title: PROseq_RG9_d78h_dTAG13

description: processed data file: PROseq_RC4_RG9_noFPKMfilter.txt

data_processing:
ChIP-seq and Calibrated ChIP-seq: For uncalibrated ChIP-seq, input and ChIP-seq reads were aligned to the 129S1/SvJm (mus) and CAST/Eih (cas) genome as previously described (Kung et al., 2015; Minajigi et al., 2015). PCR duplicates were removed and uniquely mapped reads used for further analysis. Fpm-normalized bigwig tracks were generated for all uniquely mapped (comp), mus-specific (mus), and cas-specific (cas) reads. Heatmaps and metaplots were generated using deepTools functions computeMatrix and plotHeatmap with the reference point as the summit of the called ChIP peaks.Calibrated ChIP-seq analysis was performed as previously described (Hu et al., 2015). Briefly, paired-end reads were aligned to a concatenated mouse and human genome (mm9 + hg19) using Bowtie2 with ?--no-mixed? and ?--no-discordant? options. PCR duplicates were filtered out with SAMBAMBA (Tarasov et al., 2015). Uniquely aligned mouse reads were normalized to human spike-in by subsampling mm9 reads so that total number of hg19 reads was matched between samples and bigWig tracks generated from normalized samples. For calibration of RAD21 cChIP between RAD21-FKBPdegron clones, only reads within hg19 peaks (hg19 tracks combined) were counted for normalization purposes. Subsampling factors were further adjusted based on ratio of hg19 to mm9 reads in matched input samples. After normalization factor was determined, paired end reads were aligned to mus and cas genomes as previously described, except using Bowtie2 with the same parameters as above (with ?--no-mixed? and ?--no-discordant?) instead of Novoalign. PCR duplicates were filtered out with SAMBAMBA and allelic reads normalized using the same normalization factor as above.Input subtracted H3K27me3 calibrated ChIP coverage profiles were generated with SPP (Kharchenko et al., 2008) with smoothing using 1kb windows recorded every 500 bp, as previously described (Simon et al., 2013). For input subtraction, inputs from DMSO and dTAG-13 treated samples were combined to ensure equal profiles were subtracted from each calibrated IP.Heatmaps and metaplots were generated using deepTools functions computeMatrix and plotHeatmap with the reference point as the summit of the called ChIP peaks. Plots of calibrated H3K27me3 signal over upregulated or downregulated genes were calculated using ?scale-regions? with the entire gene scaled to 3kb. To compare the allelic densities of H3K27me3 over different classes of X-linked genes, we computed average densities over gene bodies using multiBigwigSummary from deepTools with default parameters. Non-expressed genes were defined as X-linked genes have 0 RPKM in at least one RNA-seq replicate of DMSO control. Genes subject to XCI were identified as the set of genes have allelic information (see RNA-seq analysis above), with escapees, Xist and Tsix excluded. Escapees were as defined previously (Wang et al., 2018). To compare allelic densities of H3K27me3 over S1 and S2 compartments, we defined S1 compartments as regions having positive value in the first Principal Component calculated in the WAPL-FKBPdegron DMSO control days 4-7 sample and S2 compartments as regions have negative value. S1 and S2 compartments were then binned into 100kb windows using bedtools makewindows, excluding windows that overlapped with unmappable regions as defined previously (Wang et al., 2018). We then we computed average densities over these 100kb bins using multiBigwigSummary from deepTools with default parameters.
RNA-seq: RNA-seq reads were aligned allele-specifically to the 129S1/SvJm (mus) and CAST/Eih (cas) genomes using TopHat2 (Kim et al., 2013) as previously described (Kung et al., 2015; Minajigi et al., 2015). PCR duplicates were removed and unique reads mapping to exons of each gene quantified by Homer (Heinz et al., 2010). DESeq 2 was used to call differentially expressed genes with a cut off of adjusted p-value < 0.1. An expression threshold of FKPM > 0.5 was also applied. Expressed genes with a minimum of 13 allelic-specific reads in at least one sample were counted as genes with allelic information (Colognori et al., 2019). For a given gene, percent mus was calculate as the percentage of allelic reads that were mus-specific (mus / (mus+cas) reads).
in situ Hi-C: Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and merged into Hi-C summary files and filtered using HOMER as previously described (Minajigi et al., 2015). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ?pre? command of Juicer tools with the genomeID mm9 (Durand et al., 2016b). The resulting Hi-C contact maps in .hic format were visualized and normalized with the ?Coverage Square Root? option in Juicebox version 1.8.8 (Durand et al., 2016a). Filtered reads from separate RAD21-FKBPdegron clones were combined before generating Hi-C contact maps.
CHART-seq: Input and ChIP-seq reads were aligned to the 129S1/SvJm (mus) and CAST/Eih (cas) genome as previously described (Kung et al., 2015). PCR duplicates were removed and uniquely mapped reads used for further analysis. Fpm-normalized bigwig tracks were generated for all uniquely mapped (comp), mus-specific (mus), and cas-specific (cas) reads. CHART libraries were sampled to equal read depth and input subtracted CHART coverage profiles were generated with SPP (Kharchenko et al., 2008) with smoothing using 1kb windows recorded every 500 bp, as previously described (Simon et al., 2013). After scaling, we computed base 2 logarithm of the ratio of the coverage of DMSO control divided by that of dTAG-13 using bigWigCompare from deepTools with --binSize 1000 and default parameters otherwise.
PRO-seq: Paired-end reads were aligned to a concatenated mouse and fly genome (mm9 + dm6) using Bowtie2 with ?--no-mixed? and ?--no-discordant? options. DMSO and dTAG-13 samples for each clone were normalized to drosophila spike-in by subsampling mm9 reads so that total number of dm6 reads was matched between samples. For RAD21-FKBPdegron clone G9, downsampling factors corresponded to library size (i.e., were equivalent to downsampling based on total number of reads). For RAD21-FKBPdegron clone C4, downsampling factors were 1 for DMSO and 0.73 for dTAG-13 although library sizes were similar, indicating that there were overall lower levels of nascent transcription in the dTAG-13 sample. Duplicates were not removed to preserve reads corresponding to TSS and promoter proximal PolII positions. Reads mapping to genes (full gene bodies) were quantified by Homer (Heinz et al., 2010), removing miRNA, snoRNA and scaRNAs. DESeq 2 was used to call differentially expressed genes with a cut off of adjusted p-value < 0.1. For analyses on all genes, no FPKM threshold was applied, but genes were required to have at least 1 count in one sample. An expression threshold of FKPM > 0.5 was applied for analyses on expressed genes. Log2FoldChange and log2baseMean from DESeq2 were plotted for indicated classes of genes. H3K27me3 genes were defined as genes overlapping H3K27me3 cChIP-seq peaks in their respective samples (DMSO and dTAG-13 peaks combined). H3K27me3 loop genes were defined as H3K27me3 genes overlapping H3K27me3-bound loop anchors called in RAD21-FKBPdegron dTAG-13 Hi-C maps (i.e., cohesin-independent H3K27me3 anchored loops). For overlap with RAD21 loop anchors, loops were called in respective DMSO Hi-C maps.For allelic analysis, PRO-seq reads not mapping to the fly genome (dm6) were aligned to mus and cas genomes using Bowtie2 with the same parameters as above (?--no-mixed? and ?--no-discordant?) and downsampled using the same factors as calculated above. Expressed genes with a minimum of 13 allelic-specific reads in at least one sample were counted as genes with allelic information (Colognori et al., 2019). For CDPs, normalized mus and cas counts divided by gene length were plotted.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.bw), regardless of whether they are allele-specific or not, cas-specific (.cas.bw) and mus-specific (.mus.bw). All bigWig files are fpm normalized and H3K27me3 bigWig files are additionally input normalized.
Supplementary_files_format_and_content: Calibrated ChIP-seq: bigWig (bw) files for all reads (.bw), regardless of whether they are allele-specific or not, cas-specific (.cas.bw) and mus-specific (.mus.bw). All bigWig files are normalized to spike-in HEK293 control and H3K27me3 bigWig files are additionally input normalized.
Supplementary_files_format_and_content: RNA-seq: Strand specific (cwig, Crick strand, wwig, Watson strand) bigWig (bw) files for all reads (.bw), regardless of whether they are allele-specific or not, cas-specific (.cas.bw) and mus-specific (.mus.bw). All bw files are fpm normalized. Raw exonic reads in each RNA-seq library were quantified and summarized in .txt files.
Supplementary_files_format_and_content: PRO-seq: Strand specific (cwig, Crick strand, wwig, Watson strand) bigWig (bw) files for all reads (.bw), regardless of whether they are allele-specific or not, cas-specific (.cas.bw) and mus-specific (.mus.bw). All bw files are downsampled according to Drosophila spike-in. Gene body counts in each PRO-seq library were quantified and summarized in .txt files.
Supplementary_files_format_and_content: In situ Hi-C: Compressed Hi-C matrix (.hic) files for all contacts genome-wide (.hic), regardless of whether they are allele-specific or not, cas-specific chrX (chrX.cas.his) contacts and mus-specific chrX (chrX.mus.hic) contacts. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: mESC

