title: RNAseq_P5NGO_PRC1ctrl_rep2

data_processing:
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) with the parameter ‘--paired’ were aligned to the mouse (GRCm38/mm10) genome using HISAT2(38) (version 2.2.1) with default parameters.  All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 30) were filtered out by samtools(39) (version 1.9) with the parameter '-q 30' before being subjected to downstream analyses.  To identify differentially expressed genes in RNA-seq, raw read counts for each gene were generated using htseq-count function, part of the HTSeq package (40) (version 1.6.0) based on the mouse gene annotation (gencode.vM24.annotation.gtf, GRCm38/mm10). DESeq2 (41) (version 1.28.1) was used for differential gene expression analyses with cutoffs FC > 2  and Padj value < 0.05. The TPM values of each gene were generated using RSEM (42)(version 1.3.3) for comparative expression analyses and computing the Pearson correlation coefficient between biological replicates.
For CUT&RUN data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html). Briefly, raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) were aligned mouse (GRCm38/mm10) genome using Bowtie2(44) (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. E. coli DNA carried along with bacterially-produced pAG-MNase protein brings along a fixed amount of E. coli DNA and can be used as spike-in DNA.  For mapping E.coli spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).  To compare replicates, Pearson correlation coefficients were calculated and plotted by multiBamSummary bins and plot correlation from deepTools(45) (version 3.5.0).  Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85).  Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli mapping files (the formula used for calculation of scaling factors = 1/ (spike-in reads/100,000)).  For visualization of CUT&RUN using the Integrative Genomics Viewer(46) (version 2.5.3), spike-in normalized genome coverage tracks were generated using genomecov function of bedtools(47) (version 2.29.2) with ‘-bg -scale $scale_factor’ parameter. SEACR (48) (https://seacr.fredhutch.org/ ) was used for peak calling. The program ngs.plot(49) (version 2.63) was used to draw tag density plots and heatmaps for read enrichments.  The FPKM values of each gene’s promoter region (TSS±2kb) were generated using Bamscale package (50)(version 0.0.5) for comparative expression analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample from RNA-seq analyses.bedgraph files were generated using bedtools; Scores represent spike-in normalized read counts.

source_name: RNAseq

extract_protocol: Total RNA was extracted using the RNeasy plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions.  Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instruction.  Prepared RNA-seq libraries were sequenced on the HiSeq 4000 system (Illumina) with paired-ended 150-bp reads.

value: post natal day 5

tag: genotype


title: CUTRUN_H3K4me3_PRC1ctrl_rep1

status: Public on Jun 26 2022

type: SRA

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

country: USA

institute: UC Davis

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) with the parameter ‘--paired’ were aligned to the mouse (GRCm38/mm10) genome using HISAT2(38) (version 2.2.1) with default parameters.  All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 30) were filtered out by samtools(39) (version 1.9) with the parameter '-q 30' before being subjected to downstream analyses.  To identify differentially expressed genes in RNA-seq, raw read counts for each gene were generated using htseq-count function, part of the HTSeq package (40) (version 1.6.0) based on the mouse gene annotation (gencode.vM24.annotation.gtf, GRCm38/mm10). DESeq2 (41) (version 1.28.1) was used for differential gene expression analyses with cutoffs FC > 2  and Padj value < 0.05. The TPM values of each gene were generated using RSEM (42)(version 1.3.3) for comparative expression analyses and computing the Pearson correlation coefficient between biological replicates.
For CUT&RUN data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html). Briefly, raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) were aligned mouse (GRCm38/mm10) genome using Bowtie2(44) (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. E. coli DNA carried along with bacterially-produced pAG-MNase protein brings along a fixed amount of E. coli DNA and can be used as spike-in DNA.  For mapping E.coli spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).  To compare replicates, Pearson correlation coefficients were calculated and plotted by multiBamSummary bins and plot correlation from deepTools(45) (version 3.5.0).  Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85).  Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli mapping files (the formula used for calculation of scaling factors = 1/ (spike-in reads/100,000)).  For visualization of CUT&RUN using the Integrative Genomics Viewer(46) (version 2.5.3), spike-in normalized genome coverage tracks were generated using genomecov function of bedtools(47) (version 2.29.2) with ‘-bg -scale $scale_factor’ parameter. SEACR (48) (https://seacr.fredhutch.org/ ) was used for peak calling. The program ngs.plot(49) (version 2.63) was used to draw tag density plots and heatmaps for read enrichments.  The FPKM values of each gene’s promoter region (TSS±2kb) were generated using Bamscale package (50)(version 0.0.5) for comparative expression analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample from RNA-seq analyses.bedgraph files were generated using bedtools; Scores represent spike-in normalized read counts.

molecule: genomic DNA

organism: Mus musculus

source_name: CUTRUN

extract_protocol: CUT&RUN libraries of PRC1ctrl, PRC1cKO, and stella-GFP oocytes were conducted as previously described(30).  ~500 non-growing oocytes isolated from P1 ovaries were pooled as one replicate, and two independent biological replicates were used for CUT&RUN library generation.  The antibodies used were rabbit anti-H2AK119ub1 (1/100; Cell Signaling Technology; 8240), rabbit anti-H3K4me3 (1/100; Cell Signaling Technology; 9751), and rabbit anti-H3K27me3 antibody (1/100; Cell Signaling Technology; 9733).  Libraries were constructed using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).  Prepared CUT&RUN libraries were sequenced on the NovaSeq 6000 system (Illumina) with paired-ended 100-bp or 50-bp reads.

tag: strain

value: C57BL/6 X FVB/NJ

tag: tissue

value: ovary

tag: age

value: post natal day 1

value: Ring1-/-; Rnf2F/+; Ddx4-Cre

tag: cut&run antibody


title: RNAseq_P5NGO_PRC1cKO_rep1

library_source: transcriptomic

molecule: total RNA

value: Ring1-/-; Rnf2F/-; Ddx4-Cre


title: RNAseq_P1NGO_PRC1ctrl_rep1


title: CUTRUN_H3K27me3_PRC1cKO_rep1


title: RNAseq_P5NGO_PRC1cKO_rep2


title: CUTRUN_H3K4me3_PRC1cKO_rep1


title: Group A - Patient 2

status: Public on Jun 29 2022

city: Stanford

first: Han

last: Zhu

address: G1105, 265 Campus Drive

department: Cardiovascular Medicine

institute: Stanford University

description:
scRNA-seq data
A2

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (4.0.3) to demultiplex the FASTQ reads in order to align them to the human reference genome (GRCh38, v4.0.0, from 10X Genomics) and count the unique molecular identifier (UMI) (through the “cellranger count” function).
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Genome_build: h38
Supplementary_files_format_and_content: Cell Ranger output

organism: Homo sapiens

source_name: Human PBMCs

extract_protocol:
Frozen PBMCs were removed from liquid nitrogen and resuspended in warm RPMI media + 10% FBS (@ 37ºC) by adding 1 mL, 3 mL, 4 mL, 8 mL 16 mL media at 30-60 second intervals. Cells were washed and passed through a 40 um filter, centrifuged @ 300 rcf x 5 min and resuspended in PBS with 50 ul 1% BSA and Biolegend Fc Receptor Blocking Solution (Human TrueStain FcX (Cat. No. 422301) for 20 minutes. Afterwards, another 50 uL of antibody mastermix containing Biolegend TotalSeq-C antibodies for staining (Biolegend TotalSeq™-C0063 anti-human CD45RA Antibody Cat. No. 304163; Biolegend TotalSeq™-C0072 anti-human CD4 Antibody Cat. No. 300567; Biolegend TotalSeq™-C0046 anti-human CD8 Antibody Cat. No. 344753) for final manufacture-recommended concentration of 1.0 ug of antibody in 100 ul of staining buffer for every 1 million cells for a total of 10-15 minutes incubation. After incubation, cells were washed 2x by resuspending in 1.5 mL PBS + 1% RNase-free BSA (MACS BSA Stock Solution No. 130-091-376) and then 1 mL PBS + 0.04% BSA. 10 uL of cell suspension was then taken for counting and appropriate volume of PSA + 0.04% BSA was added (200-500 uL) to aim for final target concentration of 1 million cells/mL). Cells were then loaded into Chromium Next GEM Chip G (10x PN 2000177) to achieve 6000-8000 target cell recovery per sample according to the manufacture’s protocol.
All steps from cDNA isolation to library preparation were completed according to 10x’s manufacturing protocols for the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1. Isolated cDNA was amplified (14 cycles), and then cDNA was allocated for TCR enrichment, feature barcode library generation, and 5’ cDNA library generation. cDNA and library quality was evaluated using the high sensitivity DNA kit on the Agilent 2100 Bioanalyzer.

