title: 7209_IP (biol rep 2 mutant)

city: Edinburgh

first: Tadas

last: Andriuskevicius

address: Alexander Crum Brown Road

department: Institute of Cell Biology, School of Biological Sciences

institute: The University of Edinburgh

description:
indexes used for this sample - R12 (CTATCGCT) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig

data_processing:
Reads in files S0_L001_R1_001 and S0_L001_R2_001 were demultiplexed using Barcode Splitter (Galaxy Version 1.0.1). The barcode sequences used for this are indicated in the sample description. Number of allowed mismatches: 0; Number of allowed barcodes nucleotide deletions: 0.
Reads were filtered for quality and poly-A tails added during library preparation using DNA SMARTTM ChIP-Seq Kit (Takara Bio, 634865) were removed using RINSEQ (Galaxy Version 0.20.4+galaxy1). Minimum mean score threshold to conserve sequences: 15; Maximal N percentage threshold to conserve sequences 2; Minimum length of poly-A/T to trim at the 5'-end: 8; Trim sequence by quality score from the 3'-end -> Quality score threshold to trim positions: 20 -> Type of quality score calculation to use: Minimum -> Rule to use to compare quality score to calculated value: Less than -> Size of the sliding window used to calculated quality score by type: 1 -> Step size used to move the sliding window: 1.
Adapter sequences were removed using Trim Galore! (Galaxy Version 0.6.7+galaxy0). Adapter automatic detection and default settings were used.
Paired reads were interleaved using seqtk_mergepe (Galaxy Version 1.3.1) using default parameters.
Processed and interleaved reads were aligned to sacCer3 reference genome using Bowtie2 (Galaxy Version 2.4.2+galaxy0) and default settings.
Reads from aligned IP samples were normalised to those from aligned input samples using bamCompare (Galaxy Version 3.3.2.0.0). Method to use for scaling the largest sample to the smallest: read count; How to compare the two files -> Compute the ratio of the number of reads -> Pseudocount: 10 10.
Rad51-ChIP signal in PGAL1-RAD55 srs2Δ rad54Δ mutants was compared to PGAL1-RAD55 controls and in induced (GAL) NK1325 cells to uninduced (RAF) NK1325 cells using bigwigCompare (Galaxy Version 3.3.2.0.0) by computing the ratio signals using default settings. The average signal ratio for the two biological repeats was computed using bigwigCompare (Galaxy Version 3.3.2.0.0) -> compute the mean of the signal in the two files.
Assembly: reference sequence sacCer3
Supplementary files format and content: format: bigwig; content: Rad51 ChIP-seq signal comparison between mutant (treated) and control

organism: Saccharomyces cerevisiae

source_name: yeast cell

extract_protocol:
The 200 OD600 units harvested for each strain were split into four Eppendorf tubes (50 OD600 units in each) and resuspended in 400 µl of bead-beating buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1 cOmplete Mini, EDTA-free Protease Inhibitor Cocktail tablet (Roche, 11836170001) per 5 ml of buffer). An equal volume of glass beads (0.5 mm diameter, BioSpec Products) was added, and the tubes were vortexed for 25 cycles (3,000 rpm; 30 seconds of vortexing, 1 minute of resting on ice). After vortexing, cells were separated from the beads and cells and nuclei were lysed with 0.5% (w/v) SDS for 10 minutes on ice. Tubes were then centrifuged at 20,817 g for 15 minutes at 4°C, the resulting supernatants were removed, the pellets were washed with 1 ml of 0.1% SDS buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.1% (w/v) SDS, 1% Triton X-100 (w/v), 0.1% Sodium Deoxycholate, 1 mM EDTA, 1 mM PMSF, 1 cOmplete Mini, EDTA-free Protease Inhibitor Cocktail tablet (Roche, 11836170001) per 5 ml of buffer) and resuspended in 300 µl of the same buffer. Cell extracts were then sonicated in Bioruptor Plus sonicator (Diagenode) for 20 cycles (30 seconds ON / 30 seconds OFF) on the HIGH power setting. After the sonication, cell debris was spun down at 20,817 g for 15 minutes at 4°C, and supernatants were transferred into fresh Eppendorf tubes containing 1 ml of the 0.1% SDS buffer. Samples belonging to the same strain (split into 4 Eppendorf tubes at the beginning) were then pooled together. 10 µl were collected as input aliquots for each sample, mixed with 390 µl of TE (10 mM Tris-HCl, pH 8, 1 mM EDTA) and stored at -80°C. Four immunoprecipitation reactions were set up for each sample by mixing 1 ml of sonicated cell lysate with 15 µl of Anti-Rad51 (y-180) rabbit polyclonal (Santa Cruz Biotechnology sc-33626) antibody and 15 µl of Dynabeads protein A magnetic beads (Invitrogen, 10002D). The mixtures were incubated overnight at 4°C on a rotating wheel. Next day, beads were recovered using a magnet and sequentially washed with wash buffer 1 (50 mM HEPES-KOH pH 7.5, 275 mM NaCl, 0.1% (w/v) SDS, 1% Triton X-100 (w/v), 0.1% Sodium Deoxycholate, 1 mM EDTA, 1 mM PMSF, 1 cOmplete Mini, EDTA-free Protease Inhibitor Cocktail tablet (Roche, 11836170001) per 5 ml of buffer), wash buffer 2 (50 mM HEPES-KOH pH 7.5, 500 mM NaCl, 0.1% (w/v) SDS, 1% Triton X-100 (w/v), 0.1% Sodium Deoxycholate, 1 mM EDTA, 1 mM PMSF, 1 cOmplete Mini, EDTA-free Protease Inhibitor Cocktail tablet (Roche, 11836170001) per 5 ml of buffer), wash buffer 3 (10 mM Tris-HCl, pH 8, 0.25 M LiCl, 1mM EDTA, 0.5% IGEPAL, 0.5% Sodium Deoxycholate) and wash buffer 4 (10 mM Tris-HCl, pH 8, 1 mM EDTA) for 5 minutes each wash on a rotating wheel at room temperature. To elute precipitated chromatin, beads belonging to the same sample were pooled together in 200 µl of TES (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS) and then incubated at 65°C for 10 minutes with mixing. Tubes were then vortexed, incubated at 65°C for additional 10 minutes and the eluted chromatin was separated from the magnetic beads by centrifugation at 15,871 g for 3 minutes. The beads were washed with 200 µl of TE on the rotating wheel for 15 minutes at room temperature. The tubes were then centrifuged at 15,871 g for 3 minutes, and the resulting supernatants were mixed with the corresponding aliquots of the eluted chromatin.  To remove proteins from the IPed DNA, Proteinase K was added to the immunoprecipitated chromatin samples to the final concentration of 1 mg/ml, and the tubes were incubated at 65°C overnight. Next day, immunoprecipitated DNA was purified using QIAquick® PCR Purification Kit (Qiagen, 28106) and eluted in 35 µl of water.
ChIP-seq libraries were prepared using DNA SMARTTM ChIP-Seq Kit (Takara Bio, 634865) according to the manufacturer’s instructions
12 samples were indexed as indicated in the sample description. Indexed samples were pooled and sequences together.

treatment_protocol:
Cells at exponential phase were pre-grown in YP + raffinose to OD600=0.3 and synchronized with α-factor for 2.5 hours. Galactose was then added to the final concentration of 2% and cells were incubated at 30°C for another hour. After that, α-factor was washed away, cells were transferred to fresh YP + galactose media with nocodazole and incubated for 2 hours.
cells were crosslinked with 1.4% of formaldehyde at 30°C in a shaking water bath for 10 minutes. Crosslinking was stopped by adding glycine to the final concentration of 0.25 M and incubating the cultures for 5 minutes. 200 OD600 units were harvested for ChIP-seq for each sample.

value: yeast cell

value: MATa ura3-52 trp1-289 leu2-3,112 bar1::LEU2 rad55:TRP1-PGAL1-RAD55 srs2::HYG rad54::NAT


title: PDX7_AML_shMFN2

status: Public on Mar 16 2023

type: RNA

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

description: PDX7_shMFN2_(Clariom_S_Human).sst-rma-gene-full.chp Signal

hyb_protocol: cDNA were hybridized to GeneChip® Clariom S Human (Affymetrix) at 45°C for 17 hours, then washed on the fluidic station FS450 (Affymetrix)

scan_protocol: GCS3000 7G (Thermo Fischer Scientific)

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v20 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PDX AML sample transduced with expression vector

label_protocol: 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit

growth_protocol: AML cells were cultured in minimum essential medium (MEM)-α Glutamax (Life Technology, Carlsbad, CA, USA) supplemented with bovine serum albumin (BSA, Sigma-Aldrich, Saint Louis, MO, USA), 100 IU/mL penicillin and 100 µg/mL streptomycin (Life Technology) at 37°C under a 5% CO2 atmosphere.

