title: mES-E14-NANOG-FKBP-PromoterBait_4

description:
Library name: Sample 70
mES-E14-NANOG-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #4

status: Public on Nov 26 2025

type: SRA

city: Hamilton

first: Joseph

last: Nickels

state: New Jersey

address: 1000 Waterview Drive

department: Institute of Metabolic Disorders

country: USA

institute: Genesis Biotechnology Group

description:
Library name: Sample 20
G2-WT-chow-5_S7

library_source: transcriptomic

data_processing:
Libraries were sequenced using the NextSeq 550 (Illumina, San Diego, CA, United States) with NextSeq 500/550 High Output Kit v2.5 (2x75 Cycles ) (Illumina, San Diego, CA, United States).  Reads were aligned to the Ensembl Mus mm39 musculus genome using STAR 2.7.  Differential gene expression analysis was performed with DEseq2 (v 1.26.0). Genes with a Benjamini and Hochberg adjusted p ≤ 0.05 (5% False Discovery Rate) were regarded as statistically significantly regulated.  Enrichment analysis of Gene Ontology pathways were performed using the cluster Profiler package for R
Read alignment software STAR2.7
Differential gene expression analysis was performed with DEseq2 (v 1.26.0).
Assembly: reads were assigned to the Ensembl Mus mm39 musculus genome using STAR 2.7
Supplementary files format and content: tab-delimited text file that includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was isolated from liver tissue with the RNeasy® Mini kit (Qiagen, Germantown, MD). Liver tissue was homogenized in in RLT lysis buffer using a Bullet Blender® 24 Gold (Next Advance, Raymertown, NY).  200-proof (100%) ethyl alcohol (Pharmco by Greenfield Global, Toronto, Canada) was added and homogenized samples were applied to a RNeasy column.   The column was washed with RW1 buffer and subjected to DNase digestion with a RNase-Free DNase Set (Qiagen, Germantown, MD).  RNA was washed again with RNeasy RW1 and RPE buffers. Total RNA was isolated in RNase-free water, quantified using a NanoDrop® ND-1000 spectrophotometer (ThermoFisher Scientific, Waltham, MA), and stored at -80°C.
Cell extracts from 15 mg of liver tissue was used for RNASeq analysis.  RNA quantity was measured using Qubit® (Thermo Scientific, Eugene, OR, United States).  A 4150 TapeStation System was used to determine RNA quality.  An RNA integrity (RIN) score > 7 (10 is maximal) was required for going forward with sequencing.  RNA libraries were prepared using Illumina Stranded Total RNA Prep and the Ribo-Zero™ Plus” kit (Illumina, San Diego, CA, United States).

tag: tissue

value: Liver


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #9

description:
Library name: Sample 9
G1-WT-HFD-3_S11


title: mES-E14-NANOG-FKBP-PromoterBait_5

city: Oxford

first: James

last: Davies

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description:
Library name: Sample 71
mES-E14-NANOG-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Trp53_combined_chimeric.txt

library_source: genomic

data_processing:
The raw FASTQ file is processed to reconstruct a single read from paired-end sequencing data. These reads are then mapped to the 800bp region surrounding the capture oligonucleotide using the non-stringent aligner BLAT. This step allows the reads to be segmented into ‘slices’ based on their alignment to the sequence around the capture site, enabling the identification of ligation junctions with base-pair precision. After this, the resulting FASTQ file is aligned to the genome using Bowtie.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes contact frequency
Library strategy: Capture-C

molecule: genomic DNA

source_name: Embryo

growth_protocol: This research was conducted under the project license PP3929317, adhering to the European Union directive 2010/63/EU and the UK Animals (Scientific Procedures) Act of 1986. All procedures were reviewed by the Animal Welfare and Ethical Review Body of the Department of Biomedical Services at the University of Oxford. Murine erythroid cells were purified using Ter119 selection (ter119-phycoerythrin antibodies (Biolegend 116208) and anti-PE MACS beads (Miltenyi, 130-048-801)) from the spleen of C57BL/6J mice following administration of phenylyhydrazine (40 mg/g body weight, 3 doses, 12 h apart). Murine HSPCs were extracted and cultured as previously described(Wilkinson et al., 2020). Murine ES cells (E14TG2a) were maintained in gelatin (Gibco 10131-035) coated flasks in Glasgow MEM x1 liquid (Gibco 21710-025) with 10% FCS (Gibco 10270-106), 1x Glutamine (Gibco 25030-024), 1 mM sodium pyruvate (Gibco 11360-039), 1x non-essential amino acids (Gibco 11140-035), mercaptoethanol (Gibco 31350-010) and LIF (Thermo Fisher PMC9484). RPE-1 cells were maintained in Dulbecco’s Modified Eagle’s Medium (Gibco, 11960044) supplemented with 10% fetal bovine serum, 1% GLUTmax (Gibco, 35050061), 1% non-essential amino acids, and 1% penicillin-streptomycin (Gibco, 15070063) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
3C library manufacture was undertaken as described previously(Hamley et al., 2023). In brief, aliquots of 1 x 107 cells were fixed 10 ml media with Formaldehyde, 37% (vol/vol) (Sigma, 47608-250ML) at a final of concentration 2% for 10 minutes at room temperature. This reaction was quenched with 1 M glycine to a final concentration 130 mM and centrifuged (5 min, 300 g). The supernatant was removed, and the cell pellet washed with cold PBS and reconstituted in 1 ml PBS. Cells were permeabilised with Digitonin (Sigma D-141; final concentration of 0.005% wt/vol). Cells were snap frozen and stored at -80 °C. Subsequently, defrosted, permeabilised cells were centrifuged (5 min, 300 g) the supernatant discarded, and resuspended in a reduced calcium content MNase buffer (Tris-HCl pH 7.5 10 mM; CaCl2 1 mM). Cells were split into 3 separate digests to allow titration of MNase (NEB M0247) concentration, which typically ranged from 5 to 20 Kunitz units per reaction. This reaction was incubated for 1 hour at 37 °C in an Eppendorf Thermomixer at 500 rpm and was quenched by adding ethylene glycol-bis(2-aminoethylether)-N,N,N’,N’-tetraacetic acid (EGTA) (Sigma E3889) to a final concentration of 5 mM. To evaluate digestion efficiency, 20% of the reaction was removed. The remaining reaction was centrifuged (5 min, 300 g) and the supernatant containing digestion buffer was discarded. The cell pellet was washed in 1 ml PBS and the cells were resuspended in DNA ligase buffer (Thermo Scientific; final concentrations Tris-HCl pH 7.5 40 mM, MgCl2 10 mM, DTT 10 mM, 5 mM ATP) supplemented with dNTPs (final concentration 400 µM of each of dATP, dCTP, dGTP and dTTP (Thermo Fisher R0191)) and EGTA 5 mM. The reaction mixture was then treated with T4 Polynucleotide Kinase PNK (NEB M0201L) and DNA Polymerase I Large (Klenow) Fragment (NEB M0210L) at final concentrations of 200 U/ml, and 100 U/ml respectively, T4 DNA ligase (Thermo Scientific, High Concentration Ligase (30 U/µl) EL0013) was added to a final concentration of 300 U/ml and the reaction was incubated at 20°C overnight using an Eppendorf Thermomixer at 500 rpm. Chromatin was decrosslinked (proteinase K, 65 °C, >2 hours) and DNA was purified using the Qiagen DNeasy blood and tissue kit (69506). Digestion and ligation efficiencies were assessed using the Agilent Tapestation (D1000 reagents).
Sequencing library preparation. Oligonucleotide capture was performed as previously described(Hamley et al., 2023; Hua et al., 2021a). Initially, 7-10 µg of each 3C library was sonicated to an averagefragment size of 200 bp using a Covaris S220 Focussed Ultrasonicator (3 cycles of 60 seconds, duty cycle 10%, intensity 5, 200 cycles per burst). After sonication, the size of library was evaluated using an Agilent TapeStation (DNA 1000). The sample was then cleaned using Ampure XP beads (Beckman Coulter A63881). To maximise library complexity, three separate aliquots of 2 µg each of the sonicated 3C library were processed simultaneously for the addition of sequencing adaptors (NEB Ultra II (NEB 7645S)) following the standard protocol with the following alternations: 7.5 µl adapter was used in ligation reactions; all Ampure XP bead clean ups were performed at a ratio of 1 : 1.8 and  the final PCR was carried out in triplicate using the Herculase II PCR reagents (Agilent) to enhance DNA yield.

value: Embryo

tag: cell line

tag: cell type

value: Mouse embryonic stem cell

tag: genotype

value: WT


title: 2325-1 (SC)

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

description:
RD_59306
10x Chromium

library_source: transcriptomic single cell

data_processing:
The resulting scRNA-seq data were analyzed by cellranger v6.0.2 and an anchor-based approach with the Seurat package v4.30.
Assembly: hg19
Supplementary files format and content: A Seurat object as a .RDS file format provided which includes cell count data plus sample's annotation and cluster IDs.

