title: intestine, 15Gy, 6h, rep2

description:
mouse was treated with 15Gy IR, then collected intestine at 6h
Ftn6h2


title: DNAPol2-Flag_ChIP_45minHU_rep1

status: Public on Nov 10 2023

type: SRA

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

library_source: genomic

data_processing:
After adapters removal using Trim Galore!, reads were aligned to the sacCer3 genome via Bowtie2 (Langmead and Salzberg, 2012) through the Galaxy server. BigWig density files were then produced using the bamCoverage function with the following options: a bin size of 250 smoothed by a rolling window of 1000bp, cpm normalization with the exclusion of the chrM, centering fragments after their artificial extension to 250bp and a minimal Phred quality score of 20. Differential densities between time points in S-phase and G1-phase were processed through the bigwigCompare function. Metagene plots were made using the computeMatrix and plotProfile commands. The list of ARS Consensus Sequences (ACSs) was retrieved from (Soudet et al., 2018) and their orientation was taken into account. The 40 early ARSs were defined through a k-means clustering based on the DNA Pol 2 signal 10kb around the ACSs. The median Z-score was finally calculated on the 30kb-window around ACSs.
Assembly: sacCer3
Supplementary files format and content: bigWig files

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Yeast cells were grown in YEPD until exponential phase, and synchronized in G1 phase by addition of α-factor (ref) for 2 hours. After two washes, cells were released into the cell cycle in fresh YEPD medium without drugs, or supplemented with 200 mM of HU.

extract_protocol:
Cells were crosslinked with 1 % formaldehyde for 15 min at room temperature, quenched with 250 mM glycine incubated for 5 min, followed by ice-cooling for at least 10min. Before freezing, pellets were washed twice with cold 1X Phosphate Buffer Saline (PBS) and transferred into 2 mL screw-cap tubes. All subsequent steps were performed at 4°C or on ice, if not mentioned otherwise. Frozen pellets were resuspended in 1 mL cold FA lysis buffer (50 mM HEPEs-KOH pH 7.5; 140 mM NaCl; 1 mM EDTA; 1 % Triton X-100; 0.1 % sodium deoxycholate; protease inhibitor cocktail) and lysed by MagNA Lyzer (6000 rpm; 5 cycles of 30 secs; 1 min on ice between runs). Extracts were recovered in a new tube and centrifuged at 13,000 x rpm for 30min. After resuspension with 1 mL of fresh FA lysis buffer, extracts were sonicated via Bioruptor Twin (Diagenode) at 4°C for 20 cycles of 30 secs. After centrifugation at 13,000 x rpm for 15 min, supernatant was transferred in a new tube and the amount of protein was determine by Bio-Rad protein assay (cat. 500-0006).  Each immunoprecipitation was carried out with 1 mg of protein (1/10 retained as the input) incubated overnight at 4°C under rotation, with 1 uL of anti-HA antibody. Protein G sepharose beads were then added for 3 hours, at 4°C under rotation.  After incubation, beads were washed 1x with 500 µL cold FA lysis buffer, 2x with 500 µL cold FA-500 buffer (FA lysis with 500 mM NaCl), 2x with 500 µL Buffer 3 (10 mM Tris-HCl pH 8; 1 mM EDTA; 250 mM LiCl, 1 % IGEPAL; 1 % sodium deoxycholate) and 1x with 500 µL 1X TE (50 mM Tris-HCl pH 7.5; 10 mM EDTA). Elution was then performed twice with 100 µL elution buffer (50 mM Tris-HCl pH 7.5; 1 % SDS; 10 mM EDTA) incubated at 65°C for 8 minutes. Eluted sample and input were treated with 0.75 mg/mL Proteinase K and incubated at 42°C for 2 hours, followed by de-crosslinking overnight at 65°C.  Both IP and input were purified with the MinElute PCR Purification kit (Qiagen, cat. 28006), following manufacturer’s recommendations and eluted from the column twice with 30 µL of elution buffer from the kit.
NEBnext Ultra DNA library prep kit for Illumina (NEB, cat. E7370L)

tag: genotype

value: Rtt101-3HA-HIS3; Pol2-5Flag-KAN; bar1D::URA3; MATa

tag: cell type

value: yeast cell

tag: treatment

value: 45min after release fron G1-phase in HU-containing medium

tag: chip antibody

value: anti-Flag (Sigma F3165-1MG)


title: intestine, 15Gy, 3d, rep3

city: Beijing

first: wang

last: qiong

address: 27 Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

description:
mouse was treated with 15Gy IR, then collected intestine at 3d
Ftn3d3

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Intestine

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Intestine

tag: strain

tag: Sex

value: male

value: Wildtype

value: 15Gy radiation, sample at 3d


title: S2000S0546

city: Grand Rapids

first: Lena

last: Brundin

address: 333 Bostwick Ave NE

country: USA

institute: Van Andel Institute

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0; Martin, 2011). Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8; Dobin et al., 2013) with --quantMode GeneCounts.
Assembly: mm10
Supplementary files format and content: Connts per million (CPM) of each sample processed using edgeR (with low expressed genes removed)

organism: Homo sapiens

source_name: brain

extract_protocol:
Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit to remove cytoplasmic and mitochondrial rRNAs and QIAseq FastSelect –5S/16S/23S Kit to remove pan bacterial rRNAs (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to adapters for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA).

value: brain

tag: group

value: healthy


title: S2000S0545


title: intestine, 15Gy, 3d, rep2

description:
mouse was treated with 15Gy IR, then collected intestine at 3d
Ftn3d2


title: DNAPol2-Flag_ChIP_30min_rep2

value: 30min after release from G1-phase


title: Rtt101-HA_ChIP_45minHU_rep2

value: anti-HA (BioLegend 901502)


title: DNAPol2-Flag_ChIP_30min_rep1


title: S2011S1154


title: DNAPol2-Flag_ChIP_G1_rep2

value: G1-phase arrested cells


title: DNAPol2-Flag_ChIP_G1_rep1


title: Rtt101-ChEC_Gal_30sec_rep2

data_processing:
Adapters were removed from the paired-end reads using the Trim Galore! function with default options from the Galaxy server (Afgan et al., 2018; Galaxy, 2022). Trimmed paired-end reads were then aligned to the modified version of the sacCer3 (called sacCer3-Flp-nick and shared as a fasta file) containing an insertion of FRT sites together with a URA3 marker in between the ROG3 and ATG18 coding genes. The bamCoverage function of DeepTools 2.0 (Ramirez et al., 2016) was used to create bigWig density files with the following options: a bin size of 1bp, counts per million (cpm) normalization with the exclusion of the chrM, 20 as a minimum Phred quality score and centering regions with respect to the fragment length limited to 200bp. BigWig files were visualized using Integrative Genomic Viewer (IGV) (Robinson et al., 2011). The average of the two replicates and the differences between the ChEC signal in Galactose and Raffinose-containing media were produced using the bigWigCompare function of DeepTools 2.0.
Assembly: Modified sacCer3 (sacCer3-Flp-nick)
Supplementary files format and content: bigWig files
Library strategy: ChEC-seq

growth_protocol: Experiments were performed as described in (Gill et al., 2020) with minor modifications. Yeast strains were cultured in YEP medium supplemented with 2% raffinose overnight. Cells were diluted to OD600 = 0.25 in 130 mL of YEP-2% raffinose for 3 h. Then, 50 mL was separated for the induction of flp-H305L expression with 3% galactose for 2 h.

extract_protocol:
For each condition, 50 mL of cultures were harvested at room temperature at 1,500 x g for 30 seconds. Cells were quickly resuspended in 1 mL of Buffer A (15 mM Tris pH 7.5; 80 mM KCl; 0.1 mM EGTA; 0.2 mM spermine; 0.5 mM spermidine; 1 mM PMSF; protease inhibitor cocktail), transferred into 2 mL tubes and pelleted at room temperature at 1,500 x g for 30 seconds. Cells were permeabilized by resuspending in 693 mL of Buffer A supplemented with 7 mL of 10% digitonin and incubated at 30°C with shaking for 5 minutes. An aliquot of 100 mL was separated and kept as a negative control (no MNase digestion).  Then, 3.5 mL of 1 M CaCl2 (5 mM final) was added and tubes were immediately placed at 30°C to start MNase cleavage. An aliquot of 100 mL was taken at 30 seconds and immediately mixed with 100mL of Stop Buffer (400 mM NaCl; 20 mM EDTA; 4 mM EGTA; 0.1% SDS). The procedure was repeated for later timepoints.  Once all timepoints were collected, cells were treated with 4 mL of 20 mg/mL proteinase K and incubated 30 minutes at 55°C. DNA was then extracted by the addition of 200 mL of phenol:chloroform:isoamyl followed by 5 min centrifugation at maximum speed at  room temperature. Then, 150 mL of the aqueous phase was transferred into a new tube, and DNA was precipitated by the addition of 1.5 mL of 20 mg/mL glycogen and 500 mL of 100 % ethanol and incubated at -20°C overnight. Precipitated DNA was centrifuged at maximum speed at 4°C for 10 minutes. DNA pellets were washed with 1 mL of 70% ethanol and air-dried for 5 minutes. Dried pellets were resuspended in 48 mL of 10 mM Tris-HCl pH 8.0 and 2 mL of 10 mg/mL RNase A was added for RNA digestion at 37°C for 30 minutes.  For size selection, 100 mL of AmPure XP beads (Beckman Coulter, cat. A63881) was added and the bead:DNA mixture was incubated at room temperature for 5 minutes. Beads were collected by placing tubes on a magnetic rack, and the supernatant was transferred to a new tube containing 55 mL of 10 mM Tris-HCl pH 8.0 and 4 mL of 5 M NaCl. Another DNA extraction and precipitation was performed as described above.  DNA pellets were washed and resuspended in 50 mL of ultrapure water. The concentration was determined using a QuBit dsDNA high-sensitivity assay (Invitrogen, cat. Q32854).
NEBnext Ultra DNA library prep kit for Illumina (NEB, cat. E7370L)

value: bar1D::KAN; Flp-nick microscopy (CirO; LEU2-pGAL10-flp-H305L; URA3-FRT-tetOx224(iYFR020W); Rtt101-3xFLAG-Mnase-HPH; MATa

tag: medium

value: Galactose-containing media


title: intestine, 15Gy, 6h, rep1

description:
mouse was treated with 15Gy IR, then collected intestine at 6h
Ftn6h1

value: 15Gy radiation, sample at 6h


title: intestine, 6Gy, 6h, rep2

description:
mouse was treated with 6Gy IR, then collected intestine at 6h
Six6h2

value: 6Gy radiation, sample at 6h


title: S2010S1116


title: Rtt101-ChEC_Gal_30sec_rep1


title: Rtt101-ChEC_Raff_30sec_rep2

description: Rtt101-ChEC_Raff_30s_0-200bp_mean.bigwig

value: Raffinose-containing media


title: Rtt101-ChEC_Raff_30sec_rep1

value: yeast cell


title: S2010S1113


title: S2003S0696


title: intestine, control, rep3

description:
intestine from normal mouse
NC3

value: no treatment


title: LCZ11 Zfp148/281 dKO ImCD8 thymocyte

city: Bethesda

first: Remy

last: Bosselut

state: MD

address: 9000 Rockville Pike, Building 37

department: Laboratory of Immune Cell Biology

institute: National Cancer Institute, National Institute of Health

data_processing:
Filtering with Cutadapt 1.18
Alignment ot mm10 with STAR 2.6.1
Read counting with HTseq
Assembly: mm10
Supplementary files format and content: Htseq count table

source_name: Thymus

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
Clontech SMARTer Low Input mRNA following the manufacturer's protocol

value: Thymus

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre negative

tag: flow markers

value: CD44low, CD8+ CD4-, TCRb+, CD69+


title: LCZ10 Zfp148/281 dKO ImCD8 thymocyte


title: S2010S1089


title: LCZ12 Zfp148/281 dKO ImCD8 thymocyte


title: intestine, control, rep2

description:
intestine from normal mouse
NC2

value: Intestine

value: male

value: Wildtype


title: LCZ9 Ctrl ImCD8 thymocyte

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre+


title: S2010S1086

value: brain

value: healthy


title: intestine, control, rep1

description:
intestine from normal mouse
NC1


title: LCZ8 Ctrl ImCD8 thymocyte


title: LCZ7 Ctrl ImCD8 thymocyte


title: intestine, 6Gy, 6h, rep3

description:
mouse was treated with 6Gy IR, then collected intestine at 6h
Six6h3


title: S2010S1082


title: LCZ5 Zfp148/281 dKO ImCD4 thymocyte


title: LCZ6 Zfp148/281 dKO ImCD4 thymocyte


title: S2009S1039


title: CAST-seq on samples treated with SaCas9 paired with g1+g2 (paired nuclease) replicate3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq and D-CAST-Seq pipelines with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: mm10
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq and D-CAST pipelines. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

source_name: MEF CF-1 Global Stem

growth_protocol: Mouse embryonic fibroblast (MEF) CF-1 cells (Global Stem, CF-1 MEF 4M untreated, Catalog. Nr. GSC-6001, Lot #94300754) were cultured in RPMI1640 medium supplemented with GlutaMAX™ (ThermoFisher, Cat. #61870010) and 10% FBS (PAN-Biotech, Cat. #P40-47500).

