EV3

description:
Library name: EV3
F131575_EV3_TACCACAG-ACGGACTT.bam


title: EV2

description:
Library name: EV2
F131574_EV2_ATGGTCCA-TGTGGCTT.bam


title: SUM149_Resistant_ML324_CTSL_ChIPseq


title: EV1

description:
Library name: EV1
F131573_EV1_TAATGCCG-ACCATAGG.bam


title: SUM149_Parental_ML324_CTSL_ChIPseq


title: P_1080_3

description:
Library name: P_1080_3
F128492_4_lanes_dupsFlagged.bam

source_name: Fibroblasts

growth_protocol: Fibroblasts were grown from patient and healthy control lung tissue biopsy before lenti virus transduction

treatment_protocol: To investigate the global transcriptome of the transduced patient and HC primary pulmonary fibroblasts stably expressing EV, WT, or p.K360N variant, 150,000 GFP+ cells were sorted based on GFP expression using BD FACS Aria (BD Biosciences) cell sorter directly into 500 ml of cold Buffer RLT Plus (Qiagen) supplemented with 2-Mercaptoethanol according to the Qiagen RNeasy Plus Mini Kit instructions.

value: Fibroblasts

tag: disease

value: patient


title: SUM149_Resistant_Control_CTSL_ChIPseq


title: SUM149_Parental_Control_CTSL_ChIPseq


title: P_1080_2

description:
Library name: P_1080_2
F128491_4_lanes_dupsFlagged.bam


title: P_WT_3

description:
Library name: P_WT_3
F128489_4_lanes_dupsFlagged.bam


title: SUM149_Parental_ML324_INPUT_ChIPseq


title: T47D_sh177_Control_K36me3_1_ChIPseq


title: SUM149_Parental_Control_INPUT_ChIPseq


title: P_1080_1

description:
Library name: P_1080_1
F128490_4_lanes_dupsFlagged.bam


title: HCC1954_Parental_Control_CTSL_ChIPseq


title: P_WT_2

description:
Library name: P_WT_2
F128488_4_lanes_dupsFlagged.bam


title: P_WT_1

description:
Library name: P_WT_1
F128487_4_lanes_dupsFlagged.bam


title: WT2

description:
Library name: WT2
F131577_WT2_TAGCGTCT-GCAGAAGA.bam


title: T47D_sh17_Control_INPUT_ChIPseq


title: T47D_sh177_Control_K9me3_1_ChIPseq


title: T47D_sh17_Control_KDM4C_ChIPseq


title: P_EV_3

description:
Library name: P_EV_3
F128486_4_lanes_dupsFlagged.bam


title: HCC2157_Parental_Untreated_KDM4C_ChIPseq

value: Untreated


title: P_EV_2

description:
Library name: P_EV_2
F128485_4_lanes_dupsFlagged.bam


title: MCF7_Parental_Untreated_H3K9me3_ChIPseq


title: HC_1080_3

description:
Library name: HC_1080_3
F128483_4_lanes_dupsFlagged.bam

value: healthy control


title: HC_1080_2

description:
Library name: HC_1080_2
F128482_4_lanes_dupsFlagged.bam


title: HCC70_Parental_Untreated_Input_ChIPseq


title: HC_WT_2

description:
Library name: HC_WT_2
F128479_4_lanes_dupsFlagged.bam


title: MCF7_Parental_Untreated_KDM4C_ChIPseq


title: HC_WT_1

description:
Library name: HC_WT_1
F128478_4_lanes_dupsFlagged.bam


title: SUM149_Parental_Control_H3K27me3_ChIPseq


title: HCC70_Parental_Untreated_KDM4C_ChIPseq


title: HC_EV_3

description:
Library name: HC_EV_3
F128477_4_lanes_dupsFlagged.bam


title: SUM149_sh17_Control_KDM4C_4_ChIPseq


title: HC_EV_1

description:
Library name: HC_EV_1
F128475_4_lanes_dupsFlagged.bam


title: RCC_PSMA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: RCC_PSMA_20241122

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 43+50-base paired-end mode.
Raw sequencing data were converted to matrices of expression using Space Ranger (version spaceranger-3.1.1, 10X Genomics).
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.zip: zipped file of Space Ranger output folder "filtered_feature_bc_matrix" in each observation size folder
Supplementary files format and content: raw_feature_bc_matrix.zip: zipped file of Space Ranger output folder "raw_feature_bc_matrix" in each observation size folder
Supplementary files format and content: spatial.zip:  zipped file of Space Ranger output folder "spatial" in each observation size folder
Library strategy: Spatial Transcriptomics

source_name: Kidney cancer

extract_protocol:
Human Kidney cancer tissue FFPE slice gene expression were detected by 10x Visium HD Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared using Visium HD Reagent Kit (#PN-1000668, 10x Genomics) following the manufacturer’s protocol.

value: Kidney cancer

value: Renal Cell Carcinoma


title: SUM149_sh17_Control_KDM4C_1_ChIPseq


title: SUM149_sh17_Control_KDM4C_3_ChIPseq


title: P_EV_1

description:
Library name: P_EV_1
F128484_4_lanes_dupsFlagged.bam


title: CITE-seq, PBMC, M42, week6, ADT

city: Toulouse

first: Anne

last: Montfort

address: 2 avenue Hubert Curien

country: France

institute: INSERM

description:
Library name: M42_S6_ADT
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
CITE-seq data were aligned to the human transcriptome using Cell Ranger version 7.1
Assembly: 2020-A
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.tsv.gz
Library strategy: CITE-seq

molecule: protein

extract_protocol:
Droplet-based single-cell libraries were generated using Chromium Instruments and Chromium Single Cell 3′ Library & Gel Bead Kit v3. 15 000 cells injected per sample
Chromium Single Cell 3′ Library & Gel Bead Kit v3 was used

treatment_protocol: PBMC from patients before and 6 weeks after nivolumab+ipilimumab therapy.

value: Immune cells

value: nivolumab + ipilimumab

tag: library type

value: ADT

tag: adt

value: TotalSeq-A0154 anti-human CD27, TotalSeq-A0034 anti-human CD3, TotalSeq-A0080 anti-human CD8, TotalSeq-A0081 anti-human CD14, TotalSeq-A0083 anti-human CD16, TotalSeq-A0136 anti-human IgM, TotalSeq-A0045 anti-human CD4, TotalSeq-A0050 anti-human CD19, TotalSeq-A0063 anti-human CD45RA, TotalSeq-A0159 anti-human HLA-DR, TotalSeq-A0147 anti-human CD62L


title: SUM149_sh17_ML324_H3K4me3_ChIPseq


title: SUM149_sh17_Control_KDM4C_2_ChIPseq


title: MCF7_Parental_Untreated_H3K36me3_ChIPseq


title: SUM149_sh17_shKDM4C_H3K4me3_ChIPseq

value: 0.1 ug/ml Doxycycline


title: CITE-seq, PBMC, M42, week0, ADT

description:
Library name: M42_S1_ADT
Antibody-derived oligonucleotide (ADT)

value: Pre-treatment


title: HC_1080_1

description:
Library name: HC_1080_1
F128481_4_lanes_dupsFlagged.bam


title: SUM149_sh17_Control_H3K4me3_ChIPseq


title: CITE-seq, PBMC, M42, week0, GEX

description:
Library name: M42_S1_GEX
PolyA RNA

molecule: polyA RNA

value: GEX


title: SUM149_sh17_ML324_H3K36me3_4_ChIPseq

value: 10 microM ML324


title: CITE-seq, PBMC, M42, week6, GEX

description:
Library name: M42_S6_GEX
PolyA RNA

value: PBMC


title: HC_WT_3

description:
Library name: HC_WT_3
F128480_4_lanes_dupsFlagged.bam


title: CITE-seq, PBMC, M26, week6, ADT

description:
Library name: M26_S6_ADT
Antibody-derived oligonucleotide (ADT)


title: CITE-seq, PBMC, M26, week6, GEX

description:
Library name: M26_S6_GEX
PolyA RNA


title: CITE-seq, PBMC, M26, week0, ADT

description:
Library name: M26_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: CITE-seq, PBMC, M26, week0, GEX

description:
Library name: M26_S1_GEX
PolyA RNA


title: CITE-seq, PBMC, M17, week6, ADT

description:
Library name: M17_S6_ADT
Antibody-derived oligonucleotide (ADT)


title: HC_EV_2

description:
Library name: HC_EV_2
F128476_4_lanes_dupsFlagged.bam


title: BL WT 7

city: Birmingham

first: Abolfazl

last: Zarjou

state: AL

address: 618 Zeigler Research Building, 703 South 19th Street

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: Sample 7

data_processing:
Basecalls were performed using bcl2fastq version 2.18.0.12
Sequence reads were aligned to reference genome using STAR version 2.7.7a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from STAR alignment BAM files using HTSEq-count version 0.11.3 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm38.p6.ReleaseM25
Supplementary files format and content: tab delimited Excel file containing raw gene counts for each gene in each sample

source_name: FtHfl/fl (wild-type)

extract_protocol: Total RNA was isolated from kidney using Trizol from wild-type (FtHfl/fl) n=4 and myeloid specific FtH deficient (FtHΔ/Δ) n=4 mice under quiescent conditions.