extract_protocol:
ChIP-seq: ChIP-seq was performed as described previously with minor modifications (Del Rosario et al., 2019). Briefly, cells were trypsinized, resuspended in 1 million cells/mL of media and crosslinked with 1% formaldehyde for 10 min at room temperature with rotation. Cells were then quenched with 0.2 M glycine for 5 min. Crosslinked cells were washed once with cold PBS, pelleted, and snap frozen in an EtOH/dry ice bath. Cell pellets were stored at -80C until further processing. 5-10 million cross-linked cells per IP were thawed on ice and resuspended in 300ul Lysis Buffer 1 (25mM HEPES pH 7.2-7.5, 25mM EDTA, 0.5% SDS). Nuclei were sonicated (Qsonica Q800 Sonicator) in polystyrene tubes at 40% power setting, 30s ON/30s OFF for a total sonication (ON) time of 6 min. After sonication, 1.2 mL of Lysis Buffer 2 (25mM HEPES pH 7.2-7.5, 187.5mM NaCl, 1.25% Triton X-100, 0.625% Na-deoxycholate, 6.25% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail) was added. 30ul of Dynabeads Protein G (Thermo Fisher Scientific) per IP were washed 3 times with ChIP Wash Buffer 1 (25mM HEPES pH 7.2-7.5, 150mM NaCl, 5mM EDTA, 1% Triton X-100, 0.5% Na-deoxycholate, 5% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail) and resuspended in 60ul ChIP Wash Buffer 1. Each IP was blocked with 20ul washed beads for 2 hours at 4C with rotation. The other 40ul of washed beads were incubated with antibody (5ul of RAD21 antibody or 2ul of H3K27me3 antibody/IP) for 2 hours at 4C. 5% input was taken from blocked lysates. Beads conjugated to antibody were added to blocked lysates and IP allowed to proceed overnight at 4C with rotation. IPs were then washed 3 times with cold ChIP Wash Buffer 1, 3 times with cold ChIP Wash Buffer 2 (25mM HEPES pH 7.2-7.5, 300mM NaCl, 5mM EDTA, 1% Triton X-100, 0.5% Na-deoxycholate, 5% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail). And 1 time with cold TENG (50mM Tris-HCl pH 8, 1mM EDTA, 50mM NaCl, 5% glycerol, 1x cOmplete EDTA-free protease inhibitor cocktail). All washes were performed by inverting tubes and setting aside for ~2 minutes per wash. IPs were then resuspended in 500ul TENG with 100ug RNAse A (Thermo Fisher Scientific) and incubated for 30 min at 37C. IPs were then washed 2 times with cold ChIP Wash Buffer 2 and 2 times with cold TENG without protease inhibitors. IPs were resuspended in 200ul elution buffer (50mM Tris-HCl pH 7.5, 10mM EDTA, 1% SDS) and incubated 15 min at 65C. Eluate was then transferred to a new tube and 198ul TE buffer (Ambion) and 40ug Proteinase K (Sigma) added. Inputs were thawed, TE buffer added to equalize volume to IPs and 200ul elution buffer and 40ug Proteinase K added. Inputs and IPs were then incubated for 2h at 45C and crosslinks reversed overnight at 65C. DNA was purified with phenol-chloroform extraction and resuspended in 50ul TE. Efficiency of ChIP was assayed via qPCR, with samples displaying over 10-fold enrichment of positive regions over negative control prepared for sequencing. Libraries were prepared from ~500ng of input or IP DNA using the NEBNext® Ultra? II DNA Library Prep Kit for Illumina® (NEB) according to kit instructions. Experiments were performed in two biological replicates. Input and ChIP-seq libraries were sequenced on Illumina HiSeq, generating 20-50 million paired end 50 or 150 nucleotide reads per sample.
Calibrated ChIP-seq: Calibrated ChIP-seq was performed using the same protocol as ChIP-seq except that 50,000 HEK293 cells per 5 million mouse cells were mixed in at the initial lysis step. Cells were counted and equal numbers of cells used per IP.
in situ Hi-C: As described in Rao et al. (2014), 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads.
CHART-seq: Xist CHART-seq was performed as previously described (Wang et al., 2018). Briefly, cells were trypsinized, resuspended in 1 million cells/mL of media and crosslinked with 1% formaldehyde for 10 min at room temperature with rotation. Cells were then quenched with 0.2 M glycine for 5 min. Crosslinked cells were washed once with cold PBS, pelleted, and snap frozen in an EtOH/dry ice bath. Cell pellets were stored at -80C until further processing. 25 million cross-linked cells per CHART were thawed on ice and resuspended in 1 mL cold sucrose buffer. (10 mM HEPES pH 7.5, 0.3 M sucrose, 1% Triton X-100, 100 mM potassium acetate, 0.1 mM EGTA) supplemented with 0.5 mM spermidine, 0.15 mM spermine, 1 mM DTT, 1x protease inhibitor cocktail (Sigma, P8340), 10 U/mL RNase inhibitor (Roche). The cell suspension was rotated for 10 min at 4°C, after which it was diluted with additional 2 mL cold sucrose buffer. This was added to a pre-chilled 15-mL glass Wheaton dounce tissue grinder (Thermo Fisher Scientific) that had been pre-rinsed once with RNaseZAP RNase decontamination solution (Thermo Fisher Scientific), three times with DEPC-treated water, and once with 2 mL sucrose buffer. Release of nuclei was accomplished by douncing cells 20 times with a tight pestle, and verified by staining with Trypan Blue Solution (Thermo Fisher Scientific). The nuclear suspension was then layered atop a cushion of 7.5 mL cold glycerol buffer (10 mM HEPES pH 7.5, 25% glycerol, 1 mM EDTA, 0.1 mM EGTA, 100 mM potassium acetate) supplemented with 0.5 mM spermidine, 0.15 mM spermine, 1 mM DTT, 1x cOmplete EDTA-free protease inhibitor cocktail (Roche), and 5 U/mL RNase inhibitor, and centrifuged at 1500 g for 10 min at 4°C. The purified nuclear pellet was resuspended in 6 mL PBS and further cross-linked with 3% formaldehyde for 30 min at room temp with rotation. Afterward, nuclei were pelleted by centrifugation at 1,000 g for 5 min at 4°C and washed three times with cold PBS. Nuclei were resuspended in in 1 mL cold nuclear extraction buffer (50 mM HEPES pH 7.5, 250 mM NaCl, 0.1 mM EGTA, 0.5% sarkosyl, 0.1% sodium deoxycholate, 5 mM DTT, 10 U/mL RNase inhibitor) and incubated for 10 min at 4°C with rotation. Nuclei were then centrifuged at 400 g for 5 min at 4°C and resuspended in 230 uL cold sonication buffer (50 mM HEPES pH 7.5, 75 mM NaCl, 0.1 mM EGTA, 0.5% sarkosyl, 0.1% sodium deoxycholate, 0.1% SDS, 5 mM DTT, 10 U/mL RNase inhibitor) to a final volume of ?270 uL. Nuclei were sonicated for 5 min at 4°C using a Covaris E220e (140W peak incident power, 10% duty factor, 200 cycles/burst). Sonicated chromatin was centrifuged at 16,000 g for 20 min at 4°C to remove debris. The supernatant (?220 uL) was mixed with 110 uL sonication buffer to a final volume of ?330 uL, which was split into two CHART reactions (Xist capture using antisense probes and control capture using sense probes). For two CHART reactions, 600 uL MyOne Streptavidin C1 beads (Thermo Fisher Scientific) were used, which were pre-washed with 1 mL DEPC-treated water, blocked with 600 uL blocking buffer (33% sonication buffer, 67% 2x hybridization buffer, 500 ng/uL yeast RNA [Thermo Fisher Scientific], 1% BSA) at room temp for 1 hr, washed with 1 mL DEPC-treated water again, and resuspended in 610 uL 1x hybridization buffer (33% sonication buffer, 67% 2x hybridization buffer [see below for composition]). For each CHART, 160 uL chromatin was mixed with 320 iL 2x hybridization buffer (50 mM Tris pH 7.0, 750 mM NaCl, 1% SDS, 1 mM EDTA, 15% formamide, 1 mM DTT, 1 mM PMSF, 1x cOmplete EDTA-free protease inhibitor cocktail, 100 U/mL RNase inhibitor) and pre-cleared with 60 uL pre-blocked MyOne Streptavidin C1 beads at room temp for 1 hr with rotation. Pre-cleared chromatin was separated from beads, with 1% saved as ?input? sample. The remaining pre-cleared chromatin (?500 uL) was mixed with 36 pmol of either antisense (Xist-targeting) or sense (control) biotinylated capture probes. We used a pool of 9 capture probes, which were selected from the 11 probes described previously (Simon et al., 2013), excluding probes X.3 and X.8. Hybridization was carried out at 37°C for 4 hr followed by incubation with 240 uL blocked MyOne Streptavidin C1 beads at 37°C for 1 hr. The beads were washed once with 1x hybridization buffer (33% sonication buffer, 67% 2x hybridization buffer) at 37°C for 10 min, five times with wash buffer (10 mM HEPES pH 7.5, 150 mM NaCl, 2% SDS, 2 mM EDTA, 2 mM EGTA, 1 mM DTT) at 37°C for 5 min, and twice with elution buffer (10 mM HEPES pH 7.5, 150 mM NaCl, 0.5% NP-40, 3 mM MgCl2, 10 mM DTT) at 37°C for 5 min. 10% of the final wash was saved as an ?RNA capture? sample to estimate the efficiency of Xist RNA capture afterward by qRT-PCR. CHART-enriched DNA was eluted twice in 200 uL elution buffer supplemented with 5 U/uL RNase H (New England BioLabs) at 37°C for 30 min. An ?input? sample and CHART DNA were treated with 0.5 mg/mL RNase A (Thermo Fisher Scientific) at 37°C for 1 hr and then with 1% SDS, 10 mM EDTA, and 0.5 mg/mL proteinase K (Sigma) at 55°C for 1 hr. Reversal of crosslinks was performed by addition of 150 mM NaCl (final 300 mM) and incubation at 65°C overnight. DNA was purified by phenol-chloroform extraction and further sheared to < 500-bp fragments using Covaris E220e (140W peak incident power, 10% duty factor, 200 cycles/burst). Sonicated DNA was purified using 1.8x Agencourt AMPure XP beads (Beckman Coulter). Libraries were sequenced on Illumina, generating ?50 million 150-nt paired-end reads per sample
RNA-seq: Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific) and mRNA isolated using the NEBNext Poly(A) Magnetic Isolation Module (NEB) according to the kit instructions. Libraries were sequenced on the Illumina HiSeq2500 (rapid run), generated 30-50 million 50 nt paired end reads per sample.
PRO-seq: PRO-Seq library construction was performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA. Aliquots of frozen (-80°C) permeabilized cells were thawed on ice and pipetted gently to fully resuspend. An aliquot was removed and diluted 1:10 in 1xPBS for cell counting using an automatic counter (Biorad TC-20) with counts spot checked by manual recount using a hemocytometer as needed. An aliquot of each dilution was also stained with Trypan Blue and counting repeated to determine permeabilization efficiency. For each sample, 1 million permeabilized cells were used for nuclear run-on. For normalization, 50,000 permeabilized Drosophila S2 cells were added to each sample of 1 million cells. Nuclear run on assays and library preparation were then performed essentially as described [Elrod, N.D., et al. (2019) Molecular Cell 76: 738-752.e7] with modifications noted below. The nuclear run-on buffer was prepared as 4X stock (20mM Tris (pH 8), 20mM MgCl2, 2mM DTT, 600mM KCl, 40uM/ea biotin-11-NTPs (Perkin Elmer), 20U SuperaseIN (Thermo)). The 4X stock was mixed 1:1 with 2% sarkosyl (Sigma) to yield 2X complete run-on mix. The 3' adapter (RNA oligo: 5'P-GAUCGUCGGACUGUAGAACUCUGAAC-3'InvdT) was pre-adenylated prior to use (5' DNA adenylation kit, NEB, according to the manufacturer's instructions). Adenylated oligo was purified by ethanol precipitation, resuspended in water and quality was modification confirmed by electrophoresis on a 15% TBE-Urea gel (Novex) next to appropriate controls. The adapter concentration was adjusted to 10uM and 1uL was used for each ligation which used T4 RNA ligase 2, truncated KQ (NEB) with 15% PEG-8000 in the reaction mix. Reactions were incubated at 16°C overnight. Each ligation reaction was then diluted with 180uL of betaine binding buffer (1.42g of betaine brought to 10mL with binding buffer and sterile filtered) containing 1uL of 100uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/). The blocking oligo is complementary to and overhangs the 3' end of the 3' adapter and reduces 5'/3' adapter dimer formation during the 5' adapter ligation step. The blocking oligo has modifications at its 3? end, to prevent extension by reverse transcriptase. Blocking oligo was also included in final wash solution prior to the 5' adapter ligation and in the ligation reaction itself, both at 3-fold molar excess over the initial amount of 3' adapter (i.e. 1uL of 30uM per reaction). The 5' adapter ligation was performed as in Elrod except PEG-8000 was increased to 15%. Libraries were prepared using the NEBNext® Ultra? II DNA Library Prep Kit for Illumina® (NEB) according to kit instructions. PRO-seq: After reverse transcription, cDNA was immediately amplified for 5-cycles (preCR step). A PCR cocktail consisting of NEBNext Ultra II Q5 master mix (NEB) and Illumina TruSeq PCR primers (RP-1, common; and RPI-X, indexing) was added to each cDNA and amplification was done according to manufacturer's suggested 2-step cycling conditions for NGS applications. To determine optimal library amplification, the preCRs were thawed on ice and an aliquot serially diluted. Each dilution was mixed with a PCR cocktail (Q5 DNA polymerase with optional high GC enhancer) containing 10uM/ea of Illumina universal P5 and P7 primers and amplified 15-cycles. The reactions were electrophoresed on a 2.2% agarose gel (SeaKem) cast with SYBR gold (Thermo) and analyzed to determine the optimal number of cycles for final amplification. preCRs were transferred from ice to a pre-heated thermal cycler block and amplified for the appropriate number of additional cycles to reach the total determined in the test amplification.

