title: pooled repeat 1, Input

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

data_processing:
Reads were aligned to the GRCh38 transcriptome using HISAT2(2.2.1). Transcript abundance was calculated using feature Counts from the subread package (v2.0.3), and differential expression was determined in R studio (v2022.07.2, R 4.2.2) using the DESeq2 (v1.38.3) analysis package with default parameters. For ChIP-seq analysis, reads were aligned to the GRCh38 reference genome using Bowtie2 (v2.4.5) and peaks were called using MACS2 (v2.2.7.1) with a q-value ≤ 0.01. Resulting peaks were assessed and analyzed with deepTools (v3.5.4),  DiffBind (v3.8.4) and ChIPSeeker (v1.34.1)
Assembly: GRCh38
Supplementary files format and content: featurecount, narrowPeak, bdg

growth_protocol: CD34+ human hematopoietic stem cells (HSCs; StemCell, 70060) were cultured in StemSpan Leukemic Cell Culture Kit (StemCell, 09720) and Complete MethoCult Optimum media (StemCell, H4034). HEK293T cells (ATCC, CRL-11268) were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco, 31-053-028) supplemented with 10% FBS (Sigma, F2442) and 1% penicillin/streptomycin (Gibco, 15140).All cell lines were maintained at 37 °C with 5% CO2.

extract_protocol:
RNA was isolated from transduced CD34+ human hematopoietic stem cells using the RNeasy Plus mini kit (Qiagen, 74136). For ChIP-seq HEK293T Cells were harvested and washed with ice cold 1X PBS and suspended in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40) supplemented with protease inhibitor (Thermo Scientific, A32965). Cells were then pelleted and resuspended in RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitor. Approximately 2.5e7 cells were used for each ChIP experiment. Chromatin in RIPA buffer was sheared to a median fragment size of around 250 bp using a Bioruptor XL (Diagenode).  2 μg of α-FLAG antibody (Sigma-Aldrich, F1804) was incubated with 50 μl Mouse IgG magnetic beads (Life Technologies, 11202D) for ~16 hours at 4 °C, respectively.  Antibody-linked magnetic beads were washed 3 times with PBS/BSA buffer (1X PBS and 5 mg/ml BSA) and sheared chromatin was incubated with corresponding antibody-linked magnetic beads at 4° C overnight and then washed 5 times with LiCl IP wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate). Cross-links were then reversed via overnight incubation at 65°C and DNA was purified using QIAquick PCR purification kit (Qiagen, 28106) for ChIP-seq. Input DNA was prepared from ~1.0e6 cells.
Total RNA samples were normalized to 10ng each, based on picogreen quantitation. RNA-seq libraries were constructed using the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485). The Switching Mechanism at 5’ end of RNA template (SMARTer) cDNA synthesis technology generates directionally identifiable ds-cDNA, incorporated with Illumina sequencing adapters and sample barcodes. Following cDNA synthesis and purification, ribosomal cDNA reduction is achieved by using probes (R-Probes v3) which target mammalian ribosomal cDNA and human mitochondrial ribosomal cDNA and ZapR v3 cleaves these fragments. Following amplification of the library using universal primers and a final purification using Takara NucleoMag NGS Clean-up and Size Select beads, the final library is ready for quantification and sequencing. Read 1 sequenced reads map to the antisense strand of the original RNA. The resulting libraries were quantitated by picogreen and fragment size assessed with the Agilent 2100 Bioanalyzer. ChIP DNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific) and the DNA integrity was checked with 4200 TapeStation (Agilent Technologies). ChIP-seq libraries were prepared using the NEB NextUltra DNA Library Preparation kit (NEB, 7645). Briefly, the ChIP DNA was end-repaired and adapters were ligated after adenylation of the 3’ ends. Adapter-ligated DNA was size-selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation (Agilent) and quantified using Qubit 2.0 Fluorometer as well as real time PCR (KAPA Biosystems). The sequencing libraries were multiplexed and clustered onto one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 equivalent instrument. Sequencing was performed using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software

treatment_protocol: 24-well plates were treated with 20 ug/ml RetroNectin (Takara Bio, T100B) as per manufacturer’s instruction. 2e6 CD34+ human HSCs (StemCell, 70060) were then mixed with 2e9 lentiviral particles and Lentiboost-P (1:100 dilution, Siron Biotech), and were then seeded onto the RetroNectin-treated plates. After centrifugation at 800g at 4°C for 90 mins, plates were placed at 37°C overnight. The cell medium was changed and cells were cultured for another ~48 hours. The transduced cells were imaged using a fluorescent microscope (Nikon ECLIPSE Ti2-E; 541094) and EGFP-positive cells were isolated using FACS cell sorting (Sony Biotechnology, MA900) and cultured in Complete MethoCult Optimum media (StemCell, H4034) for 2 weeks. HEK293T cells were co-transfected with indicated NUP98 fusions (10 μg ) or dCas9 fusion (7.5 μg) expression vectors and gRNA (2.5 μg) constructs in 10 cm plates in biological duplicates for each condition tested. ~72 hours post-transfection, cells were cross-linked for 10 min at RT using 1% formaldehyde (Sigma F8775-25ML) and then the reaction was stopped by the addition of glycine to a final concentration of 125 mM.

value: Input repeat1, pooled

value: pooled input DNA from all repeat 1 samples


title: AsiSI_U2OS_4OHT_MCM4_ChIP_EDF8b_Seq_replicate 2

status: Public on Feb 19 2025

type: SRA

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

country: USA

institute: NIH

library_source: genomic

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: AsiSI TADs and random TADs AsiSI cut sites in U2OS NS-seq peaks AsiSI cut sites in LIG4-/- AID RAD21 AsiSI-HCT116 replication timing in U2OS
Supplementary files format and content: BigWig file format of BrdU-seq NS-seq and ChIP-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone

growth_protocol: AsiSI-U2OS cells were grown in DMEM medium 10% FBS. AID RAD21 HCT116 and AID RAD21 AsiSI HCT116 are grown in McCoy's 5A medium with 10% FBS

extract_protocol:
DNA from cell cultures was isolated size fractionated and subject to exunuclease digestion as described in Aladjem et al. Science 281 1005 1998. and Wang et al. Molecular and Cellular Biology 24:3373-86 2004. For ChipSeq DNA molecules were enriched using antibodies against proteins of interest. For BrdU seq extraction was performed using a protocol modified from Marchal et al. 2018
Samples were eluted and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB E7335S and E7500S).

treatment_protocol: 4OHT was added at a concentration of 300 nM for 4h to induce DNA DSBs. Where relevant WEE1i was added at a concentration of 10 uM for 1h.

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma

tag: genotype

value: Wild-type AsiSI_U2OS

tag: treatment


title: KLF2 WT BMM, day 7, rep 1

city: Berkeley

first: Gregory

last: Barton

state: CA

department: Molecular and Cell Biology

institute: UC Berkeley

description: Library name: sample 5

library_source: transcriptomic

data_processing:
and were aligned with Kallisto v0.43.0 (Bray et al., 2016), using the “-b 100 and -t 4” options to obtain transcript abundances in transcripts per million and estimated counts. The kallisto index used during transcript quantification was built from the Mus musculus transcriptome GRCm38 from Ensembl (ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/cdna/s). Transcript abundances were summarized to gene level using tximport (Soneson et al., 2015).
Assembly: Mus musculus transcriptome GRCm38 from Ensembl
Supplementary files format and content: Hierarchical Data Format 5 files contains run info, abundance esimates, bootstrap estimates, and transcript length information length

molecule: polyA RNA

organism: Mus musculus

source_name: in vitro-derived bone marrow macrophage (BMM)

extract_protocol:
extraction protocol, Bone Marrow Macrophage culture and transfer On Day -7, femur, tibia and iliac bones from LysMCre/+Klf2fl/fl, LysM+/+Klf2fl/fl mice were flushed with RPMI (Gibco) and red blood cells were lysed with ACK buffer (Gibco). Cells were counted and 1M cells were plated in 10cm non-TC treated plates in 8 mL RPMI with 10mM HEPES (Gibco), 1mM Sodium Pyruvate (Gibco), 2mM Glutamax (Gibco), 100U/100µg/mLPen/Strep (Gibco), 1.7µL ß-mercaptoethanol (Fisher), 10% FCS (Gibco or Omega) (RP10+), 10% titrated M-CSF 3T3-cell conditioned laboratory-made media. On Day -3, BMM were given an additional 8mL RP10+ with 10% M-CSF. On Day -1, B6.SJL recipient mice were anesthetized with 90mg/kg ketamine + 5mg/kg xyalzine i.p. Upon achieving the appropriate anesthetic level, 5mL of warm PBS was injected slowly into the peritoneal cavity with a 23 gauge needle. Mice were gently rocked and then PBS was recovered with a 21 gauge needle. Mice were kept warm during the duration of the anesthesia and monitored until recovered. On Day 0, BMM were harvested by incubating in 5mL 4mM ETDA in PBS for 20 min in a 37 deg C incubator.  ETDA was quenched by the addition of 7mL RP10+. Cells were counted and resuspended to inject 1x106 cells per recipient mouse in 100µL of RPMI i.p. Cells were harvested by lavage on day 7, stained and sorted on live, single CD45+ cells with a BD FACS Aria Fusion (BD Biosciences). TRIzol LS (Thermo) was added to sorted cells and frozen at -80˚C for RNA extraction and library generation for RNAseq. extraction protocol, Bone Marrow Macrophage culture and transduction. On Day -1, 2.5x106 293T-GP2 retroviral producer cells were plated in 10mL DMEM with 10mM HEPES (Gibco), 1mM Sodium Pyruvate (Gibco), 2mM Glutamax (Gibco), 100U/100µg/mL Pen/Strep (Gibco), 1.7µL B-mercaptoehtanol(Fisher), 10% FCS (Gibco or Omega) (DM10+) in 10cm TC treated plates. On Day 0, 293T-GP2s (Clontech/Takara, RRID:CVCL_WI48) were transfected with 100ng MSCV plasmid (MSCV multiple cloning site IRES puroR 2A mCherry or GFP) and 10ng pVSVg plasmid (Addgene 8454) with 3µL/mL Lipofectamine 2000 (Thermo). Also on Day 0, femur, tibia and iliac bones from C57BL/6 mice were flushed with RPMI (Gibco) and red blood cells were lysed with ACK buffer (Gibco). Cells were counted and 4x106 cells were plated in 10 cm non-TC treated plates in 8 mL RPMI with 10mM HEPES (Gibco), 1mM Sodium Pyruvate (Gibco), 2mM Glutamax (Gibco), 100U/100µg/mL Penicillin/Streptomycin (Gibco), 1.7 µL B-mercaptoethanol (Fisher), 10% FCS (Gibco or Omega) (RP10+), and 10% titrated M-CSF 3T3-cell conditioned laboratory-made media. On Day 1, media was replaced on the 293T-GP2 to 8 mL. On Day 2 viral supernatants were harvested from 293T-GP2s and filtered through 0.45µM PES syringe filter. Bone marrow cultures were harvested, resuspended in 293T-GP2 supernatant supplemented with 10% M-CSF 3T3 cell media and returned to the same 10 cm plate. Media was replaced on 293T-GP2s for repeating of viral infections on Day 3. On Day 4, bone marrow cells are harvested out of plates and resuspended in 8 mL RP10+ with 10% M-CSF 3T3 supe with 5 µg/mL puromycin. Media was again replaced on Day 7 with fresh RP10+ with 10% M-CSF 3T3 supe. Cells were harvested on day 8-10 by incubating in 5mL 4mM ETDA in PBS for 20 min in a 37˚C incubator.  ETDA was quenched by the addition of 7mL RP10+. Cells were counted and 1x105 cells were resuspended in TRIzol (Thermo) and stored at -80˚C for subsequent RNA isolation. extraction protocol, Whole Lung Prep. The lungs were harvested and homogenized into a single-cell suspension with C tubes on a GentleMacs (Milltenyi) with appropriate tissue programs in 0.07mg/mL LiberaseTM and 45µg/mL DNaseI in 2mL HBSS with Ca/Mg. Tissues were incubated 20min at 37˚C and then finished on the GentleMacs. Enzymes were quenched with PBS with 2mM EDTA and 2% FCS on ice and then red blood cells were lysed with room-temperature ACK lysis buffer (Gibco) and passed through a 100μm cell strainer. Cells were sorted for live, single, CD45+CD11b-CD11c+ with a BD FACS Aria.
Total RNA was isolated from cells using TRIzol or TRIzol LS reagent (Invitrogen). Chloroform extraction was performed according to the manufacturer’s protocol. RNA was recovered from the aqueous layer using RNA Clean and Concentrator-5 kit (Zymo Research). RNA was quantified with a Qubit (Invitrogen) and the integrity was evaluated with Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2014). For BMM overexpressing transcription factors, samples were generated from two independent BMM transductions, but RNA was harvested, libraries were generated, and sequencing was all performed concurrently. Samples were sequenced on an Illumina NovaSeq sequencer using paired-end 50 base pair reads.

