title: cChIP_H3K27me3_WH2_d4-7_dTAG13

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.

tag: cell type

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae

value: WAPL-FKBP(degron)

value: 3 days dTAG-13 (500nM)

tag: differentiation day

value: day 7

tag: chip antibody

value: H3K27me3 (GeneTex GTX60892)


title: RNA_WH2_d4-7_dTAG13

status: Public on Mar 15 2021

type: SRA

city: Boston

first: Andrea

middle: June

last: Kriz

state: MA

address: 185 Cambridge St

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital, Harvard Medical School

description: processed data file: WH7d4-7-comp-gene-D-13-rep1-rep2-WH2d4-7-D-13-table.nospace.noFPKM.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

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: strain

tag: genotype

tag: treatment


title: RNA_WH2_d4-7_DMSO

value: 3 days DMSO


title: Sample 5_CREBmut-head-fed1

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

description:
q3
processed data file:
1_Head-dM-KD_gene_exp_sampl1-6.diff

data_processing:
.diff file from cuffdiff comparing the samples indicated in the file name:
MiSeq Generation of fastq files
tophat2 alignment
cuffdiff Differential Gene Expression
.txt file from DESeq2 comparing thhe samples indicated in the file name:
MiSeq Generation of fastq files
STAR alignment
DESeq2 Differential Gene Expression
Genome_build: dm3 (.diff files); dm6 (DESeq2 output)
Supplementary_files_format_and_content: .diff file from cuffdiff or .txt file from DESeq2 comparing the samples indicated in the file name

organism: Drosophila melanogaster

source_name: CREBmut-head-fed

growth_protocol: standard fly media

extract_protocol:
total RNA extracted with Qiagen Rneasy kit
polyA RNA isolated and library prepared with NEBnext Ultra kit

treatment_protocol: 16h fasting

value: creb mutant fruit fly

tag: age

value: 3-5 days old

tag: tissue

value: adult fly head

value: fed


title: SAMPLE 133_641491SV151015HGU219F05

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 133

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

molecule: total RNA

organism: Homo sapiens

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

tag: time point

value: Screening Visit

tag: visit code

value: SV


title: SAMPLE 137_300934SV151015HGU219F12

description: Liver biopsy  from Non-tolerant SAMPLE 137


title: cChIP_input_WH2_d4-7_dTAG13

library_source: genomic

molecule: genomic DNA


title: SAMPLE 139_415095MF26281216A07

description: Liver biopsy  from Non-tolerant SAMPLE 139

value: Primary Endpoint Visit


title: SAMPLE 132_286326SV151015HGU219A11

description: Liver biopsy  from Non-tolerant SAMPLE 132


title: Sample 13_wt-head-fed3

description:
q1
processed data file:
3_fed-head-KO_gene_exp_sample13-15.diff
5_VolcanoPlot-DESeq2_control_fastVSfed_sample1-2-7-8-13.txt
8_VolcanoPlot-DESeq2_fed_crtckoVSwt_sample1-3-7-9-13-14.txt

source_name: wt-head-fed

value: w1118 fruit fly


title: Sample 11_CREBmut-head-fed2

description:
q5
processed data file:
2_DMHead2-gene_exp_sample7-12.diff


title: Sample 3_CRTCko-head-fed1

description:
q5
processed data file:
1_Head-dM-KD_gene_exp_sampl1-6.diff
6_VolcanoPlot-DESeq2_crtcko_fastVSfed_sample3-4-9-10-14.txt
8_VolcanoPlot-DESeq2_fed_crtckoVSwt_sample1-3-7-9-13-14.txt

source_name: CRTCko-head-fed

value: crtc ko fruit fly


title: Sample 10_CRTCko-head-fasted2

description:
q4
processed data file:
2_DMHead2-gene_exp_sample7-12.diff
6_VolcanoPlot-DESeq2_crtcko_fastVSfed_sample3-4-9-10-14.txt
7_VolcanoPlot-DESeq2_fast_crtckoVSwt_sample2-4-8-10.txt

source_name: CRTCko-head-fasted

value: 16 hours fasting treatment


title: SAMPLE 160_259491SV151015HGU219C10

description: Liver biopsy  from Tolerant SAMPLE 160

value: Tolerant


title: Sample 8_wt-head-fasted2

description:
q2
processed data file:
2_DMHead2-gene_exp_sample7-12.diff
5_VolcanoPlot-DESeq2_control_fastVSfed_sample1-2-7-8-13.txt
7_VolcanoPlot-DESeq2_fast_crtckoVSwt_sample2-4-8-10.txt

source_name: wt-head-fasted


title: Sample 7_wt-head-fed2

description:
q1
processed data file:
2_DMHead2-gene_exp_sample7-12.diff
5_VolcanoPlot-DESeq2_control_fastVSfed_sample1-2-7-8-13.txt
8_VolcanoPlot-DESeq2_fed_crtckoVSwt_sample1-3-7-9-13-14.txt


title: Sample 1_wt-head-fed1

description:
q1
processed data file:
1_Head-dM-KD_gene_exp_sampl1-6.diff
5_VolcanoPlot-DESeq2_control_fastVSfed_sample1-2-7-8-13.txt
8_VolcanoPlot-DESeq2_fed_crtckoVSwt_sample1-3-7-9-13-14.txt


title: H2Aub 4cell WT Rep2

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

description:
H2Aub_4C_WT.bw
H2Aub_4Cell_Mat.merged.bw
H2Aub_4Cell_Pat.merged.bw

data_processing:
Low quality reads and adaptor sequences of the CUT&RUN data were trimmed using Trimgalore (v0.4.5) with the parameter “--paired”. The trimmed reads were then aligned to mm10 genome using Bowtie2 (v2.3.4.3)  with parameters “‘--no-unal --no-mixed --no-discordant -I 10 -X 700”. To minimize mapping bias toward reference genome (B6) for the F1 hybrid data, SNPs between PWK and B6/129 or B6/DBA were masked as “N”, depending the maternal genetic background. Unmapped and low quality reads were removed using sambamba (v0.5.9) with parameters “-f bam -F ‘mapping_quality >= 20 and not (unmapped or mate_is_unmapped)’”. Only uniquely mapped reads were kept for downstream analyses. PCR duplicates were removed using the “MarkDuplicates” command from Picard tools (v2.8.0) (https://broadinstitute.github.io/picard/). SNPsplit (v0.3.2) was used to determine the parental origin of the CUT&RUN read pairs. The bigwig files were generated using the “bamCoverage” command from deepTools (v3.0.2) with parameters “--binSize 25 --extendReads 150 --normalizeUsing RPKM --outFileFormat bigwig --scaleFactor 1”. Reproducibility were assessed by calculating Pearson correlation coefficient of RPKM in 5-kb bins between replicates. The biological replicates were pooled using the ‘merge’ command from sambamba (v0.5.9). CUT&RUN reads within the mm10 black list regions (https://github.com/Boyle-Lab/Blacklist/tree/master/lists) were not used for subsequent analyses.
Genome_build: mm10 with SNPs masked as "N"
Supplementary_files_format_and_content: Bigwig files that can be uploaded on a genome browser to view H3K27me3 and H2Aub at different genomic locations.