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae

value: day 7


title: AAA

status: Public on Mar 15 2021

type: SRA

city: Madison

first: Bo

last: Liu

state: WI

address: 1111 Highland Avenue

country: USA

institute: University of Wisconsin-Madison

library_source: transcriptomic

data_processing:
Cell Ranger software was used to perform demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression estimation for each sample according to the 10x Genomics documentation
Downstream analysis was performed using Seurat (version 3.2.0) R (version 3.6.3) package.
Genome_build: mm9
Supplementary_files_format_and_content: TAR (of MTX, TSV)

molecule: total RNA

organism: Mus musculus

source_name: Infrarenal abdominal aortas

extract_protocol:
Mouse infrarenal abdominal aortas were collected and digested in an enzymatic mix (DMEM containing 10 mg/ml collagenase type II (C6885, Sigma Aldrich) and 1 mg/ml elastase (LS002292, Worthington Biochemistry)) for 15 minutes at 37 ̊C. The tissue suspension was filtered with a 40 µm cell strainer, then centrifuged at 500 g for 5 min. Cells were resuspended with DMEM containing 10% FBS. Single-cell suspensions from 4 aortas per group were pooled together as one sample. 5000 cells per sample were loaded on a Chromium Controller (10x Genomics).
The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ v3 Reagent Kit according to the manufacturers guidelines (10x Genomics)

treatment_protocol: AAA was induced in 12-week-old male C57BL/6J mice. Infrarenal abdominal aortas were perivascularly treated with 0.5 M CaCl2 for 10 minutes followed by PBS for 5 minutes. Mice in the sham group received 0.5 M NaCl treatment for 10 minutes followed by PBS for 5 minutes. Aortas were collected four days after AAA induction. Single-cell suspensions from four aortas were pooled as one sample.

tag: strain

tag: treatment

tag: age

tag: Sex

value: male

tag: tissue

value: Infrarenal abdominal aortas


title: iPS8_1932_d4_21

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Quality control was performed using FastQC (v. 0.11.8) and multiQC (v. 1.6), and one replicate (1938 iPS 1, day4) was eliminated from analysis
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v. 2.7.3a) (Dobin et al., 2013). The STAR parameters used were: --runMode alignReads --outSAMmode Full --outSAMattributes Standard --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1.
Annotation was done using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation) (Liao et al., 2014). The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id.
Ensembl genes without at least three samples with 10 or more reads were removed from analysis.
Normalization and differential expression analysis were performed using the R (v. 3.6.3) package DEseq2 (v. 1.28.1), (Love 2014). BiomaRt (v. 2.42.1) was used to convert Ensembl gene IDâ€™s to HUGO gene names.
Genome_build: GRCh38.p10 (GENCODE release 26)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample post filtering

organism: Homo sapiens

source_name: differentiated induced pluripotent stem cell

growth_protocol: MSCs (passage 3-4) were used for reprogramming in order to maximize reprogramming efficiency. MSCs were karyotyped both before and after reprogramming, to confirm normal chromosome number and confirm fetal sex.  Reprogramming was done using CytoTuneTM -iPSC 2.0 Sendai Reprogramming Kit (ThermoFisher) following the manufacturer’s protocol. In brief, reprogramming vectors were transduced into MSCs. Post-transduction day 5-7, MSCs were replated onto irraditated mouse embryonic feeder (MEF)-coated dishes with WiCell media (DMEM/F12 containing 20% Knockout serum replacement, 1X Glutamax, and 1X Nonessential amino acid, 0.1mM 2-mercaptoethanol and 12ng/ml b-FGF). P0 iPSC colonies appeared around 2 weeks post-transduction, and were subsequently picked for subcultures and passaged up to 10 times to dilute Sendai virus out from the culture.

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (Ambion). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by Aligent 2100 bioanalyzer. All samples had a RIN above 8.0.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit with Ribo-Zero Gold (Illumina)

treatment_protocol: Prior to differentiation, iPSCs were converted to feeder-free conditions in StemFlex (ThermoFisher) on Geltrex (ThermoFisher) coated plates (coated using 1:200 diluted Geltrex). Differentiation was performed using the two-step trophoblast differentiation established in our lab (detailed in Horii 2019) iPSC cell passages 5-10 post-StemFlex adaptation were used for all experiments.  XVIVO hypoxia workstation (Biospherix) was used for cell culture under 2% oxygen. Media was changed every day.

tag: disease state

value: Severe Preeclampsia

tag: differentiation days + oxygen%

value: day+4 under 21% oxygen

tag: differentiation end point cell type

value: Syncytiotrophoblast

tag: gender

value: Female


title: MCAO/R-2

city: Chang Chun

first: Xuan

last: Chen

state: Jilin

address: Xinmin Street

department: The First Hospital of Jilin University

country: China

institute: Jilin university

data_processing:
paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality trimmed reads were aligned to the rat reference genome (UCSC RN5).
Then, guided by the Ensembl gtf gene annotation file with hisat2 software (v2.0.4), cuffdiff software (v2.2.1, part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified
Genome_build: UCSC RN5
Supplementary_files_format_and_content: FPKM/count values for each samples

organism: Rattus norvegicus

source_name: brain tissue_middle cerebral artery occlusion and reperfusion (MCAO/R) model

extract_protocol:
Total RNA from the brain cortex was isolated using TRIzol reagent (Life Technologies)
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina NovaSeq Sequencer according to the manufacturer’s instructions.

value: brain

value: Sprague-Dawley (SD) rats

tag: time point


title: SAMPLE 29_519183LF13AG01280119_F03

type: RNA

city: Bethesda

first: Sai

last: Kanaparthi

state: MD

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

description: Liver biopsy  from Non-tolerant SAMPLE 29

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v3.1) in R.3.4.3

label: Biotin

source_name: Liver biopsy

label_protocol: Standard Affymetrix protocol

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

value: liver

tag: isw outcome (tolerant/non-tolerant)

value: Non-tolerant

value: 5yr Visit

tag: visit code


title: PROseq_RG9_d78h_DMSO

city: Boston

first: Andrea

middle: June

last: Kriz

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

growth_protocol: Undifferentiated mESCs were grown on γ-irradiated MEF feeders in medium containing DMEM, high glucose, GlutaMAX supplement, pyruvate, 15% Hyclone FBS (Sigma), 25 mM HEPES pH 7.2-7.5, 1x MEM non-essential amino acids, 1x Pen/Strep, 0.1 mM βME, and 500 U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein (Sigma, ESG1107) at 37°C with 5% CO2. To induce differentiation in EBs, mESCs were trypsinized and resuspended in the same media without LIF. For the first 3 days of differentiation, EBs were grown in suspension. On day 4 and subsequent days, EBs were grown on gelatinized plates until harvested at day 7 or day 10.

treatment_protocol: Degradation of RAD21 or WAPL in FKBPdegron lines during differentiation was induced by adding a 1:20,000 dilution of 10mM dTAG-13 in DMSO to cell culture media (500nM final concentration) for the indicated time frames. The small molecule dTAG-13 was synthesized as previously described (Erb et al., 2017; Nabet et al., 2018). For DMSO vehicle controls, the same volume of DMSO alone was added to cell culture media.

tag: cell type

tag: genotype

value: 8h DMSO

tag: differentiation day


title: MCAO/R-3


title: iPS8_1932_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: MCAO/R-1


title: HU-1-12_untreated_timepoint2

type: genomic

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

country: Germany

institute: University Hospital Ulm

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan reader with standard recommended settings

data_processing: The raw data were processed using the RnBeads package in R/Bioconductor. Probes known to be cross-reactive (43 230) or overlapping known single-nucleotide polymorphisms (SNPs; 8 710), as well as probes giving unreliable measurements (1039 as determined by the Greedycut algorithm) were excluded from analysis. The data from the remaining 432 598 probes were subjected to background subtraction using the Noob method and beta-mixture quantile normalization (BMIQ). This normalization strategy successfully mitigated the inherent bias in β-value distributions between the two different types of probes (Infinium I and II) that are present on the HumanMethylation450 BeadChip. In a subsequent step, probes of non-CpG context (1 242), probes binding to sequences on sex chromosomes (9 941), probes with missing values (198) and probes with low standard deviation (57 109) were filtered out. The data obtained by the remaining 364 108 probes were used in downstream analyses.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: CLL, untreated

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from CD19+ fractions of patients' peripheral blood mononuclear cells (PBMCs) using Qiagen AllPrep Kit according to standard instructions

value: female

tag: treated

value: no

tag: response to therapy

value: not applicable

value: unmutated


title: SAMPLE 30_286326LF13AG01280119_E05

description: Liver biopsy  from Non-tolerant SAMPLE 30


title: iPS1_1938_d0

source_name: induced pluripotent stem cell

value: Normal

value: day 0

value: induced pluripotent stem cell

value: Male


title: PROseq_RC4_d78h_DMSO

value: ES cell (Tsix-stop)

tag: strain

value: CAST/Ei x 129/Sv/Jae

value: day 7


title: SAMPLE 27_821656LF13AG01280119_A08

description: Liver biopsy  from Non-tolerant SAMPLE 27

value: liver


title: SAMPLE 28_828298LF13AG01280119_B01

description: Liver biopsy  from Non-tolerant SAMPLE 28

value: Non-tolerant


title: tra1Q3-2

city: London

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

description: MATalpha his3delta0 leu2delta0 ura3delta0 tra1Q3-HIS3+DED1pr-YHR100-LEU2

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to S. cerevisiae whole genome using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Genome_build: Saccharomyces cerevisiae S288C reference genome (assembly R64-2-1)
Supplementary_files_format_and_content: Raw gene counts table for every gene and every sample
Supplementary_files_format_and_content: Normalized counts text files for each gene for each sample

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae RNA

growth_protocol: Strains were grown to mid-log phase in synthetic complete media

extract_protocol:
RNA was extracted using the MasterPure Yeast RNA purification kit (Lucigen) according to the manufacturer’s instructions.
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)


title: PROseq_RC4_d78h_dTAG13

tag: treatment


title: iPS2_1932_d0

value: Severe Preeclampsia

value: Female


title: 20b_CO_TCCTGAGC-GCGTAAGA

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description: one sample equals cornea macrophages from 10 pooled mice

data_processing:
Base calling was performed with RTA 1.18.61 using standard parameters.
Fastq files were generated with CASAVA 1.8.2 using standard parameters.
Fastq files were aligned to the mouse genome using the subjunc aligner from the Rsubread package (Version 1.20.1) with default parameters (-nthread 12). Alignment was done against an index build on the Gencode M6 primary assembly fasta file.
Gene counts were determined using featureCounts from the Rsubread package (Version 1.20.1). Features were obtained from the Gencode M6 primary assembly gtf. Parameters used were: annot.ext=<path to gencode M6 primary assembly GTF>, isGTFAnnotationFile=TRUE, GTF.featureType="exon", GTF.attrType="gene_name", useMetaFeatures=TRUE, nthreads=12, reportReads=TRUE
Raw counts were filtered removing the genes with the lowest 32% of counts summed over all samples. Following voom transformation, differential gene expression was analyzed using the bioconductor package limma with default parameters.
Genome_build: Gencode M6 (GRCm38.p4)
Supplementary_files_format_and_content: featureCounts.txt, tab delimited text file, matrix with raw counts for each sample

source_name: cornea macrophages

extract_protocol:
Total RNA was column purified using the RNeasy Mini Kit (QIAGEN) from the ipsilateral and contralateral ventral pons (containing the facial nucleus, and parts of the gigantocellular reticular nucleus, intermediate reticular nucleus, parvicellular reticular nucleus, alpha, and spinal trigeminal nucleus, oral) of CX3CR1GFP/wt mice that underwent unilateral facial nerve axotomy at 8 weeks of age, at the corresponding time points post axotomy.
A sequencing library was constructed using the Illumina TruSeq Stranded mRNA kit (starting material 300 ng total RNA). Library quality was assessed with the KAPA qPCR System (Peqlab) prior to sequencing.