extract_protocol:
Cells were harvested on day 6 post nucleofection for genomic DNA extraction using the NucleoSpin Tissue Mini kit for DNA from cells and tissue (Macherey-Nagel REF 740952.250).
CAST-Seq was performed as previously described (Turchiano et al, 2021) with minor modifications. Briefly, genomic DNA was fragmented by enzymatic digestion (NEBNext® Ultra™ II FS DNA Library Prep Cat.# E7805S) to obtain average fragment lengths of 350-500 bp. After linker ligation (NEBNext®Ultra™ II FS DNA Library Prep Cat.# E7805S) and DNA purification, two rounds of PCR utilizing Q5 polymerase (NEB, Cat.# M0493S) were performed with the following conditions: 20 cycles at 95°C for 15 s, 61°/63°C (g1 or g1+2/g2, first reaction) or 68°C (second reaction) for 20 seconds, 72°C for 20 seconds.
A third PCR introduced the barcoded Illumina adapter for sequencing (NEB, NEBNext Multiplex Oligos for Illumina, Cat.# E7335, E7500, E7710, E7730). Libraries were sequenced by Azenta Life Sciences using the Illumina NovaSeq platform with a 2 x 150 bp configuration.

treatment_protocol: For nucleofection, 5x10 5 MEF cells were resuspended in 20 μL of P4 solution (Lonza, Cat. #V4XP-4032) and mixed with previously assembled RNPs. For RNP assembly, 3 μg of SaCas9 protein (Synthego, SaCas9 2NLS Nuclease (300 pmol)) were complexed for ten minutes with 72 pmol of gRNA (Synthego). Nucleofection was performed with a 4D-Nucleofector (Lonza, Germany), program CZ-167 in a 16-well cuvette.

value: MEFs

tag: sample

value: CAST-seq derived amplicons from gDNA


title: LCZ3 Ctrl ImCD4 Thymocyte


title: CAST-seq on samples treated with SaCas9 paired with g1+g2 (paired nuclease) replicate4


title: LCZ2 Ctrl ImCD4 Thymocyte


title: LCZ1 Ctrl ImCD4 Thymocyte


title: intestine, 6Gy, 6h, rep1

description:
mouse was treated with 6Gy IR, then collected intestine at 6h
Six6h1


title: S2009S1020


title: CAST-seq on samples treated with SaCas9 paired with g1+g2 (paired nuclease) replicate2


title: CAST-seq on samples treated with SaCas9 paired with g1+g2 (paired nuclease) replicate1


title: S2006S0926


title: S2008S0997


title: CAST-seq on samples treated with SaCas9 paired with g2 replicate4


title: HiC_Pds5a_KO_rep5_4

city: Los Angeles

first: Oliver

last: Bell

state: California

address: 1450 Biggy St, NRT6510

institute: USC

description:
Pds5a_KO.hic
Pds5a_KO.mcool

data_processing:
RNA-seq Data Analysis: Raw paired-end RNA-seq reads were aligned to the mm10 genome using STAR-2.6.1c (Dobin et al., 2013). Overlap of STAR-aligned reads with genes was performed using HTSeq count function (Anders et al., 2015) with stranded=reverse option and the GRCm38 version 94 GTF file. The HTseq count matrix was pre-filtered to exclude genes with a read count below 10. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014) using the “apeglm” method (Zhu et al., 2019) for LFC shrinkage. We applied a threshold of p-adj < 0.05 and fold change > 0.5 or -0.5 for gene expression changes to be considered significant. Visualization of RNA-seq data was performed using custom R scripts and ggplot2. Gene ontology analysis for significantly deregulated genes was performed using custom R scripts and clusterProfiler reference (Wu et al., 2021; Yu et al., 2012).
ChIP-seq Data Analysis: Raw reads were mapped to the custom concatenated mouse (mm10) and spike-in human (hg38) genome sequences using bowtie 2 with “–no-mixed” and “no-discordant” options (Langmead and Salzberg, 2012). Subsequently, low quality reads were filtered using SAMtools (Li et al., 2009), duplicated reads were discarded with the Picard toolkit (http://broadinstitute.github.io/picard/) and only unique mapped reads were retained. For visualization uniquely mapped mouse reads were normalized by random subsampling with samtools using calibration factors calculated from the corresponding hg38 spike-in reads as described previously (Bonhoure et al., 2014; Fursova et al., 2019; Hu et al., 2015). High correlation between replicates was confirmed using multiBamSummary and plotCorrelation functions from deepTools (Ramírez et al., 2016) before merging for visualization and downstream analysis. Genome coverage tracks (bigWig files) were produced with MACS2’ pileup function (Zhang et al., 2008) and heatmaps and profile plots generated with deepTools (Ramírez et al., 2016). Peaks were called on each replicate independently using MACS2 (Zhang et al., 2008). Peaks overlapping with a custom-build blacklist were discarded to remove sequencing artifacts and only peaks called in both replicates were retained for downstream analysis.
Hi-C data analysis: Hi-C data were analyzed using the HiC-Pro (2.11.1) pipeline (Servant et al., 2015). Read mapping to the mm10 genome was performed using bowtie 2 (Langmead and Salzberg, 2012) within the HiC-Pro pipeline. PCR and optical duplicates as well as reads with MAPQ < 30 were removed. Filtered valid HiC contact data was binned and raw and ICE normalized .hic contact matrices were generated. We also produced balanced single and multi-resolution .cool and .mcool cooler files for visualization in HiGlass.
Genome_build: mm10; ChIPcapseq: amended mm9 genome build

source_name: mouse embryonic stem cells

growth_protocol: All mESCs were cultivated without feeders in high-glucose-DMEM (Corning 10-013-CV) supplemented with 13.5% fetal bovine serum (Corning 35-015-CV), 10 mM HEPES pH 7.4 (Corning, 25-060-CI), 2 mM GlutaMAX (Gibco, 35050-061), 1 mM Sodium Pyruvate (Corning 25-000-Cl), 1% Penicillin/Streptomycin (Sigma, P0781), 1X non-essential amino acids (Gibco, 11140-050), 50 mM β-mercaptoethanol (Gibco, 21985-023) and recombinant LIF. Cells were incubated at 37°C and 5% CO 2 and were passaged every 48 hours by trypsinization in 0.25% 1x Trypsin-EDTA (Gibco, 25200-056). In order to reverse of TetR-CBX7 fusion protein binding 1 µg/ml Doxycycline (Sigma, D9891) was added to cell culture medium.

extract_protocol:
RNA-seq: 5 million mESCs were trypsinized and collected by centrifugation. Resulting cell pellets were washed in 1x PBS and resuspended in 1x DNA/RNA protection reagent (Monarch Total RNA Miniprep Kit, NEB). Subsequently, cells were lysed and total RNA extracted following the mammalian cell protocol including optional on-column DNase I treatment. Calibrated ChIP-seq (cChIP) and ChIPCap-seq: 30 million mESCs and HEK293T cells were collected, washed once in 1x PBS and crosslinked for 7 min in 1% formaldehyde. The crosslinking was quenched by addition of 125 mM glycine and incubated on ice. The crosslinked cells were pelleted by centrifugation for 5 min at 1200g at 4 °C. Nuclei were prepared by washes with NP-Rinse buffer 1 (10 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 0.5 mM EGTA, 0.25% Triton X-100) followed by NP-Rinse buffer 2 (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Afterwards, the nuclei were washed twice with shearing buffer (1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0, 0.1% SDS) and subsequently resuspended in 900 µL shearing buffer with added 1× protease inhibitors complete mini (Roche). Chromatin was sheared by sonication in 15 ml Bioruptor tubes (Diagenode, C01020031) with 437.5 mg sonication beads (Diagenode, C03070001) for 6 cycles (1 min on/1 min off) on a Bioruptor Pico sonicator (Diagenode). For each ChIP reaction 4 % HEK293T-derived human spike-in lysate was combined with mESC lysate and incubated in 1x IP buffer (50 mM HEPES/KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS), with following appropriate antibodies at 4 °C o/n a rotating wheel: H3K27me3 (Diagenode, C15410195), RING1B (Cell Signaling, D22F2), PDS5a (Millipore Sigma #SAB2101764), SUZ12 (Cell Signaling D39F6), H2AK119ub (Cell Signaling D27C4), PCGF1 (Abcam ab202395), RAD21 (Abcam ab992), CTCF (Millipore 070729). Antibody-bound chromatin was captured using Dynabeads protein G beads (Thermofisher #10004D) for 4 hours at 4°C. ChIP washes were performed as described previously (Farcas et al., 2012). ChIPs were washed 5x with 1x IP buffer ( 50 mM HEPES/KOH pH 7.5, 300 mM NaCl, I mM EDTA, 1% Triton-X100, 0.1% DOC, 0.1% SDS), or 1.5x IP buffer for H3K27me3 and H2AK119ub, followed by 3x washes with DOC buffer (10 mM Tris pH 8, 0.25 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% DOC) and 1x with TE/50 mM NaCl. ChIP DNA was eluted 2x in elution buffer (1% SDS, 0.1 M NaHCO3 ) at 65°C for 20 min, RNase A treated for 30 min at 37 °C, Proteinase K treated for 3 hrs at 55 °C and crosslinks were reversed o/n at 65 °C. The following day, ChIP samples and corresponding inputs were puriﬁed by PCI extraction and DNA precipitation. In Situ Hi-C: Hi-C was performed as previously described (Rao et al., 2014) with modifications described in (Boyle et al., 2020) as following: 5 million mESCs were crosslinked in 1% formaldehyde for 10 mins before the reaction was quenched by adding 0.2 M final glycine. Cells were permeabilized in lysis buffer (0.2% IGEPAL, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) and nuclei isolated in NEBuffer 3 supplemented by 0.3% SDS at 62 °C for 10 min. SDS was quenched with 1% Triton X100 at 37°C for 60 min, the nuclei pelleted and resuspended in 250 µl of 1x DpnII buffer with 600 U DpnII (NEB). Following o/n digestion at 37°C, 200 U were added for 2 hrs. DpnII was inactivated for 20 min at 65°C before the DNA ends were filled-in and biotinmarked using Klenow, d(C/G/T)TPs and biotin-14-dATP for 90 min at 37°C. Proximity ligation was performed using T4 DNA ligase (NEB) for 4 hrs at room temperature. Subsequently, nuclei were spun down, resuspended in 200 µl mQ water and digested with proteinase K for 30 min at 55°C in presence of 1% SDS. For crosslink reversal 1.85 M final NaCl was added and samples incubated at 65°C o/n. The next day, sample DNA was ethanol precipitated and sheared in 500 µL sonication buffer (50 mM Tris pH 8.0, 0.1% SDS, 10 mM EDTA) on a Bioruptor Pico sonicator (Diagenode). DNA was then concentrated on Amicon ultra 0.5 30K ﬁlter units (Millipore), biotin-pulldown performed using MyOne Streptavidin T1 beads (Life technologies, 65602) and used for NGS library preparation.
RNA-seq: For RNA-seq library preparation, 1 µg of total RNA per sample was enriched for poly-A using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and final RNA-seq libraries generated using the NEBNext Ultra II Directional RNA Library Prep kit (NEB, E7760 and NEBNext Multiplex Oligos (NEB, E7335/E7500). cChIP-seq and ChIPCap-seq library preparation: Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol. Libraries were purified using Agencourt AMPure XP (Beckman Coulter) and amplified using the KAPA Real-Time Library Amplification Kit (KAPABiosystems) following the manufacturer’s instructions. ChIPCap-seq libraries were prepared identically to ChIP-seq libraries. After PCR amplification the libraries were enriched for loci of interest using the MYbaits kit DNA capture target enrichment system (Arbor Biosciences) according to manufacturer’s manual. 120 nucleotides long MYbaits sequence capture probes (Arbor Biosciences) were custom designed against 25 mm9 genomic loci (Table S3). Library quality control including determination of average size and concentration was performed prior to sequencing by commercial Next Generation Sequencing providers. NGS libaries were eventually sequenced as 150 bp paired-end reads on the Illumina HiSeq platform. In situ HiC: DNA ends were repaired, biotin removed from unligated ends and NEXTFLEX DNA barcoded adapters (Perkin Elmer) were ligated. Desired PCR cycle numbers were determined in test endpoint PCRs using Q5 DNA polymerase (NEB M0491L). Final HiC libraries were generated from 4-6 individual PCR reactions, which were pooled and subjected to cleanup and size-selection using AMPure beads (Beckman Coulter A63882). Samples were ﬁrst test sequenced to check library quality before selected Hi-C ibraries were sequenced at greater depth (Table S2).
NGS libaries were eventually sequenced as 50 bp single-end reads or 150 bp paired-end reads on Illumina platforms

