title: GP5d p53-KO, SETDB1i Rep3

value: SETDB1 inhibition

value: 24 hours


title: Mouse liver, Sp_573_EE_3, Day 30, rep 3

status: Public on Jun 16 2025

type: SRA

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

country: China

institute: Southern University of Science and Technology

description: Library name: X342-3

library_source: genomic

data_processing:
FASTQ generation: Illumina bcl-convert v4.0
Read trimming: Trimmomatic v0.38  SLIDINGWINDOW:5:15 HEADCROP:3 AVGQUAL:15 LEADING:5 TRAILING:5 MINLEN:80.
Alignment: BSMAP v2.90 to mm39  -n 0 -v 0.08 -g 1 -p 48.
Methylation ratios: methratio.py, BSMAP package
DMCs: Radmeth v1.0  coverage >= 5×, Q < 0.05, Δβ > 0.10.
DMRs: metilene v0.2-8  --mincpgs 3 --mode 1 -mtc 2; keep regions P < 0.05, Δβ > 0.10, >= 5 CpGs, length > 50 bp.
Assembly: mm10
Supplementary files format and content: xls format table with chr, pos, strand, context, rate, depth, nC
Supplementary files format and content: csv format table with chr,start,end,meth.diff,qvalue,annotation,gene_annot

molecule: genomic DNA

organism: Mus musculus

source_name: liver

extract_protocol:
Genomic DNA was isolated from mouse liver tissue or Hepa1-6 liver cells with the QIAamp DNA Mini kit (Qiagen), quantified by Qubit fluorometry, fragment size verified on a Fragment Analyzer, and spiked with 0.5 % unmethylated λ-DNA as a bisulfite-conversion control.
One µg gDNA was sheared (~250 bp) on a Bioruptor, end-repaired, A-tailed and ligated to 5-mC Illumina adapters; DNA was bisulfite-converted (EZ DNA Methylation-Gold, Zymo), PCR-amplified (8–12 cycles, KAPA HiFi Uracil+), size-selected with AMPure XP beads, QC’d on a Bioanalyzer, quantified by qPCR, and sequenced as 2 × 150 bp reads on an Illumina NovaSeq X Plus.

tag: tissue

value: liver


title: Control 1

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: MDA_231_empty_6_3_c1_1

library_source: transcriptomic

data_processing:
Libraries were sequenced by the Illumina NextSeq 500
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: hg38
Supplementary files format and content: OVOL1_RNA-Seq.xlsx - Raw and normalized counts (genes in rows and samples in columns)

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% FBS, 1% Penicillin-Streptomycin solution

extract_protocol:
RNA was isolated using Trizol reagent following manufacturer protocol
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: MDA-MB-231 cells were stably transfected with plasmid harboring Arrdc4 overexpression

tag: cell line

tag: cell type

value: Breast Cancer

tag: genotype

value: WT


title: Mouse liver, Sp_EE_17, Day 120, rep 5

description: Library name: X330-5


title: GP5d p53-KO, SETDB1i Rep2

city: Helsinki

first: Divyesh

last: Patel

address: University of Helsinki

department: Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine,

country: Finland

institute: University of Helsinki

data_processing:
Trim Galore v.0.6.7 was used to remove adaptor/overepresented sequences, discarding reads left with < 20 bp. FastQC v.0.11.9 was used for quality control.
Reads were also aligned with STAR v.2.5.3a (Dobin et al. 2013).
Gene counts were quantified by using HTSeq-count v.0.11.2 (Anders et al. 2015)
Diffential expression analysis was performed with DESeq2 v.1.32.0 (Love et al. 2014).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include geneexpression counts for each sample.

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. OE19 cells were cultured in RPMI supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA stranded mRNA-seq kit for Illumina (Roche) as per manufacturer’s instruction

treatment_protocol:
Cells were treated with distinct chromatin modifier enzyme inhibitors. For DNMT inhibition, cells were treated with 500 nM/L DAC (MedChemExpress, HY-A0004). Media containing DAC were replaced each day for three days. For HDAC inhibition, cells were treated with 500 nmol/L SB939 (MedChemExpress, HY-13322) for 18 hours. For SETDB1 inhibition, cells were treated with 500 nM/L Mitramycin A (MedChemExpress, HY-A0122) for 24 hours. For co-inhibition of DNMT and HDAC, cells were treated with 500 nM/L DAC. DAC containing media were replaced each day for three days. Cells were treated with 500 nmol/L SB939 for 18 hours and collected for RNA isolation and ChIP-seq. For DMSO control, cells were treated with DMSO (Fisher, BP231). Media containing DMSO were replaced each day for four days.
Generation of GP5d p53-KO and GP5d KAP1 heterozygous cell line is described in Sahu et al., Nat. Gen. (2022)

value: Colon adenocarcinoma

tag: treatment

tag: time


title: RAD21-AID c9 Input

city: Freiburg im Breisgau

first: Maximilian

middle: Christian

last: von der Linde

address: Stefan-Meier-Straße 17

department: Institute for Medical Bioinformatics and Systems Medicine (IBSM)

country: Germany

institute: University Medical Center Freiburg

data_processing:
The 3' adaptors were removed using cutadapt (v1.4.2, Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were aligned to GRCh38.14 (Genome Reference Consortium Human Build 38), GCA_000001405.29 using bowtie
genome-wide coverage tracks were computed using bedtools (v2.27, bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+' ,bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools (bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024)ignoreDuplicates --nomalizeUsing CPM --exactScaling for H3 WT and KD
Assembly: GRCh38.14 (Genome Reference Consortium Human Build 38), GCA_000001405.29
Supplementary files format and content: bigwig format files containing the information about genome coverage

source_name: Ramos

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, libraries were prepared following the NEB Next Ulta II DNA library kit. Libraries were amplified with the kappa library amplification qCR master mix

value: Ramos

value: Burkitt's Lymphoma

value: untreated


title: iHCF (ATAC-seq)

city: South San Francisco

first: Ittai

middle: Ethan

last: Eres

state: CA

address: 750 Gateway Boulevard

department: CRADI

country: USA

institute: Amgen

data_processing:
We processed reads and called open chromatin ATAC peaks using the ENCODE ATAC-seq pipeline
ATAC peaks from naïve overlap peaks from two pseudo-replicates retained for downstream analyses
HINT-ATAC used in concert with TF motifs from HOCOMOCO and JASPAR to find footprinted regions with interesting TF binding
Assembly: hg38
Supplementary files format and content: narrowPeak files output by MACS2, defining called ATAC peaks (open chromatin regions)

source_name: Heart

growth_protocol: Primary cells cultured according to manufacturer instructions (PromoCell & Lonza); immortalized human cardiac fibroblasts were generated from adult heart ventricle primary cells (Applied Biological Materials).

extract_protocol:
Buenrostro et al. standard extraction protocol
Buenrostro et al. standard library construction protocol

value: Heart

value: Immortalized human cardiac fibroblast


title: Mouse liver, Sp_EE_16, Day 120, rep 4

description: Library name: X330-4


title: GP5d p53-KO, DNMTi-HDACi Rep3

value: DNMT HDAC co-inhibition

value: 96 hours


title: RAD21-AID c9 IgG


title: GP5d p53-KO, SETDB1i Rep1


title: RAD21-AID c9 8h IAA rep2

value: 8h IAA


title: rna.wt.dox.rep2

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Read pairs were aligned to the Gencode v44 transcriptome with STAR (v2.7.10b).
Transcript reads were counted with salmon (v1.9.0), then summarized at the gene level by tximport.
Assembly: hg38
Supplementary files format and content: Counts per gene in tab-delimited text format.

molecule: polyA RNA

growth_protocol: Doxycycline (dox) inducible wildtype (wt) and TA1del (ta1) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line.

extract_protocol:
Cell were harvested for ATAC-seq and remaining cell pellet was stored in RNAlater. RNA was extracted using TriZol.
RNA libraries were generated with Illumina TruSeq stranded mRNA with oligoDT capture (polyA capture).

treatment_protocol: To investiage the role that wt and ta1-GATA3 have on gene expression, GATA3 expression was induced for 24 hours with dox (1 ug/ml).

value: basal breast cancer line

value: WT GATA3 (1-444aa)

tag: induced

value: DOX


title: Mouse liver, Sp_EE_14, Day 120, rep 2

description: Library name: X330-2


title: Mouse liver, Sp_EE_15, Day 120, rep 3

description: Library name: X330-3


title: GP5d p53-KO, HDACi Rep2

value: HDAC inhibition

value: 18 hours


title: Control 3

description: Library name: MDA_231_empty_6_3_c1_3


title: RAD21-AID c9 8h IAA rep1


title: rna.wt.dox.rep3


title: rna.wt.dox.rep1


title: Control 2

description: Library name: MDA_231_empty_6_3_c1_2


title: GP5d p53-KO, DNMTi-HDACi Rep1


title: RAD21-AID c9 4h IAA rep2

value: 4h IAA


title: GP5d p53-KO, HDACi Rep1


title: rna.wt.ctrl.rep3

value: Control/Uninduced


title: Mouse liver, Sp_EE_12, Day 90, rep 6

description: Library name: X309-6

value: liver


title: GP5d p53-KO, DNMTi Rep3

value: Colon adenocarcinoma

value: DNMT  inhibition

value: 72 hours


title: RAD21-AID c9 4h IAA rep1

value: Ramos

value: Burkitt's Lymphoma


title: Mouse liver, Sp_EE_11, Day 90, rep 5

description: Library name: X309-5


title: rna.wt.ctrl.rep2


title: RAD21-AID c9 noIAA rep1

value: untreated


title: GP5d p53-KO, DNMTi Rep2


title: rna.wt.ctrl.rep1


title: Mouse liver, Sp_EE_10, Day 90, rep 4

description: Library name: X309-4


title: ATAC_rep2

data_processing:
ATACSeq
The illumina reads were adapter trimmed on their 3’ ends with cutadapt (version 1.15;  --match-read-wildcards -O 1 -f fastq -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC for read1 and cutadapt --match-read-wildcards -O 1 -f fastq -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for read2).
The paired end trimmed reads larger then 18nt were aligned with bowtie2 (version 2.1.0;  --sensitive   -p 10 -X 5000 -N 0   --trim5 0 --trim3 0) to the human hg38 genome.
The aligned reads were sorted by position with samtools (version 0.1.19).
Strand specific and undirected occupancy profiles were generated with deeptools bamCoverage v2.2.2.
Assembly: NCBI HG38
Supplementary files format and content: bigWig of rpm-normalized read densities

growth_protocol: Ramos cells were cultured in complete RPMI medium

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor modifocations in the tagmentation step where we used a homemade Tn5 enzyme and assembeld the Tn5-adapter tagmentation mix ourselves. However, the adapter sequences and primers used for library amplification are the same as in the Buenrostro et al. protocol.
transposed DNA was amplified with RT-qPCR monitoring to avoid oveamplification and the libraries were purified with AMPure XP beads.


