title: B.unvax.SA.d17.1


title: ChIP_CD34_22_2_SA2_529_1252_SA1

status: Public on Jun 18 2024

type: SRA

city: Regensburg

first: Alexander

last: Fischer

address: Franz-Josef-Strauß-Allee 11

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
CD34_SA1.peaks.ann.txt
CD34_SA1.peaks.DESEQnorm2total.txt
raw data cannot be deposited online

library_source: genomic

data_processing:
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5) in very sensitive mode
Samtools (v.1.6) was used to remove lower quality alignments with mapQ=<10 and sorting
HOMER style tagDirectories were generated using HOMER makeTagDirectory (-checkGC and -unique). For AML samples, tag directories were corrected for copy number varations based on FreeC output genereated from DNA-Input-Sequencing data.
Bigwig coverage tracks  were generated using HOMER’s makeUCSCfile function. For HSPC RAD21/CTCF/MED12/PU1/H3K27ac data sets, BigWigs were aditionally scaled based on median coverage across the top 5% common peaks detected in all samples.
For focal peaks, HOMER was used to call peaks (factor mode; -fdr 0.00001 -tbp). For region peaks, i.e. H3K27ac, HOMER was used for peak calling in region mode (-fdr 0.00001, -size 250, -L 0 -F 5 -minDist 350, -tbp -ntagThreshold 10). In case of AMLs, peak calling was performed in individual tag directories, in case of HSPCs condition-merged tag directories were used. For each data set, peak files of all conditions/groups were merged and filtered for low-mappability and blacklisted regions to generate reference peak sets. Subsequently, the individual samples were annotated to combined peak set to obtain peak coverage tables for each data set separetely.
Annotation tables with peak coverage were used for differential analysis using DESeq2 or edgeR to calculate differential Peak Coverage between controls and associated cohesin deficient samples. For H3K27ac data sets, counts were additionally normalized  for length and GC content using offsets generated by the cqn R package, which were implemented in edgeR. For STAG1 and STAG2 HPSC datasets differential analysis was performed using HOMER’s getDiffExpression.pl routine with the -batch, -rlog and -normtotal options enabled. The same applies to RAD21 ChIP-seq in RAD21 KD HSPCs.
Assembly: GRCh38.p10
Supplementary files format and content: bigWig coverage track files for individual samples
Supplementary files format and content: tab-delimited file containing peak coordinates and coverage counts for each sample (HOMER annotation output)
Supplementary files format and content: tab-delimited file containing peak coordinates and DESeq2 or edgeR statistics for differential peak testing

molecule: genomic DNA

organism: Homo sapiens

source_name: cord blood

growth_protocol: CD34+ HSPCs were enriched from fresh cord blood samples on the day of birth using the CD34 MicroBead kit (Miltenyi biotec). Cells were expanded for 7d in serum-free Stem Span media (Stem Cell Technologies) supplemented with human recombinant cytokines (Peprotech): SCF (0.1ng/mL), FLT3 (0.1ng/mL), IL6 (0.004ng/mL), TPO (0.025ng/mL) and StemRegenin1 (7500nmol/mL, Stem Cell technologies) as well as Penicillin/Streptomycin.

extract_protocol:
Cells were fixated using 0.5M DSG and 1% formaldehyde. Chromatin was sheared using Branson Sonifier 250. ChIP was performed with lysate of 2 Mio cells using a target specific antibody (anti-RAD21ab992 (abcam), anti-H3K27ac ab4729 (abcam), anti-CTCF 2899S (Cell Signaling), anti-STAG2 (custom produced), anti-STAG1 (custom produced), anti-MED12 (custom produced), anti-PU.1 sc352 (santa cruz)) and ProteinA Dynbeads. After de-crosslinking and proteinase K digest, DNA was purified using Monarch PCR & DNA clean-up kit (NEB).
Libraries were generated using the NEBNextUltra II DNA Library Prep Kit for Illumina with all available input material and 11 PCR cycles for amplification.

treatment_protocol: To obtain AML cells, PBMCS were extracted from bone marrow or whole blood samples of patients using Lymphoprep at the timepoint of first diagnosis and viably frozen. For knockdown experiments with healthy cells, HSPCs were transfected using the Neon electroporation system (Invitrogen, 1400V, 20ms, 2 pulses) at a density of 60,000 viable cells/µL with 1.33µg of chemically modified siRNAs (Axiolabs) per mio cells. Cells were kept in antibiotics-free media after transfection and harvested after 4d.

tag: tissue

value: cord blood

tag: cell line

tag: cell type

value: HSPC

tag: genotype

value: wt

tag: treatment


title: B.unvax.SA.d10.4

city: Seattle

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

country: USA

institute: Seattle Children's Research Institute

description: Lung parenchymal cells were selected for 10X Genomics scRNAseq using IV labelling and FACSAria II sorting.

library_source: transcriptomic single cell

data_processing:
The Seurat R package was used for initial QC filtering and integration. First. a filtering step was applied across all samples. requiring all passing cells to have UMIs mapped to at least 500 distinct genes. and fewer than 5% of UMIs mapped to mitochondrial genes. Genes detected in fewer than 3 cells per mouse were excluded from further analysis. The Seurat integration pipeline56 was then applied to correct for batch effects and align cells across conditions including all combinations of mouse strain. Mtb strain. time post challenge. and CoMtb status.
Initial cell type assignment was performed using the CellTypist python package.57 As CellTypist does not have an available cell type model suitable for mouse lung or mouse immune cells. we created a de novo mouse lung immune cell type model using two published mouse cell atlases. namely the Tabula Muris58 and scMCA59 resources. Cell type labels were harmonized between both sources (e.g. macrophage -> Macrophage) and both datasets were filtered to retain immune and lung-associated cell types. excluding cells specific to other organs. The CellTypist python package was then used to train a mouse lung cell type model based on this combined resource. This model was then used to assign cell types to count-normalized log transformed data on a per-cell level from mouse lung scRNAseq samples. using the python scanpy60 package to normalize total counts per cell to 10.000 and log transform as required by CellTypist.
Assembly: mm10-2020-A (10X Genomics)
Supplementary files format and content: R Seurat object containing raw and normalized counts, per-sample and per-cell metadata, cell type label assignments, calculated UMAP and PCA co-ordinates.

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
After one round of washing with ice-cold DPBS. cells were resuspended to 1000 cells/ml in DPBS. and 8000 cells were inputted into the 10X Genomics pipeline following the manufacturer’s recommendations.
Per 10x protocol

treatment_protocol: We performed single-cell RNA sequencing (scRNAseq) and flow cytometry analysis of lungs from Mtb-infected animals with and without CoMtb (10^4 CFU of Mtb injected i.d. 8 weeks prior to aerosol Mtb infection) immediately pre-infection and at 10. 17 and 34 days after CD infection. Single cell suspensions were generated from lung samples prior to Mtb infection and at days 10. 17 and 34 post-Mtb infection. Cells were resuspended in 200 ul MACS buffer (PBS containing 2.5% FBS plus 1 mM EDTA). filtered through a 70 um filter. and run on a FACS AriaII (BD) sorter. To collect parenchymal cells for single-cell RNA sequencing. alveolar macrophages (AM. SiglecF+CD11c+) were sorted separately into one collection tube to account for autofluorescence in the IV label channel. and all other IV-negative cells were sorted into another collection tube. After sorting. the two populations were combined and counted on a hemocytometer.

value: Lung

tag: mtb strain

tag: timepoint


title: ChIP_CD34_14_3_siCtrl_MED12

description: raw data cannot be deposited online

value: siCtrl


title: ChIP_CD34_14_2_SA2_529_1252_SA1


title: B.unvax.SA.d10.3


title: B.unvax.SA.d10.2


title: ChIP_CD34_28_4_SA1_2259_4094_SA1


title: B.unvax.SA.d10.1


title: B.unvax.Rv.d34.4


title: ChIP_CD34_21_4_siCtrl_MED12

description: raw data cannot be deposited online


title: ChIP_CD34_27_3_SA1_2259_4094_SA1


title: ChIP_CD34_19_2_siCtrl_MED12

description: raw data cannot be deposited online


title: B.unvax.Rv.d34.3


title: ChIP_CD34_21_2_SA1_2259_4094_SA1


title: B.unvax.Rv.d34.2


title: B.unvax.Rv.d34.1


title: ChIP_CD34_28_6_siCtrl_SA1


title: ChIP_CD34_17_1_SA1_2259_4094_SA1


title: ChIP_CD34_22_3_siCtrl_SA1


title: B.unvax.Rv.d17.4


title: B.unvax.Rv.d17.3


title: ChIP_CD34_21_4_siCtrl_SA1_Rep1


title: ChIP_CD34_21_4_siCtrl_SA1


title: B.unvax.Rv.d17.2


title: B.cotb.none.d0.4

value: CoMtb


title: ChIP_CD34_21_3_SA2_529_1252_SA1


title: B.cotb.none.d0.3


title: ChIP_CD34_17_3_siCtrl_SA1


title: ChIP_CD34_17_2_SA2_529_1252_SA1


title: B.cotb.none.d0.2


title: ChIP_CD34_14_4_Mock_SA1

value: Mock


title: B.cotb.none.d0.1


title: ChIP_AML_RAD21_28420_SA1_DQI_Rep1

description:
19733
EGAR00003889703

source_name: hematopoietic

value: hematopoietic

value: AML blasts

value: RAD21 mut


title: ChIP_CD34_14_3_siCtrl_SA1


title: B.cotb.SA.d34.1


title: B.cotb.SA.d34.4


title: ChIP_AML_Rad21_38455_SA1-DQI

description:
41580a
EGAR00003889701


title: ChIP_AML_RAD21_27650_SA1_DQI_Rep1

description:
19725
EGAR00003889702


title: B.cotb.SA.d34.2


title: ChIP_CD34_14_1_SA1_2259_4094_SA1


title: ChIP_AML_Rad21_23039_SA1-DQI

description:
7314
EGAR00003889700


title: B.cotb.SA.d17.3


title: B.cotb.SA.d17.2


title: B.cotb.SA.d17.1


title: ChIP_AML_SA2_29728_SA1-DQI

description:
24603
EGAR00003766193

value: STAG2 mut


title: ChIP_AML_SA2_27396_SA1-DQI

description:
12567
EGAR00003766192


title: ChIP_AML_SA2_24743_SA1-DQI

description:
12514
EGAR00003766191


title: B.cotb.SA.d10.4


title: ChIP_AML_SA2_9708_SA1-DQI

description:
2193
EGAR00003766189


title: ChIP_AML_SA2_15365_SA1-DQI

description:
2292
EGAR00003766190


title: B.cotb.SA.d10.2


title: B.cotb.SA.d10.3


title: B.cotb.SA.d10.1


title: ChIP_AML_ctr_19416_SA1-DQI

description:
3488
EGAR00003766187

value: cohesin wt


title: ChIP_AML_ctr_21047_SA1-DQI

description:
6246
EGAR00003766188


title: B.cotb.Rv.d34.2


title: B.cotb.Rv.d34.4


title: B.cotb.Rv.d34.1


title: B.cotb.Rv.d17.4


title: B.cotb.Rv.d34.3


title: ChIP_CD34_28_5_SA2_529_1252_SA2

description:
CD34_SA2.peaks.ann.txt
CD34_SA2.peaks.DESEQnorm2total.txt
raw data cannot be deposited online


title: ChIP_AML_ctr_16911_SA1-DQI

description:
2236
EGAR00003766183


title: ChIP_AML_ctr_19405_SA1-DQI

description:
3323
EGAR00003766186


title: ChIP_CD34_22_2_SA2_529_1252_SA2


title: B.cotb.Rv.d17.2


title: B.cotb.Rv.d17.1


title: ChIP_CD34_21_3_SA2_529_1252_SA2


title: ChIP_AML_ctr_18136_SA1-DQI

description:
1551
EGAR00003766184


title: B.cotb.Rv.d17.3


title: ChIP_CD34_20_5_SA2_529_1252_SA2


title: ChIP_CD34_17_2_SA2_529_1252_SA2


title: liver, Mettl14[fl/fl]/Alb-Cre, rep3

city: Princeton

first: Aaron

middle: E

last: Lin

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

library_source: transcriptomic

data_processing:
Reads were demultiplexed using Picard v2.25.6, from within viral-ngs v2.1.33 with the read structure ‘5S8B15M8B102T’ and Q20M1 mismatch tolerance.
Demultiplexed reads were mapped to the mouse genome mm39 using STAR v2.7.10a.
Uniquely mapped reads were counted based on the GENCODE comprehensive gene annotation on the primary assembly using htseq-count v1.99.2.
Assembly: mm39, GENCODE release M28
Supplementary files format and content: Counts matrix of genes (mm39, M28) x all 6 samples

source_name: liver

growth_protocol: Mice were bred and maintained in accordance with a protocol (3063) approved by the Institutional Animal Care and Use Committee (IACUC) at Princeton University.