value: KLF2 WT

value: day 7


title: AsiSI_U2OS_4OHT_MCM4_ChIP_EDF8b_Seq_replicate 1


title: KLF2 WT BMM, day 0, rep 2

description: Library name: sample 4

value: in vitro-derived bone marrow macrophage (BMM)

value: day 0


title: HEK293T dCas9 NUP98a-KDM5A repeat 2, ChIP

value: transient transfection with dCas9-NUP98a-KDM5A contruct

tag: antibody

value: alpha-FLAG antibody (Sigma-Aldrich, F1804)


title: AsiSI_U2OS_4OHT_MCM2pS139_ChIP_EDF8b_Seq_replicate 2


title: KLF2 KO BMM, day 0, rep 2

description: Library name: sample 3

value: KLF2 KO


title: AsiSI_U2OS_4OHT_MCM2pS139_ChIP_EDF8b_Seq_replicate 1


title: HEK293T dCas9-NUP98a-KDM5A repeat 1, ChIP


title: YF22, NS, CHL, EBV-/HIV-, Female

city: Chapel Hill

first: Yuri

last: Fedoriw

address: 160 Medical Dr

institute: University of North Carolina - Chapel Hill

description:
Library name: YF22
YF22

data_processing:
STAR 2.7.6a was used for read alignment
Salmon 1.4.0 was used for transcript quantification
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes transcripts per million (tpm) counts for each sample

molecule: total RNA

source_name: FFPE tumor

extract_protocol:
Omega FFPE RNA extraction kit
KAPA Hyper Prep RNA with Riboerase kit
[Sequencing step] Eukaryotic strand-specific mRNA sequencing, sequenced on Illumina NovaSeq 6000 S4, paired-end 150 bp

value: FFPE tumor

tag: diagnosis

value: CHL

tag: subtype

value: NS

tag: ebv/hiv status

value: EBV-/HIV-

tag: Sex

value: Female


title: HEK293T dCas9-NUP98a-HOXA9 repeat 1, ChIP

value: transient transfection with dCas9-NUP98a-HOXA9 contruct


title: AsiSI_U2OS_4OHT_BrdU_seq_Figure1c_EDF3d_replicate 2


title: YF23, NS, CHL, EBV-/HIV-, Female

description:
Library name: YF23
YF23


title: KLF2 KO BMM, day 0, rep 1

description: Library name: sample 2


title: KLF2 WT BMM, day 0, rep 1

description: Library name: sample 1


title: pooled repeat 2, Input

value: Input repeat2, pooled

value: pooled input DNA from all repeat 2 samples


title: HEK293T dCas9 NUP98a-HOXA9 repeat 2, ChIP


title: KLF2 KO BMM, day 7, rep 1

description: Library name: sample 8


title: HEK293T dCas9 NUP98a repeat 2, ChIP

value: transient transfection with dCas9-NUP98a contruct


title: K562, CTCF2-del

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: other

data_processing:
Hi-C data were mapped to the hg38 reference genome and processed using a pipeline based on the 4DN Hi-C pipeline (https://github.com/4dn-dcic/docker-4dn-hic).
Assembly: hg38
Supplementary files format and content: Juicebox contact matrix (.HiC)

molecule: other

growth_protocol: Human erythroleukemia K562 cells were grown at 37°C at 5% CO2 in RPMI 1640 (Gibco, cat. no. 11875093) supplemented with 10% FBS (Sigma, cat. no. F7524) and 1% Penicillin-Streptomycin (Gibco, cat. no. 15140122). Cells were maintained at a density below 1 million per ml and were routinely tested for mycoplasma.

extract_protocol:
Hi-C template preparation was performed as previously described (Rao et al. Cell 2014) with modifications as follows: ten million cells per sample were harvested and fixed in 2% formaldehyde; fixation was quenched by glycine at final concentration of 0.2 M. Four-cutter restriction enzyme MboI (NEB, cat. no. R0147) was used for in situ digestion (400 U/10 million cells). Digested DNA ends were labeled with biotin-14–dATP (Invitrogen, cat. no. 19524016) in a Klenow end-filling reaction. End-repaired, ligated, and reverse-crosslinked DNA was purified using isopropanol and magnetic beads (Macherey-Nagel NucleoMag PCR Beads). Purified DNA was sheared to 300-500 bp with Covaris, following manufacturer’s instructions. After AMPure XP size selection, appropriately-sized ligation fragments marked by biotin were immobilized using Dynabeads MyOne Streptavidin C1 (Invitrogen, cat. no. 65001) and ligated to indexed KAPA UDI Adapters (Roche). The non-amplified, immobilized and indexed Hi-C library was subsequently used as input for target-specific capture using RNA baits. Capture Hi-C of the targeted genomic sequences was carried out with KAPA HyperCap (Roche) with the bait library according to manufacturer’s instructions (Roche). The total output of post-capture was amplified with 12 cycles
We designed a custom biotinylated KAPA HyperCap Target Enrichment Probes (Roche) library. Biotinylated 120-mer RNA baits were designed to target MboI restriction fragments within the TPCN2-LTO1 region (hg38: chr11: 68,998,932-69,725,322) and a control region (chr18:21,427,907-22,925,680) For each MboI motif two probes were designed, each covering the MboI recognition motif and extending away from the motif in opposite directions. Probes were filtered using Roche Hyperdesign standard selection parameters (15 mer frequency of 1000, maximum allowed close matches to hg38 of 20).
Capture Hi-C


title: K562, CCND1-del


title: YF18, NS, CHL, EBV+/HIV-, Female

description:
Library name: YF18
YF18

value: EBV+/HIV-


title: K562, MYEOV-del

value: MYEOV-del


title: HEK293T NUP98a-KDM5A repeat 2, ChIP

value: transient transfection with NUP98a_KDM5A contruct


title: HEK293T dCas9-NUP98a repeat 1, ChIP


title: YF17, NA, CHL, EBV-/HIV-, Female

description:
Library name: YF17
YF17


title: WT BMDM vehicle treatment, rep 6

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

description: Library name: WT_Veh_06_19448X6

data_processing:
Raw reads were first quality and adapter-trimmed using trim galore then transcript counts were quantified using Salmon against the transcriptome from assembly GRCm38 (mm10)  70. Transcript level quantifications were read into R using the tximeta package and summarized to gene level counts before differential expression analysis with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-separated value file. DESeq2 counts summarized by gene with ENSEMBL identifiers

source_name: BMDM

growth_protocol: Leukocytes isolated from bone marrow isolation, suspended in complete DMEM and counted via trypan blue exclusion staining on a hemocytometer. Cells were plated on tissue culture treated 10cm dishes at a concentration of 5-8 x 106 cells/plate in 10mL of complete media + M-CSF (20ng/mL). Fresh media, including M-CSF was added to existing media on days 4 and days 7. Fully differentiated BMDMs were used for experimental use between days 7-9.

extract_protocol:
BMDMs were washed with cold, sterile PBS, 2x. Qiazol (Qiagen cat# 79306) RNA-stabilization reagent, was then added directly to each well. Wells were scraped with a cell scraper and collected into 1.5 Eppendorf tubes and frozen at -20°C until RNA extraction. RNA extraction was performed using, Direct-zol RNA miniprep kit (Zymo Research cat# R2070) according to manufacturer instructions.
Total RNA was first hybridized with the NEBNext rRNA Depletion kit v2 (NEB, cat# E7400) to diminish rRNA from the samples. Stranded RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat# E7760L). Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (Agilent, cat# 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (Roche, cat#07960140001).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis and sequenced on a NovaSeq 6000 with a paired-end 150 cycle sequencing run.

treatment_protocol: F. rodentium cultures were quantified by OD 600nm (using 1 OD 600nm = 1 x 10^8 cells/mL), washed 2x in sterile PBS and co-cultured with 1 x 106 cell/mL fully differentiated BMDMs at an MOI of 10 in 6-well tissue culture plates.

value: BMDM

value: WT


title: WT BMDM vehicle treatment, rep 5

description: Library name: WT_Veh_05_19448X5


title: WT BMDM vehicle treatment, rep 4

description: Library name: WT_Veh_04_19448X4


title: WT BMDM vehicle treatment, rep 3

description: Library name: WT_Veh_03_19448X3


title: K562, Enhancer-del

value: Enhancer-del


title: YF15, NS, CHL, EBV+/HIV+, Female

description:
Library name: YF15
YF15

value: EBV+/HIV+


title: K562, WT


title: HEK293T NUP98a-HOXA9 repeat 2, ChIP

value: transient transfection with NUP98a_HOXA9 contruct

value: alpha-FLAG antibody (Sigma-Aldrich, F1804)


title: YF14, NS, CHL, EBV+/HIV-, Female

description:
Library name: YF14
YF14

value: FFPE tumor

value: CHL


title: YF13, NS, CHL, EBV-/HIV-, Male

description:
Library name: YF13
YF13

value: NS

value: EBV-/HIV-

value: Male


title: AsiSI_U2OS_4OHT_BrdU_seq_Figure1c_EDF3d_replicate 1

value: Bone

value: Osteosarcoma

value: Wild-type AsiSI_U2OS


title: K562, RAD21-AID, clone2, IAA, VP:MYEOV

data_processing:
FastQ files were demultiplexed and processed using pipe4C (https://github.com/deLaatLab/pipe4C). Reads were mapped against hg38.  Blind fragments were omitted. Read counts were normalized to one-million mapped intra chromosomal reads (normalized reads) excluding the two highest covered fragments and 21 fragment end rolling mean scores were calculated for every fragment end.
Assembly: hg38
Supplementary files format and content: Wig files.
Library strategy: 4C-seq

extract_protocol:
4C template preparation was performed as previously described in PMID: 31351925. In brief, ten million cells per sample were cross-linked in 2% formaldehyde. Chromatin was digested in situ with DpnII (NEB, cat. no. R0543) followed by dilution and ligation. Subsequently, crosslinks were removed by Proteinase K treatment, followed by template trimming using Csp6I (CviQI, second cutter, Thermo Scientific, cat. no. ER0211) and re-ligation.
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using ELT PCR System (Roche, cat. no. 11681842001).

treatment_protocol: RAD21 depletion in K562 cells was induced by adding 1µM 5-Ph-IAA (MedChemExpress, cat. no. HY-134653) to cell cultures two-hour before crosslink.