title: GP5d p53-KO, HDACi Rep3


title: Mouse liver, Sp_EE_9, Day 90, rep 3

description: Library name: X309-3


title: ATAC_rep1


title: rna.ta1.dox.rep3

value: TA1del GATA3 (126-444aa)


title: GP5d p53-KO, DMSO Rep3

value: DMSO Control

value: 96 hours


title: rna.ta1.dox.rep2

value: basal breast cancer line


title: Mouse liver, Sp_EE_8, Day 90, rep 2

description: Library name: X309-2


title: rna.ta1.dox.rep1


title: GP5d p53-KO, DMSO Rep2


title: C424, T cell lymphoma, biol rep 3 [ATAC-Seq]

city: Vienna

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

country: Austria

institute: Medical University of Vienna

data_processing:
Initial data quality check was done using FastQC. Next, transposase (Tn5) sequences were removed using the cutadapt tool. All Illumina adapters were likewise removed. Next Bowite2 was used for mapping reads to the reference genome. Sorting of the mapped reads was done using samtools. Mitochondrial reads and sex chromosomes as well as reads with low mapping quality (MAPQ < 30) were removed. For deduplication rmdup and samtools were used. Peaks were called with MACS2 (Model-based analysis of ChIP-seq). FRiP scores were calculated and quality check was performed using multiQC. Counting reads per peak was accomplished with featureCounts. To annotate peaks, the package ChIPseeker was used. Differential enrichment analysis was done using edgeR.
Assembly: mm36
Supplementary files format and content: bigwig files containing peaks

source_name: ALK+ Hdac1KO, thymic lymphoma

extract_protocol:
Snap frozen tumor tissue was lyzed in homogenization buffer. Nuclei were pelleted by centrifugation (5 min, 4°C, 350 rcf). Nuclei were resuspended in homogenization buffer and gradients of iodixanol solution were used to obtain the band containing the nuclei at the 30 – 40% iodixanol interface after centrifugation (20 min, 4°C, 3000 rcf, break off). Nuclei were diluted in ATAC-RSB-Tween buffer and counted. 50,000 nuclei per sample were centrifuged (10 min, 500 rcf, 4°C) and resuspended in ATAC-seq Reaction Mix. Reactions were incubated (37°C, 30 min, 1000 rpm). After incubation, Binding Buffer (Qiagen MinElute PCR Purification kit) was added. A cleaning protocol using the MiniElute PCR Purification kit was performed according to the manufacturer and samples were eluted in Elution Buffer.
Purified DNA was amplified using qPCR with index primers in 2 rounds of amplification using the NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs). Following 2 times SPRI beads purification, library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

value: ALK+ Hdac1KO, thymic lymphoma

value: NPM-ALK+ CRE+ HDAC1delta/delta


title: Mouse liver, Sp_EE_6, Day 30, rep 6

description: Library name: X308-6


title: GP5d p53-KO, DNMTi Rep1


title: rna.ta1.ctrl.rep3


title: Mouse liver, Sp_EE_13, Day 120, rep 1

description: Library name: X330-1


title: B966, T cell lymphoma, biol rep 2 [ATAC-Seq]


title: OE19, DNMTi-HDACi Rep3

value: Esophageal  adenocarcinoma

value: WT

value: DNMT HDAC co-inhibition


title: Mouse liver, Sp_EE_5, Day 30, rep 5

description: Library name: X308-5


title: OE19, DNMTi-HDACi Rep2


title: B 840, T cell lymphoma, biol rep 1 [ATAC-Seq]


title: Mouse liver, Sp_EE_4, Day 30, rep 4

description: Library name: X308-4


title: OE19, DNMTi-HDACi Rep1


title: rna.ta1.ctrl.rep1

value: Control/Uninduced


title: cnr.wt.treatment_dmso.dox.snf5.rep3

data_processing:
Adapters were clipped from raw read pairs with TrimGalore v0.6.6.
Read pairs were mapped to the hg38 reference assembly with bowtie2 v2.4.5 using parameters "--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700", then filtered with samtools v1.19.2 for minimum MAPQ of 30.
Duplicate mapped fragments were then removed by MarkDuplicate from the Picard tool suite v.2.27.1 with parameter REMOVE_DUPLICATES=TRUE.
Biological triplicate samples were combined with samtools merge function.
Peaks calls were made with MACS2 v2.2.9.1 on the merged replicates using IgG per condition (WT Control, WT DOX, TA1del Control, TA1del DOX) with -q 0.00001;  peak sets per antibody and experimental subset were then concatenated, merged with bedtools v2.30.0 (-d 10), and filtered to remove exclusion list regions (ENCODE) and non-canonical chromosomes.
Fragments at peaks were counted by the featureCounts function of subread v2.0.3 with parameters "-p -countReadPairs".
Genomic coverage tracks were generated by deeptools bamCoverage v3.5.3 with parameters "--normalizeUsing None --binSize 10 --ignoreDuplicates --effectiveGenomeSize 2913022398 --scaleFactor", where the scale factors were calculated by 1/[(E.Coli fragment count/Sample fragment count)*100.  For lenti-empty and lenti-AFOS treated samples, only the 2nd and 3rd replicates contributed to the coverage tracks to avoid bias resulting from the separate pAG-MNase batch used for the 1st replicate.
Assembly: hg38
Supplementary files format and content: Fragment counts per peak in tab-delimited text format.
Supplementary files format and content: Normalized genomic coverage tracks in bigWig format.
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed following standard CUT&RUN conditions outlined in protocol provided by Henikoff lab on protocols.io (Skene and Henikoff 2017, Janssens 2019, Meers et al. 2019) with minor modification of increasing wash steps to 4 times. Purified pAG-MNase was provided by the NIEHS Protein Expression Core and purified using Meers et al. 2019 protocol. For each reaction, 5e5 cells were harvested. Antibody dilutions (overnight incubation) were as follows: IgG Rabbit (Antibodies online ABIN101961; 1:100), Mouse IgG (Abcam ab46540; 1:100), FLAG M2 (Sigma F1804; 1:50), FRA1 (Abcam ab252421; 1:50), p300 (CST 86377S; 1:50), H3K4me1 (Epicypher 13-0057; 1:50), H3K27ac (Millipore MABE647; 1:50), BRG1 (Abcam ab110641; 1:50), SNF5/SMARCB1 (CST 91735S; 1:50).
Library preparations were performed with NEBNext Ultra II (NEB #E7645) described for transcription factors(Liu et al. 2018, Liu 2021) at half volume reactions. Additional modifications were made using NEBNext unique Dual Index Primers (NEB #E6440, #E6442), 15 ng of input DNA, and 0.5 µM diluted adapter.

treatment_protocol: To investigate changes in histone modifications, transcirption factor/chromatin remodeler binding in WT and TA1del-GATA3 expression, cells were induced with +/- DOX (1 ug/mL) for 24 hr.To determine the effect of AP-1 binding, cells were transduced with lentivirus containing empty vector or AFOS (dominant negative AP-1 that inhibits binding) for 48 hrs prior to DOX induction for 24 hrs. To determine the effect of ATPase function by SWI/SNF, cells were treated concurrently +/- DOX (1 ug/ml) and either DMSO (8 uL) or BRM014 (8 uM) for 24 hrs.

value: WT GATA3 (1-444aa)

value: DOX

value: DMSO

tag: antibody


title: C453, T cell lymphoma, biol rep 4 [ATAC-Seq]

source_name: ALK+, thymic lymphoma

value: ALK+, thymic lymphoma

value: NPM-ALK+ HDAC1 fl/fl


title: C452, T cell lymphoma, biol rep 3 [ATAC-Seq]


title: Mouse liver, Sp_EE_2, Day 30, rep 2

description: Library name: X308-2

value: liver


title: OE19, SETDB1i Rep3

value: SETDB1 inhibition

value: 24 hours


title: C455, T cell lymphoma, biol rep 4 [ATAC-Seq]


title: Mouse liver, Sp_EE_3, Day 30, rep 3

description: Library name: X308-3


title: C413, T cell lymphoma, biol rep 2 [ATAC-Seq]


title: Mouse liver, Sp_EE_7, Day 90, rep 1

description: Library name: X309-1


title: cnr.wt.treatment_dmso.dox.snf5.rep2


title: GP5d p53-KO, DMSO Rep1

value: and

value: DMSO Control


title: OE19, SETDB1i Rep2


title: OE19, SETDB1i Rep1


title: cnr.wt.treatment_dmso.dox.fra1.rep3

value: basal breast cancer line

value: FRA1 [Abcam, ab252421]


title: Mouse liver, Sp_EE_1, Day 30, rep 1

description: Library name: X308-1


title: rna.ta1.ctrl.rep2

value: TA1del GATA3 (126-444aa)


title: C348, T cell lymphoma, biol rep 1 [ATAC-Seq]


title: OE19, HDACi Rep3

value: Esophageal  adenocarcinoma

value: HDAC inhibition

value: 18 hours


title: cnr.wt.treatment_dmso.dox.fra1.rep2


title: Mouse liver, SF01_EE_12, Day 90, rep 6

description: Library name: X372-6


title: Mouse liver, SF01_EE_11, Day 90, rep 5

description: Library name: X372-5


title: LNCAP sgAR, rep2

city: San Francisco

first: Raunak

last: Shrestha

department: Radiation Oncology

institute: University of California, San Francisco

description: Library name: sgAR_2

data_processing:
The ATAC-seq paired-end fastq files were trimmed to remove Illumina Nextera adapter sequence using Cutadapt v2.6. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Bowtie2 was then used to align the ATAC-seq reads against the Human reference genome build hg38 using. The uniquely mapped reads were obtained in SAM format. Samtools was used to convert SAM to BAM file as well as sort the BAM file. Picard was then used to flag duplicates using the MarkDuplicates tool. The resulting BAM file reads position were then corrected by a constant offset to the read start using deepTools2. This resulted in the final aligned, de-duplicated BAM file that was used in all downstream analyses. ATAC-seq peak calling was performed using MACS2 to obtain narrow peaks. The resulting peaks that map to the mitochondrial genome or genomic regions listed in the ENCODE hg38 blacklist or peaks that extend beyond the ends of chromosomes were filtered out.
Assembly: hg38
Supplementary files format and content: peaks bed file

source_name: LNCaP

extract_protocol:
ATAC-Seq on LNCaP cells were performed following knockdown of PTGES3 or control (GAL4).
ATAC-seq was carried out as described in the published method papers by Buenrostro, et al. and Corces, et al. with the following modifications. Cells were resuspended in buffer, incubated on ice for 10 minutes, and lysed using a dounce homogenizer. 50,000 nuclei were incubated with 25uL 2X TD Buffer and 1.25uL Transposase shaking at 300rpm at 37C for 30 minutes. Zymo DNA Clean and Concentrator 5 kit was then used to purify DNA. Transposed DNA was amplified using PCR master mix and indexes from Nextera DNA Library Prep kit for 5 cycles and then assessed using qPCR. Final cleanup was performed using 1.8X AMPure XP beads and libraries quantified using the DNA High Sensitivity Agilent 2100 Bioanalyzer System. Samples were sequenced at the UCSF Core Facility on the HiSeq4000 paired end 100. The entire experimental setup was performed in two technical replicates.

value: LNCaP

value: castration resistant prostate cancer

value: sgAR


title: LNCAP sgAR, rep1

description: Library name: sgAR_1


title: OE19, HDACi Rep2

value: WT


title: Mouse liver, SF01_EE_10, Day 90, rep 4

description: Library name: X372-4


title: cnr.wt.treatment_dmso.dox.fra1.rep1

value: WT GATA3 (1-444aa)

value: DOX

value: DMSO


title: cnr.wt.treatment_dmso.dox.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: Mouse liver, SF01_EE_9, Day 90, rep 3

description: Library name: X372-3

value: liver


title: OE19, HDACi Rep1


title: CM (RNA-seq)

data_processing:
RNA sequencing reads were aligned to human reference genome hg38 and fragments per kilobase per million sequenced, quantile normalized (FPKQ) were determined with ArraySuite software (OmicSoft, Cary, NC) and in-house sotware.
Genes with FPKQ values >0 were considered expressed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKQ values for each sample across assayed genes

extract_protocol:
Total RNA was harvested using Mirvana miRNA RNA isolation kits (Ambion, Grand Island, NY) with on-column DNase treatment.
RNA libraries were prepared using the Illumina Truseq RNA Sample Preparation Kit (Illumina, San Diego, CA).