value: Blood

tag: cell type

value: PBMC

tag: treatment

value: Immune Checkpoint Inhibitor

tag: disease state

value: No irAE

tag: molecule subtype

value: Total RNA


title: Intestinal_lymphatics_002

status: Public on Jun 21 2022

city: New York

first: Marina

last: Schernthanner

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Sequenced reads were mapped to mm10 genome assembly using cellranger version 6.0.1
Reads falling on each gene are counted by HT-Seq

source_name: intestine

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: large intestine

value: lymphatic endothelial cells


title: RNAseq_P1NGO_PRC1ctrl_rep2


title: CUTRUN_H2AK119ub_WT_rep1

value: stella-GFP Tg+


title: CUTRUN_H3K27me3_PRC1ctrl_rep2


title: CUTRUN_H3K4me3_PRC1cKO_rep2


title: RNAseq_P5NGO_PRC1ctrl_rep1


title: Intestinal_lymphatics_003


title: RNAseq_P1NGO_PRC1cKO_rep1


title: Group A - Patient 1

description:
scRNA-seq data
A1


title: CUTRUN_H2AK119ub_WT_rep2


title: CUTRUN_H3K27me3_PRC1ctrl_rep1


title: Intestinal_lymphatics_001


title: CUTRUN_H3K27me3_PRC1cKO_rep2


title: WTLI2

data_processing:
Sequenced reads were mapped to mm10 genome assembly using cellranger version 6.0.1
Genome_build: mm10
Supplementary_files_format_and_content: cellranger output

extract_protocol:
10X single-cell RNA-sequencing
10X Visium spatial transcriptomics
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Sicocultured-organoids

source_name: intestinal organoids

value: small intestine

tag: passages

value: Passage 1

value: COCULTURE


title: WTLI1


title: WTSI2


title: SIorganoids

value: CTRL


title: RNAseq_P1NGO_PRC1cKO_rep2

value: C57BL/6 X FVB/NJ


title: LIscRNA


title: WTSI1


title: Set1 K562 PARP1 inhibition Olaparib Replicate A2

status: Public on Jun 18 2022

city: Ithaca

first: Charles

middle: Grahe

last: Danko

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

description:
Micro-C
K562_Olaparib.mapq_30.mcool
K562_Olaparib_cis_mapq30_pairs.gz

data_processing:
All Micro-C mapping was done using the mirnylab/distiller-nf: v0.3.3 pipeline. Raw data were mapped to the hg38 human genome assembly (K562 and Jurkat) or mm10 mouse genome assembly (mESCs).
For data visualization by contact maps, multi cool (mcool) files, balanced by iterative correction and eigenvector decomposition (ICE) for resolutions of 200 bp to 10 Mb were generated from contacts with both ends having a mapq score > 30.
Assembly: hg38, mm10
Supplementary files format and content: pairs file - contains the coordinated of read pair ends, mapq and orientation.
Supplementary files format and content: mcool file -  contains all valid Micro-C pairs stored in HDF5 format and ICE-normalized with mutiple resolutions
Library strategy: Micro-C

growth_protocol: K562 and Jurkat cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1X penicillin streptomycin antibiotic. mECSs harboring a homozygous endogenous NELFB-FKBP12F36V fusion protein were cultured on 0.1% gelatin (Millipore) in PBS+/+ coated tissue-culture grade plates in a humidified 37°C incubator with 5% CO2. For routine culture, cells were grown in Serum/LIF conditions: DMEM (Gibco), supplemented with 2 mM L-glutamine (Gibco), 1x MEM non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), 100 U/ml penicillin and 100 U/ml streptomycin (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 15% Fetal Bovine Serum (Gibco), and 1000 U/ml of recombinant leukemia inhibitory factor (LIF).

extract_protocol:
Cells were crosslinked with 1 ml per million cells of 1% formaldehyde for 10 minutes at room temperature and quenched by 0.25 M Glycine for 5 min. After spin-down for 5 minutes at 300Xg at 4 °C, cells were washed at a density of 1 ml per million cells in ice cold PBS. Cells were crosslinked a second time, with 1 ml per 4 million cells of 3 mM disuccinimidyl glutarate (DSG) (ThermoFisher Scientific, 20593) for 40 min at room temperature and quenched by 0.4 M Glycine for 5 min. Following two washes with ice cold PBS, cells were flash-frozen and kept at -80 °C until further use. For MNase digestion, cells were thawed on ice for 5 min, incubated with 1ml MB#1 buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1x Roche cOmplete EDTA-free (Roche diagnostics, 04693132001)) and washed twice with MB#1 buffer. MNase concentration for each cell type was predetermined using MNase titration experiments exploring 2.5-20U of MNase per million cells. We selected the concentration that gives ~90% mononucleosomes in an MNase. Chromatin was digested with MNase for 10 min at 37 °C and digestion was stopped by adding 8 ul of 500 mM EGTA and incubating at 65 °C for 10 min.   Following dephosphorylation with rSAP (NEB #M0371) and end polishing using T4 PNK (NEB #M0201), DNA polymerase Klenow fragment (NEB #M0210) and biotinylated dATP and dCTP (Jena Bioscience #NU-835-BIO14-S and #NU-809-BIOX-S, respectively), ligation was performed in a final volume of 2.5 ml for 3h at room temperature using T4 DNA ligase (NEB #M0202). Dangling ends were removed by a 5 min incubation with Exonuclease III (NEB #0206) at 37 °C and biotin enrichment was done using 20 ul DynabeadsTM MyOneTM Streptavidin C1 beads (Invitrogen #65001).
Libraries were prepared with the NEBNext Ultra II Library Preparation Kit (NEB #E7103). Samples were sequenced on a combination of Illumina’s NovaSeq 6000 and HiSeq 2500 at Novogene.

treatment_protocol: For the PARP1 inhibition experiment, cells were treated with either 10 μM Olaparib, initially diluted in DMSO, or DMSO only, for 90 min before immediately crosslinked for Micro-C or lysed in NUN buffer (0.3 M NaCl, 1 M Urea, 1% NP-40, 20 mM HEPES, pH 7.5, 7.5 mM MgCl2, 0.2 mM EDTA, 1 mM DTT, 20 units per ml SUPERase In Rnase Inhibitor (Life Technologies, AM2694), 1X Protease Inhibitor Cocktail (Roche, 11 873 580 001)) for ChRO-seq. To induce NELFB degradation, dTAG-13 (Bio-Techne) was reconstituted in DMSO (Sigma) at 5 mM. dTAG-13 was diluted in maintenance medium to 500 nM and added to cells with medium changes for the specified amounts of time. For dTAG washes, the cells were washed 4 times, twice with PBS +/+ and twice with maintenance medium following the treatment time to ensure complete removal of the dTAG ligand. At the end of each dTAG-13 treatment time point, cells were detached using Trypsin-EDTA (0.05%) (Gibco) and counted before crosslinking for Micro-C.

tag: cell line

value: 90 minutes Olaparib


title: Set1 K562 PARP1 inhibition Olaparib Replicate B1


title: Set1 K562 PARP1 inhibition Olaparib Replicate B2


title: Set1 K562 Micro-C Replicate E

description:
Micro-C
K562.mapq_30.mcool
K562_cis_mapq30_pairs.gz


title: SIscRNA


title: Set1 Jurkat Micro-C Replicate B

description:
Micro-C
Jurkat.mapq_30.mcool
Jurkat_cis_mapq30_pairs.gz

source_name: Jurkat

value: Jurkat


title: Jurkat Micro-C Replicate A


title: Set1 K562 PARP1 inhibition DMSO Replicate A1

description:
Micro-C
K562_DMSO.mapq_30.mcool
K562_DMSO_cis_mapq30_pairs.gz

value: 90 minutes DMSO


title: Set2 K562 PARP1 inhibition Olaparib Replicate B2


title: Set1 K562 Micro-C Replicate F


title: Set1 K562 PARP1 inhibition DMSO Replicate A2


title: Set1 K562 PARP1 inhibition DMSO Replicate B1


title: Set1 K562 Micro-C Replicate A


title: Set1 K562 Micro-C Replicate D


title: K562 ChRO-seq Olaparib Replicate B

description: ChRO-seq

data_processing:
All data processing for ChRO-seq data (as well as PRO-seq and GRO-seq available raw data) in this study was done using the Proseq2.0 pipeline available from GitHub (https://github.com/Danko-Lab/proseq2.0).
Assembly: hg38
Supplementary files format and content: bigwig file - contains raw read counts
Library strategy: ChRO-seq

growth_protocol: K562 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1X penicillin streptomycin antibiotic.

extract_protocol:
For chromatin isolation from cultured K562 cells, we added 1 ml of 1X NUN buffer and vigorously vortexed the samples for 1 min. An additional 500 µl of NUN buffer was added and samples were vigorously vortexed for an additional 30 s. The samples were then incubated on ice for 30 min with a brief vortex every 10 min and centrifuged at 12,500g for 30 min at 4 °C, after which the NUN buffer was removed from the chromatin pellet. The chromatin pellet was washed 3 times with 1 ml of 50 mM Tris-HCl, pH 7.5, supplemented with 40 U/ml of RNase inhibitor, centrifuged at 10,000Xg for 5 min at 4 °C, and the supernatant discarded. After washing, 100 µl of chromatin storage buffer (50 mM Tris-HCl, pH 8.0, 25% glycerol, 5 mM Mg(CH3COO)2, 0.1 mM EDTA, 5 mM DTT, 40 U/ml Rnase inhibitor) was added to each sample. The samples were loaded into a Bioruptor and sonicated with the power setting on high, with a cycle time of 10 min with cycle durations of 30 s on and 30 s off. The sonication was repeated up to three times, as needed, to get the chromatin pellet into suspension. Samples were stored at −80 °C.
ChRO-seq library preparation was performed following a published protocol(18), with minor modifications. Chromatin from 1 million K562 cells in 25 µl chromatin storage buffer was mixed with 25 µl of 2X chromatin run-on buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2,1 mM DTT, 300 mM KCl, 10 μM Biotin-11-ATP (Perkin Elmer, NEL544001EA), 40 μM Biotin-11-CTP (Perkin Elmer, NEL542001EA), 10 μM Biotin-11-GTP (Perkin Elmer, NEL545001EA), 40 μM Biotin-11-UTP (Perkin Elmer, NEL543001EA), 2ng/μl Yeast tRNA (VWR, 80054-306), 0.8 U/μl RNase inhibitor, 1% Sarkosyl (Fisher Scientific, AC612075000)). The run-on reaction was incubated in a thermomixer at 37 °C for 5 min at 750 RPM. The reaction was stopped by adding 300 μl of Trizol LS (Life Technologies, 10296-010). To clean up the reaction prior to base hydrolysis,  40 μl of 1-bromo-3-chloropropane (BCP) (Sigma, B9673) were added to the samples and samples were vortexed for 20 sec, incubated for 3 min at RT and centrifuged at 17,000Xg at 4°C for 5 min. ~250 μl of aqueous phase was transferred to a new 1.5 ml tube and samples were pelleted at 17,000Xg at 4°C for 15 min in 650 ml ice-cold 100% EtOH  with GlycoBlue (2.5 μl) (Ambion, AM9515) to visualize the RNA pellet. The pellet was further washed with 0.5 ml ice-cold 75% by vortex-mixing and centrifugation at 17,000Xg at 4°C for 5 min. Any residual EtOH was removed by air-drying the pellet for 5 min in RT. The RNA pellet was resuspended in 20 μl of diethylpyrocarbonate (DEPC)-treated water and heat denatured at 65 °C for 40 sec. For base hydrolysis, 5 μl of 1N were added to the RNA sample to get 0.2N NaOH, and samples were incubated on ice for 8 min. Base hydrolysis was stopped by adding 25 μl of Tris-HCl pH 6.8 and gently mixing.  3′ Adapter ligation was done using T4 RNA Ligase 1 (NEB, M0204L). A first binding to streptavidin beads (NEB, S1421S) and washed as described (18). RNA was removed from beads by Trizol (Life Technologies, 15596-026) and followed by a 5′ decapping with RNA 5′ pyrophosphohydrolase (RppH, NEB, M0356S). The 5′ end was phosphorylated using T4 polynucleotide kinase (NEB, M0201L). A second bead binding was performed, and an on-beads 5′ adapter ligation followed. After bead washes, RNA was removed from beads by adding 300 μl of TRI reagent (MRC, TR 118). 40 μl of BCP were added to the samples and samples were vortexed for 20 sec, incubated for 3 min at room temperature and centrifuged at 17,000Xg at 4°C for 5 min. ~180μl of aqueous phase was transferred to a new 1.5 ml tube and samples were pelleted at 17,000Xg at 4 °C for 15 min in 450 ml ice-cold 100% EtOH with GlycoBlue (2.5 μl) to visualize the RNA pellet. The pellet was further washed with 0.4 ml ice-cold 75% EtOH by vortex-mixing and centrifugation at 17,000Xg at 4 °C for 5 min. Any residual EtOH was removed by air-drying the pellet for 5 min in RT. A reverse transcription reaction using Superscript III Reverse Transcriptase (Life Technologies, 18080-044) was used to generate cDNA. cDNA was then amplified using Q5 High-Fidelity DNA Polymerase (NEB, M0491L) to generate the ChRO-seq libraries following the protocol provided by NEB.