tag: replicate

value: IAA

tag: vp

value: MYEOV


title: HEK293T NUP98a-HOXA9 repeat 1, ChIP


title: YF19, NS, CHL, EBV+/HIV-, Male

description:
Library name: YF19
YF19

value: EBV+/HIV-


title: YF12, NS, CHL, EBV+/HIV-, Male

description:
Library name: YF12
YF12


title: WT BMDM vehicle treatment, rep 2

description: Library name: WT_Veh_02_19448X2

value: BMDM


title: WT BMDM vehicle treatment, rep 1

description: Library name: WT_Veh_01_19448X1

value: WT


title: HEK293T NUP98a repeat 1, ChIP

value: transient transfection with NUP98a contruct


title: K562, RAD21-AID, clone2, DMSO, VP:MYEOV

value: DMSO


title: Clec12a-/- BMDM vehicle treatment, rep 5

description: Library name: KO_Veh_05_19448X20


title: Clec12a-/- BMDM vehicle treatment, rep 6

description: Library name: KO_Veh_06_19448X21


title: YF11, MC, CHL, EBV+/HIV-, Male

description:
Library name: YF11
YF11

value: MC


title: YF21, MC, CHL, EBV+/HIV-, Male

description:
Library name: YF21
YF21


title: K562, RAD21-AID, clone2, IAA, VP:Enhancer

value: Enhancer


title: HEK293T NUP98a-KDM5A repeat 1, ChIP

value: transient transfection with NUP98a_KDM5A contruct

value: alpha-FLAG antibody (Sigma-Aldrich, F1804)


title: HEK293T wt repeat 1, ChIP

value: wt

value: Mock transient transfection


title: K562, RAD21-AID, clone2, IAA, VP:CTCF_4


title: HEK293T wt repeat 2, ChIP


title: Clec12a-/- BMDM vehicle treatment, rep 3

description: Library name: KO_Veh_03_19448X18


title: RPMI8226, LFch-treated-3

city: Chuncheon

first: Young-Saeng

last: Jang

state: gangwondo

address: Biomedical science B-213

country: South Korea

institute: Kangwon National University

description:
RP-ch-3
GEO_processed_data_RP_normalized_readCount_data

data_processing:
After completing quality checks on raw sequence data using FastQC (ver. 0.11.9), adapter sequences were trimmed with Trimmomatic (ver. 0.39).
The cleaned read sequences were then aligned to the reference genome (GRCh38/hg38) using STAR (ver. 2.7.10a), and HTseq (ver. 0.11.2) was employed to count the aligned sequencing reads.
Assembly: hg38
Supplementary files format and content: Differentially expressed genes (DEGs) were identified using normalized read count data with the DESeq2 package in R (ver. 1.38.3), by comparing control and LFch groups for each of the three cell lines.

growth_protocol: MM cells were maintained in KCLB medium, which consisted of RPMI 1640 medium supplemented with fetal bovine serum (FBS 10%), 1% penicillin/streptomycin, HEPES 1 M, and sodium bicarbonate 7.5% at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted using the RNAeasy Kit (QIAGEN), according to the manufacturer’s instructions.
Sequencing libraries were generated using the Next® Ultra RNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s protocol.

treatment_protocol: MM cells were treated with LFch (3µM) for 24 hours

value: multiple myeloma

value: LFch


title: K562, RAD21-AID, clone2, DMSO, VP:Enhancer


title: Clec12a-/- BMDM vehicle treatment, rep 2

description: Library name: KO_Veh_02_19448X17


title: RPMI8226, LFch-treated-2

description:
RP-ch-2
GEO_processed_data_RP_normalized_readCount_data


title: HEK293T NUP98a repeat 2, ChIP


title: YF08, LD, CHL, EBV-/HIV-, Female

description:
Library name: YF08
YF08

value: FFPE tumor

value: CHL

value: LD

value: EBV-/HIV-

value: Female


title: K562, RAD21-AID, clone2, IAA, VP:CTCF_2


title: Clec12a-/- BMDM vehicle treatment, rep 1

description: Library name: KO_Veh_01_19448X16

value: BMDM


title: YF07, MC, CHL, EBV+/HIV-, Male

description:
Library name: YF07
YF07

value: EBV+/HIV-

value: Male


title: RPMI8226, LFch-treated-1

description:
RP-ch-1
GEO_processed_data_RP_normalized_readCount_data


title: Clec12a-/- BMDM with F. rodentium, rep 6

description: Library name: KO_Fr_12_19448X27


title: YF06, MC, CHL, EBV+/HIV+, Female

description:
Library name: YF06
YF06

value: EBV+/HIV+


title: K562, RAD21-AID, clone2, DMSO, VP:CTCF_2

value: DMSO


title: K562, RAD21-AID, clone2, IAA, VP:CTCF_1


title: YF10, NS, CHL, EBV+/HIV+, Male

description:
Library name: YF10
YF10

value: NS


title: YF05, NS, CHL, EBV+/HIV-, Male

description:
Library name: YF05
YF05


title: Clec12a-/- BMDM vehicle treatment, rep 4

description: Library name: KO_Veh_04_19448X19


title: Clec12a-/- BMDM with F. rodentium, rep 5

description: Library name: KO_Fr_11_19448X26


title: YF09, LR, CHL, EBV+/HIV-, Male

description:
Library name: YF09
YF09

value: LR


title: RPMI8226, untreated-3

description:
RP-m-3
GEO_processed_data_RP_normalized_readCount_data


title: RPMI8226, untreated-2

description:
RP-m-2
GEO_processed_data_RP_normalized_readCount_data


title: YF03, MC, CHL, EBV+/HIV-, Male

description:
Library name: YF03
YF03

value: MC


title: K562, RAD21-AID, clone2, DMSO, VP:CTCF_1


title: Clec12a-/- BMDM with F. rodentium, rep 3

description: Library name: KO_Fr_09_19448X24


title: YF02, NS, CHL, EBV+/HIV+, Female

description:
Library name: YF02
YF02


title: MM1R, LFch-treated-3

description:
MR-ch-3
GEO_processed_data_MR_normalized_readCount_data


title: K562, RAD21-AID, clone2, IAA, VP:CCND1


title: K562, RAD21-AID, clone2, DMSO, VP:CTCF_4


title: Clec12a-/- BMDM with F. rodentium, rep 2

description: Library name: KO_Fr_08_19448X23


title: K562, RAD21-AID, clone2, DMSO, VP:CCND1


title: MM1R, LFch-treated-2

description:
MR-ch-2
GEO_processed_data_MR_normalized_readCount_data


title: Clec12a-/- BMDM with F. rodentium, rep 1

description: Library name: KO_Fr_07_19448X22


title: MM1R, LFch-treated-1

description:
MR-ch-1
GEO_processed_data_MR_normalized_readCount_data


title: WT BMDM with F. rodentium, rep 6

description: Library name: WT_Fr_12_19448X12

value: WT


title: K562, RAD21-AID, clone1, DMSO, VP:MYEOV

value: MYEOV


title: STARR-seq output-complement, biological replicate 2

city: Beijing

first: Jiaying

last: Li

state: Beijing

address: Dongjiaomin Road

country: China

institute: Beijing Tongren Hospital

description:
Library name: Sample10
STARR-seq
output_complement_rpe2

data_processing:
Paired-end 150 bp reads were merged into single amplicons using Flash v1.2.11 [28]. Oligo sequences from the passing reads were then mapped back to the expected oligo sequences using BWA mem version 0.7.12 [29]. Multi-mapped reads were discarded. Reads were filtered if not met the following conditions: 1) adaptor sequences ‘GCTAGCCATTGCGTGTAGAG’ was perfectly matched. 2) Exact 10bp barcode sequences between adaptors. 3) Only primary alignment would be included (-F 256). Oligo with less than 5 unique barcodes in any replicate were discarded. The abundance of unique barcode counts for each oligo per replicate were provided as input to DESeq2 [30] for normalization as well as for enhancer activity calculation.
Assembly: hg38
Supplementary files format and content: Space-delimited text file includes counts the number of unique barcodes per oligo.

growth_protocol: DMEM + 10% FBS (Thermo Fisher Scientific) or plus 10% complement competent human serum (S1-LITER, EMD Millipore).

extract_protocol:
Total RNA was extracted from transfected ARPE-19 cells using M5 HiPer Universal RNA Mini Kit (Mei5bio), and followed by poly (A) tail mRNA isolation using Dynabeads® Oligo (dT) kit (ThermoFisher Scientific). mRNA was treated with TURBO™ DNase (ThermoFisher Scientific) and purified by Agencourt RNAClean XP beads (Beckman Coulter). Target-specific first strand complementary DNA (cDNA) synthesis was performed with SuperScript III (ThermoFisher Scientific; 1.5 μg mRNA/reaction) to specifically reverse transcribe plasmid transcribed mRNAs (RT primer: 5’- CAAACTCATCAATGTATCTTATCATG-3’). All mRNA from the 10 million transfected cells was used in reverse transcription. After reverse transcription, reactions were treated with RNase A + H and pooled.
Then the first round of amplification, every 5 μL cDNA reaction was used as a template in every 50 μL PCR reaction using KAPA HiFi HotStart ReadyMix (Roche). Target amplification primers were used (gia-starrseq-2-f: 5’- ACACTCTTTCCCTACACGACGCTCTTCCGATCTattagattgatctagagcatgcaccggt-3’; gia-starrseq-2-r: 5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCtcgaagcggccggccgaattcgtcga-3’). In the final round of amplification, the enzyme used is the same as that used in the first round, but 4 sets of primer combinations with different indexes are set to complete the final construction of the library. Illumina HiSeq platform compatible primers were used (forward: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse: 5’-CAAGCAGAAGACGGCATACGAGAT-index-GTGACTGGAGTTCAGACGTG-3’). A total of 4 duplicated PCR reactions were performed for each indexing PCR. PCR products were cleaned up by DNA pure beads (VDOBIOTECH) and submitted for Illumina sequencing. Input library for sequencing was generated using similar PCR setup. Products from 4 duplicated PCR reactions were pooled (10 ng plasmid/reaction, 16 cycles of PCR).

treatment_protocol: Input plasmid library was electroporated into ARPE-19 cells using the Nucleofector™ platform (Lonza) according to manufacturer’s protocol (1 μg DNA/1 million cells). A total of 10 million cells were electroporated in each replicate and two biological replicates were generated. After transfection, cells were further cultured for 29 h until harvest.

tag: condition

value: complement


title: STARR-seq output-complement, biological replicate 3

description:
Library name: Sample11
STARR-seq
output_complement_rpe3


title: Clec12a-/- BMDM with F. rodentium, rep 4

description: Library name: KO_Fr_10_19448X25


title: STARR-seq output-complement, biological replicate 1

description:
Library name: Sample9
STARR-seq
output_complement_rpe1


title: WT BMDM with F. rodentium, rep 5

description: Library name: WT_Fr_11_19448X11


title: MM1R, untreated-2

description:
MR-m-2
GEO_processed_data_MR_normalized_readCount_data

value: multiple myeloma


title: RPMI8226, untreated-1

description:
RP-m-1
GEO_processed_data_RP_normalized_readCount_data


title: WT BMDM with F. rodentium, rep 4

description: Library name: WT_Fr_10_19448X10


title: STARR-seq output-naive, biological replicate 4

description:
Library name: Sample8
STARR-seq
output_naive_rpe4

value: naive


title: K562, RAD21-AID, clone1, DMSO, VP:Enhancer

value: Enhancer


title: WT BMDM with F. rodentium, rep 3

description: Library name: WT_Fr_09_19448X9


title: STARR-seq output-naive, biological replicate 3

description:
Library name: Sample7
STARR-seq
output_naive_rpe3


title: STARR-seq output-complement, biological replicate 4

description:
Library name: Sample12
STARR-seq
output_complement_rpe4


title: K562, RAD21-AID, clone1, IAA, VP:CTCF_4


title: WT BMDM with F. rodentium, rep 2

description: Library name: WT_Fr_08_19448X8


title: MM1S, LFch-treated-3

description:
MS-CH-3
GEO_processed_data_MS_normalized_readCount_data

value: LFch


title: MM1S, LFch-treated-2

description:
MS-CH-2
GEO_processed_data_MS_normalized_readCount_data


title: WT BMDM with F. rodentium, rep 1

description: Library name: WT_Fr_07_19448X7


title: K562, RAD21-AID, clone1, DMSO, VP:CTCF_4


title: K562, RAD21-AID, clone1, IAA, VP:CTCF_2


title: STARR-seq output-naive, biological replicate 2

description:
Library name: Sample6
STARR-seq
output_naive_rpe2


title: K562, RAD21-AID, clone1, IAA, VP:MYEOV


title: STARR-seq output-naive, biological replicate 1

description:
Library name: Sample5
STARR-seq
output_naive_rpe1


title: MM1S, LFch-treated-1

description:
MS-CH-1
GEO_processed_data_MS_normalized_readCount_data


title: MM1R, untreated-3

description:
MR-m-3
GEO_processed_data_MR_normalized_readCount_data


title: STARR-seq input, biological replicate 4

description:
Library name: Sample4
STARR-seq
input_rpe22

value: input


title: K562, RAD21-AID, clone1, DMSO, VP:CTCF_2


title: K562, RAD21-AID, clone1, IAA, VP:Enhancer


title: MM1S, untreated-3

description:
MS-M-3
GEO_processed_data_MS_normalized_readCount_data


title: K562, RAD21-AID, clone1, IAA, VP:CTCF_1


title: ko2

city: Jinan

first: Weijie

last: Wu

address: Wenhuaxilu No.107

institute: Qilu Hospital of Shandong University

description:
Library name: Sample5
10X Genomics

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger (v6.1.2) Pipeline coupled with mouse reference version GRCh38. The output filtered gene expression matrices were analyzed by R software (version 4.3.1) with the Seurat package (version 4.4.0)1. A custom R script was used to combine the expression data and metadata from all libraries corresponding to a single batch. The expression data matrix was loaded into a Seurat object along with the library metadata for downstream processing. The percentage of mitochondrial transcripts for each cell (percent.mt) was calculated and added as metadata to the Seurat object. Cells were further filtered before dimensionality reduction (nFeature_RNA-min. 200; nFeature_RNA-max. 3000; percent.mt-max. 10%).
Assembly: mm10-2020-A
Supplementary files format and content: Tap-separated values files and matrix files