value: Heart

value: Cardiac myocyte


title: OE19, DNMTi Rep3

value: DNMT  inhibition

value: 72 hours


title: cnr.wt.treatment_dmso.dox.flag.rep2

value: basal breast cancer line


title: cnr.wt.treatment_dmso.dox.snf5.rep1


title: NHCFV (RNA-seq)

value: Cardiac fibroblast--ventricular


title: Mouse liver, SF01_EE_8, Day 90, rep 2

description: Library name: X372-2


title: OE19, DNMTi Rep2

value: Esophageal  adenocarcinoma


title: NHCFV biol rep 2 (Hi-C)

data_processing:
Data were processed using both HiC-Pro version 2.8.1 and Juicer version 1.5.6 on AWS
Genome-wide loops were called at 2kb resolution using GOTHiC version 1.12.0 and HiCCUPS included in Juicer 1.5.6
Assembly: hg38
Supplementary files format and content: Common .hic format output from juicer pipeline for processed Hi-C data

growth_protocol: Primary cells cultured according to manufacturer instructions (PromoCell & Lonza)

extract_protocol:
in-situ Arima Hi-C
Arima Hi-C (10M cells each)


title: cnr.wt.treatment_dmso.dox.flag.rep1


title: cnr.wt.treatment_dmso.dox.brg1.rep2

value: BRG1 [Abcam, ab110641]


title: Mouse liver, SF01_EE_7, Day 90, rep 1

description: Library name: X372-1


title: OE19, DNMTi Rep1


title: OE19, DMSO Rep1

value: DMSO Control

value: 96 hours


title: Mouse liver, SF01_EE_5, Day 30, rep 5

description: Library name: X366-5


title: cnr.wt.treatment_dmso.dox.brg1.rep3


title: Mouse liver, SF01_EE_6, Day 30, rep 6

description: Library name: X366-6


title: CM biol rep 2 (Hi-C)


title: GP5d, SETDB1i Rep3

value: Colon adenocarcinoma

value: SETDB1 inhibition

value: 24 hours


title: OE19, DMSO Rep2

value: WT


title: Mouse liver, SF01_EE_1, Day 30, rep 1

description: Library name: X366-1


title: cnr.wt.treatment_dmso.dox.brg1.rep1

value: WT GATA3 (1-444aa)

value: DOX

value: DMSO


title: P3, cuttag-seq

city: Shanghai

first: xu

last: wu

address: 83 Fenyang Road

institute: EENT Hospital, Fudan University

data_processing:
After data quality control by software fastQC (V0.11.2), cleaned raw data was then compared to GRCh38. Using MACS2 (V3.0.1) for  peak calling involves processing aligned sequencing reads to identify and obtain genomic locations and sequences of regions. Peaks are annotated with their genomic locations and associated gene information by HOMER (V1.5.2).
Assembly: GRCh38
Supplementary files format and content: bigwig

source_name: auricular cartilage

extract_protocol:
cells are fixed to preserve protein-DNA interactions and then permeabilized to allow antibody access.C-Myc primary and secondary antibodies linked to transposase are subsequently applied to target and tag regions where proteins bind to DNA.
The final library is then refined and size-selected through magnetic bead purification.

value: auricular cartilage

value: primary chondrocyte


title: CM biol rep 1 (Hi-C)

value: Heart

value: Cardiac myocyte


title: Mouse liver, SF01_EE_4, Day 30, rep 4

description: Library name: X366-4

value: liver


title: GP5d, HDACi Rep3

value: HDAC inhibition

value: 18 hours


title: cnr.wt.treatment_dmso.ctrl.snf5.rep3

value: basal breast cancer line

value: Control/Uninduced


title: iHCF (RNA-seq)

value: Immortalized human cardiac fibroblast


title: cnr.wt.treatment_dmso.ctrl.fra1.rep2

value: FRA1 [Abcam, ab252421]


title: Mouse liver, Vehicle_5, Day 90, rep 2

description: Library name: X358-2


title: P1, cuttag-seq


title: cnr.wt.treatment_dmso.ctrl.fra1.rep1


title: CM biol rep 2 (ATAC-seq)


title: GP5d, HDACi Rep1

value: Colon adenocarcinoma


title: cnr.wt.treatment_dmso.ctrl.snf5.rep2


title: cnr.wt.treatment_dmso.ctrl.snf5.rep1


title: Mouse liver, SF01_EE_2, Day 30, rep 2

description: Library name: X366-2


title: GP5d, SETDB1i Rep2

value: SETDB1 inhibition

value: 24 hours


title: NHCFV (ATAC-seq)

value: Cardiac fibroblast--ventricular


title: P3, ATAC-seq

data_processing:
After data quality control by software fastQC (V0.11.2), cleaned raw data was then compared to GRCh38. Using MACS2 (V3.0.1) for ATAC-Seq peak calling involves processing aligned sequencing reads to identify and obtain genomic locations and sequences of regions indicative of open chromatin. ATAC-Seq peaks are annotated with their genomic locations and associated gene information by HOMER (V1.5.2).
Assembly: GRCh38
Supplementary files format and content: bigwig

extract_protocol:
Cells are washed with PBS, lysed in chilled buffer, and centrifuged to collect nuclei. Nuclei are treated with transposase, followed by DNA purification.
Transposase digestion and initial library construction involve adding transposase reaction mix to cell nuclei, followed by incubation, DNA purification, and amplification using specific primers. The final library is then refined and size-selected through magnetic bead purification.


title: Mouse liver, SF01_EE_3, Day 30, rep 3

description: Library name: X366-3


title: P6, ATAC-seq


title: cnr.wt.treatment_dmso.ctrl.fra1.rep3

value: WT GATA3 (1-444aa)


title: GP5d, SETDB1i Rep1

value: WT


title: 2L-sgPTGES3_DMSO

data_processing:
The RNA-seq single-end fastq data generated by Illumina HiSeq 4000 sequencing system were first trimmed to remove adapter sequence using Cutadapt. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Using splice-aware aligner STAR, RNA-seq reads were aligned onto the Human reference genome build hg38 and exon-exon junctions, according to the known Human gene model annotation from the GENCODE v30.  Based on the reads that can only be mapped to a single genomic location, the gene expression quantification was performed using featurecount function within Rsubread R-package.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: castration resistant prostate cancer

extract_protocol: LNCaPi cells were viral transduced with sgRNA targeting PTGES3 or control sgRNA for 3 days and selected with puromycin for pure population for 3 days. Post-selection RNA was extracted from the cells using the Zymo Quick-RNA extraction kit. QuantSeq 3’mRNA-Seq library prep kit FWD for Illumina was used to prepare the library as per the manufacturer’s protocol. Quality control was performed by using the Agilent Bioanalyzer 2100 system and the samples were sequenced in Illumina HiSeq 4000. The entire set of the experiment was done in two biological replicates.

value: castration resistant prostate cancer

value: LNCaP


title: Mouse liver, Vehicle_6, Day 90, rep 3

description: Library name: X358-3


title: NHCFV biol rep 1 (Hi-C)

value: Heart


title: CM biol rep 1 (ATAC-seq)

value: Cardiac myocyte


title: GP5d, HDACi Rep2


title: GRKO GFP-mGRtetra 100uM TCA/100nM Cort 2h Replicate 3

city: Bethesda

first: Thomas

last: Johnson

state: Maryland

address: 41 Medlars Dr. Room B307

department: CCR

institute: National Cancer Institute

description: Library name: GH4637

data_processing:
RNA reads were aligned using STAR 2.7.0f with default settings.
Cutadapt was used for adapter trimming and quality control.
RNA-Seq data processed with HOMER program version 4.10.4: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -noadj and getDiffExpression.pl -vst
Assembly: mm10
Supplementary files format and content: Excel file of normed counts (RNA-seq)

source_name: adenocarcinoma cells

growth_protocol: Cell lines use typical growth protocols with DMEM 10% FBS. All cells were grown 24h on media with 10% charcoal stripped serum 24h before Corticosterone and/or TCA treatment.

extract_protocol:
Total RNA was collected using Pure-Link RNA Mini kit (Thermo).
RNA-Seq libraries were made with TruSeq Stranded Total RNA Library Prep. With Ribo-Zero Plus

treatment_protocol: Corticosterone treatments were 100 nano-molar for 2h. TCA treatments were 100uM for 2h

value: adenocarcinoma cells

value: GRKO GFP-mGRtetra

value: TCA 100uM/Cort 100nM 2h


title: Mouse liver, Vehicle_4, Day 90, rep 1

description: Library name: X358-1

value: liver


title: Mouse liver, Vehicle_3, Day 30, rep 3

description: Library name: X302-3


title: cnr.wt.treatment_dmso.ctrl.flag.rep3

value: basal breast cancer line

value: Control/Uninduced

value: DMSO

value: FLAG M2 SIGMA [SIGMA, F1804]


title: cnr.wt.treatment_dmso.ctrl.brg1.rep2

value: BRG1 [Abcam, ab110641]


title: OE19, DMSO Rep3

value: Esophageal  adenocarcinoma

value: DMSO Control

value: 96 hours


title: GP5d, DNMTi Rep3

value: Colon adenocarcinoma

value: WT

value: DNMT  inhibition

value: 72 hours


title: Mouse liver, Vehicle_2, Day 30, rep 2

description: Library name: X302-2


title: MCF10CA1a, Bio Rep 2, Library 3

first: Kathleen

middle: Shaindel Metz

last: Reed

state: MD

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

description: Micro-C library

data_processing:
Reads are aligned to the human genome with bwa mem
Pairtools is used to parse, sort, and remove duplicates
Pairtools and samtools are used to generate .pairs and .bam files
Samtools is used to sort and index the .bam files
Juicer_tools pre is used to generate a .hic file
Assembly: hg38 (NCBI GRCh38, iGenomes)
Supplementary files format and content: .hic files
Library strategy: Micro-C

growth_protocol: Cells were grown in DMEM/F12 supplemented with 1.05 mM CaCl2, 5% horse serum, and 10mM HEPES. Media for MCF10A and MCF10AT1 cells was additionally supplemented with 10 ug/ml insulin, 20ng/ml EGF, 0.5 ug/ml hydrocortisone, and 0.1 ug/ml cholera enterotoxin. Cells were grown to ~70% confluence in 15cm plates.

extract_protocol:
Cells were trypsinized and counted. 5M cells at a time were pelleted down and resuspended in PBS. Aliquots of 1M cells were generated, spun down, supernatant was removed, and the 1M cell pellets were flash frozen in liquid nitrogen and sent to Cantata Bio for extraction and library prep.
The Micro-C library was prepared using the Dovetail® Micro-C Kit according to the manufacturer’s protocol. Briefly, the chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was then digested in situ with micrococcal nuclease (MNase). Following digestion, the cells were lysed with SDS to extract the chromatin fragments and the chromatin fragments were bound to Chromatin Capture Beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends. After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified then converted into a sequencing library using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification.

value: epithelial (metastatic)


title: MCF10CA1a, Bio Rep 2, Library 4

description: Micro-C library


title: P1, ATAC-seq

value: auricular cartilage

value: primary chondrocyte


title: GP5d, DNMTi Rep2


title: cnr.wt.treatment_dmso.ctrl.flag.rep1

value: WT GATA3 (1-444aa)


title: Mouse liver, Vehicle_1, Day 30, rep 1

description: Library name: X302-1

data_processing:
FASTQ generation: Illumina bcl-convert v4.0
Read trimming: Trimmomatic v0.38  SLIDINGWINDOW:5:15 HEADCROP:3 AVGQUAL:15 LEADING:5 TRAILING:5 MINLEN:80.
Alignment: BSMAP v2.90 to mm39  -n 0 -v 0.08 -g 1 -p 48.
Methylation ratios: methratio.py, BSMAP package
DMCs: Radmeth v1.0  coverage >= 5×, Q < 0.05, Δβ > 0.10.
DMRs: metilene v0.2-8  --mincpgs 3 --mode 1 -mtc 2; keep regions P < 0.05, Δβ > 0.10, >= 5 CpGs, length > 50 bp.
Assembly: mm10
Supplementary files format and content: xls format table with chr, pos, strand, context, rate, depth, nC
Supplementary files format and content: csv format table with chr,start,end,meth.diff,qvalue,annotation,gene_annot

extract_protocol:
Genomic DNA was isolated from mouse liver tissue or Hepa1-6 liver cells with the QIAamp DNA Mini kit (Qiagen), quantified by Qubit fluorometry, fragment size verified on a Fragment Analyzer, and spiked with 0.5 % unmethylated λ-DNA as a bisulfite-conversion control.
One µg gDNA was sheared (~250 bp) on a Bioruptor, end-repaired, A-tailed and ligated to 5-mC Illumina adapters; DNA was bisulfite-converted (EZ DNA Methylation-Gold, Zymo), PCR-amplified (8–12 cycles, KAPA HiFi Uracil+), size-selected with AMPure XP beads, QC’d on a Bioanalyzer, quantified by qPCR, and sequenced as 2 × 150 bp reads on an Illumina NovaSeq X Plus.