source_name: 4-cell embryo

extract_protocol:
As all libraries generated in this study involved low-input techniques,  samples collected were directly put into lysis buffer for further library construction.
H3K27me3 and H2Aub CUT&RUN libraries were constructed as previously described (Skene and Henikoff, 2017 eLife. 2017; 6: e21856, PMID: 28079019).
CUT&RUN

tag: background

value: B6/129 mixed x PWK

tag: manipulation

value: Eed (fl/fl) x WT

tag: embryos/oocytes

value: 60 4-cell


title: SAMPLE 135_827472SV151015HGU219G07

description: Liver biopsy  from Non-tolerant SAMPLE 135


title: cChIP_RAD21_WH2_d4-7_dTAG13

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae

value: WAPL-FKBP(degron)

value: 3 days dTAG-13 (500nM)

value: day 7

value: RAD21 (Abcam ab992)


title: cChIP_H3K27me3_WH2_d4-7_DMSO

value: 3 days DMSO

value: H3K27me3 (GeneTex GTX60892)


title: Sample 4_CRTCko-head-fasted1

description:
q6
processed data file:
1_Head-dM-KD_gene_exp_sampl1-6.diff
6_VolcanoPlot-DESeq2_crtcko_fastVSfed_sample3-4-9-10-14.txt
7_VolcanoPlot-DESeq2_fast_crtckoVSwt_sample2-4-8-10.txt

value: 3-5 days old

value: adult fly head


title: Sample 2_wt-head-fasted1

description:
q2
processed data file:
1_Head-dM-KD_gene_exp_sampl1-6.diff
5_VolcanoPlot-DESeq2_control_fastVSfed_sample1-2-7-8-13.txt
7_VolcanoPlot-DESeq2_fast_crtckoVSwt_sample2-4-8-10.txt

value: w1118 fruit fly


title: Sample 6_CREBmut-head-fasted1

description:
q4
processed data file:
1_Head-dM-KD_gene_exp_sampl1-6.diff

source_name: CREBmut-head-fasted

value: creb mutant fruit fly


title: SAMPLE 129_977303SV151015HGU219B06

description: Liver biopsy  from Non-tolerant SAMPLE 129

value: liver

value: Non-tolerant

value: Screening Visit

value: SV


title: Sample 9_CRTCko-head-fed2

description:
q3
processed data file:
2_DMHead2-gene_exp_sample7-12.diff
6_VolcanoPlot-DESeq2_crtcko_fastVSfed_sample3-4-9-10-14.txt
8_VolcanoPlot-DESeq2_fed_crtckoVSwt_sample1-3-7-9-13-14.txt

value: crtc ko fruit fly

value: fed


title: cChIP_input_WH7_d78h_dTAG13

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae


title: cChIP_input_WH2_d4-7_DMSO

value: WAPL-FKBP(degron)


title: SAMPLE 131_763869SV151015HGU219D10

description: Liver biopsy  from Non-tolerant SAMPLE 131


title: SAMPLE 125_802143SV281015HGU219A08

description: Liver biopsy  from Non-tolerant SAMPLE 125


title: SAMPLE 123_933569SV151015HGU219G11

description: Liver biopsy  from Tolerant SAMPLE 123

value: Tolerant


title: SAMPLE 130_588124FCB1281216G03

description: Liver biopsy  from Non-tolerant SAMPLE 130

value: For-cause Biopsy Visit


title: cChIP_H3K27me3_WH7_d78h_dTAG13

value: day 7


title: cChIP_RAD21_WH2_d4-7_DMSO

value: 3 days DMSO

value: RAD21 (Abcam ab992)


title: SAMPLE 128_603788SV281015HGU219H04

description: Liver biopsy  from Tolerant SAMPLE 128


title: cChIP_RAD21_WH7_d78h_dTAG13


title: cChIP_RAD21_WH7_d78h_DMSO

value: 8h DMSO


title: SAMPLE 126_636296FCB1281216F06

description: Liver biopsy  from Non-tolerant SAMPLE 126


title: SAMPLE 127_794852SV151015HGU219F07

description: Liver biopsy  from Non-tolerant SAMPLE 127


title: cChIP_H3K27me3_WH7_d78h_DMSO

value: H3K27me3 (GeneTex GTX60892)


title: SAMPLE 124_977303FCB1281216E10

description: Liver biopsy  from Non-tolerant SAMPLE 124


title: cChIP_input_WH7_d78h_DMSO


title: cChIP_RAD21_WH2_d78h_dTAG13


title: SAMPLE 121_938137SV281015HGU219G09

description: Liver biopsy  from Non-tolerant SAMPLE 121


title: SAMPLE 122_736429SV151015HGU219H09

description: Liver biopsy  from Non-tolerant SAMPLE 122


title: SAMPLE 119_828298SV151015HGU219D07

description: Liver biopsy  from Non-tolerant SAMPLE 119


title: SAMPLE 120_165255SV151015HGU219D06

description: Liver biopsy  from Non-tolerant SAMPLE 120


title: 1981_D0_iPS12

type: genomic

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

hyb_protocol: 500 ng of DNA underwent bisulfite conversion, hybridization to Infinium Human Methylation EPIC beadchip (Illumina)

scan_protocol: Arrays were imaged using iScan (Illumina) using standard recommended Illumina scanner settings

data_processing: Using the built-in quality control probes, all the samples passed quality control in GenomeStudio (Illumina). Preprocessing, and normalization steps were done by using the R (v3.6.2) package Minfi (v1.34.0) (Aryee 2014). Raw data (idat files) were combined, then normalized by noob normalization. M values were used to create PCA plots using Qlucore Omics Explorer (v3.6) and differentially methylated probes (DMP) were detected using the dmpFinder function in Minfi (v1.34.0). Cross reacting probes (Pidsley 2016) and sex chromosomes were removed from the list of DMPs.

label: Cy5 and Cy3

source_name: induced pluripotent stem cell

label_protocol: Standard Illumina Protocol

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: DNA was isolated using DNeasy kit (Qiagen) and quantified using Qubit dsDNA BR assay kit (ThermoFisher).