extract_protocol:
Liver tissue was collected from animals after perfusion with PBS via the portal vein to remove blood from tissue. RNA was extracted from bulk liver tissue using the Monarch total RNA miniprep kit (New England Biolabs, Ipswich, MA) after homogenization with steel beads using a TissueLyser LT bead mill (Qiagen, Venlo, The Netherlands).
Starting from 50 ng total RNA per sample, we performed bulk RNA barcoding and sequencing (BRB-Seq) with minor modifications. We performed reverse transcription with Template Switching RT Enzyme Mix (NEB) and a uniquely barcoded oligo(dT)30 primer for each sample, modified to use Illumina TruSeq Read 1 priming site instead of Nextera Read 1. Following the remainder of the standard BRB-Seq protocol, we pooled up to 24 barcoded first-strand cDNAs into a single tube, synthesized second-strand cDNA with Gubler-Hoffman nick translation, and tagmented cDNA pools with Tn5 produced in-house. We amplified libraries using a P5-containing primer and a unique multiplexed i7 indexing primer (Chromium i7 Multiplex Kit, 10X Genomics), then purified and size-selected libraries with SPRIselect (Beckman Coulter). We sequenced all pools on a NovaSeq SP v1.5 flowcell (Illumina) with 28 cycles of Read 1, 8 cycles of Read i7, and 102 cycles of Read 2.

treatment_protocol: C57BL/6 and B6.Cg-Tg(Alb-cre)21Mgn/J (Alb-cre) were obtained from the Jackson Laboratory (Bar Harbor, ME). Mettl14[fl/fl], (on the C57BL/6 background) were kindly provided by Dr. Chuan He (University of Chicago, HHMI). Mettl14[fl/fl]/Alb-Cre mice were generated by intercrossing mice harboring the respective alleles and typing offspring with primer combinations distinguishing wild-type and mutant alleles (typing information are available upon request).

value: liver

tag: mouse id

tag: replicate


title: liver, Mettl14[fl/fl]/Alb-Cre, rep2


title: liver, Mettl14[fl/fl]/Alb-Cre, rep1


title: liver, Mettl14[fl/fl], rep3


title: ChIP_CD34_28_4_SA1_2259_4094_SA2


title: ChIP_AML_ctr_18519_SA1-DQI

description:
1747
EGAR00003766185


title: ChIP_CD34_21_2_SA1_2259_4094_SA2


title: ChIP_CD34_27_3_SA1_2259_4094_SA2


title: liver, Mettl14[fl/fl], rep1


title: ChIP_CD34_17_1_SA1_2259_4094_SA2


title: P300 siRNA Late-2-cell rep2

city: Shenzhen

first: Di

last: Gao

address: No. 1, Haiyuan 1st Road, Futian District

country: China

institute: the University of Hong Kong Shenzhen Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Novaseq output
Sequence reads underwent trimming using Cutadapt version 4.1 with default parameters
Trimmed sequence reads were mapped to UCSC mm9 using HISAT2 version 2.2.1 with default parameters
Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation (the University of California Santa Cruz [UCSC] gene models) using Cufflinks version 2.2
Assembly: mm9
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 FPKM values for each Sample

source_name: preimplantation embryo

growth_protocol: zygotes was cultured in 50 μl KSOM (Millipore, MR-107-D) droplets at 37°C with 5% CO2 in air and saturated humidity

extract_protocol:
embryos were lysis in 4 μl lysis buffer  from a previous report (Picelli et al., 2014)
Preparation of total RNA-seq libraries from early embryos of different stages was performed using the Smart-seq2 protocol as described previously (Picelli et al., 2014)

value: preimplantation embryo

value: P300 knockdown


title: P300 siRNA Late-2-cell rep1


title: ChIP_CD34_14_1_SA1_2259_4094_SA2


title: ChIP_CD34_22_3_siCtrl_SA2


title: Control Late-2-cell rep1

value: WT


title: ChIP_CD34_28_6_siCtrl_SA2


title: Control Late-2-cell rep2


title: P300 siRNA H3K4me3 Late-8-cell rep2 ChIP

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Novaseq output
ChIP-Seq reads underwent trimming using Cutadapt version 4.1 with default parameters
ChIP-Seq reads were aligned to the UCSC mm9 genome using Bowtie2 version 2.3.5.1. Only uniquely mapping reads with a tolerance of up to two mismatches were retained.
Read counts were normalized by calculating reads per kilobase of bin per million of sequenced reads (RPKM), following the removal of non-uniquely mapped reads, unmapped reads, and PCR duplicates.
BW files were generated using the bamCoverage command from deepTools version 3.5.1.
Peaks was carried out employing MACS (model-based analysis of ChIP-seq) version 2.1.2, using default parameters and a q value cutoff of 0.05
Assembly: mm9
Supplementary files format and content: BW

extract_protocol:
embryos were lysis in 100 μl wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1x Protease inhibitor cocktail)
The protocol for the CUT&Tag library was adapted from a previous report with minor modifications (Kaya-Okur et al., 2019)


title: ChIP_CD34_14_4_Mock_SA2


title: P300 siRNA H3K4me3 Late-8-cell rep1 ChIP


title: ChIP_CD34_17_3_siCtrl_SA2


title: Control H3K27ac Late-2-cell rep2 ChIP


title: ChIP_CD34_21_4_siCtrl_SA2


title: Control H3K4me3 Late-8-cell rep2 ChIP


title: Control H3K4me3 Late-8-cell rep1 ChIP


title: ChIP_CD34_18_4_siCtrl_SA2


title: ChIP_CD34_14_2_SA2_529_1252_SA2


title: Control H3K27ac Late-2-cell rep1 ChIP


title: ChIP_AML_Rad21_29992_SA2

description:
27918
EGAR00003889699


title: ChIP_CD34_14_3_siCtrl_SA2


title: liver, Mettl14[fl/fl], rep2


title: ChIP_AML_Rad21_28420_SA2

description:
19733
EGAR00003889697


title: ChIP_AML_Rad21_UKR186_SA2

description:
UKR186
EGAR00003766214


title: ChIP_AML_Rad21_38455_SA2

description:
41580a
EGAR00003766213


title: Cornea, PBS, 7day,rep4

city: Beijing

first: yaqiong

last: li

address: youanmenwai

institute: Capital Medical University

data_processing:
Image processing and base recognition were performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
The RNA sequencing reads were aligned to the Mus musculus reference genome GRCm38 using Hisat2 (version 2.1.0) with default parameters.
The normalized expression value, fragments per kilobase of transcript per million mapped reads (FPKM), was calculated for each gene using StringTie (version 1.3.3).
FPKM at the gene level and transcript level were calculated using Ballgown (version 2.10.0).
Gene Set Enrichment Analysis (GSEA) for the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis was analysed using GSEA (version 2.2.4).
Assembly: GRCm38
Supplementary files format and content: The Express file format is xlsx, which analyses the expression of gene and transcript in the cornea of mice.
Supplementary files format and content: The Diff_express file format is xlsx, which analyses all differentially expressed genes /transcripts and differentially expressed genes /transcripts in the cornea of mice.

source_name: Cornea

extract_protocol:
RNA was harvested using Trizol reagent and  1-2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Roche) following manufacturer's protocols.

treatment_protocol: The C57BL/6 female mice aged 6 to 8 weeks were used for establishing DED models. Mice were randomly assigned to a control or DED group. Briefly, both eyes of mice in the DED groups were topically administered 5 μl of 0.2% BAC (Sigma-Aldrich) twice daily for 7 days, while the normally control mice were treated with PBS in both eyes.

value: Cornea

value: PBS


title: Cornea, PBS, 7day,rep1


title: Cornea, BAC, 7day,rep4

value: BAC


title: Cornea, PBS, 7day,rep3


title: Cornea, PBS, 7day,rep2


title: ChIP_AML_Rad21_27650_SA2

description:
19725
EGAR00003889696


title: ChIP_AML_Rad21_23039_SA2

description:
7314
EGAR00003766211


title: Cornea, BAC, 7day,rep1


title: Cornea, BAC, 7day,rep2


title: Cornea, BAC, 7day,rep3


title: ChIP_AML_Rad21_26830_SA2

description:
12557
EGAR00003766212


title: ChIP_AML_SA2_BB007_SA2

description:
BB007
EGAR00003766229


title: ChIP_AML_SA2_32635_SA2

description:
36837
EGAR00003766228


title: ChIP_AML_SA2_31501_SA2

description:
27513
EGAR00003766227


title: C2C12 cells, Prr33-gRNA-3, differentiation 3 days

city: Hangzhou

first: Xuyang

last: Fu

address: Kaixuan Road NO.258

institute: Zhejiang University

data_processing:
The image data measured by the high-throughput sequencer were converted into  sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: gene_counts text file includes raw counts for each Sample
Supplementary files format and content: gene_fpkm text file includes FPKM value for each Sample

growth_protocol: C2C12 cells were cultured in growth medium consisting of DMEM high glucose, 20% fetal bovine serum, 100 U/ml penicillin, and 100 mg/ml streptomycin in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
The total RNA was extracted from cell samples using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following mamufacturer's protocols

treatment_protocol: Once the density reached approximately 80%, the cells were shifted to differentiation medium (DMEM high glucose, 2% Horse Serum, 100 U/ml penicillin, and 100 mg/ml streptomycin), to initiate differentiation. The differentiation medium was replaced daily to ensure proper differentiation.