value: liver


title: cnr.wt.treatment_dmso.ctrl.brg1.rep3

value: basal breast cancer line


title: MCF10CA1a, Bio Rep 2, Library 2

description: Micro-C library


title: cnr.wt.treatment_brm014.dox.snf5.rep3

value: DOX


title: GRKO GFP-mGRtetra 100uM TCA/100nM Cort 2h Replicate 2

description: Library name: GH4636

value: adenocarcinoma cells

value: GRKO GFP-mGRtetra

value: TCA 100uM/Cort 100nM 2h


title: cnr.wt.treatment_dmso.ctrl.brg1.rep1

value: Control/Uninduced

value: DMSO

value: BRG1 [Abcam, ab110641]


title: cnr.wt.treatment_dmso.ctrl.flag.rep2

value: FLAG M2 SIGMA [SIGMA, F1804]


title: 1L-sgPTGES3_DMSO

value: castration resistant prostate cancer

value: LNCaP


title: cnr.wt.treatment_brm014.dox.snf5.rep2


title: GP5d, DNMTi Rep1

value: Colon adenocarcinoma

value: WT

value: DNMT  inhibition

value: 72 hours


title: MCF10CA1a, Bio Rep 2, Library 1

description: Micro-C library

value: epithelial (metastatic)


title: GRKO GFP-mGRtetra 100uM TCA/100nM Cort 2h Replicate 1

description: Library name: GH4635


title: GRKO GFP-mGRtetra 100uM TCA 2h Replicate 2

description: Library name: GH4633

value: TCA 100uM 2h


title: GRKO GFP-mGRtetra 100uM TCA 2h Replicate 1

description: Library name: GH4632


title: cnr.wt.treatment_brm014.dox.snf5.rep1

value: basal breast cancer line

value: WT GATA3 (1-444aa)


title: 2L-sgGAL4_DMSO


title: GRKO GFP-mGRtetra 100uM TCA 2h Replicate 3

description: Library name: GH4634

value: adenocarcinoma cells


title: LNCAP sgPTGES3 rep2

data_processing:
The ATAC-seq paired-end fastq files were trimmed to remove Illumina Nextera adapter sequence using Cutadapt v2.6. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Bowtie2 was then used to align the ATAC-seq reads against the Human reference genome build hg38 using. The uniquely mapped reads were obtained in SAM format. Samtools was used to convert SAM to BAM file as well as sort the BAM file. Picard was then used to flag duplicates using the MarkDuplicates tool. The resulting BAM file reads position were then corrected by a constant offset to the read start using deepTools2. This resulted in the final aligned, de-duplicated BAM file that was used in all downstream analyses. ATAC-seq peak calling was performed using MACS2 to obtain narrow peaks. The resulting peaks that map to the mitochondrial genome or genomic regions listed in the ENCODE hg38 blacklist or peaks that extend beyond the ends of chromosomes were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: peaks bed file

extract_protocol: ATAC-Seq on LNCaP cells were performed following knockdown of PTGES3 or control (GAL4). The experiment was carried out as described in the published method papers by Buenrostro, et al. and Corces, et al. with the following modifications. Cells were resuspended in buffer, incubated on ice for 10 minutes, and lysed using a dounce homogenizer. 50,000 nuclei were incubated with 25uL 2X TD Buffer and 1.25uL Transposase shaking at 300rpm at 37C for 30 minutes. Zymo DNA Clean and Concentrator 5 kit was then used to purify DNA. Transposed DNA was amplified using PCR master mix and indexes from Nextera DNA Library Prep kit for 5 cycles and then assessed using qPCR. Final cleanup was performed using 1.8X AMPure XP beads and libraries quantified using the DNA High Sensitivity Agilent 2100 Bioanalyzer System. Samples were sequenced at the UCSF Core Facility on the HiSeq4000 paired end 100. The entire experimental setup was performed in two technical replicates.


title: LNCAP sgGAL4 rep2


title: MCF10CA1a, Bio Rep 1, Library 4

description: Micro-C library


title: LNCAP sgPTGES3 rep1


title: GRKO GFP-mGRtetra 100nM Cort 2h Replicate 3

description: Library name: GH4631

value: GRKO GFP-mGRtetra

value: Cort 100nM 2h


title: cnr.wt.treatment_brm014.dox.fra1.rep3

value: DOX

value: FRA1 [Abcam, ab252421]


title: LNCAP sgGAL4 rep1


title: MCF10CA1a, Bio Rep 1, Library 3

description: Micro-C library


title: MCF10CA1a, Bio Rep 1, Library 2

description: Micro-C library


title: GRKO GFP-mGRtetra 100nM Cort 2h Replicate 2

description: Library name: GH4630


title: MCF10CA1a, Bio Rep 1, Library 1

description: Micro-C library


title: haf2_del_ethylene_rep2

city: Austin

first: Guihua

last: Wang

state: Texas

address: 2506 Speedway

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

description: sequencing instrument: Illumina NovaSeq X Plus

data_processing:
Paired-end raw fastq data were evaluated with FastQC and low-quality reads were removed with Trim Galore (Babraham Institute).
The trimmed and filtered reads were then mapped to the Arabidopsis reference genome (TAIR10) with STAR.
Mapped reads were counted by featureCounts (Subread 2.0.1) and differentially regulated genes were identified using R package DESeq2.
Assembly: TAIR10

organism: Arabidopsis thaliana

source_name: etiolated seedlings

growth_protocol: Arabidopsis seeds were first surface-sterilized with solution containing 50% bleach and 0.01% Triton X-100 for 10 minutes, washed with sterile distilled water for four times, sown on Murashige and Skoog (MS) medium plates containing 1% sucrose and 1% phytoblend agar and stratified for three days at 4°C in the dark.

extract_protocol:
RNA extraction was conducted following the manufacturer’s recommendation using the RNeasy Plant Kit (Qiagen) with DNase I digestion and clean up (Qiagen, RNeasy Mini Kit (250)).
Libraries were generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770), with 1μg RNA as input, following the manufacturer’s instructions.

treatment_protocol: After stratification and light exposure, plated seeds on MS medium were treated with a flow of hydrocarbon free air at 22°C in air-tight containers. After three days in the dark, those etiolated seedlings were subsequently treated with ethylene gas (10 ppm) or hydrocarbon-free air for indicated hours prior to sampling.

value: etiolated seedlings

value: ethylene


title: cnr.wt.treatment_brm014.dox.fra1.rep2


title: MCF10AT1, Bio Rep 2, Library 4

description: Micro-C library

value: epithelial (pre-malignant)


title: GRKO GFP-mGRtetra 100nM Cort 2h Replicate 1

description: Library name: GH4629


title: haf2_del_ethylene_rep1


title: cnr.wt.treatment_brm014.dox.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: MCF10AT1, Bio Rep 2, Library 3

description: Micro-C library


title: haf2_del_air_rep2

value: air


title: GRKO GFP-mGRtetra Veh Replicate 2

description: Library name: GH4627

value: Vehicle


title: MCF10AT1, Bio Rep 2, Library 2

description: Micro-C library


title: haf2_del_air_rep1


title: cnr.wt.treatment_brm014.dox.flag.rep2


title: GRKO GFP-mGRtetra Veh Replicate 3

description: Library name: GH4628


title: cnr.wt.treatment_brm014.dox.flag.rep1


title: GRKO GFP-mGRwt 100uM TCA/100nM Cort 2h Replicate 3

description: Library name: GH4613

value: GRKO-mGRwt

value: TCA 100uM/Cort 100nM 2h


title: haf2_ko_ethylene_rep2


title: cnr.wt.treatment_brm014.dox.brg1.rep3

value: BRG1 [Abcam, ab110641]


title: MCF10AT1, Bio Rep 1, Library 4

description: Micro-C library


title: GRKO GFP-mGRtetra Veh Replicate 1

description: Library name: GH4626


title: cnr.wt.treatment_brm014.dox.brg1.rep2


title: MCF10AT1, Bio Rep 2, Library 1

description: Micro-C library


title: GRKO GFP-mGRwt 100uM TCA/100nM Cort 2h Replicate 2

description: Library name: GH4612


title: haf2_ko_air_rep2


title: MCF10AT1, Bio Rep 1, Library 3

description: Micro-C library


title: cnr.wt.treatment_brm014.dox.fra1.rep1


title: cnr.wt.treatment_brm014.dox.brg1.rep1


title: GRKO GFP-mGRwt 100uM TCA/100nM Cort 2h Replicate 1

description: Library name: GH4611


title: haf2_ko_air_rep1


title: MCF10AT1, Bio Rep 1, Library 2

description: Micro-C library


title: cnr.wt.treatment_brm014.ctrl.snf5.rep3

value: Control/Uninduced


title: MCF10AT1, Bio Rep 1, Library 1

description: Micro-C library


title: haf2_ko_ethylene_input_rep2

data_processing:
Paired-end raw reads were first mapped to the Arabidopsis genome (TAIR10) using Bowtie2 software with default parameters. Duplicate reads were removed using SAMtools.
H3K14ac and H3K23ac ChIP-seq data for Col-0 air and ethylene treatment were obtained from previous study (GEO accession code GSE77396). ChIP-seq coverage tracks shown in the genome browser IGV were generated using deeptools3.0.2
bamCoverage function normalized by reads per genomic content (1x normalization, 1X RPGC) and bin size = 1.
Assembly: TAIR10
Supplementary files format and content: bw, bin =1
Supplementary files format and content: bw, bin =1

extract_protocol:
Three-day-old etiolated haf2_ko seedlings treated with air or 4h ethylene were harvested and crosslinked in 1% formaldehyde, and the chromatin was isolated and sheared by Bioruptor. Anti-H3K14ac (Millipore; 07-353) and anti-H3K23ac (Millipore; 07-355) antibodies together with Dynabeads were added to the sonicated chromatin followed by incubation overnight to precipitate histone bound DNA fragments.
Chromatin-immunoprecipitated DNA after elution was prepared for library construction by using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads according to standard operating procedures and then sequenced using Illumina NovaSeq X Plus.

tag: chip antibody


title: cnr.wt.treatment_brm014.ctrl.snf5.rep2

value: basal breast cancer line


title: GRKO GFP-mGRwt 100uM TCA 2h Replicate 3

description: Library name: GH4610

value: TCA 100uM 2h


title: MCF10A, Bio Rep 2, Library 4

description: Micro-C library

value: epithelial (normal-like)


title: GRKO GFP-mGRwt 100uM TCA 2h Replicate 1

description: Library name: GH4608

value: adenocarcinoma cells


title: cnr.wt.treatment_brm014.ctrl.snf5.rep1

value: WT GATA3 (1-444aa)


title: haf2_ko_ethylene_input_rep1


title: haf2_ko_ethylene_H3K23ac_rep2

value: Anti-H3K23ac (Millipore; 07-355)


title: MCF10A, Bio Rep 2, Library 3

description: Micro-C library


title: haf2_ko_ethylene_rep1


title: cnr.wt.treatment_brm014.ctrl.fra1.rep3

value: FRA1 [Abcam, ab252421]


title: MCF10A, Bio Rep 2, Library 2

description: Micro-C library


title: GRKO GFP-mGRwt 100nM Cort 2h Replicate 3

description: Library name: GH4607

value: Cort 100nM 2h


title: cnr.wt.treatment_brm014.ctrl.fra1.rep2


title: haf2_ko_ethylene_H3K23ac_rep1

value: etiolated seedlings

value: ethylene


title: GRKO GFP-mGRwt 100nM Cort 2h Replicate 2

description: Library name: GH4606


title: MCF10A, Bio Rep 2, Library 1

description: Micro-C library


title: haf2_ko_ethylene_H3K14ac_rep2

value: Anti-H3K14ac (Millipore; 07-353)


title: cnr.wt.treatment_brm014.ctrl.fra1.rep1


title: GRKO GFP-mGRwt 100nM Cort 2h Replicate 1

description: Library name: GH4605


title: haf2_ko_ethylene_H3K14ac_rep1


title: MCF10A, Bio Rep 1, Library 4

description: Micro-C library


title: haf2_ko_air_input_rep2

value: air


title: 1L-sgGAL4_DMSO

value: castration resistant prostate cancer

value: LNCaP


title: GRKO GFP-mGRwt Veh Replicate 3

description: Library name: GH4604

value: GRKO-mGRwt

value: Vehicle


title: MCF10A, Bio Rep 1, Library 3

description: Micro-C library


title: GRKO GFP-mGRwt 100uM TCA 2h Replicate 2

description: Library name: GH4609


title: cnr.wt.treatment_brm014.ctrl.flag.rep2

value: Control/Uninduced

value: FLAG M2 SIGMA [SIGMA, F1804]


title: cnr.wt.treatment_brm014.ctrl.flag.rep1

value: basal breast cancer line


title: MCF10A, Bio Rep 1, Library 2

description: Micro-C library

value: epithelial (normal-like)


title: GRKO GFP-mGRwt Veh Replicate 1

description: Library name: GH4602

value: adenocarcinoma cells


title: haf2_ko_air_H3K23ac_rep2


title: cnr.wt.treatment_brm014.ctrl.brg1.rep3

value: WT GATA3 (1-444aa)

value: BRG1 [Abcam, ab110641]


title: MCF10A, Bio Rep 1, Library 1

description: Micro-C library


title: haf2_ko_air_input_rep1


title: GRKO GFP-mGRwt Veh Replicate 2

description: Library name: GH4603


title: cnr.wt.treatment_brm014.ctrl.brg1.rep2


title: Primary Tumor, IR, biological replicate 5

city: Boston

first: Gerald

middle: V

last: Denis

state: MA

address: 72 East Concord Street

institute: Boston University

description:
Library name: IR_5
primary_tumor_salmon.merged.gene_counts.tsv

data_processing:
Sequencing reads were processed using the nf-core rnaseq pipeline.
Reads were quality trimmed using Trimmomatic to remove adapters and low-quality bases.
Quality-checked reads were aligned to the mouse reference genome using STAR aligner.
Gene expression counts were generated using featureCounts based on the GRCm38/mm10 annotation.
Differential gene expression analysis was performed using DESeq2 to compare Control and Experimental groups.
Assembly: GRCm39/mm39 mouse reference genome.
Supplementary files format and content: Tab-delimited text files containing raw gene counts for each sample.
Supplementary files format and content: Tab-delimited text files containing normalized expression values for each sample.