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Single-cell samples were profiled by  10x chromium Single Cell RNA sequensing.
Single-cell gene expression libraries were prepared according to the Chromium NextGEM Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMs (Gel Bead-In-Emulsion). Full-length cDNA was synthesized and barcoded within each GEM. Subsequently, GEMs were broken, and cDNA was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product was fragmented prior to end-repair, A-tailing, and adaptor ligation.
PDX samples were flow-sorted, gating for CD45-dim and SSC low cells; 10K–15K cells were then labeled using the 10x Genomics (Pleasanton, CA) Chromium Next GEM Single Cell 3' Kit v3.1 and sequenced at 200 M reads per sample using an Illumina NovaSeq 6000.

value: Bone Marrow

tag: pdx id2

tag: pdx model

tag: treatment

value: AraC


title: 2493-5 (SC)

description:
RD_59309
10x Chromium

value: PAWLTL


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #11

description:
Library name: Sample 11
G1-WT-HFD-3_S11


title: mES-E14-NANOG-FKBP-PromoterBait_3

description:
Library name: Sample 69
mES-E14-NANOG-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #7

description:
Library name: Sample 7
G1-WT-HFD-2_S13


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #8

description:
Library name: Sample 8
G1-WT-HFD-2_S13


title: AML901_Saline (Bulk)

description: PDXPASZ

data_processing:
RNA-Seq reads were aligned and quantified using RSEM (version 1.30) (PMID: 21816040) and Bowtie2 (version 2.10) (PMID: 22388286) to human reference GRCh38 {(GENCODE v32/Ensembl 98)(refdata-gex-GRCh38-2020-A dated 2020-07-07 downloaded from 10X Genomics with GENCODE gtf dated 2019-09-05)}.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus mini kit with a genomic DNA elimination column (74104).
Extracted RNA samples were profiled using Illumina Novaseq 6000 with 25M reads per sample.
Briefly, RNA quality was confirmed, 150bp paired-end mRNA libraries were prepared, and libraries were sequenced at a depth of 25M reads per sample on the NovaSeq 6000 platform (Illumina).

value: PASZLJ

value: Saline


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #10

description:
Library name: Sample 10
G1-WT-HFD-3_S11


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #6

description:
Library name: Sample 6
G1-WT-HFD-2_S13


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #4

description:
Library name: Sample 4
G1-WT-HFD-1_S8


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #3

description:
Library name: Sample 3
G1-WT-HFD-1_S8


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #12

description:
Library name: Sample 12
G1-WT-HFD-3_S11


title: mES-E14-M14-FKBP-PromoterBait_6

description:
Library name: Sample 66
mES-E14-M14-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #5

description:
Library name: Sample 5
G1-WT-HFD-2_S13


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #2

description:
Library name: Sample 2
G1-WT-HFD-1_S8


title: AML013_Saline (Bulk)


title: AML903_AraC (Bulk)

value: PATDRZ


title: mES-E14-M14-FKBP-PromoterBait_5

description:
Library name: Sample 65
mES-E14-M14-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Group 2 WT mice fed chow. RNASeq performed at end of the study #1

description:
Library name: Sample 17
G2-WT-chow-5_S7


title: AML903_Saline (Bulk)


title: Plasma exosome OSA_6

city: changsha

first: xing

last: lyu

address: NO.139 Renmin road

department: Laboratory Medicine

country: China

institute: The Second Xiangya Hospital, Central South University

description:
Library name: O2-6
O2-6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl 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. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality. Paired-end clean reads were aligned to the reference genome- GRCh38 using TopHat2/Bowtie2. Mapped reads were used for the Quantification of gene expression level and Differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: list file include clean counts for each sample
Supplementary files format and content: list fle include UMl-TPM values for each sample

source_name: plasma

extract_protocol:
Peripheral blood samples from individuals were collected in EDTA tubes following a regular venipuncture procedure. After centrifugation at 3,000 ×g for 15 min at 4 °C, the plasma was aspirated and stored at −80 °C before use. The UC method was optimized according to the method previously described (Théry C. et al. 2006).  After thawing at 37 °C, 1 mL plasma samples were centrifugated at 3,000 ×g for 15 min to remove cell debris. Repeat the above steps. Then, the supernatant was diluted by five-fold volume of PBS, centrifuged at 10,000 ×g for 20 min, and processed through a 0.22 μm filter to remove large particles. The supernatant was ultracentrifuged at 100,000 ×g, 4 °C for 60 min to pellet the exosomes. The pellet was resuspended in phosphate-buffered saline (PBS) and centrifuged again at 100,000 ×g 4 °C for 4 h. After PBS washing, the exosomes pellet was re-suspended in 100 µl PBS. Total RNA was extracted and purified from plasma exosome using miRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) according to the kit instruction. RNA concentration and purity were evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 250pg—10ng RNA per sample was used as input material for sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit V2 (Takara Bio USA, Inc.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. For small RNA libraries, a total amount of 1ng-500ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using QIAseq miRNA Library Kit (Qiagen, Frederick, MD) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Reverse transcription (RT) primers with unique molecular indices (UMIs) were introduced to analyze the quantification of miRNA expressions during cDNA synthesis and PCR amplification. At last, library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR. The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

value: plasma

value: plasma exosomes


title: Group 1 WT mice fed a HFD. RNASeq performed at end of study #1

description:
Library name: Sample 1
G1-WT-HFD-1_S8


title: Plasma exosome OSA_5

description:
Library name: O2-5
O2-5


title: mES-E14-M14-FKBP-PromoterBait_4

description:
Library name: Sample 64
mES-E14-M14-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Plasma exosome OSA_4

description:
Library name: O2-4
O2-4


title: mES-E14-M14-FKBP-PromoterBait_3

description:
Library name: Sample 63
mES-E14-M14-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Plasma exosome OSA_3

description:
Library name: O2-3
O2-3


title: Plasma exosome OSA_2

description:
Library name: O2-2
O2-2


title: Plasma exosome OSA_1

description:
Library name: O2-1
O2-1


title: AML006_AraC (Bulk)


title: mES-E14-NANOG-FKBP-PromoterBait_2

description:
Library name: Sample 68
mES-E14-NANOG-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: mES-E14-NANOG-FKBP-PromoterBait_1

description:
Library name: Sample 67
mES-E14-NANOG-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-NANOG-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: Plasma exosome non-OSA_4

description:
Library name: O1-4
O1-4


title: mES-E14-M14-FKBP-PromoterBait_2

description:
Library name: Sample 62
mES-E14-M14-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: AML006_Saline (Bulk)


title: AML001_Saline (Bulk)


title: mES-E14-M1-FKBP-PromoterBait_6

description:
Library name: Sample 60
mES-E14-M1-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: AML010_Saline (Bulk)


title: AML005_Saline (Bulk)


title: mES-E14-M1-FKBP-PromoterBait_4

description:
Library name: Sample 58
mES-E14-M1-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: AML905_Saline (Bulk)


title: AML010_AraC (Bulk)


title: 648T1B_IDH2-Mutant_SRSF2-WT RNA

city: Miami

first: Aristeidis

middle: G

last: Telonis

state: FL

address: 1550 NW 10th Ave

department: Biochemistry & Molecular Biology

institute: University of Miami

data_processing:
Adapters were trimmed from the acquired fastq files with cutadapt (v. 1.18) with parameter -m10
Reads were mapped on the GRCh37 human genome with STAR (v. 2.7.1a) with parameters chimSegmentMin=10, outFilterMismatchNmax=5, alignEndsType=EndToEnd, alignIntronMax=1000000 and alignSJDBoverhangMin=6
Gene expression profiles were extracted with RSEM (v. 1.2.28) using Ensembl v75 for gene annotations
Assembly: GRCh37
Supplementary files format and content: Table with counts and FPKM values per gene

molecule: polyA RNA

source_name: Blood

extract_protocol:
AllPrep DNA/RNA kit from Qiagen (Valencia, CA)
polyA-selected strand-specific SureSelect (Agilent)

value: Blood

tag: Sex

value: M

tag: idh2 genotype

value: Mutant

tag: srsf2 genotype


title: 85T1M_IDH2-WT_SRSF2-WT RNA

source_name: Marrow

value: Marrow


title: 736T3b_IDH2-WT_SRSF2-Mutant RNA

value: F


title: AML001_AraC (Bulk)


title: 556T2B_IDH2-Mutant_SRSF2-Mutant RNA


title: mES-E14-M1-FKBP-PromoterBait_2

description:
Library name: Sample 56
mES-E14-M1-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: mES-E14-M14-FKBP-PromoterBait_1

description:
Library name: Sample 61
mES-E14-M14-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M14-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: 614T1M_IDH2-Mutant_SRSF2-Mutant RNA


title: 560T3B_IDH2-WT_SRSF2-Mutant RNA


title: mES-E14-M1-FKBP-PromoterBait_3

description:
Library name: Sample 57
mES-E14-M1-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: AML005_AraC (Bulk)


title: 543T6B_IDH2-Mutant_SRSF2-WT RNA


title: mES-E14-M1-FKBP-PromoterBait_1

description:
Library name: Sample 55
mES-E14-M1-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: 523T2B_IDH2-Mutant_SRSF2-Mutant RNA


title: Plasma exosome non-OSA_3

description:
Library name: O1-3
O1-3


title: TCHnorm2.n.U (SC)

description: 10x Genomics

extract_protocol:
Single-cell samples were profiled by  10x chromium Single Cell RNA sequensing.
Single-cell gene expression libraries were prepared according to the Chromium NextGEM Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMs (Gel Bead-In-Emulsion). Full-length cDNA was synthesized and barcoded within each GEM. Subsequently, GEMs were broken, and cDNA was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product was fragmented prior to end-repair, A-tailing, and adaptor ligation.
Patient samples were flow-sorted, gating for CD45-dim and SSC low cells; 10K–15K cells were then labeled using the 10x Genomics (Pleasanton, CA) Chromium Next GEM Single Cell 3' Kit v3.1 and sequenced at 200 M reads per sample using an Illumina NovaSeq 6000.