treatment_protocol: cornea macrophages:1. put freshly dissected corneae (separate in 2-4 pieces) or ciliary body in 500 µL Collagenase D (2mg/mL) in HBSS on ice 2. start digestion by putting them on 37 °C with 800 rpm 3. after 1.5 h add another 500 µL Collagenase D solution per tube and  4. after another 1.5 h resuspend ciliary body several times with a blue tip; use the Eppi-Homogenizer several times for put the solution on a 70 µm sieve (50 mL tube) and smash remaining parts with a 2 mL syringe insert for at least 30 sec per sample 5. wash with 5 mL 20 mM EDTA in PBS 6. homogenize again 7. wash with 15 mL 20 mM EDTA in PBS (if 2 samples are pooled, do not exceed a volume of 30 mL) 8. centrifuge for 15 min at 1200 rpm 9. aspire the supernatant with a vacuum pump (tilt the tube and put the pipette at the edge of the 50 mL tube 10. use a blue tip, pipette the PBS (+20 mM EDTA) once up and down to reduce a attachement of cells at the inner surface 11. rinse the conus of the 50 mL several times and transfer to FACS tube (around 300-400 µL) 12. repeat step 10.-12. two times 15. add 0.5 µL fixable viability dye 16. wash once with PBS (without EDTA) 17. discard supernatant  18. add Fc block 1:200 in FACS Buffer 19. wash once with FACS Buffer 20. add antibody master mix (CD11b, CD45, F4/80, CD64) 21. wash once with FACS Buffer 22. sort cells by flow cytometry in RNA Protection Buffer (Qiagen) and purify RNA according to the manufacturers protocol retinal microglia: 1. put retina into 500 µL cold PBS and place on ice 2. resuspend around 20 times with blue tip, followed by a yellow tip 3. add 0.5 µL fixable viability dye for 30’ on ice 4. wash with facs buffer (FB)  1200 rpm for 5’ and discard supernatant 5. add 100 or 200 µL of 1:200 Fc Block (anti CD16/CD32) for 20’ on ice 6. wash with FB  1200 rpm for 5’ and discard supernatant 7. add antibody master mix with a concentration of 1:200 for CD11b and CD45 8. wash with FB  1200 rpm for 5’ and discard supernatant 9. sort cells by flow cytometry in RNA Protection Buffer (Qiagen) and purify RNA according to the manufacturers protocol. brain: 2. Take off the brain and shear the brain with two scalpels to small pieces 3. Transfer the tissue to the glass potter and fill the potter with ice cold dissection medium (10ml 1xHBSS, 150µl HEPES, 120µl 45% D-Glucose) 4. Shear the brain in the potter until it is a homogenous solution without any tissue pieces inside 5. Transfer the solution through a 70µm cell strainer into a 50 ml tube 6. Fill the tube until 50 ml with 1x HBSS and centrifuge the cells at 1200 rpm for 5 min at 4°C 7. Discard the supernatant and resupend the cells in 5 ml 70% Percoll 8. In the meanwhile underlay 4 ml 30% Percoll with 4 ml 37% Percoll 9. Finally underlay both layers with the cell solution (70% Percoll) 10. Centrifuge the gradient without brake for at 2200 rpm (800g) for 30 min at 4°C 11. After the centrifugation, keep the cells on ice, carefully remove the myelin from the gradient, then transfer all cells from the interphase 37/70 to a new 15 ml tube and fill up immediately with FACS buffer (480 mL PBS, 10 mL FCS, 10 mL 0.5 M EDTA) to dilute the (toxic) Percoll solution 12. Centrifuge for 10 min at 1000 rpm at 4°C 13. Discard the supernatant (try to reduce the residual volume down to 100 – 200 µL) 14. Resuspend the cells in the residual volume and transfer to a FACS tube (Greiner bio-one, 5 mL, 12x75 mm) 15. add 0.5 µL fixable viability dye 16. wash once with FACS buffer and centrifuge 17. add Fc Block for 20 minutes 18. wash once with FACS buffer and centrifuge 19. Add the pre-mixed master mix for the staining of the microglia  (e.g. CD45-e405 and CD11b-APC 1:200) and incubate for 20 min at 4°C   20. Fill up with FACS buffer and centrifuge again (see 12.)  21. Discard the supernatant and vortex before acquiring the sample with the Sorter 22. cells are collected in RNA Protection Buffer and RNA is purified according to the manufacturer’s protocol

value: purified macrophages from corneae from adult mice (8-10 weeks of age)


title: iPS2_1932_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: AdipoRonPEG5 treated liver rep2

city: Dallas

first: Toshiharu

last: Onodera

state: TX

address: 5323 Harry Hines Boulevard

department: Touchstone diabetes center

institute: UT Southwestern medical center

data_processing:
 Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
 Alignments were parsed using Tophat program
 differential expressions were determined through DESeq2/edgeR
 HTSeq v0.6.1 was used to count the read numbers mapped of each gene.
Supplementary_files_format_and_content: count, fpkm

source_name: Liver

extract_protocol:
Liver tissue was harvested and frozen in liquid nitrogen. RNA was exteracted by trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5 mg/Kg of PBS, Adiporon, AdipoRonPEG5, AdipoRonPEG6HTL were injected twice a day for five days. After 5 five days of treatment

tag: mouse strain

value: Liver


title: SAMPLE 24_736429FCB1AG01280119_B03

description: Liver biopsy  from Non-tolerant SAMPLE 24

value: For-cause Biopsy Visit


title: 18b_bMG_4-6_CGTACTAG-AAGGAGTA

description: one sample equals retinal microglia from 10 pooled mice

source_name: brain microglia

value: purified microglia from whole brain from adult mice (8-10 weeks of age)


title: AdipoRonPEG5 treated liver rep1


title: AdipoRon treated liver rep3

value: AdipoRon


title: 15b_BM-Mo_4-6_TAGGCATG-GTAAGGAG

source_name: bone marrow monocytes

value: purified monocytes from whole bone marrow from adult mice (8-10 weeks of age)


title: iPS2_1932_d4

value: day 4

value: Cytotrophoblast


title: SAMPLE 25_878825LF13AG01280119_F06

description: Liver biopsy  from Non-tolerant SAMPLE 25

value: 5yr Visit


title: 16b_BM-Mo_7-9_TAAGGCGA-ACTGCATA


title: SAMPLE 23_910844LF13AG01280119_F08

description: Liver biopsy  from Non-tolerant SAMPLE 23


title: AdipoRon treated liver rep2


title: iPS10_1932_d4


title: Sham-1

source_name: brain tissue_sham

value: brain

value: Sprague-Dawley (SD) rats


title: 19b_bMG_7-9_AGGCAGAA-CTAAGCCT


title: SAMPLE 21_588124LF13AG01280119_E08

description: Liver biopsy  from Non-tolerant SAMPLE 21

value: liver


title: AdipoRon treated liver rep1


title: ChIP_RAD21_RG9_d108h_dTAG13

library_source: genomic

source_name: RAD21 ChIP, clone G9

value: CAST/Ei x 129/Sv/Jae

tag: genotype/variation

value: ES cell (Tsix-stop)

value: day 10

tag: chip antibody

value: RAD21 (Abcam ab992)


title: AdipoRonPEG5 treated liver rep3

tag: tissue


title: iPS10_1932_d4_2

tag: disease state

value: Severe Preeclampsia

tag: differentiation days + oxygen%

value: day+4 under 2% oxygen

value: Extravillous trophoblast

value: Female


title: Control liver rep3

value: vehicle

value: Liver


title: 11b_BMG_GGACTCCT-AGAGTAGA

value: purified microglia from whole brain from adult mice (8-10 weeks of age)


title: 10b_BMG_TCCTGAGC-TATCCTCT


title: iPS10_1932_d4_21

value: day+4 under 21% oxygen

tag: differentiation end point cell type

value: Syncytiotrophoblast

tag: gender


title: SAMPLE 19_907381LF13AG01280119_D04

description: Liver biopsy  from Non-tolerant SAMPLE 19

tag: isw outcome (tolerant/non-tolerant)

value: Non-tolerant

tag: time point

value: 5yr Visit


title: Control liver rep2


title: SAMPLE 20_488136MF22221216H05

description: Liver biopsy  from Non-tolerant SAMPLE 20

value: Primary Endpoint Visit

tag: visit code


title: SAMPLE 18_944000LF13AG01280119_G11

description: Liver biopsy  from Non-tolerant SAMPLE 18

value: liver


title: iPS4_1754_d4

value: Normal

value: day 4

value: Cytotrophoblast

value: Male


title: Control liver rep1


title: iPS4_1754_d0

value: day 0

value: induced pluripotent stem cell


title: 08b_BM_CGTACTAG-GCGTAAGA

value: purified monocytes from whole bone marrow from adult mice (8-10 weeks of age)


title: Pdx1:Cre;Grg3Grg4_3

city: Aurora

first: Alexandra

last: Theis

state: Colorado

address: 1775 Aurora Ct, Room 4202A

department: Barbara Davis Center

institute: University of Colorado Anschutz Medical Campus

data_processing:
fastQC for quality check of raw fastq files
trim-galore for adapter trimming
HiSAT2 to align to Mm10 ( using Ensembl Mus_musculus.GRCm38.95.gtf)
bedtools to Align and Sort to create .sam and .bam files
HT-Seq to generate counts (.txt files)
DESeq2 for differential expression analysis
Genome_build: Mm10 (Mus_musculus.GRCm38.95.gtf)
Supplementary_files_format_and_content: .txt file with column 1 (gene) and column 2 (read counts)

source_name: e18.5 whole pancreas

extract_protocol:
Whole pancreas was dissected from e18.5 mouse embryos, pulverized in buffer RLT +beta mercaptoethanol (RNAeasy Mini Kit Qiagen, Cat# 74134), frozen on dry ice. RNA was extracted using Qiagen RNAeasy Mini kit, eluted in 30ul RNAse free H2O.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed, C57BL6

value: pancreas

tag: Stage


title: 04b_CO_TAAGGCGA-CTAAGCCT

value: purified macrophages from corneae from adult mice (8-10 weeks of age)


title: SAMPLE 26_455735LF13AG01280119_D02

description: Liver biopsy  from Non-tolerant SAMPLE 26


title: 09b_BM_AGGCAGAA-CTCTCTAT


title: iPS10_1932_d0

value: Severe Preeclampsia

value: Female


title: iPS2_1932_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: iPS4_1754_d4_2


title: iPS4_1754_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: Pdx1:Cre;Grg3Grg4_1


title: 03_MG10000_AGGCAGAA-AGAGTAGA

source_name: retinal microglia

value: purified microglia from retinae from adult mice (8-10 weeks of age)


title: 03b_MG10000_R1-6_TAGGCATG-AAGGAGTA


title: Sham

value: NaCl

tag: age

tag: Sex

value: male

value: Infrarenal abdominal aortas


title: Pdx1:Cre;Grg3Grg4_2


title: SAMPLE 32_603788LF13AG01280119_C10

description: Liver biopsy  from Non-tolerant SAMPLE 32

value: liver

value: Non-tolerant

value: 5yr Visit


title: iPS3_1754_d4

value: Normal

value: day 4

value: Cytotrophoblast

value: Male


title: Pdx1:Cre;Grg3_3

value: mixed, C57BL6

value: pancreas


title: SAMPLE 15_636296LF13AG01280119_F02

description: Liver biopsy  from Non-tolerant SAMPLE 15


title: iPS3_1754_d4_21


title: 01b_CO_TCCTGAGC-GTAAGGAG

value: purified macrophages from corneae from adult mice (8-10 weeks of age)


title: Pdx1:Cre;Grg3_2


title: SAMPLE 12_769999LF13AG01280119_D08

description: Liver biopsy  from Non-tolerant SAMPLE 12


title: 02b_MG7500_R8-10_GGACTCCT-ACTGCATA


title: iPS3_1754_d0

value: day 0

value: induced pluripotent stem cell


title: iPS3_1754_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: SAMPLE 16_983489LF13AG01280119_C04

description: Liver biopsy  from Non-tolerant SAMPLE 16


title: SAMPLE 22_990077LF13AG01280119_F11

description: Liver biopsy  from Non-tolerant SAMPLE 22


title: SAMPLE 13_393758LF13AG01280119_A06

description: Liver biopsy  from Non-tolerant SAMPLE 13


title: iPS2_1754_d4


title: SAMPLE 17_300934LF13AG01280119_H04

description: Liver biopsy  from Non-tolerant SAMPLE 17


title: 01_CO3000_TAAGGCGA-CTCTCTAT

description: one sample equals cornea macrophages from 10 pooled mice


title: Pdx1:Cre;Grg3_1


title: SAMPLE 14_233127FCB3AG01280119_E11

description: Liver biopsy  from Non-tolerant SAMPLE 14

value: For-cause Biopsy Visit


title: 02_MG10000_CGTACTAG-TATCCTCT

description: one sample equals retinal microglia from 10 pooled mice

value: purified microglia from retinae from adult mice (8-10 weeks of age)


title: iPS2_1933_d4_2

value: Severe Preeclampsia


title: iPS2_1754_d0


title: IIDP-AFC2208-2 snATAC (CB)

first: Kyle

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

data_processing:
Note: Barcodes for combinatorial barcoding snATAC-seq experiments are integrated into the original read names.
Alignment: Trimmed Nextera adapter sequences using trim_galore v.0.4.4 and aligned reads to hg19 using bwa mem v.0.7.17-r1188.
Filtering: Low mapping quality (MAPQ<30), mitochondrial reads, duplicate reads on a per-barcode basis with MarkDuplicates from picard.
Clustering: Custom code for processing snATAC-seq datasets is available at https://github.com/kjgaulton/pipelines/tree/master/T1D_snATAC_pipeline.
Peak calling: MACS2 (v.2.1.2) with --nomodel --keep-dup all on aggregate chromatin accessibility profiles for each cluster.
Genome_build: hg19
Supplementary_files_format_and_content: merged peaks
Supplementary_files_format_and_content: single cell cluster labels

source_name: pancreatic islets

extract_protocol:
Nuclei were isolated from fresh pancreatic islets using a glass dounce homogenizer with a tight-fitting pestle, frozen whole pancreas using a mortar and pestle, and PBMCs using a lysis buffer.
(CB; combinatorial barcoding) Permeabilized nuclei were distributed to 96 wells and tagmentation was carried out to introduce a first barcode combination. After pooling, 20 nuclei were sorted into each well of a 96 well plate and a second barcode was introduced by PCR. Libraries were purified according to the MinElute PCR Purification Kit manual using a vacuum manifold and size selection was performed with SPRI Beads. (10X; 10X Genomics) Libraries were generated using the 10X Genomics Chromium Chip E Single Cell ATAC kit following the manufacturers instructions.