source_name: blood

extract_protocol:
Blood samples from anesthetized mice were collected into anticoagulant tubes and peripheral blood mononuclear cells (PBMCs) were prepared by a centrifugation method using HISTOPAQUE (Cat. 10771, Sigma-Aldrich, USA). After centrifugation, the PBMC layers were carefully harvested by a Pasteur pipette. Collected cells were further purified using a PBS solution, followed by centrifugation (250 x g, 4°C, 10 min).  Contaminant red blood cells (RBCs) were lysed using an RBC lysis buffer (Cat. 130-094-183, Miltenyi, Germany). After termination of RBC lysis with 2% FBS, purified PBMCs were collected by centrifugation
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics)

value: blood

value: PBMC


title: STARR-seq input, biological replicate 3

description:
Library name: Sample3
STARR-seq
input_rpe21


title: MM1S, untreated-2

description:
MS-M-2
GEO_processed_data_MS_normalized_readCount_data


title: STARR-seq input, biological replicate 2

description:
Library name: Sample2
STARR-seq
input_rpe18


title: MM1S, untreated-1

description:
MS-M-1
GEO_processed_data_MS_normalized_readCount_data


title: MM1R, untreated-1

description:
MR-m-1
GEO_processed_data_MR_normalized_readCount_data


title: K562, RAD21-AID, clone1, DMSO, VP:CTCF_1


title: STARR-seq input, biological replicate 1

description:
Library name: Sample1
STARR-seq
input_rpe17


title: con3

description:
Library name: Sample3
10X Genomics


title: K562, RAD21-AID, clone1, DMSO, VP:CCND1


title: K562, RAD21-AID, clone1, IAA, VP:CCND1


title: K562, MYEOV-del, clone2, VP:CCND1

value: MYEOV-del


title: con1

description:
Library name: Sample1
10X Genomics


title: con2

description:
Library name: Sample2
10X Genomics


title: C28/I2 cells, DPP4OE2

city: Chengdu

first: zhang

last: zhao

address: Guoxue Lane, Wuhou District

institute: Sichuan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: chondrocytes

value: DPP4 overexpression


title: siHOIP rep2

city: Shinagawa-ku

first: Fumiaki

last: Ohtake

state: Tokyo

country: Japan

institute: Hoshi University

description: Library name: Sample 11

data_processing:
Trimmed reads are mapped to reference genome with HISAT2.
After the read mapping, Stringtie was used for transcript assembly.
Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
Assembly: GRCh38, NCBI_109.20200522
Supplementary files format and content: Excel file containing FPKM and TPM for each sample

growth_protocol: Human HT1080 cells were obtained from the American Type Culture Collection (ATCC) and maintained at 37 °C with 5% CO2 in DMEM high-glucose medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich), penicillin–streptomycin (100 U/mL, Gibco, 15140148), sodium pyruvate (1 mM, Gibco, 11360070), and MEM nonessential amino acids (1×, Gibco, 11140050).

extract_protocol:
Total RNA was isolated using RNeasy kit (QIAGEN)
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA LT Sample Prep Kit following manufacturer's protocol.

treatment_protocol: Transfection was performed using Lipofectamine RNAiMax (Thermo Fisher Scientific) for siRNAs. Transfected cells were used for experiments 72h after transfection.

value: human sarcoma cell line


title: C28/I2 cells, DPP4OE3


title: C28/I2 cells, DPP4OE1


title: ko3

description:
Library name: Sample6
10X Genomics


title: K562, MYEOV-del, clone1, VP:CCND1


title: siHOIP rep1

description: Library name: Sample 10


title: C28/I2 cells, OENC3


title: K562, CTCF2-del, clone2, VP:MYEOV


title: siUBR5 rep3

description: Library name: Sample 9


title: C28/I2 cells, OENC2


title: siUBR5 rep2

description: Library name: Sample 8


title: K562, CTCF2-del, clone2, VP:Enhancer


title: ko1

description:
Library name: Sample4
10X Genomics


title: C28/I2 cells, OENC1


title: siUBR5 rep1

description: Library name: Sample 7


title: K562 cells, water 31d, biol rep3, sRNA-seq

city: Xiamen

first: Fan

last: Gao

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

data_processing:
Raw reads in which >10% of bases were N or > 50% of bases had low (<= 5) quality scores, as well as reads containing sequence adapters or long homopolymeric tracks, were removed. After removing low quality reads, the reads were then aligned to the GRCh37/hg19 version of the human genome using Bowtie2 (v2.2.9) with default settings.
The  sRNA-seq data from the three K562 bio-replicates were combined and used to generate RPKM for each sRNA.
The expression fold change (FC) of each unique sRNA alignment in each sample (each biological replicate for each time point of 13 or 31 days) was calculated.
Assembly: GRCh37/hg19
Supplementary files format and content: The processed files contain read counts (columns 5) and RPKM values (columns 6)  of dox-control sample, read counts (columns 7) and RPKM values (columns 8)  of dox-treated sample and fold-change (columns 9) for each unique small RNA with unique 5’ and 3’ coordinates.

source_name: cell line

growth_protocol: K562 cells were maintained in respectively RPMI 1640 (ThermoFisher Scientific, US) and DMEM (Sigma) supplemented with 10% fetal bovine serum (ThermoFisher Scientific, US) and 1% pen/strep (ThermoFisher Scientific, US) at 37 °C in 5% CO2.

extract_protocol:
Total RNA was isolated from two million cells of each biological replicate with TRNzol Universal reagent (TIANGEN, Beijing, China) following the manufacturer’s protocol.
Small RNA-seq libraries for small RNA-seq were constructed using NEB Next Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer's protocols. After library construction, PCR products corresponding to small RNAs in the range of 20-40 nt were purified by PAGE and used for small RNA-seq.

treatment_protocol: The K562 cells harboring the Drosha shRNA were plated into 3 mL culture medium supplemented with 1 μg/mL Dox (Macklin Inc, 24390-14-5) at 5´ 105 cells/mL in 6-well plates and incubated for 3, 13 and 31 days with Dox always present in the medium. The cells were also grown in parallel without Dox as control. For each well, the medium with or without Dox was changed every 2 days. Two independent biological replicates were performed for the 3-day treatment, and three for the 13- and 31-day treatments.

value: cell line

value: human erythroleukemic cell line

value: Induced with water for 31d


title: K562, CTCF2-del, clone2, VP:CCND1


title: K562, CCND1-del, clone2, VP:MYEOV


title: siTRIP12 rep3

description: Library name: Sample 6

value: WT


title: siHOIP rep3

description: Library name: Sample 12


title: K562 cells, water 31d, biol rep2, sRNA-seq


title: K562, CCND1-del, clone2, VP:Enhancer


title: siTRIP12 rep1

description: Library name: Sample 4


title: siTRIP12 rep2

description: Library name: Sample 5


title: K562 cells, water 13d, biol rep2, sRNA-seq

value: Induced with water for 13d


title: Scrambled siRNA rep3

description: Library name: Sample 3


title: Scrambled siRNA rep2

description: Library name: Sample 2


title: K562, CCND1-del, clone1, VP:CTCF_2


title: K562 cells, water 13d, biol rep3, sRNA-seq


title: Scrambled siRNA rep1

description: Library name: Sample 1


title: K562, 3xhCTCF-U, clone2, VP:MYEOV

value: MYEOV


title: K562 cells, water 13d, biol rep1, sRNA-seq


title: K562, CCND1-del, clone1, VP:Enhancer


title: K562, 3xhCTCF-U_CRE_deleted, clone2, VP:MYEOV


title: K562, 3xhCTCF-U, clone2, VP:Enhancer


title: ZNF217_rep2

city: Boston

first: Yifei

last: Liao

state: Massachusetts

address: 181 Longwood Ave, 8th Floor

institute: Brigham and Women's hospital

description:
Library name: ZNF217_rep2
ChIP with ZNF217 antibody_rep2

data_processing:
ChIP-seq reads were first aligned to the Akata EBV genome using Bowtie2 v2.5.1 with the parameters -k 1". PCR duplicated reads were marked and removed using Picard (http://broadinstitute.github.io/picard/) and Samtools. The EBV tracks were normalized to total mapping reads and generated using bedtools (https://github.com/arq5x/bedtools2) v2.30.0 with the parameters “genomecov -bga -split -scale” together with bedGraghToBigWig (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig). The tracks were visualized using Integrative Genomics Viewer (IGV).
Assembly: Akata EBV genome
Supplementary files format and content: bw files

source_name: EBV+ Akata cell line

growth_protocol: EBV+ Akata cells were cultured in RPMI1640 with 10% FBS at 37 degrees C and 5% CO2.

extract_protocol:
Akata cells were crosslinked with a 1% formaldehyde solution in growth medium and then quenched with 2.5M glycine in distilled water. The cells were washed with ice-cold PBS and lysed in 1% SDS lysis buffer (50 mM Tris, 10 mM EDTA, and 1% SDS) supplemented with 1X cOmplete EDTA-free protease inhibitor. Chromatin was sheared to 100-300 bp with Bioruptor Pico sonication, followed by centrifugation at 15,000 x g for 10 minutes at 4 °C. The resulting supernatant was diluted at a 1:10 ratio in ChIP dilution buffer (1.2 mM EDTA, 16.7 mM Tris, 167 mM NaCl, 0.01% SDS, and 1.1% Triton X-100) supplemented with 1X cOmplete EDTA-free protease inhibitor. 1% of the sheared chromatin was saved as Input and stored at -80 °C until use. The diluted chromatin was rotated overnight at 4 °C with antibody and 20 μl protein A/G magnetic beads. Next day, the immunocomplexes were subsequently washed twice with low-salt buffer (150 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl, 0.1% SDS, 1% Triton X-100) and high-salt buffer (500 mM NaCl, 2 mM EDTA, 20 mM Tris-HCl, 0.1% SDS, 1% Triton X-100), and once with LiCl buffer (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris) and TE buffer (1 mM EDTA, 10 mM Tris). After eluting in Elution buffer (100 mM NaHCO3, 1% SDS), DNA was reverse cross-linked for 2 hours at 65 °C. Immunoprecipitated DNA was purified with QIAquick PCR purification kit.
Immunoprecipitated DNA were subjected to library preparation using NEBNext Ultra DNA Library Prep Kit