source_name: Primary Tumor

growth_protocol: Murine 4T1 cells as a TNBC model and murine 3T3-L1 pre-adipocytes to be differentiated into mature adipocytes were obtained from the American Type Culture Collection. The 4T1 cells and 3T3L1 cells were cultured in RPMI1640 and DMEM medium, respectively, supplemented with 10% fetal bovine serum (FBS), and 100 units/mL penicillin, 10 μg/mL streptomycin (Corning), and incubated at 37°C with 100% humidity and 5% CO2.

extract_protocol:
Total RNA was extracted from 4T1 cells treated with IS and IR adipocyte derived exosome using the RNeasy Plus Mini Kit (QIAGEN, Cat. No. 74136), following the manufacturer's protocol. Exosomal RNA was extracted from culture media using the exoRNA Easy Kit(Qiagen, Cat. No. 77144).  RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, as per the manufacturer's protocol. Final libraries were checked for quality using an Agilent Bioanalyzer and quantified using a Qubit fluorometer.

treatment_protocol: 4T1 cells were treated with exosomes isolated from IS and IR adipocytes on Day 0 and cultured for 72 hours until 70% confluency was reached.

value: Primary Tumor

value: Mammary adenocarcinoma cells

value: IR group, primary tumor


title: haf2_ko_air_H3K14ac_rep2

value: etiolated seedlings


title: haf2_ko_air_H3K23ac_rep1

value: Anti-H3K23ac (Millipore; 07-355)


title: NEXO_8

city: Oxford

first: Tamiris

last: Borges da Silva

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina NovaSeq platform NovaSeq 6000
Illumina Casava 1.8 was used for quality control and Phred score for determination of sequence error rate
Sequence reads were trimmed for adaptor sequence/low quality sequences (Base Quality less than 5)
Raw sequences were provided after quality control assessment by Novogene
Paired reads were concatenated and salmon quant was used for quantification
Assembly: GRCh38.p14
Supplementary files format and content: Salmon quantification files in the format quant.sf using Galaxy Europe

source_name: normal human dermal fibroblasts

growth_protocol: Bone marrow mesenchymal stromal cells were cultured with PromoCell Mesenchymal Stem Cell Growth Media 2 supplemented with provided supplement pack. Normal Human dermal fibroblasts were cultured with PromoCell Fibroblast Growth Media 2 according to manufacturer's instructions

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
Poly-A enrichment (performed by Novogene Limited (Cambridge, UK)

treatment_protocol: Normal human dermal fibroblasts were cultured to confluency in 6 well plates and had their medium changed for 48 hours to DMEM 1% Penicillin/Streptomycin with 30 µg/ml of secretome fractions. Controls were only exposed to DMEM 1% Penicillin/Streptomycin

value: normal human dermal fibroblasts

value: NHDFs exposed to non small extracellular vesicles

tag: batch


title: NEXO_7


title: Primary Tumor, IR, biological replicate 3

description:
Library name: IR_3
primary_tumor_salmon.merged.gene_counts.tsv


title: haf2_ko_air_H3K14ac_rep1

value: Anti-H3K14ac (Millipore; 07-353)

value: air


title: cnr.wt.treatment_brm014.ctrl.brg1.rep1


title: Primary Tumor, IR, biological replicate 2

description:
Library name: IR_2
primary_tumor_salmon.merged.gene_counts.tsv


title: NEXO_5


title: Primary Tumor, IR, biological replicate 1

description:
Library name: IR_1
primary_tumor_salmon.merged.gene_counts.tsv


title: cnr.wt.lenti_empty.dox.p300.rep2

value: DOX


title: cnr.wt.lenti_empty.dox.p300.rep3


title: cnr.wt.treatment_brm014.ctrl.flag.rep3

value: Control/Uninduced


title: EV_8

value: NHDFs exposed to small extracellular vesicles


title: 5 dpf hematopoietic zebrafish cells, posterior region, replicate 2

city: Paris

first: Lea

last: Torcq

address: 25 Rue du docteur Roux

country: France

institute: Institut Pasteur

description: Library name: 5dpf_hematopoietic_posterior_2

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoding processing, aligment, gene count and agregation was done using the CellRanger  (version v6.1.2)
Assembly: zebrafish genome (Lawson lab version 4.3.2).
Supplementary files format and content: Tab-separated value files and matrix files

organism: Danio rerio

source_name: posterior region

extract_protocol:
Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources (Bresciani et al., 2018; Manoli and Driever, 2012; Samsa et al., 2016). All steps were performed with cooled solutions (4°C), and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly, 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine, at a final concentration of 640 µg/ml. Larvae (between 20 and 30 whole larvae or 60-80 dissected segments per tube) were washed twice in PBS before centrifugation (300 x g for 1 min @4°C) and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium (Life Technologies, Cat#: 12605-010) for 10 min on ice, with gentle pipetting every 3 mins, first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g, before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium (Genlantis, Cat#: T200100). Ultimately, samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow-through was transferred to a FACS tube and kept on ice until sorting (within the hour). Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples, gating was done on SSC-A vs. FSC-A to collect cells, then on FSC-W vs. FSC-A to keep only singlets and on APC-A to remove dead cells marked by Draq7 (Thermofisher, Cat#: D15106).
Based on the 10XGenomics Chromium V3.1 guidelines, a mix of single and double positive cells from approximately 100 dissected 5dpf outcrossed Tg(cd41:eGFP) X Tg(gata2b:RFP) double-positives larvae were collected in PBS and diluted at a concentration of around 400 cells/µL in order to load ~20 000 cells per condition (anterior and posterior halves of larvae). Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10XGenomics, Cat#: PN-1000269) kit was used, and library preparation was performed according to the manufacturer recommendations (17 PCR cycles were performed for final library amplification, and library quality and concentration were assessed using the BioAnalyzer and Qubit systems). Two independent biological replicates were generated. The sequencing was performed on a Novaseq6000 platform to generate 150-bp paired-end reads, and a theoretical count of 40 000 reads per cell were sequenced.

value: posterior region

value: hematopoietic cells


title: 5 dpf hematopoietic zebrafish cells, anterior region, replicate 2

description: Library name: 5dpf_hematopoietic_anterior_2

source_name: anterior region

value: anterior region


title: Primary Tumor, control, biological replicate 4

description:
Library name: Control_5
primary_tumor_salmon.merged.gene_counts.tsv

value: No treatment, primary tumor


title: cnr.wt.lenti_empty.dox.p300.rep1

value: basal breast cancer line

value: WT GATA3 (1-444aa)


title: EV_7


title: Primary Tumor, control, biological replicate 3

description:
Library name: Control_3
primary_tumor_salmon.merged.gene_counts.tsv

value: Primary Tumor

value: Mammary adenocarcinoma cells


title: cnr.wt.lenti_empty.dox.fra1.rep3

value: FRA1 [Abcam, ab252421]


title: Primary Tumor, IR, biological replicate 4

description:
Library name: IR_4
primary_tumor_salmon.merged.gene_counts.tsv

value: IR group, primary tumor


title: 5 dpf hematopoietic zebrafish cells, anterior region, replicate 1

description: Library name: 5dpf_hematopoietic_anterior_1


title: EV_6

value: normal human dermal fibroblasts


title: cnr.wt.lenti_empty.dox.fra1.rep2


title: Primary Tumor, control, biological replicate 2

description:
Library name: Control_2
primary_tumor_salmon.merged.gene_counts.tsv


title: NEXO_6

value: NHDFs exposed to non small extracellular vesicles


title: EV_5


title: Primary Tumor, control, biological replicate 1

description:
Library name: Control_1
primary_tumor_salmon.merged.gene_counts.tsv


title: zebrafish embryos, EW treatment group-3

city: Baotou

first: Xiaoe

last: Jia

address: 31# Jian She Road, Baotou Medical College, Baotou, 014040, Inner Mongolia Autonomous Region, China

institute: Baotou Medical College

description:
Library name: HD0005405-EW48-3
EW48-3.txt

data_processing:
Illumina/BGI platform
Assembly: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: csv files include FPKM values for each sample

source_name: whole embryo

extract_protocol:
RNA was harvested using TRIzol Reagent Kit (Magen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Abclonal mRNA-seq Lib Prep  Kit (Abclonal, China) following manufacturer's protocols.

value: whole embryo

value: wildtype

value: MTZ +EW treatment


title: zebrafish embryos, EW treatment group-2

description:
Library name: HD0005404-EW48-2
EW48-2.txt


title: cnr.wt.lenti_empty.dox.fra1.rep1

data_processing:
Adapters were clipped from raw read pairs with TrimGalore v0.6.6.
Read pairs were mapped to the hg38 reference assembly with bowtie2 v2.4.5 using parameters "--local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700", then filtered with samtools v1.19.2 for minimum MAPQ of 30.
Duplicate mapped fragments were then removed by MarkDuplicate from the Picard tool suite v.2.27.1 with parameter REMOVE_DUPLICATES=TRUE.
Biological triplicate samples were combined with samtools merge function.
Peaks calls were made with MACS2 v2.2.9.1 on the merged replicates using IgG per condition (WT Control, WT DOX, TA1del Control, TA1del DOX) with -q 0.00001;  peak sets per antibody and experimental subset were then concatenated, merged with bedtools v2.30.0 (-d 10), and filtered to remove exclusion list regions (ENCODE) and non-canonical chromosomes.
Fragments at peaks were counted by the featureCounts function of subread v2.0.3 with parameters "-p -countReadPairs".
Genomic coverage tracks were generated by deeptools bamCoverage v3.5.3 with parameters "--normalizeUsing None --binSize 10 --ignoreDuplicates --effectiveGenomeSize 2913022398 --scaleFactor", where the scale factors were calculated by 1/[(E.Coli fragment count/Sample fragment count)*100.  For lenti-empty and lenti-AFOS treated samples, only the 2nd and 3rd replicates contributed to the coverage tracks to avoid bias resulting from the separate pAG-MNase batch used for the 1st replicate.
Assembly: hg38
Supplementary files format and content: Fragment counts per peak in tab-delimited text format.
Supplementary files format and content: Normalized genomic coverage tracks in bigWig format.
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed following standard CUT&RUN conditions outlined in protocol provided by Henikoff lab on protocols.io (Skene and Henikoff 2017, Janssens 2019, Meers et al. 2019) with minor modification of increasing wash steps to 4 times. Purified pAG-MNase was provided by the NIEHS Protein Expression Core and purified using Meers et al. 2019 protocol. For each reaction, 5e5 cells were harvested. Antibody dilutions (overnight incubation) were as follows: IgG Rabbit (Antibodies online ABIN101961; 1:100), Mouse IgG (Abcam ab46540; 1:100), FLAG M2 (Sigma F1804; 1:50), FRA1 (Abcam ab252421; 1:50), p300 (CST 86377S; 1:50), H3K4me1 (Epicypher 13-0057; 1:50), H3K27ac (Millipore MABE647; 1:50), BRG1 (Abcam ab110641; 1:50), SNF5/SMARCB1 (CST 91735S; 1:50).
Library preparations were performed with NEBNext Ultra II (NEB #E7645) described for transcription factors(Liu et al. 2018, Liu 2021) at half volume reactions. Additional modifications were made using NEBNext unique Dual Index Primers (NEB #E6440, #E6442), 15 ng of input DNA, and 0.5 µM diluted adapter.