value: embryonic stem cells


title: S2008S0977


title: HiC_Pds5a_KO_rep5_5

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: HiC_Pds5a_KO_rep5_6

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: S2006S0913


title: CTLA4-Tumor

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

library_source: transcriptomic single cell

data_processing:
Sequence reads for each sample were aligned and processed using cellranger/6.0.0
Assembly: mm10
Supplementary files format and content: hdf5 count matrix in sparse matrix format

molecule: polyA RNA

source_name: Flank tumor section

extract_protocol:
Single-cell suspensions were prepared by enzymatic digestion, using a MACS tumor dissociation kit (cat. #130-095-929; Miltenyi Biotec). Cells were strained through MACS strainer (cat. # 130-098-458; Miltenyi Biotec). The cell count and viability were analyzed by staining the cells with AO/PI stain on the Nexcelom Cellometer K2. The cells were then resuspended at a concentration of 500 cells/μL in PBS (cat. #SH30256FS; Fisher Scientific) + 0.4% nonacetylated BSA (cat. #BP1605100; Fisher Scientific).
The samples were then loaded onto 10X Genomics Chromium Single-Cell Controller (10X Genomics) to prepare scRNA-seq libraries. Around 50,000 to 1,000,000 mean sequencing reads per cell were generated on Illumina NextSeq 500 instrument using v2.5 flow cells.

value: Flank tumor section

tag: cell line

value: Tumor cells


title: CAST-seq on samples treated with SaCas9 paired with g2 replicate3


title: PD1-Plus-CTLA4-Tumor


title: Lag3-Tumor


title: S2005S0894


title: HiC_Pds5a_KO_rep5_1

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: CAST-seq on samples treated with SaCas9 paired with g1 replicate2


title: IgG-Tumor

value: IgG


title: S2005S0899


title: LCZ4 Zfp148/281 dKO ImCD4 thymocyte


title: CAST-seq on samples treated with SaCas9 paired with g2 replicate2


title: CAST-seq on samples treated with SaCas9 paired with g2 replicate1


title: S2005S0877


title: S2005S0879


title: PD1-Tumor


title: HiC_Pds5a_KO_rep5_3

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: Untreated sample used as control replicate4

description: use as un-treated control


title: HiC_Pds5a_KO_rep4_6

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: PD1-Plus-Lag3-Tumor


title: S2005S0831


title: HiC_Pds5a_KO_rep4_3

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: CAST-seq on samples treated with SaCas9 paired with g1 replicate1


title: S2005S0875


title: HiC_Pds5a_KO_rep4_2

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: Untreated sample used as control replicate3

description: use as un-treated control


title: HiC_Pds5a_KO_rep5_2

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: pdKO, dLN, rep2_rna

data_processing:
The standard 10x Genomics cellranger ARC (version 2.0.1) pipeline was used to perform data processing.
Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence
Assembly: mm10
Supplementary files format and content: h5; Feature and barcode matrix
Supplementary files format and content: tsv; fragment file for ATAC fragments
Supplementary files format and content: csv; statistics

source_name: Lung draining lymph nodes

extract_protocol:
Nuclei were isolated following the recommended protocol from 10X Genomics, using a 3 minute lysis time.
Chromium NextGem Single Cell ATAC + Gene Expression

value: Lung draining lymph nodes

tag: replicate

value: Rep 2

value: CD44+ CD4+ CD19- CD8- Rosa26-YFP+

value: Activated CD4+ T cells

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd2-Cre+


title: HiC_Pds5a_KO_rep4_1

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: Th2_ChIP_aZfp281_Rep2

data_processing:
ChIP-seq reads were aligned with Bowtie2 to the mm10 genome
Reads were sorted and indexed with samtools
Count per million bigwig traces were generated with Deeptools
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Spleen

growth_protocol: Activated for five days in vitro with irradiated APCs, aCD3, aCD28, aIFNg, aIL-12, and IL-4.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was digested and immunoprecipitated as indiciated in the Cell Signaling Technology Simple ChIP protocol with anti-Zfp281 or anti-Gata3 antibody.
Libraries were prepared as indicated in the Cell Signaling Technology Simple ChIP library single-index library construction kit.

value: Spleen

tag: antibody


title: Th2_ChIP_IgG_Rep2

value: Activated for five days in vitro with irradiated APCs, aCD3, aCD28, aIFNg, aIL-12, and IL-4.


title: Untreated sample used as control replicate2

description: use as un-treated control

value: no treatment


title: Ctrl, dLN, rep2_rna

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd2-Cre-


title: S2004S0808

value: brain


title: S2004S0795

value: healthy


title: pdKO, dLN, rep2_atac

library_source: genomic single cell


title: S2004S0782


title: pdKO, dLN, rep1_rna

value: Rep 1


title: Untreated sample used as control replicate1

description: use as un-treated control

value: MEFs

value: CAST-seq derived amplicons from gDNA


title: S2004S0797


title: S2004S0765


title: HiC_Pds5a_KO_rep3_6

description:
Pds5a_KO.hic
Pds5a_KO.mcool

value: embryonic stem cells


title: HiC_Pds5a_KO_rep3_4

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: LPS_28h_nucleus_GY15_N

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

description: Sig_p_adj_FisherScoredSites_ByCondition_Nuclear_0hr_28hr.tsv

data_processing:
STAR v2.7.9a
REDItools2
Assembly: mm10
Supplementary files format and content: A list of differentially expressed A-to-I editing sites in bed format

molecule: nuclear RNA

source_name: kidney

extract_protocol:
One-third of the minced tissue was transferred to a 1.2 mL of fractionation/lysis buffer, which consisted of 10 mM Tris pH 7.0, 10 mM NaCl, 5 mM MgCl2, 0.5% IGEPAL CA-630, 0.5% Triton X-100, DNase I (Zymo E1011A 10 U/mL), and Superase*In (2 uL per 1 mL). The lysate was centrifuged at 3,000 g for 3 minutes at 4 °C. The supernatant was further centrifuged at 21,000 g for 5 minutes. The resulting supernatant represents the cytoplasmic fraction. The pellet obtained from the initial centrifugation was resuspended in 1 mL of the fractionation/lysis buffer and homogenized using a Minilys tissue homogenizer (Bertin Instruments) at the highest speed for 45 seconds. After homogenization, the lysate was centrifuged at 21,000 g for 5 minutes. This supernatant serves as the nuclear fraction. Each fraction was then incubated with anti-dsRNA monoclonal antibody J2 (SCICONS/Jena Bioscience; IgG2a kappa light chain) at a concentration of 10 µg per 600 µl of lysate for 2 hours at 4 °C. Mouse IgG2a kappa (clone eBM2a) was used as an isotype control. Protein G Dynabeads (Invtrogen) were washed in the immunoprecipitation buffer described below and then incubated with the sample-antibody mix for 1 hour at 4 °C. The dsRNA-antibody-Dynabeads complex was washed on a magnetic rack using 500 µL x 4 immunoprecipitation buffer consisting of 50 mM Tris pH 7.4, 100 mM NaCl, 3 mM MgCl2, IGEPAL 0.5%. RNA was extracted from Dynabeads using 1 mL TRIzol and 200 µL chloroform per sample. After the second round of TRIzol chloroform RNA purification, RNA precipitation was done using ice cold isopropanol, sodium acetate and GlycoBlue on ice for 1 hour. The RNA was resuspended in 7 µL of water. The RNA yields were approximately 6 ng/µl to 16 ng/µl for J2 antibody immunoprecipitation (lower in the nuclear fraction), while the isotype control yielded less than 300 pg/µl (hence no sequenceing was performed).
cDNA library preparation was carried out using the Clontech SMARTer Stranded Total RNA-Seq Kit v2. The pooled libraries were loaded onto a NovaSeq 6000 sequencer.

value: kidney

value: LPS 4 mg/kg iv 28 h


title: LPS_28h_cytoplasm_GY15_C

description: Sig_p_adj_FisherScoredSites_ByCondition_Cytoplasm_0hr_28hr.tsv

molecule: cytoplasmic RNA


title: pdKO, dLN, rep1_atac

value: Lung draining lymph nodes


title: HiC_Pds5a_KO_rep4_4

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: Ctrl, dLN, rep2_atac

value: Rep 2


title: HiC_Pds5a_KO_rep3_5

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: LPS_28h_nucleus_GY14_N


title: LPS_28h_cytoplasm_GY14_C


title: S2004S0761


title: Ctrl, dLN, rep1_rna


title: LPS_28h_nucleus_GY13_N


title: S2003S0744


title: HiC_Pds5a_KO_rep3_3

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: HiC_Pds5a_KO_rep3_1

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: HiC_Pds5a_KO_rep3_2

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: LPS_28h_cytoplasm_GY13_C


title: S2003S0724


title: HiC_Pds5a_KO_rep2_2

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: Th2_tdKO_Zfp281_cpm.bw

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was digested and immunoprecipitated as indiciated in the Cell Signaling Technology Simple ChIP protocol with anti-Zfp281 or anti-Gata3 antibodies.
Libraries were prepared as indicated in the Cell Signaling Technology Simple ChIP library single-index library construction kit.