value: pancreatic islets

value: male

tag: bmi

tag: donor id


title: KO_YolkSac_Rep3

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Read alignment and mapping done with TopHat2, version 2.1.0
Gene and transcript level computation done with CuffQuant, Version 2.2.1
Normalized abundance measurements generated by CuffNorm, Version 2.2.1, calculate FPKM values using quartile normalization
CuffDiff, Version 2.2.1, geometric normalization, per-condition dispersion
Genome_build: mm9
Supplementary_files_format_and_content: YolkSac_HNF4AKOvsCtrl_gene_exp.diff containing significant changes in transcript expression outputted by Cuffdiff

extract_protocol:
RNAs were extracted from yolk sac tissues of indicated genotypes. The whole yolk sac samples were washed with PBS, and then quick frozen in liquid nitrogen and stored at -80°C for later processing for RNA extraction. Yolk sac samples were homogenized in Trizol (Invitrogen) and processed for RNA extraction according to the manufacturer’s instructions.
BGI in-house kit (BGI-Shenzhen, China)

treatment_protocol: Pregnant UBC-CreERT2 negative female mice (crossed with UBC-CreERT2 positive male) were treated with tamoxifen and progesterone (1:1 mix, 5 mg each) by oral gavage at embryonic day (E) 12.5 and E13.5. Yolk sac tissues were collected at E18.5.

value: YolkSac

tag: genotype

value: Hnf4af/f; UBC-CreERT2 positive (HNF4AKO)

tag: treatment

value: Tamoxifen and progesterone (1:1 mix, 5 mg each)


title: Pdx1:Cre_1

tag: strain


title: KO_YolkSac_Rep4


title: SAMPLE 11_679850LF13AG01280119_A03

description: Liver biopsy  from Non-tolerant SAMPLE 11

value: liver

value: Non-tolerant

value: 5yr Visit


title: MEL/ch11_Con_H3K27ac_ChIP-Seq

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

description: MEL/ch11 cells are murine erythroleukemia cells containing human chromosome 11.

data_processing:
ChIP-seq raw reads were trimmed to 36 bp using trim sequences tool. Trimmed reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the hg19 canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files.  Peak regions were identified using MACS2 providing input chromatin data as control.
Genome_build: hg19 chromosome11
Supplementary_files_format_and_content: bigwig

growth_protocol: MEL/ch11 cells were cultured in DMEM medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K27ac) was processed using NEBNext ChIP-seq library (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. The concentration of adaptors was 1.5 µM for H3K27ac ChIP DNA. Adaptor-ligated DNA was selected at 200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles for H3K27ac). The fragments are purified using NEBNext sample purification beads. Final libraries were quantified with Qubit dsDNA HS assay (Invitrogen) and were sequenced single-end with a read length of 100 bp on an Illumina NovaSeq system.

treatment_protocol: For transcriptional activation of the β-globin gene, MEL/ch11 cells were induced at a concentration of 1.5x10^5 cells/ml with 5 mM HMBA for 72 h.

tag: cell type

value: erythroleukemia cells

tag: cell line

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: iPS2_1754_d4_2

tag: disease state

value: Normal

tag: differentiation days + oxygen%

value: Male


title: MEL/ch11_HS3∆∆GA_H3K27ac_ChIP-Seq


title: KO_YolkSac_Rep1

tag: tissue


title: SAMPLE 9_393758MF26281216H08

description: Liver biopsy  from Non-tolerant SAMPLE 9

tag: isw outcome (tolerant/non-tolerant)

value: Primary Endpoint Visit


title: Pdx1:Cre_3

value: mixed, C57BL6

value: pancreas


title: SAMPLE 6_843475LF13AG01280119_F07

description: Liver biopsy  from Non-tolerant SAMPLE 6

tag: time point


title: Aortic VSMCs, DOKO2

city: Oslo

first: Kuan

last: Yang

address: Sognsvannsveien 20

department: Research Institute of Internal Medicine

country: Norway

institute: Oslo University Hospital

data_processing:
Contaminated adapter and low quality reads were trimmed with fastp (v0.20.0).
Reads were mapped to mouse cDNA (GRCm38.p6, NCBI Mus musculus Annotation Release 108) using kallisto (v0.46.0) with 100 bootstrap iterations.
sleuth (v0.30.0) was used to obtain deferentially expressed transcripts with Wald test from HDF5 file outputed by kallisto.
Genome_build: GRCm38.p6, NCBI Mus musculus Annotation Release 108
Supplementary_files_format_and_content: HDF5 (.h5) binary file which contains estimated counts, TPM, effective length of main quantification and boostraps as well as run info
normalized_kallisto_abundance_all_samples.csv.gz

source_name: Aortic Vascular Smooth Muscle Cells

extract_protocol:
Aortas were lysated before subsequent selection with mouse CD31 and CD90.1 microbeads, with cell sorting taking place in an autoMACS Pro Separator (Miltenyi Biotec). Total RNA was extracted using RNeasy spin columns (Qiagen).
Library was constructed by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacture's protocol.

value: ApoE/Neil3 double knockout

tag: background strain

value: 26 weeks

value: Aortic Vascular Smooth Muscle Cells


title: Aortic VSMCs, DOKO3


title: Aortic VSMCs, S2

data_processing:
Contaminated adapter and low quality reads were trimmed with fastp (v0.20.0).
Reads were mapped to mouse cDNA (GRCh38.p13, NCBI Homo sapiens Updated Annotation Release 109.20190905) using kallisto (v0.46.0) with 100 bootstrap iterations.
sleuth (v0.30.0) was used to obtain deferentially expressed transcripts with Wald test from HDF5 file outputed by kallisto.
Genome_build: GRCh38.p13, NCBI Homo sapiens Updated Annotation Release 109.20190905
Supplementary_files_format_and_content: HDF5 (.h5) binary file which contains estimated counts, TPM, effective length of main quantification and boostraps as well as run info
normalized_kallisto_abundance_all_samples.csv.gz

growth_protocol: Cells were grown in PromoCell Growth medium and 1% penicillin Streptomycin at 37 Celsius degrees and 5% carbon dioxide.

extract_protocol:
Experimental cells cultures were lysated before and total RNA was extracted using RNeasy spin columns (Qiagen).
Library was constructed by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacture's protocol.

treatment_protocol: NEIL3 mRNA-abrogated cells were treated with 0.5 µM NEIL3 antisense oligonucleotides for 48 hours, whereas controls were treated in parallel with a scramble version of the same antisense oligonucleotides.

value: Scramble control

value: Aortic Vascular Smooth Muscle Cells (primary)


title: Aortic VSMCs, G3

value: NEIL3 mRNA-abrogated


title: SAMPLE 8_488136FCB2AG01280119_C07

description: Liver biopsy  from Non-tolerant SAMPLE 8

value: For-cause Biopsy Visit

tag: visit code


title: Ctrl_YolkSac_Rep3

value: YolkSac

value: Hnf4af/f; UBC-CreERT2 negative (Control)

value: Tamoxifen and progesterone (1:1 mix, 5 mg each)


title: Aortic VSMCs, DOKO1

tag: age


title: SAMPLE 3_794852LF13AG01280119_G09

description: Liver biopsy  from Non-tolerant SAMPLE 3

value: liver

value: Non-tolerant

value: 5yr Visit


title: iPS2_1754_d4_21

value: Normal

value: day+4 under 21% oxygen

tag: differentiation end point cell type

value: Syncytiotrophoblast

tag: gender

value: Male


title: Aortic VSMCs, G2


title: Aortic VSMCs, G1


title: Ctrl_YolkSac_Rep2


title: SAMPLE 4_933569LF13AG01280119_H06

description: Liver biopsy  from Non-tolerant SAMPLE 4


title: Pdx1:Cre_2

value: mixed, C57BL6

value: pancreas

tag: Stage


title: Ctrl_YolkSac_Rep4

tag: genotype


title: Aortic VSMCs, S1

tag: treatment


title: SAMPLE 1_540674LF13AG01280119_E12

description: Liver biopsy  from Non-tolerant SAMPLE 1


title: SgRNA-seq sgRNA_K562_TimeCourse_Day6

status: Public on Mar 14 2021

city: STANFORD

first: Jeffrey

middle: Michael

last: Granja

address: 279 Campus Drive W

institute: Stanford University

description:
SgRNA-seq
SgRNA-seq

data_processing:
The Cell Ranger ATAC Software Suite (version 1.2.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the Tn5 transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified with MACS2
Barcodes likely associated with whole cells were identified by analyzing the number of fragments (1000) mapped near TSS regions (enriched over background) and a peak-barcode matrix is defined using ArchR
Genome_build: hg38
Supplementary_files_format_and_content: ArchR Processed scATAC-seq data is provided as an R SummarizedExperiment object. This object contains counts alongth with row and column metadata corresponding to the individual cells and peak/motif/gene chromatin accessibility. Fragments file contain Tn5 corrected cut sites per cell.
Fastq reads containg 10x scATAC cell barcodes were matched to the nearest cell barcode in the 10x cell barcode list allowing for 1 mismatch in R.
Fastq reads containing sgRNA barcodes were exact matched to sgRNA sequences in R.
The combination of cell barcodes and sgRNA were counted and converted into a frequency table csv.
Genome_build: hg38
Supplementary_files_format_and_content: Frequency CSV table of 10x scATAC cell barcodes and sgRNA barcode counts to identify combinations that were highly specific to assign spearATAC cells.

source_name: Immortalized cell line

extract_protocol:
Up to 500,000 FACS-isolated immortalized cell line cells were processed for scATAC-seq. Cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3-5 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the pelleted nuclei were resuspended in Diluted Nuclei Buffer (10x Genomics). The nuclei stock concentration was determined for each cell line using Trypan Blue and a total of 5,000 nuclei from each cell line were pooled together and loaded into the 10x Genomics scATAC-seq (v1) transposition reaction.
In brief, after the final scATAC-seq libraries were prepared (~150nM final concentration in 20uL ddH2O), 2.5uL of the libraries were used as input for a targeted sgRNA linear amplification PCR reaction using a 5’ biotinylated, sgRNA-specific primer (oSP2053: 5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTaagtatcccttggagaaccaccttg-3’) for 25 cycles. PCR product was pooled and purified using a Qiagen Minelute kit (Qiagen). Biotinylated sgRNA fragments were then enriched using Streptavidin MyOne C1 beads (ThermoFisher) and re-suspended in 40uL ddH2O, which was used as input for an exponential PCR amplification reaction for 15 cycles using primers corresponding to P5 (oSP1594: 5’- AATGATACGGCGACCACCGAGA-3’) and an indexed P7-containing primer (5’- CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTG-3’, where NNNNNNNN is replaced with the index of choice).