value: skeletal muscle cells

value: PRR33 knocked down

value: myoblast differentiation


title: ChIP_AML_SA2_29728_SA2

description:
24603
EGAR00003766226


title: ChIP_AML_SA2_28041_SA2

description:
19892
EGAR00003766225


title: ChIP_AML_Rad21_29047_SA2

description:
19740
EGAR00003889698


title: C2C12 cells, Prr33-gRNA-2, differentiation 3 days


title: C2C12 cells, Ctrl-gRNA-3, differentiation 3 days


title: C2C12 cells, Prr33-gRNA-1, differentiation 3 days


title: ChIP_AML_SA2_27396_SA2

description:
12567
EGAR00003766223


title: C2C12 cells, Ctrl-gRNA-2, differentiation 3 days


title: WT articular cartilage_2

city: Shanghai

first: Junjie

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: cartilage

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: cartilage


title: ChIP_AML_SA2_27493_SA2

description:
48386
EGAR00003766224


title: WT articular cartilage_3


title: ChIP_AML_SA2_25458_SA2

description:
48380
EGAR00003766222


title: ChIP_AML_SA2_24743_SA2

description:
12514
EGAR00003766221


title: ChIP_AML_SA2_22525_SA2

description:
7325
EGAR00003766220


title: WT articular cartilage_1


title: Parkin KO articular cartilage_3

value: Parkin KO


title: Parkin KO articular cartilage_1


title: ChIP_AML_SA2_22464_SA2

description:
7323
EGAR00003766219

value: hematopoietic


title: ChIP_AML_SA2_15640_SA2

description:
2216
EGAR00003766217

value: AML blasts


title: Articular cartilage of 18-month-old mice_2


title: ChIP_AML_SA2_15365_SA2

description:
2292
EGAR00003766216


title: Articular cartilage of 18-month-old mice_1


title: ChIP_AML_SA2_9708_SA2

description:
2193
EGAR00003766215


title: ChIP_AML_ctr_22023_SA2

description:
6374
EGAR00003766210


title: ChIP_AML_SA2_19142_SA2

description:
3315
EGAR00003766218


title: C2C12 cells, Ctrl-gRNA-1, differentiation 3 days


title: ChIP_AML_ctr_21290_SA2

description:
5285
EGAR00003766209


title: ChIP_AML_ctr_20899_SA2

description:
5286
EGAR00003766207


title: ChIP_AML_ctr_21047_SA2

description:
6246
EGAR00003766208


title: P300 siRNA NaCr Late-8-cell rep2

value: P300 knockdown NaCr rescue


title: ChIP_AML_ctr_20458_SA2

description:
4338
EGAR00003766206


title: Articular cartilage of 2-month-old mice_1


title: ChIP_AML_ctr_20180_SA2

description:
4334
EGAR00003766205


title: P300 siRNA NaCr Late-8-cell rep1


title: Parkin KO articular cartilage_2


title: P300 siRNA I1394G Late-8-cell rep2

value: P300 knockdown I1394G rescue


title: ChIP_AML_ctr_19405_SA2

description:
3323
EGAR00003766203

value: cohesin wt


title: P300 siRNA I1394G Late-8-cell rep1


title: ChIP_AML_ctr_19416_SA2

description:
3488
EGAR00003766204


title: ChIP_AML_ctr_19284_SA2

description:
3319
EGAR00003766202


title: P300 siRNA Late-8-cell rep2


title: ChIP_AML_ctr_18519_SA2

description:
1747
EGAR00003766200


title: ChIP_AML_ctr_19049_SA2

description:
3313
EGAR00003766201


title: Articular cartilage of 18-month-old mice_3


title: Control Late-8-cell rep1


title: Control Early-8-cell rep2


title: ChIP_CD34_22_2_SA2_529_1252_CTCF

description:
CD34_CTCF.peaks.ann.txt
raw data cannot be deposited online

value: cord blood

value: HSPC

value: wt


title: Rat cortical neuron, Pam3CSK4, 6h, rep1

city: Philadelphia

first: Trevor

last: Griesman

state: PA

address: 459 Stemmler hall, 3450 Hamilton Walk

department: Pathology and laboratory medicine

institute: University of Pennsylvania

description:
pam3_a
log2CPM_filter_norm.txt

data_processing:
Raw reads were mapped to the indexed Rnor_6.0 genome using Kallisto, with an estimated average fragment length of 72 and an estimated standard deviation of 4
Kallisto output was imported into Rstudio at the gene level, and gene names were obtained from Ensembl (release 104)
edgeR was used to extract Log2 Counts Per Million (CPM) for each gene, and genes with greater than 1 Log2 CPM in 2 or fewer samples were filtered out.
Log2 CPM were normalized using edgeR, with trimmed mean of M-values (TMM) normalization
Assembly: Rnor_6.0
Supplementary files format and content: Tab-delimited text file includes filtered, normalized log2 CPM: log2CPM_filter_norm.txt

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Cortical neurons day 7 ex vivo

growth_protocol: Cortical neurons were isolated from E18 Sprague Dawley rat embryos and were grown in neurobasal media + 2% B27 supplement, 33mM glucose, 40mM HEPES, and 1% penicillin/streptomycin for 7 days prior to treatment

extract_protocol:
RNA was collected in Trizol, and purified using a Zymo RNA clean & concentrator-25 kit according to the instructions, with duplicate wells pooled during purification.
PolyA enriched cDNA libraries were constructed with an Illumina TruSeq RNA library prep kit, according to the manufacturers instructions.

treatment_protocol: Cells were treated with vehicle (water), Pam3CSK4 (10ug/mL), or Pam2CSK4 (10ug/mL) diluted in DPBS for 6h

value: Cortical neurons day 7 ex vivo

tag: strain

value: Sprague Dawley

value: Pam3CSK4 10ug/mL

tag: time

value: 6 hours


title: P300 siRNA Late-8-cell rep1

value: preimplantation embryo

value: P300 knockdown


title: Rat cortical neuron, Mock, 6h, rep3

description:
mock_c
log2CPM_filter_norm.txt

value: Vehicle


title: P300 siRNA Early-8-cell rep1


title: P300 siRNA 4-cell rep2


title: ChIP_CD34_28_5_SA2_529_1252_CTCF


title: ChIP_AML_ctr_11374_SA2

description:
2207
EGAR00003766195


title: P300 siRNA 4-cell rep1


title: Rat cortical neuron, Pam2CSK4, 6h, rep1

description:
pam2_a
log2CPM_filter_norm.txt

value: Pam2CSK4 10ug/mL


title: ChIP_AML_ctr_14094_SA2

description:
2273
EGAR00003766196


title: ChIP_AML_ctr_16911_SA2

description:
2236
EGAR00003766197


title: ChIP_CD34_28_1_RAD21_467_2031_CTCF


title: ChIP_CD34_21_3_SA2_529_1252_CTCF


title: Rat cortical neuron, Pam3CSK4, 6h, rep3

description:
pam3_c
log2CPM_filter_norm.txt


title: ChIP_CD34_27_1_RAD21_467_2031_CTCF


title: ChIP_CD34_22_1_RAD21_467_2031_CTCF


title: Control Late-8-cell rep2

value: WT


title: Rat cortical neuron, Pam3CSK4, 6h, rep2

description:
pam3_b
log2CPM_filter_norm.txt


title: Rat cortical neuron, Pam2CSK4, 6h, rep3

description:
pam2_c
log2CPM_filter_norm.txt


title: Articular cartilage of 2-month-old mice_3

value: cartilage


title: Control Early-8-cell rep1


title: ChIP_CD34_20_5_SA2_529_1252_CTCF


title: ChIP_AML_ctr_18136_SA2

description:
1551
EGAR00003766198

value: hematopoietic

value: AML blasts


title: ChIP_CD34_17_2_SA2_529_1252_CTCF


title: Rat cortical neuron, Mock, 6h, rep2

description:
mock_b
log2CPM_filter_norm.txt


title: Rat cortical neuron, Pam2CSK4, 6h, rep2

description:
pam2_b
log2CPM_filter_norm.txt


title: ChIP_CD34_28_4_SA1_2259_4094_CTCF


title: Rat cortical neuron, Mock, 6h, rep1

description:
mock_a
log2CPM_filter_norm.txt


title: ChIP_CD34_27_3_SA1_2259_4094_CTCF


title: Control 4-cell rep2


title: Articular cartilage of 2-month-old mice_2


title: ChIP_CD34_18_1_RAD21_467_2031_CTCF


title: ChIP_CD34_21_2_SA1_2259_4094_CTCF


title: Control 4-cell rep1


title: Orc2-Flag ChIP-Exo from cells released from G1-phase (24min), biol rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
*library strategy: ChIP-Exo
Primary analysis RTA 2.11.3 and Secondary analysis bcl2fastq2_2.20.0
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to sacCer3 genome using Bowtie2 aligner (v. 2.3.5)
Bigwig files were generated for visualizing with genome browser using deeptools (version 3.2.1)
Normalisation of each sample to sequencing read depth using deeptools  --normalizeUsing CPM option. Strand seperated Bigwig files were generated for visualizing with genome browser using bedtools (version 2.27.1) and UCSC wigToBigWig program.
Assembly: sacCer3
Supplementary files format and content: Bigwig files of normalised data
Supplementary files format and content: Strand seperated Bigwig files of normalised data

organism: Saccharomyces cerevisiae

source_name: cells released from G1-phase (24min)

growth_protocol: Cells were grown in 100ml YPD from overnight cultures to OD600 0.6 at 220 rpm and 30°C followed by 2 hrs α-factor arrest at 25°C, 220 rpm and released in 100 ml warm media.

extract_protocol:
Lysates were prepared using standard procedures, sonicated chromatin clarified and Flag-tagged proteins immunprecipitated.
Immunoprecipitated DNA was treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation. After phosphorylation, the first adapter was ligated using T4 DNA Ligase and T4 Polynucleotidekinase. Gaps were filled with phi29 polymerase and 5’ DNA ends were digested using lambda exonuclease. DNA was eluted from resin, de-crosslinked and purified. The second adapter was ligated and DNA purified. After 18 cycles of amplification, DNA libraries were gel extracted using the NEB Monarch PCR & DNA Cleanup Kit according to the manufacturer’s instructions to allow elution with smaller volumes. Libraries were quantified using Qubit fluorometry (Thermo Fisher, dsDNA HS Assay) and qPCR (KAPA Illumina library quantification) before pooling and Illumina next generation sequencing.

treatment_protocol: cells were arrested in G1 using alpha-factor and releases (S) and G2 using Nocodazole

value: cells released from G1-phase (24min)

value: crosslinked culture, IP with anti-Flag F-1804, Sigma


title: ChIP_CD34_17_1_SA1_2259_4094_CTCF

value: cord blood


title: P300 siRNA POL(II) Late-8-cell rep2 ChIP


title: ChIP_CD34_14_1_SA1_2259_4094_CTCF

value: HSPC


title: Orc2-Flag ChIP-Exo from cells released from G1-phase (24min), biol rep1


title: ChIP_CD34_28_6_siCtrl_CTCF

value: wt

value: siCtrl


title: P300 siRNA POL(II) Late-8-cell rep1 ChIP


title: ChIP_CD34_14_2_SA2_529_1252_CTCF


title: P300 siRNA NaCr H3K18cr Late-8-cell rep2 ChIP

value: P300 knockdown NaCr rescue


title: IN_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep3

data_processing:
Primary analysis RTA 2.11.3 and Secondary analysis bcl2fastq2_2.20.0
Sequencing reads were mapped to sacCer3 genome using Bowtie2 aligner (v. 2.3.5)
Bigwig files were generated for visualizing with genome browser using bedtools (version 2.27.1) and UCSC wigToBigWig program.
Normalisation of each sample to sequencing read depth was done using bedtools (2.22.0) genomecov. -scale Scale factor used was generated by division of read depth by an arbitrary large number for each sample.
Assembly: sacCer3
Supplementary files format and content: Strand seperated Bigwig files of normalised data

growth_protocol: Cells were grown in 100ml YPD from overnight cultures to OD600 0.5 at 220 rpm and 23°C followed by a 3hrs shift to 37C.