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% or msc

value: day 0

tag: differentiation end point cell type or parental line (msc)

value: induced pluripotent stem cell

tag: gender

value: Female


title: cChIP_input_WH2_d78h_dTAG13

tag: cell type

tag: differentiation day


title: cChIP_RAD21_WH2_d78h_DMSO

tag: strain

tag: chip antibody


title: cChIP_H3K27me3_WH2_d78h_DMSO

tag: genotype

tag: treatment


title: cChIP_H3K27me3_WH2_d78h_dTAG13


title: SAMPLE 117_182516SV151015HGU219D09

description: Liver biopsy  from Non-tolerant SAMPLE 117

tag: tissue

value: liver

value: Non-tolerant

value: Screening Visit

value: SV


title: 1933_D0_iPS2

value: Male


title: 1754_D0_iPS3

value: Normal


title: 1933_D4_21%_iPS5

source_name: differentiated induced pluripotent stem cell

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: 1754_D4_2%_iPS3

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: 1933_D4_2%_iPS5


title: 1932_MSC

value: MSC

value: parental line


title: SAMPLE 118_160690SV281015HGU219B03

description: Liver biopsy  from Non-tolerant SAMPLE 118

tag: isw outcome (tolerant/non-tolerant)


title: cChIP_input_WH2_d78h_DMSO

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae

value: WAPL-FKBP(degron)

value: 8h DMSO

value: day 7


title: 1938_MSC


title: SAMPLE 116_455735SV151015HGU219C08

description: Liver biopsy  from Non-tolerant SAMPLE 116

value: liver

tag: time point


title: 1938_D4_2%_iPS3


title: 1947_D0_iPS8

value: day 0

value: induced pluripotent stem cell

value: Female


title: SAMPLE 115_810205SV151015HGU219B09

description: Liver biopsy  from Tolerant SAMPLE 115

value: Tolerant

value: Screening Visit

tag: visit code

value: SV


title: cChIP_H3K27me3_RG9_d78h_dTAG13

value: H3K27me3 (GeneTex GTX60892)


title: cChIP_RAD21_RG9_d78h_dTAG13

value: RAD21 (Abcam ab992)


title: SAMPLE 114_376456SV281015HGU219B06

description: Liver biopsy  from Tolerant SAMPLE 114


title: cChIP_input_RG9_d78h_dTAG13


title: SAMPLE 113_324363SV151015HGU219D05

description: Liver biopsy  from Tolerant SAMPLE 113


title: 1938_D0_iPS1

value: Normal

value: Male


title: 1932_D4_21%_iPS8

value: Severe Preeclampsia

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: SAMPLE 112_417706SV281015HGU219D08

description: Liver biopsy  from Tolerant SAMPLE 112


title: cChIP_H3K27me3_RG9_d78h_DMSO

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae


title: 1981_D0_iPS11


title: 1938_D0_iPS2


title: 1947_D0_iPS2


title: 1981_D0_iPS4


title: 1932_D0_iPS8


title: 1933_MSC

value: MSC

value: parental line


title: cChIP_input_RG9_d78h_DMSO

value: 8h DMSO

value: day 7


title: 1938_D4_21%_iPS3


title: cChIP_RAD21_RG9_d78h_DMSO


title: Control 8

city: Belo Horizonte

first: Luzia

middle: Helena

last: Carvalho

state: Minas Gerais

address: Av. Augusto de Lima, 1715

country: Brazil

institute: Instituto René Rachou, FIOCRUZ

data_processing: Raw data was analysed with NanoString nSolver 4.0, using default quality control standards. For normalization, spike in oligos (cel-miR-248 and cel-miR-254) were used. Following manufacturer’s instructions, only targets that presented average raw count above 100 were considered for further differential expression analysis in Partek Genomics Suite 7.0. Principal component analysis plot was also generated with the same software with batch effects removed.

label: not provided

label_protocol: Extraction product (3 uL) was analyzed using nCounter Human v3 miRNA Expression Assay (NanoString Technologies), according to the manufacturer’s instructions.

extract_protocol: Circulating and exosomal RNA were purified from plasma using Plasma/Serum Circulating and Exosomal RNA Purification kit (Norgen Biotek Corp., Canada), according to manufacturer instructions. In order to control extraction efficiency, a panel contained 5 spiked in probes (ath-miR-159a, cel-miR-248, cel-miR-254, osa-miR-414, osa-miR-442; IDT Technologies, USA) was added after second lysis buffer incubation. After purification, RNA portion was concentrated using RNA Clean-Up and Concentration kit (Norgen Biotek Corp., Canada), following manufacturer instructions.

tag: subject status

value: Healthy subject

value: plasma


title: 1947_D0_iPS7

value: day 0

value: induced pluripotent stem cell

value: Female


title: cChIP_H3K27me3_RC4_d78h_dTAG13

value: H3K27me3 (GeneTex GTX60892)


title: SAMPLE 109_983489SV281015HGU219F09

description: Liver biopsy  from Non-tolerant SAMPLE 109

value: liver

value: Non-tolerant

value: Screening Visit

value: SV


title: LM3_siNC

city: Changchun

first: Shui

last: Liu

state: Jilin Province

address: Ziqiang Stree No.218

department: The Second Hospital of Jilin University

country: China

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
The quality of the original data was statistically analyzed, and the sequencing data quality of the samples was visually evaluated by FastQC.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, HISAT2 was used to compare the quality-controlled sequencing sequence with the reference genome, and the results were statistically compared by RSeQC.
Fragments Per Kilobase of exon transcript per Million fragments mapped reads(FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: hepatocellular  carcinoma

growth_protocol: The LM3 and RBE cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimitotic solution. All cells were maintained at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
The transfected cells were digested with trypsin and washed three times with PBS, and total RNA was harvested using Trizol reagent. Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (Cat#12301ES96) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The LM3 and RBE cells were transfected with si-FENDRR or si-NC using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis.

tag: cell line

value: LM3 cell

value: hepatocellular  carcinoma

value: Transfection with si-NC


title: MCF7 tamoxifen resistant cells

city: Guangzhou

first: Yinghua

last: Zhu

address: 107 Yanjiang West Road

institute: Sun Yat-Sen University

description: lncRNA and mRNA expression

hyb_protocol: The labeled cRNAs were hybridized onto the microarray based on the manufacturer’s standard protocols.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: MCF7 tamoxifen resistant cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF7 cell were cultured in DMEM supplemented with 10% FBS and 0.01 mg/ml human recombinant insulin , MCF7 tamoxifen resistant cells were cultured in phenol red free RPMI-1640 containing 5% charcoal stripped steroid depleted FBS.

extract_protocol: Total RNA was extracted using Trizol reagent(Invitrogen) following the manufacturer's instructions.

treatment_protocol: MCF7 cells were plated in six well plate and culture for 24 hours. Then, the cells were washed with PBS, the culture medium was changed with phenol red free RPMI-1640 containing 5% charcoal stripped steroid depleted FBS(css),  and harvested the cells 48 hours later. MCF7 tamoxifen resistant cells cultured in css medium four 48 hours, then harvested for extracting total RNA.

value: MCF7 tamoxifen resistant cells


title: MCF7 parent cells

description: lncRNA and mRNA expression

source_name: MCF7 parent cells

value: MCF7 parent cells


title: RBE_siNC

source_name: intrahepatic cholangiocarcinoma

value: RBE cell

value: intrahepatic cholangiocarcinoma


title: SAMPLE 108_318921SV151015HGU219C07

description: Liver biopsy  from Non-tolerant SAMPLE 108


title: 1932_D4_2%_iPS8

value: Severe Preeclampsia

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: cChIP_H3K27me3_RC4_d78h_DMSO