tag: timepoint

value: Normal Donor


title: Plasma exosome non-OSA_2

description:
Library name: O1-2
O1-2


title: Plasma exosome non-OSA_1

description:
Library name: O1-1
O1-1


title: AML905_AraC (Bulk)


title: 495T1M_IDH2-Mutant_SRSF2-Mutant RNA


title: 587T2B_IDH2-WT_SRSF2-WT RNA


title: 475T1B_IDH2-WT_SRSF2-Mutant RNA


title: TCHnorm2.n.S (SC)

description: 10x Genomics


title: mES-E14-M13-FKBP-PromoterBait_5

description:
Library name: Sample 53
mES-E14-M13-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Trp53_combined_chimeric.txt

value: Embryo


title: 287T1M_IDH2-WT_SRSF2-Mutant RNA


title: 283T9B_IDH2-Mutant_SRSF2-Mutant RNA


title: 584T3M_IDH2-WT_SRSF2-Mutant RNA


title: 247T2Ba_IDH2-Mutant_SRSF2-Mutant RNA


title: TCHnorm1.n.S (SC)

description: 10x Genomics


title: 247T2Bb_IDH2-Mutant_SRSF2-Mutant RNA


title: 246T9B_IDH2-Mutant_SRSF2-WT RNA


title: 225T15B_IDH2-WT_SRSF2-Mutant RNA


title: mES-E14-M13-FKBP-PromoterBait_4

description:
Library name: Sample 52
mES-E14-M13-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Trp53_combined_chimeric.txt

value: Mouse embryonic stem cell


title: mES-E14-M13-FKBP-PromoterBait_3

description:
Library name: Sample 51
mES-E14-M13-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Trp53_combined_chimeric.txt

value: WT


title: 54T1B_IDH2-WT_SRSF2-WT RNA


title: PAVTLN_D (SC)

description: 10x Genomics

value: Bone Marrow

value: Diagnosis


title: Huh7_HiChIP_rep1

city: Seoul

first: Sunyoung

last: Jang

state: Not required for this country

address: Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul

country: South Korea

institute: Sookmyung Women's University

library_source: other

data_processing:
*library strategy: HiChIP
Paired-end sequencing reads were mapped to the human reference genome (hg19), and reads from multiple sequencing libraries were merged to enhance coverage. H3K27ac HiChIP data were analyzed using the Juicer pipeline (Durand, et al., 2016). Chromatin loops were identified by HiCCUPS with default settings.
Assembly: hg19
Supplementary files format and content: hic

molecule: other

growth_protocol: Hep3B cells were maintained in DMEM containing 10% FBS and 1% penicillin-streptomycin. Huh7 cells were maintained in RPMI containing 10% FBS and 1% penicillin-streptomycin. Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Cells (4 x 10^6) in serum-free media were cross-linked by incubating for 10 minutes at room temperature with 1% methanol-free formaldehyde solution (Thermo Scientific, 28906) and quenched by adding 0.125 M glycine. After collecting by centrifugation, cross-linked cell pellets were resuspended in 500 μL of ice-cold HiC lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP-40) containing protease inhibitor (Sigma-Aldrich, 11697498001), and incubated at 4°C for 30 minutes. Nuclei were pelleted and washed once with 500 μL of ice-cold HiC lysis buffer.
After removing the supernatant, nuclei were incubated in 100 μL of 0.5% SDS at 62°C for 10 minutes. SDS was quenched by adding 50 μL 10% Triton X-100 (and 285 μL water), and nuclei were incubated for 15 minutes at 37°C. Chromatin was digested by adding 50 μL of 10x NEB Buffer2 and 375 U MboI (NEB, R0147) and incubating for 4 hours at 37°C with rotation; MboI was inactivated by incubating at 62°C for 20 minutes. Restriction fragment ends were biotinylated by adding 52 μl of fill-in master mix (37.5 μL of 0.4 mM biotin-dATP [Thermo Scientific, 19524016]; 1.5 μL of 10 mM dCTP; 1.5 μL of 10 mM dGTP; 1.5 μL of 10 mM dTTP; and 10 μL of 5 U/μL DNA polymerase I, large (Klenow) fragment [NEB, M0210]) and incubating at 37°C for 1 hour with shaking. Ligation was performed by adding 948 μL of ligation master mix (150 μL of 10X NEB T4 ligase buffer [NEB, B0202] containing 10 mM ATP, 125 μL of 10% Triton X-100, 7.5 μL of 20 mg/mL bovine serum albumen [BSA] and 10 μL of 400 U/μL T4 DNA ligase [NEB, M0202]), and incubating at room temperature overnight with slow rotation. Pellets containing nuclei were resuspended in lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris pH 8.0, and protease inhibitor cocktail) and sonicated using a Diagenode Bioruptor to generate chromatin fragments; fragment size range was determined by agarose gel electrophoresis. For ChIP procedures, chromatin was diluted with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 7.5, 167 mM NaCl). The amount of Tn5 (Illumina, 20034197) needed to generate libraries of the correct size was estimated by quantifying ChIP DNA using a Nanodrop microvolume spectrophotometer. ChIP DNA underwent biotin capture and was simultaneously fragmented and tagged (tagmented) with Tn5. The bead-bound, tagmented DNA was then PCR amplified and size selected using AMPure XP beads (Beckman, A63880). After size selection, libraries were quantified by qPCR. HiChIP libraries were constructed and sequenced on a HiSeq 2500 system (Illumina).

value: Liver

value: Hepatocellular carcinoma tumor

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: mES-E14-M1-FKBP-PromoterBait_5

description:
Library name: Sample 59
mES-E14-M1-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M1-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: mES-E14-M13-FKBP-PromoterBait_2

description:
Library name: Sample 50
mES-E14-M13-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: 201T1B_IDH2-Mutant_SRSF2-WT RNA


title: Huh7_HiChIP_rep2


title: mES-E14-M13-FKBP-PromoterBait_1

description:
Library name: Sample 49
mES-E14-M13-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: PAVTLN_R (SC)

description: 10x Genomics

value: Relapse


title: mES-E14-M13-FKBP-PromoterBait_6

description:
Library name: Sample 54
mES-E14-M13-FKBP-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-MYC_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-M13-FKBP-PromoterBait-Trp53_combined_chimeric.txt


title: HSPC-WT-PromoterBait_6

description:
Library name: Sample 48
HSPC-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
HSPC-WT-PromoterBait-Hba-a1_combined_chimeric.txt
HSPC-WT-PromoterBait-HBB-b1_combined_chimeric.txt
HSPC-WT-PromoterBait-Idh2_combined_chimeric.txt
HSPC-WT-PromoterBait-Klf4_combined_chimeric.txt
HSPC-WT-PromoterBait-Med13l_combined_chimeric.txt
HSPC-WT-PromoterBait-MYC_combined_chimeric.txt
HSPC-WT-PromoterBait-Nanog_combined_chimeric.txt
HSPC-WT-PromoterBait-Setd1b_combined_chimeric.txt
HSPC-WT-PromoterBait-slc25a37_combined_chimeric.txt
HSPC-WT-PromoterBait-SOX2_combined_chimeric.txt
HSPC-WT-PromoterBait-Tet2_combined_chimeric.txt
HSPC-WT-PromoterBait-Trp53_combined_chimeric.txt

source_name: Bone-marrow

value: Bone-marrow

value: c-KIT+


title: PAVBFN_R (SC)

description: 10x Genomics


title: Hep3B_HiChIP_rep2


title: Huh7_structure_Input

data_processing:
The reads in ChIP-seq were trimmed of the adapter sequences and low-quality reads using Cutadapt (version 4.1). The reads were then aligned to the human reference genome by Bowtie2 (version 2.4.2), and duplicate reads were removed from the mapped reads using Picard tools. Index generation was performed by Samtools. HOMER (version 4.11) was used to identify target protein binding sites and generate bedGraph files for visualization.
Assembly: hg19
Supplementary files format and content: bedGraph.gz