value: Kidney

value: FtHfl/fl (wild-type)

value: Quiescent


title: BL WT 5

description: Library name: Sample 5


title: CITE-seq, PBMC, M17, week6, GEX

description:
Library name: M17_S6_GEX
PolyA RNA


title: CITE-seq, PBMC, M17, week0, GEX

description:
Library name: M17_S1_GEX
PolyA RNA


title: CITE-seq, PBMC, M17, week0, ADT

description:
Library name: M17_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: BL WT 8

description: Library name: Sample 8


title: SUM149_sh17_ML324_H3K36me3_1_ChIPseq


title: BL KO 4

description: Library name: Sample 4

source_name: FtHΔ/Δ (myeloid-specific FtH-deficient)

value: FtH-/- (myeloid-specific FtH-deficient)


title: SUM149_sh17_shKDM4C_H3K36me3_3_ChIPseq


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 17

type: genomic

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description: No biochemical recurrence

hyb_protocol: Genomic DNA of ~250 ng was bisulfite converted using Zymo EZ-96 DNA Methylation kit (Zymo Research, CA, USA) and restored with Illumina Infinium HD FFPE DNA Restore kit (Illumina, CA, USA). Samples were then processed on Illumina Human Methylation EPIC version 2.0 BeadChip (Illumina, CA, USA) following the Illumina Infinium HD Methylation Assay (Illumina, CA, USA).

scan_protocol: Arrays were imaged using BeadArray reader (HiScan) and standard Illumina scanner setting

data_processing: The IDAT files were processed using the minfi package as part of a cross-package workflow in R Studio. The probes in the array were annotated using the annotation IlluminaHumanMethylationEPICv2anno.20a1.hg38 file and IlluminaHumanMethylationEPICv2manifest manifest file. The RnBeads package was used to check the data quality. The mean detection P-value was calculated for each sample, and those samples with P-values > 0.05 were excluded from the analysis. Samples with reliable signals (P-value < 0.05) were further filtered to exclude probes overlapping with single nucleotide polymorphisms (SNPs) identified by Pidsley et al. (2016) . After this, the functional normalisation method from the minfi package was used to minimise technical variation. This was followed by retaining only those probes with a mean detection P-value < 0.05 across all samples. Probes with SNPs at the CpG interrogation site or single nucleotide extension were removed using the dropLociWithSnps function in minfi, along with those showing cross-hybridization as reported by Pidsley et al. (2016). Beta values were calculated for each CpG probe that was retained after the filtering steps for each sample.

label: Cy3 and Cy5

source_name: FFPE radical prostatectomy

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted using a modified protocol of the QIAamp DNA FFPE Kit (Qiagen, Hilden, Germany), in conjunction with a supplementary deparaffinization solution protocol.

value: FFPE radical prostatectomy

tag: disease state

value: Localised prostate cancer

tag: tumour gleason grade

tag: tumour stage

value: pT2 pNx

tag: age of tissue (years)


title: BL KO 3

description: Library name: Sample 3


title: CITE-seq, PBMC, M16, week6, ADT

description:
Library name: M16_S6_ADT
Antibody-derived oligonucleotide (ADT)


title: BL KO 1

description: Library name: Sample 1


title: BL KO 2

description: Library name: Sample 2


title: CITE-seq, PBMC, M16, week0, GEX

description:
Library name: M16_S1_GEX
PolyA RNA


title: CITE-seq, PBMC, M16, week0, ADT

description:
Library name: M16_S1_ADT
Antibody-derived oligonucleotide (ADT)


title: CITE-seq, PBMC, M16, week6, GEX

description:
Library name: M16_S6_GEX
PolyA RNA


title: SUM149_sh17_Control_H3K36me3_5_ChIPseq

value: DMSO


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 17

description: No biochemical recurrence

data_processing:
RNA-Sequencing reads were evaluated for quality using FastQC v0.12.1 and summarised with the MultiQC v1.12 tool. Trim Galore v0.6.10 was used to remove adapter sequences and filter out low-quality reads. The trimming was performed with a Phred quality score threshold of 30 and the default settings, which include adapter auto-detection. The FastQ Screen v0.15.3 tool was utilised to analyse overrepresented sequences and identify potential contamination in the trimmed reads by aligning the reads to a set of reference genomes.
The trimmed reads were then aligned to the following human ribosomal (rRNA) reference sequences: NR_023363, NR_003285, NR_003286 and NR_003287, using Bowtie2 v2.5.1 aligner to determine the proportion of reads mapped to rRNA, allowing for the assessment of rRNA depletion.
The reads were subsequently mapped to the human genome using STAR aligner v2.7.11b. While performing STAR alignment, the Ensembl Homo sapiens GRCh37 reference genome (with version 87 annotation) was used with default settings. STAR alignment generated SAM files, which were converted into BAM files and sorted using Samtools v1.19.2.
Gene counts for each gene ID were obtained using featureCounts v2.0.6 with BAM files as the input. The featureCounts analysis was conducted with default settings using the Ensembl Homo sapiens GRCh37 version 87 annotation file. Subsequently, genes with very low counts were excluded by retaining only genes with Counts Per Million (CPM) > 0.5 in at least nine samples (i.e., 50% of the samples) and then count values were normalised to Transcripts Per Million (TPM).
The R package biomaRt v2.54.1 was used to retrieve gene names and gene biotypes, using the hsapiens_gene_ensembl database (accessed via the Ensembl GRCh37, URL: grch37.ensembl.org). Common protein-coding and non-coding genes were identified between replicates. Spearman correlation analyses were conducted using log2(TPM + 1) values.
Assembly: Ensembl Homo sapiens GRCh37 reference genome (with version 87 annotation)
Supplementary files format and content: Comma-separated values (CSV) include TPM values for each sample post filtering

extract_protocol:
Total RNA was extracted with Qiagen RNeasy FFPE Kit (Qiagen, Hilden, Germany), following a modified version of the manufacturer's protocol.
TruSeq stranded total RNA libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, CA, USA) and ribosomal RNA (rRNA) was depleted using the Ribo-Zero Gold kit (Illumina, CA, USA) according to the manufacturer’s protocol. Quality of the libraries were checked on an Illumina iSeq flow cell (Illumina, CA, USA) and the sequencing was performed on two flow cell lanes of an Illumina NovaSeq (Illumina, CA, USA) generating 150 bp paired-end reads.

tag: tumour gleason_grade

tag: age of_tissue_(years)


title: SUM149_sh17_shKDM4C_H3K36me3_1_ChIPseq


title: SUM149_sh17_shKDM4C_H3K36me3_2_ChIPseq


title: BL WT 6

description: Library name: Sample 6


title: SUM149_sh17_ML324_H3K36me3_2_ChIPseq


title: SUM149_sh17_ML324_H3K36me3_3_ChIPseq


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 14

description: No biochemical recurrence


title: PER_GD21_Triz_18-22_60b

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

institute: Inserm U1085-Irset

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Gévezé, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the rat reference transcriptome from the UCSC website (release rn6, downloaded August 2020) using BWA version 0.7.4.4 with the parameter “−l 24”
Assembly: rn6
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,484 genes detected.

organism: Rattus norvegicus

source_name: Triticonazole_Gestational Day 21

growth_protocol: Animals were housed in pairs (until GD17) or individually (GD17-21) under standard conditions with 12 h light/dark cycles in ScanTainers (Ventilated Cabinets from SCANBUR, Karlslunde, Denmark) with 50–60 air changes per hour at 22 °C ± 10 and humidity kept at 55% ± 5. High Temperature polysulfone cages with wood chip bedding, nesting material and a wooden shelter (Tapvei, Denmark). Animals were fed Altromin 1314 (Altromin GmbH, Lage, Germany, soy and alfalfa-free) and tap water was freely available in polysulfone bottles (84-ACBT0702SU Tecniplast, VA, Italy).

extract_protocol:
Dams were exposed 1 h ± 15 min before decapitation under CO2/O2-anesthesia on GD17 or 21. For gene expression analyses, the perineum including the genital tubercle (GT) was more finely dissected and placed in RNAlater. Total RNA was extracted (n = 11-12 samples/group) using an RNeasy Micro Kit (Qiagen, Germany) according to manufacturer’s instructions, including on-column DNase I digestion.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

treatment_protocol: Exposure was initiated at GD7 and continued until necropsy on GD17 or 21. Rats were weighed and gavaged each morning with vehicle (corn oil) or triticonazole (450 mg/kg bw/day) with a dosing volume of 2 ml/kg bw.