treatment_protocol: For the PARP1 inhibition experiment, cells were treated with either 10 μM Olaparib, initially diluted in DMSO, or DMSO only, for 90 min before immediately crosslinked for Micro-C or lysed in NUN buffer (0.3 M NaCl, 1 M Urea, 1% NP-40, 20 mM HEPES, pH 7.5, 7.5 mM MgCl2, 0.2 mM EDTA, 1 mM DTT, 20 units per ml SUPERase In Rnase Inhibitor (Life Technologies, AM2694), 1X Protease Inhibitor Cocktail (Roche, 11 873 580 001)) for ChRO-seq.


title: Set1 K562_Micro-C Replicate B


title: Set1 K562 Micro-C Replicate C


title: K562 ChRO-seq DMSO Replicate B

description: ChRO-seq


title: Set2 K562 PARP1 inhibition Olaparib Replicate A1


title: Set2 K562 PARP1 inhibition DMSO Replicate B1


title: K562 ChRO-seq DMSO Replicate A

description: ChRO-seq


title: Set2 K562 PARP1 inhibition DMSO Replicate B2


title: K562 ChRO-seq Olaparib Replicate A

description: ChRO-seq


title: Set2 K562 PARP1 inhibition Olaparib Replicate B1


title: Set2 K562 PARP1 inhibition DMSO Replicate A2


title: Set2 K562 PARP1 inhibition Olaparib Replicate A2


title: Set2 K562 PARP1 inhibition DMSO Replicate A1


title: Set1 K562 PARP1 inhibition Olaparib Replicate A1


title: Set1 K562 PARP1 inhibition DMSO Replicate B2


title: Set2 Jurkat Micro-C Replicate B


title: Set2 K562 Micro-C Replicate E


title: Set2 K562 Micro-C Replicate F


title: mESCs, NELFB-dTAG  T=24h post washout Replicate B1

description:
Micro-C
mESC_NELFB_dTAB_T24h_post_washout.mapq_30.mcool
mESC_NELFB_dTAG_T24h_post_washout_cis_mapq30_pairs.gz

source_name: mESCs

value: mESCs

value: 60 minutes dTAG-13 + 24h post dTAG-13 washout


title: mESCs, NELFB-dTAG  T=24h post washout Replicate B2


title: Set2 K562_Micro-C Replicate B


title: Set2 K562 Micro-C Replicate C


title: Set2 K562 Micro-C Replicate D


title: mESCs, NELFB-dTAG  T=24h post washout Replicate A1


title: Set2 K562 Micro-C Replicate A


title: mESCs, NELFB-dTAG  T=8h post washout Replicate B1

description:
Micro-C
mESC_NELFB_dTAB_T8h_post_washout.mapq_30.mcool
mESC_NELFB_dTAG_T8h_post_washout_cis_mapq30_pairs.gz

value: 60 minutes dTAG-13 + 8h post dTAG-13 washout


title: mESCs, NELFB-dTAG  T=60min Replicate A1

description:
Micro-C
mESC_NELFB_dTAB_T60min.mapq_30.mcool
mESC_NELFB_dTAG_T60min_cis_mapq30_pairs.gz

value: 60 minutes dTAG-13


title: mESCs, NELFB-dTAG  T=30min Replicate B1

description:
Micro-C
mESC_NELFB_dTAB_T30min.mapq_30.mcool
mESC_NELFB_dTAG_T30min_cis_mapq30_pairs.gz

value: 30 minutes dTAG-13


title: mESCs, NELFB-dTAG  T=8h post washout Replicate A1


title: mESCs, NELFB-dTAG  T=60min Replicate B1


title: mESCs, NELFB-dTAG  T=60min Replicate B2


title: mESCs, NELFB-dTAG  T=24h post washout Replicate A2


title: mESCs, NELFB-dTAG  T=30min Replicate B2


title: mESCs, NELFB-dTAG  T=8h post washout Replicate B2


title: mESCs, NELFB-dTAG  T=0 Replicate B1

description:
Micro-C
mESC_NELFB_dTAB_T0.mapq_30.mcool
mESC_NELFB_dTAG_T0_cis_mapq30_pairs.gz

value: No dTAG-13


title: mESCs, NELFB-dTAG  T=30min Replicate A2


title: mESCs, NELFB-dTAG  T=0 Replicate B2


title: mESCs, NELFB-dTAG  T=0 Replicate A2


title: pro-B miR-15 dKO 3

status: Public on Jun 09 2022

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

description: RNA was amplified and reverse transcribed into cDNA using the SMART-seq protocol

data_processing:
single end reads were trimmed using Trimmomatic
aligned using STAR aligner
counted with FeatureCounts
Assembly: GRCm39
Supplementary files format and content: Excel file including all samples

source_name: bone marrow

extract_protocol:
RNeasy Micro Kit (Qiagen; 74004)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: FACS sorted pro-B cells

value: miR-15a/bfl/fl Vav-Cre

value: 10-12 weeks

tag: strain background


title: pro-B miR-15 dKO 4


title: mESCs, NELFB-dTAG  T=0 Replicate A1


title: pro-B miR-15 dKO 2


title: pro-B, control 4

value: miR-15a/b+/+ Vav-Cre


title: pro-B miR-15 dKO 1


title: mESCs, NELFB-dTAG  T=60min Replicate A2


title: iCLIP-3xFlag-U1A_IP1_biol rep3

status: Public on May 23 2022

city: San Sebastian

first: Lorea

last: Blazquez

address: Dr Begiristain

country: Spain

institute: Biogipuzkoa Health Research Institute

data_processing:
iCLIP sequencing reads was performed using the iMaps server (https://imaps.genialis.com/) following the iCount demultiplex and analyse complete worrkflow
Assembly: hg38
Supplementary files format and content: U1A_IP2_1_Paraclu_grouped_cdna.bedgraph file contains a list of genes which showed U1A binding
Supplementary files format and content: U1A_IP2_1_Paraclu_grouped_cdna.bedgraph file contains read counts to upload in a Genome Browser

source_name: HeLa_3xFlag-U1A stable cell line

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

extract_protocol: Followed the iCLIP protocol explained in PMID 24184352 with modifications detailed in Rovira, Moreno et al. MTNA 2022

treatment_protocol: Doxycyclin at 200ng/ml was added to cell media to induce transgene expression

value: HeLa_3xFlag-U1A stable cell line

value: First IP; Replicate 3


title: mESCs, NELFB-dTAG  T=30min Replicate A1


title: pro-B, control 3


title: iCLIP-3xFlag-U1A_IP1_biol rep1

value: First IP; Replicate 1


title: pro-B, control 2


title: iCLIP-3xFlag-U1A_IP2_biol rep2

value: Second IP; Replicate 2


title: pro-B, control 1


title: mESCs, NELFB-dTAG  T=8h post washout Replicate A2


title: iCLIP-3xFlag-U1A_IP1_biol rep2

value: First IP; Replicate 2


title: gDNA_Dnmt3a_cKO_rep2

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: DNA-seq
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., 2019 (in submission)
We followed the GATK “best practices for germline SNPs and indels in whole genomes and exomes” pipeline. Briefly, raw data were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 20) using Trim Galore in the paired-end mode. Clean data were then mapped to the mm10 genome using BWA (v0.7.13-r1126). Duplicates reads were marked with Picard.
The analysis-ready reads were fed into GATK (v3.7) to perform two rounds of joint genotyping and base recalibration. Variants were then filtered using the following criteria: QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0 .
A substituted genome to mask out all these SNPs (replaced with Ns) was generated with the maskfasta tool in the BEDTools suite73 (v2.27.1). This substituted genome was used in the methylC-seq data processing pipeline.
Genome_build: mm10

source_name: Excitatory pyramidal neurons from frontal cortex of Dnmt3a cKO mice

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee.