extract_protocol:
ChIP lysates were prepared using standard procedures, sonicated chromatin clarified and Flag-tagged proteins immunprecipitated.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina following the manufacturer’s instructions

treatment_protocol: After 1 hr of the 3 hrs shift, α-factor or Nocodazole was added for the entire remainder of the 3hrs temperature shift to induce arrest in G1 or G2.


title: ChIP_CD34_27_4_siCtrl_CTCF


title: ChIP_AML_ctr_18367_SA2

description:
2305
EGAR00003766199

value: cohesin wt


title: ChIP_CD34_24_2_siCtrl_CTCF


title: ChIP_CD34_21_4_siCtrl_CTCF


title: IN_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep2


title: ChIP_CD34_19_2_siCtrl_CTCF


title: ChIP_CD34_22_3_siCtrl_CTCF


title: P300 siRNA NaCr H3K18cr Late-8-cell rep1 ChIP


title: P300 siRNA I1394G H3K18cr Late-8-cell rep2 ChIP

value: P300 knockdown I1394G rescue


title: IN_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep1


title: IN_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G1 at the non-permissive temperature 37C, biol re3


title: ChIP_CD34_14_4_Mock_CTCF

value: Mock


title: ChIP_CD34_18_4_siCtrl_CTCF


title: P300 siRNA I1394G H3K18cr Late-8-cell rep1 ChIP

value: preimplantation embryo


title: P300 siRNA H3K18cr Late-8-cell rep2 ChIP

value: P300 knockdown


title: ChIP_AML_SA2_29728_CTCF

description:
24603
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766137

value: STAG2 mut


title: ChIP_AML_ctr_9873_SA2

description:
2194
EGAR00003766194


title: ChIP_AML_SA2_27396_CTCF

description:
12567
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766136


title: ChIP_CD34_17_3_siCtrl_CTCF


title: IN_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep1


title: IN_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep2


title: ChIP_AML_SA2_9708_CTCF

description:
2193
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766134


title: ChIP_AML_SA2_24743_CTCF

description:
12514
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766135


title: P300 siRNA H3K18cr Late-8-cell rep1 ChIP


title: IN_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep3


title: Control POL(II) Late-8-cell rep2 ChIP

value: WT


title: ChIP_AML_SA2_25458_CTCF

description:
48380
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766132


title: IN_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep2


title: ChIP_AML_SA2_31501_CTCF

description:
27513
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766133


title: ChIP_AML_SA2_22464_CTCF

description:
7323
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766131


title: ChIP_AML_SA2_15640_CTCF

description:
2216
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766130


title: IN_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep1


title: ChIP_AML_SA2_15365_CTCF

description:
2292
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766129


title: ChIP_CD34_14_3_siCtrl_CTCF


title: IN_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep3


title: ChIP_AML_SA2_BB007_CTCF

description:
BB007
Allpat_CTCF.peaks.ann.filt.txt
SA2mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766128


title: Control H3K18cr Late-8-cell rep2 ChIP


title: ChIP_AML_Rad21_26830_CTCF

description:
12557
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766127

value: RAD21 mut


title: Control H3K18cr Late-8-cell rep1 ChIP


title: ChIP_AML_Rad21_23039_CTCF

description:
7314
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766126

value: hematopoietic


title: ChIP_AML_Rad21_UKR186_CTCF

description:
UKR186
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766125

value: AML blasts


title: IN_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep2


title: IN_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep1


title: Control H3K18cr Morula rep2 ChIP


title: ChIP_AML_Rad21_29047_CTCF

description:
19740
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766122


title: ChIP_AML_Rad21_28420_CTCF

description:
19733
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766121


title: IN_Orc2-FLAG ChIP_Seq from wt cells arrested in G2 at the non-permissive temperature 37C, biol rep1


title: ChIP_AML_Rad21_38455_CTCF

description:
41580a
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766124


title: IN_Orc2-FLAG ChIP_Seq from wt cells arrested in G2 at the non-permissive temperature 37C, biol rep3


title: ChIP_AML_Rad21_27650_CTCF

description:
19725
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766120


title: IN_Orc2-FLAG ChIP_Seq from wt cells arrested in G1 at the non-permissive temperature 37C, biol rep3


title: Control POL(II) Late-8-cell rep1 ChIP


title: IN_Orc2-FLAG ChIP_Seq from wt cells arrested in G2 at the non-permissive temperature 37C, biol rep2


title: Control H3K18cr Morula rep1 ChIP


title: ChIP_AML_ctr_21047_CTCF

description:
6246
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766118


title: ChIP_AML_ctr_19416_CTCF

description:
3488
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766117


title: Control H3K18cr MEF rep1 ChIP


title: ChIP_AML_ctr_19405_CTCF

description:
3323
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766116


title: ChIP_AML_Rad21_29992_CTCF

description:
27918
Allpat_CTCF.peaks.ann.filt.txt
RAD21mutvsCTRL.CTCF.Peaks_DESEQ.model.all.txt
EGAR00003766123


title: IN_Orc2-FLAG ChIP_Seq from wt cells arrested in G1 at the non-permissive temperature 37C, biol rep2


title: Wild type 18M rep3

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore (v.0.6.6)
Alignment to GRCm38.p13.101 or mm10 whole genome with STAR (v.2.7.1a) and read feature counting with RSEM (v.1.3.3)
FPKM were calculated using a fpkm function from DESeq2 (v.1.32.0) and differential gene expression by edgeR (v.3.36.0)
genome build: GRCm38.p13.101 (mm10)
processed data files format and content: txt files include normalized counts (FPKM)

source_name: mouse retina

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead using TruSeq Stranded mRNA Library Prep kit (Illumina, #20020595).
Each 100 ng total RNA from retinas were isolated and an oligo-dT primer including an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was carried out. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The double-stranded library was purified by employing AMPure magnetic beads (A63881, Beckman coulter, CA, USA) to get rid of all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components.

value: mouse retina

value: Kdm3b wild type


title: ChIP_AML_ctr_18136_CTCF

description:
1551
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766114


title: Control H3K18cr MEF rep2 ChIP


title: ChIP_AML_ctr_16911_CTCF

description:
2236
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766113


title: ChIP_AML_ctr_21290_CTCF

description:
5285
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766119


title: Wild type 18M rep2


title: IN_Orc2-FLAG ChIP_Seq from wt cells arrested in G1 at the non-permissive temperature 37C, biol rep1

value: crosslinked culture, IP with anti-Flag F-1804, Sigma


title: Kdm3b Hetero 12M rep3

value: Kdm3b heterogeneous gene


title: ChIP_AML_ctr_9873_CTCF

description:
2194
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766112


title: ChIP_AML_ctr_22023_CTCF

description:
6374
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766111


title: ChIP_AML_ctr_20899_CTCF

description:
5286
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766110


title: Wild type 18M rep1


title: ChIP_AML_ctr_18519_CTCF

description:
1747
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766115


title: IP_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep3


title: ChIP_AML_ctr_20180_CTCF

description:
4334
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766108


title: Wild type 12M rep1


title: IP_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep2


title: ChIP_AML_ctr_14094_CTCF

description:
2273
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766104


title: IP_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep1


title: ChIP_AML_ctr_19049_CTCF

description:
3313
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766106


title: ChIP_AML_ctr_19284_CTCF

description:
3319
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766107


title: ChIP_AML_ctr_18367_CTCF

description:
2305
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766105


title: Wild type 06M rep3


title: Wild type 06M rep1


title: ChIP_CD34_28_1_RAD21_467_2031_H3K27ac

description:
mergedCD34_H3K27ac.CD34.ann.table.txt
qstat.RAD21KDvsCTRL.upperQ0.95.cqn.CD34.txt
raw data cannot be deposited online

value: cord blood

value: HSPC

value: wt


title: IP_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep3


title: ChIP_AML_ctr_11374_CTCF

description:
2207
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766103

value: cohesin wt


title: ChIP_CD34_27_1_RAD21_467_2031_H3K27ac


title: Wild type 06M rep2


title: ChIP_CD34_22_1_RAD21_467_2031_H3K27ac


title: IP_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep2


title: IP_Orc2-FLAG ChIP_Seq from  cdc46-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep1


title: ChIP_CD34_18_1_RAD21_467_2031_H3K27ac


title: P300 siRNA Early-8-cell rep2


title: ChIP_CD34_28_5_SA2_529_1252_H3K27ac

description:
mergedCD34_H3K27ac.CD34.ann.table.txt
qstat.SA1KDvsCTRL.upperQ0.95.cqn.CD34.txt
raw data cannot be deposited online


title: ChIP_AML_ctr_20458_CTCF

description:
4338
Allpat_CTCF.peaks.ann.filt.txt
EGAR00003766109


title: Wild type 01M rep1


title: IP_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep3


title: ChIP_CD34_21_3_SA2_529_1252_H3K27ac


title: IP_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep2


title: AFB1-fed larvae, 5 day + 72h, replicate 4

city: Wageningen

first: Parth

last: Shah

state: Gelderland

address: Droevendaalsesteeg 1

department: Laboratory of Entomology

country: Netherlands

institute: Wageningen University

data_processing:
Raw data filtering was performed to remove reads with adaptor contamination.
Clean paired-end reads were mapped on Hermetia illucens genome (GCF_905115235.1) using STAR and default parameters.
Gene counts were obtained STAR (with gene count function) on the RefSeq assembly GCF_905115235.1.
Assembly: GCF_905115235.1
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

organism: Hermetia illucens

source_name: larvae

growth_protocol: The larvae of Hermetia illucens were reared at 16 h light / 8 h dark cycle at 27°C and 65% humidity.

extract_protocol:
Five replicates (of two pooled larvae each) were collected from control and AFB1-treatments, respectively at each time point and flash-frozen in liquid nitrogen. Total RNA was extracted with TriZol reagent and subjected to DNase treatment, protein purification and stored at -80 degree C. The quality of total RNA was evaluated using Agilent Bioanalyzer and DeNovix Bioanalyzer.
Library preparation was performed at BaseClear B.V. (Leiden, Netherlands). Sequencing libraries were sequenced paired-ended (150 bp read-length) on an Illumina NovaSeq 6000 platform.

treatment_protocol: Five-day old larvae were fed on either control or AFB1-spiked chickenfeed diet respectively. Samples were collected at 6 h, 24 h and 72 h post-treatment.