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit)

tag: tissue source

value: patient with AML

tag: genotype


title: PDX8_AML_shCTL

description: PDX8_shCTL_(Clariom_S_Human).sst-rma-gene-full.chp Signal

value: shCTL


title: 7209_input (biol rep 2 mutant)

type: SRA

country: United Kingdom

description:
indexes used for this sample - R11 (GCGCGAGA) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig

library_source: genomic

molecule: genomic DNA

tag: strain

tag: cell type

tag: chip antibody


title: PDX1_shCTL

description: PDX1_shCTL_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX7_AML_shCTL

description: PDX7_shCTL_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Light_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg38 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping qualit and duplicate reads were removed after the aligment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (https://eg.readthedocs.io/en/latest/text.html#longrange).
Assembly: hg38
Supplementary files format and content: Pairwise Interaction Format

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies) with 50 ng/ml SCF, 3 IU/ml EPO, 10-6 M dexamethasone, 1 ug/ml doxycycline, and passaged every three days.

extract_protocol:
10 ng of 3C DNA was processed for library generation using the NEBNext Ultra II DNA Library prep kit following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg38) were retained for downstream data analysis.
CAPTURE-3C-seq

treatment_protocol: HeLa cells were exposed to blue light (488nM) for 5 min to induce light-activated phase separation.

tag: tissue

value: Human HeLa cells


title: PDX8_AML_shMFN2

description: PDX8_shMFN2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: WT P7_rep1_multiome_snRNA

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger ARC v2.0.0 (10x Genomics) was used (‘count’ option with default parameters) to filter and align raw reads, identify transposase cut sites, detect accessible chromatin peaks, call cells and generate raw count matrices for the multiome samples.
Sequencing reads were aligned to the mm10 genome, coupled with the Gencode vM23 (Ensembl 98) gene annotation.
Assembly: mm10
Supplementary files format and content: *features.tsv.gz, *barcodes.tsv.gz, *matrix.mtx.gz: compressed filtered features (genes and peaks), barcodes and expression matrices generated by Cell Ranger.

organism: Mus musculus

source_name: cortex

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
multiome (scRNA-seq + ATAC-seq)

value: cortex

tag: age

value: postnatal day 7

tag: Sex

value: M


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Light-rep2


title: PDX5_AML_shMFN2

description: PDX5_shMFN2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: M-4_SK070_G34R_P7_crx_DNMT3A

data_processing:
ChIP-seq datasets were processed using the chipseq module of GenPipes v.3.1.2 (Bourgey et al., 2019).
Briefly, raw reads were trimmed using Trimmomatic v0.32 (Bolger et al., 2014) to remove adaptor and sequencing-primer associated reads, then aligned to mm10 using bwa-mem v0.7.12 (Li and Durbin, 2009) with default parameters.
PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard v2.0.1 to produce uniquely aligned reads.
Uniquely aligned reads with mapping quality of 5 or greater were then used to quantify enrichment (q > 5). Visualization tracks were generated using Homer v4.9.1 (Heinz et al., 2010).
Assembly: mm10
Supplementary files format and content: Bigwig files generated with Homer v4.9.1, read coverage for each sample over the mouse genome

source_name: mouse cortex

extract_protocol:
Crosslinked ChIP-seq   Crosslinked ChIP-seq was performed as described previously (Harutyunyan et al., 2019). Briefly, 30-50mg pulverized tissue fixed with 1% formaldehyde (Sigma), followed by reverse crosslinking with glycine. Fixed tissues were then pelleted and stored at −80 °C until use. To isolate nuclei from tissue, pellets were dounced briefly with syringe and needle (25 5/8 gauge) prior to incubation with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate) for 30 mins on ice. Sonication of lysed nuclei was performed on a BioRuptor (Diagenode) for 20 cycles of 30s and 300s off. Samples were checked for sonication efficiency using the criteria of 150–500 bp by gel electrophoresis.   ChIP reaction for DNMT3A was performed as follows: anti-DNMT3A (1:250, ab2850), were incubated with 35 ul protein A Dynabeads at 4 °C for 3 h, then chromatin from ~1-4 million cells was added in RIPA buffer, incubated at 4 °C o/n, washed using buffers from Ideal ChIP-seq Kit (one wash with each buffer, corresponding to RIPA, RIPA + 500 mM NaCl, LiCl, TE), eluted from beads by incubating with Elution buffer for 30 min. at room temperature.   Reverse cross linking took place on a heat block at 65°C for 4 h. ChIP samples were then treated with 2µl RNase Cocktail at 65°C for 30 min followed by 2µl Proteinase K at 65°C for 30 min. Samples were purified with QIAGEN MiniElute PCR purification kit. In parallel, input samples (chromatin from 50,000 cells) were reverse crosslinked, and DNA isolated following the same protocol.    Native ChIP-seq   For histone post-translational modifications, native ChIP were performed as described previously (Chen et al., 2018) with minor adjustments. Briefly, 30-50mg pulverized tissue was dissociated passing through a syringe (25 5/8 gauge) 20x in douncing buffer (10mM Tris Cl pH7.5, 4mM MgCl2, 1mM CaCl2, and protease inhibitor cocktail (Roche)). Disassociated cells were then digested with 30U of micrococcal nuclease (Worthington) at 37°C for 7 mins, yielding predominantly mono- and di-nucleosomes. Cells were then lysed in ice-cold hypotonic lysis buffer (0.2 mM EDTA, 0.1 mM benzamidine, 0.1 mM PMSF, 1.5 mM DTT, and protease inhibitor cocktail (Roche)) to yield chromatin. Chromatin was then incubated with pre-conjugated antibody:bead complex containing H3K27me3 (CST 9733, 4 μL / IP), H3K27ac (CST 8173, 4 μL / IP), H3K36me3 (Active Motif 61022, 4 μL / IP), or H3K36me2 (Active Motif 39255, 4 μL / IP) complexed to Protein A Dynabeads (Invitrogen, 20 μL / IP) or Anti-Mouse Dynabeads (Invitrogen, 40 μL / IP) rotating at 4°C overnight. Beads were then washed twice in ChIP Wash Buffer (20 mM Tris-HCl pH 8, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, and protease inhibitor cocktail) and once more in Final Wash Buffer (20 mM Tris-HCl pH 8, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, and protease inhibitor cocktail). DNA was then eluted in 100mM NaHCO3 and 1% SDS at 65°C for 2h, and purified using phenol:choloroform extraction followed by ethanol precipitation.
ChIP library preparation was carried out using KAPA HTP Illumina library preparation reagents (Roche), following manufacturer’s instructions. Briefly, 50 µl of ChIP DNA sample was incubated with 45 µl end repair mix at 20 °C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50 µl buffer enzyme mix at 30 °C for 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead-bound sample was incubated with 45 µl buffer enzyme mix and 5 µl of TruSeq DNA adapters (Illumina), for 20 °C 15 min, followed by Ampure XP bead purification. Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using gel excision to collect 200–700 bp fragments.

value: Cortex

tag: mark

value: 7 days


title: M-3306_SK059_WT_P7_crx_DNMT3A


title: 6934_IP (biol rep 2 control)

description:
indexes used for this sample - R10 (TTCGCGGA) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig

value: Anti-Rad51 (y-180) rabbit polyclonal (Santa Cruz Biotechnology sc-33626) antibody

value: MATa ura3-52 trp1-289 leu2-3,112 bar1::LEU2 rad55:TRP1-PGAL1-RAD55


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Dark_combined


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Dark-rep2


title: PDX5_AML_shCTL

description: PDX5_shCTL_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: 7208_IP (biol rep 1 mutant)

description:
indexes used for this sample - R8 (GCGCATTA) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig


title: 6934_input (biol rep 2 control)

description:
indexes used for this sample - R9 (CATAGCCG) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Light-rep1


title: CAPTURE-3C-seq_FUSNLAMPS-HS2-Dark-rep1


title: M-2727_SK002_WT_10W_crx_H3K27me3

value: 10 weeks


title: M-2617_SK010_G34R_10W_crx_H3K27me3


title: 6933_IP (biol rep 1 control)

description:
indexes used for this sample - R6 (ACGAATTC) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig


title: G34R P7_rep1_multiome_snRNA

description: 10x Genomics


title: 6933_input (biol rep 1 control)

description:
indexes used for this sample - R5 (TTCTGAAT) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Light_combined


title: M-2616_SK006_WT_10W_crx_H3K27me3


title: 7208_input (biol rep 1 mutant)

description:
indexes used for this sample - R7 (AGCTTCAG) and F2 (ATAGAGGC)
mutant_7208_7208_control_6933_6934_ratio_mean.bigwig


title: 1325_GAL_IP

description:
indexes used for this sample - R4 (GGAATCTC) and F2 (ATAGAGGC)
1325_induced_uninduced_ratio.bigwig

treatment_protocol:
Cells at exponential phase were pre-grown in YP + raffinose to OD600=0.4. Then galactose was added to the final concentration of 2% (HO-mediated break induced) and cells were incubated at 30°C for another 2 hours.
cells were crosslinked with 1.4% of formaldehyde at 30°C in a shaking water bath for 10 minutes. Crosslinking was stopped by adding glycine to the final concentration of 0.25 M and incubating the cultures for 5 minutes. 200 OD600 units were harvested for ChIP-seq for each sample.