extract_protocol: Cells were crosslinked by incubating with 1% formaldehyde (Merck, F8775) for 10 minutes at 37°C, after which the reaction was quenched by adding glycine (final concentration, 0.125 M). Crosslinked cells were scraped out with filtered Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40) supplemented with protease inhibitor (ROCHE, 25530-049) and phenylmethylsulfonyl fluoride (PMSF) (Merck, P7626), then incubated on ice for 10 minutes. Crosslinked cells were subsequently lysed in filtered 1x RIPA buffer (10 mM Tris pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-DOC, 1% Triton X-100 ) containing protease inhibitor and PMSF, then sonicated to achieve a chromatin fragment size range of 200-500 bp. The sonicated chromatin was immunoprecipitated with anti-H3K4me3 (Millipore, 17-614), anti-H3K27ac (Abcam, ab4729), anti-pSTAT3 (Cell Signaling, 9145), anti-CTCF (Cell Signaling, 2899), anti-SMC1 (Bethyl Laboratories, A300-055A) and anti-SMC3 (Abcam, ab9263) antibodies, and the resulting ChIP DNA was captured by incubating with protein A and protein G Dynabeads (1:1 mix) at 4°C overnight with rotation. Dynabead protein-antibody complexes were subsequently washed with filtered low-stringency wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-DOC, 1% Triton X-100 ), high-stringency wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-DOC, 1% Triton X-100, 300 mM NaCl) and LiCl wash buffer (50 mM Tris pH 7.5, 250 mM LiCl, 0.5% NP-40, 0.5% Na-DOC), followed by two washes with 1x PBS. ChIP DNA was reverse-crosslinked and purified for DNA library construction using a MinElute PCR Purification kit (Qiagen, 28004). ChIP-seq libraries were constructed and sequenced using a HiSeq 2500 system and NextSeq 500 (Illumina).

treatment_protocol: Cells were treated with IL-6 (100ng/mL) for 24h. Cells treated with UltraPure distilled water served as control. Cells were also treated with IL-6 (100ng/mL) for 24h and/or sorafenib (10 μM) for 24h. Cells treated with DMSO served as control.


title: Hep3B_HiChIP_rep1


title: Hep3B_structure_Input


title: Huh7_H3K4me3

value: H3K4me3 (Millipore, #17-614)


title: PAUVAT_R (SC)

description: 10x Genomics


title: PAWNPU_R (SC)

description: 10x Genomics

value: M


title: HSPC-WT-PromoterBait_5

description:
Library name: Sample 47
HSPC-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
HSPC-WT-PromoterBait-Hba-a1_combined_chimeric.txt
HSPC-WT-PromoterBait-HBB-b1_combined_chimeric.txt
HSPC-WT-PromoterBait-Idh2_combined_chimeric.txt
HSPC-WT-PromoterBait-Klf4_combined_chimeric.txt
HSPC-WT-PromoterBait-Med13l_combined_chimeric.txt
HSPC-WT-PromoterBait-MYC_combined_chimeric.txt
HSPC-WT-PromoterBait-Nanog_combined_chimeric.txt
HSPC-WT-PromoterBait-Setd1b_combined_chimeric.txt
HSPC-WT-PromoterBait-slc25a37_combined_chimeric.txt
HSPC-WT-PromoterBait-SOX2_combined_chimeric.txt
HSPC-WT-PromoterBait-Tet2_combined_chimeric.txt
HSPC-WT-PromoterBait-Trp53_combined_chimeric.txt


title: PAVBFN_D (SC)

description: 10x Genomics


title: Hep3B_H3K4me3


title: HSPC-WT-PromoterBait_4

description:
Library name: Sample 46
HSPC-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
HSPC-WT-PromoterBait-Hba-a1_combined_chimeric.txt
HSPC-WT-PromoterBait-HBB-b1_combined_chimeric.txt
HSPC-WT-PromoterBait-Idh2_combined_chimeric.txt
HSPC-WT-PromoterBait-Klf4_combined_chimeric.txt
HSPC-WT-PromoterBait-Med13l_combined_chimeric.txt
HSPC-WT-PromoterBait-MYC_combined_chimeric.txt
HSPC-WT-PromoterBait-Nanog_combined_chimeric.txt
HSPC-WT-PromoterBait-Setd1b_combined_chimeric.txt
HSPC-WT-PromoterBait-slc25a37_combined_chimeric.txt
HSPC-WT-PromoterBait-SOX2_combined_chimeric.txt
HSPC-WT-PromoterBait-Tet2_combined_chimeric.txt
HSPC-WT-PromoterBait-Trp53_combined_chimeric.txt


title: Huh7_CTCF

value: CTCF (Cell Signaling, #2899)


title: Huh7_SMC1

value: SMC1 (Benthyl Laboratories,  A300-055A)


title: Huh7_SMC3

value: SMC3 (Abcam, ab9263)


title: Hep3B_SMC1


title: Hep3B_SMC3


title: PAUNSV_D (SC)

description: 10x Genomics


title: Hep3B_CTCF


title: PAUMTZ_R (SC)

description: 10x Genomics


title: HSPC-WT-PromoterBait_1

description:
Library name: Sample 43
HSPC-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
HSPC-WT-PromoterBait-Hba-a1_combined_chimeric.txt
HSPC-WT-PromoterBait-HBB-b1_combined_chimeric.txt
HSPC-WT-PromoterBait-Idh2_combined_chimeric.txt
HSPC-WT-PromoterBait-Klf4_combined_chimeric.txt
HSPC-WT-PromoterBait-Med13l_combined_chimeric.txt
HSPC-WT-PromoterBait-MYC_combined_chimeric.txt
HSPC-WT-PromoterBait-Nanog_combined_chimeric.txt
HSPC-WT-PromoterBait-Setd1b_combined_chimeric.txt
HSPC-WT-PromoterBait-slc25a37_combined_chimeric.txt
HSPC-WT-PromoterBait-SOX2_combined_chimeric.txt
HSPC-WT-PromoterBait-Tet2_combined_chimeric.txt
HSPC-WT-PromoterBait-Trp53_combined_chimeric.txt


title: HSPC-WT-PromoterBait_2

description:
Library name: Sample 44
HSPC-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
HSPC-WT-PromoterBait-Hba-a1_combined_chimeric.txt
HSPC-WT-PromoterBait-HBB-b1_combined_chimeric.txt
HSPC-WT-PromoterBait-Idh2_combined_chimeric.txt
HSPC-WT-PromoterBait-Klf4_combined_chimeric.txt
HSPC-WT-PromoterBait-Med13l_combined_chimeric.txt
HSPC-WT-PromoterBait-MYC_combined_chimeric.txt
HSPC-WT-PromoterBait-Nanog_combined_chimeric.txt
HSPC-WT-PromoterBait-Setd1b_combined_chimeric.txt
HSPC-WT-PromoterBait-slc25a37_combined_chimeric.txt
HSPC-WT-PromoterBait-SOX2_combined_chimeric.txt
HSPC-WT-PromoterBait-Tet2_combined_chimeric.txt
HSPC-WT-PromoterBait-Trp53_combined_chimeric.txt


title: PAUNSV_R (SC)

description: 10x Genomics


title: Hep3BnIL6_H3K27ac_rep1


title: PAUMTZ_D (SC)

description: 10x Genomics


title: Hep3BpIL6_H3K27ac_rep1

value: 100ng/mL IL-6


title: PARBIU_R (SC)

description: 10x Genomics

value: F


title: Erythroid-WT-PromoterBait-R1R2_5

description:
Library name: Sample 41
Erythroid-WT-PromoterBait-R1R2-Hba_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Hbb_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Slc25a37_combined_chimeric.txt

source_name: Fetal liver

value: Fetal liver

value: Mouse embryonic stem cell


title: Erythroid-WT-PromoterBait-R1R2_4

description:
Library name: Sample 40
Erythroid-WT-PromoterBait-R1R2-Hba_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Hbb_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Slc25a37_combined_chimeric.txt

value: WT


title: PARBIU_D (SC)

description: 10x Genomics

value: Bone Marrow

value: Diagnosis


title: PAUVAT_D (SC)

description: 10x Genomics


title: Erythroid-WT-PromoterBait-R1R2_3

description:
Library name: Sample 39
Erythroid-WT-PromoterBait-R1R2-Hba_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Hbb_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Slc25a37_combined_chimeric.txt


title: Huh7nIL6_H3K27ac_rep1

value: Liver

value: Hepatocellular carcinoma tumor


title: HSPC-WT-PromoterBait_3

description:
Library name: Sample 45
HSPC-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
HSPC-WT-PromoterBait-Hba-a1_combined_chimeric.txt
HSPC-WT-PromoterBait-HBB-b1_combined_chimeric.txt
HSPC-WT-PromoterBait-Idh2_combined_chimeric.txt
HSPC-WT-PromoterBait-Klf4_combined_chimeric.txt
HSPC-WT-PromoterBait-Med13l_combined_chimeric.txt
HSPC-WT-PromoterBait-MYC_combined_chimeric.txt
HSPC-WT-PromoterBait-Nanog_combined_chimeric.txt
HSPC-WT-PromoterBait-Setd1b_combined_chimeric.txt
HSPC-WT-PromoterBait-slc25a37_combined_chimeric.txt
HSPC-WT-PromoterBait-SOX2_combined_chimeric.txt
HSPC-WT-PromoterBait-Tet2_combined_chimeric.txt
HSPC-WT-PromoterBait-Trp53_combined_chimeric.txt