value: DOX


title: In vitro, miR-145a-3p, biological replicate 3

description:
Library name: ScRNA4D_3
mirna_salmon.merged.gene_counts.tsv

source_name: In vitro

value: In vitro

value: miRNA miR-145a-3p treatment


title: cnr.wt.lenti_empty.dox.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: zebrafish embryos, EW treatment group-1

description:
Library name: HD0005403-EW48-1
EW48-1.txt


title: DMEM_7

value: NHDFs incubated with DMEM (controls)


title: cnr.wt.lenti_empty.dox.flag.rep2


title: In vitro, miR-145a-3p, biological replicate 2

description:
Library name: ScRNA4D_2
mirna_salmon.merged.gene_counts.tsv


title: DMEM_6


title: zebrafish embryos, MTZ model group-3

description:
Library name: HD0005402-MTZ48-3
MTZ48-3.txt

value: MTZ treatment


title: In vitro, miR-145a-3p, biological replicate 1

description:
Library name: ScRNA4D_1
mirna_salmon.merged.gene_counts.tsv


title: cnr.wt.lenti_empty.dox.flag.rep1

value: basal breast cancer line


title: zebrafish embryos, MTZ model group-2

description:
Library name: HD0005401-MTZ48-2
MTZ48-2.txt


title: 5 dpf hematopoietic zebrafish cells, posterior region, replicate 1

description: Library name: 5dpf_hematopoietic_posterior_1

value: posterior region

value: hematopoietic cells


title: DMEM_5


title: cnr.wt.lenti_empty.dox.brg1.rep3

value: WT GATA3 (1-444aa)

value: BRG1 [Abcam, ab110641]


title: In vitro, scramble miRNA negative control, biological replicate 2

description:
Library name: miR1454D_2
mirna_salmon.merged.gene_counts.tsv

value: Mammary adenocarcinoma cells

value: scrambled miRNA treatment


title: zebrafish embryos, MTZ model group-1

description:
Library name: HD0005400-MTZ48-1
MTZ48-1.txt


title: cnr.wt.lenti_empty.dox.brg1.rep2


title: In vitro, scramble miRNA negative control, biological replicate 1

description:
Library name: miR1454D_1
mirna_salmon.merged.gene_counts.tsv


title: zebrafish embryos, control group-3

description:
Library name: HD0005399-DMSO48-3
DMSO48-3.txt

value: DMSO treatment


title: NEXO_3

value: normal human dermal fibroblasts

value: NHDFs exposed to non small extracellular vesicles


title: Brain, Clonogenic Assay, IR, biological replicate 5

description:
Library name: Brain_IR5
brain_rsem_expected_counts.tsv

source_name: Brain Clonogenic Assay

value: Brain Clonogenic Assay

value: IR group, Brain clonogenic assay


title: DMEM_8


title: zebrafish embryos, control group-2

description:
Library name: HD0005398-DMSO48-2
DMSO48-2.txt

value: whole embryo

value: wildtype


title: NEXO_2


title: Brain, Clonogenic Assay, IR, biological replicate 4

description:
Library name: Brain_IR4
brain_rsem_expected_counts.tsv


title: NEXO_1


title: cnr.wt.lenti_empty.ctrl.p300.rep3

value: Control/Uninduced


title: cnr.wt.lenti_empty.ctrl.p300.rep2


title: Brain, Clonogenic Assay, IR, biological replicate 3

description:
Library name: Brain_IR3
brain_rsem_expected_counts.tsv


title: zebrafish embryos, control group-1

description:
Library name: HD0005397-DMSO48-1
DMSO48-1.txt


title: Brain, Clonogenic Assay, IR, biological replicate 2

description:
Library name: Brain_IR2
brain_rsem_expected_counts.tsv


title: EV_3

value: NHDFs exposed to small extracellular vesicles


title: PNT36-MGUS_12

type: RNA

city: Barcelona

first: David

middle: F.

last: Moreno

state: Barcelona

address: Villarroel 170

department: Hematology

country: Spain

institute: IDIBAPS - Hospital Clínic de Barcelona

description: RNA was isolated using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA)

hyb_protocol: A minimum of 100 ng of total RNA per sample was loaded and run on the HuV1_Cancer Immu_v1_1_Nanostring for analysis of the NanoString PanCancer Immune Profiling Panel

scan_protocol: The sample cartridge was scanned by an nCounter Digital Analyse (NanoString Technologies) at 555 fields of view.

data_processing: Quality control of the raw data followed the recommendations of the nSolver software. The R package NanoTube (version 1.10.0) with standard parameters was used to preprocess the gene expression counts, including nSolver normalization.

label: NanoString

source_name: CD19 depleted bone marrow

label_protocol: Capture probes and reporter probes (NanoString Technologies) were added to the extracted mRNA (a minimum of 100 ng) according to manufacturer instructions

growth_protocol: Fresh bone marrow samples collected in EDTA tubes obtained from patients with IgM MGUS and WM were used.

extract_protocol: Total RNA was isolated from the CD19-depleted samples using TRIzol® reagent (Thermo Fisher Scientific, Waltham, MA). The isolated RNA was quantified using Qubit 2.0 Fluorometer (ThermoFischer).

treatment_protocol: Immediately, the samples were subjected to immunomagnetic separation with CD19 microbeads (AutoMACS, Milteny Biotec, Bergisch Gladbach, Germany) to deplete B cells.

tag: diagnosis

value: IgM MGUS

tag: risk

value: Intermediate risk


title: EV_4


title: EV_2


title: Brain, Clonogenic Assay, IR, biological replicate 1

description:
Library name: Brain_IR1
brain_rsem_expected_counts.tsv


title: Brain, Clonogenic Assay, IS, biological replicate 5

description:
Library name: Brain_IS5
brain_rsem_expected_counts.tsv

value: IS group, Brain clonogenic assay


title: cnr.wt.lenti_empty.ctrl.fra1.rep3

value: basal breast cancer line

value: FRA1 [Abcam, ab252421]


title: cnr.wt.lenti_empty.ctrl.fra1.rep2

value: WT GATA3 (1-444aa)


title: NEXO_4


title: cnr.wt.lenti_empty.ctrl.p300.rep1


title: cnr.wt.lenti_empty.dox.brg1.rep1

value: DOX

value: BRG1 [Abcam, ab110641]


title: cnr.wt.lenti_empty.ctrl.fra1.rep1


title: PNT34-MGUS_03


title: PNT27-MGUS_11


title: Brain, Clonogenic Assay, IS, biological replicate 4

description:
Library name: Brain_IS4
brain_rsem_expected_counts.tsv

value: Mammary adenocarcinoma cells


title: DMEM_2

value: normal human dermal fibroblasts

value: NHDFs incubated with DMEM (controls)


title: cnr.wt.lenti_empty.ctrl.flag.rep2

value: FLAG M2 SIGMA [SIGMA, F1804]


title: cnr.wt.lenti_empty.ctrl.flag.rep3


title: Brain, Clonogenic Assay, IS, biological replicate 3

description:
Library name: Brain_IS3
brain_rsem_expected_counts.tsv

value: Brain Clonogenic Assay


title: cnr.wt.lenti_empty.ctrl.flag.rep1


title: DMEM_3


title: DMEM_1


title: Brain, Clonogenic Assay, IS, biological replicate 1

description:
Library name: Brain_IS1
brain_rsem_expected_counts.tsv


title: PNT22-WM_06

value: Waldenström Macroglobulinemia


title: PNT23-WM_08

value: High risk


title: Brain, Clonogenic Assay, control, biological replicate 5

description:
Library name: Brain_C5
brain_rsem_expected_counts.tsv

value: No treatment, Brain clonogenic assay


title: PNT35-MGUS_07


title: cnr.wt.lenti_empty.ctrl.brg1.rep3

value: Control/Uninduced


title: Brain, Clonogenic Assay, IS, biological replicate 2

description:
Library name: Brain_IS2
brain_rsem_expected_counts.tsv


title: Brain, Clonogenic Assay, control, biological replicate 4

description:
Library name: Brain_C4
brain_rsem_expected_counts.tsv


title: DM_4

value: NHDFs exposed to depleted medium


title: DM_3


title: PNT21-MGUS_05

value: IgM MGUS

value: Intermediate risk


title: DMEM_4


title: cnr.wt.lenti_empty.ctrl.brg1.rep1

value: basal breast cancer line


title: PNT20-MGUS_04


title: Brain, Clonogenic Assay, control, biological replicate 3

description:
Library name: Brain_C3
brain_rsem_expected_counts.tsv


title: DM_2


title: cnr.wt.lenti_empty.ctrl.brg1.rep2


title: PNT24-MGUS_09


title: PNT19-MGUS_02


title: cnr.wt.lenti_afos.dox.p300.rep3


title: Brain, Clonogenic Assay, control, biological replicate 2

description:
Library name: Brain_C2
brain_rsem_expected_counts.tsv


title: In vitro, IR adipocyte exosome treated, biological replicate 3

description:
Library name: T_IR_3
invitro_rsem_expected_counts.tsv

value: In vitro

value: Insulin resistant adipocyte derived exosomes


title: PNT33-WM_09

value: Low risk


title: CM_2

value: NHDFs exposed to conditioned medium


title: PNT32-WM_08


title: In vitro, IR adipocyte exosome treated, biological replicate 2

description:
Library name: T_IR_2
invitro_rsem_expected_counts.tsv

value: Mammary adenocarcinoma cells


title: Brain, Clonogenic Assay, control, biological replicate 1

description:
Library name: Brain_C1
brain_rsem_expected_counts.tsv


title: CM_4

value: normal human dermal fibroblasts


title: PNT31-MGUS_07


title: CM_3


title: cnr.wt.lenti_afos.dox.fra1.rep2

value: WT GATA3 (1-444aa)

value: DOX

value: FRA1 [Abcam, ab252421]


title: CM_1


title: cnr.wt.lenti_afos.dox.fra1.rep1


title: In vitro, IS adipocyte exosome treated, biological replicate 3

description:
Library name: T_IS_3
invitro_rsem_expected_counts.tsv

value: Insulin sensitive adipocyte derived exosomes


title: cnr.wt.lenti_afos.dox.flag.rep3

value: FLAG M2 SIGMA [SIGMA, F1804]


title: cnr.wt.lenti_afos.dox.p300.rep2


title: PNT30-WM_04

value: Waldenström Macroglobulinemia


title: cnr.wt.lenti_afos.dox.p300.rep1


title: cnr.wt.lenti_afos.dox.flag.rep2


title: PNT17-WM_12


title: In vitro, IS adipocyte exosome treated, biological replicate 1

description:
Library name: T_IS_1
invitro_rsem_expected_counts.tsv


title: Peripheral blood CD8+ T cells CITE

city: Hwasun-eup, Hwasun-gun

first: Jae-Ho

last: Cho

state: Jeollanam-do

address: 264, Seoyang-ro

country: South Korea

institute: CHONNAM NATIONAL UNIVERSITY

description: 10x Genomics

data_processing:
Data processing procedures were carried out using Cell Ranger-6.1.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and a matrix file

source_name: peripheral blood

extract_protocol:
CD3+CD8+CD4- cells were purified using CytoFLEX SRT
Cells were resuspended in PBS and filtered through a 40 µm filter. After cells were counted using LUNA-FL™ Automated Fluorescence Cell Counter (Logos Biosystems), 10X Genomics Chromium Instrument and cDNA synthesis kit (Chromium Next GEM Single Cell 5ʹ Kit v2 & Chromium Next GEM Chip K Single Cell Kit) were used to generate a barcoded cDNA library for single Cell RNA-sequencing. cDNA library quality was determined using an Agilent Bioanalyzer (Agilent technologies). Two paired-end 200bp FlowCells were ran on an Illumina NovaSeq6000 S2 Rgt Kit v1.5 (200 cycles (Read lengths: 28 bp Read1, 10 bp I7 Index, 10 bp I5 Index, and 90 bp Read2) (Illumina).