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
1.5 µg of genomic DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 400 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Half of adapter-ligated DNA molecules were enriched by 6 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 6 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads and size selection done from 400 – 600 bp. Libraries were sequenced on Illumina HiSeq 4000.

value: C57BL6J/129 (name in Jackson Labs:B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ)

value: brain (frontal cortex)

value: excitatory pyramidal neurons

value: Postnatal day 39

tag: Sex

value: male


title: gDNA_Dnmt3a_cKO_rep1


title: ChIP-seq_Control_IgG

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., 2019 (in submission)
ChIP-seq reads were pre-processed with the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6). Briefly, paired-end reads were mapped to the mm10 genome with BWA (v0.7.13-r1126). Reads were then filtered using samtools (v1.2) to remove unmapped, mate unmapped, not primary alignment and duplicates reads (-F 1804). Properly paired reads were retained (-f 2). Multi-mapped reads (MAPQ < 30) were removed. PCR duplicates were removed using the MarkDuplicates tool in Picard (v2.10.6). Reads mapped to the blacklist regions in mouse mm10 genome (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were also removed.
Peak calling was performed using epic2 (v0.0.16), a reimplementation of SICER. For H3K4me3 and H3K27ac, we used the following parameters: “--bin-size 200 --gaps-allowed 1”. For H3K27me3, we used the following parameters: “--bin-size 200 --gaps-allowed 3”. The IgG sample was used as a control.
Differential binding analysis of ChIP-seq peak data was performed using DiffBind (v2.10.0) in DESeq2 (v1.22.1) mode. Regions with FDR < 0.05 were considered significant.
Bigwig files for visualization were generated using the bamCoverage tool in the deepTools package (v3.3.1) with the bin size 10 and normalized using RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq and ChIP-seq datasets

source_name: Excitatory pyramidal neurons from frontal cortex of control mice

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Sorted nuclei were crosslinked for 15min in 1% formaldehyde solution and quenched afterward with glycine at a final concentration of 0.125 M. After crosslinking, nuclei were sonicated in Lysis buffer (50 mM Tris HCl pH 8, 20 mM EDTA, 1% SDS, 1X EDTA free protease inhibitor cocktail). ChIP assays were conducted with antibodies against H3K27me3 (39156, Active Motif), H3K27ac (39133, Active Motif) and H3K4me3 (04-745, Millipore Sigma). Mouse IgG (015-000-003, Jackson ImmunoResearch) served as negative control. H3K4me3 ChIP-seq assays were conducted with 100K nuclei and 500K nuclei were used for H3K27me3 and H3K27ac ChIP-seq assays. The respective antibodies and IgG were coupled for 4-6 hours to Protein G Dynabeads (50µl, 10004D, Thermo Fisher Scientific). Equal amounts of sonicated chromatin were diluted with 9 volumes of Binding buffer (1% Triton X-100, 0.1% Sodium Deoxycholate, 2X EDTA free protease inhibitor cocktail) and subsequently incubated overnight with the respective antibody-coupled Protein G beads. Beads were washed successively with high salt buffer (50 mM Tris HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.5% Triton X-100) low salt (50 mM Tris HCl pH 7.4, 500 mM NaCl, 2 mM EDTA, 0.5% Triton X-100) and wash buffer (50 mM Tris HCl pH 7.4, 50 mM NaCl, 2 mM EDTA) before de-crosslinking, proteinase K digestion and DNA precipitation.
Libraries were generated with the Accel-NGS 2S Plus DNA Library Kit (21024, Swift Biosciences) and sequenced on the Illumina HiSeq 4000 Sequencing system.


title: gDNA_Control_rep1


title: gDNA_Control_rep2


title: ChIP-seq_Dnmt3a_cKO_H3K4me3_rep2


title: ChIP-seq_Dnmt3a_cKO_H3K27me3_rep2


title: ChIP-seq_Control_H3K27me3_rep1


title: ChIP-seq_Dnmt3a_cKO_H3K27me3_rep1


title: ChIP-seq_Control_H3K27me3_rep2


title: iCLIP-3xFlag-U1A_IP2_biol rep3

value: Second IP; Replicate 3


title: ChIP-seq_Control_H3K27ac_rep2


title: ChIP-seq_Dnmt3a_cKO_H3K27ac_rep1


title: ChIP-seq_Dnmt3a_cKO_H3K27ac_rep2


title: iCLIP-3xFlag-U1A_IP2_biol rep1

value: Second IP; Replicate 1


title: ChIP-seq_Control_H3K27ac_rep1


title: ChIP-seq_Dnmt3a_cKO_H3K4me3_rep1


title: MethylC-seq_Dnmt3a_cKO_rep1 (technical replicate)

description: Note: this sample was not used in the manuscript.

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., 2019 (in submission)
MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequceing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
To find DMVs, we first identified UMRs (undermethylated regions) and LMRs (low methylated regions) using MethylSeekR95 (v1.22.0) with m = 0.5, n = 7 and FDR < 0.05. DMVs were then defined as UMRs that with length ≥ 5 kb and mean methylation level ≤ 15%.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls (allC tables); columns in allc files are: column 1 - chromosome; column 2 - position (1-based); column 3 - strand; column 4 - class (context); column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value 0 or 1 indicating the result of statistical test for methylated cytosines)

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Urich M. et al. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols. 2015 Mar;10(3):475-83.]. All DNA obtained from the extraction was spiked with 0.5% unmethylated Lambda DNA. The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 8 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample. MethylC-seq libraries were sequenced on Illumina HiSeq 4000.


title: ChIP-seq_Control_H3K4me3_rep2


title: MethylC-seq_Control_rep2


title: MethylC-seq_Control_rep1


title: MethylC-seq_Dnmt3a_cKO_rep2 (technical replicate)


title: ChIP-seq_Control_H3K4me3_rep1


title: RNA-seq_Dnmt3a_cKO_rep1 (technical replicate)

description:
nuclear RNA
Note: this sample was not used in the manuscript.

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., 2019 (in submission)
Reads were trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 20) using Trim Galore (v0.5.0) in the paired-end mode.
Clean reads were mapped to the mouse mm10 (GRCm38) genome and the GENCODE annotated transcriptome (release M10) with STAR (Spliced Transcripts Alignment to a Reference, v2.5.1b).
Gene expression was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.30).
Gene-level “expected count” from the RSEM results were rounded and fed into edgeR (v3.24.1) to call differentially expressed genes. Only genes that were expressed (with counts per million > 2) in at least two samples were kept. These counts were then normalized using the TMM method, and DE genes were then called in the quasi-likelihood F-test mode, requiring FDR < 0.05 and FC > 20%
Bigwig files for visualization were generated by running STAR in "inputAlignmentsFromBAM" with the previous generated BAM files as input to generate bedgraph files, and then converted to bigWig format using UCSC bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq and ChIP-seq datasets
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using RSEM v1.2.30. Gene IDs were from GENCODE annotation (M10).

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in RL buffer for RNA purification using the Single-Cell RNA Purification Kit (Norgen 51800) with on-column DNase digestion following the standard kit protocol. The nuclear RNA concentration was determined using TapeStation (Agilent).
RNA was diluted to 1 ng/µl and a total of 5 ng processed for RNA-seq library preparation. RNA libraries were prepared using NuGen Ovation® RNA‑Seq System V2 for cDNA preparation following the product manual, cDNA purification using Zymo Research DNA Clean & Concentrator™-25 with modification from Ovation protocol. cDNA elution on 30-40 ul of TE. 1 ug of each sample was fragmented at 300bp using Covaris S2 (Sonolab S-series V2) and the rest of the library was prepared following protocol for KAPA LTP Library Preparation Kit, using Illumina indexed adapters.


title: ChIP-seq_P0_Dnmt3a_cKO_H3K27me3_rep2

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., 2019 (in submission)
ChIP-seq reads were pre-processed with the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2, v1.1.6). Briefly, paired-end reads were mapped to the mm10 genome with BWA (v0.7.13-r1126). Reads were then filtered using samtools (v1.2) to remove unmapped, mate unmapped, not primary alignment and duplicates reads (-F 1804). Properly paired reads were retained (-f 2). Multi-mapped reads (MAPQ < 30) were removed. PCR duplicates were removed using the MarkDuplicates tool in Picard (v2.10.6). Reads mapped to the blacklist regions in mouse mm10 genome (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were also removed.
Peak calling was performed using epic2 (v0.0.16), a reimplementation of SICER. For H3K4me3 and H3K27ac, we used the following parameters: “--bin-size 200 --gaps-allowed 1”. For H3K27me3, we used the following parameters: “--bin-size 200 --gaps-allowed 3”. The IgG sample was used as a control.
Differential binding analysis of ChIP-seq peak data was performed using DiffBind (v2.10.0) in DESeq2 (v1.22.1) mode. Regions with FDR < 0.05 were considered significant.
ChIP-seq: Bigwig files for visualization were generated using the bamCoverage tool in the deepTools package (v3.3.1) with the bin size 10 and normalized using RPKM.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq and ChIP-seq datasets

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Sorted nuclei were crosslinked for 15min in 1% formaldehyde solution and quenched afterward with glycine at a final concentration of 0.125 M. After crosslinking, nuclei were sonicated in Lysis buffer (50 mM Tris HCl pH 8, 20 mM EDTA, 1% SDS, 1X EDTA free protease inhibitor cocktail). ChIP assays were conducted with antibodies against H3K27me3 (39156, Active Motif), H3K27ac (39133, Active Motif) and H3K4me3 (04-745, Millipore Sigma). Mouse IgG (015-000-003, Jackson ImmunoResearch) served as negative control. H3K4me3 ChIP-seq assays were conducted with 100K nuclei and 500K nuclei were used for H3K27me3 and H3K27ac ChIP-seq assays. The respective antibodies and IgG were coupled for 4-6 hours to Protein G Dynabeads (50µl, 10004D, Thermo Fisher Scientific). Equal amounts of sonicated chromatin were diluted with 9 volumes of Binding buffer (1% Triton X-100, 0.1% Sodium Deoxycholate, 2X EDTA free protease inhibitor cocktail) and subsequently incubated overnight with the respective antibody-coupled Protein G beads. Beads were washed successively with high salt buffer (50 mM Tris HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.5% Triton X-100) low salt (50 mM Tris HCl pH 7.4, 500 mM NaCl, 2 mM EDTA, 0.5% Triton X-100) and wash buffer (50 mM Tris HCl pH 7.4, 50 mM NaCl, 2 mM EDTA) before de-crosslinking, proteinase K digestion and DNA precipitation.
Libraries were generated with the Accel-NGS 2S Plus DNA Library Kit (21024, Swift Biosciences) .