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre+


title: LPS_16h_nucleus_GY12_N

description: Sig_p_adj_FisherScoredSites_ByCondition_Nuclear_0hr_16hr.tsv

value: LPS 4 mg/kg iv 16 h


title: Th2_tdKO_Gata3


title: S2002S0679


title: Ctrl, dLN, rep1_atac

value: Activated CD4+ T cells


title: LPS_16h_cytoplasm_GY12_C

description: Sig_p_adj_FisherScoredSites_ByCondition_Cytoplasm_0hr_16hr.tsv


title: S2000S0528


title: LPS_16h_nucleus_GY11_N


title: S2016S1215

value: suicide


title: HiC_Pds5a_KO_rep1_1

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: HiC_Pds5a_KO_rep2_1

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: S2001S0579


title: Th2_WT_Gata3

value: Spleen

value: Activated for five days in vitro with irradiated APCs, aCD3, aCD28, aIFNg, aIL-12, and IL-4.


title: HiC_Pds5a_KO_rep1_2

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: S2014S1207


title: LPS_16h_cytoplasm_GY10_C


title: ChIP DNA, aZfp281 rep1

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was digested and immunoprecipitated as indiciated in the Cell Signaling Technology Simple ChIP protocol.
Libraries were prepared as indicated in the Cell Signaling Technology Simple ChIP library single-index library construction kit.


title: LPS_16h_cytoplasm_GY11_C


title: HiC_wt_rep5_5

description:
wt.hic
wt.mcool


title: LPS_04h_nucleus_GY9_N

description: Sig_p_adj_FisherScoredSites_ByCondition_Nuclear_0hr_4hr.tsv

value: LPS 4 mg/kg iv 4 h


title: dKO, thymocyte, rep2

data_processing:
The standard 10x Genomics cellranger (version 5.0.1) pipeline was used to extract Fastqs and 10X Genomics cellranger (version 5.0.1) pipeline was used to perform data processing.
Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A).
Assembly: mm10
Supplementary files format and content: h5 file; Feature and barcode matrix

extract_protocol: Single Cell NextGem 5' V1.1 chemistry from 10X genomics

value: Thymus

value: CD69+ mixed with CD69-CD8+CD4+ and CD69- CD8- CD4-

value: 8:1:1 mixture of sorted CD69+, CD69- DP, and CD69- DN thymocytes


title: HiC_Pds5a_KO_rep4_5

description:
Pds5a_KO.hic
Pds5a_KO.mcool


title: ChIP DNA, IgG Control

value: IgG


title: S2013S1194

value: brain


title: HiC_wt_rep5_3

description:
wt.hic
wt.mcool

value: embryonic stem cells


title: LPS_04h_nucleus_GY8_N

value: kidney


title: LPS_04h_cytoplasm_GY8_C

description: Sig_p_adj_FisherScoredSites_ByCondition_Cytoplasm_0hr_4hr.tsv


title: LPS_16h_nucleus_GY10_N


title: HiC_wt_rep5_6

description:
wt.hic
wt.mcool


title: HiC_wt_rep5_1

description:
wt.hic
wt.mcool


title: S2016S1214


title: S2012S1175


title: ChIP DNA, 2% Input rep 1


title: U937 cells, Epigenetic CRISPR pool, Day 5 GFP-low, clone E6

city: La Jolla

first: Karina

middle: Ofelia

last: Barbosa Guerra

state: CA

address: 10901 North Torrey Pines Rd, Deshpande Lab RM6210B

department: Tumor Initiation & Maintenance Program

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
library strategy: CRISPR Library preparation for Amplicon sequencing
MAGeCK-VSIPR MLE pipeline (Li et al., 2015)
Gene rankings were generated comparing the GFP -low and -high fractions to the T0 timepoints. Both clones (E6 and D5) were considered biological replicates.
Both experimental conditions (GFP -high and -low) were further compared using MAGeCKFlute (Wang et al., 2019).
Assembly: hg38
Supplementary files format and content: An Excel spreadsheet containing sgRNA normalized counts and gene- level statistics.

growth_protocol: U937 cells expressing a GFP-MEIS1 transgene were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Genomic DNA was extracted from cell pellets using Zymo QuickDNA™ Miniprep Plus Kit.
A library preparation strategy (Canver et al., 2018) with custom PCR primers  was employed to index sgRNA sequences with Illumina adapters to sequence with 1x75 bp single-end reads.

treatment_protocol:
U937 cells expressing a GFP-MEIS1 transgene were transduced with a pooled CRISPR sgRNA library  lentivirus targeting Epigenetic regulator genes and controls, altogether ~600 genes. Puromycin (1ug/ul) was added 2 days after transduction to select for transduced cells and removed from the culture upon selection completion.
Cells were harvested by centrifugation at an initial timepoint after puromycin selection and 5 days later subjected to flow-cytometry sorting on the basis of GFP-MEIS1 fluorescence. The top and bottom quintile fractions were collected for genomic DNA preparation.

value: Monocytes

tag: disease

value: Acute Myeloid Leukemia

tag: condition

value: GFP-high fraction

tag: clone

tag: time

value: Day 5


title: S2014S1202


title: WT, thymocyte, rep2

value: Rep 2

tag: cell type

tag: genotype

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre negative


title: LPS_04h_cytoplasm_GY9_C

tag: treatment


title: HiC_wt_rep5_2

description:
wt.hic
wt.mcool


title: S2013S1182

tag: tissue

value: suicide


title: LPS_04h_nucleus_GY7_N


title: S2011S1148


title: U937 cells, Epigenetic CRISPR pool, Day 0 unsorted, clone E6

value: Day 0


title: WT, thymocyte, rep1

value: Rep 1


title: LPS_01h_nucleus_GY6_N

description: Sig_p_adj_FisherScoredSites_ByCondition_Nuclear_0hr_1hr.tsv

value: LPS 4 mg/kg iv 1 h


title: HiC_wt_rep5_4

description:
wt.hic
wt.mcool


title: dKO, thymocyte, rep1

value: Thymus

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre+


title: HiC_wt_rep4_6

description:
wt.hic
wt.mcool


title: U937 cells, Epigenetic CRISPR pool, Day 5 GFP-low, clone D5

value: GFP-low fraction


title: U937 cells, Epigenetic CRISPR pool, Day 5 GFP-high, clone E6


title: HiC_wt_rep4_5

description:
wt.hic
wt.mcool


title: S2010S1104


title: S2011S1132


title: S2010S1058


title: HiC_wt_rep4_3

description:
wt.hic
wt.mcool


title: HiC_wt_rep4_4

description:
wt.hic
wt.mcool


title: S2009S1042


title: LPS_01h_nucleus_GY5_N


title: U937 cells, Epigenetic CRISPR pool, Day 0 unsorted, clone D5

value: Control unsorted


title: LPS_01h_cytoplasm_GY6_C

description: Sig_p_adj_FisherScoredSites_ByCondition_Cytoplasm_0hr_1hr.tsv


title: S2009S1027

value: brain


title: HiC_wt_rep4_2

description:
wt.hic
wt.mcool

value: embryonic stem cells


title: LPS_04h_cytoplasm_GY7_C

value: kidney

value: LPS 4 mg/kg iv 4 h


title: HiC_wt_rep4_1

description:
wt.hic
wt.mcool


title: MOLM13 cells, non-targeting control, rep 3

description:
MOLM_NTC_3
SGF29_RNASeq_gene.results.merged.tpm.xlsx

data_processing:
Raw reads were preprocessed by trimming Illumina Truseq adapters, polyA, and polyT sequences using cutadapt v2.3 with parameters “cutadapt -j 4 -m 20 --interleaved -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Fastq1 Fastq2 | cutadapt --interleaved -j 4 -m 20 -a "A{100}" -A "A{100}" - | cutadapt -j 4 -m 20 -a "T{100}" -A "T{100}" -”.
Trimmed reads were subsequently aligned to human genome version hg38 using STAR aligner  v2.7.0d_0221 with parameters according to ENCODE long RNA-seq pipeline.
Gene expression levels were quantified using RSEM v1.3.1. Ensembl v84 gene annotations were used for the alignment and quantification steps. RNA-seq sequence, alignment, and quantification qualities were assessed using FastQC v0.11.5 and MultiQC v1.8. Lowly expressed genes were filtered out by retaining genes with estimated counts (from RSEM) ≥ number of samples times 5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM Glutamine and 100 U/ml penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen) and 900ng of total RNA per sample were used for library preparation.
RNA library prep was performed with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) follownig the manufacturer's instructions.

treatment_protocol:
Cells were transduced with CRISPR sgRNA lentivirus targeting MLL, CSNK2A1, SGF29 or non-targeting control. Puromycin (1ug/ul) was added 2 days after to select for transduced cells and removed from the culture upon selection completion.
Cells were harvested by centrifugation 7 days after puromycin removal and washed with 1X PBS and protease inhibitors.

value: Monocytes

value: Acute Myeloid Leukemia

value: Non-targeting control

value: CRISPR sgRNA lentiviral transduction


title: S2009S1011


title: MOLM13 cells, non-targeting control, rep 2

description:
MOLM_NTC_2
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: HiC_wt_rep3_6

description:
wt.hic
wt.mcool


title: LPS_01h_cytoplasm_GY4_C


title: HiC_wt_rep3_5

description:
wt.hic
wt.mcool


title: S2007S0945


title: HiC_wt_rep3_4

description:
wt.hic
wt.mcool


title: MOLM13 cells, SGF29 knockout, rep 2

description:
MOLM_SGF_2
SGF29_RNASeq_gene.results.merged.tpm.xlsx

value: SGF29 knockout


title: LPS_00h_cytoplasm_GY3_C

value: Saline


title: U937 cells, Epigenetic CRISPR pool, Day 5 GFP-high, clone D5

value: GFP-high fraction

value: Day 5


title: S2007S0962

value: suicide


title: S2006S0936


title: MOLM13 cells, SGF29 knockout, rep 1

description:
MOLM_SGF_1
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: HiC_wt_rep3_3

description:
wt.hic
wt.mcool


title: LPS_01h_cytoplasm_GY5_C

value: LPS 4 mg/kg iv 1 h


title: LPS_00h_nucleus_GY2_N


title: LPS_00h_nucleus_GY3_N


title: S2006S0935


title: HiC_wt_rep3_2

description:
wt.hic
wt.mcool


title: LPS_01h_nucleus_GY4_N


title: LPS_00h_cytoplasm_GY2_C


title: U937 cells, non-targeting control, SGF29 batch, rep 3

description:
U937_NTC_3
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: S2006S0922


title: U937 cells, non-targeting control, SGF29 batch, rep 2

description:
U937_NTC_2
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: LPS_00h_nucleus_GY1_N


title: HiC_wt_rep2_1

description:
wt.hic
wt.mcool


title: S2005S0866


title: U937 cells, non-targeting control, SGF29 batch, rep 1

description:
U937_NTC_1
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: MOLM13 cells, non-targeting control, rep 1

description:
MOLM_NTC_1
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: LPS_00h_cytoplasm_GY1_C


title: HiC_wt_rep1_2

description:
wt.hic
wt.mcool


title: U937 cells, SGF29 knockout, rep 3

description:
U937_SGF_3
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: ATAC-Seq SRR2-18_47D_biol_rep3

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
Demultiplexed raw ATAC-seq reads were processed using the ENCODE ATAC-seq pipeline (v.1.10.0) established by the Kundaje Lab (https://github.com/ENCODE-DCC/atac-seq-pipeline) including reproducible peak calls using the IDR method
The alignment BAM files for each biological replicate were used to create track formatted bedGraph files that were normalized to counts per million mapped reads (CPM) using Deeptools bamCoverage (https://github.com/deeptools/deepTools)
Assembly: mm10
Supplementary files format and content: bedGraph; track formatted histogram of ATAC-seq signal
Supplementary files format and content: narrowPeak; coordinates of accessible chromatin regions

source_name: neural stem/progenitor cell

growth_protocol: All cells were maintained on poly-d-lysine and laminin coated plates in N2B27 media supplemented with EGF and bFGF

extract_protocol:
30,000 ESC-derived NSPCs were dissociated with Accutase and washed once with 0.04% BSA in PBS. Cells were lysed in cold resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin for three minutes. Cell lysis was halted by dilution with 0.1% Tween-20 in resuspension buffer before pelleting nuclei at 500 RCF for 10 minutes in a 4 °C microcentrifuge. Isolated nuclei were resuspended in a 50 μL transposition mix (25 μL of 2X Tagment DNA buffer [20 mM Tris-HCl, 10 mM MgCl2, 20% dimethyl formamide], 2.5 μL transposase (100 nM final), 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, and 5 μL water) and incubated at 37°C for 30 minutes in a thermomixer, with shaking at 1000 RPM.
Transposed fragments were cleaned up with the MinElute kit (Quiagen). Libraries were amplified for 11-14 cycles with universal and indexing primers using NEBNext HiFi 2X PCR Master Mix and dual size selection with 0.7X and 0.3X volumes of AMPure XP beads (Beckman Coulter). Library size was assessed using the 2100 Bioanalyzer (Agilent) before NovaSeq 6000 sequencing using paired-end 50 cycle parameters at a depth of 50-60 million reads per sample.

treatment_protocol: Enhancer deleted clones contain heterozygous or homozygous deletions of enhancer clusters within the study. Deletions were generated in mouse embryonic stem cells using Cas9 endonuclease and guide RNA.