tag: strain

value: Perineum

tag: age

value: Gestational Day 21

value: Triticonazole

value: wildtype


title: SUM149_sh17_Control_H3K36me3_4_ChIPseq

tag: chip target


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 16

description: No biochemical recurrence

value: pT3a pN0


title: PER_GD21_Triz_18-22_60a


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 15

description: Biochemical recurrence


title: Prostate tumour Biochemical recurrence EPIC V2, Patient 13, Replicate 1

description: Biochemical recurrence


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 11

description: No biochemical recurrence


title: PER_GD21_Triz_18-22_59b


title: PER_GD21_Triz_18-22_59c


title: SUM149_sh17_Control_H3K36me3_2_ChIPseq

tag: cell line


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 14, Replicate 2

description: No biochemical recurrence


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 16

description: No biochemical recurrence


title: PER_GD21_Triz_18-22_58c


title: SUM149_sh17_Control_H3K36me3_1_ChIPseq


title: PER_GD21_Triz_18-22_57b


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 13

description: Biochemical recurrence


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 10, Replicate 1

description: No biochemical recurrence


title: SUM149_sh17_ML324_H3K9me3_2_ChIPseq


title: SUM149_sh17_ML324_H3K9me3_3_ChIPseq


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 9

description: No biochemical recurrence

value: pT2 pN0


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 14, Repicate 1

description: No biochemical recurrence


title: Prostate tumour Biochemical recurrence EPIC V2, Patient 13, Replicate 2

description: Biochemical recurrence


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 12

description: No biochemical recurrence


title: PER_GD21_Triz_18-22_20b


title: SUM149_sh17_Control_H3K36me3_3_ChIPseq


title: PER_GD21_Triz_18-22_19b


title: SUM149_sh17_shKDM4C_H3K9me3_3_ChIPseq

value: 0.1 microgram/ml Doxycycline


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 11

description: No biochemical recurrence


title: SUM149_sh17_ML324_H3K9me3_1_ChIPseq

value: 10 microM ML324


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 10

description: No biochemical recurrence


title: PER_GD21_Triz_18-22_19a


title: SUM149_sh17_shKDM4C_H3K9me3_2_ChIPseq


title: Prostate tumour Biochemical Persistence EPIC V2, Patient 1

description: Biochemical persistence


title: Prostate tumour No biochemical recurrence EPIC V2, Patient 10, Replicate 2

description: No biochemical recurrence


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 9

description: No biochemical recurrence


title: SUM149_sh17_shKDM4C_H3K9me3_1_ChIPseq


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 8

description: Biochemical recurrence

value: pT2c  pNx


title: N1E-115 cells, Day 0_3

city: Hachioji

first: Hideji

last: Yako

state: Tokyo

address: 1432-1, Horinouchi

institute: Tokyo University of Farmacy and Life Science

description: Library name: N1E-115 cells, Day 0_3

data_processing:
The paired-end 42 bp or paired-end 150 (full transcript assays, PE42 or PE150) or single-end 75 bp (DGE assays, SE75) sequencing reads generated by Illumina sequencing are mapped to the genome using the STAR algorithm with default settings. Alignment information for each read is stored in the BAM format. nfcore/rnaseq pipeline is applied to perform the alignment.
The number of fragments overlapping predefined genomic features of interest (e.g. genes) are counted. For full transcript assays: only read pairs that have both ends aligned are counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded.
Assembly: mm10
Supplementary files format and content: Raw count file for each sample

source_name: N1E-115 cells

extract_protocol:
Total RNAs were prepared using ISOGEN (NIPPON GENE).
RNA libraries for RNA-seq were prepared using  NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit,, following the manufacturer’s instructions.

tag: time

value: Day 0

value: N1E-115 cells

tag: cell type

value: Neuroblast

value: Wyld type

value: no treatment


title: PER_GD21_Triz_18-22_18b

tag: treatment

tag: genotype


title: N1E-115 cells, Day 0_2

description: Library name: N1E-115 cells, Day 0_2


title: SUM149_sh17_Control_H3K9me3_5_ChIPseq


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 7

description: Biochemical recurrence

tag: tissue

value: FFPE radical prostatectomy

value: Localised prostate cancer


title: N1E-115 cells, Day 0_1

description: Library name: N1E-115 cells, Day 0_1


title: PER_GD21_Triz_18-22_17a


title: Prostate tumour Biochemical recurrence EPIC V2, Patient 7

description: Biochemical recurrence

value: pT2 pNx


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 6

description: Biochemical recurrence


title: SUM149_sh17_Control_H3K9me3_3_ChIPseq

value: DMSO


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 5

description: Biochemical recurrence


title: SUM149_sh17_Control_H3K9me3_1_ChIPseq


title: PER_GD21_Ctrl_18-22_28c

source_name: Control_Gestational Day 21

value: Perineum

value: Gestational Day 21

value: Control


title: SUM149_sh17_Control_H3K9me3_2_ChIPseq


title: Prostate tumour No biochemical recurrence RNA-seq, Patient 3

description: No biochemical recurrence


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 4

description: Biochemical recurrence

value: pT3a pN0


title: PER_GD21_Ctrl_18-22_27c

value: wildtype


title: PER_GD21_Triz_18-22_18a

value: Triticonazole


title: Csf1rfl/fl brain macrophages and vascular cells

city: Zurich

first: Hannah

middle: Jade

last: Van Hove

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description: Library name: Control

data_processing:
The libraries were sequenced on a NovaSeq sequencer in line with 10x Genomics recommendations (paired-end reads) with a depth of 50,000 reads per cell. Cell Ranger software (10x Genomics, v.3.1.0) was used to demultiplex, process raw data, and align the reads to the GENCODE reference build GRCm38.p6 Release M23, followed by summarizing the unique molecular identifier (UMI) counts. A filtered gene-cell count matrix was generated by Cell Ranger’s built-in cell-calling algorithms.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Whole Brain

extract_protocol:
All methods are listed in the associated manuscript.
The quality of the single-cell suspension was assessed using a hemocytometer under a Leica DM IL LED Fluo microscope, and cell quantity was evaluated with an automated cell counter (LUNA-FX7, Logos). Cells were loaded into the 10x Genomics Chromium platform, and library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent kits v3.1 protocol).

value: Whole Brain

value: mural cells (MCs) and fibroblasts (FBs) (CD13+ and/or CD140a+O4- cells), endothelial cells (ECs) (CD31+), astrocytes (AC) (ACSA-2+), BAMs (CD11bhiF4/80+) and microglia (CD11b+F4/80hi)


title: Mrc1Cre:Csf1rfl/fl brain macrophages and vascular cells

description: Library name: Mutant


title: SUM149_sh17_Control_Input_3_ChIPseq

value: Input


title: PER_GD21_Ctrl_18-22_25c


title: Prostate tumour Biochemical recurrence RNA-seq, Patient 2

description: Biochemical recurrence

value: pT3b pNx


title: HCC1954_sh17_ML324_H3K4me3_ChIPseq

value: 10 microM ML324


title: PER_GD21_Ctrl_18-22_25b


title: Prostate tumour Biochemical persistence RNA-seq, Patient 1

description: Biochemical persistence


title: K1

city: changsha

first: Cheng

last: Xing

state: Hunan Province

address: Department of Hematology, the Second Xiangya Hospital, Central South University,

department: Department of Hematology

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: murine bone marrow

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: murine bone marrow

value: heterozygous knockout


title: SUM149_sh17_Control_H3K9me3_4_ChIPseq

data_processing:
ChIP-seq and ATAC-seq data processing were based on chips pipeline (Qiu et al., 2021; Taing et al., 2021). Peak calling was performed using MACS2 v2.1.2 with FDR<0.01 as the cutoff (Feng et al., 2012).
Reads were aligned to hg19 genome using BWA-MEM aligner (Li, 2013).
Seqplots (Stempor and Ahringer, 2016) was used to make the ChIP-Seq heatmaps and intensity plots using Bigwig files. DiffBind package was used for principle component analysis and peak set interaction based on Bed file (Stark and Brown, 2011). Genomic track visualization were conducted using WashU Epigenome Browser (Zhou and Wang, 2012). For motif enrichment analysis, fasta sequence files were extracted based on Bed files using BEDtools (Quinlan and Hall, 2010) and then input into MEME Suite AME module (Bailey et al., 2015) using HOCOMOCO full v11 database (Kulakovskiy et al., 2018) for calculation. E value below 10-5 is considered as a significant enrichment.
CTSL Hi-ChIP data were processed using the HiC-Pro pipeline (Servant et al., 2015). Briefly, reads were aligned to hg19 reference genome using Bowtie2 (Langmead and Salzberg, 2012). After restriction site detection and 2nd round of alignment was performed. Validated pairs were filtered and distributed to the whole genome binned in 500kb resolution. Inter- and intra-chromosomal interactions were visualized using HiTC package (Servant et al., 2012) after ICE normalization. Differential inter- and intra-chromosomal interaction sites were called using HiCCompare package (Stansfield et al., 2018) using the cutoff of interaction frequency (IF) >50 and padj<0.05.
Assembly: hg19
Supplementary files format and content: BED, Iced matrix


title: PER_GD21_Ctrl_18-22_28b


title: HCC1954_QC6352_rep2_RNAseq

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Briefly, fastq files were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out. The gene-level counts from all studies were then normalized using TMM with edgeR  (Robinson et al., 2010). Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)] were used for analysis. For samples sequenced on different days, batch correction was applied using removeBatchEffect function from limma package (Smyth, 2005).
Assembly: hg19
Supplementary files format and content: Matrix table (in .csv format) with raw gene counts for every gene and every sample

source_name: Breast Cancer

growth_protocol: HCC1954 and HCC1806 cells were cultured in RPMI-1640 medium with 10% FBS and 100U/ml Penicillin-Streptomycin. SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin.  HDQP1 cells were cultured in DME with 10% FBS and 100U/ml Penicillin-Streptomycin.

extract_protocol:
Total RNA were extracted following manufacturer's protocol pf Qiagen Rneasy Mini Kit. (Qiagen, #74106)
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

treatment_protocol: Cells were seeded in six well plates and treatment of 0.1% DMSO, 0.1μg/ml doxycycline, 10 μM ML324 or 1 μM QC6352 were added the next day. Cells were treated for 5 days until RNA collection.