value: EBV+ Akata cell line

value: B cells


title: K562 cells, dox 31d, biol rep3, sRNA-seq

value: Induced with Dox for 31d


title: ZNF217_rep1

description:
Library name: ZNF217_rep1
ChIP with ZNF217 antibody_rep1


title: K562, 3xhCTCF-U_CRE_deleted, clone2, VP:Enhancer

value: Enhancer


title: KDM1A_rep2

description:
Library name: KDM1A_rep2
ChIP with KDM1A antibody_rep2


title: KDM1A_rep1

description:
Library name: KDM1A_rep1
ChIP with KDM1A antibody_rep1


title: K562, 3xhCTCF-U, clone2, VP:CCND1


title: K562 cells, dox 31d, biol rep2, sRNA-seq


title: K562, 3xhCTCF-U_CRE_deleted, clone2, VP:CCND1


title: K562, CCND1-del, clone2, VP:CTCF_2


title: K562 cells, dox 31d, biol rep1, sRNA-seq


title: INPUT_rep2

description:
Library name: INPUT_rep2
Input_rep2


title: K562 cells, water 31d, biol rep1, sRNA-seq


title: K562, 3xhCTCF-U, clone1, VP:MYEOV


title: K562 cells, dox 13d, biol rep3, sRNA-seq

value: Induced with Dox for 13d


title: K562 cells, water 3d, biol rep3, sRNA-seq

value: Induced with water for 3d


title: K562 cells, dox 13d, biol rep2, sRNA-seq


title: K562 cells, dox 13d, biol rep1, sRNA-seq


title: INPUT_rep1

description:
Library name: INPUT_rep1
Input_rep1


title: K562, 3xhCTCF-U, clone1, VP:Enhancer


title: K562, 3xhCTCF-U_CRE_deleted, clone1, VP:MYEOV


title: hPSC, PDX and NKX6.1, DOX + TMP, 2ug/mL - 10uM, 7-8 days, rep3

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description:
Library name: EB_diff_DT_3
EB_diff_DT_3

data_processing:
Paired-end FASTQ files were processed using the nf-core-rnaseq pipeline (v3.12.0) (auto strandedness).
Adapter sequences were removed with Trim Galore.
Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.
Downstream analysis was performed using Pluto (https://pluto.bio).
Assembly: GRCh38 (NCBI, p.14, release 110)
Supplementary files format and content: comma-delimited text file includes raw counts for each Sample

source_name: hPSC

growth_protocol: Undifferentiated human pluripotent stem cells (hPSC) were maintained on hPSC qualified Matrigel (Corning #354277) in mTeSR+ media (STEMCELL Technologies #05826). hPSCs were dissociated into single cells and counted using the Countess cell counter. Homogeneous hPSC clusters with 1000 cells/cluster were generated by plating ~5.9 x10^6 cells into a 6-well 400 Agrewell plate (STEMCELL) and spun down. Clusters culture in this plate with mTeSR plus media supplemented with 10uM ROCKi. After 24 hours, media was changed and supplemented with the different treatments; DOX, DOX + TMP + dTAG (DTG), and DOX + TMP (DT) for 48 hours. After this incubations, hPSC clusters were then transferred into a suspension 6-well plate with EB differentiation media (DMEM F12 supplemented with 10% FBS) and culture for 7-8 days in a shaker plate (100rpms) at 37C, 5% CO2 and 95% humidity.

extract_protocol:
Clusters of cells were pelleted and washed twice with PBS. Pellet clusters were then frozen at -80 C for shipping to Novogene for RNA purification, library construction and sequencing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: hPSC

value: PDX1 and NKX6.1

tag: drug

value: DOX + TMP

tag: dose

value: 2ug/mL - 10uM

tag: timepoint

value: 7-8 days


title: K562 cells, dox 3d, biol rep3, sRNA-seq

value: cell line

value: Induced with Dox for 3d


title: K562 cells, water 3d, biol rep1, sRNA-seq

value: human erythroleukemic cell line


title: hPSC, PDX and NKX6.1, DOX + TMP, 2ug/mL - 10uM, 7-8 days, rep1

description:
Library name: EB_diff_DT_1
EB_diff_DT_1


title: K562, 3xhCTCF-U_CRE_deleted, clone1, VP:Enhancer


title: K562, 3xhCTCF-U, clone1, VP:CCND1


title: K562 cells, untreated, sRNA-seq

value: Untreated


title: hPSC, NKX6.1, DOX + TMP + dTAG, 2ug/mL - 10uM - 250nM, 7-8 days, rep3

description:
Library name: EB_diff_DTd_3
EB_diff_DTd_3

value: DOX + TMP + dTAG


title: K562, 3xhCTCF-U_CRE_deleted, clone1, VP:CCND1


title: hPSC, NKX6.1, DOX + TMP + dTAG, 2ug/mL - 10uM - 250nM, 7-8 days, rep2

description:
Library name: EB_diff_DTd_2
EB_diff_DTd_2


title: K562, 3xhCTCF-D, clone2, VP:MYEOV

value: MYEOV


title: hPSC, NKX6.1, DOX + TMP + dTAG, 2ug/mL - 10uM - 250nM, 7-8 days, rep1

description:
Library name: EB_diff_DTd_1
EB_diff_DTd_1


title: hPSC, PDX1, DOX, 2ug/mL, 7-8 days, rep3

description:
Library name: EB_diff_DOX_3
EB_diff_DOX_3

value: DOX


title: K562, 3xhCTCF-D_CRE_deleted, clone2, VP:MYEOV


title: totalRNASeq_WT_ID_NoLIF_rep2

city: new york

first: Jane

middle: A

last: Skok

state: NEW YORK

address: Smilow Research Center, Third floor, Room 307, 522 First Avenue

institute: NYU

data_processing:
Data were processed using Seq-N-Slide pipeline.
The Illumina adaptor and the T overhang were trimmed as per Illumina recommendation using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the STAR aligner.
Read count extraction and normalization were performed using the Seq-N-Slide pipeline.
Differentially expressed genes were called using DESeq2 with an adjusted p-value of 0.05 and a fold change cutoff of 1.5
Assembly: mm10
Supplementary files format and content: counts.tpm.LIFvsNoLIF.csv, comma-separated TPM matrix
Supplementary files format and content: counts.normalized.LIFvsNoLIF.csv, comma-separated normalized count matrix

source_name: mESC

growth_protocol: Mouse embryonic stem cells E14Tg2a and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin coated dishes at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM supplemented with 15% fetal bovine serum , 100 U/ml penicillin - 100 μg/ml streptomycin, 1 X GlutaMax supplement, 1 mM sodium pyruvate, 1 X MEM non-essential amino-acids, 50 μM b-mercaptoethanol, 104 U/ml leukemia inhibitory factor, 3 μM CHIR99021 and 1 μM MEK inhibitor PD0325901. The cells were passaged every alternate day by dissociation with TrypLE.For the exit from pluripotency, mESCs were cultured for 3 days in the same medium but without the addition of LIF (leukemia inhibitory factor, CHIR99021 (Sigma, SML1046)) and MEK inhibitor (PD0325901).

extract_protocol:
mESCs were dissociated using TrypLE, washed in 1X PBS, pelletted and 2.5 million cells were used for extracting RNA with RNeasy plus kit (Qiagen #74134) in each case.
RNA quality was checked in Tapestation (Agilent High Sensitivity RNA ScreenTape) and quantified by Nanodrop. 500ng were used for Total RNA libraries preparation using Illumina kit (Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus #20040529). Libraries were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 100 million 150bp paired-end total per sample.

treatment_protocol: For degradation of endogenous CTCF, the auxin-inducible degron was induced by adding 500 μM indole-3-acetic acid (IAA, chemical analog of auxin) to the media. Expression of transgenes was achieved by the addition of doxycycline (Dox, 1 μg/ml) to the media. The cells were treated with IAA and/or Dox for 2 days.

value: mESC

tag: strain

value: WT

value: IAA+Doxyxycline

tag: media

value: No LIF

value: replicate 2


title: hPSC, PDX1, DOX, 2ug/mL, 7-8 days, rep2

description:
Library name: EB_diff_DOX_2
EB_diff_DOX_2

value: hPSC


title: K562, 3xhCTCF-D, clone2, VP:Enhancer

tag: cell line

value: Enhancer


title: totalRNASeq_WT_ID_NoLIF_rep1

value: replicate 1


title: K562, 3xhCTCF-D_CRE_deleted, clone2, VP:Enhancer


title: hPSC, PDX1, DOX, 2ug/mL, 7-8 days, rep1

description:
Library name: EB_diff_DOX_1
EB_diff_DOX_1

tag: cell type


title: hPSC, PDX and NKX6.1, DOX + TMP, 2ug/mL - 10uM, 7-8 days, rep2

description:
Library name: EB_diff_DT_2
EB_diff_DT_2

value: PDX1 and NKX6.1

value: DOX + TMP

value: 2ug/mL - 10uM


title: totalRNASeq_WT_ID_LIF_rep2

tag: genotype

value: LIF


title: K562, 3xhCTCF-D, clone2, VP:CCND1

tag: treatment


title: hPSC, Control, None, NA, 7-8 days, rep3

description:
Library name: EB_diff_Control_3
EB_diff_Control_3

value: Control

value: 7-8 days


title: totalRNASeq_WT_ID_LIF_rep1


title: K562, 3xhCTCF-D_CRE_deleted, clone2, VP:CCND1


title: hPSC, Control, None, NA, 7-8 days, rep2

description:
Library name: EB_diff_Control_2
EB_diff_Control_2


title: totalRNASeq_R342C_ID_NoLIF_rep2


title: K562 cells, dox 3d, biol rep1, sRNA-seq

tag: tissue

value: cell line

value: human erythroleukemic cell line

value: Induced with Dox for 3d


title: hPSC, Control, None, NA, 7-8 days, rep1

description:
Library name: EB_diff_Control_1
EB_diff_Control_1


title: K562, 3xhCTCF-D, clone1, VP:MYEOV

value: MYEOV


title: totalRNASeq_R342C_ID_NoLIF_rep1

value: mESC


title: K562, 3xhCTCF-D_CRE_deleted, clone1, VP:MYEOV


title: totalRNASeq_R342C_ID_LIF_rep2

value: IAA+Doxyxycline


title: K562, 3xhCTCF-D, clone1, VP:Enhancer


title: K562,E50; dCas9-KRAB,3

data_processing:
Raw reads were used as input for STARsolo 2.7.11a with parameters --soloType CB_UMI_Simple, --soloCBstart 7, --soloCBlen 8, --soloUMIstart 1, --soloUMIlen 6, --soloBarcodeReadLength 0, --soloStrand Forward, --soloCBmatchWLtype 1MM_multi, --soloUMIdedup NoDedup, --soloMultiMappers Unique EM, --soloUMIfiltering -. As reference GENCODE hg38 (release V44) was used.
Raw counts of the two replicates with the lowest counts were collapsed, resulting in 2 replicates per factor. Next counts were normalized using DeSeq2 1.38.3 with gRNA Control_T as reference.
Assembly: hg38
Supplementary files format and content: raw counts (tsv), DESeq2 normalized counts (tsv) and CEL-seq2 barcodes per sample (tsv)

growth_protocol: K562 cells were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS (Sigma) and 1% pen–strep (Gibco) and refreshed every 2-3 days. Cells were grown at a maximal density of 5x10^5 cells/ml.

extract_protocol: High-throughput bulk RNA-seq plates were prepared by adding 1 μl of 7.5 ng/μl CEL-seq2 primers(Hashimshony, Senderovich et al. 2016) to 96-well plates. These primers contain sample-specific barcodes that were used to barcode and amplify the mRNA from each sample. After combination of cell suspension with the sample barcode, a mixture of dNTP’s and synthetic ERCC spike in molecules were added to the plates using a liquid handling platform and cells were lysed at 65 degrees Celsius. Then, a Reverse Transcription mix with Superscript II enzyme was added to barcode and reverse transcribe the mRNA from all samples to cDNA. After incubation at 42 degrees Celsius, second strand synthesis was done by adding a mixture of DNA polymerase, ligase and RNAseH enzyme, after which material from all samples was pooled and purified. Next, material from all samples was frozen and stored, and part of it was amplified using In Vitro Transcription. The resulting amplified RNA was prepared into sequencing ready libraries following the SORT-seq library preparation protocol(Muraro, Dharmadhikari et al. 2016). Sequencing libraries were indexed with Illumina Truseq small RNA primers.

treatment_protocol: K562 cells expressing dCas9-KRAB were transduced with lentivirus containing an sgRNA-BFP against a target factor or control. Transductions were performed by incubating cells overnight with 50% medium and 50% lentivirus-containing supernatant. The next day, cells were refreshed. From day 2 to 6, cells were selected using  1 ug/ml Puromycin (Sigma, Cat#P9620) and refreshed daily. At sample harvest, cells were sorted BFP-high to contain an sgRNA.