tag: ho-mediated break

value: induced

value: MATa-inc trp1-289 ura3::NAT leu2::LEU2-Pgal-HO HEM13::HOsite-URA3 pif1-m2-TRP1-pif1-m1


title: PDX4_AML_shMFN2

description: PDX4_shMFN2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: M-2428_SK014_G34R_10W_crx_H3K27me3


title: PDX4_AML_shCTL

description: PDX4_shCTL_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX3_AML_shMFN2

description: PDX3_shMFN2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX3_AML_shCTL

description: PDX3_shCTL_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX5_OE_EMPTY

description: PDX5_EMPTY_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Light-rep2


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Light-rep1


title: PDX5_OE_MFN2

description: PDX5_MFN2OE_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: M-1998_CC431_WT_P7_crx_H3K36me3


title: 1325_RAF_IP

description:
indexes used for this sample - R2 (TCTCCGGA) and F2 (ATAGAGGC)
1325_induced_uninduced_ratio.bigwig

treatment_protocol:
Cells at exponential phase were pre-grown in YP + raffinose to OD600=0.4. More raffinose was then added to the final concentration of 4% (HO-mediated break not induced) and cells were incubated at 30°C for another 2 hours.
cells were crosslinked with 1.4% of formaldehyde at 30°C in a shaking water bath for 10 minutes. Crosslinking was stopped by adding glycine to the final concentration of 0.25 M and incubating the cultures for 5 minutes. 200 OD600 units were harvested for ChIP-seq for each sample.

value: not induced


title: M-1998_CC435_WT_P7_crx_Input

value: Input


title: 1325_GAL_input

description:
indexes used for this sample - R3 (AATGAGCG) and F2 (ATAGAGGC)
1325_induced_uninduced_ratio.bigwig

value: yeast cell


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Dark_combined


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Light_rep3


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Dark-rep2


title: M-1998_CC429_WT_P7_crx_H3K27ac


title: M-1998_CC430_WT_P7_crx_H3K27me3


title: CAPTURE-3C-seq_BRD4LAMPS-HS2-Dark-rep1


title: SK-MEL-147 Cells S-4879 (Replicate_3)

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: SK-MEL-147 Cells

growth_protocol: A375MA2 Cells  were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin and SK-MEL-147 Cells  were grown in RPMI-1640 medium with 10% Fetal bovine serum and Penicillin  at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375MA2 cells and SK-MEL-147 Cells used for preparing the total RNA and to perfrom gene expression array.

tag: genotype/variation

value: G3BP1 shRNA#2 Expressing cells

tag: sample type

value: Cell line


title: M-1964_SK052_WT_P7_crx_H3K36me2


title: PDX4_OE_MFN2

description: PDX4_MFN2OE_(Clariom_S_Human).sst-rma-gene-full.chp Signal

value: patient with AML


title: M-1815_SK049_G34R_P7_crx_H3K36me2


title: Spt7 degron, plus auxin, total RNA replicate 2

city: Seattle

first: Jeremy

middle: Aspin

last: Schofield

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
Paired-end reads were aligned to the yeast genome (SacCer3) using bowtie2 (--local).
Aligned reads were processed from .sam to sorted and duplicate removed .bam files (view, fixmate, sort, and markdup) using Samtools.
Per-gene counts were determined using HTSeq and a standard gene feature reference file (SacCer3 RefSeq GTF from NCBI).
Assembly: SacCer3
Supplementary files format and content: Tables (.txt files) of read counts for yeast genes

source_name: Spt7-degron (SHY1045)

growth_protocol: UAS-core plasmid libraries were transformed into yeast using the LiOAC method. Yeast cultures were grown for several days with occasional dilution in synthetic complete (SC) media -Ura at 30degC to select for positive transformants. On the day of treatment, yeast cultures were grown to mid log phase (~0.8).

extract_protocol: Total RNA was isolated using a RiboPure RNA Purification Kit (Thermo Fisher).

treatment_protocol: Yeast cultures were treated with 500uM auxin (or DMSO alone for negative controls) for 30 minutes to degrade coactivators. Samples for RNA-seq were pelleted, snap frozen and stored at -80degC until processing.

tag: treatment

value: 30 min auxin (500uM)


title: Spt7 degron, no auxin, total RNA replicate 1

value: 30 min DMSO


title: PDX4_OE_EMPTY

description: PDX4_EMPTY_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX3_OE_MFN2

description: PDX3_MFN2OE_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX3_OE_EMPTY

description: PDX3_EMPTY_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: SK-MEL-147 Cells S-4879 (Replicate_2)


title: PDX1_OE_MFN2

description: PDX1_MFN2OE_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: PDX1_OE_EMPTY

description: PDX1_EMPTY_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: M-1815_CC433_G34R_P7_crx_Input


title: AML cells_shMFN2_72h_rep3 [OCI-AML2 shMFN2 3]

description: OCI-AML2_shMFN2_3_(Clariom_S_Human).sst-rma-gene-full.chp Signal

source_name: AML cell line incubated with doxycycline for 72h

treatment_protocol: Doxycycline was used at 1µg/mL

tag: cell line

value: leukemia cell line


title: Med15 degron, plus auxin, total RNA replicate 2

source_name: Med15-degron (SHY1055)


title: SK-MEL-147 Cells S-4879 (Replicate_1)


title: Med15 degron, plus auxin, total RNA replicate 1


title: 1325_RAF_input

description:
indexes used for this sample - R1 (CGAGTAAT) and F2 (ATAGAGGC)
1325_induced_uninduced_ratio.bigwig


title: M-1815_CC425_G34R_P7_crx_H3K36me3


title: Spt7 degron, plus auxin, total RNA replicate 1


title: SK-MEL-147 Cells S-2539 (Replicate_2)

value: G3BP1 shRNA#1 Expressing cells


title: Med15 degron, no auxin, total RNA replicate 2


title: SK-MEL-147 Cells S-2539 (Replicate_3)


title: M-1815_CC420_G34R_P7_crx_H3K27ac

value: Cortex


title: Spt7 degron, no auxin, total RNA replicate 2


title: M-1815_CC424_G34R_P7_crx_H3K27me3

value: 7 days


title: Taf13 degron, plus auxin, nascent RNA replicate 4

description: Nascent RNA (targeted)

data_processing:
Consensus sequence counts were determined by clustering read 1 RNA library sequences using VSEARCH with 99% similarity.
Assembly: NA
Supplementary files format and content: Table. Column 1 "size" = number of sequence reads in cluster. Column 2 = consensus cluster sequence.

source_name: Taf13-degron (SHY1043)

extract_protocol:
Total RNA was isolated using a RiboPure RNA Purification Kit (Thermo Fisher). Kit buffers were supplemented with 10mM BME. Nascent RNAs were purified using MTS-biotin and streptavidin beads as described in Duffy et al. 2015.
Nascent RNA barcodes were reverse transcribed with a reporter-specific primer. PCR1 was performed with primers complementary to the RT product and containing overhanging regions for multiplexing PCR. qPCR was used to determine the number of amplification cycles for PCR2. PCR2 was perfomed using unique dual indexes.

treatment_protocol: Yeast cultures were treated with 500uM auxin (or DMSO alone for negative controls) for 30 minutes to degrade coactivators. Yeast cultures were then treated with 5mM 4-thiouracil (4-TU) to label nascent RNAs. Samples for RNA-seq were pelleted, snap frozen and stored at -80degC until processing. Samples for DNA-seq were collected immediately prior to auxin/DMSO treatment.