tag: source

value: human derived

tag: growth media

value: RPMI; 10% FBS; 1% pen-strep


title: SgRNA-seq sgRNA_K562_TimeCourse_Day9

description:
SgRNA-seq
SgRNA-seq

tag: cell type


title: SgRNA-seq sgRNA_K562_TimeCourse_Day21

description:
SgRNA-seq
SgRNA-seq


title: Ctrl_YolkSac_Rep1


title: SgRNA-seq sgRNA_MCF7_LargeScreen_Rep2

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_MCF7_LargeScreen_Rep1

description:
SgRNA-seq
SgRNA-seq


title: KO_YolkSac_Rep2

value: Hnf4af/f; UBC-CreERT2 positive (HNF4AKO)


title: SAMPLE 5_751760LF13AG01280119_A10

description: Liver biopsy  from Non-tolerant SAMPLE 5


title: SgRNA-seq sgRNA_K562_LargeScreen_Rep6

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_K562_Pilot_Rep1

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_MCF7_LargeScreen_Rep3

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_K562_LargeScreen_Rep5

description:
SgRNA-seq
SgRNA-seq


title: Aortic VSMCs, APOE2

value: ApoE knockout

value: 26 weeks

value: Aortic Vascular Smooth Muscle Cells


title: Aortic VSMCs, APOE1


title: SgRNA-seq sgRNA_K562_LargeScreen_Rep3

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_K562_LargeScreen_Rep1

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_K562_LargeScreen_Rep4

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_GM_LargeScreen_Rep2

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_GM_LargeScreen_Rep4

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_K562_TimeCourse_Day3

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_K562_LargeScreen_Rep2

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_GM_LargeScreen_Rep1

description:
SgRNA-seq
SgRNA-seq


title: SgRNA-seq sgRNA_GM_LargeScreen_Rep3

description:
SgRNA-seq
SgRNA-seq


title: SAMPLE10_324363LF13AG01280119_C03

description: Liver biopsy  from Non-tolerant SAMPLE10


title: Single Cell ATAC-seq scATAC_K562_TimeCourse_Day9

description:
Single Cell ATAC-seq
Single Cell ATAC-seq
scATAC_K562_TimeCourse_Peak_Matrix_SE.rds
scATAC_K562_TimeCourse_Motif_Matrix_SE.rds

extract_protocol:
Up to 500,000 FACS-isolated immortalized cell line cells were processed for scATAC-seq. Cells were pelleted in a fixed-angle rotor at 300 RCF for 5 minutes at 4°C. The supernatant was removed, and the pellet was resuspended in 100 uL of ice-cold lysis buffer (RSB containing 0.1% Tween-20, 0.1% NP-40, and 0.01% digitonin) and incubated on ice for 3-5 minutes. To dilute lysis, 1 mL of chilled RSB-T was added to each tube and the cells were pelleted as before. The supernatant was removed and the pelleted nuclei were resuspended in Diluted Nuclei Buffer (10x Genomics). The nuclei stock concentration was determined for each cell line using Trypan Blue and a total of 5,000 nuclei from each cell line were pooled together and loaded into the 10x Genomics scATAC-seq (v1) transposition reaction.
scATAC-seq library preparation was performed as recommended by the manufacturer (10x Genomics scATAC-seq (v1)).


title: SAMPLE 7_461082LF13AG01280119_H01

description: Liver biopsy  from Non-tolerant SAMPLE 7


title: Single Cell ATAC-seq scATAC_MCF7_LargeScreen_Rep4

description:
Single Cell ATAC-seq
Single Cell ATAC-seq
scATAC_MCF7_LargeScreen_Peak_Matrix_SE.rds
scATAC_MCF7_LargeScreen_Motif_Matrix_SE.rds


title: Single Cell ATAC-seq scATAC_K562_TimeCourse_Day3


title: Single Cell ATAC-seq scATAC_K562_TimeCourse_Day21


title: Single Cell ATAC-seq scATAC_MCF7_LargeScreen_Rep3


title: Single Cell ATAC-seq scATAC_MCF7_LargeScreen_Rep1


title: Single Cell ATAC-seq scATAC_K562_LargeScreen_Rep2

description:
Single Cell ATAC-seq
Single Cell ATAC-seq
scATAC_K562_LargeScreen_Peak_Matrix_SE.rds
scATAC_K562_LargeScreen_Motif_Matrix_SE.rds


title: Single Cell ATAC-seq scATAC_K562_LargeScreen_Rep1


title: Single Cell ATAC-seq scATAC_K562_LargeScreen_Rep5


title: Single Cell ATAC-seq scATAC_MCF7_LargeScreen_Rep2


title: Single Cell ATAC-seq scATAC_K562_LargeScreen_Rep4


title: Single Cell ATAC-seq scATAC_K562_LargeScreen_Rep6


title: Single Cell ATAC-seq scATAC_GM_LargeScreen_Rep4

description:
Single Cell ATAC-seq
Single Cell ATAC-seq
scATAC_GM_LargeScreen_Peak_Matrix_SE.rds
scATAC_GM_LargeScreen_Motif_Matrix_SE.rds


title: Single Cell ATAC-seq scATAC_K562_LargeScreen_Rep3


title: Single Cell ATAC-seq scATAC_K562_Pilot_Rep1

description:
Single Cell ATAC-seq
Single Cell ATAC-seq
scATAC_K562_Pilot_Peak_Matrix_SE.rds
scATAC_K562_Pilot_Motif_Matrix_SE.rds


title: PTECs MYC-OE SETD2-KO rep2

city: Shanghai

first: Hanyu

last: Rao

address: Huashan Rd, No. 1954

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <50 bp) and low quality reads using Cutadapt (v1.9.1)(Anthony M et al., Bioinformatics 2014) and Trimmomatic (v0.35) (Martin M et al., EMBnet.J 2011).
Then FastQC (Andrews S et. al., FastQC 2010) is used to ensure high reads quality.
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 (Kim, D et al., Nat. Methods 2015) software.
Peak detection was performed using the MACS (v2.1.1) (Zhang et al., Genome Biol 2008) peak finding algorithm with 0.01 set as the p-value cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie. Ballgown, a R package, were used to measure differential gene expression.The false discovery rate (FDR) control method was used to calculate the adjusted P-values in multiple testing in order to evaluate the significance of the differences. Here, only gene with an adjusted P-value <0.05 were used for subsequent analysis.

source_name: Kidney

growth_protocol: renal primary tubular epithelial cells were isolated from mice kidney cortex segment

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies Corp.), and further treated with DNase to remove genomic DNA contamination.
Isolation of mRNA was performed using the NEBNext PolyA mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and the mRNA was then used for RNA-Seq library preparation with the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA). The library was then subjected to Illumina sequencing with paired-end 2x150 as the sequencing mode.

value: Renal primary tubular epithelial cells

tag: strain

value: Kidney

value: Ksp1.3/cre; MYCfl/fl;Setd2fl/fl


title: SAMPLE 2_938137LF13AG01280119_B02

description: Liver biopsy  from Non-tolerant SAMPLE 2

value: liver

value: Non-tolerant


title: PTECs MYC-OE rep3

value: Ksp1.3/cre; MYCfl/fl


title: PTECs MYC-OE rep2


title: PTECs MYC-OE SETD2-KO rep1


title: Single Cell ATAC-seq scATAC_GM_LargeScreen_Rep3


title: PTECs MYC-OE SETD2-KO rep3


title: PTECs SETD2-KO rep1

value: Ksp1.3/cre; Setd2fl/fl


title: PTECs SETD2-KO rep2


title: Single Cell ATAC-seq scATAC_GM_LargeScreen_Rep1


title: PTECs WT rep3


title: SgRNA-seq sgRNA_MCF7_LargeScreen_Rep4

description:
SgRNA-seq
SgRNA-seq


title: PTECs WT rep2


title: Single Cell ATAC-seq scATAC_GM_LargeScreen_Rep2


title: PTECs MYC-OE rep1


title: PTECs WT rep1


title: ChIPSeq_IP_H3K27ac_nothing_IAA_48hrs

city: New York

first: Iris

last: Mueller

state: New York

address: 430 East 67th Street

institute: MSKCC

data_processing:
Reads were first trimmed using Trim Galore (Version 0.4.5) using --illumina and default parameters. Mapping was done with STAR (Version 2.5.3a) allowing multimappers (--winAnchorMultimaNmax 100 --outFilterMultimapNmax 100 --outFilterMismatchNmax 3) to mm10 assembly. Peaks were called for using epic2 peak caller (version 0.0.41) using the epic2-df function. Peaks were subsequently filtered to fulfil wildtype read number requirements (>= 100 && <=5000) and for peaks that are overrepresented in the wildtype condition (FC_WT > 1) yielding 55 high confidence peaks. For visualization, bigWig coverage files normalized to sequencing depth *10000000 were generated with deepTools (version 2.29.2) with the following configurations: bamCoverage --bam --ignoreDuplicates --scaleFactor --centerReads. BigWig were subsequently loaded into IGV (version 2.8.0). For average profiles ngsplot (Version 2.63) was applied using default parameters.
Genome_build: mm10

source_name: Embryonic stem cells

growth_protocol: Cells were maintained at 37°C in a 5% CO2 atmosphere. ESCs were generally grown in 2i/LIF medium (1:1 mix of Dulbecco’s Modified Eagle Medium: Nutrient Mixture F-12 + Glutamax (DMEM/F-12, Gibco) and Neurobasal Medium (Gibco), supplemented with N2 and B27 supplement (final 1X, Gibco), 1% Penicillin/Streptomycin (Gibco), 2 mM Glutamax (Gibco), 50 µM β-Mercaptoethanol (Gibco), 1 mM Sodium Pyruvate (Gibco), 0.1 mM MEM Non-Essential Amino Acids Solution (MEM-NEAS, Gibco), 1 µM MEK inhibitor PD0325901 (Sigma-Aldrich), 3 µM GSK3b inhibitor CHIR99021 (Sigma-Aldrich) and Leukaemia Inhibitory Factor (LIF, made in-house). Cells were passaged every second day. For this purpose, the medium was aspirated, cells were once washed in PBS, and approximately 1.5 ml of Accutase (Sigma) were added per 10 cm dish. Cells were gently disrupted into single cells by pipetting, resuspended in medium and pelleted by centrifugation at 300 x g for 5 min. The supernatant was aspirated and an appropriate number of cells was re-seeded in fresh medium on plates coated with 0.15% gelatin (Sigma) in PBS. For indicated experiments, ESCs were grown in serum/LIF medium (Glasgow Minimum Essential Media (GMEM) supplemented with 10% heat-inactivated Fetal Bovine Serum (HI-FBS), 1% Penicillin/Streptomycin, 2 mM Glutamax (Gibco), 100 µM β-Mercaptoethanol (Gibco), 1 mM Sodium Pyruvate (Gibco), 0.1 mM MEM Non-Essential Amino Acids Solution (MEM-NEAS, Gibco) and Leukaemia Inhibitory Factor (LIF, made in-house) in which they were passaged every second day by washing the cells once in PBS, trypsinization for 1 min at 37°C, followed by resuspension in medium, centrifugation and re-plating.