tag: strain

value: 129S1/Cast F1 Hybrid

value: Clone 47D

value: neural stem/progenitor cell

value: Sox2-mCherry (129), homozygous SRR2-18 deletion

value: homozygous enhancer deletion


title: S2005S0840

value: brain


title: U937 cells, SGF29 knockout, rep 2

description:
U937_SGF_2
SGF29_RNASeq_gene.results.merged.tpm.xlsx


title: S2004S0776


title: HiC_wt_rep1_1

description:
wt.hic
wt.mcool

value: embryonic stem cells


title: ATAC-Seq SRR2-18_47D_biol_rep2


title: S2004S0775


title: U937 cells, SGF29 knockout, rep 1

description:
U937_SGF_1
SGF29_RNASeq_gene.results.merged.tpm.xlsx

value: Monocytes


title: ATAC-Seq SRR2-18_47D_biol_rep1


title: cChIPseq_GT_wt_Suz12_rep2


title: S2003S0748


title: U937 cells, non-targeting control, rep 4

description:
NTCR01
TPM_MLL-CK2-NTC.xlsx

value: Acute Myeloid Leukemia


title: HiC_wt_rep3_1

description:
wt.hic
wt.mcool


title: cChIPseq_GT_wt_Suz12_rep1


title: S2003S0746


title: ATAC-Seq F1_parent_biol_rep3

value: Clone 5B

value: Sox2-mCherry (129)

value: no deletion


title: S2001S0577


title: ATAC-Seq F1_parent_biol_rep2


title: cChIPseq_GT_wt_Ring1B_rep2


title: ATAC-Seq F1_parent_biol_rep1


title: U937 cells, non-targeting control, rep 3

description:
NTC4
TPM_MLL-CK2-NTC.xlsx

value: Non-targeting control

value: CRISPR sgRNA lentiviral transduction


title: U937 cells, non-targeting control, rep 2

description:
NTC3
TPM_MLL-CK2-NTC.xlsx


title: cChIPseq_GT_wt_Ring1B_rep1


title: S2000S0574


title: cChIPseq_GT_wt_Rad21_rep2


title: S2000S0520


title: Beta-glucan/anti-CD40_2

city: Philadelphia

first: Max

middle: M

last: Wattenberg

state: PENNSYLVANIA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Data was processed using the Cell Ranger pipeline (10x Genomics, v.6.1.2) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome and creation of feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: tar archives include barcodes.tsv, features.tsv, matrix.mtx, and filtered_feature_bc_matrix.h5 Cell Ranger pipeline outputs.

source_name: Orthotopic tumor (PDA.7940B tumor cells)

extract_protocol:
Tumors were minced with micro-dissecting scissors at 4°C in DMEM containing collagenase (1mg/mL, Sigma-Aldrich) and DNase (150 U/mL, Sigma) and incubated at 37°C for 45 minutes with intermittent agitation. Tissues were filtered through a 70-um nylon strainer (Corning). Cells were then incubated in ACK lysing buffer (Life Technologies) for 5 minutes, washed with DMEM and filtered through a 40-um strainer and dead cells were removed by magnetic bead sorting per the manufacturer's protocol (Miltenyi).
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3.1 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run.

treatment_protocol: Mice were implanted with PDA.7940B tumor cells into the pancreas. Ten days later mice were left untreated or were treated with a single dose of beta-glucan (1.2mg/kg) intravenous, anti-CD40 (0.1 mg) intraperitoneal or the combination and eight days later necropsy was performed.

value: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma

value: WT

value: Beta-glucan + anti-CD40


title: cChIPseq_GT_wt_Rad21_rep1


title: U937 cells, non-targeting control, rep 1

description:
NTC1
TPM_MLL-CK2-NTC.xlsx


title: U937 cells, CNK2A1 knockout, rep 3

description:
CK2R03
TPM_MLL-CK2-NTC.xlsx

value: CSNK2A1 knockout


title: Beta-glucan/anti-CD40_1

value: Orthotopic tumor (PDA.7940B tumor cells)


title: U937 cells, CNK2A1 knockout, rep 2

description:
CK2R02
TPM_MLL-CK2-NTC.xlsx


title: cChIPseq_GT_wt_PDS5A_rep2


title: cChIPseq_GT_wt_PDS5A_rep1


title: HCC3153_dH3_dox_long_H3K27ac_ChIP_Input_2

city: Boston

first: Daniel

last: Temko

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

data_processing:
Reads were aligned to hg19 with BWA-mem v0.7.17 (http://bio-bwa.sourceforge.net).
Duplicates were removed using Picard MarkDuplicates v2.18.17 (http://broadinstitute.github.io/picard/), with parameters (REMOVE_DUPLICATES=TRUE, VALIDATION_STRINGENCY=LENIENT).
ChIP-signal was quantified and peaks were called using MACS2 v2.1.2 {Zhang, 2008, PMID:18798982}, with parameters (--SPMR -B --keep-dup=1 --extsize=146 --nomodel, -q 0.05).
Assembly: hg19
Supplementary files format and content: bigwig of signals
Supplementary files format and content: bed files of called peaks

source_name: breast cancer

growth_protocol: Cells were grown in their respective media prepared per provider's guidelines, at 37 degree C, 5% CO2.

extract_protocol:
Cells were cross-linked in fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube, and immunoprecipitation (IP) was conducted overnight at 4 °C. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using xGen DNA EZ Library Prep Kit from (IDT) with xGen™ UDI Primer Pairs according to manufacturers protocol.

treatment_protocol: cells were treated with (dox) or without (no_dox) Doxycyclin to induce TRE promoter gene expression

value: breast cancer

tag: parental cell_line

value: tumor cells

value: doxycycline

tag: time point

value: 42 days


title: U937 cells, MLL knockout, rep 3

description:
MLL4
TPM_MLL-CK2-NTC.xlsx

value: MLL knockout


title: HCC3153_dH3_dox_long_H3K27ac_ChIP_Input_1


title: Beta-glucan_2

value: Beta-glucan (1.2mg IV x1)


title: cChIPseq_GT_wt_Pcgf1_rep2

value: embryonic stem cells


title: HCC3153_dH3_no_dox_long_H3K27ac_ChIP_Input_2

value: no doxycycline


title: U937 cells, MLL knockout, rep 2

description:
MLL2
TPM_MLL-CK2-NTC.xlsx

value: Monocytes

value: Acute Myeloid Leukemia


title: cChIPseq_GT_wt_Input_2


title: U937 cells, MLL knockout, rep 1

description:
MLL1
TPM_MLL-CK2-NTC.xlsx


title: untreated_2

value: untreated


title: HCC3153_dH3_no_dox_long_H3K27ac_ChIP_Input_1


title: cChIPseq_GT_wt_Input_1


title: S1998S0461

extract_protocol:
Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit to remove cytoplasmic and mitochondrial rRNAs and QIAseq FastSelect –5S/16S/23S Kit to remove pan bacterial rRNAs (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to adapters for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA).
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA).

value: brain

tag: group

value: suicide


title: untreated_1

value: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma

value: WT


title: HCC3153_wt_dox_long_H3K27ac_ChIP_Input_2

value: wild type


title: cChIPseq_GT_wt_H3K27me3_rep2


title: HCC3153_wt_dox_long_H3K27ac_ChIP_Input_1


title: HCC3153_wt_no_dox_long_H3K27ac_ChIP_Input_2


title: N2a cells, PT2, rep2

city: changchun

first: junchao

last: Shi

state: jilin

address: xi'an road

department: College of Veterinary Medicine

institute: Jilin University

description:
FPKMs_allsamples.txt
raw_counts.txt

data_processing:
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
Differential expression analysis of two conditions/groups (3 biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: N2a cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Mock or PHEV-infected N2a cells were treated with 1 μM Thapsigargin or DMSO for 24 h

value: Mouse neuroblastoma

value: PHEV infection and Thapsigargin treatment


title: cChIPseq_GT_wt_H3K27me3_rep1


title: anti-CD40_1

value: Orthotopic tumor (PDA.7940B tumor cells)

value: anti-CD40 (FGK45, 0.1mg IP x1)


title: N2a cells, PT1, rep1

description:
FPKMs_allsamples.txt
raw_counts.txt


title: U937 cells, CNK2A1 knockout, rep 1

description:
CK2R01
TPM_MLL-CK2-NTC.xlsx

value: CSNK2A1 knockout

value: CRISPR sgRNA lentiviral transduction


title: cChIPseq_GT_wt_Pcgf1_rep1


title: cChIPseq_GT_wt_H2AK119ub_rep2


title: anti-CD40_2


title: Beta-glucan_1

value: Beta-glucan (1.2mg IV x1)


title: Femur 2-1

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

data_processing:
SpaceRanger
Seurat
Assembly: mm10
Supplementary files format and content: spatial files, matrix.h5 files and text file for suture coordinates and genotype
Library strategy: Visium Spatial Transcriptomics

source_name: Femur

growth_protocol: 10 week old mice

extract_protocol:
FFPE (manufacturer's protocol)
10X Visium Spatial Gene Expression (manufacturer's protocol)

treatment_protocol: Decalcified in EDTA for 2 weeks

tag: developmental stage

value: 10 week old

value: Femur


title: HCC3153_wt_no_dox_long_H3K27ac_ChIP_Input_1

value: breast cancer

value: tumor cells

value: no doxycycline

value: 42 days


title: Femur 1-2


title: HCC3153_dH3_dox_short_H3K27ac_ChIP_Input_2

value: doxycycline

value: 7 days


title: Femur 1-1


title: Femur 2-2


title: HCC3153_dH3_dox_short_H3K27ac_ChIP_Input_1


title: N2a cells, P1, rep1

description:
FPKMs_allsamples.txt
raw_counts.txt

value: WT

value: PHEV infection


title: cChIPseq_GT_wt_H2AK119ub_rep1

value: embryonic stem cells


title: N2a cells, P2, rep2

description:
FPKMs_allsamples.txt
raw_counts.txt

value: Mouse neuroblastoma


title: HCC3153_dH3_no_dox_short_H3K27ac_ChIP_Input_2


title: cChIPseq_GT_wt_CTCF_rep1


title: cChIPseq_GT_wt_Cbx7_rep2


title: N2a cells, T2, rep2

description:
FPKMs_allsamples.txt
raw_counts.txt

value: Thapsigargin treatment


title: HCC3153_dH3_no_dox_short_H3K27ac_ChIP_Input_1


title: N2a cells, T3, rep3

description:
FPKMs_allsamples.txt
raw_counts.txt


title: HCC3153_wt_dox_short_H3K27ac_ChIP_Input_2

value: wild type


title: cChIPseq_GT_wt_CTCF_rep2


title: N2a cells, T1, rep1

description:
FPKMs_allsamples.txt
raw_counts.txt


title: cChIPseq_GT_Pds5a_KO_Suz12_rep2


title: N2a cells, M3, rep3

description:
FPKMs_allsamples.txt
raw_counts.txt

value: DMSO treatment


title: cChIPseq_GT_wt_Cbx7_rep1


title: tdKO, bio1, tech2

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using spaceranger v2.0.0 (Bcl2fastq 2.20.0), and alignment was performed using spaceranger v2.0.0 (STAR2.7.2a). Sequenced reads were aligned to the 10x Genomics provided mouse reference sequence (refdata-gex-mm10-2020-A) and probe set (Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A).
Assembly: mm10
Supplementary files format and content: jpg; aligned tissue images
Supplementary files format and content: jpg; aligned fiducials
Supplementary files format and content: tiff; cytassist image
Supplementary files format and content: jpg; detected tissue images
Supplementary files format and content: png; tissue images
Supplementary files format and content: csv; spatial enrichment
Supplementary files format and content: csv; tissue positions
Supplementary files format and content: h5; matrix file
Supplementary files format and content: json; scalefactors
Library strategy: Spatial Transcriptomics

extract_protocol:
Probe hybridization and all subsequent steps were performed as per 10X User guide for Visium CytAssist Spatial Gene Expression (CG000495).
Subsequently, probe extension was carried out and the ligation product was eluted, and a pre-amplification step performed. A subset of the pre-amplification product was used for library construction.