value: Taf13-degron (SHY1043)

value: S. cerevisiae

value: 30 min auxin (500uM), 5 min 4-thiouracil (5mM)


title: SK-MEL-147 Cells S-2539 (Replicate_1)


title: SK-MEL-147 Cells TRC-NS (Replicate_3)

value: Non-silencing shRNA Expressing cells


title: M-1791_SK069_WT_P7_crx_DNMT3A


title: M-1790_SK068_G34R_P7_crx_DNMT3A


title: AML cells_shMFN2_72h_rep2 [OCI-AML2 shMFN2 2]

description: OCI-AML2_shMFN2_2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: Taf13 degron, plus auxin, nascent RNA replicate 3

description: Nascent RNA (targeted)


title: SK-MEL-147 CellsTRC-NS (Replicate_2)


title: Taf13 degron, no auxin, nascent RNA replicate 4

description: Nascent RNA (targeted)

value: 30 min DMSO, 5 min 4-thiouracil (5mM)


title: M-1752_SK048_WT_P7_crx_H3K36me2


title: AML cells_shCTL_72h_rep3 [OCI-AML2 shCTL 3]

description: OCI-AML2_shCTRL3_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: AML cells_shCTL_72h_rep2 [OCI-AML2 shCTL 2]

description: OCI-AML2_shCTRL2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: SK-MEL-147 Cells TRC-NS (Replicate_1)


title: AML cells_shMFN2_72h_rep1 [OCI-AML2 shMFN2 1]

description: OCI-AML2_shMFN2_1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: A375MA2 Cells S-4879 (Replicate_3)

source_name: A375MA2 Cells


title: Taf13 degron, no auxin, nascent RNA replicate 3

description: Nascent RNA (targeted)


title: Spt7 degron, plus auxin, nascent RNA replicate 4

description: Nascent RNA (targeted)

value: Spt7-degron (SHY1045)


title: AML cells_shMFN2_72h_rep2 [MOLM-14 shMFN2 2]

description: MOLM14_shMFN2_2(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: AML cells_shMFN2_72h_rep3 [MOLM-14 shMFN2 3]

description: MOLM14_shMFN2_3(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: Spt7 degron, plus auxin, nascent RNA replicate 3

description: Nascent RNA (targeted)


title: M-1752_CC409_WT_P7_crx_H3K27ac


title: M-1751_CC412_G34R_P7_crx_H3K36me3


title: M-1751_SK047_G34R_P7_crx_H3K36me2


title: A375MA2 Cells S-4879 (Replicate_2)


title: A375MA2 Cells S-4879 (Replicate_1)


title: Med15 degron, no auxin, total RNA replicate 1


title: AML cells_shMFN2_72h_rep1 [MOLM-14 shMFN2 1 ]

description: MOLM14_shMFN2_1(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: Spt7 degron, no auxin, nascent RNA replicate 4

description: Nascent RNA (targeted)


title: A375MA2 Cells S-2539 (Replicate_3)


title: A375MA2 Cells S-2539 (Replicate_2)


title: Spt7 degron, no auxin, nascent RNA replicate 3

description: Nascent RNA (targeted)


title: AML cells_shCTL_72h_rep1 [OCI-AML2 shCTL 1]

description: OCI-AML2_shCTRL1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: AML cells_shCTL_72h_rep2 [MOLM-14 shCTL 2]

description: MOLM14_shCTRL2_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: M-2617_SK061_G34R_10W_crx_WGBS

data_processing:
WGBS datasets were processed using the methylseq module of GenPipes v3.1.2 (Bourgey et al., 2019).
Briefly, raw reads were trimmed using Trimmomatic v0.32 (Bolger et al., 2014) to remove adaptor and sequencing-primer associated reads, then aligned to bisulfite-converted mm10 genome using Bismark v0.18.11 (Krueger and Andrews, 2011) with default parameters.
PCR duplicate reads as defined by reads with identical mapping coordinates were then collapsed by Picard v2.0.1 to produce uniquely aligned reads.
Methylation status is then called using Bismark v0.18.11 at CpG and CHH genomic contexts to generate visualization tracks.
Assembly: mm10
Supplementary files format and content: *mCG.methylation.bw, bigWig files, methylation % at individual CG sites
Supplementary files format and content: *mCG.coverage.bw, bigWig files, read depth coverage at individual CG sites
Supplementary files format and content: *mCHH.methylation.bw, bigWig files, methylation % at individual non-CG sites
Supplementary files format and content: *mCHH.coverage.bw, bigWig files, read depth coverage at individual non-CG sites

source_name: Mouse cortex

extract_protocol:
Whole-genome sequencing libraries were generated from 700 to 1000 ng of genomic DNA spiked with 0.1% (w/w) unmethylated λ DNA (Promega) previously fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent).
The KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied. End repair of the generated dsDNA with 3′ or 5′ overhangs, adenylation of 3′ ends, adaptor ligation, and clean-up steps were carried out as per KAPA Biosystems’ recommendations. The cleaned-up ligation product was then analyzed on a Bioanalyzer High Sensitivity DNA Chip (Agilent) and quantified by PicoGreen (Life Technologies). Samples were then bisulfite converted using the Epitect Fast DNA Bisulfite Kit (Qiagen) according to the manufacturer’s protocol. Bisulfite-converted DNA was quantified using OliGreen (Life Technologies) and, based on quantity, amplified by 9–12 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems) according to the manufacturer’s protocol. The amplified libraries were purified using Ampure XP Beads (Beckman Coulter), validated on Bioanalyzer High Sensitivity DNA Chips, and quantified by PicoGreen.

value: 10 weeks


title: AML cells_shCTL_72h_rep1 [MOLM-14 shCTL 1 ]

description: MOLM14_shCTRL1_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: M-2616_SK060_WT_10W_crx_WGBS


title: AML cells_shCTL_72h_rep3 [MOLM-14 shCTL 3]

description: MOLM14_shCTRL3_(Clariom_S_Human).sst-rma-gene-full.chp Signal


title: Med15 degron, plus auxin, nascent RNA replicate 3

description: Nascent RNA (targeted)

value: Med15-degron (SHY1055)


title: M-2428_SK062_G34R_10W_crx_WGBS


title: A375MA2 Cells TRC-NS (Replicate_3)


title: M-2427_SK059_WT_10W_crx_WGBS


title: A375MA2 Cells S-2539 (Replicate_1)


title: Med15 degron, plus auxin, nascent RNA replicate 4

description: Nascent RNA (targeted)


title: M-1751_CC408_G34R_P7_crx_H3K27ac


title: A375MA2 Cells TRC-NS (Replicate_2)


title: A375MA2 Cells TRC-NS (Replicate_1)


title: WM266-4SCG2 OE, biological rep2

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

description: Gene expression data from melanoma cells overexpressing SCG2 vector

hyb_protocol: (according to user manual Applied Biosystems™ WT PLUS Reagent Kit) 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Applied Biosystems™ human Clariom™ S Array.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore.

source_name: melanoma cell lines

label_protocol: The Applied Biosystems™ WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA.

growth_protocol: Melanoma cells were cultured in DMEM medium containing 10% heat-inactivated fetal calf serum, 0.1 mM β-mercaptoethanol, 1% non-essential amino acids, and 1% penicillin/streptomycin. Cells were stored in a humidified incubator at 37°C and 5% CO2.

extract_protocol: Total RNA was isolated from cultured cells using the RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.

treatment_protocol: Melanoma cells were transfected with a control vector (EV) or a SCG2 vector (SCG2 OE)

value: melanoma cell line WM266-4

value: overexpressing SCG2 vector


title: WM266-4 SCG2 OE, biological rep3


title: M-3295_G34W_10W_crx_RNA

data_processing:
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Bedgraph files were generated with bedtools 2.27.1 genomeCoverageBed function using a normalization factor of number of mapping read/100,000,000. Then bedGraphtoBigWig was used to convert the bedgraph files to bigwig.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4  and the mm10 ensGene annotation set from Ensembl.
Assembly: mm10
Supplementary files format and content: bigWig files generated with bedtools 2.27.1, read coverage for each sample over the mouse genome
Supplementary files format and content: mm10.Ensembl.raw_counts.tsv, tab-separated values file, raw counts of all the RNA-seq samples.

extract_protocol:
Total RNA was extracted from pulverized tissue using the Aurum Total RNA Mini Kit (Bio-Rad) according to manufacturer’s instructions.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre).

value: Female

tag: gentoype


title: WM266-4 SCG2 OE, biological rep1


title: Med15 degron, no auxin, nascent RNA replicate 3

description: Nascent RNA (targeted)


title: M-3294_G34W_10W_crx_RNA

value: Male


title: M-3293_WT_10W_crx_RNA


title: Taf13 degron, plus auxin, nascent RNA replicate 1

description: Nascent RNA (targeted)


title: Taf13 degron, plus auxin, nascent RNA replicate 2

description: Nascent RNA (targeted)


title: CAPTURE-ChIP-seq_LAMPS_dCas9-HS2-INPUT_rep2

description: ChIP DNA

data_processing:
Raw reads were aligned to human (hg38)  genome assembly using Bowtie2  with -k 1.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The bigwig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file, peak bed file

growth_protocol: HeLa cells were cultured in DMEM medium containing 10% FBS.