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae

value: 8h DMSO

value: day 7


title: XPC_3

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
TPM determined using Kallisto v0.43.1
Genome_build: hg38
Supplementary_files_format_and_content: Table with TPMs per sample

source_name: MCF-10A Cells

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: shRNA

value: shXPC

tag: rep


title: 1754_MSC

tag: disease state

value: Normal

tag: differentiation days + oxygen% or msc

value: MSC

value: parental line

value: Male


title: 1947_D4_21%_iPS8

value: day+4 under 21% oxygen

tag: differentiation end point cell type or parental line (msc)

value: Syncytiotrophoblast

tag: gender

value: Female


title: Patient 24

hyb_protocol: according to the manufacturer’s instructions.

value: Plasmodium vivax patient

value: plasma


title: Patient 25

scan_protocol: according to the manufacturer’s instructions.


title: Control 7

value: Healthy subject


title: Patient 26


title: cChIP_input_RC4_d78h_dTAG13

tag: cell type

tag: differentiation day


title: cChIP_RAD21_RC4_d78h_DMSO

tag: strain

tag: chip antibody

value: RAD21 (Abcam ab992)


title: XPC_2


title: cChIP_RAD21_RC4_d78h_dTAG13

tag: genotype

tag: treatment


title: SAMPLE 111_332151SV151015HGU219E05

description: Liver biopsy  from Tolerant SAMPLE 111

tag: tissue

value: liver

tag: isw outcome (tolerant/non-tolerant)

value: Tolerant

value: Screening Visit

value: SV


title: RBE_siRNA

value: RBE cell

value: intrahepatic cholangiocarcinoma

value: Transfection with si-FENDRR


title: cChIP_input_RC4_d78h_DMSO

value: ES cell (Tsix-stop)

value: CAST/Ei x 129/Sv/Jae

value: 8h DMSO

value: day 7


title: XPC_1

value: shXPC


title: SAMPLE 110_234924SV151015HGU219C05

description: Liver biopsy  from Non-tolerant SAMPLE 110

value: Non-tolerant

tag: time point

tag: visit code


title: Patient 23

tag: subject status

value: Plasmodium vivax patient


title: XPA_2

tag: shRNA

value: shXPA

tag: cell line


title: Control_MEF_3_RNA

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM24 transcript reference.
Ribosome profiling data were adaptor trimmed with fastx_clipper using -a CTGTAGGCACCATCAAT and rRNA was removed using bowtie2 version 2.2.3 using the parameter -L 13.
Remaining ribosome profiling reads were mapped to the mm10 genome with a Gencode vM24 transcript annotation using hisat2 version 2.1.0.
Ribosome profiling reads were counted at the gene-level using featureCounts for reads overlapping CDS features.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include featureCounts estimated gene counts ribosome profiling samples.

source_name: Mouse Embryonic Fibroblast

extract_protocol:
Whole mouse embryos, mouse embryonic fibroblasts, or adult mouse tissues were isolated and immediately frozen in liquid nitrogen. Total RNA was extracted with Trizol reagent.
RNA-Seq libraries were prepared using the KAPA Stranded mRNA-Seq Kit. Briefly, total RNA was isolated and RNA quality was assessed on Agilent TapeStation. mRNA was purified using biotin-tagged polydT oligonucleotides and streptavidin-coated magnetic beads. After fragmentation of mRNA, libraries were prepared according to manufacturer’s instructions. Paired end reads (2x100bp) were obtained using the HiSeq 4000 (Illumina). Ribosome profiling libraries were generated as previously described (Ingolia et al., 2012; Ishimura et al., 2014) and sequenced on an Illumina HiSeq 4000 (1x75 bp).

value: Mouse Embryonic Fibroblast

value: CAG-Cre ER

tag: batch

value: Batch 6

value: Tamoxifen


title: XPA_3

tag: rep


title: XPA_1


title: SAMPLE 102_588124SV281015HGU219F10

description: Liver biopsy  from Non-tolerant SAMPLE 102

value: liver

value: Screening Visit


title: 1933_D0_iPS1

tag: disease state

value: Severe Preeclampsia

tag: differentiation days + oxygen% or msc

value: day 0

tag: differentiation end point cell type or parental line (msc)

value: induced pluripotent stem cell

value: Male


title: 1981_D4_21%_iPS11

value: day+4 under 21% oxygen

value: Syncytiotrophoblast

tag: gender

value: Female


title: SAMPLE 103_910844SV281015HGU219C10

description: Liver biopsy  from Non-tolerant SAMPLE 103

value: SV


title: LM3_siRNA

value: LM3 cell

tag: cell type

value: hepatocellular  carcinoma

value: Transfection with si-FENDRR


title: SAMPLE 101_809997FCB1281216E02

description: Liver biopsy  from Non-tolerant SAMPLE 101

value: Non-tolerant

value: For-cause Biopsy Visit


title: ERCC6_3


title: Patient 19

value: Plasmodium vivax patient

value: plasma


title: Patient 21


title: Patient 20


title: Patient 18


title: Patient 22


title: Control_MEF_2_RNA

tag: strain

value: Mouse Embryonic Fibroblast

value: CAG-Cre ER

value: Batch 6

value: Tamoxifen


title: SAMPLE 100_809997SV281015HGU219E08

description: Liver biopsy  from Non-tolerant SAMPLE 100

value: liver

value: Screening Visit


title: Control_MEF_1_RNA

tag: genotype


title: 1981_D4_2%_iPS11

value: Severe Preeclampsia

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: Upf2_MEF_3_RNA

value: CAG-Cre ER; Upf2 cKO

tag: treatment


title: Upf2_MEF_2_RNA

tag: tissue


title: SAMPLE 107_813272SV151015HGU219H06

description: Liver biopsy  from Non-tolerant SAMPLE 107

tag: isw outcome (tolerant/non-tolerant)