value: Breast Cancer

value: Human breast cancer epithelial cell

value: Dox-inducible shKDM4C


title: HCC1954_sh17_shKDM4C_H3K4me3_ChIPseq

source_name: Human breast cancer cell line

extract_protocol:
ChIP-seq: For histone modification ChIP-seq, 150 mm plates tissue culture plates were fixed in 1% formaldehyde (Electron Microscopy Sciences, 15714) containing fixing buffer (50 mM HEPESKOH pH7.5, 100 mM NaCl, 1 mM EDTA pH8 and 0.5 mM EGTA pH8) for 10 min at 37°C. For CTSL and GRHL2 ChIP-seq, 15 mM (ethylene glycol bis(succinimidyl succinate) (EGS) was diluted 1:10 in PBS and used to fix the cells for 30 min at RT, with the addition of 1% formaldehyde during the last 10 min. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M and further rocking the plates for 5 min. Cell monolayers were washed twice with ice-cold PBS and scrapped off the plate in 10 ml PBS, spun at 200g for 5 min, and flash frozen after removing the supernatant. Frozen pellets were resuspended in 1 ml of Cell Lysis Buffer (50 mM HEPES pH8, 140 mM NaCl, 1 mM EDTA pH8, 10 % glycerol, 0.5% NP-40, 0.25% Triton X-100 and PPI) and incubated for 10 min at 4°C with gentle rotation. Nuclei were then centrifuged at 1,700g for 5 min at 4°C. Pelleted nuclei were washed twice with 1 ml Wash Buffer (10 mM Tris-HCl pH8, 200 mM NaCl, 1mM EDTA pH8, 0.5 mM EGTA pH8 and PPI) and then resuspended in 1 ml of Shearing Buffer (10 mM Tris-HCl pH7.4, 1 mM EDTA pH8, 0.1% SDS, 1% Triton-X100, 0.1% Sodium Deoxycholate, 0.25% NLauroylsarcosine, 1 mM DTT and PPI) and sonicated in a Covaris E220 focused-ultrasonicator (peak intensity: 140, 5% duty cycle, 200 cycles per burst, 10-12 min) using 1 ml AFA fiber tubes. An equivalent of 5 x 106 cells was sonicated in each tube and used for each ChIP. Lysates were centrifuged for 15 min at 10,000g in a refrigerated centrifuge. Cleared supernatants were transferred to new tubes and NaCl was added to a final concentration of 150 mM. Samples were then incubated with Dynabeads Protein G (LifeTechnologies,10003D, 40 µl/ml of lysate) for 1 hour at 4°C, with constant rotation (pre-clearing). After magnetic separation of the beads, the appropriate primary antibody was added to each tube for an overnight immunoprecipitation, at 4°C, with gentle rotation. Antibody-bound cross-linked chromatin was precipitated with prewashed Dynabeads Protein G for 2 h at 4°C and with constant rotation. Beads were then washed sequentially with low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS), high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS), LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) and twice with 1X TE buffer. Each wash was performed for 5 min at 4°C with gentle rotation. DNA was eluted from the beads with 300 µl of 100 mM sodium bicarbonate and 1% SDS for 30 min at RT with constant shaking. Crosslinking was reversed overnight at 65°C and RNA and protein were then sequentially digested by adding 0.2 mg/ml RNase A for 30 min at 37°C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was extracted with 300 µl of phenol/chloroform/isoamyl-alcohol (Calbiochem, #516726) and centrifuged at 20,000g for 5 min at RT. DNA in the upper layer was then precipitated with 1 volume isopropanol, 1/3 volume of 2 M sodium perchlorate and 5 µl glycogen and centrifuged at 20,000g for 10 min at RT. Pelleted DNA was washed twice with 70% ethanol and resuspended in 20 µl low TE. For ATAC-seq: Fifty thousand cells were resuspended in 1ml of cold ATAC-seq resuspension buffer (RSB) (10mM Tris-HCl (pH 7.4), 10mM NaCl and 3mM MgCl2 in water). Cells were centrifuged at maximum speed for 10min in a prechilled (4 °C) fixed-angle centrifuge. After centrifugation, supernatant was carefully aspirated. Cell pellets were then resuspended in 50μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubated on ice for 3min. After lysis, 1ml of ATAC-seq RSB containing only 0.1% Tween-20 was added and the tubes were inverted to mix. Nuclei were then centrifuged for 5min at max speed in a prechilled fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50μl of transposition mix (25μl 2X TD buffer, 2.5μl transposase (100nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween20 and 5μl water46) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen MinElute columns.
ChIP-seq/Hi-ChIP: Libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) according to the manufacturer’s protocol. Library fragments were size-selected by PAGE within a 150kb and 700kb range. ATAC-seq: Libraries were amplified as previously described (Buenrostro et al., 2015).

value: 0.1 microgram/ml Doxycycline


title: PER_GD21_Ctrl_18-22_4a

value: Perineum


title: HCC1954_QC6352_rep1_RNAseq


title: H1

institute: the Second Xiangya Hospital, Central South University,

value: homozygous knockout mice for Fabp4


title: HCC1954_sh17_Control_H3K4me3_ChIPseq

value: DMSO


title: W1

value: wild type


title: HCC1954_Vehicle_rep2_RNAseq


title: PER_GD21_Ctrl_18-22_3a

value: Gestational Day 21

value: Control

value: wildtype


title: HCC1954_sh17_Control_KDM4C_2_ChIPseq


title: PER_GD21_Ctrl_18-22_26c


title: S3

city: Shanghai

first: Xiya

last: Ding

state: Shanghai

address: 227 Chongqing South Road

department: Departments of Neonatology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.

data_processing:
The main steps of applying Seqtk for filtering are as follows: removing the connector sequences contained in reads; Remove bases with a mass Q of less than 20 at the 3 'end, resulting in a base error rate of less than 0.01; Remove reads with a length less than 25; Remove ribosome RNA reads from the corresponding species. Apply the split mapping algorithm of Hisat2 (version: 2.0.4) to perform Genome mapping on preprocessed reads. This algorithm allows for the segmentation of reads that cannot be fully matched for mapping, making it more suitable for eukaryotic (with intron inter region) transcriptome sequencing data; Using default parameters In transcriptome sequencing, we can estimate the level of gene expression by mapping the number of reads to the gene region, but the number of reads is not only proportional to the gene expression level, but also related to the length of the gene itself and the amount of sequencing data. In order to ensure comparability of gene expression levels among different genes and samples, reads were transformed into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for standardization of gene expression levels.
Assembly: GRCm38.p4
Supplementary files format and content: gene_expression.xls.gz: Tab-delimited text file includes raw counts and FPKMs for each sample.

extract_protocol:
Total RNA was extracted using MJzol animal RNA Extraction Kit(MagBeads) (Cat#T102096)following the manufacturers instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
The purified Total RNA was subjected to steps such as mRNA isolation, fragmentation, synthesis of first stranded cDNA, synthesis of second stranded cDNA, end repair, addition of A at the 3 'end, ligation of ligands, and enrichment to complete the construction of the sequencing sample library.

value: mouse lung epithelial cells

value: pCMV-SPORT6 vector control


title: S2

institute: International Peace Maternity and Child Health Hospital


title: HCC1954_Vehicle_rep1_RNAseq


title: HCC1954_sh17_Control_KDM4C_1_ChIPseq


title: PER_GD21_Ctrl_18-22_2b


title: HCC1954_sh17_ML324_H3K36me3_2_ChIPseq


title: HDQP1_sh20_QC6352_2_RNAseq


title: N3

value: NR4A1 overexpression plasmids


title: S1


title: PER_GD21_Ctrl_18-22_2a


title: HCC1954_sh17_ML324_H3K36me3_1_ChIPseq

value: 10 microM ML324


title: HDQP1_sh20_QC6352_1_RNAseq


title: N2


title: PER_GD21_Ctrl_18-22_1a


title: HDQP1_sh20_ML324_2_RNAseq


title: PER_GD21_Ctrl_18-22_3b


title: HCC1954_sh17_shKDM4C_H3K36me3_2_ChIPseq


title: PER_GD17_Triz_18-22_56c

source_name: Triticonazole_Gestational Day 17

value: Gestational Day 17

value: Triticonazole


title: PER_GD17_Triz_18-22_56b


title: HCC1954_sh17_shKDM4C_H3K36me3_1_ChIPseq


title: HDQP1_sh20_ML324_1_RNAseq

value: Breast Cancer


title: HCC1954_sh17_Control_H3K36me3_2_ChIPseq


title: HDQP1_sh20_shKDM4C_1_RNAseq

value: Human breast cancer epithelial cell

value: 1 ug/ml doxycycline


title: PER_GD17_Triz_18-22_56a


title: HDQP1_sh20_shKDM4C_2_RNAseq

value: Dox-inducible shKDM4C


title: HCC1954_sh17_ML324_H3K9me3_2_ChIPseq


title: HCC1954_sh17_Control_H3K36me3_1_ChIPseq


title: PER_GD17_Triz_18-22_55c

value: Perineum


title: G85

type: RNA

city: Lleida

first: Robert

last: Montal

address: Av. Alcalde Rovira Roure 80

country: Spain

institute: IRBLleida

description: Tumor

hyb_protocol: Samples were run on the nCounter prep station and scanner

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions

data_processing: Data importing, normalization, and sample calibration were conducted on the RCC files in nSolver Version 4.0. Files were imported with QC in the default setting. Next, positive control normalization followed the default setting. The CodeSet normalization was applied against 11 housekeeping genes with >150 counts and low mean standard deviation (%CV<60). The panel standard in each batch was selected in the CodeSet calibration step