extract_protocol: 10-20 ng of ChIP DNA was processed for library generation using the NEBNext Ultra II DNA Library prep kit following the manufacturer’s protocol (New England Biolabs).

treatment_protocol: Cells were exposed to blue light (488nM) for 5 min to induce light-activated phase separation

value: Human HeLa cells

tag: streptavidin dynabeads

value: ThermoFisher 65602


title: CAPTURE-ChIP-seq_LAMPS_dCas9-HS2-INPUT_rep1

description: ChIP DNA


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-NosgRNA-Light_rep2

description: ChIP DNA


title: Taf13 degron, no auxin, nascent RNA replicate 2

description: Nascent RNA (targeted)


title: M-2618_G34R_10W_crx_RNA


title: Taf13 degron, no auxin, nascent RNA replicate 1

description: Nascent RNA (targeted)


title: M-3292_WT_10W_crx_RNA


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-NosgRNA-Light_rep1

description: ChIP DNA


title: Med15 degron, no auxin, nascent RNA replicate 4

description: Nascent RNA (targeted)


title: Spt7 degron, plus auxin, nascent RNA replicate 2

description: Nascent RNA (targeted)


title: M-2616_WT_10W_crx_RNA


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-NosgRNA-Dark_rep2

description: ChIP DNA


title: Spt7 degron, plus auxin, nascent RNA replicate 1

description: Nascent RNA (targeted)


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-NosgRNA-Dark_rep1

description: ChIP DNA


title: Spt7 degron, no auxin, nascent RNA replicate 2

description: Nascent RNA (targeted)


title: M-2499_G34V_10W_crx_RNA


title: MSC_H3K27ac

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using bwa v.0.7.12 with default settings.
Duplicate reads were removed using picard-tools v.1.95. Aligned reads were extended to 150 bp to approximate fragment sizes
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bedtools; scores show fragments normalized to 10M mapped fragments.

source_name: Primary Mesenchymal stem cells

growth_protocol: Primary pediatric mesenchymal stem cells were cultured in Iscove’s modified Dulbecco’s medium containing 10% fetal calf serum (FCS) and 10 ng/ml platelet-derived growth factor. shRNA mediated knock-down was used to remove EWS-FLI1 protien  from ewing cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the H3K27ac (abcam#39133) antibody using standard protocol.
Precipitated DNA samples were used to prepare sequencing libraries with  TruSeq ChIP Library Kit  (illumina, IP-202-1012), and DNA samples were sequenced with the Nextseq 500 Illumina genome analyzer.

treatment_protocol: untreated

value: mesenchymal stem cells

value: untreated

value: H3k27ac, abcam39133


title: Spt7 degron, no auxin, nascent RNA replicate 1

description: Nascent RNA (targeted)


title: WM266-4 control, biological rep3

description: Gene expression data from melanoma cells expressing empty vector (control)

value: expressing empty vector (control)


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-HS2-Light_rep2

description: ChIP DNA


title: M-2617_G34R_10W_crx_RNA

value: Cortex


title: M-2498_WT_10W_crx_RNA-1


title: RNA-seq, vel3, 24HAI, R2

city: Norwich

first: Xiaochao

last: Chen

address: Norwich Research Park, Colney Ln

department: Crop Genetics

institute: John Innes Centre

description:
24HAI_endosperm_TPM
vel3_R2

data_processing:
For RNA-seq, raw reads were trimmed using cutadapt-1.9.1 (Martin, 2011) and mapped to Arabidopsis thaliana TAIR10 reference genome using STAR-2.5.a (Dobin et al., 2013). featureCounts (Liao et al., 2014) was used to count the numbers of reads mapped to each gene. Sense reads were selected for downstream analysis. edgeR (Robinson et al., 2010) was used to calculate differentially expressed genes (DEGs), based on the threshold of FDR<0.05 and fold change≥2. For data visualization, bigwig files were generated using deepTools-3.1.1 (Ramírez et al., 2016) with a bin size of 50bp, before visualization in IGV -2.12.3 (Robinson et al., 2011).     For ChIP-seq, raw reads were trimmed using cutadapt-1.9.1 (Martin, 2011) and mapped to Arabidopsis thaliana TAIR10 reference genome using bowtie2 (Langmead et al., 2018). Only uniquely mapped reads were kept for downstream analysis using Samtools-1.9 and Sambamba-6.7 (Li et al., 2009; Tarasov et al., 2015). For data visualization, bigwig files were calculated using deepTools-3.1.1(Ramírez et al., 2016) with a bin size of 50bp, before visualization in IGV -2.12.3 (Robinson et al., 2011). Peaks were called using SICER 1.1 for H3K27me3 (Zhang et al., 2009) or MACS2 for VEL3 (Zhang et al., 2008), based on the threshold of FDR<0.05. Only common peaks between two biological replicates were considered.  Different H3K27me3 peaks between Col0 and vel3 were calculated using DiffBind (Ross-Innes et al.,2012) and DESeq2 (Love et al., 2014), based on the threshold of FDR<0.05 and fold change≥2. Genes were identified for these peaks are located in genebody or 1kb promoter using bedtools-2.28.0 (Quinlan & Hall, 2010).
Supplementary files format and content: For RNA-seq, csv files with TPM are provided. For ChIP-seq, bigwig files are provided

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: water-imbibed endosperm

extract_protocol:
RNA of endosperm and seeds were extracted using Qiagen RNeasy Plant Mini Kit
Libraries of RNA-seq and H3K27me3 ChIP-seq were construed by Novogene (China) and BGI (China) respectively.  For libraries of VEL3 ChIP-seq, Tn5 tagmentation was performed on 1ng ChIP-ed DNA or input DNA for 5 min at 55°C, with 0.1ul enzyme and 2.5ul buffer in 5ul reaction (Illumina, 20034197). PCR amplification was conducted using the following programs: 72°C  5min, 98°C 30s, N cycles of 98°C 10s, 63°C 30s and 72°C 1min. cycle number (N) was determined by the qpcr of each partially-amplified library. 0.8X Agencourt AMPure XP beads (Beckman Coulter, A63880) was used for the library size selection. Libraries were sequenced at Novogene (Beijing, China) using a Novaseq system, 150-bp paired-end sequences with a minimum of 30 million reads acquired per sample.

value: water-imbibed endosperm


title: M-2493_G34V_10W_crx_RNA


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-HS2-Dark_rep1

description: ChIP DNA


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-HS2-Dark_rep2

description: ChIP DNA


title: CAPTURE-ChIP-seq_BRD4LAMPS-dCas9-HS2-Light_rep1

description: ChIP DNA


title: RNA-seq, vel3, 24HAI, R1

description:
24HAI_endosperm_TPM
vel3_R1


title: M-2498_WT_10W_crx_RNA-2


title: Med15 degron, no auxin, nascent RNA replicate 2

description: Nascent RNA (targeted)

value: S. cerevisiae


title: Med15 degron, plus auxin, nascent RNA replicate 1

description: Nascent RNA (targeted)

value: 30 min auxin (500uM), 5 min 4-thiouracil (5mM)


title: M-2492_WT_10W_crx_RNA


title: RNA-seq, Col0, 24HAI, R3

description:
24HAI_endosperm_TPM
Col0_R3

value: wildtype


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-NosgRNA-Light_rep2

description: ChIP DNA


title: Med15 degron, plus auxin, nascent RNA replicate 2

description: Nascent RNA (targeted)


title: RNA-seq, Col0, 24HAI, R2

description:
24HAI_endosperm_TPM
Col0_R2


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-NosgRNA-Light_rep1

description: ChIP DNA


title: M-2494_G34V_10W_crx_RNA

value: 10 weeks


title: WM266-4 control, biological rep1


title: RNA-seq, vel3, 24HAI, R3

description:
24HAI_endosperm_TPM
vel3_R3


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-NosgRNA-Dark_rep2

description: ChIP DNA


title: Med15 degron, no auxin, nascent RNA replicate 1

description: Nascent RNA (targeted)

value: Med15-degron (SHY1055)

value: 30 min DMSO, 5 min 4-thiouracil (5mM)


title: RNA-seq, vel3, mature, R3

description:
mature_endosperm_TPM
vel3_R8

source_name: mature endosperm

value: mature endosperm


title: miR-501KO mouse 5

city: Zurich

first: Alexandra

last: Fahrner

address: Rämistrasse 100

department: Division of Endocrinology, Diabetes and Clinical Nutrition

country: Switzerland

institute: University Hospital Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the gene annotation as provided by ENCODE release 91.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
R version 3.5.1
Assembly: Mus_musculus/Ensembl/GRCm38.p5/Annotation/Release_91-2018-02-26
Supplementary files format and content: text files include identifiers and raw counts