value: Thymus

value: Rep 1

tag: technical replicate

value: Zfp148 fl/fl; Zfp281 fl/fl; Cd4-Cre+


title: HCC3153_wt_dox_short_H3K27ac_ChIP_Input_1


title: Ctrl, bio2


title: tdKO, bio1, tech1


title: Ctrl, bio1, tech2


title: tdKO, bio2


title: HCC3153_wt_no_dox_short_H3K27ac_ChIP_Input_1


title: N2a cells, PT3, rep3

description:
FPKMs_allsamples.txt
raw_counts.txt

tag: cell line

value: PHEV infection and Thapsigargin treatment


title: Ctrl, bio1, tech1

tag: replicate


title: N2a cells, M2, rep2

description:
FPKMs_allsamples.txt
raw_counts.txt


title: N2a cells, M1, rep1

description:
FPKMs_allsamples.txt
raw_counts.txt


title: p53-/-, TBI, Day1 rep2

city: NEW BRUNSWICK

first: Jianming

last: Wang

state: NJ

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.

source_name: Small intestine

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: 12 Gy TBI with a Cs-137 γ-source irradiator

value: Small intestine

value: 12Gy TBI


title: cChIPseq_GT_Pds5a_KO_Ring1B_rep2

extract_protocol:
RNA-seq: 5 million mESCs were trypsinized and collected by centrifugation. Resulting cell pellets were washed in 1x PBS and resuspended in 1x DNA/RNA protection reagent (Monarch Total RNA Miniprep Kit, NEB). Subsequently, cells were lysed and total RNA extracted following the mammalian cell protocol including optional on-column DNase I treatment. Calibrated ChIP-seq (cChIP) and ChIPCap-seq: 30 million mESCs and HEK293T cells were collected, washed once in 1x PBS and crosslinked for 7 min in 1% formaldehyde. The crosslinking was quenched by addition of 125 mM glycine and incubated on ice. The crosslinked cells were pelleted by centrifugation for 5 min at 1200g at 4 °C. Nuclei were prepared by washes with NP-Rinse buffer 1 (10 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 0.5 mM EGTA, 0.25% Triton X-100) followed by NP-Rinse buffer 2 (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Afterwards, the nuclei were washed twice with shearing buffer (1 mM EDTA pH 8.0, 10 mM Tris-HCl pH 8.0, 0.1% SDS) and subsequently resuspended in 900 µL shearing buffer with added 1× protease inhibitors complete mini (Roche). Chromatin was sheared by sonication in 15 ml Bioruptor tubes (Diagenode, C01020031) with 437.5 mg sonication beads (Diagenode, C03070001) for 6 cycles (1 min on/1 min off) on a Bioruptor Pico sonicator (Diagenode). For each ChIP reaction 4 % HEK293T-derived human spike-in lysate was combined with mESC lysate and incubated in 1x IP buffer (50 mM HEPES/KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS), with following appropriate antibodies at 4 °C o/n a rotating wheel: H3K27me3 (Diagenode, C15410195), RING1B (Cell Signaling, D22F2), PDS5a (Millipore Sigma #SAB2101764), SUZ12 (Cell Signaling D39F6), H2AK119ub (Cell Signaling D27C4), PCGF1 (Abcam ab202395), RAD21 (Abcam ab992), CTCF (Millipore 070729). Antibody-bound chromatin was captured using Dynabeads protein G beads (Thermofisher #10004D) for 4 hours at 4°C. ChIP washes were performed as described previously (Farcas et al., 2012). ChIPs were washed 5x with 1x IP buffer ( 50 mM HEPES/KOH pH 7.5, 300 mM NaCl, I mM EDTA, 1% Triton-X100, 0.1% DOC, 0.1% SDS), or 1.5x IP buffer for H3K27me3 and H2AK119ub, followed by 3x washes with DOC buffer (10 mM Tris pH 8, 0.25 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% DOC) and 1x with TE/50 mM NaCl. ChIP DNA was eluted 2x in elution buffer (1% SDS, 0.1 M NaHCO3 ) at 65°C for 20 min, RNase A treated for 30 min at 37 °C, Proteinase K treated for 3 hrs at 55 °C and crosslinks were reversed o/n at 65 °C. The following day, ChIP samples and corresponding inputs were puriﬁed by PCI extraction and DNA precipitation. In Situ Hi-C: Hi-C was performed as previously described (Rao et al., 2014) with modifications described in (Boyle et al., 2020) as following: 5 million mESCs were crosslinked in 1% formaldehyde for 10 mins before the reaction was quenched by adding 0.2 M final glycine. Cells were permeabilized in lysis buffer (0.2% IGEPAL, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) and nuclei isolated in NEBuffer 3 supplemented by 0.3% SDS at 62 °C for 10 min. SDS was quenched with 1% Triton X100 at 37°C for 60 min, the nuclei pelleted and resuspended in 250 µl of 1x DpnII buffer with 600 U DpnII (NEB). Following o/n digestion at 37°C, 200 U were added for 2 hrs. DpnII was inactivated for 20 min at 65°C before the DNA ends were filled-in and biotinmarked using Klenow, d(C/G/T)TPs and biotin-14-dATP for 90 min at 37°C. Proximity ligation was performed using T4 DNA ligase (NEB) for 4 hrs at room temperature. Subsequently, nuclei were spun down, resuspended in 200 µl mQ water and digested with proteinase K for 30 min at 55°C in presence of 1% SDS. For crosslink reversal 1.85 M final NaCl was added and samples incubated at 65°C o/n. The next day, sample DNA was ethanol precipitated and sheared in 500 µL sonication buffer (50 mM Tris pH 8.0, 0.1% SDS, 10 mM EDTA) on a Bioruptor Pico sonicator (Diagenode). DNA was then concentrated on Amicon ultra 0.5 30K ﬁlter units (Millipore), biotin-pulldown performed using MyOne Streptavidin T1 beads (Life technologies, 65602) and used for NGS library preparation.
RNA-seq: For RNA-seq library preparation, 1 µg of total RNA per sample was enriched for poly-A using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and final RNA-seq libraries generated using the NEBNext Ultra II Directional RNA Library Prep kit (NEB, E7760 and NEBNext Multiplex Oligos (NEB, E7335/E7500). cChIP-seq and ChIPCap-seq library preparation: Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol. Libraries were purified using Agencourt AMPure XP (Beckman Coulter) and amplified using the KAPA Real-Time Library Amplification Kit (KAPABiosystems) following the manufacturer’s instructions. ChIPCap-seq libraries were prepared identically to ChIP-seq libraries. After PCR amplification the libraries were enriched for loci of interest using the MYbaits kit DNA capture target enrichment system (Arbor Biosciences) according to manufacturer’s manual. 120 nucleotides long MYbaits sequence capture probes (Arbor Biosciences) were custom designed against 25 mm9 genomic loci (Table S3). Library quality control including determination of average size and concentration was performed prior to sequencing by commercial Next Generation Sequencing providers. NGS libaries were eventually sequenced as 150 bp paired-end reads on the Illumina HiSeq platform. In situ HiC: DNA ends were repaired, biotin removed from unligated ends and NEXTFLEX DNA barcoded adapters (Perkin Elmer) were ligated. Desired PCR cycle numbers were determined in test endpoint PCRs using Q5 DNA polymerase (NEB M0491L). Final HiC libraries were generated from 4-6 individual PCR reactions, which were pooled and subjected to cleanup and size-selection using AMPure beads (Beckman Coulter A63882). Samples were ﬁrst test sequenced to check library quality before selected Hi-C ibraries were sequenced at greater depth (Table S2).
NGS libaries were eventually sequenced as 50 bp single-end reads or 150 bp paired-end reads on Illumina platforms


title: HCC3153_wt_no_dox_short_H3K27ac_ChIP_Input_2

value: breast cancer

value: tumor cells

value: no doxycycline

tag: antibody


title: RNA-Seq SRR2-18_47D_Diff10_rep2

data_processing:
Reads were trimmed using fastp/0.20 (https://github.com/OpenGene/fastp) with standard settings.
Reads were aligned to mm10 using STAR/2.7.9a (https://github.com/alexdobin/STAR) with the following options: --alignEndsType Local --outFilterMultimapNmax 20
The alignment BAM files for each biological replicate were used to create track formatted bedGraph files that were normalized to counts per million mapped reads (CPM) using Deeptools bamCoverage (https://github.com/deeptools/deepTools)
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: mixed neural differentiated cell progeny

growth_protocol: All neural stem and progenitor cells were maintained on poly-d-lysine and laminin coated plates in N2B27 media supplemented with EGF and bFGF. To induce differentiation of NSPCs into neurons and astrocytes, cells were cultured in complete NeuroCult™ Differentiation Kit (Mouse & Rat) medium for 10 days.

extract_protocol:
RNA was extracted using silica-membrane RNeasy columns (Qiagen) and treated with TURBO DNase (Thermo Fisher) prior to library construction
Total ribo-depleted RNA-seq libraries were prepared for Illumina HiSeq2500 125bp paired-end sequencing

value: 129S1/Cast F1 Hybrid

value: Clone 47D

value: Sox2-mCherry (129), SRR2-18 deletion (129/Cast)

value: homozygous enhancer deletion


title: N2a cells, P3, rep3

description:
FPKMs_allsamples.txt
raw_counts.txt

value: Mouse neuroblastoma

value: WT

value: PHEV infection


title: cChIPseq_GT_Pds5a_KO_Ring1B_rep1

value: embryonic stem cells


title: cChIPseq_GT_Pds5a_KO_Rad21_rep2


title: SUM185_dH3_dox_long_H3K27ac_ChIP_Input_1

value: doxycycline

value: 42 days


title: RNA-Seq SRR2-18_47D_Diff10_rep1

value: mixed neural differentiated cell progeny


title: cChIPseq_GT_Pds5a_KO_Suz12_rep1


title: WT, TBI, Day1 rep2


title: cChIPseq_GT_Pds5a_KO_Rad21_rep1


title: SUM185_dH3_no_dox_long_H3K27ac_ChIP_Input_1


title: RNA-Seq F1_parent_Diff10_rep2

value: Clone 5B

value: Sox2-mCherry (129)

value: no deletion


title: WT, TBI, Day1 rep1

value: Small intestine

value: 12Gy TBI


title: cChIPseq_GT_Pds5a_KO_PDS5A_rep1


title: RNA-Seq F1_parent_Diff10_rep1


title: cChIPseq_GT_Pds5a_KO_PDS5A_rep2


title: SUM185_wt_dox_long_H3K27ac_ChIP_Input_2

value: breast cancer

value: tumor cells

value: wild type


title: cChIPseq_GT_Pds5a_KO_Input_2


title: SUM185_wt_dox_long_H3K27ac_ChIP_Input_1


title: RNA-Seq SRR2-18_47D_rep2

value: 129S1/Cast F1 Hybrid

value: Clone 47D

value: neural stem/progenitor cell

value: Sox2-mCherry (129), SRR2-18 deletion (129/Cast)


title: RNA-Seq SRR2-18_44D_rep1

value: Clone 44D

value: homozygous enhancer deletion


title: SUM185_dH3_dox_long_H3K27ac_ChIP_Input_2

value: doxycycline


title: MEF_Ifng_A

city: Gainesville

first: Zongliang

last: Jiang

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
Multiplexed sequencing reads that passed filters were trimmed to remove low-quality reads and adaptors by TrimGalore (version 0.6.7) (-q 25 --length 20 --max_n 3 --stringency 3). The quality of reads after filtering was assessed by fastQC, followed by alignment to the mouse genome (GRCm39) by HISAT2 (version 2.2.1) with default parameters. The output SAM files were converted to BAM files and sorted using SAMtools6 (version 1.14). Read counts of all samples were quantified by using FeatureCount (Version 2.0.1) with mouse genome as a reference and were adjusted to provide CPM (Counts per million mapped reads). Principal component analysis (PCA) and cluster analysis were performed by using R (a free software environment for statistical computing and graphics). Differentially expressed genes (DEGs) was identified by using edgeR in R. The genes were considered differentially expressed if they provided a false discovery rate of <0.05 and fold change >2. ClusterProfiler was used to reveal the Gene Ontology (GO) and KEGG pathways in R.
Assembly: GRCm39
Supplementary files format and content: txt, normalized read counts

source_name: MEF

extract_protocol:
RNA isolation from cultured cells was used Trizol reagent.
RNA-seq libraries were prepared using the NEBNext RNA Library Prep Kit (New England Biolabs, NEB) .