extract_protocol:
Immunopreciptiation of cross-linked and sonicated cell lysates.
NEBNext Ultra II protocol (NEB, E7645S)

value: Embryonic stem cells

tag: developmental stage

tag: chip antibody

value: H3K27ac (Active motive, 39685)

value: Mpp8mAID; OsTIR1

value: 48 hours IAA (500 µM)


title: ChIPSeq_IP_H3K27ac_Npart_untreated_48hrs

tag: tissue

value: Mpp8mAID; OsTIR1; Mpp81-729

value: untreated


title: ChIPSeq_IP_H3K27ac_Npart_IAA_48hrs


title: ChIPSeq_IP_H3K27ac_wt_untreated_48hrs

value: Mpp8mAID; OsTIR1; Mpp8wt


title: ChIPSeq_IP_H3K27ac_wt_IAA_48hrs


title: ChIPSeq_IP_H3K27ac_nothing_untreated_48hrs


title: ChIPSeq_IP_H3K27ac_Cpart_IAA_48hrs

value: Mpp8mAID; OsTIR1; Mpp8112-858


title: ChIPSeq_IP_H3K4me3_wt_IAA_48hrs

value: H3K4me3 (Cell signaling, 9715S)


title: ChIPSeq_IP_H3K4me3_wt_untreated_48hrs


title: ChIPSeq_IP_H3K4me3_Npart_untreated_48hrs


title: ChIPSeq_IP_H3K4me3_Npart_IAA_48hrs


title: PTECs SETD2-KO rep3


title: ChIPSeq_IP_H3K4me3_nothing_IAA_48hrs


title: RNASeq_Mpp8mAID_Cpart_IAA_48hrs_Rep2

description:
RNASeq_Mpp8mAID_Cpart_DMSO_vs_IAA_48hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_Cpart_DMSO_vs_IAA_48hrs_cntTable.txt

data_processing:
Reads were mapped to mm10 genome with STAR-2.5.3a allowing multimappers (--winAnchorMultimaNmax 100 --outFilterMultimapNmax 100 --outFilterMismatchNmax 3) and further processed with TEtranscripts (--mode multi --stranded no) using GRCm38.95.gtf for transcript annotation and mm10_rmsk_TE.gtf for TE annotation (Jin et al., 2015). DESeq results were further analyzed in R environment. Significantly differentially regulated genes were defined as FDR-adjusted pvalue < 0.05 and abs(fold change) > 1.5. Data was filtered for genes that were significantly changed upon 6 hour auxin treatment in E14; OsTIR1 cells.
Genome build: mm10
Reads were first trimmed using Trim Galore (Version 0.4.5) using --illumina and default parameters. Mapping was done with STAR (Version 2.5.3a) allowing multimappers (--winAnchorMultimaNmax 100 --outFilterMultimapNmax 100 --outFilterMismatchNmax 3) to mm10 assembly. Peaks were called for using epic2 peak caller (version 0.0.41) using the epic2-df function. Peaks were subsequently filtered to fulfil wildtype read number requirements (>= 100 && <=5000) and for peaks that are overrepresented in the wildtype condition (FC_WT > 1) yielding 55 high confidence peaks. For visualization, bigWig coverage files normalized to sequencing depth *10000000 were generated with deepTools (version 2.29.2) with the following configurations: bamCoverage --bam --ignoreDuplicates --scaleFactor --centerReads. BigWig were subsequently loaded into IGV (version 2.8.0). For average profiles ngsplot (Version 2.63) was applied using default parameters.
Genome build: mm10

molecule: polyA RNA

extract_protocol:
Total RNA was isolated from cells using the RNeasy kit (74104, Qiagen) and RNA quality was assed using the RNA 600 Nano kit (Agilent Technologies).
TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001)

tag: cell line

value: ESC line derivative of feeder-independent E14-TG2a parental cells (129/Ola strain)


title: ChIPSeq_Input_Npart_IAA_48hrs

value: Input


title: ChIPSeq_Input_Npart_untreated_48hrs


title: ChIPSeq_IP_H3K4me3_Cpart_IAA_48hrs


title: ChIPSeq_Input_Cpart_IAA_48hrs


title: ChIPSeq_Input_wt_IAA_48hrs


title: ChIPSeq_IP_H3K4me3_nothing_untreated_48hrs


title: ChIPSeq_IP_H3K4me3_Cpart_untreated_48hrs


title: ChIPSeq_Input_nothing_untreated_48hrs


title: ChIPSeq_Input_nothing_IAA_48hrs


title: ChIPSeq_IP_H3K27ac_Cpart_untreated_48hrs


title: RNASeq_Mpp8mAID_Cpart_IAA_48hrs_Rep1


title: RNASeq_Mpp8mAID_Npart_IAA_48hrs_Rep1

description:
RNASeq_Mpp8mAID_Npart_DMSO_vs_IAA_48hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_Npart_DMSO_vs_IAA_48hrs_cntTable.txt


title: RNASeq_Mpp8mAID_Npart_untreated_48hrs_Rep2


title: RNASeq_Mpp8mAID_WT_IAA_48hrs_Rep2

description:
RNASeq_Mpp8mAID_WT_DMSO_vs_IAA_gene_48hrs_TE_analysis.txt
RNASeq_Mpp8mAID_WT_DMSO_vs_IAA_48hrs_cntTable.txt


title: RNASeq_Mpp8mAID_Npart_untreated_48hrs_Rep1


title: RNASeq_Mpp8mAID_Npart_IAA_48hrs_Rep2


title: RNASeq_Mpp8mAID_WT_IAA_48hrs_Rep1


title: RNASeq_Mpp8mAID_WT_untreated_48hrs_Rep2


title: Single Cell ATAC-seq scATAC_K562_TimeCourse_Day6

value: human derived

value: RPMI; 10% FBS; 1% pen-strep


title: ChIPSeq_Input_wt_untreated_48hrs


title: RNASeq_Mpp8mAID_nothing_IAA_48hrs_Rep2

description:
RNASeq_Mpp8mAID_nothing_DMSO_vs_IAA_48hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_nothing_DMSO_vs_IAA_48hrs_cntTable.txt


title: RNASeq_OsTIR1_nothing_IAA_6hrs_Rep2

description:
RNASeq_OsTIR1_nothing_DMSO_vs_IAA_6hrs_gene_TE_analysis.txt
RNASeq_OsTIR1_nothing_DMSO_vs_IAA_6hrs_cntTable.txt

value: 6 hours IAA (500 µM)


title: RNASeq_Mpp8mAID_nothing_IAA_48hrs_Rep1


title: ChIPSeq_Input_Cpart_untreated_48hrs


title: RNASeq_Mpp8mAID_nothing_untreated_48hrs_Rep2


title: RNASeq_Mpp8mAID_WT_untreated_48hrs_Rep1


title: RNASeq_Mpp8mAID_nothing_untreated_48hrs_Rep1


title: RNASeq_Mpp8mAID_Cpart_IAA_6hrs_Rep2

description:
RNASeq_Mpp8mAID_Cpart_DMSO_vs_IAA_6hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_Cpart_DMSO_vs_IAA_6hrs_cntTable.txt


title: RNASeq_Mpp8mAID_Cpart_untreated_48hrs_Rep1


title: RNASeq_Mpp8mAID_Npart_untreated_6hrs_Rep1

description:
RNASeq_Mpp8mAID_Npart_DMSO_vs_IAA_6hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_Npart_DMSO_vs_IAA_6hrs_cntTable.txt


title: RNASeq_Mpp8mAID_Npart_IAA_6hrs_Rep2


title: RNASeq_Mpp8mAID_Cpart_untreated_6hrs_Rep2


title: RNASeq_Mpp8mAID_Cpart_untreated_6hrs_Rep1


title: RNASeq_OsTIR1_nothing_IAA_6hrs_Rep1


title: RNASeq_OsTIR1_nothing_untreated_6hrs_Rep1


title: RNASeq_Mpp8mAID_Npart_IAA_6hrs_Rep1


title: RNASeq_Mpp8mAID_Npart_untreated_6hrs_Rep2


title: RNASeq_Mpp8mAID_Cpart_untreated_48hrs_Rep2


title: RNASeq_Mpp8mAID_WT_IAA_6hrs_Rep2

description:
RNASeq_Mpp8mAID_WT_DMSO_vs_IAA_6hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_WT_DMSO_vs_IAA_6hrs_cntTable.txt


title: Mayo_19_prert [A230]

first: Xin

last: Pei

state: NY

address: 417 E 68th St,Mortimer B. Zuckerman Research Center

department: Radiation Oncology

institute: Memorial Sloan Kettering Cancer Center

description:
A230
A230-MSK-RNA

data_processing:
aligned against human genome assembly hg19 by STAR 2-pass alignment
QC metrics, for example general sequencing statistics as well as gene feature and body coverage, were then calculated based on the alignment result through the tool package RSeQC
RNA-seq gene level count values were computed by using the R package GenomicAlignments function over aligned reads with UCSC hg19 KnownGene as the base gene model.
The Union counting mode was used and only mapped paired reads after alignment quality filtering were considered. Gene level FPKM (Fragments Per Kilobase Million) and raw read count values were computed by the R package DESeq2.
To account for this batch effect in RNA expression, we used the ComBat  batch correction method through the implementation in R sva package.
Genome_build: hg19
Supplementary_files_format_and_content: Batch corrected RNA expression of UCSC hg19 KnownGene

source_name: oropharyngeal tumor biopsy

extract_protocol:
Quant-iTTM RiboGreen® RNA Assay Kit
Illumina’s TruSeq RNA Access Library Prep kit

tag: tissuetype

value: FFPE tumor

tag: studytimepoint

value: prert

tag: site

value: Mayo


title: Mayo_18_prert [A228]

description:
A228
A228-MSK-RNA


title: RNASeq_Mpp8mAID_nothing_IAA_6hrs_Rep2

description:
RNASeq_Mpp8mAID_nothing_DMSO_vs_IAA_6hrs_gene_TE_analysis.txt
RNASeq_Mpp8mAID_nothing_DMSO_vs_IAA_6hrs_cntTable.txt


title: Mayo_18_recur [A234]

description:
A234
A234-MSK-RNA

value: recur


title: Mayo_17_prert [A226]

description:
A226
A226-MSK-RNA


title: RNASeq_Mpp8mAID_nothing_IAA_6hrs_Rep1


title: RNASeq_Mpp8mAID_WT_untreated_6hrs_Rep2


title: RNASeq_OsTIR1_nothing_untreated_6hrs_Rep2


title: Mayo_14_prert [A222]

description:
A222
A222-MSK-RNA


title: Mayo_13_prert [MAYO13]

description:
MAYO13
RNA2019-MAYO13-FFPE-tumor-pretx


title: Mayo_16_prert [A227]

description:
A227
A227-MSK-RNA


title: RNASeq_Mpp8mAID_nothing_untreated_6hrs_Rep1


title: RNASeq_Mpp8mAID_Cpart_IAA_6hrs_Rep1


title: Mayo_15_prert [A223]

description:
A223
A223-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_Cpart_IAA_48hrs

data_processing:
Reads were first trimmed using Trim Galore (Version 0.4.5) using --illumina and default parameters. Mapping was done with STAR (Version 2.5.3a) allowing multimappers (--winAnchorMultimaNmax 100 --outFilterMultimapNmax 100 --outFilterMismatchNmax 3) to mm10 assembly. Peaks were called for using epic2 peak caller (version 0.0.41) using the epic2-df function. Peaks were subsequently filtered to fulfil wildtype read number requirements (>= 100 && <=5000) and for peaks that are overrepresented in the wildtype condition (FC_WT > 1) yielding 55 high confidence peaks. For visualization, bigWig coverage files normalized to sequencing depth *10000000 were generated with deepTools (version 2.29.2) with the following configurations: bamCoverage --bam --ignoreDuplicates --scaleFactor --centerReads. BigWig were subsequently loaded into IGV (version 2.8.0). For average profiles ngsplot (Version 2.63) was applied using default parameters.
Genome build: mm10
Reads were first trimmed using Trim Galore (Version 0.4.5) using --illumina and default parameters. Mapping was done with STAR (Version 2.5.3a) allowing multimappers (--winAnchorMultimaNmax 100 --outFilterMultimapNmax 100 --outFilterMismatchNmax 3) to mm10 assembly. Peaks were called for using epic2 peak caller (version 0.0.41) using the epic2-df function. Peaks were subsequently filtered to fulfil wildtype read number requirements (>= 100 && <=5000) and for peaks that are overrepresented in the wildtype condition (FC_WT > 1) yielding 55 high confidence peaks. For visualization, bigWig coverage files normalized to sequencing depth *10000000 were generated with deepTools (version 2.29.2) with the following configurations: bamCoverage --bam --ignoreDuplicates --scaleFactor --centerReads. BigWig were subsequently loaded into IGV (version 2.8.0). For average profiles ngsplot (Version 2.63) was applied using default parameters.
Genome build: mm10

tag: crosslinking strategy

value: 10 min formaldehyde (1%)