label: Nanostring

source_name: Gastric Adenocarcinoma

label_protocol: Up to 5μl of RNA was used for gene expression profiling through the nCounter PanCancer IO 360

growth_protocol: Samples collected after surgical resection

extract_protocol: Total RNA was isolated from frozen samples using the Maxwell RSC Simply RNA kit

treatment_protocol: Not applicable. Archived tissue was obtained at our Insitution upon patient's consent

tag: gender

value: Female

tag: anatomic location

value: Distal

tag: histology

value: Intestinal


title: G82

description: Tumor

value: Male


title: Sham operation

city: Niigata

first: Yuya

last: Suzuki

address: 1-757 Asahimachi, Chuo-ku, Niigata

institute: Niigata university

description:
Library name: Control
10x Genomics

data_processing:
The resulting FASTQ file was processed using Cell Ranger v7.1.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix file

source_name: kidney

extract_protocol:
The right kidney was exposed through a flank incision and removed. After a week, the left kidney was exposed and the upper and the lower poles were ligated with a 3-0 non-absorbable suture until the coil diameter was half of the kidney. For control animals (sham), each flank of the kidney underwent sham surgery by incising flanks, exposing the kidney, and suturing each flank. Four weeks after surgery, the mice were sacrificed under anesthesia to collect kidney samples.
Nuclei were isolated from frozen kidney tissue using a Chromium Nuclei Isolation Kit (10x Genomics), following the manufacturer's protocol. Single nuclei, diluted to a concentration of 1000 nuclei/mL, were captured using the Chromium System (10x Genomics) in accordance with the manufacturer’s protocol.

treatment_protocol: 5/6 nephrectomy

value: kidney


title: 5/6 nephrectomy

description:
Library name: Nephrectomy
10x Genomics


title: PER_GD17_Triz_18-22_55b

value: wildtype


title: PER_GD17_Triz_18-22_55a


title: HDQP1_sh20_Vehicle_1_RNAseq

value: DMSO


title: HCC1954_sh17_ML324_H3K9me3_1_ChIPseq


title: HDQP1_sh20_Vehicle_2_RNAseq


title: N1

value: mouse lung epithelial cells


title: HDQP1_sh17_QC6352_1_RNAseq


title: HCC1954_sh17_shKDM4C_H3K9me3_1_ChIPseq

value: 0.1 microgram/ml Doxycycline


title: G80

description: Tumor


title: HCC1954_sh17_shKDM4C_H3K9me3_2_ChIPseq


title: PER_GD17_Triz_18-22_54b


title: G78

description: Tumor


title: HDQP1_sh17_ML324_2_RNAseq


title: PER_GD17_Triz_18-22_54a


title: G76

description: Tumor

value: Mixed


title: G75

description: Tumor


title: HCC1954_sh17_Control_H3K9me3_2_ChIPseq


title: HDQP1_sh17_ML324_1_RNAseq


title: HCC1954_sh17_Control_H3K9me3_1_ChIPseq


title: G73

description: Tumor


title: PER_GD17_Triz_18-22_53b

value: Gestational Day 17


title: G81

description: Tumor

value: Body


title: HDQP1_sh17_QC6352_2_RNAseq

value: Breast Cancer


title: HDQP1_sh17_shKDM4C_2_RNAseq

value: Human breast cancer epithelial cell


title: PER_GD17_Ctrl_18-22_24c

source_name: Control_Gestational Day 17

value: Control


title: PER_GD17_Triz_18-22_54c

value: Triticonazole


title: PER_GD17_Triz_18-22_53a

value: Perineum


title: PER_GD17_Ctrl_18-22_24b


title: HDQP1_sh17_shKDM4C_1_RNAseq

value: Dox-inducible shKDM4C

value: 1 ug/ml doxycycline


title: HDQP1_sh17_Vehicle_2_RNAseq


title: SUM149_QC6352_1_RNAseq

description:
SUM149_Scramble_QC6352_1
SUM149_CTSLKO_counts_matrix.csv

growth_protocol: HCC1954 and T47D cells were cultured in RPMI-1640 medium with 10% FBS and 100U/ml Penicillin-Streptomycin. SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin.

value: 1 microM QC6352


title: SUM149_QC6352_2_RNAseq

description:
SUM149_Scramble_QC6352_2
SUM149_CTSLKO_counts_matrix.csv


title: G70

description: Tumor

value: Female


title: SUM149_Vehicle_2_RNAseq

description:
SUM149_Scramble_Vehicle_2
SUM149_CTSLKO_counts_matrix.csv


title: G71

description: Tumor

value: Male

value: Intestinal


title: PER_GD17_Ctrl_18-22_24a

value: wildtype


title: SUM149_Vehicle_1_RNAseq

description:
SUM149_Scramble_Vehicle_1
SUM149_CTSLKO_counts_matrix.csv

value: DMSO


title: HDQP1_sh17_Vehicle_1_RNAseq


title: SUM149_CTSLKO_QC6352_rep2_RNAseq

value: CTSL KO


title: SUM149_ML324_Resistant_ML324_5_RNAseq

description:
SUM149_ML324_Resistant_ML324_5
SUM149_Parental_MLR_counts_matrix.csv

value: 10 microM ML324


title: SUM149_CTSLKO_QC6352_rep1_RNAseq


title: HCC1954_sh17_Control_Input_ChIPseq

value: Input


title: PER_GD17_Ctrl_18-22_23c

value: Gestational Day 17


title: G67

description: Tumor

value: Body


title: G64

description: Tumor

value: Distal


title: PER_GD17_Ctrl_18-22_23b

value: Control


title: G63

description: Tumor

value: Mixed


title: SUM149_ML324_Resistant_ML324_4_RNAseq

description:
SUM149_ML324_Resistant_ML324_4
SUM149_Parental_MLR_counts_matrix.csv


title: PER_GD17_Ctrl_18-22_23a

value: Perineum


title: SUM149_CTSLKO_Vehicle_rep2_RNAseq

value: Breast Cancer

value: Human breast cancer epithelial cell


title: PER_GD17_Ctrl_18-22_22c


title: SUM149_ML324_Resistant_ML324_3_RNAseq

description:
SUM149_ML324_Resistant_ML324_3
SUM149_Parental_MLR_counts_matrix.csv


title: SUM149_CTSLKO_Vehicle_rep1_RNAseq


title: SUM149_sgScramble_QC6352_rep2_RNAseq

value: sgScramble


title: G68

description: Tumor


title: G62

description: Tumor

value: Female


title: SUM149_ML324_Resistant_ML324_2_RNAseq

description:
SUM149_ML324_Resistant_ML324_2
SUM149_Parental_MLR_counts_matrix.csv


title: PER_GD17_Ctrl_18-22_22b


title: SUM149_ML324_Resistant_Control_5_RNAseq

description:
SUM149_ML324_Resistant_Control_5
SUM149_Parental_MLR_counts_matrix.csv


title: SUM149_sgScramble_QC6352_rep1_RNAseq


title: PER_GD17_Ctrl_18-22_22a


title: SUM149_sgScramble_Vehicle_rep2_RNAseq


title: SUM149_ML324_Resistant_ML324_1_RNAseq

description:
SUM149_ML324_Resistant_ML324_1
SUM149_Parental_MLR_counts_matrix.csv


title: PER_GD17_Ctrl_18-22_21c


title: G61

description: Tumor

value: Diffuse


title: SUM149_ML324_Resistant_Control_4_RNAseq

description:
SUM149_ML324_Resistant_Control_4
SUM149_Parental_MLR_counts_matrix.csv


title: G58

description: Tumor

value: Male

value: Intestinal


title: G60

description: Tumor


title: G59

description: Tumor


title: PER_GD17_Ctrl_18-22_21a

value: wildtype


title: SUM149_ML324_Resistant_Control_3_RNAseq

description:
SUM149_ML324_Resistant_Control_3
SUM149_Parental_MLR_counts_matrix.csv

value: DMSO


title: HCC1806_sh20_QC6352_2_RNAseq

value: Dox-inducible shKDM4C


title: SUM149_ML324_Resistant_Control_2_RNAseq

description:
SUM149_ML324_Resistant_Control_2
SUM149_Parental_MLR_counts_matrix.csv


title: PHA_GD21_Triz_18-22_60a

value: Genital tubercle

value: Gestational Day 21

value: Triticonazole


title: HCC1806_sh20_QC6352_1_RNAseq


title: G57

description: Tumor

value: Distal


title: G56

description: Tumor


title: G55

description: Tumor

value: Body


title: SUM149_ML324_Resistant_Control_1_RNAseq

description:
SUM149_ML324_Resistant_Control_1
SUM149_Parental_MLR_counts_matrix.csv