title: PAPZCL_R (SC)

description: 10x Genomics

value: Relapse


title: Huh7pIL6_H3K27ac_rep1

value: H3K27ac (Abcam, ab4729)


title: PAPZCL_D (SC)

description: 10x Genomics


title: Total RNA  of  S. Typhimurium SL1344  cells growing in LB at 37°C OD=2 (ESP condition GFP+) Replicate 1

city: Gif-sur-Yvette

first: Virginia

last: Lioy

address: 1 Avenue de la Terrasse

department: Genome Biology

country: France

institute: Institute for Integrative Biology of the Cell (I2BC)

description:
Library name: MKR21
RNA-seq

data_processing:
Hi-C libraries were proccessed using the OHCA pipeline from Bioconductor: https://jserizay.com/OHCA/docs/devel/. Hi-C matrices were binned at 1Kb, plasmids were exluded of the analyses
For the ChIP-seq analysis, each read was aligned to the reference genome (Salmonella enterica serovar Typhimurium strain SL1344) using Bowtie2 (v 2.4.2).  Paired-end reads were then Merged and sorted with Samtools, and PCR duplicates were removed using the Picard MarkDuplicates tool. Subsequently, SAM files were converted to BAM files, indexed, and processed to generate bedGraph and bigWig files with using bamCompared from DeepTools2. This tool allowed us to compare the ChIP-seq data to the INPUT and normalize it in Bins Per Million mapped reads (BPM). For Hi-C correlations and determination of protein occupancy (H-NS and RNA polymerase), 1Kb bins were used. No binning was used for the rest of analyses.
For RNA-seq analysis, paired-end reads were mapped to the reference genome using Bowtie2 (v 2.4.2). After alignment, SAM files were sorted, converted to BAM format, and indexed. BAM files were subsequently converted to WIG format using bamCoverage or Galaxy with CPM normalization. Read quantification in sense and antisense orientations was performed using featureCounts program (v 2.0.1)70. Differential gene expression analysis was conducted in R using the SARTools pipeline (Statistical Analysis of RNA-Seq data Tools, v1.8.1), which is based on DESeq2. Quality controls, raw count normalization, and identification of differentially expressed genes were systematically performed. Principal Component Analysis (PCA) and hierarchical clustering were applied to data transformed using Variance Stabilizing Transformation (VST) to ensure homoscedasticity. The Benjamini-Hochberg method was used for p-value adjustment with a statistical significance threshold of 0.05. The condition "GFP negative" was defined as the reference for comparisons. Genes with null counts across all samples and predefined low-quality features were excluded prior to analysis.  Additionally, to facilitate correlations with Hi-C data, DESeq2-normalized counts per kilobase for each gene under all experimental conditions were determined
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium SL1344 complete genome, GenBank: FQ312003.1
Supplementary files format and content: 4879x4879 Hi-C contact matrices in txt format

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacteria

growth_protocol: Bacteria were cultured in Lennox Broth (LB) medium at 37°C with shaking at 180 rpm. Overnight cultures were diluted 1:1000 and grown to an OD600 of 0.1 (early exponential phase, EEP) or OD600 of 2 (early stationary phase, ESP). When required, antibiotics were added to the liquid medium or agar plates at the following final concentrations: 100 μg/mL ampicillin (Amp), 50 μg/mL kanamycin (Kan), or 30 μg/mL chloramphenicol (Cm). Include oxygen shock and microanaerobiosis

extract_protocol:
Hi-C: Frozen pellets were thawed on ice, resuspended in 200 μL of 1× Tris-EDTA (TE) buffer (Sigma-Aldrich, Cat# T928) containing a complete protease inhibitor cocktail (Roche, Cat# 11873580001). Then, 1 µl of ready-lyse lysozyme (LGC Biosearch, Cat# LU-R1804M) was added and the mixture was incubated at RT for 20 minutes.  Next, 10 µl of 10% SDS (Sigma-Aldrich, Cat#  05030) was added to the cells and incubated for 10 minutes at RT. Subsequently, the lysed cells were transferred into a 2 mL Eppendorf tube containing 800 μL of digestion mix: 100 μL of 10× NEB1 buffer (New England Biolabs, Cat# B7001S), 100 μL of 10% Triton (Sigma-Aldrich, Cat# T8787), and 600 μL of sterile water. After removing 80 μL of non-digested control, 20 μL of HpaII enzyme (New England Biolabs, Cat# R0171L) were added to the digestion mix. Both tubes were then incubated for 3 hours at 37°C with agitation. Following DNA digestion, 80 μL of the digested control were removed and kept on ice with the non-digested control. The remaining digestion mix was centrifuged for 20 minutes at 16,000 × g, 4°C, and the pellet was re-suspended in 80 µL of sterile water. The 80 µL of digested DNA was then added to the biotinylation mix containing 10 µL of 10× ligation buffer, 1 µL of 10 mM dAGTP mix, 3 µL of 1 mM biotin-14-dCTP (Jena Biosciences, Cat# E-NU-956-BIO14-S), and 2 µL of DNA polymerase I, large (Klenow) fragment (New England Biolabs, Cat# M0210L), and incubated for 1 hour at 37°C with agitation. Following biotinylation, proximity ligation of DNA fragments was performed by adding the ligation mix: 24 µL of 10× ligation buffer (without ATP), 2.4 µL of 100 mM ATP, 2.4 µL of 10 mg/mL BSA (New England Biolabs, Cat# B9000S), and 3.2 µL of of T4 DNA ligase (Thermo Fisher Scientific, Cat# EL0013). Ligation was performed at 25°C for 3 hours with gentle agitation. The crosslink was then reversed by incubating the samples (including the non-digested and digested controls) overnight at 65°C in the presence of proteinase K (20 mg/mL; Eurobio Scientific, Cat# GEXPROK01-B5), EDTA (500 mM; Sigma-Aldrich, Cat# 03690), and 10% SDS. The next day, DNA was purified by phenol extraction and ethanol precipitation. Briefly, one volume of phenol:chloroform:isoamyl alcohol (25:24:1) (Thermo Fisher Scientific, Cat# 10308293) was added to the samples. Following centrifugation, the upper aqueous phase was transferred to a new 1.5 mL tube, and DNA was precipitated with 1/10 volume of 3 M Na-acetate (pH 5.2) and two and a half volumes of cold ethanol. After incubation at −80°C for 30 minutes, the DNA was pelleted, washed once with 70% ethanol, and dried using an Eppendorf concentrator plus speed vac. The DNA was resuspended in 130 µL of 1× TE buffer containing 10 μg/mL RNase A (Thermo Fisher Scientific, Cat# EN0531) ChIP-seq: frozen cell pellets, fixed with 1% formaldehyde, were thawed on ice and re-suspended in 500 μl of lysis buffer I: 20% sucrose (Sigma-Aldrich, Cat# S7903), 10 mM Tris-HCl (pH 8), 50 mM NaCl, and 10 mM EDTA, supplemented with 4 μl of ready-lyse lysozyme. The mixture was incubated at 37°C for 30 minutes. Next, 500 μl of lysis buffer II (50 mM Tris-HCl (pH8), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 and complete protease inhibitor cocktail) was added. The cells were transferred to a 1 mL Covaris tube and sonicated using a Covaris S220 focused Ultrasonicator. Sonication parameters were set to 210 seconds for EEP samples and 270 seconds for ESP samples (peak power = 140 W; duty factor = 5%; cycles per burst = 200). Following sonication, the samples were centrifuged at 18,000 × g for 30 minutes at 4°C. The supernatant was transferred into a new 1.5 mL tube, with 50 μL set aside as input and stored at −20°C until further use. Immunoprecipitation of FLAG-tagged proteins was performed by incubating the cell extracts with 100 μL of ANTI-FLAG M2 affinity gel (Sigma-Aldrich, Cat# A2220) overnight at 4°C on a rotator. The beads were washed twice with 400 μL of TBS (Tris-HCl 50mM pH 7.4, 150mM NaCl) containing 0.05% Tween 20, followed by three washes with 400 μL of cold TBS. Each wash step was performed under rotation for 10 minutes at 4°C. The 3xFLAG-protein-DNA complexes were eluted by adding 2.5 volumes of 3xFLAG peptide solution (Sigma-Aldrich, Cat# F4799) relative to the total packed gel volume. The samples were incubated for 90 minutes on a rotator at 4°C, centrifuged for 30 seconds at 5000 × g at 4°C, and the supernatant was transferred to 1.5 mL LoBind DNA tubes. A second elution step was performed similarly. The IP and input samples were treated with RNase A (10 μg/mL) for 1 hour at 37°C and then incubated overnight at 65°C with proteinase K (final concentration: 50 μg/mL) to reverse the formaldehyde crosslinks. DNA was then purified using a Qiagen MinElute PCR Purification Kit (Qiagen, Cat# 28004) and stored at -20°C until further processing. RNA-seq:Frozen pellets of sorted cells were thawed on ice and resuspended in 1 mL of TRIzol (Qiagen, Cat# 79306), followed by the addition of 400 µL of chloroform. After a 3-minute incubation, the mixture was centrifuged at 20,000 × g for 15 minutes at 4°C. The upper aqueous phase containing RNA was carefully transferred to a new tube, and 600 µL of isopropanol was added to precipitate the RNA at room temperature. Following a 30-minute centrifugation at 20,000 × g at 4°C, the supernatant was discarded. The RNA pellet was washed with 500 µL of 70% ethanol, air-dried, and resuspended in RNase-free water by shaking at 900 rpm for 5 minutes. RNA was treated with DNase according to the manufacturer’s instructions (Invitrogen™ TURBO DNA-free™ Kit, Cat# AM1907). RNA concentrations were determined using either a Nanodrop spectrophotometer or a Qubit fluorometer (Invitrogen). RNA quality was assessed with an Agilent 2100 Bioanalyzer, and samples were stored at −20°C.
For Hi-C and ChIP-seq libraries preparation, samples were first sheared to a target fragment size of 300 bp using a Covaris S220 instrument. Then, Hi-C libraries were prepared as described in (Ckrockram et al, STAR protocol, 2021). For ChIP-seq libraries, after sonication, IP and input samples were purified using 1.6x volume of AMPure XP beads according to manufacturer instructions (Beckman Coulter, Cat# A63881). DNA was eluted into 40 μL of elution buffer (EB, 10 mM Tris-HCl pH 7.5). After adjusting the volume of the samples to 80 μL with sterile water, DNA fragments were end-repaired by adding 40 μL of the following mix: 12 μL 10× T4 DNA ligase buffer (New England Biolabs, Cat# B0202S), 4 μL 10 mM dNTP mix, 5 μL T4 DNA polymerase (3 U/μL, New England Biolabs, Cat# M0203L), 5 μL T4 Polynucleotide Kinase (10 U/μL, Thermo Fisher Scientific, Cat# EK0032), 1 μL DNA polymerase I, large (Klenow) fragment (5 U/μL, New England Biolabs, Cat# M0210L), and 13 μL H2O . The reaction was incubated at room temperature (RT) for 30 minutes, purified using 1.6× AMPure XP beads, and DNA was eluted in 30 μL of EB. Purified DNA was then dA-tailed by adding 5 μL of 10× NEBuffer 2 (New England Biolabs, Cat# B7002S), 10 μL of 1 mM dATP (Sigma-Aldrich, Cat# D4788), 3 μL of Klenow Fragment (3'–5' exo-), (5 U/μL, New England Biolabs, Cat# M0212L), and 2 μL of H2O. The reaction was incubated at 37 °C for 30 minutes, followed by heat inactivation at 65 °C for 20 minutes to deactivate the Klenow Fragment (3’–5’ exo-). After purification with 1.6× volume of AMPure XP beads, DNA was eluted in 12 μL of EB. Illumina adapters were ligated using the NEBNext Quick Ligation Module (New England Biolabs, Cat# E6056S) for 15 minutes at RT. The ligation reaction was then purified using AMPure XP beads. First, the sample volume was adjusted to 50 μL with water, and a double size selection step was performed with the beads at a ratio of 0.7×-1.1×. For 3xFLAG-H-NS and 3xFLAG-RpoC libraries, PCR amplification was performed in a single 15-cycle reaction using  5 µl of library, 10 µl of 2 µM Illumina primers P1 and P2 mix, 10 µl Phusion 2× High Fidelity Master Mix (New England Biolabs, Cat#  M0531S) and 10 µl of H2O (for both IP and input). For the 3xFLAG-HilD and 3xFLAG-H-NS on sorted populations, three PCR reactions were performed for IP samples and one for the input sample. PCR products were purified using Qiagen MinElute PCR purification columns, and primer dimers were removed using AMPure XP beads. The concentration of Hi-C and ChIP-seq libraries was quantified using a Qubit fluorometer (Invitrogen) with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Cat# 10606433). Libraries were diluted to 0.5 ng/μL, and their quality was assessed on an Agilent 4150 TapeStation system using Agilent High Sensitivity D5000 ScreenTape (Agilent, Cat# 5067-5592). RNA-seq libraries.....