treatment_protocol: No treatment

value: peripheral blood


title: DM_1

value: NHDFs exposed to depleted medium


title: Peripheral blood CD8+ T cells 5GE

description: 10x Genomics


title: cnr.wt.lenti_afos.dox.fra1.rep3


title: PNT18-MGUS_01

value: IgM MGUS

value: High risk


title: cnr.wt.lenti_afos.dox.flag.rep1

value: basal breast cancer line


title: In vitro, control, biological replicate 2

description:
Library name: T_Control_2
invitro_rsem_expected_counts.tsv

value: In vitro

value: No treatment


title: PNT15-MGUS_10

description: RNA was isolated using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA)

value: Intermediate risk


title: PNT16-MGUS_11


title: PNT14-MGUS_06

value: Low risk


title: OVCAR8ip1 cells, BARD1 expressed_2, biol rep 2, 48h

city: Houston

first: Emine

last: Bayraktar

address: 1881 East Road

institute: MD Anderson Cancer Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Raw reads filtering is as follows: Removing reads with adapter contamination. Removing reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%). Removing reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38 (hg38) from Genome Reference Consortium

source_name: SKOV3ip1 tumors

growth_protocol: OVCAR8ip1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 0.1% gentamicin sulfate.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: A BARD1-expressing OVCAR8 cell line was generated by transduction with a BARD1 plasmid (EX-Q0613-Lv122, GeneCopoeia, Inc). Lentivirus particles containing BARD1 open reading frames were produced using the Lenti-Pac HIV Expression Packaging Kit protocol (HPK-LvTR-20; GeneCopoeia) and transduced into OVCAR8 cells. Virus particles and polybrene were diluted in Opti-MEM and added to the cells the following day, and the cells were incubated overnight at 37 °C with 5% CO2. The next day, the media was replaced with complete media, and after 48 hours, the infected cells were analyzed for transient expression of GFP-BARD1 using a fluorescent microscope.

value: SKOV3ip1 tumors

value: High grade ovarian serous adenocarcinoma

value: stable cells


title: OVCAR8ip1 cells, BARD1 expressed_1, biol rep 1, 48h


title: cnr.wt.lenti_afos.dox.brg1.rep3

value: WT GATA3 (1-444aa)

value: DOX

value: BRG1 [Abcam, ab110641]


title: OVCAR8ip1 cells, Control _3, biol rep 3, 48h

value: control


title: In vitro, IS adipocyte exosome treated, biological replicate 2

description:
Library name: T_IS_2
invitro_rsem_expected_counts.tsv

value: Mammary adenocarcinoma cells

value: Insulin sensitive adipocyte derived exosomes


title: In vitro, control, biological replicate 1

description:
Library name: T_Control_1
invitro_rsem_expected_counts.tsv


title: cnr.wt.lenti_afos.dox.brg1.rep2


title: PNT13-MGUS_05


title: cnr.wt.lenti_afos.dox.brg1.rep1


title: nPA_611271, control replicate 4

city: Durham

first: Vennesa

last: Valentine

address: 308 Research Drive

institute: Duke Univerisity

description:
Library name: nPA_611271
nPA_611271 Genome-wide DNA Methylation

data_processing:
High-throughput sequencing generates massive raw data, which must meet quality standards for reliable bioinformatics analysis. FastQC is used to assess the quality of raw data and provide basic statistics.
FastQC was used to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software. The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the clean data reads.
DSS-single(DSS) was used to analyze differentially methylated regions (DMR) between K27M samples and nPA controls.  Smoothing was applied when conducting the analysis.
Assembly: The Bismark software was used for aligning bisulfite-treated reads to a reference genome.  The process involves converting C to T and G to A (reverse complement) in both the sequencing reads and the reference genome. The mouse genome used was GRCm39.
Supplementary files format and content: The processed data files are stored as K27M_vs_nPA.DMR.all.result.xls

source_name: mouse brain

extract_protocol:
Tumor-bearing mouse brains were cut in half sagitally and then formalin fixed and parrafin embedded (FFPE).  Tumor areas were identified on H+E slides cut from the surface of each FFPE block.  Tumor was then microdissected from the corresponding areas of two unstained ten-micron sections from the FFPE block.  Genomic DNA was extracted from the microdissected tumor tissue via standard methods.
The genomic DNA, spiked with lambda DNA, was fragmented into 200–400 bp pieces and bisulfite-treated to generate single-stranded DNA (ssDNA). During this process, unmethylated cytosines were converted to uracil, while methylated cytosines remained unchanged. Methylation sequencing adapters were ligated, and double-stranded DNA was synthesized. After size selection and PCR amplification, the library was prepared.

value: mouse brain

value: Nestin-TVA/TVA; p53-FL/FL; ATM-FL/FL

value: Irradiated


title: OVCAR8ip1 cells, BARD1 expressed_3, biol rep 3, 48h


title: PNT12-WM_03

value: Waldenström Macroglobulinemia


title: nPA_610769, control replicate 3

description:
Library name: nPA_610769
nPA_610769 Genome-wide DNA Methylation

value: Nestin-TVA/+; p53-FL/FL; ATM-FL/FL


title: OVCAR8ip1 cells, Control _2, biol rep 2, 48h


title: OVCAR8ip1 cells, Control _1, biol rep 1, 48h


title: cnr.wt.lenti_afos.ctrl.p300.rep3

value: basal breast cancer line

value: Control/Uninduced


title: nPA_610705, control replicate 2

description:
Library name: nPA_610705
nPA_610705 Genome-wide DNA Methylation

value: Nestin-TVA/TVA; p53-FL/FL; ATM-FL/+


title: cnr.wt.lenti_afos.ctrl.p300.rep2


title: In vitro, control, biological replicate 3

description:
Library name: T_Control_3
invitro_rsem_expected_counts.tsv

value: In vitro

value: No treatment


title: PNT10-WM_01

value: Low risk


title: PNT11-MGUS_02

value: IgM MGUS


title: nPA_612035, control replicate 1

description:
Library name: nPA_612035
nPA_612035 Genome-wide DNA Methylation


title: cnr.wt.lenti_afos.ctrl.fra1.rep3

value: WT GATA3 (1-444aa)

value: FRA1 [Abcam, ab252421]


title: cnr.wt.lenti_afos.ctrl.fra1.rep2


title: PT4

city: Zhengzhou

first: ting

last: sun

address: No. 100 Science Avenue

institute: Zhengzhou University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline (version 4.0.0) 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.
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat[1] (version 3.1.1). To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we apply a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CESC

extract_protocol:
Tumor and normal tissues were washed with PBS for three times and then were cut into 1-3 mm3. Tissue pieces were subsequently transferred to 10ml digestion medium containing 0.2% collagenase I/II, DNAse I (Sigma) and 25 units dispase in DMEM. Samples were placed on an incubated orbital shaker at 37C for 15 min with 250 RPM. 20mL ice-cold PBS containing 5% fetal bovine serum were added into sample and then samples were filtered with 40 µm cell strainer. After centrifugation with 1500 RPM, 5min at 4C, 5mL red blood cell lysis buffer were added for 15 min and then sample were centrifuged, single cell were re-suspended in sorting buffer and counted by automatic cell counter.
Library for single cell data were performed by Chromium Single Cell 3’Library, Gel Bead &Multiplex Kit and Chip Kit (10x Genomics) according to manufacturer’s instructions.

value: CESC

value: all cells

tag: age


title: PNT9-MGUS_12

value: Intermediate risk


title: cnr.wt.lenti_afos.ctrl.p300.rep1


title: PT3

description: 10x Genomics


title: PT5

description: 10x Genomics


title: K27M_612395, experimental replicate 1

description:
Library name: K27M_612395
K27M_612395 Genome-wide DNA Methylation

value: mouse brain

value: Nestin-TVA/TVA; p53-FL/FL; H3f3a-LSL-K27M/H3f3a-LSL-K27M; ATM-FL/FL


title: K27M_612408, experimental replicate 3

description:
Library name: K27M_612408
K27M_612408 Genome-wide DNA Methylation

value: Nestin-TVA/TVA; p53-FL/FL; H3f3a-LSL-K27M/H3f3a-LSL-K27M; ATM-FL/+


title: PNT7-MGUS_10


title: PNT8-WM_11

value: Waldenström Macroglobulinemia


title: PT1

description: 10x Genomics


title: PNT5-WM_06

value: High risk


title: PNT6-WM_07


title: PNT4-WM_05


title: cnr.wt.lenti_afos.ctrl.flag.rep2

value: basal breast cancer line

value: FLAG M2 SIGMA [SIGMA, F1804]


title: cnr.wt.lenti_afos.ctrl.fra1.rep1

value: Control/Uninduced


title: LNCAP 181-40 rep2

data_processing:
The RNA-seq paired-end fastq data generated by Illumina NovaSeq sequencing system were first trimmed to remove adapter sequence using Cutadapt. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Using splice-aware aligner STAR, RNA-seq reads were aligned onto the human reference genome build hg38 and exon-exon junctions, according to the known human gene model annotation from the GENCODE v30. Based on the reads that can only be mapped to a single genomic location, the gene expression quantification was performed using featurecount function within Rsubread R-package.
Assembly: hg38
Supplementary files format and content: raw_gene_counts_matrix_gencode_v30.txt: Matrix table with raw gene counts for every gene and every sample.

extract_protocol: RNA was extracted from the cells using the Zymo Quick-RNA extraction kit. QuantSeq 3’mRNA-Seq library prep kit FWD for Illumina was used to prepare the library as per the manufacturer’s protocol. Quality control was performed by using the Agilent Bioanalyzer 2100 system and the samples were sequenced in Illumina NovaSeq. The entire set of the experiment was done in two biological replicates.

treatment_protocol: LNCaP cells were treated with the PTGES3 inhibitor 181-40 or DMSO.

value: LNCaP

value: castration resistant prostate cancer

value: PTGES3 inhibitor 181-40


title: K27M_612409, experimental replicate 2

description:
Library name: K27M_612409
K27M_612409 Genome-wide DNA Methylation

value: Irradiated


title: trnE-mutant, 75-week-old, replicate 2, 80% mutation load, mtscATAC-seq

city: Hangzhou

first: Guo-shi

last: Chai

state: --- Select One ---

address: No. 600 Dunyu Road, Sandun Town, Xihu District, Hangzhou, Zhejiang PR China

institute: Westlake University

description: 10x Genomics

library_source: other

data_processing:
The nuclear mitochondrial DNA segments (NUMTs) were masked in the mm10 genome (PMID: 32788668 and PMID: 36792778). Raw sequencing data were aligned to the modified mm10 reference genome using CellRanger-ATAC (v 2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: Kidney

extract_protocol:
After obtaining the single-cell suspensions, we first fixed, lysed, and permeabilized the cells according to the method described in Nature Protocols (PMID:36792778). Briefly, the cells were fixed in 1% paraformaldehyde at room temperature for 10 minutes, with the tube being vortexed and inverted occasionally. The fixation was terminated with 0.125 M glycine. The cells were then lysed on ice for 3-5 minutes using 100 μL of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% digitonin and 1% BSA), with a cell concentration of 100,000 to 300,000 cells per 100 μL of lysis buffer. After centrifugation to remove the supernatant, the cells were resuspended in 1× dilution buffer (10x Genomics; 2000207). 5 µl cell suspension was mixed 1:1 with trypan blue for counting using a Countess II FL automated cell counter. Finally, 20,000 to 30,000 cells were used for mtscATAC-seq library preparation.
scATAC-seq libraries were prepared following the manufacturer protocol of Chromium Next GEM Single Cell ATAC Kit v2 (10x Genomics, PN-1000390). Briefly, the required number of cells were incubated in a Transposition Mix that includes ATAC Buffer B and ATAC Enzyme at 37 °C for 30 min. Subsequently, a pre-mix comprising Barcoding Reagent B, Reducing Agent B, and Barcoding Enzyme, along with the transposed cells, Single Cell ATAC Gel Beads, and partitioning oil, was loaded onto a Chromium Chip E. The resulting single-cell GEMs were collected, and linear amplification was performed in a C1000 Touch Thermal Cycler with the following conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 12 cycles of 98°C for 10 seconds, 59°C for 30 seconds, and 72°C for 1 minute. Emulsions were then coalesced using the Recovery Agent and purified with Dyna beads. Indexed sequencing libraries were constructed, purified, and sequenced on an Illumina-x-plus instrument at Novogene Biotechnology Co., Ltd. (Beijing, China).
mtscATAC-seq

value: Kidney

value: 80% trnE mutation load


title: PT2

description: 10x Genomics

value: CESC


title: cnr.wt.lenti_afos.ctrl.flag.rep3

first: Paul

last: Wade

institute: NIEHS

value: WT GATA3 (1-444aa)


title: LNCAP 181-40 rep1


title: trnE-mutant, 75-week-old, replicate 1, 75% mutation load, mtscATAC-seq

description: 10x Genomics

value: 75% trnE mutation load


title: PNT29-WM_08


title: LNCAP DMSO rep2

value: DMSO


title: PT6

description: 10x Genomics

value: all cells


title: K27M_612137, experimental replicate 4

description:
Library name: K27M_612137
K27M_612137 Genome-wide DNA Methylation

value: mouse brain

value: Nestin-TVA/TVA; p53-FL/FL; H3f3a-LSL-K27M/H3f3a-LSL-K27M; ATM-FL/+


title: cnr.wt.lenti_afos.ctrl.flag.rep1


title: trnE-mutant, 3-week-old, 80% mutation load, mtscATAC-seq

description: 10x Genomics


title: PCOS-3

city: Jinan

first: Shan

last: Han

address: Wenhua West road

institute: Shandong University

description: Library name: Sample 6

data_processing:
these cDNA libraries were then sequenced using an Illumina HiSeq X Ten platform
Following sequencing, the obtained reads were subjected to a filtering process to remove any low-quality reads,
and the remaining clean reads were aligned to a reference genome using the HISAT2 software
Differentially expressed genes were identified with the P-value<0.05 and fold change>1.5 between the two groups.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM for each Sample

source_name: granulosa cell

extract_protocol:
Total RNAs of granulosa cells from PCOS and control patients were extracted using RNA lysis from BGI.
The extracted RNAs were used to construct RNA libraries using the SMRTbell Template Prep Kit for Illumina from BGI Tech Co., Ltd.