title: HCC1806_sh20_shKDM4C_2_RNAseq

value: 1 ug/ml doxycycline


title: G53

description: Tumor


title: PHA_GD21_Triz_18-22_59c


title: HCC1806_sh20_shKDM4C_1_RNAseq


title: SUM149_Parental_ML324_4_RNAseq

description:
SUM149_Parental_ML324_4
SUM149_Parental_MLR_counts_matrix.csv

value: 10 microM ML324


title: PHA_GD21_Triz_18-22_59b


title: G96

description: Tumor


title: HCC1806_sh20_Vehicle_2_RNAseq

value: Breast Cancer


title: SUM149_sgScramble_Vehicle_rep1_RNAseq

value: Human breast cancer epithelial cell


title: PHA_GD21_Triz_18-22_58c


title: HCC1806_sh20_Vehicle_1_RNAseq


title: SUM149_Parental_ML324_2_RNAseq

description:
SUM149_Parental_ML324_2
SUM149_Parental_MLR_counts_matrix.csv


title: G95

description: Tumor


title: PHA_GD21_Triz_18-22_57b


title: SUM149_Parental_ML324_1_RNAseq

description:
SUM149_Parental_ML324_1
SUM149_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_QC6352_2_RNAseq


title: G94

description: Tumor


title: PHA_GD21_Triz_18-22_60b


title: G51

description: Tumor


title: SUM149_Parental_Control_4_RNAseq

description:
SUM149_Parental_Control_4
SUM149_Parental_MLR_counts_matrix.csv


title: PHA_GD21_Triz_18-22_20b


title: SUM149_Parental_Control_3_RNAseq

description:
SUM149_Parental_Control_3
SUM149_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_QC6352_1_RNAseq


title: HCC1806_sh5_shKDM4C_2_RNAseq


title: PHA_GD21_Triz_18-22_19a


title: PHA_GD21_Triz_18-22_19b


title: SUM149_Parental_ML324_3_RNAseq

description:
SUM149_Parental_ML324_3
SUM149_Parental_MLR_counts_matrix.csv


title: G50

description: Tumor


title: G49

description: Tumor

value: Proximal


title: G48

description: Tumor


title: HCC1806_sh5_Vehicle_2_RNAseq


title: SUM149_Parental_Control_1_RNAseq

description:
SUM149_Parental_Control_1
SUM149_Parental_MLR_counts_matrix.csv


title: PHA_GD21_Triz_18-22_18b


title: PHA_GD21_Triz_18-22_18a


title: HCC1806_sh5_shKDM4C_1_RNAseq


title: HCC1954_ML324_Resistant_ML324_3_RNAseq

description:
HCC1954_ML324_Resistant_ML324_3
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_Vehicle_1_RNAseq


title: G47

description: Tumor

value: Female


title: G45

description: Tumor

value: Mixed


title: PHA_GD21_Triz_18-22_17a


title: HCC1806_sh5_QC6352_rep2_ATACseq

data_processing:
ChIP-seq and ATAC-seq data processing were based on chips pipeline (Qiu et al., 2021; Taing et al., 2021). Peak calling was performed using MACS2 v2.1.2 with FDR<0.01 as the cutoff (Feng et al., 2012).
Reads were aligned to hg19 genome using BWA-MEM aligner (Li, 2013).
Seqplots (Stempor and Ahringer, 2016) was used to make the ChIP-Seq heatmaps and intensity plots using Bigwig files. DiffBind package was used for principle component analysis and peak set interaction based on Bed file (Stark and Brown, 2011). Genomic track visualization were conducted using WashU Epigenome Browser (Zhou and Wang, 2012). For motif enrichment analysis, fasta sequence files were extracted based on Bed files using BEDtools (Quinlan and Hall, 2010) and then input into MEME Suite AME module (Bailey et al., 2015) using HOCOMOCO full v11 database (Kulakovskiy et al., 2018) for calculation. E value below 10-5 is considered as a significant enrichment.
CTSL Hi-ChIP data were processed using the HiC-Pro pipeline (Servant et al., 2015). Briefly, reads were aligned to hg19 reference genome using Bowtie2 (Langmead and Salzberg, 2012). After restriction site detection and 2nd round of alignment was performed. Validated pairs were filtered and distributed to the whole genome binned in 500kb resolution. Inter- and intra-chromosomal interactions were visualized using HiTC package (Servant et al., 2012) after ICE normalization. Differential inter- and intra-chromosomal interaction sites were called using HiCCompare package (Stansfield et al., 2018) using the cutoff of interaction frequency (IF) >50 and padj<0.05.
Assembly: hg19
Supplementary files format and content: BigWig, Iced matrix

source_name: Human breast cancer

growth_protocol: HCC1954, HCC1806, HCC70, HCC2157 and T47D cells were cultured in RPMI-1640 medium with 10% FBS and 100U/ml Penicillin-Streptomycin. SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin. MCF7 cells were cultured in DMEM medium with 10% FBS and 100U/ml Penicillin-Streptomycin.

value: Human breast cancer


title: HCC1954_ML324_Resistant_ML324_1_RNAseq

description:
HCC1954_ML324_Resistant_ML324_1
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_QC6352_rep1_ATACseq


title: G40

description: Tumor

value: Intestinal


title: PHA_GD21_Ctrl_18-22_28b

value: Control

value: wildtype


title: G38

description: Tumor


title: HCC1954_ML324_Resistant_Control_3_RNAseq

description:
HCC1954_ML324_Resistant_Control_3
HCC1954_Parental_MLR_counts_matrix.csv

value: DMSO


title: HCC1806_sh5_shKDM4C_rep2_ATACseq

value: Dox-inducible shKDM4C

value: 1 ug/ml Doxycycline


title: PHA_GD21_Ctrl_18-22_28c

value: Genital tubercle

value: Gestational Day 21


title: HCC1954_ML324_Resistant_ML324_2_RNAseq

description:
HCC1954_ML324_Resistant_ML324_2
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_shKDM4C_rep1_ATACseq


title: G36

description: Tumor

value: Male

value: Distal

value: Diffuse


title: PHA_GD21_Ctrl_18-22_27c


title: SUM149_Parental_Control_2_RNAseq

description:
SUM149_Parental_Control_2
SUM149_Parental_MLR_counts_matrix.csv


title: HCC1954_ML324_Resistant_Control_2_RNAseq

description:
HCC1954_ML324_Resistant_Control_2
HCC1954_Parental_MLR_counts_matrix.csv


title: PHA_GD21_Ctrl_18-22_26c


title: HCC1954_ML324_Resistant_Control_1_RNAseq

description:
HCC1954_ML324_Resistant_Control_1
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_Vehicle_rep2_ATACseq


title: PHA_GD21_Ctrl_18-22_25c


title: HCC1954_Parental_ML324_3_RNAseq

description:
HCC1954_Parental_ML324_3
HCC1954_Parental_MLR_counts_matrix.csv

value: 10 microM ML324


title: G35

description: Tumor


title: G34

description: Tumor


title: HCC1806_sh5_Vehicle_rep1_ATACseq

value: Human breast cancer epithelial cell


title: PHA_GD21_Ctrl_18-22_25b


title: HCC1806_sh5_QC6352_H3K36me3_rep2_ChIPseq


title: PHA_GD21_Ctrl_18-22_4a


title: HCC1954_Parental_ML324_2_RNAseq

description:
HCC1954_Parental_ML324_2
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1954_Parental_ML324_1_RNAseq

description:
HCC1954_Parental_ML324_1
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_QC6352_H3K36me3_rep1_ChIPseq


title: HCC1954_Parental_Control_3_RNAseq

description:
HCC1954_Parental_Control_3
HCC1954_Parental_MLR_counts_matrix.csv


title: PHA_GD21_Ctrl_18-22_3b


title: G28

description: Tumor

value: Proximal


title: G87

description: Tumor


title: PHA_GD21_Ctrl_18-22_2b


title: G31

description: Tumor

value: Female

value: Body


title: G32

description: Tumor


title: HCC1954_Parental_Control_1_RNAseq

description:
HCC1954_Parental_Control_1
HCC1954_Parental_MLR_counts_matrix.csv


title: HCC1806_sh5_QC6352_H3K9me3_rep2_ChIPseq

value: Human breast cancer


title: HCC1806_sh5_QC6352_Input_ChIPseq


title: PHA_GD21_Ctrl_18-22_2a


title: HCC1954_Parental_Control_2_RNAseq

description:
HCC1954_Parental_Control_2
HCC1954_Parental_MLR_counts_matrix.csv


title: SUM149_sh20_ML324_2_RNAseq

description:
SUM149_shKDM4C_20_ML324_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HCC1806_sh5_shKDM4C_H3K36me3_rep2_ChIPseq


title: G22

description: Tumor

value: Intestinal


title: HCC1806_sh5_shKDM4C_H3K36me3_rep1_ChIPseq


title: PHA_GD17_Triz_18-22_56c

value: Gestational Day 17

value: Triticonazole


title: PHA_GD21_Ctrl_18-22_3a

value: Control

value: wildtype


title: HCC1806_sh5_QC6352_H3K9me3_rep1_ChIPseq

value: Dox-inducible shKDM4C


title: PHA_GD21_Ctrl_18-22_1a

value: Genital tubercle


title: SUM149_sh20_ML324_1_RNAseq

description:
SUM149_shKDM4C_20_ML324_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HCC1806_sh5_shKDM4C_H3K9me3_rep2_ChIPseq