title: RNA-seq_Dnmt3a_cKO_rep2 (technical replicate)


title: ChIP-seq_P0_Dnmt3a_cKO_H3K27me3_rep1


title: RNA-seq_Control_rep2


title: RNA-seq_Control_rep1


title: ChIP-seq_P0_Control_H3K27me3_rep2


title: ChIP-seq_P0_Control_H3K27me3_rep1


title: ChIP-seq_E14_Dnmt3a_cKO_H3K27me3_rep2

source_name: Excitatory pyramidal neurons from cortex of Dnmt3a cKO mice

value: brain (cortex)

value: Embryonic day 14


title: MethylC-seq_P0_Dnmt3a_cKO_rep1

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq and ChIP-seq datasets were performed as described in Li et al., 2019 (in submission)
MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequceing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
MethylC-seq: To find DMVs, we first identified UMRs (undermethylated regions) and LMRs (low methylated regions) using MethylSeekR95 (v1.22.0) with m = 0.5, n = 7 and FDR < 0.05. DMVs were then defined as UMRs that with length ≥ 5 kb and mean methylation level ≤ 15%.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls (allC tables); columns in allc files are: column 1 - chromosome; column 2 - position (1-based); column 3 - strand; column 4 - class (context); column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value 0 or 1 indicating the result of statistical test for methylated cytosines)

extract_protocol:
The frontal cortex tissue was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Urich M. et al. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols. 2015 Mar;10(3):475-83.]. All DNA obtained from the extraction was spiked with 0.5% unmethylated Lambda DNA. The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart Uracil+ Readymix (Kapa Biosystems, Woburn, MA) and 5 µl TruSeq PCR Primer Mix (Illumina) (50 µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 8 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure XP beads. Up to two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to two independent libraries from the same biological sample.

value: Postnatal day 0


title: ChIP-seq_E14_Control_H3K27me3_rep1

source_name: Excitatory pyramidal neurons from cortex of control mice


title: ChIP-seq_E14_Dnmt3a_cKO_H3K27me3_rep1


title: MethylC-seq_P0_Dnmt3a_cKO_rep2


title: MethylC-seq_P0_Control_rep1


title: MethylC-seq_P0_Control_rep4


title: MethylC-seq_P0_Control_rep5


title: MethylC-seq_P0_Control_rep2


title: MethylC-seq_P0_Control_rep3


title: MC38 dLN + TILS

status: Public on May 16 2022

first: Thomas

last: Ciucci

description: GP66:I-Ab+ CD4+

library_source: transcriptomic single cell

data_processing:
Basecalling was performed using RTA 2.4.11
Sequencing reads were demultiplexed using Bcl2fastq 2.17
The fastq files are processed throgh the cellranger count to get differential expression counts.
For hashtagged sequencing, samples were demultiplexed based on the expression of barcoded antibodies
Barcodes =  dLN-1 ACCCACCAGTAAGAC, dLN-2 GGTCGAGAGCATTCA, TIL-1 CTTGCCGCATGTCAT, TIL-2 AAAGCATTCTTCACG
Supplementary files format and content: mm10

source_name: Draining lymph node and Tumor

extract_protocol:
Single Cell  5'  Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and  sequenced with paired-end reads on a Illumina sequencers.

value: Wild-type


title: LCMV memory CD4

data_processing:
Basecalling was performed using RTA 1.12.4.2
Sequencing reads were demultiplexed using Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger software to produce the fastqfiles
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10
Supplementary_files_format_and_content: barcode file, gene file and gene expression matrix

source_name: Spleen

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and  sequenced with paired-end reads  on a NextSeq500 sequencer (Illumina).

tag: infection

value: LCMV Arm

tag: population

value: CD4(+) TCRb(+) CD25(-) GP66tetramer(+) CD44(hi) CD62L(lo)


title: MethylC-seq_P0_Control_rep6


title: JFL12

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.6 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.4.0 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were normalized by total number of reads per each samples and multiplied by 10E6.
Genome_build: Homo sapiens (GRCm38)
Supplementary_files_format_and_content: Counts matrix with gene expression value for all samples.

source_name: WPMY cells in androgen deprivation medium treated with Olaparib

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

treatment_protocol: WPMY-1 cells were growth with or without androgens (ADT) and treated with DMSO or 10 uM Olaparib for 4 days

tag: tissue source

value: Prostate

value: Prostate stromal cell line


title: JFL10

value: androgen deprivation medium treated with Olaparib


title: WPMY_LACTATE_rep0 [ATAC-seq]

data_processing:
FASTQ.gz files were concatenated into two files per sample and used as input for Taiji software (https://taiji-pipeline.github.io/documentation/)
Taiji software uses BWA to allign the data to hg38 genome.
Taiji uses samtools, bedGraphToBigWig to generate bigwig files, and MACS2 to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content: processed data file consist of a bigwig file per sample

source_name: Prostate stromal cell line

growth_protocol: WPMY-1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Corning), supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, and 100 U/ml penicillin and 100 µg/ml streptomycin, in an atmosphere of 95% air and 5% CO2

extract_protocol:
The cell pellet was resuspended in 50 μl lysis buffer and then spun down 500 × g for 10 min at 4 °C. The nuclei pellet was resuspended into 50 μl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, 5 μl of amplified DNA after the first 5 cycles was used to do qPCR of 20 cycles to decide the number of cycles for the second round of PCR.
The total amplified DNA was size selected to fragments less than 800 bp using SPRI beads. Quantification of the ATAC-seq library was done with QuBit. The size of the pooled library was examined by TapeStation. Barcoded ATAC-seq libraries were pooled and paired end sequenced (sX75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego, CA).

treatment_protocol: WPMY-1 cells treated or not with 24 mM lactate, 48h

value: prostate

value: Lactate 24mM, 48h


title: WPMY_CTR_rep0 [ATAC-seq]

value: Control cells, 48h


title: JFL11


title: JFL9

source_name: WPMY cells in androgen deprivation medium treated with DMSO


title: JFL8

value: androgen deprivation medium treated with DMSO


title: WPMY_OLA_rep0

source_name: WPMY-1 treated with 10 uM olaparib for 4 days

extract_protocol:
The cell pellet was resuspended in 50 μl lysis buffer and then spun down 500 × g for 10 min at 4 °C. The nuclei pellet was resuspended into 50 μl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, 5 μl of amplified DNA after the first 5 cycles was used to do qPCR of 20 cycles to decide the number of cycles for the second round of PCR.
The total amplified DNA was size selected to fragments less than 800 bp using SPRI beads. Quantification of the ATAC-seq library was done with QuBit. The size of the pooled library was examined by TapeStation. Barcoded ATAC-seq libraries were pooled and paired end sequenced (sX75) on the Illumina NextSeq 500 using the Mid output V2.5 kit (Illumina Inc., San Diego, CA).

treatment_protocol: DMSO or 10 uM Olaparib for 4 days

value: 10 uM olaparib for 4 days


title: JFL7


title: ChIP-seq_E14_Control_H3K27me3_rep2

value: C57BL6J/129 (name in Jackson Labs:B6.129-Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/MmbeJ)

value: excitatory pyramidal neurons

value: male


title: JFL5

source_name: WPMY cells in complete medium treated with Olaparib

value: complete medium treated with Olaparib


title: WPMY_DMSO_rep0

source_name: WPMY-1 treated with DMSO for 4 days

value: DMSO for 4 days


title: JFL3

source_name: WPMY cells in complete medium treated with DMSO

value: complete medium treated with DMSO


title: JFL6


title: JFL1


title: JFL2


title: Oct-RNA-1-05

data_processing:
FASTq files were processed using RNAseq Alignment module in BaseSpace (Illumina), using default parameters. Reads were aligned to mouse (hg38) genome using STAR. Differentially expressed genes were calculated using DeSeq2.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM gene expression values for all human genes (hg38) for all samples

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X76) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

treatment_protocol: WPMY-1 cells were  treated or not with 24 mM Lactate for 48h

value: Lactate treatment


title: Oct-RNA-1-03

value: Control


title: Oct-RNA-1-06


title: Oct-RNA-1-02


title: iTCE_D7_pos_rep6

status: Public on May 12 2022

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

description: WNT/FGF stimulated three-component embryoids (TCEs)

data_processing:
Sequencing raw data (bcl) were demultiplexed and transformed in fastq files using cassava v1.8.2.
The fastq files were aligned against the reference genome by RNAstar v2.5.3a.
The raw sequencing counts per gene were generated using htseq_count v2.16.2 using gencode.v25.annotation.exon.tls1.tlsNA-nopseudogene.gff3 or  Mus_musculus.GRCm38.93_proteinCoding_lincRNA.gtf.
To eliminate reads that were mapped on genomes from both human and mouse species we used picard tools.  Readnames from mouse mapped bam were filtered out of human mapped bam using picard FilterSamReads tools as well as  readnames from human mapped bam were filtered out of mouse mapped bam.
Assembly: hs_GRCh38.p2
Assembly: GRCm38
Supplementary files format and content: Comma separated value file including counts per gene (row)  for each sample (column)

organism:
Homo sapiens
Mus musculus

growth_protocol: hiPSCs alone or in combination with support cell types were prepared for 3D-aggregation by adding a total of 5.5×106 cells per-well in Corning Costar ultra-low attachment 6-well plates (CLS3471, Sigma Aldrich) in STEMdiff APEL2 medium (05270, STEMCELL Technologies) supplemented with 10 μM ROCK inhibitor (Y-27632, 1254, Tocris Bioscience) with constant shaking (Orbi-Shaker CO2, Benchmark Scientific) at 95 rpm at 37 °C and 8% CO2 overnight.

extract_protocol:
RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical).
Libraries were quantified using Quant-iT Picogreen (Invitrogen, Carlsbad, California, USA) on a Spectramax M2 (Molecular Devices, Sunnyvale, California, USA). Size pattern was controlled using a Fragment Analyzer-96 with the DNF-474-0500 High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies, Santa Clara, California, USA).
Libraries (Average size: 295 bp) were pooled at an equimolar ratio and clustered at a concentration of 9 pM on a single read sequencing flow cell.

treatment_protocol: For Wnt/FGF pathway stimulation, the medium was then replaced with STEMdiff APEL2 medium (05270, STEMCELL Technologies), supplemented with 2.5 μM of GSK3-inhibitor CHIR99021 (Tocris Bioscience) for 6 days.