value: SV


title: Patient 17


title: SAMPLE 106_990077SV151015HGU219C06

description: Liver biopsy  from Non-tolerant SAMPLE 106

tag: time point


title: 1947_MSC

value: Normal

value: MSC

value: parental line

value: Female


title: ERCC6_2


title: ERCC5_3


title: Patient 16

value: Plasmodium vivax patient


title: Pelo_MEF_2_RNA

value: CAG-Cre ER; Pelo cKO


title: Upf2_MEF_1_RNA

value: Mouse Embryonic Fibroblast


title: Patient 15

value: plasma


title: Pelo_MEF_1_RNA

value: Batch 6


title: ERCC5_2


title: SAMPLE 104_843475SV281015HGU219G08

description: Liver biopsy  from Tolerant SAMPLE 104

value: Tolerant

tag: visit code


title: SAMPLE 105_542636SV281015HGU219H07

description: Liver biopsy  from Non-tolerant SAMPLE 105

value: liver

value: Non-tolerant


title: ERCC6_1


title: SAMPLE 97_649391SV281015HGU219C09

description: Liver biopsy  from Non-tolerant SAMPLE 97

value: Screening Visit


title: ERCC5_1


title: SAMPLE 99_664737SV281015HGU219A09

description: Liver biopsy  from Tolerant SAMPLE 99


title: SAMPLE 95_276711FCB1281216C11

description: Liver biopsy  from Non-tolerant SAMPLE 95

value: For-cause Biopsy Visit


title: SAMPLE 96_768987SV151015HGU219H04

description: Liver biopsy  from Tolerant SAMPLE 96


title: 1932_D0_iPS2

value: Severe Preeclampsia

value: day 0

value: induced pluripotent stem cell


title: Hbs1l_MEF_2_RNA

value: CAG-Cre ER; Hbs1l cKO

value: Tamoxifen


title: SAMPLE 94_649391FCB1281216B08

description: Liver biopsy  from Non-tolerant SAMPLE 94


title: 1981_MSC

value: MSC

value: parental line


title: ERCC4_3


title: Patient 14

tag: subject status

value: Plasmodium vivax patient


title: Patient 13


title: Hbs1l_MEF_1_RNA


title: 1938_D0_iPS3

value: Normal

value: Male


title: Patient 12

value: plasma


title: Hbs1l_MEF_3_RNA

value: Mouse Embryonic Fibroblast

value: Batch 6


title: Control 6

value: Healthy subject


title: 1932_D0_iPS10

value: Female


title: ERCC4_2

tag: shRNA


title: SAMPLE 93_677482FCB1281216G10

description: Liver biopsy  from Non-tolerant SAMPLE 93

value: liver

value: Non-tolerant


title: Control_Upf2_batch_MEF_3_ribo

description: Ribosome protected RNA fragments

value: CAG-Cre ER

value: Batch 5


title: Control_Upf2_batch_MEF_2_ribo

description: Ribosome protected RNA fragments


title: SAMPLE 92_384384SV281015HGU219G07

description: Liver biopsy  from Non-tolerant SAMPLE 92

value: Screening Visit

value: SV


title: 1754_D4_21%_iPS3

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: SAMPLE 98_349892SV281015HGU219C02

description: Liver biopsy  from Tolerant SAMPLE 98

value: Tolerant


title: CON_3

value: shCON

tag: cell line


title: Control 5


title: 1933_D0_iPS5

value: Severe Preeclampsia

value: day 0

value: induced pluripotent stem cell


title: CON_2


title: Control_Upf2_batch_MEF_1_ribo

description: Ribosome protected RNA fragments

value: Mouse Embryonic Fibroblast

tag: batch

value: Tamoxifen


title: 1947_D4_2%_iPS8

value: Normal

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: Upf2_MEF_3_ribo

description: Ribosome protected RNA fragments

value: CAG-Cre ER; Upf2 cKO


title: SAMPLE 91_772315SV151015HGU219B05

description: Liver biopsy  from Non-tolerant SAMPLE 91

value: liver

value: Non-tolerant


title: 1754_D0_iPS2

value: Male


title: Upf2_MEF_2_ribo

description: Ribosome protected RNA fragments

value: Batch 5


title: CON_1

tag: rep


title: SAMPLE 89_540674SV281015HGU219H09

description: Liver biopsy  from Tolerant SAMPLE 89

value: Screening Visit

value: SV


title: ERCC4_1


title: Patient 10

value: Plasmodium vivax patient

value: plasma


title: Patient 9


title: Control_Pelo_batch_MEF_3_ribo

description: Ribosome protected RNA fragments

value: CAG-Cre ER

value: Batch 4


title: Control_Pelo_batch_MEF_2_ribo

description: Ribosome protected RNA fragments


title: Patient 8


title: SAMPLE 87_636296SV281015HGU219B02

description: Liver biopsy  from Non-tolerant SAMPLE 87


title: Patient 7


title: Control_Pelo_batch_MEF_1_ribo

description: Ribosome protected RNA fragments


title: Patient 11


title: SAMPLE 90_379054SV281015HGU219D07

description: Liver biopsy  from Tolerant SAMPLE 90

value: Tolerant


title: Control 4

value: Healthy subject


title: Pelo_MEF_3_ribo

description: Ribosome protected RNA fragments

value: Mouse Embryonic Fibroblast

value: CAG-Cre ER; Pelo cKO

value: Tamoxifen


title: 1754_D0_iPS4

tag: disease state

value: Normal

value: day 0

value: induced pluripotent stem cell


title: Upf2_MEF_1_ribo

description: Ribosome protected RNA fragments

value: CAG-Cre ER; Upf2 cKO


title: Pelo_MEF_1_ribo

description: Ribosome protected RNA fragments


title: SAMPLE 88_462021SV281015HGU219H05

description: Liver biopsy  from Non-tolerant SAMPLE 88

value: liver

value: Non-tolerant


title: Control_Hbs1l_batch_MEF_3_ribo

description: Ribosome protected RNA fragments

value: Batch 3


title: Pelo_MEF_2_ribo

description: Ribosome protected RNA fragments


title: SAMPLE 85_733922SV151015HGU219E09

description: Liver biopsy  from Tolerant SAMPLE 85

value: Screening Visit

value: SV


title: SAMPLE 86_794910SV281015HGU219C08

description: Liver biopsy  from Non-tolerant SAMPLE 86


title: Patient 2

value: Plasmodium vivax patient

value: plasma


title: SAMPLE 84_878825SV281015HGU219H08

description: Liver biopsy  from Tolerant SAMPLE 84


title: Control_Hbs1l_batch_MEF_2_ribo

description: Ribosome protected RNA fragments

value: CAG-Cre ER


title: Control 3


title: SAMPLE 83_597774SV281015HGU219E07

description: Liver biopsy  from Tolerant SAMPLE 83

value: Tolerant


title: Control 2

value: Healthy subject


title: SAMPLE 82_878825FCB1281216G07

description: Liver biopsy  from Non-tolerant SAMPLE 82

value: For-cause Biopsy Visit


title: SAMPLE 81_751760SV151015HGU219H05

description: Liver biopsy  from Non-tolerant SAMPLE 81


title: Hbs1l_MEF_3_ribo

description: Ribosome protected RNA fragments

value: Mouse Embryonic Fibroblast

value: CAG-Cre ER; Hbs1l cKO


title: Control_Hbs1l_batch_MEF_1_ribo

description: Ribosome protected RNA fragments

value: Tamoxifen


title: Patient 4


title: iPS4_1981_d4

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

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)

value: Severe Preeclampsia

tag: differentiation days + oxygen%

value: day 4

tag: differentiation end point cell type

value: Cytotrophoblast

value: Female


title: Patient 5


title: Control 1


title: Patient 3


title: Hbs1l_MEF_2_ribo

description: Ribosome protected RNA fragments


title: Hbs1l_MEF_1_ribo

description: Ribosome protected RNA fragments


title: iPS4_1981_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast

tag: gender


title: Mpbes1_rep3

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

description: CRISPR-generated mutant plant

data_processing:
quality filter and read trimming: BBDuk software. Read minimum length of 35bo and quality score of 25
Alignment to Marchantia polymorpha v3.1 genome using STAR v2.5.2b
Features quantification: Gene expression calculated as raw fragment counts, at gene level,  using FeatureCounts v1.5.1
Downstream processing included low-counts and high variability filter using HSTfilter (R package) and TMM normalization and differential expression analysis using edgeR (R package)
Genome_build: Marchantia polymorpha v3.1
Supplementary_files_format_and_content: Tab-separated text file containing raw fragment counts of each Marchantia polymorpha gene and for each sample

organism: Marchantia polymorpha

source_name: CRISPR-generated mutant plant

growth_protocol: Marchantia polymorpha subsp. ruderalis cv. Tak-1 plants were grown on half-strength Gamborg’s B5 basal medium (Duchefa) supplemented with 1% phytoagar (Duchefa), under white light (50 μmol/m2/s) and long-day conditions (16 h light at 22°C, 8 h dark at 20°C) for 30 days.