value: E50; dCas9-KRAB

tag: plate


title: K562,E50; dCas9-KRAB,4


title: totalRNASeq_R342C_ID_LIF_rep1


title: K562, 3xhCTCF-D_CRE_deleted, clone1, VP:Enhancer


title: K562, 3xhCTCF-D, clone1, VP:CCND1


title: K562,E50; dCas9-KRAB,2


title: totalRNASeq_Q418R_ID_NoLIF_rep1

value: No LIF


title: K562, 3xhCTCF-D_CRE_deleted, clone1, VP:CCND1


title: ANGPTL3_KO_5

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: ANG3 KO 12

data_processing:
Base calling:  RTA-1.18.64.0
FASTQ generation:  bcl2fastq-1.8.4
Read trimming:  trimmomatic-0.35
Read QC:  fastQC-0.10.1
Alignment:  STAR-2.4.2
Mapping statistics:  bamtools-2.3.0
Differential expression:  cufflinks-2.2.1
Assembly: hg19
Supplementary files format and content: tab-delimited gene-level differential expression output from Cuffdiff

source_name: ANGPTL3 KO HepG2 cell clone transfected with lentivirus containing CRISPR/cas9 and EDEM3 sgRNA

growth_protocol: Standard culture with DMEM medium suppplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s procedures
Ilumina TruSeq Stranded Total RNA with Ribo-Zero Globin

treatment_protocol: The cells were infected with lentiviruses containing CRISPR/cas9 with control and ANGPTL3 sgRNAs

value: Huh7 hepatoma cells

value: ANGPTL3 KO


title: K562,E50; dCas9-KRAB,1


title: totalRNASeq_Q418R_ID_LIF_rep2

value: replicate 2


title: D19 PPs, LatB, 24hr, rep3

city: København N

first: Adam Kappel

last: Rump

address: Blegdamsvej 3

department: DanStem

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were mapped using Salmon 1.3.0 with  --gcBias --seqBias tags
Transcript counts were mapped to genes and analyzed for differential expression using DESeq2
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing results of the pseudoalignment
Supplementary files format and content: comma-delimited file containing differential expression analysis of each time point, as well as normalized gene counts for each gene in each sample

growth_protocol: SA121-derived NGN3-GFP cells were differentiated into pancreatic progenitor cells (Day 19) following a previously established protocol (Ameri et al., Cell Reports, 2017)

extract_protocol:
RNA was harvested using the RNeasy mini kit (Qiagen) with on-column DNAse digestion.
Library was constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Bionordika) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Bionordika)

treatment_protocol: LatB samples were treated with 0.5micromolar latrunculin B and harvested at indicated time points. Control samples 24hr were treated with DMSO.

value: ESC-derived pancreatic progenitor cells

value: LatB

tag: time


title: resistant,3

city: Shanghai

first: Shuwen

last: Dong

address: Huangpu District

institute: Shanghai Jiao Tong University

data_processing:
CLC Genomics Workbench 12.0.3
Assembly: hg38
Supplementary files format and content: text file includes raw counts for each sample

extract_protocol:
Total mRNA was extracted via TRIzol (Invitrogen, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA via poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized via random hexamer primers and M-MuLV reverse transcriptase (RNase H-). Second-strand cDNA synthesis was subsequently performed via DNA polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of the DNA fragments, adaptors with hairpin loop structures were ligated to prepare for hybridization. To preferentially select cDNA fragments 370~420 bp in length, the library fragments were purified with the AMPure XP system. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primers. Finally, the PCR products were purified (AMPure XP system), and library quality was assessed on an Agilent Bioanalyzer 2100 system.

value: carboplatin


title: ANGPTL3_KO_4

description: ANG3 KO G2


title: ANGPTL3_KO_3

description: ANG3 KO G1


title: resistant,2


title: totalRNASeq_K365T_ID_NoLIF_rep2


title: ANGPTL3_KO_2

description: ANG3 KO 12


title: D19 PPs, LatB, 24hr, rep1


title: K562,E50; dCas9-KRAB,5


title: D19 PPs, LatB, 12hr, rep2


title: sensitive,3

value: no treatment


title: totalRNASeq_K365T_ID_LIF_rep2

value: LIF


title: totalRNASeq_Q418R_ID_NoLIF_rep2


title: totalRNASeq_Q418R_ID_LIF_rep1

value: replicate 1


title: ANGPTL3_KO_1

description: ANG3 KO G2


title: D19 PPs, LatB, 12hr, rep1


title: D19 PPs, LatB, 24hr, rep2


title: sensitive,2


title: totalRNASeq_K365T_ID_LIF_rep1


title: ANGPTL3_KO_0

description: ANG3 KO G1


title: D19 PPs, LatB, 6hr, rep3


title: resistant,1


title: sensitive,1


title: Control_5

description: ANG3 WT3

source_name: ANGPTL3 WT Huh7 cell clone transfected with lentivirus containing CRISPR/cas9 and control sgRNA

value: WT ANGPTL3


title: D19 PPs, LatB, 6hr, rep2


title: Control_4

description: ANG3 WT2


title: THP-1, 48hr LPS, heavy digest

city: Tallahassee

first: Jonathan

middle: H

last: Dennis

state: FL

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

description: 48hr post LPS

data_processing:
adapter sequences and poor quality reads were removed with Trimmomatic (version 0.39)
Bowtie2 was used to align the sequences to the T2T reference human genome with the --end-to-end --no-mixed --no-discordant flags
Mitochondrial and duplicate reads were filtered with samtools (version  1.10) and picardtools (version 2.27.3)
Nucleosome footprints  (>120bp) for light and heavy digests were calculated with DANPOS3 and the log2 ratio of light to heavy digests was calculated for each time point to determine nucleosome sensitivity to MNase digest with deeptools (version 3.5.1) .
Small fragments (<110bp) from light digests were used for regulatory factor footprinting. Peaks were called with MACS3. Xstreme was used to identify enriched motifs under small fragment footprint peaks and FIMO was used to identify the locations of specific motifs. Coverage files for small fragments over promoter regions were generated with bedtools gencov
Assembly: T2T
Supplementary files format and content: bigwig files of light and heavy digests
Supplementary files format and content: bigwig files of nucelosome occupancy and sensitivity to MNase digestion
Supplementary files format and content: The *sensitivity*bw files are generated from a log2 ratio of light/heavy digests. These files are linked on the GSE record since they were derived from multiple samples.

growth_protocol: Cells were grown in RPMI-1640 media (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO2

extract_protocol:
Cells were crosslinked in 1% v/v formaldehyde (Sigma-Aldrich) and incubated for 10 minutes at room temperature while rocking. Excess formaldehyde was quenched with 125mM glycine and cells were washed twice in PBS. Cells were resuspended in nuclei isolation buffer (10mM HEPES at pH 7.8, 2mM MgOAc2, 0.3M sucrose, 1mM CaCl2 and 1% Triton-X) and pelleted by centrifugation at 1000×g for 10 min at 4°C. Nuclei were washed twice in nuclei isolation buffer and chromatin was digested with either 5U or 200U MNase for 10 minutes at 37°C. MNase reactions were halted with 50mM EDTA. Protein-DNA crosslinks were reversed by treating the MNase-digested nuclei with 0.2 mg/mL proteinase K and 1% sodium dodecyl sulfate, and incubating overnight at 65°C. DNA was isolated using guanidinium-isopropanol and washed with ethanol on a silica column. Mononucleosomal and sub-mononucleosomal DNA was isolated from a 2% agarose gel slice and purified by glycogen precipitation.
MNase sequencing libraries were prepared for each replicate using the Accel-NGS®2S Plus DNA Library Kit (Swift) for Illumina® using 10ng of input DNA from each digestion. Libraries were indexed with the Accel-NGS 2S Unique Dual Indexing Kit and normalized with Normalase. We used a previously validated custom designed Roche Nimblegen SeqCap EZ Library SR to capture 2000 bp regions flanking the Transcription Start Site (TSS) for every pol II gene in the human genome(Druliner et al. 2016; Sexton et al. 2016). The TSS sequences were repeat masked using human COT DNA and library adapters were masked with universal blocking oligos. Biotinylated sequence capture oligos were hybridized to input libraries for 48 hours and purified with streptavidin beads. Enriched sequences were amplified in a 15 cycle PCR amplification using TruSeq primers.

treatment_protocol: Cells were exposed to 25nM phorbol 12-myristate 13-acetate (Sigma-Aldrich) for 48 hours and recovered in complete medium for 24 hours following differentiation. Cells were then treated with 10ng/ml LPS for 0hr, 5min, 30min, 1hr, 4hr, 12hr, 24hr, and 48hr prior to harvest

value: LPS treated macrophage

tag: digest condition

value: 200U MNase

value: LPS


title: KO, Replicate2, scRNA-seq

city: wuhan

first: wei

last: jiang

address: No.1, Shizishan Street, Hongshan District, Wuhan, China

institute: Huazhong Agricultural University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 7.2.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: leg muscles

extract_protocol:
Muscle tissues were transported in 10 ml of 1x DPBS on ice, minced, and digested with 0.25% trypsin and 10 ug/mL DNase I in PBS with 5% FBS. The digestion occurred at 37°C with shaking at 50 rpm for 40 minutes. Cells were collected every 20 minutes to enhance yield and viability, filtered through a 40 um strainer, and red blood cells were lysed with 1X RBC Lysis Solution. The cells were then washed in 1x DPBS with 2% FBS and viability was assessed with 0.4% Trypan blue on a Countess® II Automated Cell Counter.
Beads with UMIs and cell barcodes were paired with cells in GEMs, and after lysis, polyadenylated RNAs were reverse transcribed with 5’ cDNA ends tagged with UMIs and cell labels. Libraries were prepared focusing on 3’ transcript ends and sequenced on a NovaSeq6000 using 2x150 chemistry. Library quality was assessed using a High Sensitivity DNA Chip and Qubit assay, following the Chromium Single Cell 3ʹ v3 protocol.

value: leg muscles


title: KO, Replicate1, scRNA-seq

description: 10X Genomics


title: D19 PPs, LatB, 6hr, rep1


title: totalRNASeq_K365T_ID_NoLIF_rep1

value: mESC

value: IAA+Doxyxycline


title: THP-1, 24hr LPS, heavy digest

description: 24hr post LPS


title: Control_3

description: ANG3 WT1


title: D19 PPs, LatB, 3hr, rep3


title: WT, Replicate2, scRNA-seq

description: 10X Genomics


title: WT, Replicate1, scRNA-seq

description: 10X Genomics


title: THP-1, 12hr LPS, heavy digest

description: 12hr post LPS


title: THP-1, 4hr LPS, heavy digest

description: 4hr post LPS


title: Control_2

description: ANG3 WT3


title: D19 PPs, LatB, 3hr, rep2


title: THP-1, 1hr LPS, heavy digest

description: 1hr post LPS


title: Control_1

description: ANG3 WT2


title: D19 PPs, control, 24hr, rep1

value: DMSO


title: THP-1, 30min LPS, heavy digest

description: 30min post LPS


title: Control_0

description: ANG3 WT1

value: Huh7 hepatoma cells


title: D19 PPs, LatB, 3hr, rep1


title: DHMC12-2_Day10_2

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters: -O 5 --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG ATCTCGTATGCCGTCTTCTGCTTG CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Trimmed reads were mapped to and filtered of human-specific repeat elements (RepBase 18.05) with STAR (2.4.0i) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn  r1.fastq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the human genome with STAR using the same parameters as the previous step, using an hg19 index in place of the repeat element index
Subread featureCounts 1.5.3 (-a gencode.v19.annotation.gtf -s 2 -o counts.txt *.bam) was used to count features using human annotations (Gencode v19)
Genome_build: hg19
Supplementary_files_format_and_content: counts.txt contains read counts from hg19-mapped BAM files

source_name: colon

extract_protocol:
Tissue samples were homogenized with zirconia beads and Trizol, and RNA extraction was performed according to the manufacturer’s instructions. Libraries were prepared using the Illumina non-stranded TruSeq kit and sequenced on an Illumina HiSeq2500.
Libraries were prepared and sequenced on an Illumina HiSeq2500