value: larvae

tag: developmental stage

value: 5 day + 72 h

value: AFB1-fed larvae


title: ChIP_CD34_20_5_SA2_529_1252_H3K27ac


title: ChIP_CD34_17_2_SA2_529_1252_H3K27ac


title: IP_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G2 at the non-permissive temperature 37C, biol rep1


title: Wild type 01M rep3


title: AFB1-fed larvae, 5 day + 72h, replicate 3


title: AFB1-fed larvae, 5 day + 72h, replicate 2


title: IP_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep3


title: ChIP_CD34_21_2_SA1_2259_4094_H3K27ac


title: ChIP_CD34_14_2_SA2_529_1252_H3K27ac


title: ChIP_CD34_17_1_SA1_2259_4094_H3K27ac


title: ChIP_CD34_14_1_SA1_2259_4094_H3K27ac


title: Wild type 01M rep2


title: IP_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep2


title: AFB1-fed larvae, 5 day + 72h, replicate 1


title: AFB1-fed larvae, 5 day + 24h, replicate 4

value: 5 day + 24 h


title: IP_Orc2-FLAG ChIP_Seq from  cdc6-1 cells arrested in G1 at the non-permissive temperature 37C, biol rep1


title: ChIP_CD34_28_6_siCtrl_H3K27ac

description:
mergedCD34_H3K27ac.CD34.ann.table.txt
raw data cannot be deposited online

value: siCtrl


title: IP_Orc2-FLAG ChIP_Seq from wt cells arrested in G2 at the non-permissive temperature 37C, biol rep3


title: ChIP_CD34_27_4_siCtrl_H3K27ac


title: ChIP_CD34_22_2_SA2_529_1252_H3K27ac


title: ChIP_CD34_24_2_siCtrl_H3K27ac


title: AFB1-fed larvae, 5 day + 24h, replicate 3


title: IP_Orc2-FLAG ChIP_Seq from wt cells arrested in G2 at the non-permissive temperature 37C, biol rep2


title: AFB1-fed larvae, 5 day + 24h, replicate 2


title: ChIP_CD34_28_4_SA1_2259_4094_H3K27ac


title: ChIP_CD34_27_3_SA1_2259_4094_H3K27ac


title: ChIP_CD34_21_4_siCtrl_H3K27ac


title: ChIP_CD34_17_3_siCtrl_H3K27ac


title: ChIP_CD34_19_2_siCtrl_H3K27ac


title: IP_Orc2-FLAG ChIP_Seq from wt cells arrested in G2 at the non-permissive temperature 37C, biol rep1


title: AFB1-fed larvae, 5 day + 24h, replicate 1


title: IP_Orc2-FLAG ChIP_Seq from wt cells arrested in G1 at the non-permissive temperature 37C, biol rep3


title: ChIP_CD34_14_4_Mock_H3K27ac


title: ChIP_CD34_18_4_siCtrl_H3K27ac


title: ChIP_CD34_14_3_siCtrl_H3K27ac


title: AFB1-fed larvae, 5 day + 6h, replicate 4

value: 5 day + 6 h


title: AFB1-fed larvae, 5 day + 6h, replicate 3


title: IP_Orc2-FLAG ChIP_Seq from wt cells arrested in G1 at the non-permissive temperature 37C, biol rep2


title: ChIP_CD34_22_3_siCtrl_H3K27ac


title: ChIP_AML_SA2_9708_H3K27ac

description:
2193
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766268

value: STAG2 mut


title: AFB1-fed larvae, 5 day + 6h, replicate 2


title: ChIP_AML_SA2_BB007_H3K27ac

description:
BB007
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766269

value: hematopoietic


title: Orc2-Flag ChIP-Exo from cells arrested in G2, rep2

data_processing:
Primary analysis RTA 2.11.3 and Secondary analysis bcl2fastq2_2.20.0
Sequencing was conducted on an Illumina HiSeq 2500 system with 50 base pair single-end reads
Sequencing reads were mapped to sacCer3 genome using Bowtie2 aligner (v. 2.3.5)
Bigwig files were generated for visualizing with genome browser using deeptools (version 3.2.1)
Normalisation of each sample to sequencing read depth using deeptools  --normalizeUsing CPM option.
Peaks were called using ChExMix software (v 0.45) .
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files of normalised data
Supplementary_files_format_and_content: Bed files with called peaks

source_name: crosslinked culture

treatment_protocol: cells were arrested in G1 using alpha-factor and G2 using Nocodazole

tag: chip antibody

value: anti-Flag F-1804, Sigma

tag: cell cycle status

value: arrested in G2


title: ChIP_AML_SA2_32635_H3K27ac

description:
36837
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766267

value: AML blasts


title: IP_Orc2-FLAG ChIP_Seq from wt cells arrested in G1 at the non-permissive temperature 37C, biol rep1

value: crosslinked culture, IP with anti-Flag F-1804, Sigma


title: ChIP_AML_SA2_31501_H3K27ac

description:
27513
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766266


title: ChIP_AML_SA2_29728_H3K27ac

description:
24603
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766265


title: Orc2-Flag ChIP-Exo from cells arrested in G2, rep1


title: ChIP_AML_SA2_28041_H3K27ac

description:
19892
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766264


title: Control larvae, 5 day + 72h, replicate 4

value: Untreated control


title: ChIP_AML_SA2_27493_H3K27ac

description:
48386
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766263


title: ChIP_AML_SA2_27396_H3K27ac

description:
12567
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766262


title: Orc2-Flag ChIP-Exo from cells arrested in G1, rep2

value: arrested in G1


title: Control larvae, 5 day + 72h, replicate 3


title: ChIP_AML_SA2_24743_H3K27ac

description:
12514
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766260


title: ChIP_AML_SA2_25458_H3K27ac

description:
48380
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766261


title: Orc2-Flag ChIP-Exo from cells arrested in G1, rep1


title: ChIP_AML_SA2_22464_H3K27ac

description:
7323
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766258


title: Control larvae, 5 day + 72h, replicate 1


title: ChIP_AML_SA2_22525_H3K27ac

description:
7325
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766259


title: Control larvae, 5 day + 72h, replicate 2


title: ChIP_AML_SA2_15640_H3K27ac

description:
2216
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766256


title: ChIP_AML_Rad21_UKR186_H3K27ac

description:
UKR186
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766254

value: RAD21 mut


title: ChIP_AML_SA2_15365_H3K27ac

description:
2292
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766255


title: ChIP_AML_Rad21_29992_H3K27ac

description:
27918
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766252


title: Mcm4-Flag ChIP-Exo from cells arrested in G1, rep1


title: ChIP_AML_Rad21_29047_H3K27ac

description:
19740
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766251


title: Mcm4-Flag ChIP-Exo from cells arrested in G1, rep2


title: ChIP_AML_Rad21_38455_H3K27ac

description:
41580a
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766253


title: Control larvae, 5 day + 24h, replicate 4


title: H4K16ac BJ-hTERT/HRAS day8 RepB

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

description: H4K16ac at day 8

data_processing:
Basecalls performed using the FastQC/MultiQC programs
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
Peak calling was performed against input sequences using EDD for H2AX ChIP (--write-log-ratios and --write-bin-scores options) and MACS2 for HDAC4, H2BK120ac and H4K16ac (--nomodel, --extsize 150 and -q 0.05 options). ChIP-seq replicates were compared using the Irreproducibility Discovery Rate (IDR) framework, with MACS2 narrow peaks as input and applying the following settings: --input-file-type narrowPeak, --rank signal.value, --output-file-type narrowPeak.
Assembly: hg38
Supplementary files format and content: Coverage tracks were generated using the bamCoverage (deepTools) tool, taking an alignment of reads as input (BAM file) and generating a coverage track (bigWig) as output, applying the following parameters: --outFileFormat bigwig --binSize 50 -p 10 --normalizeUsing RPKM

source_name: BJ

growth_protocol: BJ cells were grown in EMEM supplemented with 10% FBS, 2mM L-glutamine, penicillin–streptomycin and NEAA (Euroclone, Milan, Italy). For each ChIP, 3.2*10^6 cells were used.

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with the relative antibodies and 8ul protein A Dynabeads (ThermoFisher). Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Drmanac et al. (Science 2010, PMID 19892942) with combinatorial probe anchor ligation chemistry generating patterned nanoarrays of self-assembling DNA nanoballs. Briefly, after End repairing, A-tailing and Ad153 index adapter ligation of 50 ng size-selected DNA, DNA was puriefied with Ampure XP beads.  KAPA HiFi Hot Start Ready Mix was used for pre-PCR amlification: 95 °C 3 ', (98 °C 20s, 60 °C 15 s, 72 °C 30s) 8 cycles, 72 °C 10'. 4 °C hold thermal cycles using , the product was purified with 1X Ampure XP beads and quantified with Qubit BR ds DNA kit. For Illumina platform, Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSseq550 following the manufacturer's protocols.    Exome capture  The hybridization of BGISEQ-500 library was performed according to the Agilent SureSelect protocol with the following optimized parameters: 1000 ng purified DNA was used for hybridization, the index block and PCR block of Agilent were replaced by a corresponding Ad153_index block (one for all indexes) and Ad153_PCR block. KAPA HiFi Hot Start Ready Mix was used for Post-PCR following the 95 °C 3 min, (98 °C 20s, 60 °C 15 s, 72 °C 30s) 13 cycles, 72 °C 10 min, 4 °C hold thermal cycle. Post-PCR products were purified and single strand DNA (ssDNA) circle was performed by using adapters; T4 DNA ligae was used for ligation (NEB, Ipswich, Massachusetts). Uncirculated DNA was digested with Exo I and Exo III. The libraries were purified with 168 μL of Ampure XP beads and quantified with Qubit BR ssDNA kit. The resulting ssDNA circle is the final library. Rolling circle amplification (RCA) was performed on ssDNA with Phi29 DNA polymerase (Thermo-Fisher, Waltham, Massachusetts) to generate DNA nanoballs (DNBs).
DNBseq Nanoballs library and TruSeq ChIP Library

treatment_protocol: Cells were seeded in 200 mm plates. 4-OHT was used to induce HRAS (or empty ER) for 2 days or 8 days. At the moment of the ChIP, cross-linking was performed for 15' with 1% formaldeyde (Sigma-Aldrich, Darmstadt, Germany) and then blocked with 125 mM Glycine (Sigma-Aldrich, Darmstadt, Germany).

value: foreskin fibroblasts

tag: passages

value: below 20


title: ChIP_AML_Rad21_27650_H3K27ac

description:
19725
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766249


title: Control larvae, 5 day + 24h, replicate 2

value: larvae


title: Control larvae, 5 day + 24h, replicate 1


title: ChIP_AML_SA2_19142_H3K27ac

description:
3315
Allpat_H3K27ac.peaks.ann.txt
qstat.SA2mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766257


title: ChIP_AML_Rad21_23039_H3K27ac

description:
7314
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766247


title: H4K16ac BJ-hTERT day8 RepB

description: H4K16ac at day 8


title: ChIP_AML_Rad21_28420_H3K27ac

description:
19733
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766250


title: ChIP_AML_ctr_9873_H3K27ac

description:
2194
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766246

value: cohesin wt


title: Control larvae, 5 day + 6h, replicate 3


title: H2BK120ac BJ-hTERT/HRAS day8 RepB

description: H2BK120ac at day 8

value: H2BK120ac (Active Motif AB_2615080)


title: ChIP_AML_ctr_22023_H3K27ac

description:
6374
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766245


title: ChIP_AML_ctr_20899_H3K27ac

description:
5286
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766242


title: Control larvae, 5 day + 6h, replicate 2


title: ChIP_AML_ctr_21290_H3K27ac

description:
5285
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766244


title: H2BK120ac BJ-hTERT day8 RepB

description: H2BK120ac at day 8


title: Control larvae, 5 day + 6h, replicate 1


title: ChIP_AML_ctr_20458_H3K27ac

description:
4338
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766241


title: ChIP_AML_ctr_20180_H3K27ac

description:
4334
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766240


title: Pan-GFP,CUT&Run,anti-GFP,Rep3

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

description:
Pan_IgG-3
normalized bigwig file
pan.bw

library_source: other

data_processing:
*library strategy: CUT&Run
RNA-Star alignment to dm6 reference with default setting
Gathering counts with FeatureCount with default setting
DESeq2 to normalize counts and generate differential gene expression table with p.adj < 0.05 filter
CUT&Run reads went through nf-core/cutandrun pipeline for trimming, alignment and deduplication
MACS3 for peak calling and normalization
Assembly: dm6
Supplementary files format and content: tab delimited table, count table
Supplementary files format and content: bigwig file, normalized CUT&Run reads