extract_protocol:
RNA extraction from thalli (ca. 100mg including apical notches) was done using the Rneasy plant mini kit (Qiagen 74904). To remove contaminating DNA, the TURBO DNAfreeTM Kit. (Ambion AM1907) was used according to the manufacturer’s recommendations.  Quality of RNA was checked with Bioanalyzer. All samples had a RNA Integrity Number (RIN) > 7.
TruSeq Stranded mRNA Sample Prep kit

treatment_protocol: No treatments were applied to the samples

value: thalli including apical notches


title: iPS4_1981_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: SAMPLE 80_461059SV281015HGU219B09

description: Liver biopsy  from Tolerant SAMPLE 80

value: liver

value: Screening Visit

value: SV


title: Mpbes1_rep2

description: CRISPR-generated mutant plant


title: iPS4_1981_d0

value: day 0

value: induced pluripotent stem cell


title: Patient 1

value: Plasmodium vivax patient

value: plasma


title: iPS12_1981_d4


title: SAMPLE 79_769999SV151015HGU219G12

description: Liver biopsy  from Non-tolerant SAMPLE 79

value: Non-tolerant


title: SAMPLE 77_461082SV151015HGU219B08

description: Liver biopsy  from Tolerant SAMPLE 77

value: Tolerant


title: SAMPLE 76_677482LF13AG01280119_A01

description: Liver biopsy  from Non-tolerant SAMPLE 76

value: 5yr Visit


title: SAMPLE 78_145471FCB1281216F01

description: Liver biopsy  from Non-tolerant SAMPLE 78

value: For-cause Biopsy Visit


title: Control_cerebellum_3_ribo

description: Ribosome protected RNA fragments

source_name: Cerebellum

value: Cerebellum

tag: age

value: Atoh-Cre;Hbs1l +/+

value: Batch 2


title: Mpbes1_rep1

description: CRISPR-generated mutant plant

value: thalli including apical notches


title: iPS12_1981_d0

value: Severe Preeclampsia

value: Female


title: Tak-1_WT_rep3

description: Wild-type plant

source_name: Wild-type plant


title: Control_cerebellum_1_ribo

description: Ribosome protected RNA fragments

tag: strain


title: SAMPLE 75_777934LF13AG01280119_D09

description: Liver biopsy  from Non-tolerant SAMPLE 75

source_name: Liver biopsy

value: liver


title: Tak-1_WT_rep2

description: Wild-type plant

tag: genotype


title: Hbs1l_cerebellum_3_ribo

description: Ribosome protected RNA fragments

value: Atoh-Cre;Hbs1l cKO


title: iPS12_1981_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: Tak-1_WT_rep1

description: Wild-type plant


title: Patient 6


title: iPS12_1981_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: SAMPLE 72_621964LF13AG01280119_F10

description: Liver biopsy  from Non-tolerant SAMPLE 72


title: Control_cerebellum_2_ribo

description: Ribosome protected RNA fragments


title: iPS11_1981_d4

value: day 4

value: Cytotrophoblast


title: SAMPLE 71_461059LF13AG01280119_B08

description: Liver biopsy  from Non-tolerant SAMPLE 71

value: Non-tolerant


title: Control_embryo_3_ribo

description: Ribosome protected RNA fragments

source_name: Whole embryo

value: Whole embryo

value: Wildtype

value: Batch 1


title: SAMPLE 9

first: Izabela

middle: Mamede Costa Andrade

last: Conceição

address: Av. Pres. Antônio Carlos, 6627

department: Genetics

institute: UFMG

data_processing:
Normalization was performed using the SNORD95, SNORD96A, RNU6-6P and cel-miR-39 from the housekeeping panel in the array. Relative quantification was calculated using the comparative 2(-Delta Delta CT) method (Livak and Schmittgen, 2001).
Normalized by 2(-Delta Delta CT)  and FoldChange by 2^(- Delta Ct)

label: SYBR

source_name: Plasma of pregnant who developed preeclampsia

label_protocol: commercial Kits

growth_protocol: [No cells were grown or maintained prior to extract preparation] Plasma samples of cases and controls were stored at -80°C until analysis.

extract_protocol: Total RNA from plasma samples (200 μL) from control and case groups was isolated using the miRNeasy Serum/Plasma Kit (Qiagen®, Leusden, Netherlands) according to the manufacturer’s instructions

treatment_protocol: [No treatment was applied to biological material prior to extract preparation]

value: developed preeclampsia

value: plasma


title: iPS11_1981_d4_21


title: Control_embryo_2_ribo

description: Ribosome protected RNA fragments


title: iPS11_1981_d4_2


title: SAMPLE 70_376456LF13AG01280119_A07

description: Liver biopsy  from Non-tolerant SAMPLE 70

value: 5yr Visit


title: SAMPLE 74_276711LF13AG01280119_G02

description: Liver biopsy  from Non-tolerant SAMPLE 74


title: SAMPLE 68_632724LF13AG01280119_G05

description: Liver biopsy  from Non-tolerant SAMPLE 68


title: Control_embryo_1_ribo

description: Ribosome protected RNA fragments


title: SAMPLE 69_182516LF13AG01280119_D05

description: Liver biopsy  from Non-tolerant SAMPLE 69


title: Hbs1l_embryo_3_ribo

description: Ribosome protected RNA fragments

value: Hbs1l -/-


title: Hbs1l_cerebellum_2_ribo

description: Ribosome protected RNA fragments

value: Cerebellum

value: Batch 2


title: SAMPLE 73_664737LF13AG01280119_F09

description: Liver biopsy  from Non-tolerant SAMPLE 73

value: liver


title: SAMPLE 7

value: Female


title: iPS8_1947_d4

value: Normal


title: SAMPLE 8


title: SAMPLE 67_384384LF13AG01280119_F01

description: Liver biopsy  from Non-tolerant SAMPLE 67


title: SAMPLE 5


title: SAMPLE 4

source_name: Plasma of controls

value: control


title: Hbs1l_cerebellum_1_ribo

description: Ribosome protected RNA fragments

value: Atoh-Cre;Hbs1l cKO


title: Hbs1l_embryo_2_ribo

description: Ribosome protected RNA fragments


title: SAMPLE 6


title: iPS11_1981_d0

value: Severe Preeclampsia

value: day 0

value: induced pluripotent stem cell


title: iPS8_1947_d0


title: SAMPLE 66_550115MF26281216F09

description: Liver biopsy  from Non-tolerant SAMPLE 66

value: Non-tolerant

value: Primary Endpoint Visit


title: Hbs1l_embryo_1_ribo

description: Ribosome protected RNA fragments

value: Whole embryo

value: Batch 1


title: SAMPLE 3

value: plasma


title: iPS8_1947_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: iPS8_1947_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: SAMPLE 2