value: granulosa cell


title: PNT28-MGUS_03

value: IgM MGUS

value: Intermediate risk


title: PNT26-WM_09

value: Waldenström Macroglobulinemia

value: High risk


title: PNT3-WM_04


title: cnr.wt.dox.p300.rep3

city: Research Triangle Park

address: 111 TW Alexander Drive

value: basal breast cancer line

value: DOX


title: cnr.wt.lenti_afos.ctrl.brg1.rep2

value: Control/Uninduced

value: BRG1 [Abcam, ab110641]


title: LNCAP DMSO rep1

first: Raunak

last: Shrestha

institute: University of California, San Francisco

source_name: castration resistant prostate cancer

value: LNCaP

value: castration resistant prostate cancer


title: PNT2-WM_02


title: THP-1 Cells-Uninfected-Untreated, Control, 4hrs, Rep 3

city: Cape Town

first: Bienyameen

last: Baker

state: Western

address: Francie Van Zijl Drive, Tygerberg

department: Department of Biomedical Sciences

country: South Africa

institute: Stellenbosch University Tygerberg Medical Campus, SAMRC Centre for TB Research

description:
Library name: IonCode_0128
UU – 2 (4hrs TP) (Exp 3)

data_processing:
Reads were quality trimmed during the base calling step using a moving window of 30pb and a cutoff of quality value (QV) 15. Reads were mapped to the hg19_AmpliSeq_Transcriptome_v1.1 reference genome and only reads with an alignment length of 17 and more were retained.
Assembly: hg19 Ampliseq transcriptome V1.1
Supplementary files format and content: CSV file, matrix counts

source_name: THP-1 cells

extract_protocol:
RNeasy ®Plus Mini Kit (Qiagen) was used to extract the total RNA.
Ion AmpliSeq™ Transcriptome Human Gene Expression Panel Chef-Ready Kit was used to prepare the RNA libraries according to manufacturer's protocol.

value: THP-1 cells

value: monocytes

value: WT

value: macrophage differentiation


title: PNT25-MGUS_10

value: Low risk


title: cnr.wt.lenti_afos.ctrl.brg1.rep3

value: WT GATA3 (1-444aa)


title: THP-1 Cells-Infected-Untreated, Control, 4hrs, Rep 3

description:
Library name: IonCode_0126
IU – 1 (4hrs TP) (Exp 3)


title: cnr.wt.lenti_afos.ctrl.brg1.rep1


title: cnr.wt.dox.p300.rep1


title: THP-1 Cells -Uninfected-Untreated, Control, 12hrs, Rep 3

description:
Library name: IonCode_0125
UU – 2 (12hrs TP) (Exp 3)


title: cnr.wt.dox.p300.rep2


title: PCOS-2

description: Library name: Sample 5

value: granulosa cell


title: PNT1-WM_01


title: THP-1 Cells-Infected-Untreated, Control, 12hrs, Rep 3

description:
Library name: IonCode_0123
IU – 1 (12hrs TP) (Exp 3)


title: PCOS-1

description: Library name: Sample 4


title: cnr.wt.dox.igg.rep3

value: IgG Rabbit (Guinea pig anti-rabbit) [Antibodies Online, ABIN101961]


title: THP-1 Cells-Infected, CKB-induced, 12hrs, Rep 3

description:
Library name: IonCode_0124
CKB – 1 (Exp 3)

value: CKB-Knockup


title: SKNBE shRIN1shRNF2 comb, replicate 2

city: Kita-adachi-gun

first: Shunpei

last: Satoh

state: Saitama

address: Komuro 818, Ina

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

description: Gene expression four days after the transduction

hyb_protocol: and subsequently hybridized to a SurePrint G3 Human GE v3 8 × 60 K Microarray (Agilent Technologies).

scan_protocol: standard agilent protocol

data_processing:
Raw data from the same cell line were normalized to the 75th percentile using GeneSpring 14.9.1 (Agilent Technologies).
The cut-off for up-regulated and down-regulated genes was defined as |fold change (FC)| > 1.5 and a false discovery rate (q-value) of ANOVA < 0.05.

label_protocol: 200 ng of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies)

growth_protocol: NB and HEK293T cells were cultured in RPMI-1640 and D-MEM (Fujifilm Wako, Japan), respectively, under humidified 5% CO2 conditions. The medium was supplemented with 10% inactivated fetal bovine serum (Thermo Fisher Scientific, Massachusetts, USA) and 100 units/mL of penicillin/streptomycin (Fujifilm Wako).

extract_protocol: 1–5 × 10^6 cells were washed twice with cold PBS and homogenized in 500 μL of ISOGEN II reagent (NIPPON GENE, Japan). We followed manufacturer’s protocol to extract RNAs.

treatment_protocol: shRNAs were packaged into lentivirus in HEK293T cells, and subsequently transduced in NB cell lines with 8 μg/ml of polybrene.

value: Neuroblastoma cell line


title: Ctrl-2

description: Library name: Sample 2


title: Ctrl-1

description: Library name: Sample 1


title: THP-1 Cells-Infected-EmptyVector-induced, 12hrs, Rep 3

description:
Library name: IonCode_0127
EV – 1 (Exp 3)

value: EmptyVector-knockup


title: THP-1 Cells-Infected, IFIT2-induced,12hrs, Rep 3

description:
Library name: IonCode_0121
IFIT2 – 2 (Exp 3)

value: IFIT2 -Knockup


title: THP-1 Cells-Uninfected-Untreated, Control, 4hrs, Rep 2

description:
Library name: IonCode_0118
UU – 2 (4hrs TP) (Exp 2)


title: cnr.wt.dox.igg.rep1

value: basal breast cancer line

value: DOX


title: cnr.wt.dox.igg.rep2


title: cnr.wt.dox.h3k4me1.rep2

value: H3K4me1 [Epicypher, 13-0057]


title: Ctrl-3

description: Library name: Sample 3


title: SKNBE shRIN1shRNF2 comb, replicate 1


title: K-1461

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Library name: K-1461

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.0f
Read count extraction via STRINGTIE v1.3.6 and prepDE.py (following Protocol stringtie webpage)
Assembly: GRCh38/hg38
Supplementary files format and content: tsv file including raw counts for all samples

source_name: quadriceps

extract_protocol:
RNA was extracted using the miRNA micro kit (Qiagen, Hilden, Germany)
done by BGI (Yantian District Shenzhen China)

value: quadriceps


title: K-1470

description: Library name: K-1470


title: THP-1 Cells-Infected-EmptyVector-induced, 12hrs, Rep 2

description:
Library name: IonCode_0117
EV  – 1 (Exp 2)


title: cnr.wt.dox.h3k4me1.rep3


title: EV_1

value: normal human dermal fibroblasts

value: NHDFs exposed to small extracellular vesicles


title: THP-1 Cells-Infected-Untreated, Control, 4hrs, Rep 2

description:
Library name: IonCode_0116
IU – 2 (4hrs TP) (Exp 2)

value: THP-1 cells

value: monocytes


title: J-1487

description: Library name: J-1487


title: THP-1 Cells -Uninfected-Untreated, Control, 12hrs, Rep 2

description:
Library name: IonCode_0115
UU – 2 (12hrs TP) (Exp 2)

value: WT

value: macrophage differentiation


title: cnr.wt.dox.h3k27ac.rep3

value: WT GATA3 (1-444aa)

value: H3K27Ac [Millipore, MABE647]


title: THP-1 Cells-Uninfected, IFIT2-induced,12hrs, Rep 3

description:
Library name: IonCode_0122
UT – 1 (Exp 3)


title: SKNBE shRNF2, replicate 1


title: J-1488

description: Library name: J-1488


title: THP-1 Cells-Infected, CKB-induced, 12hrs, Rep 2

description:
Library name: IonCode_0114
CKB – 1 (Exp 2)


title: SKNBE shRNF2, replicate 2


title: cnr.wt.dox.h3k4me1.rep1


title: SKNBE mock control, replicate 1

source_name: mock control

value: mock control


title: cnr.wt.dox.h3k27ac.rep2


title: J-1486

description: Library name: J-1486


title: J-1485

description: Library name: J-1485


title: cnr.wt.dox.h3k27ac.rep1


title: SKNBE shRING1, replicate 1


title: NGP shRIN1shRNF2 comb, replicate 2


title: SKNBE shRING1, replicate 2


title: cnr.wt.dox.fra1.rep3

value: FRA1 [Abcam, ab252421]


title: J-1483

description: Library name: J-1483


title: SKNBE mock control, replicate 2

value: Neuroblastoma cell line


title: cnr.wt.dox.fra1.rep2


title: THP-1 Cells-Infected-Untreated, Control, 12hrs, Rep 2

description:
Library name: IonCode_0113
IU – 1 (12hrs TP) (Exp 2)


title: THP-1 Cells-Infected, IFIT2-induced,12hrs, Rep 2

description:
Library name: IonCode_0111
IFIT2 – 1 (Exp 2)


title: J-1484

description: Library name: J-1484


title: THP-1 Cells-Uninfected, IFIT2-induced, 12hrs, Rep 2

description:
Library name: IonCode_0112
UT – 2 (Exp 2)


title: NGP shRIN1shRNF2 comb, replicate 1


title: NGP shRNF2, replicate 1


title: THP-1 Cells-Infected-EmptyVector-induced, 12hrs, Rep 1

description:
Library name: IonCode_0107
EV – 2 (Exp 1)

value: EmptyVector-knockup


title: NGP shRNF2, replicate 2


title: J-1482

description: Library name: J-1482


title: THP-1 Cells-Uninfected-Untreated, Control, 4hrs, Rep 1

description:
Library name: IonCode_0108
UU – 2 (4hrs TP) (Exp 1)


title: cnr.wt.dox.flag.rep2

value: FLAG M2 SIGMA [SIGMA, F1804]


title: cnr.wt.dox.flag.rep3

value: basal breast cancer line


title: THP-1 Cells-Infected-Untreated, Control, 4hrs, Rep 1

description:
Library name: IonCode_0106
IU – 1 (4hrs TP) (Exp 1)


title: cnr.wt.dox.fra1.rep1

value: DOX


title: NGP shRING1, replicate 1


title: J-1481

description: Library name: J-1481


title: J-1480

description: Library name: J-1480


title: THP-1 Cells -Uninfected-Untreated, Control, 12hrs, Rep 1

description:
Library name: IonCode_0105
UU – 2 (12hrs TP) (Exp 1)


title: J-1479

description: Library name: J-1479


title: cnr.wt.ctrl.p300.rep3

value: Control/Uninduced


title: J-1478

description: Library name: J-1478

value: quadriceps


title: cnr.wt.dox.flag.rep1


title: NGP mock control, replicate 2


title: cnr.wt.ctrl.p300.rep2


title: THP-1 Cells-Infected, CKB-induced, 12hrs, Rep 1

description:
Library name: IonCode_0104
CKB – 2 (Exp 1)

value: CKB-Knockup


title: NGP shRING1, replicate 2

description: Gene expression four days after the transduction


title: NGP mock control, replicate 1