molecule: other

organism: Drosophila melanogaster

source_name: 3rd instar larval wing imaginal disc

extract_protocol:
Total RNA was extracted by standard protocol with Trizol; 1ug RNA was used for librariy construction
RNA-seq library was prepared by using Illumina TruSeq Stranded Total RNA kit, CUT&Run library was prepared by using illumina TruSeq ChIP library preparation kit

value: 3rd instar larval wing imaginal disc

value: Pan-EGFP


title: ChIP_AML_ctr_21047_H3K27ac

description:
6246
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766243


title: gammaH2AX BJ-hTERT/HRAS day8 RepB

description: Estimation of DSBs at day 8

value: gammaH2AX (Millipore PA5-28778)


title: gammaH2AX BJ-hTERT/HRAS/HDAC4 day8 RepB

description: Estimation of DSBs at day 8


title: ChIP_AML_ctr_19416_H3K27ac

description:
3488
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766239


title: Pan-GFP,CUT&Run,anti-GFP,Rep2

description:
Pan_IgG-2
normalized bigwig file
pan.bw


title: AFB1-fed larvae, 5 day + 6h, replicate 1

value: 5 day + 6 h

value: AFB1-fed larvae


title: ChIP_AML_ctr_19405_H3K27ac

description:
3323
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766238

value: hematopoietic


title: ChIP_AML_ctr_19284_H3K27ac

description:
3319
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766237


title: gammaH2AX BJ-hTERT day8 RepB

description: Estimation of DSBs at day 8


title: H4K16ac BJ-hTERT/HRAS/HDAC4 day8 RepB

description: H4K16ac at day 8


title: ChIP_AML_ctr_19049_H3K27ac

description:
3313
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766236


title: HDAC4 BJ-hTERT/HRAS/HDAC4 day2 RepB

description: HDAC4 binding at day 2

value: HDAC4 (Paroni et al, 2004 PMID 15075374 )


title: Pan-GFP,CUT&Run,anti-GFP,Rep1

description:
Pan_IgG-1
normalized bigwig file
pan.bw


title: ChIP_AML_ctr_18519_H3K27ac

description:
1747
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766235

value: AML blasts


title: ChIP_AML_Rad21_26830_H3K27ac

description:
12557
Allpat_H3K27ac.peaks.ann.txt
qstat.RAD21mutvsCTRL.upperQ0.95.cqn.txt
EGAR00003766248


title: Control larvae, 5 day + 24h, replicate 3

value: 5 day + 24 h


title: Control larvae, 5 day + 6h, replicate 4

value: Untreated control


title: H2BK120ac BJ-hTERT/HRAS/HDAC4 day8 RepB

description: H2BK120ac at day 8


title: ChIP_AML_ctr_18367_H3K27ac

description:
2305
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766234


title: Pan-GFP,CUT&Run,IgG,Rep3

description:
Pan_GFP-3
normalized bigwig file
pan.bw


title: HDAC4 BJ-hTERT/HRAS day2 RepB

description: HDAC4 binding at day 2


title: H2BK120ac BJ-hTERT/HRAS/HDAC4 day2 RepB

description: H2BK120ac at day 2


title: ChIP_AML_ctr_14094_H3K27ac

description:
2273
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766231


title: HDAC4 BJ-hTERT day2 RepB

description: HDAC4 binding at day 2


title: H2BK120ac BJ-hTERT day2 RepB

description: H2BK120ac at day 2


title: ChIP_AML_ctr_18136_H3K27ac

description:
1551
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766233


title: ChIP_CD34_17_2_SA2_529_1252_RAD21

description:
CD34_RAD21.peaks.ann.txt
qstat_SA1KDvsCTRL.RAD21.Peaks_edgeR.all.txt
raw data cannot be deposited online

value: cord blood

value: HSPC

value: wt


title: Pan-GFP,CUT&Run,IgG,Rep2

description:
Pan_GFP-2
normalized bigwig file
pan.bw


title: axn RNAi,RNA-seq,Rep2 [a2]

description:
axn RNAi 2
axn slmb RNAi count table
axni_slmbi_cts.txt

data_processing:
RNA-Star alignment to dm6 reference with default setting
Gathering counts with FeatureCount with default setting
DESeq2 to normalize counts and generate differential gene expression table with p.adj < 0.05 filter
CUT&Run reads went through nf-core/cutandrun pipeline for trimming, alignment and deduplication
MACS3 for peak calling and normalization
Assembly: dm6
Supplementary files format and content: tab delimited table, count table
Supplementary files format and content: bigwig file, normalized CUT&Run reads

source_name: 3rd instar larval fat body

value: 3rd instar larval fat body

value: SREBP-Gal4>axn RNAi


title: ChIP_CD34_14_2_SA2_529_1252_RAD21

data_processing:
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5) in very sensitive mode
Samtools (v.1.6) was used to remove lower quality alignments with mapQ=<10 and sorting
HOMER style tagDirectories were generated using HOMER makeTagDirectory (-checkGC and -unique). For AML samples, tag directories were corrected for copy number varations based on FreeC output genereated from DNA-Input-Sequencing data.
Bigwig coverage tracks  were generated using HOMER’s makeUCSCfile function. For HSPC RAD21/CTCF/MED12/PU1/H3K27ac data sets, BigWigs were aditionally scaled based on median coverage across the top 5% common peaks detected in all samples.
For focal peaks, HOMER was used to call peaks (factor mode; -fdr 0.00001 -tbp). For region peaks, i.e. H3K27ac, HOMER was used for peak calling in region mode (-fdr 0.00001, -size 250, -L 0 -F 5 -minDist 350, -tbp -ntagThreshold 10). In case of AMLs, peak calling was performed in individual tag directories, in case of HSPCs condition-merged tag directories were used. For each data set, peak files of all conditions/groups were merged and filtered for low-mappability and blacklisted regions to generate reference peak sets. Subsequently, the individual samples were annotated to combined peak set to obtain peak coverage tables for each data set separetely.
Annotation tables with peak coverage were used for differential analysis using DESeq2 or edgeR to calculate differential Peak Coverage between controls and associated cohesin deficient samples. For H3K27ac data sets, counts were additionally normalized  for length and GC content using offsets generated by the cqn R package, which were implemented in edgeR. For STAG1 and STAG2 HPSC datasets differential analysis was performed using HOMER’s getDiffExpression.pl routine with the -batch, -rlog and -normtotal options enabled. The same applies to RAD21 ChIP-seq in RAD21 KD HSPCs.
Assembly: GRCh38.p10
Supplementary files format and content: bigWig coverage track files for individual samples
Supplementary files format and content: tab-delimited file containing peak coordinates and coverage counts for each sample (HOMER annotation output)
Supplementary files format and content: tab-delimited file containing peak coordinates and DESeq2 or edgeR statistics for differential peak testing


title: ChIP_CD34_28_4_SA1_2259_4094_RAD21


title: Input BJ-hTERT day8 RepB

description: Input

value: foreskin fibroblasts

value: below 20


title: Input BJ-hTERT/HRAS/HDAC4 day2 RepB

description: Input


title: ChIP_AML_ctr_16911_H3K27ac

description:
2236
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766232

value: cohesin wt


title: ChIP_AML_ctr_11374_H3K27ac

description:
2207
Allpat_H3K27ac.peaks.ann.txt
EGAR00003766230


title: Input BJ-hTERT/HRAS/HDAC4 day8 RepB

description: Input


title: SREBP-Gal4 control,RNA-seq,Rep2 [w2]

description:
SREBP-Gal4 control 2
axn slmb RNAi count table
axni_slmbi_cts.txt


title: ChIP_CD34_21_3_SA2_529_1252_RAD21


title: axn RNAi,RNA-seq,Rep1 [a1]

description:
axn RNAi 1
axn slmb RNAi count table
axni_slmbi_cts.txt


title: slmb RNAi,RNA-seq,Rep1 [s1]

description:
slmb RNAi 1
axn slmb RNAi count table
axni_slmbi_cts.txt

value: SREBP-Gal4>slmb RNAi


title: ChIP_CD34_28_5_SA2_529_1252_RAD21


title: ChIP_CD34_22_2_SA2_529_1252_RAD21


title: HDAC4 BJ-hTERT/HRAS/HDAC4 day2 RepA

description: HDAC4 binding at day 2


title: ChIP_CD34_27_3_SA1_2259_4094_RAD21


title: ChIP_CD34_18_1_RAD21_467_2031_RAD21

description:
CD34_RAD21.peaks.ann.txt
RAD21KDvsCTRL.RAD21.Peaks_DESEQn2t.model.all.txt
raw data cannot be deposited online


title: Input BJ-hTERT/HRAS day8 RepB

description: Input


title: axn RNAi,RNA-seq,Rep3 [a3]

description:
axn RNAi 3
axn slmb RNAi count table
axni_slmbi_cts.txt


title: ChIP_CD34_17_1_SA1_2259_4094_RAD21


title: SREBP-Gal4 control,RNA-seq,Rep3 [w3]

description:
SREBP-Gal4 control 3
axn slmb RNAi count table
axni_slmbi_cts.txt


title: ChIP_CD34_14_1_SA1_2259_4094_RAD21


title: Input BJ-hTERT day2 RepB

description: Input


title: ChIP_CD34_27_4_siCtrl_RAD21

description:
CD34_RAD21.peaks.ann.txt
raw data cannot be deposited online

value: siCtrl


title: ChIP_CD34_28_6_siCtrl_RAD21


title: ChIP_CD34_21_2_SA1_2259_4094_RAD21


title: Input BJ-hTERT/HRAS day2 RepB

description: Input


title: ChIP_CD34_20_5_SA2_529_1252_RAD21


title: SREBP-Gal4 control,RNA-seq,Rep1 [w1]

description:
SREBP-Gal4 control 1
axn slmb RNAi count table
axni_slmbi_cts.txt


title: Kdm3b Hetero 12M scRNA

data_processing:
Fastq files were aligned to GRCm38 (index provided by 10x) using Cellranger (v.6.1.2)
For QC, filtering, normalization, batch effect correction and doublet exclusion, Scanpy (v.1.9.1), anndata (v.0.8.0) and scrublet (v.0.2.3) were used.
The veloicty of scRNA are calculated by scVelo (v.0.2.4).
genome build: GRCm38
processed data files format and content: txt file include gene list, fold change and P value of each clusters

extract_protocol:
Dissociated retina cells were filtered out using 30 um cell strainer (miltenyi biotech, cat no. 130-098-458), and washed 2 times with cold Ca2+ and Mg2+ free 0.04 % BSA/PBS at 300 g for 5 min at 4 °C. After the final centrifugation, supernatant was removed, and dead cells were removed from cells using Dead cells removal kit (miltenyi biotech, cat no. 130-090-101) and MS columns (miltenyi biotech, cat no. 130-042-201) according to the manufacture’s protocol. Then, the collected live cells were gently resuspended in 1ml of ice cold 0.04 % BSA/PBS and counted with a LUNA-FX7™ Automated Fluorescence Cell Counter (logos boisystems).
According to the 10x Chromium Single Cell 3’ v3.1 protocol (10x Genomics, document no. CG000315) Single Cell RNA-seq libraries were prepared using the 10x Chromium controller and Next Gem Single cell 3’ Reagent v3.1 kits (10x genomics, PN-1000123). Briefly, the cell suspension (target recovery 10,000 cells) was mixed with reverse transcription master mix and loaded with Single Cell 3′ Gel Beads and Partitioning Oil into a Single Cell G Chip (10x genomics, PN-1000120) to generate single-cell Gel Bead-in-emulsion (GEM). Poly-adenylated mRNA from single cells were uniquely barcoded and reverse-transcribed within GEM. After barcoded full-length cDNA was generated from mRNA through GEM-RT incubation, the barcoded cDNA molecules were amplified with PCR. For 3’ Gene Expression Library construction, the enriched cDNA was sequentially subjected to the enzymatic fragmentation, end-repair, A-tailing, adaptor ligation and index PCR.