title: iPS7_1947_d4

value: day 4

value: Cytotrophoblast


title: SAMPLE 64_641491LF13AG01280119_H03

description: Liver biopsy  from Non-tolerant SAMPLE 64

value: liver

value: 5yr Visit


title: iPS7_1947_d0

value: Normal

value: Female


title: SAMPLE 1

value: control


title: IGF2BP2_input_2

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of IGF2BP2 on genome using “ABLIRC” strategy.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: BMDMs

growth_protocol: BMDMs were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from IGF2BP2-RNA complexes and another for the western blotting assay for IGF2BP2 immunoprecipitation.The IGF2BP2-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: antibody


title: IGF2BP2_input_1


title: iPS7_1947_d4_21


title: CHART_Xist_WH7_d4-7_dTAG13.rep2

source_name: Xist CHART, rep2

value: CAST/Ei x 129/Sv/Jae

tag: genotype/variation

value: WAPL-FKBP(degron)

tag: cell type

value: ES cell (Tsix-stop)

tag: treatment

value: 3 days dTAG-13 (500nM)

tag: differentiation day

value: day 7


title: SAMPLE 65_996155LF13AG01280119_A09

description: Liver biopsy  from Non-tolerant SAMPLE 65

tag: tissue

tag: isw outcome (tolerant/non-tolerant)

value: Non-tolerant

tag: time point

tag: visit code


title: IGF2BP2_IP_2

value: name:IGF2BP2 Antibody; vendor:proteintech; catalog#:11601-1-AP; lot#:00082294


title: CHART_Xist_WH7_d4-7_DMSO.rep2

value: 3 days DMSO


title: CHART_input_WH7_d4-7_DMSO.rep2

source_name: CHART input, rep2


title: iPS7_1947_d4_2

source_name: differentiated induced pluripotent stem cell

value: day+4 under 2% oxygen


title: CHART_input_WH7_d4-7_dTAG13.rep2


title: IGF2BP2_IP_1


title: iPS2_1947_d4


title: SAMPLE 62_809997LF13AG01280119_E02

description: Liver biopsy  from Non-tolerant SAMPLE 62


title: SAMPLE 63_234924LF13AG01280119_C06

description: Liver biopsy  from Non-tolerant SAMPLE 63


title: SAMPLE 60_802143LF13AG01280119_C01

description: Liver biopsy  from Non-tolerant SAMPLE 60


title: iPS2_1947_d0

source_name: induced pluripotent stem cell

value: day 0

value: induced pluripotent stem cell


title: CHART_Xist_WH7_d4-7_dTAG13.rep1

source_name: Xist CHART, rep1


title: SAMPLE 57_733922LF13AG01280119_C12

description: Liver biopsy  from Non-tolerant SAMPLE 57


title: SAMPLE 59_542636LF13AG01280119_F05

description: Liver biopsy  from Non-tolerant SAMPLE 59


title: SAMPLE 58_214859FCB2AG01280119_D01

description: Liver biopsy  from Non-tolerant SAMPLE 58

value: For-cause Biopsy Visit


title: iPS2_1947_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: CHART_Xist_WH7_d4-7_DMSO.rep1


title: CHART_input_WH7_d4-7_dTAG13.rep1

source_name: CHART input, rep1


title: iPS3_1938_d4

value: Normal

value: day 4

value: Cytotrophoblast

value: Male


title: CHART_input_WH7_d4-7_DMSO.rep1

value: CAST/Ei x 129/Sv/Jae

value: WAPL-FKBP(degron)


title: SAMPLE 56_145471LF13AG01280119_E10

description: Liver biopsy  from Non-tolerant SAMPLE 56

value: liver

value: 5yr Visit


title: iPS3_1938_d0


title: cChIP_H3K27me3_WH7_d4-7_dTAG13.rep2

source_name: H3K27me3 cChIP, clone H7 rep2

value: ES cell (Tsix-stop)

value: 3 days dTAG-13 (500nM)

value: day 7

tag: chip antibody

value: H3K27me3 (GeneTex GTX60892)


title: iPS3_1938_d4_2

tag: disease state

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: cChIP_H3K27me3_WH7_d4-7_DMSO.rep2

value: 3 days DMSO


title: iPS2_1938_d4

tag: differentiation days + oxygen%


title: SAMPLE 55_148518LF13AG01280119_H10

description: Liver biopsy  from Non-tolerant SAMPLE 55

value: Non-tolerant


title: SAMPLE 61_702777LF13AG01280119_H07

description: Liver biopsy  from Non-tolerant SAMPLE 61


title: SAMPLE 53_214859LF13AG01280119_A04

description: Liver biopsy  from Non-tolerant SAMPLE 53


title: cChIP_input_WH7_d4-7_DMSO.rep2

source_name: cChIP input, clone H7, rep2


title: cChIP_input_WH7_d4-7_dTAG13.rep2


title: iPS2_1938_d0

value: day 0

tag: differentiation end point cell type

value: induced pluripotent stem cell


title: iPS2_1947_d4_2

value: Normal

tag: gender

value: Female


title: SAMPLE 52_550115LF13AG01280119_A05

description: Liver biopsy  from Non-tolerant SAMPLE 52


title: SAMPLE 51_813272LF13AG01280119_D06

description: Liver biopsy  from Non-tolerant SAMPLE 51


title: cChIP_RAD21_WH7_d4-7_DMSO.rep2

source_name: RAD21 cChIP, clone H7, rep2

value: RAD21 (Abcam ab992)


title: cChIP_RAD21_WH7_d4-7_dTAG13.rep2

value: CAST/Ei x 129/Sv/Jae


title: iPS3_1938_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast

value: Male


title: SAMPLE 48_313003LF13AG01280119_H02

description: Liver biopsy  from Non-tolerant SAMPLE 48

value: liver

value: 5yr Visit


title: SAMPLE 54_113192LF13AG01280119_B12

description: Liver biopsy  from Non-tolerant SAMPLE 54


title: SAMPLE 47_794910LF13AG01280119_G08

description: Liver biopsy  from Non-tolerant SAMPLE 47


title: SAMPLE 50_160690LF13AG01280119_B04

description: Liver biopsy  from Non-tolerant SAMPLE 50


title: cChIP_H3K27me3_WH7_d4-7_dTAG13.rep1

source_name: H3K27me3 cChIP, clone H7 rep1

value: WAPL-FKBP(degron)

value: ES cell (Tsix-stop)

value: 3 days dTAG-13 (500nM)

value: day 7


title: iPS2_1938_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: SAMPLE 49_510267LF13AG01280119_B05

description: Liver biopsy  from Non-tolerant SAMPLE 49

value: Non-tolerant


title: iPS1_1938_d4_21


title: iPS2_1938_d4_21


title: cChIP_RAD21_WH7_d4-7_dTAG13.rep1

source_name: RAD21 cChIP, clone H7, rep1


title: cChIP_input_WH7_d4-7_dTAG13.rep1

source_name: cChIP input, clone H7, rep1


title: iPS1_1938_d4

value: day 4

value: Cytotrophoblast


title: cChIP_H3K27me3_WH7_d4-7_DMSO.rep1

value: 3 days DMSO

value: H3K27me3 (GeneTex GTX60892)