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Npart_IAA_48hrs


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Cpart_untreated_48hrs


title: ChIPSeq_Input_Mpp8mAID_Cpart_untreated_48hrs


title: Mayo_11_prert [A219]

description:
A219
A219-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Npart_untreated_48hrs


title: Mayo_12_prert [A224]

description:
A224
A224-MSK-RNA


title: RNASeq_Mpp8mAID_WT_IAA_6hrs_Rep1

value: Mpp8mAID; OsTIR1


title: RNASeq_Mpp8mAID_WT_untreated_6hrs_Rep1


title: ChIPSeq_Input_Mpp8mAID_Npart_untreated_48hrs


title: Mayo_08_prert [A229]

description:
A229
A229-MSK-RNA


title: Mayo_10_recur [A233]

description:
A233
A233-MSK-RNA


title: Mayo_09_prert [A225]

description:
A225
A225-MSK-RNA


title: Mayo_10_prert [A231]

description:
A231
A231-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_WT_IAA_48hrs

value: 48 hours IAA (500 µM)


title: RNASeq_Mpp8mAID_nothing_untreated_6hrs_Rep2


title: Mayo_06_prert [A220]

description:
A220
A220-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_WT_IAA_48hrs


title: Mayo_07_prert [A221]

description:
A221
A221-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Cpart_IAA_48hrs

value: Mpp8mAID; OsTIR1; Mpp81-729


title: Mayo_05_prert [A232]

description:
A232
A232-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_WT_untreated_48hrs

value: untreated


title: Mayo_04_prert [A218]

description:
A218
A218-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_WT_untreated_48hrs

value: Mpp8mAID; OsTIR1; Mpp8wt


title: ChIPSeq_Input_Mpp8mAID_Npart_IAA_48hrs

value: Mpp8mAID; OsTIR1; Mpp8112-858


title: Mayo_02_prert [A216]

description:
A216
A216-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_nothing_IAA_48hrs


title: Mayo_03_prert [A217]

description:
A217
A217-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_nothing_IAA_48hrs


title: ChIPSeq_Input_Mpp8mAID_nothing_untreated_48hrs


title: Mayo_01_prert [A215]

description:
A215
A215-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_nothing_untreated_48hrs


title: MSK50_prert [A214]

description:
A214
A214-MSK-RNA

value: MSKCC


title: MSK49_prert [A213]

description:
A213
A213-MSK-RNA


title: MSK48_prert [A209]

description:
A209
A209-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_Cpart_IAA_6hrs

value: ESC line derivative of feeder-independent E14-TG2a parental cells (129/Ola strain)


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Cpart_untreated_6hrs


title: MSK47_prert [A210]

description:
A210
A210-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Cpart_IAA_6hrs


title: MSK46_prert [MSK46]

description:
MSK46
RNA2019-MSK46-FFPE-tumor-pretx


title: MSK23_prert [A208]

description:
A208
A208-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_Cpart_untreated_6hrs


title: MSK24_prert [A211]

description:
A211
A211-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Npart_IAA_6hrs


title: MSK22_prert [A207]

description:
A207
A207-MSK-RNA


title: MSK20_prert [MSK20]

description:
MSK20
RNA2019-MSK20-FFPE-tumor-pretx


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_WT_IAA_6hrs


title: ChIPSeq_Input_Mpp8mAID_Npart_untreated_6hr


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_Npart_untreated_6hrs


title: MSK21_prert [A212]

description:
A212
A212-MSK-RNA


title: MSK19_prert [A206]

description:
A206
A206-MSK-RNA

value: Frozen tumor


title: MSK17_prert [A204]

description:
A204
A204-MSK-RNA


title: MSK18_prert [A205]

description:
A205
A205-MSK-RNA


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_WT_untreated_6hrs


title: ChIPSeq_Input_Mpp8mAID_WT_IAA_6hrs


title: ChIPSeq_Input_Mpp8mAID_WT_untreated_6hrs


title: MSK16_prert [A203]

description:
A203
A203-MSK-RNA


title: MSK14_prert [A201]

description:
A201
A201-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_nothing_IAA_6hrs


title: MSK13_ND [MSK13]

description:
MSK13
RNA2019-MSK13-FFPE-tumor-ND

value: ND


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_nothing_IAA_6hrs


title: AML1956_at_day_29_sample_2

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
RNAseq fastq files were trimmed using Trim Galore and cutadapt to remove adapter sequences. Trimmed fastq files were aligned using STAR (version 2.5.3a) to the human genome (hg19) using Gencode (v19)  transcriptome assembly.  Coding genes were quantified using subread featureCounts (v1.4.5-p1) to annotate uniquely mapped reads to Gencode annotation.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: primary AML1956

growth_protocol: Patient-derived AML cells engrafted in NSG mice.

extract_protocol: RNA-seq libraries were prepared using the TruSeq RNA Kit according to the manufacturer

treatment_protocol: PDX models were treated with AraC (Cytarabine) for 5 consecutive days with 60 mg/kg (i.p.).

value: primary AML1956

value: PDX models were treated with AraC for 5 consecutive days with 60 mg/kg (i.p.) and harvested on day 29


title: AML1956_at_day_29_sample_1


title: MSK15_prert [A202]

description:
A202
A202-MSK-RNA


title: ChIPSeq_Input_Mpp8mAID_Npart_IAA_6hrs

value: 6 hours IAA (500 µM)


title: ChIPSeq_IP_FLAG_Tasorflag

value: TCF2.2 (F1 hybrid 129S6;C57BL/6N lines)

value: 30 min disuccinimidyl glutarate (0.4 mM), 10 min formaldehyde (1%)

value: FLAG (Sigma, affinity gel A2220)

value: Tasorflag2 homozygous knockin


title: AML1956_at_day_8_sample_1

value: PDX models were treated with AraC for 5 consecutive days with 60 mg/kg (i.p.) and harvested on day 8


title: ChIPSeq_IP_FLAG_wt

value: wt


title: AML1956_at_day_0_sample_2

value: Control mice, untreated


title: ChIPSeq_Input_Mpp8flag

value: untreated


title: ChIPSeq_IP_FLAG_Mpp8flag

value: Mpp8Flag2 homozygous knockin


title: AML1956_at_day_0_sample_1


title: ChIPSeq_Input_Mpp8mAID_nothing_untreated_6hrs

value: 10 min formaldehyde (1%)

value: Mpp8mAID; OsTIR1


title: AML2837_at_day_29_sample_2

source_name: primary AML2837

value: primary AML2837


title: AML2837_at_day_29_sample_3


title: ChIPSeq_IP_MPP8_Mpp8mAID_nothing_untreated

value: ESC line derivative of feeder-independent E14-TG2a parental cells (129/Ola strain)

value: MPP8 (Proteintech, 16796-1-1AP)


title: AML2837_at_day_8_sample_2


title: ChIPSeq_IP_MPP8_Mpp8mAID_Cpart_IAA_16hrs

value: Mpp8mAID; OsTIR1; Mpp8112-858

value: 16 hours IAA (500 µM)


title: ChIPSeq_IP_MPP8_Mpp8mAID_Npart_IAA_16hrs

value: Mpp8mAID; OsTIR1; Mpp81-729


title: ChIPSeq_IP_H3K9me3_Mpp8mAID_nothing_untreated_6hrs


title: ChIPSeq_IP_FLAG_Mpp8mAID_Npart_IAA_16hrs


title: ChIPSeq_IP_MPP8_Mpp8mAID_nothing_IAA_16hrs


title: AML2837_at_day_8_sample_3


title: AML2837_at_day_0_sample_3


title: ChIPSeq_IP_FLAG_Mpp8mAID_Cpart_IAA_16hrs


title: AML1956_at_day_0_sample_3

value: primary AML1956


title: AML2837_at_day_0_sample_2


title: AML2837_at_day_0_sample_1


title: Sample_9_AML2741_AraC_repl1_RNAseq

description: human patient-derived AML cells

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 using STAR with default parameters
TPM were obtained using Rsubread using RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: TPM

source_name: AML ex vivo

treatment_protocol: Included as additional column of SAMPLES section

tag: agent

value: AraC  (100nM)

tag: time point


title: ChIPSeq_IP_FLAG_Mpp8mAID_WT_IAA_16hrs

value: 30 min disuccinimidyl glutarate (0.4 mM), 10 min formaldehyde (1%)

value: FLAG (Sigma, affinity gel A2220)

value: Mpp8mAID; OsTIR1; Mpp8wt


title: ChIPSeq_Input_Mpp8mAID_Cpart_IAA_16hrs


title: ChIPSeq_Input_Mpp8mAID_Npart_IAA_16hrs


title: ChIPSeq_IP_FLAG_wt_nothing_untreated

value: wt


title: ChIPSeq_Input_Mpp8mAID_WT_IAA_16hrs


title: Sample_8_AML2741_Vehicle_repl2_RNAseq

description: human patient-derived AML cells

value: DMSO vehicle control


title: Sample_7_AML2741_Vehicle_repl1_RNAseq

description: human patient-derived AML cells


title: ChIPSeq_IP_MPP8_Mpp8mAID_WT_IAA_16hrs


title: female-tg-7

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to mouse genome (mm10) using the STAR RNA-seq aligner software (version STAR_2.5.0a )
The STAR genome database was built with the gencode annotation file (version M12)
Raw read counts for 49585 Gencode-annotated gene-level features were determined using HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: liver

growth_protocol: Mice were grouped housed in IVC cages (up to 5 animals/cage) in a specific pathogen free environment and fed standard chow diet (Altromin 1324; total pathogen free, irradiated with 25kGy) and water ad libitum.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: Sex

value: Female

tag: age

value: 5-7 months


title: female-tg-6

tag: genotype


title: Sample_6_AML1566_AraC_repl3_RNAseq

description: human patient-derived AML cells

value: AraC  (1000nM)


title: Sample_4_AML1566_AraC_repl1_RNAseq

description: human patient-derived AML cells


title: Sample_3_AML1566_Vehicle_repl3_RNAseq

description: human patient-derived AML cells


title: female-tg-5


title: female-tg-4


title: AML2837_at_day_29_sample_1

value: primary AML2837

tag: treatment

value: PDX models were treated with AraC for 5 consecutive days with 60 mg/kg (i.p.) and harvested on day 29


title: Sample_2_AML1566_Vehicle_repl2_RNAseq

description: human patient-derived AML cells


title: female-tg-2


title: female-tg-1


title: AML2837_at_day_8_sample_1

value: PDX models were treated with AraC for 5 consecutive days with 60 mg/kg (i.p.) and harvested on day 8


title: female-wt-7

value: wild type


title: female-wt-6


title: female-wt-5


title: ChIPSeq_IP_FLAG_Pphln1flag

value: TCF2.2 (F1 hybrid 129S6;C57BL/6N lines)

value: Pphln1Flag2 homozygous knockin

value: untreated


title: ChIPSeq_Input_wt_nothing_untreated

value: ESC line derivative of feeder-independent E14-TG2a parental cells (129/Ola strain)


title: MCF7_siUSP1_2

city: shanghai

first: aihui

last: ma

address: 800, Dongchuan Road

institute: shanghai cancer institute

data_processing:
Illumina HiSeq 2500 reads were trimmed for adaptor sequences, ribosome RNA reads and low-quality sequences by Seqtk (https://github.com/lh3/seqtk).
Clean reads were mapped to human genome (hg19) with TopHat (version:2.0.9).
The gene fragments were counted by HTSeq (Bioinformatics, 2015. 31(2):p.166-9). Fragments Per Kilobase of exon model per Million mapped reads (FPKM) were normalized by TMM (trimmed mean of M values) method (Genome Biol, 2010. 11(3):p.R25).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM/count values for each gene in each sample.

source_name: breast cancer cell line MCF7, transfected with USP1 specific siRNA-2

growth_protocol: MCF7 cells were grown in Dulbecco’s Modified Eagle Medium plus 10% fetal bovine serum, 100 units/ml penicillin and 100  μg/mL streptomycin.

extract_protocol:
Total RNA was extracted by TRIZOL Reagent (Life Technologies, Inc) and quantified by Agilent Bioanalyzer 2100 (Agilent technologies).
The cDNA fragments were subjected to an end repair process, added a single ‘A’ base, and ligated with the adapters. The products were then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Cells were maintained at 37 °C with 5% CO2, grown to 80% confluence, and then transfected with control siRNA or USP1-specific siRNA using Lipofectamine 2000 Transfection Reagent (Thermo Fisher Scientific).

tag: transfection

value: USP1 siRNA-2

value: breast cancer cell line