treatment_protocol: Eyes were enucleated from animals and retinas dissected in fresh and cold 1X PBS. Dissected retinas were transferred to 1 ml of accutase (Gibco, #A1110501-01) per retina and incubated at 37 °C for 20 min at shaking heat block (1,000 rpm), with gentle pipetting performed every 10 minutes.

value: mouse retina

value: Kdm3b heterogeneous gene


title: Wild type 18M scRNA

value: Kdm3b wild type


title: HDAC4 BJ-hTERT day2 RepA

description: HDAC4 binding at day 2

value: HDAC4 (Paroni et al, 2004 PMID 15075374 )


title: ChIP_CD34_22_3_siCtrl_RAD21


title: HDAC4 BJ-hTERT/HRAS day2 RepA

description: HDAC4 binding at day 2


title: ChIP_CD34_21_4_siCtrl_RAD21


title: H2BK120ac BJ-hTERT/HRAS day2 RepA

description: H2BK120ac at day 2

value: H2BK120ac (Active Motif AB_2615080)


title: ChIP_AML_SA2_BB007_Rad21

description:
BB007
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766102

value: hematopoietic

value: AML blasts

value: STAG2 mut


title: slmb RNAi,RNA-seq,Rep2 [s2]

description:
slmb RNAi 2
axn slmb RNAi count table
axni_slmbi_cts.txt


title: ChIP_CD34_19_2_siCtrl_RAD21

value: cord blood

value: HSPC


title: Pan-GFP,CUT&Run,IgG,Rep1

description:
Pan_GFP-1
normalized bigwig file
pan.bw

value: 3rd instar larval wing imaginal disc

value: Pan-EGFP


title: ChIP_CD34_27_1_RAD21_467_2031_RAD21

value: wt


title: ChIP_AML_SA2_31501_Rad21

description:
27513
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766100


title: Wild type 01M scRNA


title: H2BK120ac BJ-hTERT/HRAS day2 RepB

description: H2BK120ac at day 2

value: foreskin fibroblasts

value: below 20


title: ChIP_CD34_28_1_RAD21_467_2031_RAD21


title: slmb RNAi,RNA-seq,Rep3 [s3]

description:
slmb RNAi 3
axn slmb RNAi count table
axni_slmbi_cts.txt

value: 3rd instar larval fat body

value: SREBP-Gal4>slmb RNAi


title: ChIP_CD34_18_4_siCtrl_RAD21

value: siCtrl


title: ChIP_CD34_22_1_RAD21_467_2031_RAD21


title: H2BK120ac BJ-hTERT/HRAS/HDAC4 day2 RepA

description: H2BK120ac at day 2


title: ChIP_AML_SA2_28041_Rad21

description:
19892
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766098


title: ChIP_CD34_14_4_Mock_RAD21


title: ChIP_CD34_17_3_siCtrl_RAD21


title: ChIP_CD34_24_2_siCtrl_RAD21


title: Wild type 12M scRNA

value: mouse retina


title: ChIP_CD34_14_3_siCtrl_RAD21


title: ChIP_AML_SA2_25458_Rad21

description:
48380
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766095


title: ChIP_AML_SA2_32635_Rad21

description:
36837
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766101


title: ChIP_AML_SA2_29728_Rad21

description:
24603
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766099


title: H2BK120ac BJ-hTERT day2 RepA

description: H2BK120ac at day 2


title: Input BJ-hTERT day2 RepA

description: Input


title: Input BJ-hTERT/HRAS/HDAC4 day2 RepA

description: Input


title: ChIP_AML_SA2_27493_Rad21

description:
48386
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766097


title: ChIP_AML_SA2_9708_Rad21

description:
2193
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766088


title: ChIP_AML_Rad21_38455_Rad21

description:
41580a
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766085

value: RAD21 mut


title: ChIP_AML_Rad21_UKR186_Rad21

description:
UKR186
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766086


title: Input BJ-hTERT/HRAS day2 RepA

description: Input


title: control

city: SUITA

first: WANG

last: YAN

state: OSAKA

address: 2-2 YAMADAOKA

country: Japan

institute: Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode. Illumina RTA v3.4.4 software was used for base calling. Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18. Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: RPKM values for each sample

source_name: Ovary

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Venlo, Netherlands).
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: Ovary

value: Ovarian clear cell carcinoma

value: No drugs


title: As2O3_1uM

value: As2O3 1uM 48 h


title: ChIP_AML_Rad21_29047_Rad21

description:
19740
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766083

extract_protocol:
Cells were fixated using 0.5M DSG and 1% formaldehyde. Chromatin was sheared using Branson Sonifier 250. ChIP was performed with lysate of 2 Mio cells using a target specific antibody (anti-RAD21ab992 (abcam), anti-H3K27ac ab4729 (abcam), anti-CTCF 2899S (Cell Signaling), anti-STAG2 (custom produced), anti-STAG1 (custom produced), anti-MED12 (custom produced), anti-PU.1 sc352 (santa cruz)) and ProteinA Dynbeads. After de-crosslinking and proteinase K digest, DNA was purified using Monarch PCR & DNA clean-up kit (NEB).
Libraries were generated using the NEBNextUltra II DNA Library Prep Kit for Illumina with all available input material and 11 PCR cycles for amplification.

value: hematopoietic

value: AML blasts


title: ChIP_AML_SA2_27396_Rad21

description:
12567
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766096

value: STAG2 mut


title: ChIP_AML_Rad21_28420_Rad21

description:
19733
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766082


title: ChIP_AML_SA2_22525_Rad21

description:
7325
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766093


title: ChIP_AML_SA2_19142_Rad21

description:
3315
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766091


title: HiC_CD34_28_1_RAD21_KD

description:
RAD21KDvsCTRL.merged.loop.scores.txt
RAD21KDvsCTRL.normTotalaverage.merged.loop.scores.txt
RAD21KDvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_CD34_rad21_10kb.hic
raw data cannot be deposited online

data_processing:
Reads were trimmed for GATC sequences using Skewer (v0.2.2)
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5).
HOMER style tagDirectories were generated using HOMER makeTagDirectory (-checkGC and -unique) and filtered using “-restrictionSite GATC -both -genome hg38 -removePEbg -removeSelfLigation -removeSpikes 10000 5“ options
HOMERs findTADsAndLoops.pl  was run to determine loop positions which were subsetquently merged to obtian consensus positions. Individual tag directories were scored for merged loop positions using findTADsAndLoops.pl -score function in default and normTotal mode. Sex chromosomes (X/Y) were filtered out after this step.
DESeq2 analysis was run on combined loop score tables of CTRL-AMLs vs. Either STAG2 or RAD21-mutant AMLs implementing a normalization factor calculated by dividing total scores from scoring to total counts by total scores derived from the regular interaction normalized scoring
For visualization of interactions, Hi-C data was analyzed using the FAN-C v.0.9.25 suite. The genome was binned at 10kb resolution and Hi-C matrices summarizing the number of valid pairs per bin were constructed and merged by patient group (.hic files)
Assembly: GRCh38.p10
Supplementary files format and content: Tab delimited file containing loop coordinates and loop scores for individual samples generated by HOMER with default HiC normalization (merged.loop.scores)
Supplementary files format and content: Tab delimited file containing loop coordinates and loop scores for individual samples generated by HOMER with normTotal HiC normalization (.normTotalaverage.merged.loop.scores)
Supplementary files format and content: Tab delimited file containing loop coordinates and DESeq2 differnetial loop statistics testing STAG2/RAD21-mutant AMLs vs CTRL-AMLs  or cohesin depleted HSPCs (SA1/SA2/RAD21 KD) vs CTRL HSPCs (DESeq.norm2Total.loopcoords2.txt)
Supplementary files format and content: .hic file generated by FAN-C at 10 kb resolution

extract_protocol:
2Mio Cells were fixated using 1% formaldehyde. Nuclei were extracted, a restriction digest using DpnII was performed, followed by incorporation of biotin-dATP and in situ proximity ligation using T4 DNA ligase. Ligated fragments were sheared on a Covaris S series sonicator and biotionylated fragments were purified using MyOne Streptavidin T1 Dynabeads.
Libraries were constructed on-bead following an in-house protocol with 12 cycles of PCR amplification using NEBNext High-Fidelity Q5 2x PCR Mix and Bioo Nextflex DNA sequencing adapters .

value: cord blood

value: HSPC


title: GSK458_0_1uM


title: ChIP_AML_SA2_15365_Rad21

description:
2292
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766089


title: ChIP_AML_Rad21_26830_Rad21

description:
12557
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766080


title: ChIP_AML_SA2_24743_Rad21

description:
12514
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766094


title: As2O3_1uM_GSK458_0_1uM


title: ChIP_AML_SA2_15640_Rad21

description:
2216
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766090


title: ChIP_AML_Rad21_23039_Rad21

description:
7314
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766079


title: ChIP_AML_Rad21_AML0117_Rad21

description:
AML0117
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766087


title: ChIP_AML_Rad21_29992_Rad21

description:
27918
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766084


title: FGF replicate 2

city: Guangzhou

first: LIHUA

last: CHEN

state: Guangdong

address: Guangzhou International Bioland

institute: Guangzhou Laboratory

description: 10x genomics

data_processing:
Raw FASTAQ files were processed using the Cell Ranger pipeline (v4.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references) with the default options
To filter out low quality cells, only cells expressing more than 200 genes (defined as genes detected in at least 3 cells) and less than 20% mitochondrial genes were selected. Datasets were integrated based on 'anchors' identified between datasets (nfeatures=2000, normalization.method='SCT') before performing linear dimension reduction by principal component (PC) analysis. The top 30 PCs were used in a Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction.
Assembly: GRCh38
Supplementary files format and content: Matrix files and Tab-separated values files

source_name: delta cell-containing islet organoids

extract_protocol:
Briefly, S7D14 cell clusters were dispersed with TrpLE. Single cells with more than 85% viability were adjusted to 1,000 cells per μL. Approximately 16,000 cells were added to each channel of a 10X loading chip and then approximately 10,000 cells were captured.
Single-cell libraries were constructed using the Single Cell 3 Library & Gel Bead Kit v.3 according to the manufacturer's instructions (10X Genomics)120. Briefly, S7D14 cell clusters were dispersed with TrpLE. Single cells with more than 85% viability were adjusted to 1,000 cells per μL. Approximately 16,000 cells were added to each channel of a 10X loading chip and then approximately 10,000 cells were captured. The captured cells were divided into Gel Beads in Emulsion (GEMs) and lysed, and the isolated RNA was reverse transcribed, barcoded, and amplified.