treatment_protocol: Mouse TSCs (provided by Dr. Wei Hsu, University of Rochester Medical Center) were routinely maintained in the medium that contains 70% mouse embryonic fibroblast (MEF)-conditioned medium and 30% basal TSC culture medium (RPMI 1640 containing 20% FBS, 1 mM sodium pyruvate, 2 mM L-glutamine, 50 units/mL penicillin, 50 μg/mL streptomycin, 0.1 μM 2-mercaptoethanol, 25 ng/mL FGF4, and 1 μg/mL heparin). TSC differentiation was carried out according the published protocols.  Briefly, TSCs were promoted to differentiate by withdrawing FGF4, heparin, and MEF-conditioned medium and were cultured in basal TSC culture medium for 5-6 days. The differentiated cells were designated as TSC-TBs.  The culture conditions for ESC-FBs and MEFs were previously described.  All cells were maintained at 37 °C in a humidified incubator with 5% CO2.

value: MEF

value: IFNγ


title: RNA-Seq SRR2-18_11C_rep2

value: Clone 11C

value: Sox2-mCherry (129), SRR2-18 deletion (Cast)

value: heterozygous enhancer deletion


title: cChIPseq_GT_Pds5a_KO_Input_1

data_processing:
RNA-seq Data Analysis: Raw paired-end RNA-seq reads were aligned to the mm10 genome using STAR-2.6.1c (Dobin et al., 2013). Overlap of STAR-aligned reads with genes was performed using HTSeq count function (Anders et al., 2015) with stranded=reverse option and the GRCm38 version 94 GTF file. The HTseq count matrix was pre-filtered to exclude genes with a read count below 10. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014) using the “apeglm” method (Zhu et al., 2019) for LFC shrinkage. We applied a threshold of p-adj < 0.05 and fold change > 0.5 or -0.5 for gene expression changes to be considered significant. Visualization of RNA-seq data was performed using custom R scripts and ggplot2. Gene ontology analysis for significantly deregulated genes was performed using custom R scripts and clusterProfiler reference (Wu et al., 2021; Yu et al., 2012).
ChIP-seq Data Analysis: Raw reads were mapped to the custom concatenated mouse (mm10) and spike-in human (hg38) genome sequences using bowtie 2 with “–no-mixed” and “no-discordant” options (Langmead and Salzberg, 2012). Subsequently, low quality reads were filtered using SAMtools (Li et al., 2009), duplicated reads were discarded with the Picard toolkit (http://broadinstitute.github.io/picard/) and only unique mapped reads were retained. For visualization uniquely mapped mouse reads were normalized by random subsampling with samtools using calibration factors calculated from the corresponding hg38 spike-in reads as described previously (Bonhoure et al., 2014; Fursova et al., 2019; Hu et al., 2015). High correlation between replicates was confirmed using multiBamSummary and plotCorrelation functions from deepTools (Ramírez et al., 2016) before merging for visualization and downstream analysis. Genome coverage tracks (bigWig files) were produced with MACS2’ pileup function (Zhang et al., 2008) and heatmaps and profile plots generated with deepTools (Ramírez et al., 2016). Peaks were called on each replicate independently using MACS2 (Zhang et al., 2008). Peaks overlapping with a custom-build blacklist were discarded to remove sequencing artifacts and only peaks called in both replicates were retained for downstream analysis.
Hi-C data analysis: Hi-C data were analyzed using the HiC-Pro (2.11.1) pipeline (Servant et al., 2015). Read mapping to the mm10 genome was performed using bowtie 2 (Langmead and Salzberg, 2012) within the HiC-Pro pipeline. PCR and optical duplicates as well as reads with MAPQ < 30 were removed. Filtered valid HiC contact data was binned and raw and ICE normalized .hic contact matrices were generated. We also produced balanced single and multi-resolution .cool and .mcool cooler files for visualization in HiGlass.
Genome_build: mm10; ChIPcapseq: amended mm9 genome build

value: embryonic stem cells


title: p53-/-, TBI, Day1 rep1

value: Small intestine

value: 12Gy TBI


title: MEF_Ifng_B


title: SUM185_wt_no_dox_long_H3K27ac_ChIP_Input_2

value: breast cancer

value: tumor cells

value: no doxycycline

value: 42 days


title: SUM185_dH3_no_dox_long_H3K27ac_ChIP_Input_2


title: cChIPseq_GT_Pds5a_KO_H3K27me3_rep2


title: RNA-Seq SRR2-18_23C_rep1

value: 129S1/Cast F1 Hybrid

value: Clone 23C

value: neural stem/progenitor cell


title: TSC_TB_TNFa_B

value: TNFα


title: TSC_TB_TNFa_A


title: SUM185_dH3_dox_short_H3K27ac_ChIP_Input_2

value: doxycycline

value: 7 days


title: cChIPseq_GT_Pds5a_KO_H3K27me3_rep1


title: TSC_TB_TNFa_C


title: MEF_Ifng_C

value: MEF

value: IFNγ


title: RNA-Seq SRR2-18_43B_rep2

value: Clone 43B

value: Sox2-mCherry (129), SRR2-18 deletion (129)


title: cChIPseq_GT_Pds5a_KO_H2AK119ub_rep2

value: embryonic stem cells


title: RNA-Seq SRR2-18_18B_rep1

value: Clone 18B

value: heterozygous enhancer deletion


title: cChIPseq_GT_Pds5a_KO_H2AK119ub_rep1


title: RNA-Seq F1_parent_rep4

value: Clone 5B

value: Sox2-mCherry (129)

value: no deletion


title: TSC_TB_T_G_B

value: TNFα and IFNγ


title: SUM185_wt_no_dox_long_H3K27ac_ChIP_Input_1

value: breast cancer

value: tumor cells

value: wild type

value: no doxycycline

value: 42 days


title: RNA-Seq F1_parent_rep2

value: 129S1/Cast F1 Hybrid

value: neural stem/progenitor cell


title: TSC_TB_T_G_A


title: TSC_TB_T_G_C


title: ChIPCapseq_reporter_TetRCbx7_Suz12 rep1


title: TSC_IFNG_C

source_name: TSC

value: TSC

value: IFNγ


title: RNA-Seq F1_parent_rep3


title: SUM185_dH3_no_dox_short_H3K27ac_ChIP_Input_1

value: 7 days


title: SUM185_wt_no_dox_short_H3K27ac_ChIP_Input_2


title: ChIPCapseq_reporter_TetRCbx7_Ring1B rep1

value: embryonic stem cells


title: ChIPCapseq_reporter_TetRCbx7_Suz12 rep2


title: SUM185_wt_dox_short_H3K27ac_ChIP_Input_2

value: doxycycline


title: ChIPCapseq_reporter_TetRCbx7_H2AK119ub rep1


title: TSC_IFNG_A


title: HCC3153_dH3_dox_long_H3K27ac_ChIP_1

value: anti-H3K27ac (Diagenode, C15410196)


title: SUM185_wt_dox_short_H3K27ac_ChIP_Input_1


title: RNA-Seq F1_parent_rep1

value: Clone 5B


title: Ctbp2 KO, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 2

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Sequencing adapters were removed using Trimmomatic v.0.33 (Bolger et al., 2014) . Quality control at each processing step was performed using the FastQC tool v0.11.2 (quality base calls, CG content distribution, duplicate levels, complexity level). The Mouse GRCm38/mm10 reference genome was obtained from UCSC Genome Browser Gateway (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz), and the corresponding gene annotation file was obtained from Ensemble (ftp://ftp.ensembl.org/pub/release-83/ gtf/mus_musculus/Mus_musculus.GRCm38.83.gtf.gz). Only autosomes, mitochondrial, and sex chromosomes were used. Reads were aligned using the subread v.1.6.2 aligne.
We obtained gene counts for each sample based on the last hg38 version of Ensembl transcriptome (v.87) using the featureCounts v.1.2.6 software (Liao et al., 2014) . RNA-seq counts were preprocessed and analyzed for differential expression using edgeR v.3.24.3 (Robinson et al., 2010). p-values for differentially expressed genes were corrected using a False Discovery Rate (FDR) multiple testing correction method (Benjamini & Hochberg, 1995).
Functional enrichment analysis (GO, KEGG) was performed using enrichr (Chen et al., 2013). Enrichment analysis using custom signatures was performed using a hypergeometric test in the clusterProfiler v.3.10.1 R package (Yu et al., 2012). Row-median centered log2(T P M + 1) expression profiles for selected genes were visualized using the pheatmap package v.1.0.12. All statistical calculations were performed within R/Bioconductor environment v3.5.3.
Assembly: GRCm38/mm10
Supplementary files format and content: txt

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
Quickly after euthanizing the mice, pancreata were harvested under ice-cold conditions. The isolated tissues were powdered by triturating using liquid nitrogen, and RNA was extracted by performing Triazole-Chloroform extraction method (Chougoni & Grossman et al).
Total RNA was isolated using RNeasy Mini kit (Qiagen) according to the manufacturer’s recommendations. RNA integrity number (RIN) value was assessed on an Agilent 2100 Bioanalyzer, and samples with RIN value above 9 were selected for sequencing purposes. Prior to the RNA-Seq, ribosomal RNA was depleted from the samples using the RiboMinusTM Human/Mouse Transcriptome Isolation Kit (Thermo Fisher Scientific, Waltham, MA). All samples were sequenced on the Illumina Hi-Seq sequencer; ~29 million 50 bp single-end reads per sample were obtained.

value: Pancreatic ductal adenocarcinoma

value: KO


title: ChIPCapseq_reporter_TetRCbx7_Ring1B rep2


title: Ctbp2 KO, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 5


title: ChIPCapseq_reporter_TetRCbx7_H3K27me3 rep1


title: TSC_IFNG_B


title: SUM185_wt_no_dox_short_H3K27ac_ChIP_Input_1


title: HCC3153_dH3_no_dox_long_H3K27ac_ChIP_1


title: Ctbp2 KO, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 4


title: ChIPCapseq_reporter_TetRCbx7_Input rep1


title: SUM185_dH3_dox_short_H3K27ac_ChIP_Input_1


title: HCC3153_dH3_no_dox_long_H3K27ac_ChIP_2


title: Ctbp2 KO, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 3


title: TSC_TB_IFNG_C


title: TSC_TB_IFNG_A


title: ChIPCapseq_reporter_TetRCbx7_H2AK119ub rep2


title: WT, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 5

value: WT


title: TSC_TNFa_A

value: TNFα


title: ChIPCapseq_reporter_TetRCbx7_H3K27me3 rep2


title: SUM185_dH3_no_dox_short_H3K27ac_ChIP_Input_2

value: breast cancer

value: tumor cells


title: TSC_TB_IFNG_B


title: HCC3153_dH3_dox_long_H3K27ac_ChIP_2


title: Ctbp2 KO, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 1


title: TSC_TNFa_B


title: ChIPCapseq_reporter_TetRCbx7_Input rep2


title: HCC3153_wt_dox_long_H3K27ac_ChIP_2

value: wild type


title: WT, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 4


title: HCC3153_wt_dox_long_H3K27ac_ChIP_1

value: 42 days


title: ChIPCapseq_reporter_Suz12 rep1


title: WT, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 3


title: WT, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 2


title: HCC3153_wt_no_dox_long_H3K27ac_ChIP_2

value: no doxycycline


title: ChIPCapseq_reporter_Ring1B rep1


title: MEF_Con_B

value: MEF

value: control


title: ChIPCapseq_reporter_Suz12 rep2


title: TSC_Con_B

value: TSC


title: HCC3153_dH3_dox_short_H3K27ac_ChIP_2

value: 7 days


title: WT, CKP, a mouse PDAC cell line derived from PDAC tumors of  C57BL/6J Pdx1-Cre; LSL-K-rasG12D; p53fl/fl, rep 1


title: HCC3153_wt_no_dox_long_H3K27ac_ChIP_1


title: HCC3153_dH3_dox_short_H3K27ac_ChIP_1


title: ChIPCapseq_reporter_Ring1B rep2

value: embryonic stem cells


title: TSC_Con_C


title: MEF_Con_A


title: OTI_sgTmed_Veh_Act_rep2

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description:
replicate 2
5894_32_OT-I_Tmed10_Act_rep2_AGTTCCG_S44_R1_001

data_processing:
Sequence samples were mapped to the mouse genome (GRCm38) using STAR(2.6.0c) using 2-pass mapping with default settings. Sequence reads were counted using HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Un-processed read count data

source_name: Mouse T-cells

growth_protocol: T cells were maintained in RPMI/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL) with IL-2 (10ng/mL), IL-7 (0.5ng/mL), IL-15 (1ng/mL), betamercaptoethanol (50uM) and puromycin (4ug/mL) and passaged every day at a density of 1*10^6/mL.