value: 1 ug/ml Doxycycline


title: SUM149_sh20_Vehicle_1_RNAseq

description:
SUM149_shKDM4C_20_Control_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv

value: DMSO


title: G15

description: Tumor

value: Male


title: G26

description: Tumor

value: Distal


title: HCC1806_sh5_shKDM4C_H3K9me3_rep1_ChIPseq


title: SUM149_sh17_ML324_4_RNAseq

description:
SUM149_shKDM4C_17_ML324_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv

value: 10 microM ML324


title: PHA_GD17_Triz_18-22_56a


title: G23

description: Tumor


title: SUM149_sh17_ML324_3_RNAseq

description:
SUM149_shKDM4C_17_ML324_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HCC1806_sh5_Vehicle_H3K36me3_rep2_ChIPseq

value: Human breast cancer epithelial cell


title: PHA_GD17_Triz_18-22_55b


title: SUM149_sh20_Vehicle_2_RNAseq

description:
SUM149_shKDM4C_20_Control_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: PHA_GD17_Triz_18-22_55c


title: G12

description: Tumor


title: SUM149_sh17_shKDM4C_4_RNAseq

description:
SUM149_shKDM4C_17_Doxy_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv

value: 0.1 microg/ml doxycycline


title: G9

description: Tumor

value: Female

value: Mixed


title: PHA_GD17_Triz_18-22_55a


title: HCC1806_sh5_Vehicle_H3K36me3_rep1_ChIPseq

value: Human breast cancer


title: G18

description: Tumor

value: Body


title: G10

description: Tumor

value: Intestinal


title: SUM149_sh17_shKDM4C_3_RNAseq

description:
SUM149_shKDM4C_17_Doxy_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HCC1806_sh5_Vehicle_H3K9me3_rep2_ChIPseq


title: PHA_GD17_Triz_18-22_56b

value: Gestational Day 17

value: Triticonazole


title: G8

description: Tumor


title: SUM149_sh17_Vehicle_4_RNAseq

description:
SUM149_shKDM4C_17_Control_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HCC1806_sh5_shKDM4C_Input_ChIPseq


title: PHA_GD17_Triz_18-22_54c

value: wildtype


title: PHA_GD17_Triz_18-22_54b


title: PHA_GD17_Triz_18-22_54a


title: HCC1806_sh5_Vehicle_H3K9me3_rep1_ChIPseq

value: Dox-inducible shKDM4C


title: G11

description: Tumor


title: SUM149_sh17_Vehicle_3_RNAseq

description:
SUM149_shKDM4C_17_Control_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HEK293 PR8 infected nuclear lysate biol rep2

city: Gothenburg

first: Aishe

middle: A

last: Sarshad

address: Medicinaregatan 9c

country: Sweden

institute: Universiry of Gothenburg

data_processing:
Illumina Nova-seq 6000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg38 genome using PARalyzer
normalized reads and clusters were combined in a csv file
Assembly: hg38
Supplementary files format and content: PARalyzer output

growth_protocol: HEK293 cells were cultured in DMEM media supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin.

extract_protocol:
Cells were fractinated into cytoplasmic and nulcear lysates or lysed into total lysates and clarified by centrifugation. First AGO proteins were enriched by immunoprecipitation with T6B peptide. After washing the beads, RNase T1 digestion was performed, 3´ends of the RNA fragments were dephosphorylated using CIP, and RNA was fluorescently 3´end-labeled using T4 Rnl2(1–249)K227Q, followed by dephosporylation with T4 PNK. RNA-protein complexes were separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed.
Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: 16 h before cell harvesting cells were infected with PR8 viral infection at MOI 10 for 16 hrs in serum free DMEM media with  1% Penicillin-Streptomycin. Cells were also treated  with  4-thiouridine (4SU)  at a final concentration of 100 μM. Just before harvesting cells were crosslinked with 312 nm UV-light for 5 min.

tag: ip molecule

value: T6B peptide

value: WT

value: 4SU and 312 UV light


title: SUM149_sh17_ML324_1_RNAseq

first: Kornelia

last: Polyak

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description:
SUM149_shKDM4C_17_3_ML324_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: G6

description: Tumor

value: Male

value: Proximal


title: G7

description: Tumor


title: SUM149_sh17_ML324_2_RNAseq

description:
SUM149_shKDM4C_17_3_ML324_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv

value: 10 microM ML324


title: PHA_GD17_Triz_18-22_53b

value: Genital tubercle


title: HCC1806_sh5_Vehicle_Input_ChIPseq

value: Human breast cancer epithelial cell

value: DMSO


title: HEK293 PR8 infected nuclear lysate biol rep1


title: G3

description: Tumor


title: G4

description: Tumor

value: Female

value: Distal


title: HEK293 PR8 infected cytoplasmic lysate biol rep2


title: PHA_GD17_Triz_18-22_53a


title: SUM149_sh17_shKDM4C_1_RNAseq

description:
SUM149_shKDM4C_17_3_Doxy_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv

value: 0.1 microg/ml doxycycline


title: HEK293 PR8 infected cytoplasmic lysate biol rep1


title: Hxk2-S15A_Glycerol6h_rep3

city: Nagoya-shi

first: Kazuki

last: Nonaka

address: Furo-cho

institute: Nagoya University

description:
Library name: Hxk2-S15A_Glycerol6h_rep3
deltaHxkS15A3

data_processing:
Raw sequencing reads were filtered using the fastp preprocessor (v0.23.2) with threshould for Phred scale quality scores (>15) and read lengths (> 15 bp).
Mapping and quantification were performed using HISAT2 (v2.2.1) and RSEM (v1.3.1) with default settings.
Assembly: sacCer3
Supplementary files format and content: csv files include raw counts for each Sample

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was isolated using the NucleoSpin® RNA Plus kit (MACHEREY-NAGEL, North Rhine-Westphalia) according to the manufacturer’s protocol. One µg of total RNA was used for mRNA purification using NEBNext Oligo d(T)25 beads (NEBNext poly(A) mRNA Magnetic Isolation Module; New England Biolabs, MA, USA).
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs) following the manufacturer’s guidelines.

treatment_protocol: Cultured in YP 2% glucose medium until log phase, then cultured in YP 3% glycerol medium for 6 hours.

value: YP 3% Glycerol medium 6 hour


title: Hxk2-S15A_Glycerol6h_rep2

description:
Library name: Hxk2-S15A_Glycerol6h_rep2
deltaHxkS15A2


title: HEK293 control nuclear lysate biol rep2


title: SUM149_sh17_Vehicle_2_RNAseq

city: Boston

description:
SUM149_shKDM4C_17_3_Control_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: PHA_GD17_Ctrl_18-22_24b

value: Gestational Day 17

value: Control


title: Hxk2-S15A_Glycerol6h_rep1

description:
Library name: Hxk2-S15A_Glycerol6h_rep1
deltaHxkS15A1


title: SUM149_sh17_Vehicle_1_RNAseq

description:
SUM149_shKDM4C_17_3_Control_1
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: PHA_GD17_Ctrl_18-22_24a

value: wildtype


title: snf1deletion_Glycerol6h_rep3

description:
Library name: snf1deletion_Glycerol6h_rep3
deltaSNF3

value: snf1 deletion


title: HEK293 control cytoplasmic lysate biol rep2

value: T6B peptide


title: PHA_GD17_Ctrl_18-22_23c


title: SUM149_sh17_shKDM4C_2_RNAseq

description:
SUM149_shKDM4C_17_3_Doxy_2
SUM149_shKDM4C_Dox_ML324_counts_matrix.csv


title: HCC1954_sh17_ML324_3_RNAseq

description:
HCC1954_shKDM4C_17_ML324_3
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: HEK293 control nuclear lysate biol rep1

value: WT


title: HCC1954_sh17_ML324_2_RNAseq

description:
HCC1954_shKDM4C_17_ML324_2
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: snf1deletion_Glycerol6h_rep2

description:
Library name: snf1deletion_Glycerol6h_rep2
deltaSNF2


title: HEK293 control cytoplasmic lysate biol rep1

value: 4SU and 312 UV light


title: HCC1954_sh17_ML324_1_RNAseq

description:
HCC1954_shKDM4C_17_ML324_1
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: snf1deletion_Glycerol6h_rep1

description:
Library name: snf1deletion_Glycerol6h_rep1
deltaSNF1


title: PHA_GD17_Ctrl_18-22_23b


title: HEK293 PR8 viral infected cells biol rep3

description:
rna_seq_virus_no_virus_counts
VE-3295-HCPR83_S30

data_processing:
RNAseq data were preprocessed using the RNAseq nf-core pipeline  (https://nf-co.re/rnaseq)
Assembly: hg38
Supplementary files format and content: format: xlsx content: TPM

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (BioSite-R1055, Zymo Research).
Libraries were prepared from 300 ng RNA using the Illumina Stranded Total RNA library preparation kit, including Ribo-Zero Plus treatment (20040525/20040529, Illumina Inc.) according to manufacturer’s instructions. For indexing Unique Dual Indexes (20040553/20040554, Illumina Inc.) were used.

treatment_protocol: PR8 viral infection was done at MOI 10 for 16 hrs in serum free DMEM media with  1% Penicillin-Streptomycin.