tag: disease state

value: ulcerative colitis patients hospitalized for moderate-severe flares

value: colon

tag: day

value: HBOT

tag: type

value: Responder


title: D19 PPs, control, 0hr, rep3

value: ESC-derived pancreatic progenitor cells


title: D19 PPs, control, 24hr, rep2


title: DHMC7_Day10_2

value: Non-responder


title: D19 PPs, control, 0hr, rep2


title: THP-1, 48hr LPS, light digest

description: 48hr post LPS

value: 5U MNase


title: DHMC11_Day10_2

value: Sham


title: THP-1, 24hr LPS, light digest

description: 24hr post LPS


title: DHMC9_Day10_2


title: D19 PPs, control, 0hr, rep1


title: DHMC3_Day10_2


title: THP-1, 12hr LPS, light digest

description: 12hr post LPS


title: DHMC12_Day10_1


title: CS, static, antiox, rep2

city: Golden

first: Davinia

last: Salvachua

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters trimq=10, qtrim="rl", maq=10.
Reads were aligned to the Trametes versicolor and Gelatoporia subvermispora genomes using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). using parameters -local, --sensitive-local
Aligned reads were mapped to genes using htseq-count (https://pubmed.ncbi.nlm.nih.gov/25260700/) with parameters -a=1, --mode="union".
Assembly: Trametes versicolor genome https://www.ncbi.nlm.nih.gov/assembly/GCF_000271585.1/
Assembly: Gelatoporia subvermispora genome https://www.ncbi.nlm.nih.gov/assembly/GCA_000320605.2/
Supplementary files format and content: read counts per gene

organism: Gelatoporia subvermispora

growth_protocol: For fungal strain maintenance, we developed a minimal and defined medium which is an adapted version of Czapek-Dox medium (CDM). CDM consists of 2 g ammonium tartrate (Sigma-Aldrich, St. Louis, MO), 0.5 g MgSO4 x 7H2O (Fisher Scientific, NJ, USA), 1 g KH2PO4 (Sigma-Aldrich, St. Louis, MO), 0.5 g KCl (Sigma-Aldrich, St. Louis, MO), 1 mL sterile vitamins supplement (ATCC® MD-VS™), and 1 mL trace elements solution per liter in H2O. The trace elements solution contains 0.1 g Na2B4O7 x 10H2O (Sigma-Aldrich, St. Louis, MO), 0.07 g ZnSO4 x 7H2O (Sigma-Aldrich, St. Louis, MO), 0.01 g CuSO4 x 5H2O (Sigma-Aldrich, St. Louis, MO), 0.01 g MnSO4  x 4H2O (Sigma-Aldrich, St. Louis, MO), 0.05 g FeSO4 x 7H2O (Fisher Scientific, NJ, USA), and 0.01 (NH4)6MoO2 x 4H2O (Fluka, NC, USA) per liter in H2O. Trace element solution was filter sterilized through 0.2 µM PES filters (Millipore, MA, USA) and added after autoclaving (30 min at 121°C) of the rest of the CDM components. For seed culture preparation, an agar plug with fungal mycelia was taken from agar plates maintained at 4°C, deposited in the center of an YMPG agar plate, and incubated for 7 days at 28°C. Then, 4-5 agar plugs with mycelia were inoculated in 50 mL of liquid YMPG and incubated at 220 rpm and 28°C for 7 days (pre-seed). Fungal pellets were then homogenized (10 s, speed 6) in sterile conditions using an Omni Mixer 115V with a 50 mL SS Chamber PTFE (Omni International, GA, USA). The fungal suspension (2 mL) was re-inoculated in YMPG under the same conditions than the pre-seed culture and incubated for 5 days. A ratio of 2:25 (v:v) of further homogenized fungal suspension per media volume was used to inoculate the cultivations.

extract_protocol:
Frozen fungal cultures (100-200 mg) were transferred to a pre-chilled mortar and ground to a fine powder in liquid nitrogen.  The liquid nitrogen was allowed to evaporate and the sample was transferred to a pre-chilled 15 mL centrifuge tube. All steps were performed on dry ice to ensure samples remained frozen. RLT buffer (700 µL)(Qiagen) containing 10% β-mercaptoethanol was added to the frozen samples and the samples were allowed to thaw with periodic vortexing at high speed. Samples were vortexed at high speed continuously for 1 min or until the sample was completely homogenous. Samples were transferred to a QIAshredder column (Qiagen) and processed using the RNeasy mini kit and subjected to DNase gDNA digestion according to the manufacturers protocol (Qiagen). The RNA samples are assessed using the Agilent 2100 Bioanalyzer, RNA with RIN >7 proceed with cDNA library.
TruSeq Stranded Total RNA (cat#20020596) is used to generate cDNA library for illumina NextSeq550 platform according to the manufacture protocol.

treatment_protocol: T. versicolor and G. subvermispora cultivations were conducted in 250 mL flasks containing 25 mL of Czapek-Dox medium (CDM) with cellobiose (15 mM). Cultivations were incubated at 28°C in either agitation (220 rpm) or static conditions using a humidity-controlled incubator (˃50 % humidity). After 6 and 10 days of incubation with T. versicolor and G. subvermispora, respectively, we induced all the cultivations with 4-HBA (~2 mM) from a 4-HBA stock solution of xxx. Antioxidants (5 mM ascorbic acid and 1 mM α-tocopherol), and prepared as previously described,6 were also added in the media 30 min before the induction in half of the cultivations incubated in either static or agitation conditions. Cultivations were harvested 24 h after the induction, corresponding to 7 days and 11 days for T. versicolor and G. subvermispora, respectively.

tag: growth medium

value: Czapek-Dox medium w/15mM cellobiose

value: static

tag: culture temperature

value: 28 deg C

tag: incubation time

value: 10 days

value: 2 mM HBA, antioxidants

tag: additional incubation

value: 24 hours


title: CS, static, antiox, rep3

tag: strain


title: DHMC7_Day10_1


title: THP-1, 1hr LPS, light digest

description: 1hr post LPS

value: LPS treated macrophage

value: LPS


title: THP-1, 4hr LPS, light digest

description: 4hr post LPS


title: UPMC2_Day10_1


title: JP1260

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: kidney

value: Rbpj c/+ ; Foxd1cre/+

tag: age


title: JP1175

description: 10X Genomics


title: THP-1, 5min LPS, heavy digest

description: 5min post LPS

tag: cell line

value: 200U MNase


title: CS, static, antiox, rep1


title: THP-1, 0hr LPS, heavy digest

description: untreated

tag: cell type

value: macrophage


title: DHMC13-2_Day10_2

value: ulcerative colitis patients hospitalized for moderate-severe flares

value: colon

value: HBOT

value: Responder


title: THP-1, 5min LPS, light digest

description: 5min post LPS

value: 5U MNase


title: CS, static, no antiox, rep3

value: Czapek-Dox medium w/15mM cellobiose

value: 2 mM HBA


title: FLAG_CTCF_R377C_ID_rep1

data_processing:
Data were processed using Seq-N-Slide pipeline.
Nextera adaptor were trimmed using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the Bowtie2 aligner.
PCR duplicates were removed using Sambamba.
After scaling down each samples to 100M reads, replicates were merged per condition. Narrow peaks were called using MACS2 in pair-end mode with IgG as control for Smc3 ChIP-seq or WT untreated condition (in which FLAG CTCF is not expressed) for CTCF FLAG ChIP-seq to control for unspecific binding. Peaks overlapping ENCODE blacklisted regions were filtered out. Bigwig files were generated using deeptools (bamCoverage) with RPKM normalization (1bp bin).
Assembly: mm10
Supplementary files format and content: Bigwig with RPKM normalization, merged per condition after scaling down to 100M reads
Supplementary files format and content: narrow peaks (except for IgG and WT untreated, q<0.05) using merged replicates

growth_protocol: Mouse embryonic stem cells E14Tg2a and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin coated dishes at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM supplemented with 15% fetal bovine serum , 100 U/ml penicillin - 100 μg/ml streptomycin, 1 X GlutaMax supplement, 1 mM sodium pyruvate, 1 X MEM non-essential amino-acids, 50 μM b-mercaptoethanol, 104 U/ml leukemia inhibitory factor, 3 μM CHIR99021 and 1 μM MEK inhibitor PD0325901. The cells were passaged every alternate day by dissociation with TrypLE.

extract_protocol:
mESCs were dissociated using TrypLE and and double cross linked using 25mM EGS (ethylene glycol bis(succinimidyl succinate)) and 1% formaldehyde. Fixed cells (10 million) were resuspended in 350 μl ice cold lysis buffer (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% sodium deoxycholate, 0.5% N-lauroysarcosine and 1X protease inhibitors) and lysed for 10 min by rotating at 4° C. Chromatin was sheared using a bioruptor (Diagenode) for 15 minutes ( 30 sec on, 30 sec off, high output level). FLAG M2 Magnetic Beads were used for FLAG immunoprecipitation. In other cases ( Cohesin, IgG) antibodies were bound to protein A magnetic beads by incubation on a rotator for one hour at room temperature.
Samples were washed and tagmentation were performed as per the original ChIPmentation protocol (Schmidl et al., 2015) using 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina #20034198 ). Chromatin was then eluted and de-crosslinked and DNA was purified using MinElute Reaction Cleanup Kit. Purified DNA was amplified as per the ChIPmentation protocol (Schmidl, Rendeiro et al. 2015) using indexed and non-indexed primers and NEBNext High-Fidelity 2X PCR Master Mix. Library quality and quantity were estimatred using Tapestation and were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 200 million 150bp paired-end total per sample.

value: mESC

tag: genotype

value: IAA+Doxyxycline

tag: replicate

value: replicate 1

tag: antibody

value: FLAG (CTCF)


title: THP-1, 30min LPS, light digest

description: 30min post LPS

value: LPS treated macrophage

tag: treatment


title: DHMC11_Day10_1

tag: tissue

value: Sham

value: Non-responder


title: FLAG_CTCF_R377C_ID_rep2

value: replicate 2


title: CS, static, no antiox, rep1

value: static

value: 28 deg C

value: 10 days

value: 24 hours


title: CS, static, no antiox, rep2


title: THP-1, 0hr LPS, light digest

description: untreated

value: macrophage

tag: digest condition


title: Colon_naive_STAT6vt_control_rep3

city: Erlangen

first: David

last: Voehringer

address: Wasserturmstrasse 3-5

department: Department of Infection Biology

country: Germany

institute: University Clinic Erlangen

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Paired-end clean reads were aligned to the reference genome mm39 using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Deseq2 (1.20.0) was used to generate normalized counts.
Assembly: mm39
Supplementary files format and content: Westermann_et_al_villinSTAT6_gene_count_colon.txt
Supplementary files format and content: Westermann_et_al_villinSTAT6_Deseq2_normalized_counts_colon.txt

extract_protocol:
We collected colon tissue in RNA protect (Qiagen) and isolated RNA withe the Rneasy Mini Kit (Qiagen). DNA was digested with the DNAse1 Amplification Kit (Merck) and RNA integrity measured at an Agilent tape station (Agilent). RNA was sequenced by Illumina sequencing (Illumina).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: colon

tag: background

tag: Sex

value: female

value: naive


title: CS, agit, antiox, rep3

value: Czapek-Dox medium w/15mM cellobiose

value: agitation 220 rpm

value: 2 mM HBA, antioxidants


title: THP-1, 48hr LPS, merged digests

description: 48hr post LPS

value: 5U + 200U MNase

value: LPS


title: DHMC9_Day10_1

tag: disease state

value: ulcerative colitis patients hospitalized for moderate-severe flares

tag: day

tag: type

value: Responder


title: CS, agit, antiox, rep2

tag: growth medium

tag: culture temperature

tag: incubation time


title: THP-1, 24hr LPS, merged digests

description: 24hr post LPS

value: LPS treated macrophage


title: Colon_naive_STAT6vt_control_rep2


title: THP-1, 4hr LPS, merged digests

description: 4hr post LPS


title: CS, agit, antiox, rep1

tag: strain

tag: additional incubation


title: CS, agit, no antiox, rep3

value: 2 mM HBA


title: Illumina-RFTS-KD-IAA_R3

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

country: France

institute: INSERM

data_processing:
Nanopore: All datasets were subsequently basecalled (high accuracy basecalling) with Dorado base-caller with a Q score cutoff of >7. Long read alignment was performed by Minimap2. Sam files were converted to bam and sorted using Samtools 1.4.
Illumina: The quality of the raw sequencing reads was assessed using FastQC (www.bioinformatics. babraham.ac.uk/projects/fastqc/) and MultiQC. For the expression data quantification and normalization, the FASTQ reads were aligned to the ToxoDB-49 build of the T. gondii ME49 genome using Subread version 2.0.1 with the following options ‘subread-align -d 50 -D 600 --sortReadsByCoordinates’. Read counts for each gene were calculated using featureCounts from the Subread package. Transcripts were quantified and normalized using TPMCalculator.
Assembly: Toxoplasma gondii genome (ME49 strain)
Supplementary files format and content: Nanopore: No processed data files, only quality filetered fastq files. | Illumina: excel file with subread raw counts and TPMCalculator normalized counts

organism: Toxoplasma gondii

source_name: RH

growth_protocol: Toxoplasma gondii type I strains were maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen).
Nanopore: the mRNA library preparation followed the SQK-RNA004 kit (Oxford Nanopore)–recommended protocol, the only modification was the input mRNA quantity increased from 500 to 900 ng (300ng from each replicate), and all other consumables and parameters were standard. | Illumina: RNA sequencing was performed following standard Illumina protocols, by Novogene (Cambridge, United Kingdom).