source_name: Tibialis anterior

growth_protocol: 12 week old male mice were used for experimentation

extract_protocol:
TA muscles were removed, snap frozen, and RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer´s instruction.
Illumina TruSeq Stranded mRNA Library Prep kit (Cat# 20020594) was used with 500 ng of total RNA for the construction of sequencing libraries. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: Intramuscular injection of Cardiotoxin into Tibialis Anterior, RNA extraction at day 6 of regeneration

value: male

value: 12 weeks

value: cardiotoxin-induced muscle regeneration

tag: time point

value: day 6

value: Tibialis anterior


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-NosgRNA-Dark_rep1

description: ChIP DNA

value: Human HeLa cells

value: ThermoFisher 65602


title: M-2427_WT_10W_crx_RNA

value: Male


title: M-2428_G34R_10W_crx_RNA

value: Cortex


title: miR-501KO mouse 4


title: miR-501KO mouse 3


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-HS2-Light_rep2

description: ChIP DNA


title: RNA-seq, vel3, mature, R2

description:
mature_endosperm_TPM
vel3_R7


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-HS2-Light_rep1

description: ChIP DNA


title: RNA-seq, Col0, 24HAI, R1

description:
24HAI_endosperm_TPM
Col0_R1

value: water-imbibed endosperm


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-HS2-Dark_rep2

description: ChIP DNA


title: miR-501KO mouse 2


title: CAPTURE-ChIP-seq_FUSNLAMPS-dCas9-HS2-Dark_rep1

description: ChIP DNA


title: RNA-seq, vel3, mature, R1

description:
mature_endosperm_TPM
vel3_R6


title: RNA-seq, Col0, mature, R3

description:
mature_endosperm_TPM
Col0_R10


title: miR-501KO mouse 1


title: Pax7Cre mouse 5

value: wild type


title: ATAC-seq_FUSNLAMPS-HS2-Light_rep1

data_processing:
Sequencing reads were aligned to human genome assembly hg38 using Bowtie v1.0.0 with the following parameters: --best --strata -k 1 -m 1. Duplicate reads were removed after the aligment with the Picard command-line tools.
The bigwig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ATAC-seq data generated by NextSeq500.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file

source_name: HeLa

extract_protocol: ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human genome (hg38) were retained for downstream data analysis.

treatment_protocol: Cells were exposed with blue light (488nM) for 5 min to induce light-activated phase separation


title: RNA-seq, Col0, mature, R1

description:
mature_endosperm_TPM
Col0_R3


title: Pax7Cre mouse 4


title: RNA-seq, vel3, globular, R3

description:
globular_seeds_TPM
vel3D8R3

source_name: seeds

value: seeds


title: RNA-seq, vel3, globular, R2

description:
globular_seeds_TPM
vel3D8R2


title: ATAC-seq_FUSNLAMPS-HS2-Dark_rep2


title: ATAC-seq_FUSNLAMPS-HS2-Dark_rep1


title: Pax7Cre mouse 3


title: RNA-seq, Col0, mature, R2

description:
mature_endosperm_TPM
Col0_R9

value: wildtype


title: Pax7Cre mouse 2


title: C32 control, biological rep1

value: melanoma cell line C32

value: expressing empty vector (control)


title: RNA-seq, vel3, globular, R1

description:
globular_seeds_TPM
vel3D8R1


title: C32 SCG2 OE, biological rep3

value: overexpressing SCG2 vector


title: WM266-4 control, biological rep2

value: melanoma cell line WM266-4


title: ATAC-seq_FUSNLAMPS-HS2-Light_rep2


title: C32 SCG2 OE, biological rep2


title: RNA-seq, Col0, globular, R3

description:
globular_seeds_TPM
Col0D8R3


title: Pax7Cre mouse 1

value: male


title: Spt7 degron, plasmid library replicate 1

description: Plasmid DNA (targeted)

data_processing:
Read pairs were joined into amplicons.
Consensus sequence counts were determined by clustering all DNA library sequences using VSEARCH with 97% similarity.
Assembly: NA
Supplementary files format and content: Table. Column 1 "size" = number of sequence reads in cluster. Column 2 = consensus cluster sequence.

extract_protocol:
Plasmid libraries were isolated from yeast transformants using a modified Mini Prep (Qiagen) protocol. Briefly, sample pellets were resuspended in buffer P1, added to tubes containing ~100ul silica beads, and physically lysed using a bead beater. The lysate was transferred to a fresh tube and the remainder of the Mini Prep protocol was followed.
PCR1 was performed with primers complementary to the reporter plasmid library and containing overhanging regions for multiplexing PCR. qPCR was used to determine the number of amplification cycles for PCR2. PCR2 was perfomed using unique dual indexes.

value: Spt7-degron (SHY1045)

value: S. cerevisiae


title: Taf13 degron, plasmid library replicate 1

description: Plasmid DNA (targeted)

value: Taf13-degron (SHY1043)


title: Taf13 degron, plasmid library replicate 4

description: Plasmid DNA (targeted)


title: Med15 degron, plasmid library replicate 2

description: Plasmid DNA (targeted)

value: Med15-degron (SHY1055)


title: Taf13 degron, plasmid library replicate 2

description: Plasmid DNA (targeted)


title: Taf13 degron, plasmid library replicate 3

description: Plasmid DNA (targeted)


title: Med15 degron, plasmid library replicate 3

description: Plasmid DNA (targeted)


title: Spt7 degron, plasmid library replicate 2

description: Plasmid DNA (targeted)


title: Med15 degron, plasmid library replicate 4

description: Plasmid DNA (targeted)


title: Spt7 degron, plasmid library replicate 4

description: Plasmid DNA (targeted)


title: Spt7 degron, plasmid library replicate 3

description: Plasmid DNA (targeted)


title: C32 control, biological rep3


title: Med15 degron, plasmid library replicate 1

description: Plasmid DNA (targeted)


title: Pre-selection DP thymocytes (Live Lin- CD4+ CD8+ CD3-), Eα(ΔE1ΔE3/ΔE1ΔE3)

city: Durham

first: Ariana

last: Mihai

state: North Carolina

address: 207 Research Dr

institute: Duke University School of Medicine

description: (300 x 300 bp)

data_processing:
Base calling performed by Miseq software from Illumina.
Migec v1.2.9 Migec v1.2.9 was used to perform: (1) demultiplexing of raw fastq files (function: Checkout; parameters: -cute); (2) assessment of molecular identifier group (MIG) size distribution (function: Histogram; parameters: default); (3) collapse of UMIs and filtering (function: AssembleBatch; parameters: -force-collision-filter –force-overseq 5).was used to perform: (1) demultiplexing of raw fastq files (function: Checkout; parameters: -cute); (2) assessment of molecular identifier group (MIG) size distribution (function: Histogram; parameters: default); (3) collapse of UMIs and filtering (function: AssembleBatch; parameters: -force-collision-filter –force-overseq 5).
Collapsed reads were merged using MiTools v1.5 (function: merge; parameters: -I –s 0.7).
MiXCR v3.0.13 was used to perform: (1) read alignment (function: align; parameters: -s mmu –OvParameters.geneFeatureToAlign=VTranscript); (2) assemble clonotypes (function: assemble; parameters: -OassemblingFeatures=[CDR2+FR3+CDR3] –OclusteringFilter.specificMutationProbability=1E-4); (3) clones export (function: exportClones; parameters: default).
VDJTools v1.2.1 was used to convert files (function: Convert; parameters: default). Converted files were used to determine Ja segment usage VDJTools v1.2.1 (function: CalcSegmentUsage; parameters: -u).
Assembly: Default reference sequence of MiXCR v3.0.13 was used.
Supplementary files format and content: Tab delimited text (.txt) file of the frequency at which each Jα segment is represented in the respective sample. (file name: SegmentUsage_U.segments.unwt.J.txt)
Supplementary files format and content: Tab delimited text (.txt) file of sample barcodes for demultiplexing. (file name: barcodes-1.txt)

source_name: Thymus

growth_protocol: Total thymocytes were harvested from 3-4 week-old mice.

extract_protocol:
Sorted cells were resuspended in TRIzol (Invitrogen). RNA was purified using Direct-Zol RNA Microprep (Zymo Research) kit with on-column DNase digestion.
Protocol is adapted from Mamedov et al. (2013) and Turchaninova et al. (2016). Tcra transcripts were amplified by 5’ rapid amplification of cDNA ends. 5 ng of total RNA was reverse transcribed using template switch oligo and Trac specific primer. cDNA was amplified, dual-indexing of amplified cDNA was performed, indexed samples were pooled at equal concentration and final library preparation carried out using NEBNext Ultra II DNA library preparation kit (NEB). Sequencing performed on MiSeq sequencer (Illumina) (300 x 300 bp).