tag: time

value: TCE

tag: group

value: pos


title: Oct-RNA-1-01

value: Prostate stromal cell line


title: Memory-phenotype CD4

tag: strain

value: CD4(+) TCRb(+) CD25(-) CD1tetramer(-) CD44(hi) CD62L(lo)


title: iTCE_D7_pos_rep2


title: iTCE_D7_pos_rep4


title: iTCE_D7_pos_rep5


title: iTCE_D7_pos_rep3


title: iTCE_D7_pos_rep1


title: Mono-aggregates_hiPSC_D7_pos_rep4

description: WNT/FGF stimulated hiPSC mono-aggregates

value: iPSC


title: R-BHTH (Reprogramming Intermediate Refractory) rep2 (ATAC-seq)

status: Public on May 06 2022

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

description:
R-BHTH_peaks.narrowPeak
R-BHTH_peaks.txt
R-BHTH_summits.bed
consensus_peak.bed
consensus_peak.counts

data_processing:
Sequencing reads are aligned to the Ensembl mouse reference version 93 using bwa mem version 0.7.15
BAM files are Encode blacklist filtered and quality filtered at mapping quality 10.
Peaks are called with MACS2 version 2.1.1.20160309. Replicates are joined at this stage.
Peaks are merged with homer's mergePeak command for a consensus peak set
Coverage in consensus peak set is determined with multiBamCov from Bedtools2 version 2.25.0
Genome_build: mm9
Supplementary_files_format_and_content: peak counts and bed files

source_name: mouse embryonic fibroblasts

growth_protocol: MEF were generated from E13.5 Bcl11b-tdTomato mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol. iPS cells were grown in DMEM containing 15% KnockOut™ Serum Replacement, 1,000 U/ml leukemia inhibitory factor, 100U/ml PS, 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM NEAA and 0.1mM b-mercaptoethanol. Transformed cells were cultivated in the same medium than MEF.

extract_protocol:
Cells were freeze in medium containing 5% DMSO. ATAC-seq DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: MEF are infected by OSKM retroviruses to induce Repro or by K-Ras G12V, shp53 lentiviruses combined with cMyc retroviral infection to induce Transfo and FACS-cell sorted after 5 days.

value: mouse embryonic fibroblast (MEF)

value: mouse embryonic fibroblasts FACS-sorted after 5 days of Repro

tag: antibody

value: CD90.2-APC (eBioscience, 17-0902)


title: R-BHTH (Reprogramming Intermediate Refractory) rep1 (ATAC-seq)


title: T-BHTH (Transforming Intermediate Refractory) rep2 (ATAC-seq)

description:
T-BHTH_peaks.narrowPeak
T-BHTH_peaks.txt
T-BHTH_summits.bed
consensus_peak.bed
consensus_peak.counts

value: mouse embryonic fibroblasts FACS-sorted after 5 days of Transfo


title: T-BLTL (Transforming Intermediate Prone) rep1 (ATAC-seq)

description:
T-BLTL_peaks.narrowPeak
T-BLTL_peaks.txt
T-BLTL_summits.bed
consensus_peak.bed
consensus_peak.counts


title: R-BLTL (Reprogramming Intermediate Prone) rep2 (ATAC-seq)

description:
R-BLTL_peaks.narrowPeak
R-BLTL_peaks.txt
R-BLTL_summits.bed
consensus_peak.bed
consensus_peak.counts


title: Mono-aggregates_hiPSC_D7_pos_rep1


title: Mono-aggregates_hiPSC_D7_pos_rep3


title: Mono-aggregates_hiPSC_D7_pos_rep2


title: Mono-aggregates_hiPSC_D7_pos_rep5


title: Mono-aggregates_hiPSC_D7_pos_rep6


title: R-BLTL (Reprogramming Intermediate Prone) rep1 (ATAC-seq)


title: Oct-RNA-1-04

value: prostate


title: T-BHTH  (Transforming Intermediate Refractory) rep2  (RNA-seq)

data_processing:
Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DeSeq2 package.
Genome_build: mm9
Supplementary_files_format_and_content: raw_count.csv: tab delimited csv file including raw counts for each sample
Supplementary_files_format_and_content: normalized_count.csv: tab delimited csv file including normalized counts for the each sample
Supplementary_files_format_and_content: model_fc.csv: tab delimited csv file including FC, p-value and adjusted p-value

growth_protocol: MEF were generated from E13.5 Bcl11b-tdTomato mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol. iPS cells were grown in DMEM containing 15% KnockOut™ Serum Replacement, 1,000 U/ml leukemia inhibitory factor, 100U/ml PS, 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM NEAA and 0.1mM b-mercaptoethanol. Malignant cells were cultivated in the same medium than MEF.

extract_protocol:
RNAs were extracted with Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic fibrobalsts FACS-sorted after 5 days of Transfo


title: T-BHTH (Transforming Intermediate Refractory) rep1 (ATAC-seq)


title: T-BHTH  (Transforming Intermediate Refractory) rep1  (RNA-seq)


title: R-BHTH (Reprogramming Intermediate Refractory) rep2 (RNA-seq)

value: mouse embryonic fibrobalsts FACS-sorted after 5 days of Repro


title: T-BLTL (Transforming Intermediate Prone) rep1  (RNA-seq)


title: T-BLTL (Transforming Intermediate Prone) rep2  (RNA-seq)


title: R-BHTH (Reprogramming Intermediate Refractory) rep1 (RNA-seq)


title: R-BLTL (Reprogramming Intermediate Prone) rep1 (RNA-seq)


title: FOXA2_input_PP2_HHEXKO

status: Public on Apr 29 2022

first: Dapeng

last: Yang

address: 1275 YORK AVE

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Align to hg19 reference genome using bowtie2 2.3.4.1
Peak calling to generate signal tracks on on individual replicates using macs2 2.1.1.20160309 with options -B -p 1e-2
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format

source_name: ES-derived progenitors

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM).  DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PP1 stage. The PP1 cells were then further differentiated toward PP2 stage using S3/4 media supplemented with 2 ng/ml of FGF7, 0.25 mM vitamin C, 0.1 µM RA, 200 nM LDN, 0.25 µM SANT-1, 100 nM TPB, and 1:200 ITS-X for 4 days. Cells collected at PP2 stage for FOXA2 ChIP-seq were differentiated at PP1 and PP2 using following condition; Cells were exposed to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, 1µM retinoic acid (RA), 100 nM LDN (Stemgent, 04-0019), 0.25 µM SANT-1 (Sigma, S4572), 200 nM TPB (EMD Millipore, 565740), and 1:200 ITS-X for two days.

extract_protocol:
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
Samples were amplified using NEBNext Q5 Hot Start HiFi PCR Master Mix. The concentration of samples was checked using PicoGreen and median fragment size was checked using the Agilent D1000 screentape on the Agilent Technologies 2200 TapeStation. Samples were sequenced single end or paired, as specified, on Illumina HiSeq 2500.

tag: differentiation stages

value: Pancreatic progenitor 2

tag: genotype

value: HHEX -/-

value: FOXA2 input


title: FOXA2_input_PP2_WT

value: wild type


title: FOXA2_PP2_HHEXKO_2


title: T-BLTL (Transforming Intermediate Prone) rep2 (ATAC-seq)

tag: cell type


title: FOXA2_PP2_WT_1


title: FOXA2_PP2_WT_2


title: FOXA2_PP2_HHEXKO_1


title: JFL4

tag: treatment

value: complete medium treated with Olaparib


title: HHEX_input_PP2_HHEXKO

data_processing:
Align to hg19 reference genome using bowtie2 2.3.4.1
Peak calling to generate signal tracks on on individual replicates using macs2 2.1.1.20160309 with options -B -p 1e-2
Genome_build: hg19
Supplementary_files_format_and_content: Coverage track in bigWig format

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM).  DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PP1 stage. The PP1 cells were then further differentiated toward PP2 stage using S3/4 media supplemented with 2 ng/ml of FGF7, 0.25 mM vitamin C, 0.1 µM RA, 200 nM LDN, 0.25 µM SANT-1, 100 nM TPB, and 1:200 ITS-X for 4 days.

value: HHEX


title: HHEX_PP2_HHEXKO_2


title: HHEX_PP2_WT_1


title: HHEX_input_PP2_WT


title: HHEX_PP2_HHEXKO_1


title: HHEX_PP1_WT_1

value: Early pancreatic progenitor


title: HHEX_input_GTPP1_WT

value: Gut tube


title: HNF4A_PP1_HHEXKO_2


title: HNF4A_PP1_WT_2


title: HHEX_GT_WT_2


title: R-BLTL (Reprogramming Intermediate Prone) rep2 (RNA-seq)


title: HHEX_GT_WT_1


title: HNF4A_input_PP1_WT_1


title: HNF4A_PP1_HHEXKO_1


title: HNF4A_PP1_WT_1


title: HNF4A_input_PP1_WT_2


title: ONECUT1_input_PP1_WT


title: ONECUT1_input_PP1_HHEXKO


title: ONECUT1_PP1_HHEXKO_2


title: HHEX_PP2_WT_2


title: ONECUT1_PP1_HHEXKO_1


title: ONECUT1_PP1_WT_1


title: ONECUT1_PP1_WT_2


title: HNF4A_input_PP1_HHEXKO_2


title: FOXA2_input_PP1_WT


title: HNF4A_input_PP1_HHEXKO_1


title: FOXA2_input_GT_WT


title: FOXA2_PP1_HHEXKO_2


title: FOXA2_PP1_WT_2


title: HHEX_PP1_WT_2


title: FOXA2_GT_HHEXKO_2


title: FOXA2_GT_WT_1


title: FOXA2_input_GT_HHEXKO


title: FOXA2_PP1_WT_1


title: FOXA2_PP1_HHEXKO_1


title: RSQ_184

status: Public on Apr 25 2022

city: Oxford

first: Breeshey

middle: Jane

last: Roskams-Hieter

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
Sickle tool version 1.33 for trimming
STAR version 2.5.3a for alignment with --twopassMode Basic flag
Picard version 1.119 for duplicate read removal
Samtools version 1.9 for bam file sorting and indexing
deeptools v3.5.0 for generating bigwigs
Genome_build: hg38, gencode v27 (ensembl v90)
Supplementary_files_format_and_content: bigwig files generated from aligned, de-duplicated bam files