value: delta cell-containing islet organoids

value: islet cells


title: FGF replicate 1

description: 10x genomics


title: ChIP_AML_ctr_22874_Rad21

description:
7326
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766078

value: cohesin wt


title: ChIP_AML_ctr_21290_Rad21

description:
5285
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766075


title: HiC_CD34_27_1_RAD21_KD

source_name: cord blood

value: wt


title: HiC_CD34_18_1_RAD21_KD


title: ChIP_AML_ctr_22759_Rad21

description:
7308
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766077


title: HiC_CD34_20_1_RAD21_KD


title: ChIP_AML_Rad21_27650_Rad21

description:
19725
Allpat_RAD21.peaks.stringent.ann.filt.txt
RAD21mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766081


title: ChIP_AML_ctr_19504_Rad21

description:
3326
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766070


title: HiC_CD34_28_5_SA2_KD

description:
SA2KDvsCTRL.merged.loop.scores.txt
SA2KDvsCTRL.normTotalaverage.merged.loop.scores.txt
SA2KDvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_CD34_stag2_10kb.hic
raw data cannot be deposited online


title: ChIP_AML_ctr_19416_Rad21

description:
3488
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766069


title: ChIP_AML_SA2_22464_Rad21

description:
7323
Allpat_RAD21.peaks.stringent.ann.filt.txt
SA2mutvsCTRL.RAD21.stringentPeaks_DESEQ.model.all.txt
EGAR00003766092


title: HiC_CD34_22_2_SA2_KD


title: ChIP_AML_ctr_22023_Rad21

description:
6374
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766076


title: ChIP_AML_ctr_19405_Rad21

description:
3323
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766068


title: ChIP_AML_ctr_19049_Rad21

description:
3313
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766066


title: ChIP_AML_ctr_20899_Rad21

description:
5286
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766073


title: HiC_CD34_22_1_RAD21_KD

description:
RAD21KDvsCTRL.merged.loop.scores.txt
RAD21KDvsCTRL.normTotalaverage.merged.loop.scores.txt
RAD21KDvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_CD34_rad21_10kb.hic
raw data cannot be deposited online


title: ChIP_AML_ctr_20458_Rad21

description:
4338
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766072


title: HiC_CD34_21_3_SA2_KD


title: ChIP_AML_ctr_20180_Rad21

description:
4334
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766071


title: ChIP_AML_ctr_21047_Rad21

description:
6246
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766074


title: HiC_CD34_20_5_SA2_KD


title: HiC_CD34_17_2_SA2_KD


title: ChIP_AML_ctr_18367_Rad21

description:
2305
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766064


title: ChIP_AML_ctr_18519_Rad21

description:
1747
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766065


title: ChIP_AML_ctr_14094_Rad21

description:
2273
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766061


title: ChIP_AML_ctr_18136_Rad21

description:
1551
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766063


title: HiC_CD34_14_2_SA2_KD


title: ChIP_AML_ctr_11374_Rad21

description:
2207
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766060


title: ChIP_IN_AML_RAD21_UKR186

description:
UKR186
EGAR00003766182

data_processing:
Sequences wer aligned to the human reference genome (GRCh38.p10) using bowtie2 (v. 2.4.5) in very sensitive mode
Samtools (v.1.6) was used to remove lower quality alignments with mapQ=<10 and sorting
FREEC (v. 11.0) 41 was run on the generated sam files including mappability filtering (unique match =TRUE) based on a hg38 mappabiltiy track created with the GEM library to optain copy number variations.
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited files containing  position, copy number and type of CNV (FreeC output)
Library strategy: low pass whole genome DNA-seq

extract_protocol:
DNA was is extracted using AllPrep DNA/RNA mini kit (Qiagen). 32.5ng of DNA was sheared to 200bp using the Covaris S-series sonication device.
DNA libriaries were generated using the NebNext library preparation kit (NEB).

treatment_protocol: PBMCS were extracted from bone marrow or whole blood samples using Lymphoprep at the timepoint of first diagnosis and viably frozen.


title: HiC_CD34_27_3_SA1_KD

description:
SA1KDvsCTRL.merged.loop.scores.txt
SA1KDvsCTRL.normTotalaverage.merged.loop.scores.txt
SA1KDvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_CD34_stag1_10kb.hic
raw data cannot be deposited online


title: ChIP_AML_ctr_9873_Rad21

description:
2194
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766058


title: ChIP_IN_AML_SA2_BB007

description:
BB007
EGAR00003766181


title: ChIP_IN_AML_RAD21_AML0117

description:
AML0117
EGAR00003766180


title: HiC_CD34_28_4_SA1_KD


title: ChIP_AML_ctr_19284_Rad21

description:
3319
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766067


title: ChIP_IN_AML_RAD21_38455

description:
41580a
EGAR00003766179


title: ChIP_IN_AML_SA2_32635

description:
36837
EGAR00003766178


title: HiC_CD34_20_4_SA1_KD


title: HiC_CD34_21_2_SA1_KD


title: ChIP_IN_AML_RAD21_29992

description:
27918
EGAR00003766176


title: ChIP_IN_AML_SA2_29728

description:
24603
EGAR00003766175


title: ChIP_IN_AML_SA2_28041

description:
19892
EGAR00003766172


title: ChIP_IN_AML_RAD21_29047

description:
19740
EGAR00003766174


title: ChIP_IN_AML_RAD21_28420

description:
19733
EGAR00003766173


title: HiC_CD34_28_6_siCtrl

description:
CD34.merged.loop.scores.txt
CD34.normTotalaverage.merged.loop.scores.txt
SA2KDvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_CD34_siCtrl_10kb.hic
raw data cannot be deposited online


title: ChIP_IN_AML_SA2_31501

description:
27513
EGAR00003766177


title: ChIP_IN_AML_RAD21_27650

description:
19725
EGAR00003766171


title: ChIP_IN_AML_SA2_27493

description:
48386
EGAR00003766170


title: ChIP_AML_ctr_16911_Rad21

description:
2236
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766062


title: HiC_CD34_22_3_siCtrl


title: HiC_CD34_27_4_siCtrl


title: ChIP_IN_AML_SA2_27396

description:
12567
EGAR00003766169


title: ChIP_AML_ctr_10156_Rad21

description:
2195
Allpat_RAD21.peaks.stringent.ann.filt.txt
EGAR00003766059


title: ChIP_IN_AML_RAD21_26830

description:
12557
EGAR00003766168


title: ChIP_IN_AML_SA2_24743

description:
12514
EGAR00003766166


title: ChIP_IN_AML_SA2_25458

description:
48380
EGAR00003766167


title: ChIP_IN_AML_RAD21_23039

description:
7314
EGAR00003766165


title: HiC_CD34_17_1_SA1_KD


title: ChIP_IN_AML_ctr_22874

description:
7326
EGAR00003766164


title: ChIP_IN_AML_SA2_22525

description:
7325
EGAR00003766162


title: ChIP_IN_AML_ctr_22759

description:
7308
EGAR00003766163


title: HiC_CD34_20_6_siCtrl


title: HiC_CD34_18_4_siCtrl


title: HiC_CD34_17_3_siCtrl


title: ChIP_IN_AML_ctr_21290

description:
5285
EGAR00003766159


title: ChIP_IN_AML_SA2_22464

description:
7323
EGAR00003766161


title: ChIP_IN_AML_ctr_22023

description:
6374
EGAR00003766160


title: HiC_CD34_14_1_SA1_KD


title: ChIP_IN_AML_ctr_21047

description:
6246
EGAR00003766158


title: ChIP_IN_AML_ctr_20458

description:
4338
EGAR00003766156


title: HiC_AML_SA2_29728

description:
24603
CohAML_CTRL_SA2_merged.loop.scores.XYrm.txt
CohAML_CTRL_SA2_merged.normTotalaverage.loop.scores.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_sa2_mut_10kb.hic
EGAR00003764778


title: HiC_CD34_14_3_siCtrl


title: ChIP_IN_AML_ctr_20899

description:
5286
EGAR00003766157


title: ChIP_IN_AML_ctr_19416

description:
3488
EGAR00003766153


title: ChIP_IN_AML_ctr_19504

description:
3326
EGAR00003766154


title: HiC_AML_SA2_9708

description:
2193
CohAML_CTRL_SA2_merged.loop.scores.XYrm.txt
CohAML_CTRL_SA2_merged.normTotalaverage.loop.scores.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_sa2_mut_10kb.hic
EGAR00003764779


title: ChIP_IN_AML_ctr_20180

description:
4334
EGAR00003766155


title: ChIP_IN_AML_ctr_19284

description:
3319
EGAR00003766151


title: HiC_AML_SA2_27396

description:
12567
CohAML_CTRL_SA2_merged.loop.scores.XYrm.txt
CohAML_CTRL_SA2_merged.normTotalaverage.loop.scores.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_sa2_mut_10kb.hic
EGAR00003764777


title: ChIP_IN_AML_ctr_19049

description:
3313
EGAR00003766149


title: ChIP_IN_AML_SA2_19142

description:
3315
EGAR00003766150


title: ChIP_IN_AML_ctr_19405

description:
3323
EGAR00003766152


title: HiC_AML_SA2_24743

description:
12514
CohAML_CTRL_SA2_merged.loop.scores.XYrm.txt
CohAML_CTRL_SA2_merged.normTotalaverage.loop.scores.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_sa2_mut_10kb.hic
EGAR00003764776


title: HiC_CD34_21_4_siCtrl


title: ChIP_IN_AML_ctr_18519

description:
1747
EGAR00003766148


title: HiC_AML_RAD21_38455

description:
41580a
CohAML_CTRL_RAD21_merged.loop.scores.XYrm.txt
CohAML_CTRL_RAD21_merged.normTotalaverage.loop.scores.txt
RAD21mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_rad21_mut_10kb.hic
EGAR00003764775


title: ChIP_IN_AML_ctr_18136

description:
1551
EGAR00003766146


title: HiC_AML_RAD21_23039

description:
7314
CohAML_CTRL_RAD21_merged.loop.scores.XYrm.txt
CohAML_CTRL_RAD21_merged.normTotalaverage.loop.scores.txt
RAD21mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_rad21_mut_10kb.hic
EGAR00003764773


title: HiC_AML_RAD21_26830

description:
12557
CohAML_CTRL_RAD21_merged.loop.scores.XYrm.txt
CohAML_CTRL_RAD21_merged.normTotalaverage.loop.scores.txt
RAD21mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_rad21_mut_10kb.hic
EGAR00003764774


title: ChIP_IN_AML_ctr_16911

description:
2236
EGAR00003766145


title: ChIP_IN_AML_ctr_10156

description:
2195
EGAR00003766140


title: ChIP_IN_AML_ctr_11374

description:
2207
EGAR00003766141


title: HiC_AML_ctr_21290

description:
5285
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764771


title: ChIP_IN_AML_SA2_15365

description:
2292
EGAR00003766143


title: ChIP_IN_AML_SA2_15640

description:
2216
EGAR00003766144


title: ChIP_IN_AML_ctr_9873

description:
2194
EGAR00003766139


title: ChIP_IN_AML_SA2_9708

description:
2193
EGAR00003766138


title: HiC_AML_ctr_21047

description:
6246
CohAML_allpat_merged.loop.scores.XYrm.txt
CohAML_allpat_merged.normTotalaverage.loop.scores.XYrm.txt
SA2mutvsCTRL.merged.loop.scores.DESeq.norm2Total.loopcoords2.txt
merged_aml_ctrl_10kb.hic
EGAR00003764770