title: SAMPLE 45_233127LF13AG01280119_H05

description: Liver biopsy  from Non-tolerant SAMPLE 45

source_name: Liver biopsy


title: HU-1-36_refractory_timepoint2

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

source_name: CLL, refractory

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

tag: Sex

value: male

tag: treated

value: yes

tag: response to therapy

value: refractory

value: mutated


title: SAMPLE 44_736429LF13AG01280119_D03

description: Liver biopsy  from Non-tolerant SAMPLE 44

value: liver


title: HU-1-36_refractory_timepoint1

value: not applicable


title: iPS1_1938_d4_2

value: Normal

value: Male


title: SAMPLE 46_488136FCB1AG01280119_D12

description: Liver biopsy  from Non-tolerant SAMPLE 46

value: For-cause Biopsy Visit


title: SAMPLE 42_415095LF13AG01280119_A11

description: Liver biopsy  from Non-tolerant SAMPLE 42

value: 5yr Visit


title: HU-1-23_refractory_timepoint1

value: unmutated


title: SAMPLE 41_977303LF13AG01280119_G01

description: Liver biopsy  from Non-tolerant SAMPLE 41


title: SAMPLE 43_488136LF13AG01280119_B10

description: Liver biopsy  from Non-tolerant SAMPLE 43


title: iPS5_1933_d4

value: Severe Preeclampsia


title: HU-1-05_treatment_timepoint1

source_name: CLL, treatment

value: stable disease


title: ChIP_RAD21_RG9_d108h_DMSO

source_name: RAD21 ChIP, clone G9

tag: strain

value: CAST/Ei x 129/Sv/Jae

value: ES cell (Tsix-stop)

value: 8h DMSO

value: day 10

value: RAD21 (Abcam ab992)


title: cChIP_RAD21_WH7_d4-7_DMSO.rep1

tag: genotype/variation

value: WAPL-FKBP(degron)

value: 3 days DMSO

value: day 7


title: iPS5_1933_d4_21

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: iPS5_1933_d4_2

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: SAMPLE 40_462021LF13AG01280119_G07

description: Liver biopsy  from Non-tolerant SAMPLE 40

value: liver

value: Non-tolerant


title: ChIP_RAD21_RC4_d108h_DMSO

source_name: RAD21 ChIP, clone C4

tag: cell type


title: HU-1-05_refractory_timepoint2

value: male

value: yes

value: refractory

value: unmutated


title: HU-1-23_refractory_timepoint2


title: ChIP_RAD21_RC4_d108h_dTAG13

value: CAST/Ei x 129/Sv/Jae

value: ES cell (Tsix-stop)

tag: treatment


title: ChIP_input_RG9_d108h

source_name: ChIP input, clone G9

value: 8h DMSO

tag: differentiation day

value: day 10


title: tra1Q3-3

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)

tag: genotype


title: iPS2_1933_d4

source_name: differentiated induced pluripotent stem cell

value: Severe Preeclampsia

value: day 4

value: Cytotrophoblast

value: Male


title: HU-1-11_relapsed_timepoint2

source_name: CLL, relapsed

value: relapsed


title: ChIP_input_RC4_d108h

source_name: ChIP input, clone C4


title: SAMPLE 38_971198LF13AG01280119_H08

description: Liver biopsy  from Non-tolerant SAMPLE 38

tag: tissue

tag: isw outcome (tolerant/non-tolerant)

value: 5yr Visit


title: iPS2_1933_d0

source_name: induced pluripotent stem cell

value: day 0

value: induced pluripotent stem cell


title: cChIP_input_WH7_d4-7_DMSO.rep1

value: WAPL-FKBP(degron)

value: 3 days DMSO

value: day 7


title: HU-1-07_relapsed_timepoint2

value: male

value: yes


title: SAMPLE 37_419162LF13AG01280119_B11

description: Liver biopsy  from Non-tolerant SAMPLE 37

value: liver

value: Non-tolerant

tag: time point

tag: visit code


title: SAMPLE 36_951840LF13AG01280119_A02

description: Liver biopsy  from Non-tolerant SAMPLE 36


title: HU-1-19_untreated_timepoint2

source_name: CLL, untreated

value: no

value: not applicable

value: unmutated


title: iPS2_1933_d4_21

tag: disease state

value: Severe Preeclampsia

value: day+4 under 21% oxygen

value: Syncytiotrophoblast


title: HU-1-31_refractory_timepoint2

value: refractory


title: SAMPLE 39_162449LF13AG01280119_G12

description: Liver biopsy  from Non-tolerant SAMPLE 39

value: 5yr Visit


title: iPS5_1933_d0

tag: differentiation days + oxygen%

value: day 0

value: Male


title: tra1Q3-1

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


title: WT-3

description: MATalpha his3delta0 leu2delta0 ura3delta0 TRA1-HIS3 +DED1pr-YHR100-LEU2


title: iPS1_1933_d4

value: day 4

tag: differentiation end point cell type

value: Cytotrophoblast


title: SAMPLE 35_810205LF13AG01280119_A12

description: Liver biopsy  from Non-tolerant SAMPLE 35


title: iPS1_1933_d4_21

tag: gender


title: WT-2

value: MATalpha his3delta0 leu2delta0 ura3delta0 TRA1-HIS3 +DED1pr-YHR100-LEU2


title: Sham-3

city: Chang Chun

first: Xuan

last: Chen

state: Jilin

address: Xinmin Street

department: The First Hospital of Jilin University

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_sham

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


title: iPS1_1933_d0

value: induced pluripotent stem cell


title: HU-1-09_untreated_timepoint2

tag: Sex

value: male

value: no

value: mutated


title: iPS1_1933_d4_2

value: Severe Preeclampsia

value: day+4 under 2% oxygen

value: Extravillous trophoblast


title: HU-1-09_untreated_timepoint1

tag: treated

value: not applicable


title: SAMPLE 33_550115FCB2AG01280119_D11

description: Liver biopsy  from Non-tolerant SAMPLE 33

value: liver

value: Non-tolerant

value: For-cause Biopsy Visit


title: Sham-2


title: SAMPLE 34_318921LF13AG01280119_F12

description: Liver biopsy  from Non-tolerant SAMPLE 34

value: 5yr Visit


title: HU-1-32_refractory_timepoint2

value: yes

tag: response to therapy

value: refractory

value: unmutated


title: SAMPLE 31_420006LF13AG01280119_B06

description: Liver biopsy  from Non-tolerant SAMPLE 31


title: iPS8_1932_d4

value: day 4

value: Cytotrophoblast

value: Female


title: WT-1

tag: strain

value: MATalpha his3delta0 leu2delta0 ura3delta0 TRA1-HIS3 +DED1pr-YHR100-LEU2


title: iPS8_1932_d0

value: day 0

value: induced pluripotent stem cell