source_name: Human multiple myeloma plasma

extract_protocol:
Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format)
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

tag: tissue

value: plasma

tag: age

tag: gender

value: Female

tag: cohort

value: validation


title: RSQ_190

source_name: Human liver cancer plasma

value: Male


title: RSQ_183


title: RSQ_192


title: RSQ_188


title: RSQ_182


title: RSQ_181


title: RSQ_179


title: RSQ_180


title: RSQ_177


title: RSQ_178


title: RSQ_169b


title: FOXA2_GT_WT_2


title: RSQ_171b


title: FOXA2_GT_HHEXKO_1


title: RSQ_160b


title: RSQ_138


title: RSQ_141


title: RSQ_135


title: RSQ_132


title: RSQ_077

source_name: Human non-cancer donor plasma


title: RSQ_078


title: RSQ_134


title: RSQ_076


title: RSQ_067


title: RSQ_074


title: RSQ_073


title: RSQ_055


title: RSQ_071


title: RSQ_051


title: RSQ_072


title: RSQ_070


title: RSQ_069


title: RSQ_049


title: RSQ_066


title: RSQ_068


title: RSQ_065


title: RSQ_054


title: PP103

source_name: Human MGUS plasma

value: pilot


title: PP102


title: PP098


title: PP116


title: RSQ_041b


title: PP097


title: PP114


title: PP091


title: PP111


title: PP109


title: PP105


title: RSQ_060


title: PP099


title: PP078

source_name: Human liver cirrhosis plasma


title: RSQ_047


title: PP087


title: PP058


title: PP055


title: PP075


title: PP049


title: PP048


title: PP060


title: PP073


title: PP061


title: PP062


title: PP050


title: FOXA2_input_PP1_HHEXKO


title: PP047


title: PP035


title: PP031


title: PP046


title: PP043


title: PP029


title: PP074


title: PP084


title: PP041


title: PP019


title: PP018


title: PP036


title: PP032


title: PP026


title: PP016


title: PP012


title: PP027


title: PP020


title: PP011


title: PP015


title: PP010


title: PP007


title: PP004


title: PP002


title: PP008


title: PP005


title: PP017


title: Total_macrophages_unfixed_sample_fractions_3

status: Public on Apr 06 2022

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR and Salmon.
Genome_build: mm10
Supplementary_files_format_and_content: Count table

source_name: Mouse microglia

extract_protocol:
Libraries were prepared using SMARTer Stranded Total RNAseq v3 Pico Input Mammalian sample preparation kits from 1ng of purified total RNA according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: microglia


title: Total_macrophages_unfixed_sample_fractions_2


title: Total_Macrophages_fixed_and_permeabilised_samples_2


title: Total_Macrophages_fixed_and_permeabilised_samples_3


title: Total_macrophages_unfixed_sample_fractions_1


title: Total_Macrophages_fixed_and_permeabilised_samples_1


title: Non_Tumor_microglia_Brain_3


title: PP003


title: Non_Tumor_microglia_Brain_2


title: EDUplus_microglia_1


title: Non_Tumor_microglia_Brain_1


title: EDUplus_microglia_3


title: EDUneg_microglia_1


title: EDUplus_microglia_2


title: BmTx (Ccr2-/-) IRI 3weeks HFD 4

status: Public on Apr 14 2022

type: RNA

city: Bonn

first: Sibylle

last: von Vietinghoff

address: Venusbergcampus 1

country: Germany

institute: University Clinic Bonn

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 750ng (only 500ng of M7342) of each fluorescently labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

label: Alexa Fluor 555

source_name: kidney

label_protocol: 200ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Just one half of the generated cDNA was used for aaUTP-cRNA synthesis. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; Thermo Fisher Scientific) as recommended in the manual of the Amino Allyl MessageAmp™ II Kit (twofold downscaled reaction volumes).

extract_protocol: RNA was extracted according to manufacturer's instructions (NucleoSpin RNA kit; #740955.250; Macherey-Nagel)

treatment_protocol: 8-week old male LDLr-/- mice were lethally irradiated, reconstituted with either wildtype or Ccr2-/- bone marrow and subjected to unilateral renal ischemia reperfusion (IR) for 27 min or control (ctrl.) surgery followed by a high fat diet for three weeks.

value: male

tag: genotype/variation

value: LDLr-/-

value: reconstituted with Ccr2-/-


title: EDUneg_microglia_2


title: BmTx (Ccr2-/-) IRI 3weeks HFD 1


title: Contralateral_microglia_unfixed_sample_3


title: IRI 3 weeks HFD

status: Public on Apr 13 2022

description: pooled sample from three male mice

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2000-2500ng of labeled cRNA were used for hybridization.

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: aorta

label_protocol: 150ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

treatment_protocol: Male LDLr-/- mice were subjected to unilateral ischemia reperfusion (IR)  or control (ctrl.) surgery followed by a high fat diet for three or ten weeks.

value: unilateral ischemia reperfusion


title: BmTx (wt) IRI 3weeks HFD 4

value: reconstituted with wildtype


title: ctrl. 10 weeks HFD

description: pooled sample from three male mice

value: control


title: BmTx (Ccr2-/-) IRI 3weeks HFD 3


title: IRI 10 weeks HFD

description: pooled sample from three male mice


title: BmTx (wt) IRI 3weeks HFD 2


title: BmTx (wt) IRI 3weeks HFD 1


title: BmTx (wt) IRI 3weeks HFD 3


title: Contralateral_microglia_unfixed_sample_1


title: ctrl. 3 weeks HFD

description: pooled sample from three male mice


title: BmTx (Ccr2-/-) IRI 3weeks HFD 2


title: mm_DC_UT_ChIP-seq_STAT1_rep2

status: Public on Apr 01 2022

city: Debrecen

first: Lajos

last: Széles

address: Egyetem tér 1.

country: Hungary

institute: University of Debrecen

description: unstimulated CD8-positive dendritic cells

data_processing:
read trimming with Trimmomatic using SE and -phread33 parameters, TruSeq3-SE.fa:2:30:10 adapter and LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 values
alignment with bwa v0.7.17 using default parameters
bam generation with Picard tools v2.8.1 using SortSam, AddOrreplaceReadGroups, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, MarkDuplicates with default parameters
tag directory generation with homer v4.9.1 makeTagDirectory using -checkGC and -single parameter
peak calling with MACS2 using -B, -q 0.001, --call-summits parameters
mm10 ENCODE blacklist were subtracted from the peak list
in case of ATAC-seq: calculating FPKM values from the previously created BAM and BED files
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (continuous-valued data in track format), bed (position of peaks)
Supplementary_files_format_and_content: table (tsv) of expression values

source_name: dendritic cells from the spleen

growth_protocol: CD8-positive dendritic cells were cultured in IMDM-glutamax medium supplemented with 10% FCS, 1% penicillin + streptomycin and 0,1% β-mercaptoethanol

extract_protocol:
Cells were double cross-linked with DSG (40 min) and  formaldehyde (10 min). Nuclei were isolated using lysis buffer containing 150 mM NaCl, 1 nM EDTA pH 8, 20 mM Tris-HCl pH 8, 1% Triton x-100, 1% SDS with EDTA-free protease inhibitor (Roche). Chromtain was sheared with sonication and immunoprecipitated overnight using antibodies against IRF3 (D83B9, Cell Signaling), IRF5 (ab21689, Abcam), IRF9 (AF5629, R&D Systems). Chromatin-antibody complexes were washed and eluted after pull-down by superparamagnetic beads (ThermoFisher Scientific). Eluted complexes were decrosslinked overnight and purified by NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). ChIP-DNA was quantified by Qubit fluorometer. In case of unstimulated cells for ATAC-seq after lysis, nuclei were subjected to tagmentation.
Indexed cDNA libraries were prepared from 1-10 ng ChIP-DNA using TruSeq ChIP Library Preparation Kit (Illumina) or Ovation Ultralow System V2 (Tecan Genomics) according to manufacturer’s instructions. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol (Illumina) for ATAC-seq. RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs) according to the manufacturer’s protocol. Libraries were sequenced on NextSeq 500 or HiSeq 2500.

treatment_protocol: Cells were left unstimulated or stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG)  or 10U IFN-beta for 90 min.

value: CD8-positive dendritic cell line

tag: stimulation

tag: chip antibody

value: STAT1 (sc-346, Santa Cruz Biotechnology),


title: EDUneg_microglia_3


title: Contralateral_microglia_unfixed_sample_2


title: TRIzol Liver LPS sample #1 [TLI2L1]

status: Public on Mar 31 2022

city: Seattle

first: Karol

last: Bomsztyk

state: WA

address: 850 Republican St

department: UW Medicine South Lake Union

institute: University of Washington

description: 2mg sample from frozen organ in CryoTray

data_processing:
Illumina RTA version 3.9.25
Index for alignment was built using the 'buildindex'  function from the Bioconductor 'Rsubread' (version 2.3.2) package. Index was assembled from the NCBI Genome Reference Consortium Mouse Build 39 (GRCm39) RefSeq assembly
Reads were aligned and counted in RStudio using the Bioconductor ‘RSubread’ (version 2.8.2) package. Alignment was done with the ‘align’ function on the paired gzFASTQ files creating sorted BAM files. Align commands:  type = "rna", input_format = "gzFASTQ", output_format = "BAM", sortReadsByCoordinates = TRUE, PE_orientation = "fr"
‘featureCounts’ function was used with the NCBI GRCm39 RefSeq Annotation and the commands: isGTFAnnotationFile=TRUE, countMultiMappingReads = FALSE, strandSpecific = 2, isPairedEnd=TRUE.
Assembly: mm39
Supplementary files format and content: tab deliminted text files include raw gene counts and gene annotation for each sample.
Supplementary files format and content: .csv table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
1-2mg samples of frozen tissue were sampled with the CryoCore and put into separate wells of a 96 well plates.  100ul of either PIXUL PK Buffer or TRIZOL buffer wer added to the wells and then all samples were sonicated in PIXUL sonicator (Matchstick Technologies, Inc Kirkland WA and Active Motif Carlsbad, CA). Samples are processed for 30 seconds in PIXUL with settings: Pulse=50, PRF=1.0 Burst=20.  TRIZOL samples then received additional 100ul of TRIZOL and followed manufacturers protocol for RNA isolation.  PIXUL PK Buffer samples are immediately incubated (After sonication) in the same PIXUL plate at 95C for 20 minutes, and then put on ice for 5 minutes. Cooled samples are centrifuged in a plate centrifuge for 10 minutes at 4,200g and 4C and then put back on ice. 60ul of clear supernatant (without any floating residue) from each well is carefully transferred via pipette to a new semi-skirted 96 well PCR plate on ice. Isolation of nucleic acids with 1.8x SPRI beads is done as per the Omega Bio-tek protocol (Norcross, GA) with a two-minute final SPRI bead drying time and final elution to 50ul of ultrapure ddH2O and then put samples on ice. Finally, DNase I and RNAse Out are added to the eluted RNA samples and DNase I digestion is done as per the manufacturer’s protocol.
Sequencing libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit with starting RNA between 205-480ng and libraries amplified between 13-14 cycles of PCR as per manufacturers protocol. Libraries were diluted as per Illumina NextSeq2000 Sequencing System Guide to a final pooled loading concentration of 650pM in resuspension buffer (RSB) plus Tween 20 with a 10% PhiX spike-in and sequenced in Illumina P2 cartridges on NextSeq 2000 that employed a dual-index, paired-end, 75 base read length (PE75).