value: PR8 infected


title: PHA_GD17_Ctrl_18-22_24c


title: PHA_GD17_Triz_18-22_53c

value: Triticonazole


title: HCC1954_sh17_shKDM4C_3_RNAseq

description:
HCC1954_shKDM4C_17_Doxy_3
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: tda1deletion_Glycerol6h_rep3

description:
Library name: tda1deletion_Glycerol6h_rep3
deltaTDA3

value: tda1 deletion


title: tda1deletion_Glycerol6h_rep2

description:
Library name: tda1deletion_Glycerol6h_rep2
deltaTDA2


title: PHA_GD17_Ctrl_18-22_22c

value: Genital tubercle


title: G2

description: Tumor

value: Male

value: Intestinal


title: PHA_GD17_Ctrl_18-22_22b


title: HEK293 PR8 viral infected cells biol rep1

description:
rna_seq_virus_no_virus_counts
VE-3295-HCPR81_S28


title: HCC1954_sh17_shKDM4C_2_RNAseq

description:
HCC1954_shKDM4C_17_Doxy_2
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: HEK293 mock infected cells biol rep3

description:
rna_seq_virus_no_virus_counts
VE-3295-HCC3_S27


title: tda1deletion_Glycerol6h_rep1

description:
Library name: tda1deletion_Glycerol6h_rep1
deltaTDA1


title: PHA_GD17_Ctrl_18-22_22a


title: HCC1954_sh17_Vehicle_3_RNAseq

description:
HCC1954_shKDM4C_17_Control_3
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv

value: DMSO


title: HEK293 mock infected cells biol rep2

description:
rna_seq_virus_no_virus_counts
VE-3295-HCC2_S26


title: PHA_GD17_Ctrl_18-22_23a


title: HEK293 PR8 viral infected cells biol rep2

description:
rna_seq_virus_no_virus_counts
VE-3295-HCPR82_S29


title: WT_Glycerol6h_rep3

description:
Library name: WT_Glycerol6h_rep3
WT3


title: PHA_GD17_Ctrl_18-22_21c


title: WT_Glycerol6h_rep2

description:
Library name: WT_Glycerol6h_rep2
WT2


title: HCC1954_sh17_Vehicle_2_RNAseq

description:
HCC1954_shKDM4C_17_Control_2
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: WT_Glycerol6h_rep1

description:
Library name: WT_Glycerol6h_rep1
WT1


title: HCC1954_sh17_Vehicle_1_RNAseq

description:
HCC1954_shKDM4C_17_Control_1
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv


title: HEK293 mock infected cells biol rep1

description:
rna_seq_virus_no_virus_counts
VE-3295-HCC1_S25


title: MKN74-Myc-MTSS1-2

status: Public on Mar 22 2025

city: Hangzhou

first: Guangzhao

last: Pan

address: Dongfang street

department: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences

description:
Library name: sample 5
Experimental-2

data_processing:
Quality Control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis:In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis:Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis:GOSeq (v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less or equal than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: Hisat2 (v2.2.1) was used to index reference genome sequence.
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

source_name: stomachs

growth_protocol: MKN74 cells were maintained in RPMI 1640 suppiemented with 10% fetal bovine serum (FBS) and antibiodics in humidied atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: The stable cell lines were generated by infecting MKN74 cells with the respective overexpressing lentivirus.

value: stomachs

value: human gastric cancer cells

value: Myc-MTSS1 overexpression

value: TRANSFECTION


title: MKN74-Myc-MTSS1-3

institute: Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences

description:
Library name: sample 6
Experimental-3


title: MKN74-Myc-MTSS1-1

description:
Library name: sample 4
Experimental-1


title: MKN74-pCDH-3

description:
Library name: sample 3
control-3


title: MKN74-pCDH-2

description:
Library name: sample 2
control-2


title: HeLa, Mid S, untreated, Rep1, ATM, ChIP

city: Bangalore

first: Radhakrishnan

last: Sabarinathan

state: Karnataka

address: GKVK, Kodigehalli

country: India

institute: National Centre for Biological Sciences- Tata Institute of Fundamental Research

description: Library name: ATM_HeLa_Mid_S_Rep1

data_processing:
ChIP-seq data were analysed using the nfcore/ChIPseq pipeline version 20.10.0. Briefly, the pipeline trims the adapters (Trim Galore!), aligns the reads to reference genome (BWA), marks duplicates (picard), quality filters (SAMtools and BEDTools), performs alignment-level QC and library complexity estimation (picard, Preseq), creates normalised bigWig files (BEDTools, bedGraphToBigWig) and calls peaks (MACS2)
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: Cervical

growth_protocol: HeLa cells were grown in DMEM with 10% FBS and 1% Penicillin/Streptomycin. Cells were cultured at 37 degree C at 5% CO2

extract_protocol:
Cells were cross-linked using 1% formaldehyde for 10 minutes and then were quenched with 125 mM glycine for 5 minutes at 60 rpm at RT. Cells were washed thrice with icecold PBS, scraped and pelleted down at 2000 rpm at 4°C for 5 minutes. The cell pellet was either stored at -80°C or directly used in further steps. First, the cells were lysed with L1A buffer (10 mM HEPES/KOH pH 7.9, 95 mM KCl, 1 mM EDTA pH 8 and 1% NP-40) for 10 minutes on ice and centrifuge at 3500 rpm for 5 minutes. Nuclei were obtained by adding a nuclear lysis buffer (L2) (50 mM Tris-HCl pH 7.4, 1% SDS and 10 mM EDTA pH 8) supplemented with 1x PIC, to the pellet for 10 minutes on ice. The chromatin was fragmented to an average size of 400-500 bp by 22 cycles of 30 seconds ON and 30 seconds OFF pulses using a Diagenode Bioruptor sonicator. Fragment size was 27 visualised by running the chromatin on 1% Agarose gel. The DNA concentration was checked in NanoDrop. Chromatin lysate was cleared by centrifugation at 12000 rpm at 4°C for 12 minutes. One hundred µg of chromatin lysate was diluted in the Dilution buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl, 2 mM EDTA pH 8 and 0.5% Triton X-100) in a 1:1.5 ratio and 10% of chromatin lysate was taken as input. The antibody was added and incubated overnight at 4°C with a constant rotation. Antibodies used are: CTCF (D31H2: Cell Signaling Technology, 1µg), RAD21 (ab992: Abcam, 1µg), MRE11 (ab208020: Abcam, 2µg), γH2AX (ab81299: Abcam, 2µg), H2AX (ab :Abcam, 2ug,), ATM (ab : Abcam, 2ug), FANCD2 (NB180, Novus Biologicals, 2ug) and RAD51 (ab176458: Abcam, 2µg). The next day, Protein A/G Dynabeads  which were blocked in 5% BSA for 1 hour, were added (15µl per tube) for 4 hours at 4°C at 12 rpm. This was followed by washes with wash buffer I (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% SDS, 2 mM EDTA pH 8 and 1% Triton X-100), wash buffer II (20 mM Tris-HCl pH 7.4, 500 mM NaCl, 2 mM EDTA pH 8 and 1% Triton X-100), wash buffer III (20 mM Tris-HCl pH 7.4, 250 mM LiCl, 1% NP40, 1 mM EDTA pH 8 and 10% Sodium deoxycholate) and 1xTE buffer (10 mM Tris pH 8, 1 mM EDTA pH 8) in sequence for 5 minutes at 4°C. Flow through was discarded after each wash step. Then the proteinDNA complex was eluted in 200µl of Elution Buffer (100 mM NaHCO3, 1% SDS) at 37°C. Decrosslinking was performed by adding 14 µl of 5M NaCl to the eluate at 65°C overnight. The DNA was purified using the Phenol:Chloroform:IAA method followed by ethanol precipitation. Finally, the pellet was dissolved in water and the extracted DNA was used in a qPCR reaction to verify the ChIP and proceeded for sequencing
library preparation was done using NEBNext Ultra II DNA library Prep kit with Sample Purification Beads (E7103L).

treatment_protocol: To synchronize cells in Mid S phase, HeLa cells were treted with 2mM Thymidine for 16h and released for 4 hours. DNA damage was induced using 2mM HU or 25uM Etoposide for 3 hours in the Mid S phase. For prolonged DNA damage asynchronous HeLa cells were treted with 2mM HU for 16 hours

value: Cervical

value: HeLa

value: Epithelial

tag: chip antibody

value: Anti-ATM antibody [EPR20100] - ChIP Grade, ab201022, abcam


title: HeLa, Mid S, untreated, Rep1, FANCD2, ChIP

description: Library name: FANCD2_HeLa_Mid_S_Rep1

value: Anti-FANCD2 antibody , NB100-182, Novus Biologicals


title: HeLa, Mid S, HU treatment 3h, Rep1, FANCD2, ChIP

description: Library name: FANCD2_Hela_Mid_S_HU_3h_Rep1

value: 2mM HU treatment for 3h


title: HCC1954_sh17_shKDM4C_1_RNAseq

description:
HCC1954_shKDM4C_17_Doxy_1
HCC1954_shKDM4C_Dox_ML324_counts_matrix.csv

value: 0.1 microg/ml doxycycline


title: HeLa, Mid S, HU treatment 3h, Rep1, ATM, ChIP

description: Library name: ATM_Hela_Mid_S_HU_3h_Rep1


title: MKN74-pCDH-1

description:
Library name: sample 1
control-1

value: WT