value: hisG46, PprgH-gfp::Cm

value: bacteria


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP-) Replicate 1

description: Library name: MKL120

value: hisG46, hns-3xFLAG, PprgH-gfp::Cm


title: Total RNA  of  S. Typhimurium SL1344  cells growing in LB at 37°C OD=2 (ESP condition GFP-) Replicate 2

description:
Library name: MKR24
RNA-seq


title: Erythroid-WT-PromoterBait-R1R2_6

description:
Library name: Sample 42
Erythroid-WT-PromoterBait-R1R2-Hba_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Hbb_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Slc25a37_combined_chimeric.txt


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP-) Replicate 2

description:
Library name: MKL122
ChIP-seq merge rep1& rep2


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP+) Replicate 1

description: Library name: MKL119


title: TCH4-TCH6, D and R (SC)

description: 10x Genomics

value: pooled male and female

value: Diagnosis and Relapse


title: Total RNA  of  S. Typhimurium SL1344  cells growing in LB at 37°C OD=2 (ESP condition GFP+) Replicate 2

description:
Library name: MKR23
RNA-seq


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP-) Replicate 2

description:
Library name: MKL118
ChIP-seq merge rep1& rep2


title: Erythroid-WT-PromoterBait_6

description:
Library name: Sample 36
Erythroid-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Hba-a1_combined_chimeric.txt
Erythroid-WT-PromoterBait-HBB-b1_combined_chimeric.txt
Erythroid-WT-PromoterBait-Idh2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Klf4_combined_chimeric.txt
Erythroid-WT-PromoterBait-Med13l_combined_chimeric.txt
Erythroid-WT-PromoterBait-MYC_combined_chimeric.txt
Erythroid-WT-PromoterBait-Nanog_combined_chimeric.txt
Erythroid-WT-PromoterBait-Setd1b_combined_chimeric.txt
Erythroid-WT-PromoterBait-slc25a37_combined_chimeric.txt
Erythroid-WT-PromoterBait-SOX2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Tet2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Trp53_combined_chimeric.txt

source_name: Spleen

value: Spleen


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP-) Replicate 1

description: Library name: MKL116


title: Erythroid-WT-PromoterBait_5

description:
Library name: Sample 35
Erythroid-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Hba-a1_combined_chimeric.txt
Erythroid-WT-PromoterBait-HBB-b1_combined_chimeric.txt
Erythroid-WT-PromoterBait-Idh2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Klf4_combined_chimeric.txt
Erythroid-WT-PromoterBait-Med13l_combined_chimeric.txt
Erythroid-WT-PromoterBait-MYC_combined_chimeric.txt
Erythroid-WT-PromoterBait-Nanog_combined_chimeric.txt
Erythroid-WT-PromoterBait-Setd1b_combined_chimeric.txt
Erythroid-WT-PromoterBait-slc25a37_combined_chimeric.txt
Erythroid-WT-PromoterBait-SOX2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Tet2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Trp53_combined_chimeric.txt


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP+) Replicate 1

description: Library name: MKL115


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description:
Library name: MKL114
ChIP-seq merge rep1& rep2

value: hisG46, hns-3xFLAG:Cm


title: Erythroid-WT-PromoterBait-R1R2_2

description:
Library name: Sample 38
Erythroid-WT-PromoterBait-R1R2-Hba_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Hbb_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Slc25a37_combined_chimeric.txt


title: TCH6_R(Bulk)

data_processing:
RNA-Seq reads were aligned and quantified using RSEM (version 1.30) (PMID: 21816040) and Bowtie2 (version 2.10) (PMID: 22388286) to human reference GRCh38 {(GENCODE v32/Ensembl 98)(refdata-gex-GRCh38-2020-A dated 2020-07-07 downloaded from 10X Genomics with GENCODE gtf dated 2019-09-05)}.
Assembly: hg19
Supplementary files format and content: Excel file includes count values for each Sample

source_name: marrow

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plus mini kit with a genomic DNA elimination column (74104).
Extracted RNA samples were profiled using Illumina Novaseq 600 with 25M reads per sample.
Briefly, RNA quality was confirmed, 150bp paired-end mRNA libraries were prepared, and libraries were sequenced at a depth of 25M reads per sample on the NovaSeq 6000 platform (Illumina).

value: marrow

value: M


title: Total RNA  of  S. Typhimurium SL1344  cells growing in LB at 37°C OD=2 (ESP condition GFP-) Replicate 1

description:
Library name: MKR22
RNA-seq


title: TCH1-TCH3, D and R (SC)

description: 10x Genomics


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL112


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description:
Library name: MKL109
ChIP-seq merge rep1& rep2


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL108


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description:
Library name: MKL110
ChIP-seq merge rep1& rep2