extract_protocol:
RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For drug treatment, H2O or AGN192403 (100uM) was added to the culture where indicated. For activation, a 24-well non-tissue-culture-treated plate was coated with anti-CD3 antibodies overnight and on the day of the experiment, cells were seeded on this plate at a density of 1*10^6/mL where indicated.

value: OT-I/Cas9 CD8 T cells

value: Tmed10 KO

tag: activation

value: Act


title: OTI_sgTmed_Veh_Act_rep1

description:
replicate 1
5894_31_OT-I_Tmed10_Act_rep1_AGTCAAC_S43_R1_001


title: ChIPCapseq_reporter_H3K27me3 rep1


title: HCC3153_dH3_no_dox_short_H3K27ac_ChIP_2

tag: condition

value: anti-H3K27ac (Diagenode, C15410196)


title: OTI_sgTmed_Veh_Rest_rep2

description:
replicate 2
5894_30_OT-I_Tmed10_Rest_rep2_CTTGTAA_S42_R1_001

value: Rest


title: TSC_Con_A


title: HCC3153_dH3_no_dox_short_H3K27ac_ChIP_1


title: ChIPCapseq_reporter_H2AK119ub rep1


title: TSC_TNFa_C


title: OTI_sgTmed_Veh_Rest_rep1

description:
replicate 1
5894_29_OT-I_Tmed10_Rest_rep1_CAGATCA_S41_R1_001


title: TSC_T_G_B

value: TNFα and IFNγ


title: ChIPCapseq_reporter_H2AK119ub rep2


title: OTI_Ctrl2_AGN_Act_rep2

description:
replicate 2
5894_28_OT-I_Ctrl-2_AGN_Act_rep2_GCCAATA_S40_R1_001

value: Ctrl

value: AGN


title: HCC3153_wt_dox_short_H3K27ac_ChIP_2

value: breast cancer

value: tumor cells

value: doxycycline


title: MEF_Con_C


title: TSC_T_G_C


title: ChIPCapseq_reporter_Input rep2


title: HCC3153_wt_dox_short_H3K27ac_ChIP_1

value: wild type


title: OTI_Ctrl2_AGN_Act_rep1

description:
replicate 1
5894_27_OT-I_Ctrl-2_AGN_Act_rep1_ACAGTGA_S34_R1_001


title: ChIPCapseq_reporter_Input rep1


title: TSC_T_G_A


title: OTI_Ctrl2_Veh_Act_rep2

description:
replicate 2
5894_26_OT-I_Ctrl-2_Veh_Act_rep2_TGACCAA_S31_R1_001


title: MEF_Tnfa_B

value: MEF

value: TNFα


title: OTI_Ctrl2_Veh_Act_rep1

description:
replicate 1
5894_25_OT-I_Ctrl-2_Veh_Act_rep1_CGATGTA_S29_R1_001


title: MEF_Tnfa_C


title: HCC3153_wt_no_dox_short_H3K27ac_ChIP_2

value: no doxycycline


title: HCC3153_wt_no_dox_short_H3K27ac_ChIP_1

value: 7 days


title: ATACseq_Pds5a_KO_rep3

value: embryonic stem cells


title: MEF_T_G_A


title: OTI_Ctrl2_Veh_Rest_rep2

description:
replicate 2
5894_22_OT-I_Ctrl-2_Veh_Rest_rep2_TAGCTTA_S35_R1_001

value: OT-I/Cas9 CD8 T cells


title: ChIPCapseq_reporter_H3K27me3 rep2


title: ATACseq_wt_rep3


title: SUM185_dH3_dox_long_H3K27ac_ChIP_2

value: 42 days


title: ATACseq_Pds5a_KO_rep1


title: OTI_Ctrl2_AGN_Rest_rep1

description:
replicate 1
5894_23_OT-I_Ctrl-2_AGN_Rest_rep1_GTGGCCT_S38_R1_001


title: SUM185_dH3_dox_long_H3K27ac_ChIP_1


title: MEF_Tnfa_A


title: OTI_Ctrl2_AGN_Rest_rep2

description:
replicate 2
5894_24_OT-I_Ctrl-2_AGN_Rest_rep2_GGCTACA_S39_R1_001


title: ATACseq_Pds5a_KO_rep2


title: SUM185_dH3_no_dox_long_H3K27ac_ChIP_1


title: MEF_T_G_B


title: SUM185_dH3_no_dox_long_H3K27ac_ChIP_2


title: OTI_Ctrl2_Veh_Rest_rep1

description:
replicate 1
5894_21_OT-I_Ctrl-2_Veh_Rest_rep1_GATCAGA_S37_R1_001


title: ATACseq_wt_rep2


title: MEF_T_G_C


title: ATACseq_wt_rep1


title: RNAseq_dSuz12_Pcgf1KO_+IAA_rep2

description: DeSeq2_dSuz12_Pcgf1KO_+IAA_vs_untreated.csv


title: SUM185_wt_dox_long_H3K27ac_ChIP_2


title: OTI_sgATP_Veh_Act_rep1

description:
replicate 1
5894_19_OT-I_Atp2a2_Act_rep1_ACTGATA_S32_R1_001

growth_protocol: B16F10 were maintained in DMEM/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL)/Puromycin (1ug/mL) and passaged 1:10 every two days. T cells were maintained in RPMI/10%FCS/Penicillin (100U/mL)/Streptomycin (100ug/mL) with IL-2 (10ng/mL), IL-7 (0.5ng/mL), IL-15 (1ng/mL), betamercaptoethanol (50uM) and puromycin (4ug/mL) and passaged every day at a density of 1*10^6/mL.

treatment_protocol: For drug treatment, DMSO or thapsigargin (50ng/mL) was added to the culture where indicated. For activation, a 24-well non-tissue-culture-treated plate was coated with anti-CD3 antibodies overnight and on the day of the experiment, cells were seeded on this plate at a density of 1*10^6/mL where indicated.

value: Atp2a2 KO

tag: activation?

value: Activated

value: DMSO


title: TSC_TB_Con_A

value: control


title: TSC_TB_Con_C


title: TSC_TB_Con_B


title: SUM185_wt_dox_long_H3K27ac_ChIP_1

value: anti-H3K27ac (Diagenode, C15410196)


title: OTI_sgATP_Veh_Rest_rep2

description:
replicate 2
5894_18_OT-I_Atp2a2_Rest_rep2_GAGTGGA_S33_R1_001

value: Resting


title: RNAseq_dSuz12_Pcgf1KO_untreated_rep2


title: LK4804-20

first: Philip

last: Murphy

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
SP 300 cycle kit
LK4804-20

data_processing:
Libraries were sequenced using paired-end 150-bp reads on an Illumina Novaseq 6000.
The FASTQ sequence reads were aligned to the mouse genome GRC m38 using HISAT2 v2.1.0.
Mapped reads were quantified with FeatureCounts v1.6.3 (gencode.vM23.annotation.gtf).
Gene expression analysis was completed in R version 3.6.0 using the limma 3.40.6 package.
Assembly: GRCm38/M23
Supplementary files format and content: raw_counts_gene_based_featureCounts.csv contains raw counts

source_name: C57BL/6N mouse heart tissue, WT, vehicle treatment

growth_protocol: Mice were fed a standard NIH-31 diet.

extract_protocol:
Hearts were excised from mice, weighed, and flash-frozen using liquid nitrogen-chilled clamps. Frozen hearts were ground in to a fine powder in a chilled mortar and pestle. A small aliquot of heart powder was then used to extract RNA using Qiagen's RNeasy RNA extraction kit. Isolated RNA was stored at -80 until ready for sequencing analysis.
The library was constructed using Illumina's Truseq stranded total RNA library prep kit.

treatment_protocol: WT and OGFOD1-KO mice aged 3-5 months were treated with either vehicle (1X PBS and Sodium Ascorbate) or isoproterenol (1X PBS, Sodium Ascorbate, and Isoproterenol) for 2 weeks by osmotic minipump. Hearts were isolated from these mice and RNA was extracted and subjected to RNAsequencing.

tag: diet

value: Heart

value: WT

tag: treatment (2_weeks)

value: Vehicle (PBS, Sodium ascorbate)


title: RNAseq_dSuz12_Pcgf1KO_+IAA_rep1

tag: cell type


title: OTI_Ctrl_TG_Act_rep1

description:
replicate 1
5894_15_OT-I_Ctrl-1_TG_Act_rep1_ACTTGAA_S27_R1_001

tag: genotype

value: Ctrl

tag: treatment

value: Thapsigargin


title: OTI_sgATP_Veh_Rest_rep1

description:
replicate 1
5894_17_OT-I_Atp2a2_Rest_rep1_GTTTCGG_S30_R1_001


title: SUM185_wt_no_dox_long_H3K27ac_ChIP_1

tag: tissue

value: breast cancer

value: tumor cells

value: wild type


title: OTI_Ctrl_TG_Act_rep2

description:
replicate 2
5894_16_OT-I_Ctrl-1_TG_Act_rep2_CGTACGT_S28_R1_001


title: OTI_sgATP_Veh_Act_rep2

description:
replicate 2
5894_20_OT-I_Atp2a2_Act_rep2_ATTCCTT_S36_R1_001


title: SUM185_dH3_dox_short_H3K27ac_ChIP_1

tag: parental cell_line

value: doxycycline

value: 7 days


title: OTI_Ctrl_Veh_Act_rep2

description:
replicate 2
5894_14_OT-I_Ctrl-1_Veh_Act_rep2_TTAGGCA_S26_R1_001

value: OT-I/Cas9 CD8 T cells


title: RNAseq_GT_Pds5a_KO_rep1

value: embryonic stem cells


title: RNAseq_dSuz12_Pcgf1KO_untreated_rep1


title: LK4804-17

description:
SP 300 cycle kit
LK4804-17

tag: strain


title: LK4804-19

description:
SP 300 cycle kit
LK4804-19

source_name: C57BL/6N mouse heart tissue, WT, isoproterenol treatment

value: Vehicle (PBS, Sodium ascorbate, isoproterenol)


title: RNAseq_GT_wt_rep2

source_name: mouse embryonic stem cells


title: LK4804-18

description:
SP 300 cycle kit
LK4804-18


title: SUM185_dH3_no_dox_short_H3K27ac_ChIP_2

value: no doxycycline

tag: time point


title: SUM185_dH3_no_dox_short_H3K27ac_ChIP_1


title: OTI_Ctrl_Veh_Act_rep1

description:
replicate 1
5894_13_OT-I_Ctrl-1_Veh_Act_rep1_ATCACGA_S25_R1_001

value: Activated

value: DMSO


title: LK4804-16

description:
SP 300 cycle kit
LK4804-16


title: SUM185_wt_no_dox_long_H3K27ac_ChIP_2

value: 42 days

value: anti-H3K27ac (Diagenode, C15410196)


title: RNAseq_GT_wt_rep1


title: SUM185_dH3_dox_short_H3K27ac_ChIP_2


title: RNAseq_GT_Pds5a_KO_rep2


title: SUM185_wt_dox_short_H3K27ac_ChIP_2


title: OTI_Ctrl_TG_Rest_rep2

description:
replicate 2
5894_12_OT-I_Ctrl-1_TG_Rest_rep2_GTGAAAC_S24_R1_001

value: Resting


title: OTI_Ctrl_TG_Rest_rep1

description:
replicate 1
5894_11_OT-I_Ctrl-1_TG_Rest_rep1_GTCCGCA_S18_R1_001