treatment_protocol: Isolation of preselection thymocytes: sorting (FACS) was performed using an Astrios (Beckman-Coulter) cell sorter. Sample staining included a lineage dump (B220, CD11b, CD11c, CD19, GR-1, TER119, F4/80, and TCRd antibodies). Sample was sorted as Live Lin-CD4+ D8+ D3-.

tag: mouse strain

value: mixed C57BL/6 and SJL/J strain background

value: Thymus

value: Not applicable

value: 3-4 weeks


title: RNA-seq, Col0, globular, R2

description:
globular_seeds_TPM
Col0D8R2

tag: genotype


title: SuRE49, transfection in K562, rep1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2500, or Illumina HiSeq-X10.
For polyA-RNA samples the barcode sequence was extracted from the read (using cutadapt and custom scripts) and counted.
For gDNA samples the barcode and the gDNA was extracted from the paired-end reads (using cutadapt and custom scripts). gDNA was then aligned to the reference genome (using bowtie2). Barcodes were then associated with genomic regions.
gDNA barcode, locations and counts were associated with polyA-RNA counts using barcode
counts for barcodes with same start and end location were summed up
Assembly: hg19
Supplementary files format and content: Tabular text file containing location on hg19, gDNA counts, and polyA-RNA counts for 2 biological replicates

growth_protocol: K562 (ATCC® CCL-243™) and HepG2 ((#HB 8065; ATCC) were cultured according to supplier's protocol.

extract_protocol:
To find out which barcodes were associated with which genomic fragments, we digested 4 µg SuRE library with I-CeuI (#R0699S; NEB), followed by magnetic bead purification (1:1 ratio beads:DNA solution). Of this, 2 µg was self-ligated overnight at 16 °C in a total volume of 2 ml (#10799009001 Roche), and purified using phenol-chloroform extraction and isopropanol precipitation. This material was treated with 25 units of Plasmid-Safe™ ATP-Dependent DNase for 1 hour and purified again with phenol-chloroform and isopropanol precipitation. To facilitate PCR, the resulting mini-circles were linearized by digesting with I-SceI (#R0694S; NEB) in a volume of 25 µl. Finally, 8 cycles of PCR (1¢ at 98°C, 10x(15¢ at 98°,15¢ at 60°, 20¢ at 72°)) with KAPA high-fidelity DNA Polymerase (#KE2502; KAPA biosystems) were performed on 1/10th of the I-SceI digested material using primers 151AR (containing the S1 and p5 adapter) and (index variants of) 117JvA (containing the S2, index and p7 adapter). The PCR product was bead purified and subjected to high-throughput paired-end sequencing on the Illumina HiseqX10 platform.
PolyA RNA was divided into 10 µl reactions containing 500 ng RNA and DNase treated with 10 units for 30 minutes (#04716728001; Roche) and DNAse was inactivated by addition of 1µl of 25mM EDTA and incubation at 70ºC for 10 minutes. Next, cDNA was produced by first adding 1 µl of 10 mM gene specific primer targeting the GFP ORF (247JvA) and 1 µl dNTP (10mM each) and incubating for 5 minutes at 65°C. Then 4 µl of RT buffer, 20 units RNAse inhibitor (#EO0381; ThermoFisher Scientific), 200 units of Maxima reverse transcriptase (#EP0743; ThermoFisher Scientific) and 2.5 µl water was added and the reaction was incubated for 30 minutes at 50°C followed by heat-inactivation at 85° for 5 minutes. Per biological replicate, 20-30 reactions were done in parallel. Each 20 µl reaction was then PCR amplified (1’ 96 °C, 20x(15’’ 96 °C, 15’’ 60 °C, 15’’ 72 °C)) in a 100 µl reaction with MyTaq™ Red Mix and primers 151AR (containing the S1 and p5 adapter) and (index variants of) 211JvA (containing the S2, index and p7 adapter) for 21 cycles. Reactions were then pooled and 500 µl was purified using CleanPCR beads (#CPCR-0050; GC biotech) and subjected to single read 50 bp high throughput sequencing on an Illumina HiSeq2000 or HiSeq2500.

value: Erythroleukemia

value: K562 cells transfected with SuRE49 library

value: transfected with SuRE49 library


title: SuRE49, transfection in K562, rep2


title: Smad3-KO neutrophils

city: New Territories

first: Patrick Ming-Kuen

last: Tang

address: Cancer center, Prince of Wales Hospital,30-32 Ngan Shing Street, Shatin

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Sequencing data were cleaned and processed using 10x CellRanger pipeline
Genome_build: mm10
Supplementary_files_format_and_content: csv files include normalized values for each sample and feature for clustering.  CellRanger output files (in barcodes.tsv.gz, BC-1 corresponds to Smad3-KO neutrophils, BC-2 corresponds to Smad3-WT neutrophils)

source_name: LLC-transplanted tumor

extract_protocol:
CD11b+Ly6G TANs were FACS-sorted from the single-cell digestion of s.c LLC tumor inoculated in C57BL6 (wild-type) and Smad3-deficient (Smad3-/- ) mice and submitted for cell encapsulation and library construction by Chromium controller with 5’ expression kit (10x genomics).
Single-cell sequencing RNA libraries were prepared for sequencing using standard 10x Genomics single-cell droplet generation protocols and next-generation sequencing Illumina protocols
10x single-cell RNA-Seq

tag: strain

value: LLC-transplanted tumor

value: neutrophils

value: 8-12 weeks

value: Smad3-deficient (Smad3-/-)


title: C32 control, biological rep2

value: melanoma cell line C32

value: expressing empty vector (control)


title: Smad3-WT neutrophils

tag: cell type

value: Smad3-wildtype (Smad3+/+)


title: RNA-seq, Col0, globular, R1

description:
globular_seeds_TPM
Col0D8R1

value: seeds

value: wildtype


title: protonema, wt_rep3

city: Tel Aviv

first: Ofir

last: Griess

address: Haim Levanon 31

department: Plant Sciences and Food Security

country: Israel

institute: Tel Aviv University

data_processing:
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Assembly: Ppatens v3.0 (Phypa V3 https://www.ncbi.nlm.nih.gov/assembly/GCF_000002425.4)
Supplementary files format and content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample.  The accession numbers are according to the latest P. patens genome assembly - with accessions such as Pp1c.. being genes, and numbers such as 986... being transposable elements.  These accessions can be found in the plant database, Phytozome for this assembly of P. patens.

organism: Physcomitrium patens

source_name: protonema

growth_protocol: 7 days on BCDAT media, 25 °C,  16-h light and 8-h dark regime

extract_protocol:
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).

value: protonema

value: Grandsen

value: wt

value: 7 days

tag: batch


title: E14  mESC, CAPS+, rep2

status: Public on Mar 15 2023

city: Oxford

first: Linzhen

last: Kong

address: University of Oxford Old Road Campus Research Building

department: Nuffield Department of Medicine

institute: Ludwig Institute for Cancer Research

description: mESC_merged_astair_CpG_filtered.bedGraph.gz

data_processing:
Fastp (v.0.12.4) was used to filter bad reads, trim low-quality bases and cut adaptors
Trimmed reads were then aligned to either mm9 (for mESC samples) or hg38 (for human healthy brain and glioblastoma samples) reference genome using BWA mem (v.0.7.17)
PCR duplicates were removed by MarkDuplicate in Picard tools (v.2.23.0) (http://broadinstitute.github.io/picard/)
Methylation calling was performed by asTair (v3.3.2) using reads with MAPQ > 10. Regions prone to cause mapping artefacts were excluded from subsequent analysis(https://sites.google.com/site/anshulkundaje/projects/blacklists)
For mESC samples, known single nucleotide variants in E14 cell lines (http://epigenetics.hugef-research.org/data.php) were also excluded. For human normal brain and glioblastoma samples, CpG sites overlapping with common single nucleotide polymorphisms (SNPs) (dbSNP153) and centromeres were further excluded from downstream analysis
Assembly: mm9, hg38
Supplementary files format and content: Tab-delimited bedGraph files include chr (first column), start position (second), end position (third), modification level (fourth), unmodified reads (fiveth) and modified reads (sixth)

source_name: E14 mouse embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen) supplemented with 15% FBS (GIBCO), 2 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco), 1% penicillin/streptavidin (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 1000 units/mL LIF (Millipore), 1 µM PD0325901 (Stemgent), and 3 µM CHIR99021 (Stemgent). mESCs were maintained at 37°C and 5% CO2 and passaged every 2 days.