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description:
Library name: MKL113
ChIP-seq merge rep1& rep2


title: TCH4_R(Bulk)

value: F


title: mES-E14-WT-EnhancerBait_12

description:
Library name: Sample 30
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt

value: Embryo

value: Mouse embryonic stem cell

value: WT


title: Erythroid-WT-PromoterBait_3

description:
Library name: Sample 33
Erythroid-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Hba-a1_combined_chimeric.txt
Erythroid-WT-PromoterBait-HBB-b1_combined_chimeric.txt
Erythroid-WT-PromoterBait-Idh2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Klf4_combined_chimeric.txt
Erythroid-WT-PromoterBait-Med13l_combined_chimeric.txt
Erythroid-WT-PromoterBait-MYC_combined_chimeric.txt
Erythroid-WT-PromoterBait-Nanog_combined_chimeric.txt
Erythroid-WT-PromoterBait-Setd1b_combined_chimeric.txt
Erythroid-WT-PromoterBait-slc25a37_combined_chimeric.txt
Erythroid-WT-PromoterBait-SOX2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Tet2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Trp53_combined_chimeric.txt


title: Erythroid-WT-PromoterBait-R1R2_1

description:
Library name: Sample 37
Erythroid-WT-PromoterBait-R1R2-Hba_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Hbb_combined_chimeric.txt
Erythroid-WT-PromoterBait-R1R2-Slc25a37_combined_chimeric.txt

value: Fetal liver


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL111


title: Erythroid-WT-PromoterBait_4

description:
Library name: Sample 34
Erythroid-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Hba-a1_combined_chimeric.txt
Erythroid-WT-PromoterBait-HBB-b1_combined_chimeric.txt
Erythroid-WT-PromoterBait-Idh2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Klf4_combined_chimeric.txt
Erythroid-WT-PromoterBait-Med13l_combined_chimeric.txt
Erythroid-WT-PromoterBait-MYC_combined_chimeric.txt
Erythroid-WT-PromoterBait-Nanog_combined_chimeric.txt
Erythroid-WT-PromoterBait-Setd1b_combined_chimeric.txt
Erythroid-WT-PromoterBait-slc25a37_combined_chimeric.txt
Erythroid-WT-PromoterBait-SOX2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Tet2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Trp53_combined_chimeric.txt


title: H-NS ChIP of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP+) Replicate 2

description:
Library name: MKL121
ChIP-seq merge rep1& rep2


title: TCH5_R(Bulk)


title: TCH6_D(Bulk)

value: Diagnosis


title: TCH5_D(Bulk)


title: Erythroid-WT-PromoterBait_2

description:
Library name: Sample 32
Erythroid-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Hba-a1_combined_chimeric.txt
Erythroid-WT-PromoterBait-HBB-b1_combined_chimeric.txt
Erythroid-WT-PromoterBait-Idh2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Klf4_combined_chimeric.txt
Erythroid-WT-PromoterBait-Med13l_combined_chimeric.txt
Erythroid-WT-PromoterBait-MYC_combined_chimeric.txt
Erythroid-WT-PromoterBait-Nanog_combined_chimeric.txt
Erythroid-WT-PromoterBait-Setd1b_combined_chimeric.txt
Erythroid-WT-PromoterBait-slc25a37_combined_chimeric.txt
Erythroid-WT-PromoterBait-SOX2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Tet2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Trp53_combined_chimeric.txt


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL100

value: hisG46, rpoC-3xFLAG:Cm


title: mES-E14-WT-EnhancerBait_10

description:
Library name: Sample 28
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: TCH4_D(Bulk)


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description: Library name: MKL106


title: mES-E14-WT-EnhancerBait_11

description:
Library name: Sample 29
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL103


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition GFP+) Replicate 2

description:
Library name: MKL117
ChIP-seq merge rep1& rep2


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL104


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description: Library name: MKL102


title: TCH3_D(Bulk)


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description: Library name: MKL101


title: INPUT gDNA  of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL99


title: RpoC ChIP of  S. Typhimurium SL1344 rpoC-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description: Library name: MKL105


title: TCH3_R(Bulk)

value: Relapse


title: mES-E14-WT-EnhancerBait_9

description:
Library name: Sample 27
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: TCH2_R(Bulk)


title: INPUT gDNA  of  S. Typhimurium SL1344 hns-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL107


title: Erythroid-WT-PromoterBait_1

description:
Library name: Sample 31
Erythroid-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Hba-a1_combined_chimeric.txt
Erythroid-WT-PromoterBait-HBB-b1_combined_chimeric.txt
Erythroid-WT-PromoterBait-Idh2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Klf4_combined_chimeric.txt
Erythroid-WT-PromoterBait-Med13l_combined_chimeric.txt
Erythroid-WT-PromoterBait-MYC_combined_chimeric.txt
Erythroid-WT-PromoterBait-Nanog_combined_chimeric.txt
Erythroid-WT-PromoterBait-Setd1b_combined_chimeric.txt
Erythroid-WT-PromoterBait-slc25a37_combined_chimeric.txt
Erythroid-WT-PromoterBait-SOX2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Tet2_combined_chimeric.txt
Erythroid-WT-PromoterBait-Trp53_combined_chimeric.txt


title: mES-E14-WT-EnhancerBait_7

description:
Library name: Sample 25
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: INPUT gDNA  of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description:
Library name: MKL93
ChIP-seq merge rep1 & rep2

value: hisG46, hilD-3XFLAG:Cm


title: INPUT gDNA  of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL92

value: bacteria


title: HilD ChIP   of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description:
Library name: MKL97
Chip-seq merge rep1 & rep2


title: mES-E14-WT-EnhancerBait_6

description:
Library name: Sample 24
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: TCH1_D(Bulk)


title: TCH2_D(Bulk)


title: mES-E14-WT-EnhancerBait_8

description:
Library name: Sample 26
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: HilD ChIP   of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL96


title: mES-E14-WT-EnhancerBait_5

description:
Library name: Sample 23
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: INPUT gDNA  of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL91


title: INPUT gDNA  of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description:
Library name: MKL94
Chip-seq merge rep1 & rep2


title: TCH1_R(Bulk)


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP GFP- condition)

description: Library name: MKL82

value: hisG46, PprgH-gfp::Cm


title: HilD ChIP   of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL95


title: Merge of libraries MKL82, MKL82bis,

description:
Library name: MKL82_Merged
Hi-C matrix 1kb bin


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP GFP- condition) Resequenced

description: Library name: MKL82_bis


title: U2 TNF treated replicate 3

city: Graz

first: Sebastian

last: Vosberg

address: Auenbruggerplatz 15

country: Austria

institute: Medical University of Graz

data_processing:
Sequencing reads were mapped using STAR with reference genome hg38. Gene expression counts were retreived using featureCounts. Default parameters have been used for all individual steps
Assembly: hg38
Supplementary files format and content: tab-separated values: gene_symbol / raw_count

source_name: CD34+ HSPCs

extract_protocol:
Total RNA were isolated using peq gold total RNA kit (VWR)
mRNA library was made with poly A enrichment using a kit developed by Novogene (Novogene GmbH)

treatment_protocol: The following reagents were used for treatment of AML cell lines: recombinant human LTα3 (5 ng/ml or 100 ng/ml rh-LTα3; R&D Systems), recombinant human TNF (5 ng/ml or 100 ng/ml rh-TNF; R&D Systems) for 24h, if indicated

value: CD34+ HSPCs

value: recombinant human TNF, 100 ng/ml


title: U2 TNF treated replicate 2


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP GFP+ condition) Resequenced

description: Library name: MKL81_bis


title: Merge of libraries MKL81, MKL81bis,

description:
Library name: MKL81_Merged
Hi-C matrix 1kb bin


title: mES-E14-WT-EnhancerBait_4

description:
Library name: Sample 22
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: Hi-C of ΔhilD  S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description: Library name: MKL134

value: hisG46, DhilD::Cm


title: mES-E14-WT-EnhancerBait_3

description:
Library name: Sample 21
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: Merge of libraries MKL72, MKL134,

description:
Library name: DhilD_ESP_Merged
Hi-C matrix 1kb bin


title: mES-E14-WT-EnhancerBait_2

description:
Library name: Sample 20
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: U2 LTA treated replicate 3

value: recombinant human Lymphotoxin A, 100 ng/ml


title: U2 TNF treated replicate 1


title: mES-E14-WT-MycPromoterBait_6

description:
Library name: Sample 18
mES-E14-WT-MycPromoterBait-MYC_combined_chimeric.txt


title: Hi-C of ΔhilE  S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP GFP- condition)

description: Library name: MKL42

value: hisG46, DhilE,PprgH-gfp::Cm


title: Hi-C of ΔhilE  S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP GFP+ condition)

description: Library name: MKL41


title: U2 LTA treated replicate 1


title: mES-E14-WT-EnhancerBait_1

description:
Library name: Sample 19
mES-E14-WT-EnhancerBait-MYC_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Nanog_combined_chimeric.txt
mES-E14-WT-EnhancerBait-SOX2_combined_chimeric.txt
mES-E14-WT-EnhancerBait-Tet2_combined_chimeric.txt


title: U2 LTA treated replicate 2


title: Hi-C of ΔhilD  S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP condition) Replicate 1