treatment_protocol: HFF cells were grown to confluence and infected with RHKu80 SNF2h KD or RHKu80 RFTS KD strains.Transcriptome profiles in each strain left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours.

tag: cell line

value: RH

tag: cell type

value: Intracellular tachyzoites

value: IAA treated for 24h


title: Colon_naive_Villincre_STAT6vt_rep3

tag: genotype


title: CS, agit, no antiox, rep1

value: 28 deg C

value: 10 days

value: 24 hours


title: Colon_naive_STAT6vt_control_rep1

value: colon

value: female


title: THP-1, 12hr LPS, merged digests

description: 12hr post LPS


title: CS, agit, no antiox, rep2

value: Czapek-Dox medium w/15mM cellobiose


title: DHMC10_Day10_2

value: Sham

value: Non-responder


title: Colon_naive_Villincre_STAT6vt_rep2

value: naive


title: THP-1, 30min LPS, merged digests

description: 30min post LPS

value: 5U + 200U MNase

value: LPS


title: Illumina-RFTS-KD-IAA_R2


title: TV, static, antiox, rep3

organism: Trametes versicolor

value: static

value: 6 days

value: 2 mM HBA, antioxidants


title: Colon_naive_Villincre_STAT6vt_rep1

value: male


title: THP-1, 1hr LPS, merged digests

description: 1hr post LPS

value: LPS treated macrophage


title: Illumina-RFTS-KD-UT_R2

value: RH

value: Intracellular tachyzoites

value: untreated sample


title: DHMC4_Day10_2

value: ulcerative colitis patients hospitalized for moderate-severe flares

value: Responder


title: THP-1, 5min LPS, merged digests

description: 5min post LPS


title: Illumina-RFTS-KD-UT_R3


title: HIC_WT_ID_rep2

description:
HIC_WT_ID_rep2
HIC_WT_ID_rep1_rep2_10kb.matrix
HIC_WT_ID_rep1_rep2_10kb_abs.bed

data_processing:
HiC-Pro (and bowtie2) was used to align and filter the Hi-C data.
Alignemnet was performed using local mode for the second step of HiC-Pro alignment (--very-sensitive -L 20 --score-min G,20,8 --local) to ignore the molecular barcode UMI sequences and dark bases introduced by Arima library prep kit at the 5’ end of the read. Singleton, ambiguous and duplicated reads were filtered out.
Ligation sites for Arima HiC kit were set up using GATCGATC,GANTGATC,GANTANTC,GATCANTC. Low mapping quality (MAPQ<30), self circle, dangling ends and re-ligation reads were filtered out through the HiC-pro pipeline.
Samples were downscaled to the same number of good quality uniquely aligned reads using HiCExplorer. Of note, we did not use the number of valid pairs to downscale the samples to not overcorrect some conditions such as IAA and mutant H455R which were expected to show a dramatic biological decrease in valid interactions.
After downscaling, replicates were merged and interaction matrices were generated using Hic-pro.
Assembly: mm10
Supplementary files format and content: Hic-pro matrices and bin files (bed)  generated at 10 kb resolution for each condition

extract_protocol:
Hi-C was performed using around 1 million cells each. mESCs were dissociated using TrypLE. Cells were  double cross linked using 25mM EGS (ethylene glycol bis(succinimidyl succinate)) followed by 1% formaldehyde.
Samples were subsequently processed using the Arima Hi-C kit as per the manufacturer's protocol and sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 600 million 150bp paired-end reads per sample.

value: mESC

value: WT

value: IAA+Doxyxycline

tag: replicate

value: replicate 2


title: HIC_WT_ID_rep1

description:
HIC_WT_ID_rep1
HIC_WT_ID_rep1_rep2_10kb.matrix
HIC_WT_ID_rep1_rep2_10kb_abs.bed

tag: treatment

value: replicate 1


title: TV, static, antiox, rep2

value: Czapek-Dox medium w/15mM cellobiose

value: 28 deg C

value: 24 hours


title: THP-1, 0hr LPS, merged digests

description: untreated

value: macrophage

value: 5U + 200U MNase


title: TV, static, antiox, rep1

value: static

value: 6 days

value: 2 mM HBA, antioxidants


title: HIC_WT_IAA_rep2

description:
HIC_WT_IAA_rep2
HIC_WT_IAA_rep1_rep2_10kb.matrix
HIC_WT_IAA_rep1_rep2_10kb_abs.bed

value: IAA


title: Illumina-RFTS-KD-IAA_R1

value: RH

value: Intracellular tachyzoites

value: IAA treated for 24h


title: Illumina-SNF2h-KD-IAA_R3


title: HIC_WT_IAA_rep1

description:
HIC_WT_IAA_rep1
HIC_WT_IAA_rep1_rep2_10kb.matrix
HIC_WT_IAA_rep1_rep2_10kb_abs.bed

value: mESC


title: HIC_S354F_ID_rep2

description:
HIC_S354F_ID_rep2
HIC_S354F_ID_rep1_rep2_10kb.matrix
HIC_S354F_ID_rep1_rep2_10kb_abs.bed


title: retinal organoid, knockout, fasudil treated, rep2

city: London

first: Michael

last: Cheetham

address: 11-43 Bath St

department: Institute of Ophthalmology

country: United Kingdom

institute: University College London

data_processing:
FastQC 0.12.1 to check for sequence quality and adaptor contamination
BBDuk (from BBMap 39.01) to trim Illumina TruSeq adaptors from samples with adaptor contamination (options ‘ktrim=r, k=23, mink=12, hdist=1, tpe, tbo’)
Decoy-aware Gencode v44 hg38 index generated with Salmon 1.10.2, using the entire genome as decoy sequence
Trimmed sequences underwent transcript quantification with Salmon 1.10.2 in mapping-based mode (options ‘--validateMappings --gcBias --numBootstraps 30')
Salmon quantification results imported directly into DESeq2 1.40.2 with tximeta 1.18.3
Assembly: Hg38
Supplementary files format and content: Each sample has a tab-delimited quant.sf file containing information on transcript length, TPM, and number of reads for each transcript

source_name: retinal organoids

growth_protocol: iPSCs were grown in 6-well plates coated in Geltrex and in (Essential 8™ Flex Medium) and when they reached about 90-95% confluency, Essential 6 medium was added for two days (Day 0 and Day 1 of differentiation). At Day 2, cells were maintained in Neural induction medium (NIM) (Advanced DMEM/F-12 (1:1) supplemented with 1% N2 supplement (100X), 100  mM Glutamine and 100 U/m penicillin/streptomycin. On Day 6, 1.5 nM bone morphogenetic protein 4 (BMP4 R&D Systems) was added to fresh NIM and half media changes were performed every other day until Day 16. Neuroretinal vesicles (NRVs) started to form between (2-4 weeks) and when they were fully defined, they manually dissected and /or checkerboarded, transferred to 96 ultra - low attachment plates and cultured in retinal differentiation medium (RDM) (DMEM/F12 nutrient mix (3:1 ratio), 10% fetal bovine serum (FBS), 2% B27 supplement (without vitamin A), 2 mM GlutaMAX and 100U/ml penicillin/streptomycin) for 6 days. At D30 medium was changed to Retinal maturation media 1 (RMM1) (DMEM/F12 nutrient mix (3:1 ratio), 10% fetal bovine serum (FBS), 2% B27 supplement (without vitamin A), 100uM taurine (Tocris Bioscience), 2 mM GlutaMAX and 100U/ml penicillin/streptomycin). From Day 50-70, medium was supplemented with 1  μM Retinoic Acid (RA) which was added fresh in every media change and from Day 70 RA was reduced to 0.5  μM and 1% N2 supplement was added to the media (RMM2). From Day 100, RA and B27 were removed from media (RMM3) and retinal organoids were transferred in 25 cm dishes until collection.

extract_protocol:
Control and LCA5 KO retinal organoids were processed for RNA extraction using an RNeasy MicroKit (QIAGEN)
cDNA synthesis was performed using a Tetro cDNA synthesis kit (Bioline)

treatment_protocol: Retinal organoids were treated from D190-D220 with either vehicle (DMSO), eupatilin (Adipogen) (10  μM), fasudil hydrochloride (Cell Guidance Systems (SM-49) (5  μM) or a combination of eupatilin (10  μM) and fasudil (5  μM) (FAS/EUP). Drug treatments were carried out at routine media changes with RMM3, three times per week.

value: retinal organoids

value: homozygous LCA5 KO

value: Fasudil treated

tag: age

value: 220 days old


title: TV, static, no antiox, rep3

value: Czapek-Dox medium w/15mM cellobiose

value: 2 mM HBA


title: retinal organoid, knockout, fasudil treated, rep3


title: Illumina-SNF2h-KD-IAA_R2


title: HIC_S354F_ID_rep1

description:
HIC_S354F_ID_rep1
HIC_S354F_ID_rep1_rep2_10kb.matrix
HIC_S354F_ID_rep1_rep2_10kb_abs.bed

value: IAA+Doxyxycline

value: replicate 1


title: Illumina-SNF2h-KD-UT_R3

value: untreated sample


title: retinal organoid, knockout, eupatilin treated, rep4

value: Eupatilin treated


title: HIC_R448Q_ID_rep2

description:
HIC_R448Q_ID_rep2
HIC_R448Q_ID_rep1_rep2_10kb.matrix
HIC_R448Q_ID_rep1_rep2_10kb_abs.bed

value: replicate 2


title: Illumina-SNF2h-KD-UT_R2


title: retinal organoid, knockout, fasudil treated, rep1


title: TV, static, no antiox, rep2

value: static

value: 28 deg C

value: 6 days

value: 24 hours


title: retinal organoid, knockout, eupatilin treated, rep3


title: HIC_R448Q_ID_rep1

description:
HIC_R448Q_ID_rep1
HIC_R448Q_ID_rep1_rep2_10kb.matrix
HIC_R448Q_ID_rep1_rep2_10kb_abs.bed


title: Illumina-SNF2h-KD-UT_R1

value: RH

value: Intracellular tachyzoites


title: HIC_R377H_ID_rep2

description:
HIC_R377H_ID_rep2
HIC_R377H_ID_rep1_rep2_10kb.matrix
HIC_R377H_ID_rep1_rep2_10kb_abs.bed

value: mESC


title: TV, agit, antiox, rep2

value: agitation 220 rpm

value: 2 mM HBA, antioxidants


title: TV, agit, antiox, rep1


title: Illumina-RFTS-KD-UT_R1


title: Illumina-SNF2h-KD-IAA_R1

value: IAA treated for 24h


title: TV, agit, no antiox, rep3

value: Czapek-Dox medium w/15mM cellobiose


title: TV, agit, antiox, rep3


title: retinal organoid, knockout, eupatilin treated, rep1

value: retinal organoids

value: homozygous LCA5 KO

value: 220 days old


title: HIC_R377C_ID_rep2

description:
HIC_R377C_ID_rep2
HIC_R377C_ID_rep1_rep2_10kb.matrix
HIC_R377C_ID_rep1_rep2_10kb_abs.bed

value: IAA+Doxyxycline