treatment_protocol: Female 8–12-week-old C57bl/6 mice were injected intraperitoneally (IP) with 5mg/kg lipopolysaccharide (LPS) in 200ml PBS or with 200ml PBS as control. The specific protocol was approved by Institutional Animal Care and Use Committee (IACUC) at the University of Washington. After 12 hours mice were euthanized by isoflurane overdose and confirmatory cervical dislocation. Brains, hearts, kidneys, and livers were harvested, immediately placed on ice, and then frozen in CryoTrays

value: Liver

tag: tissue treatment

value: Lipopolysaccharide (LPS) treated

tag: rna isolation buffer

value: TRIzol

tag: mouse number

value: Female 8-12 week-old C57bl/6


title: mm_DC_UT_ChIP-seq_STAT2_rep1

value: STAT2 (07-140, Merck Millipore)


title: mm_DC_IFNb_ChIP-seq_STAT2_rep1

description: IFNB-stimulated dendritic cell (90 min)

value: 90 min; 10U IFN-beta


title: AA-E316-Jurkat_PHF6KO

status: Public on Apr 05 2022

first: Robert

last: Albero

address: 1130 St Nicholas Ave

institute: Columbia University

data_processing:
Data was aligned to hg19 genome using Bowtie2 and further processed the data using SAMtools.
SICER pipeline was used to identify spatial clusters of ChIP-enriched regions( 1000 bp window,3000 bp gap size)
PHF6-bound regions were defined as a FC>1.5 and FDR< 10EXP-20 compairing PHF6wt and PHF6 KO samples. Chromosome Y peaks were filtered out.
Bigwigs were generated and analyzed using Deeptools 3.3.0. Bigwigs were RPKM normalized.
Genome_build: hg19
Supplementary_files_format_and_content: bw and bed files

growth_protocol: We routinely split Jurkat cells every 2-3 days (typically 1 × 10e6 cells / ml ) on Falcon Tissue Culture Treated Flasks (Fisher-Scientific, #353136) and cultured the cells in RPMI-1640 containing 10% fetal bovine serum (FBS), 100 U ml–1 penicillin G and 100 μg ml–1 streptomycin

extract_protocol:
We extracted nuclear fractions and incubated with Mnase (1.5 U μL-1 ) before isolating nuclear complexes with antibody.
We used the Diagenode MicroPlex kit for Illumina platforms (Diagenode, #C05010012) following manufacturer’s instructions for library preparation. We quantified the libraries using the KAPA Library Quantification Kit for Illumina Platforms (KapaBiosystems, #KR0405) and AMPure XP (Beckman, # A63880) for library purification. We sequenced amplicon pools in an Illumina NextSeq500/505.

treatment_protocol: Cells were untreated

tag: disease state

value: Acute T cell leukemia

tag: cell line

value: Jurkat cells

value: Peripheral blood

value: Anti-PHF6 Antibody (HPA001023)

value: Untreated


title: AA-E316-Jurkat_WT

value: WT


title: TRIzol Liver PBS sample #1 [TLI2P1]

value: Phosphate Buffered Saline (PBS) treated


title: TRIzol Liver PBS sample #2 [TLI1P2]


title: TRIzol Liver LPS sample #2 [TLI1L2]


title: TRIzol Kidney LPS sample #2 [TK1L2]

source_name: Kidney

value: Kidney


title: TRIzol Kidney PBS sample #1 [TK1P1]


title: TRIzol Heart PBS sample #1 [TH2P31]

source_name: Heart

value: Heart


title: TRIzol Heart PBS sample #2 [TH2P33]


title: TRIzol Heart LPS sample #1 [TH2L31]


title: TRIzol Heart LPS sample #2 [TH2L33]


title: TRIzol Brain LPS sample #2 [TB2L2]

source_name: Brain

value: Brain


title: TRIzol Brain LPS sample #1 [TB1L1]


title: TRIzol Kidney PBS sample #2 [TK1P2]


title: PKBuffer Liver PBS sample #2 [BLI2P2]

value: PIXUL Proteinase K Buffer


title: TRIzol Brain PBS sample #1 [TB1P1]


title: TRIzol Kidney LPS sample #1 [TK1L1]


title: PKBuffer Liver LPS sample #1 [BLI1L1]

value: Liver


title: PKBuffer Liver PBS sample #1 [BLI1P1]


title: PKBuffer Heart PBS sample #2 [BH2P32]


title: PKBuffer Kidney LPS sample #2 [BK2L40]

value: Lipopolysaccharide (LPS) treated


title: PKBuffer Kidney PBS sample #1 [BK1P40]


title: PKBuffer Heart LPS sample #2 [BH1L32]


title: PKBuffer Brain LPS sample #2 [BB1L2]


title: TRIzol Brain PBS sample #2 [TB2P2]

value: TRIzol


title: PKBuffer Kidney PBS sample #2 [BK2P40]

value: Female 8-12 week-old C57bl/6


title: PKBuffer Heart PBS sample #1 [BH2P30]


title: PKBuffer Brain LPS sample #1 [BB1L1]


title: PKBuffer Brain PBS sample #2 [BB1P2]


title: mes4_l1pgcs_rep05

status: Public on Mar 16 2022

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

address: 329 sinsheimer labs

institute: University of California at Santa Cruz

description: Single set of sister Primordial Germ Cells (2 cells) dissected from an L1 larva (fed for 30-60 minutes immediately after hatching).

data_processing:
Libraries were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.
Illumina reads were mapped to the ce10 genome and  92 ERCC spike-in sequences  (Life Technologies, #4456740) using HISAT2 (v2.2.1) and parameters: --no-unal, --no-discordant, --no-mixed.  Known exons and splice sites were extracted from an Ensembl ce10 (WS220) GTF annotation file and given to HISAT2 for read mapping. Reads were de-duplicated using Samtools (v1.10) and then counted over exons and at the gene level (same ce10 annotation) using featureCounts from the Subread package (Liao et al., 2014).
Low quality transcript profiles from PGCs and EGCs were filtered from the dataset using scuttle in R (v1.2.0) (McCarthy et al., 2017). All PGCs and EGCs were used to calculate Median Absolute Deviations (MADs) for library size, number of detected features (genes), and % of library that aligned to ERCC spike-in transcripts. Samples were considered outliers and filtered from the dataset if they had a library size >3 MADs lower than the median, or a number of detected features >3 MADs lower than the median, or a % of library that aligned to ERCC spike-in transcripts >3 MADs greater than the median.
Scaling factors to normalize raw read counts were calculated using scran in R (v1.20.1) (Lun et al., 2016) for PGCs and EGCs and using DESeq2 (v1.32.0) (Love et al., 2014) for gonads. A matrix of normalized counts for samples of PGCs and EGCs is included in this submission: pgc_egcs_countsNormalized.txt
Differentially expressed genes were identified using DESeq2 (v1.32.0) (Love et al., 2014) as those with a Benjamini Hochberg-adjusted p-value < 0.05.
Assembly: ce10
Supplementary files format and content: allsamples_rawcounts_matrix.txt is a matrix containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file that also includes entries for 92 ERCC spike-in transcripts. Counts were generated using featureCounts from the subread package (Liao et al. 2014). pgcs_egcs_countsNormalized_matrix.txt contains normalized counts for all samples of PGCs and EGCs. adgerm_batch01_countsNormalized_matrix.txt contains normalized counts for adult gonad samples sequenced in "adgerm_batch01".  adgerm_batch02_countsNormalized_matrix.txt contains normalized counts for adult gonad samples sequenced in "adgerm_batch02".

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Primordial Germ Cells

growth_protocol: Animals were reared at 20˚C using standard protocols.

extract_protocol:
Single sets of 2 Primordial Germ Cells (PGCs) or 2 Early Germ Cells (EGCs) were dissected from L1 larvae or L2 larvae, respectively. PGCs and EGCs were used directly as starting material for library preparation. 20-60 gonads were dissected from 1st day adult hermaphrodites and then cut at the gonad bend. Only the distal halves were kept to exclude oocytes and several somatic gonad cells from our analysis. Gonads were vortexed in Trizol and stored at -80˚C. RNAs were then extract from those gonads using 1-bromo-3-chloropropane (Sigma #B9673), precipitated using isopropanol, pelleted by a 13,000 rcf spin for 15 minutes at 4˚C, and washed using ethanol.
Libraries were constructed according to manufacturer's recommendation. PGCs/EGCs: RNAs were converted into double-stranded cDNAs using a modified smart-seq2 protocol (Picelli et al., 2014). Illumina sequencing libraries were then prepared from those cDNAs using Illumina's Nextera XT kit. Gonads: mRNAs were isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then used to prepare Illumina sequencing libraries using the NEBNext Ultra RNA Library Prep Kit (#E7530).

tag: source strain

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

tag: stage and sex

value: L1 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no