description: Library name: MKL72


title: re-secuencing of MKL16

description: Library name: MKL16_bis


title: Merge of fastq files MKL15, MKL15bis

description:
Library name: MKL15_Merged
Hi-C matrix 1kb bin


title: mES-E14-WT-MycPromoterBait_5

description:
Library name: Sample 17
mES-E14-WT-MycPromoterBait-MYC_combined_chimeric.txt


title: Merge of libraries MKL16, MKL16_bis

description:
Library name: MKL16_Merged
Hi-C matrix 1kb bin


title: U2 untreated replicate 3


title: mES-E14-WT-MycPromoterBait_4

description:
Library name: Sample 16
mES-E14-WT-MycPromoterBait-MYC_combined_chimeric.txt


title: U2 untreated replicate 2


title: mES-E14-WT-MycPromoterBait_3

description:
Library name: Sample 15
mES-E14-WT-MycPromoterBait-MYC_combined_chimeric.txt


title: Hi-C of WT S. Typhimurium SL1344 cells growing statically in LB OD=0.3 in a filled and sealed 50 mL Falcon tube

description: Library name: MKL15


title: HiC WT Salmonella in LB, 37C OD0.3 then transferred into a filled and sealed 50mL Falcon w/o agitation at 37C for 30 min

description: Library name: MKL16


title: mES-E14-WT-MycPromoterBait_2

description:
Library name: Sample 14
mES-E14-WT-MycPromoterBait-MYC_combined_chimeric.txt


title: re-secuencing of MKL15

description: Library name: MKL15_bis


title: U2 untreated replicate 1


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2(ESP condition) Replicate 4

description: Library name: MKL20


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2(ESP condition) Replicate 3

description: Library name: MKL9


title: mES-E14-WT-MycPromoterBait_1

description:
Library name: Sample 13
mES-E14-WT-MycPromoterBait-MYC_combined_chimeric.txt


title: U1 TNF treated replicate 3


title: U1 TNF treated replicate 2


title: HilD ChIP   of  S. Typhimurium SL1344 hilD-3xFLAG cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description:
Library name: MKL98
Chip-seq merge rep1 & rep2


title: mES-E14-WT-PromoterBait-optimized_6

description:
Library name: Sample 12
mES-E14-WT-PromoterBait-optimized-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Trp53_combined_chimeric.txt


title: mES-E14-WT-PromoterBait-optimized_5

description:
Library name: Sample 11
mES-E14-WT-PromoterBait-optimized-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Trp53_combined_chimeric.txt


title: U1 LTA treated replicate 3


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 3

description: Library name: MKL19


title: U1 TNF treated replicate 1


title: Merge of libraries MKL3, MKL8, MKL19

description:
Library name: WT_EEP_Merged
Hi-C matrix 1kb bin


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP GFP+ condition)

description: Library name: MKL81


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 1

description: Library name: MKL3


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=0,1 (EEP condition) Replicate 2

description: Library name: MKL8


title: mES-E14-WT-PromoterBait-optimized_3

description:
Library name: Sample 9
mES-E14-WT-PromoterBait-optimized-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Trp53_combined_chimeric.txt


title: CD90+ HSC resorted after 7 day culture with DMSO - Replicate 2

city: Rye

first: Larry

middle: L

last: Luchsinger

state: NY

address: 601 Midland Ave

department: Stem Cell Regenerative Research

institute: New York Blood Center

description:
Library name: D2
processed data file column assignment: Column G-K

data_processing:
Paired-end 150 bp sequencing was performed on an Illumina HiSeq 4000.
Trimmed sequence reads were aligned to the human genome (hg37) and expression counts (STAR) was performed BasePair (https://basepairtech.com).
Read counts were extracted and normalized (FPKM) followed by statistical analyses.
Assembly: hg19 (GRCh37)
Supplementary files format and content: Normalized STAR Expression Analysis (NCBI RefSeq ID, Gene Symbol, count, FPKM and TPM)

source_name: Cord Blood

growth_protocol: HSCs were cultured in StemSpan SFM with 100ng SCF, TPO, FLT3L, 50ng/mL IL-3, 20ng/mL IL-6 in 5% CO2 and 5% O2 humidified chamber.

extract_protocol:
RNA was extracted with LS Trizol in the presence of linear acrylamide, according to manufacturer's instructions.
Sequencing libraries were prepared using an SMartR 2 RNA-seq system V2 kit following manufacturer's protocols.

treatment_protocol: Cultures were treated with 0.01% DMSO or 5nM Compound B.  Half media was refreshed every day for 7 days.

value: Cord Blood

value: CD90+ HSC

tag: batch


title: U1 LTA treated replicate 2


title: CD90+ HSC resorted after 7 day culture with DMSO - Replicate 3

description:
Library name: D3
processed data file column assignment: Column M-Q


title: CD90+ HSC resorted after 7 day culture with Compound B - Replicate 3

description:
Library name: B4
processed data file column assignment: Column AG-AK

value: 5nM Compound B


title: Hi-C of WT S. Typhimurium SL1344 cells growing in LB at 37°C OD=2 (ESP condition) Replicate 2

description: Library name: MKL4


title: Merge of libraries MKL1, MKL4, MKL9

description:
Library name: WT_ESP_Merged
Hi-C matrix 1kb bin


title: E59 human distal femur RNA

city: Boston

first: April

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
the Cell Ranger pipeline was used to process the fastq files
the Cell Ranger-ARC pipeline v2.0.0 was used to generate the count matrix
Assembly: hg38
Supplementary files format and content: Cell ranger output files - barcodes.tsv, features.tsv, matrix.mtx, atac_fragments.tsv

source_name: distal femur

extract_protocol:
collagenase digestion
RNA and ATAC seq libraries were prepared using the 10x Chromium Single Cell Multiome ATAC + Gene Expression kit following the manufacturer's protocols

value: distal femur

tag: age

value: Collagenase digestion


title: U1 LTA treated replicate 1

value: WT


title: mES-E14-WT-PromoterBait-optimized_2

description:
Library name: Sample 8
mES-E14-WT-PromoterBait-optimized-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Trp53_combined_chimeric.txt

value: Embryo

value: Mouse embryonic stem cell


title: Group C-20

city: Guangzhou

first: Wen

last: Ni

state: Guangdong

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer after quality filtering.
Firstly, Q30 was used to perform quality control.
The high quality reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl gtf gene annotation file with hisat2 software (v2.04).
Then, cuffdiff software (part of cufflinks, v2.2.1) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes.
Fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Assembly: UCSC hg19
Supplementary files format and content: processed_data.xlsx: Excel file includes raw counts and normalized counts for each Sample.

source_name: normal intestinal mucosal tissues

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.

value: normal intestinal mucosal tissues

tag: donor


title: U1 untreated replicate 2


title: CD90+ HSC resorted after 7 day culture with Compound B - Replicate 2

description:
Library name: B2
processed data file column assignment: Column AA-AE


title: mES-E14-WT-PromoterBait-optimized_1

description:
Library name: Sample 7
mES-E14-WT-PromoterBait-optimized-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-optimized-Trp53_combined_chimeric.txt


title: mES-E14-WT-PromoterBait_6

description:
Library name: Sample 6
mES-E14-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Trp53_combined_chimeric.txt


title: E59 human distal femur ATAC

library_source: genomic single cell


title: CD90+ HSC resorted after 7 day culture with Compound B - Replicate 1

description:
Library name: B1
processed data file column assignment: Column U-Y


title: Group B-20

source_name: liver metastases

value: liver metastases


title: mES-E14-WT-PromoterBait_4

description:
Library name: Sample 4
mES-E14-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Trp53_combined_chimeric.txt


title: Group A-20

source_name: CRC tissues

value: CRC tissues


title: Group A-19


title: Group C-18


title: Group B-19


title: U1 untreated replicate 3


title: A2 TNF treated replicate 2

source_name: bone marrow

value: bone marrow

value: acute myeloid leukemia


title: Group A-18


title: A2 TNF treated replicate 1

value: recombinant human TNF, 100 ng/ml


title: mES-E14-WT-PromoterBait_3

description:
Library name: Sample 3
mES-E14-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Trp53_combined_chimeric.txt

source_name: Embryo


title: mES-E14-WT-PromoterBait_2

description:
Library name: Sample 2
mES-E14-WT-PromoterBait-Cbfa2t2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Hba-a1_combined_chimeric.txt
mES-E14-WT-PromoterBait-HBB-b1_combined_chimeric.txt
mES-E14-WT-PromoterBait-Idh2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Klf4_combined_chimeric.txt
mES-E14-WT-PromoterBait-Med13l_combined_chimeric.txt
mES-E14-WT-PromoterBait-MYC_combined_chimeric.txt
mES-E14-WT-PromoterBait-Nanog_combined_chimeric.txt
mES-E14-WT-PromoterBait-Setd1b_combined_chimeric.txt
mES-E14-WT-PromoterBait-slc25a37_combined_chimeric.txt
mES-E14-WT-PromoterBait-SOX2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Tet2_combined_chimeric.txt
mES-E14-WT-PromoterBait-Trp53_combined_chimeric.txt


title: Group B-17