extract_protocol:
For isolation of genomic DNA, cells were harvested by centrifugation for 5 min at 1,000× g and room temperature. DNA was extracted with Quick-DNA Plus kit (Zymo Research) according to the manufacturer’s protocol.
Genomic DNA was spiked with 0.5% of CpG-methylated lambda DNA and 0.25% of unmodified 2 kb spike-in control. DNA samples were fragmented by Covaris M220 and size-selected to 300–500 bp with 0.55–0.85× Ampure XP beads according to the manufacturer’s protocol. The sonicated DNA was additionally spiked with 0.05% of 144 mer spike-in after size-selection with Ampure XP beads. End-repair and A-tailing reaction and ligation of NEBNext Adaptor for Illumina were prepared with KAPA HyperPrep Kit according to the manufacturer’s protocol. The uracil in the loop of NEBNext Adaptor was removed by adding 6  ml of USER Enzyme (New England Biolabs) to the ligation reaction and incubating at 37 °C for 45 min. The reaction was purified with 0.8× Ampure XP beads by washing twice with 80% acetonitrile/water (v/v).

value: E14 mouse embryonic stem cells


title: SPT16_AID_V5_Clone2_EtOH_12h [TT-Seq]

city: Pittsburgh

first: David

middle: Charles

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description:
4sU-labeled RNA
Incubated with 4sU for 5 minutes at 37C
PROMPT_12h_results.csv
eRNA_12h_results.csv
gene_12h_results.csv
DHS_12h_results.csv

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using STAR, with options --outFilterMismatchNoverReadLmax 0.02 and --outFilterMultimapNmax 1
Aligned reads were processed in deepTools by using the bamCoverage command to generate stranded bigwig files detailing coverage genome-wide in 1 bp bins with BPM normalization
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: TT-seq

source_name: E14 mES cell line

growth_protocol: Murine embryonic stem cells were grown under feeder-free conditions in DMEM, supplemented with 10% Fetal Bovine Serum, 2 mM-Glutamine, 1X non-essential amino acids, 0.129mM 2-mercaptoethanol, 1000U/mL Leukemia Inhibitory Factor (LIF), 3 µM CHIR99021 GSK inhibitor (p212121), and 1 µM PD0325091 MEK inhibitor (p212121). Cells were passaged every 48 hours using trypsin (Gibco) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol:
Cells were trypsinized, quenched, pelleted, washed with cold PBS, and crosslinked with 1% formaldehyde for 15 minutes. Crosslinking was quenched with .5M glycine for 5 minutes. Fixed cells were pelleted and washed with cold PBS
Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and replaced with fresh medium containing 500 mM 4-thiouridine (4sU). Cells were incubated at 37 degrees Celsius with 5% CO2 for five minutes, then washed with DPBS and trypsinized. Cells were pelleted, washed with DPBS, and RNA was extracted with TRIzol per manufacturer's instructions.
TT-seq

treatment_protocol: After 48 hours of undisturbed growth on 10 cm plates, medium was aspirated and cells were washed with DPBS. DPBS was aspirated and fresh medium was added containing 500 nM 3-Indoleacetic acid (3-IAA) or an equivalent volume of 100% ethanol. Plates were then left at 37 degrees Celsius with 5% CO2 for 24 hours before extraction.

tag: tag integration

value: osTIR1 was integrated into the genome using CRISPR-directed homologous recombination

value: Cells were left undisturbed on 10 cm plates for 48 hours prior to treatment. Cells were treated with 0.1% ethanol mixed into medium for the indicated time (hours). Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment.


title: SPT16_AID_V5_Clone2_3-IAA_12h [TT-Seq]

value: osTIR1 was integrated into the genome using CRISPR-directed homologous recombination; separately, Supt16 was C-terminally tagged with the 37 kDa mini-AID tag and a triple V5 tag


title: C32 SCG2 OE, biological rep1

value: overexpressing SCG2 vector


title: protonema, ddm1_rep3

tag: tissue

tag: age


title: SPT16_AID_V5_Clone2_3-IAA_3h [TT-Seq]

description:
4sU-labeled RNA
Incubated with 4sU for 5 minutes at 37C
PROMPT_3h_results.csv
eRNA_3h_results.csv
gene_3h_results.csv
DHS_3h_results.csv

value: Cells were left undisturbed on 10 cm plates for 48 hours prior to treatment. Cells were treated with 500 nM 3-IAA mixed into medium for the indicated time (hours). Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment.


title: SPT16_AID_V5_Clone1_0h [TT-Seq]

description:
4sU-labeled RNA
Incubated with 4sU for 5 minutes at 37C
PROMPT_0h_results.csv
eRNA_0h_results.csv
gene_0h_results.csv
DHS_0h_results.csv


title: SPT16_AID_V5_Clone1_3-IAA_6h [TT-Seq]

description:
4sU-labeled RNA
Incubated with 4sU for 5 minutes at 37C
PROMPT_6h_results.csv
eRNA_6h_results.csv
gene_6h_results.csv
DHS_6h_results.csv


title: Untagged_3-IAA_Rep2_12h [TT-Seq]


title: SPT16_AID_V5_Clone1_3-IAA_12h [TT-Seq]


title: SPT16_AID_V5_Clone1_EtOH_6h [TT-Seq]


title: SPT16_AID_V5_Clone2_3-IAA_6h [TT-Seq]


title: SPT16_AID_V5_Clone1_EtOH_12h [TT-Seq]


title: SPT16_AID_V5_Clone2_EtOH_3h [TT-Seq]


title: SPT16_AID_V5_Clone1_3-IAA_3h [TT-Seq]


title: Untagged_3-IAA_Rep1_6h [TT-Seq]


title: Untagged_Rep1_0h [TT-Seq]


title: Untagged_3-IAA_Rep1_3h [TT-Seq]


title: Untagged_Rep2_0h [TT-Seq]


title: Untagged_3-IAA_Rep2_3h [TT-Seq]


title: SPT16_AID_V5_Clone2_3-IAA_24h

description: Transposed for 30 minutes at 37C with 100 rpm shaking and Tn5 transposome (Diagenode). Libraries were amplified for 10 cycles of high-fidelity PCR

data_processing:
Reads were trimmed to 25 bp and barcode adapter sequences removed using trim_galore
Reads mapped to mm10 genome using bowtie2, allowing for 1 mismatch
Duplicates were removed using Picard
Reads were filtered for quality using SAMtools (MAPQ ≥ 10)
Reads were size-selected into nucleosome-free (1-100 bp) size class
Reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 1 bp bins with RPGC normalization, using an effectiveGenomeSize of 2308125349
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Cells were trypsinized, quenched, pelleted, washed with cold PBS, and resuspended in hypotonic buffer. Nuclei were pelleted and lysed cell debris (supernatant) removed. Nuclei were flash-frozen until time of use.
Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and cells were trypsinized. Cells were pelleted, washed with DPBS, and resuspended in hypotonic buffer. Nuclei were pelleted and lysed cell debris (supernatant) removed. Nuclei were flash-frozen until time of use. Nuclei were transposed for 30 minutes at 37C with 100 rpm shaking and Tn5 transposome (Diagenode). Libraries were amplified for 10 cycles of high-fidelity PCR
ATAC-seq

treatment_protocol: After 48 hours of undisturbed growth on 10 cm plates, medium was aspirated and cells were washed with DPBS. DPBS was aspirated and fresh medium was added containing 500 nM 3-Indoleacetic acid (3-IAA) or an equivalent volume of 100% ethanol. Plates were then left at 37 degrees Celsius with 5% CO2 for the indicated time before extraction.

value: E14 mES cell line


title: E14  mESC, CAPS+, rep1


title: SPT16_AID_V5_Clone2_EtOH_24h


title: SPT16_AID_V5_Clone2_3-IAA_12h


title: SPT16_AID_V5_Clone2_EtOH_12h


title: SPT16_AID_V5_Clone2_0h [TT-Seq]


title: SPT16_AID_V5_Clone2_EtOH_6h [TT-Seq]


title: Untagged_3-IAA_Rep1_12h [TT-Seq]


title: SPT16_AID_V5_Clone1_EtOH_3h [TT-Seq]


title: SPT16_AID_V5_Clone2_EtOH_6h


title: SPT16_AID_V5_Clone2_3-IAA_6h


title: SPT16_AID_V5_Clone2_3-IAA_3h


title: Untagged_3-IAA_Rep2_6h [TT-Seq]


title: SPT16_AID_V5_Clone1_3-IAA_24h


title: SPT16_AID_V5_Clone2_0h


title: SPT16_AID_V5_Clone1_0h


title: SPT16_AID_V5_Clone1_EtOH_3h


title: SPT16_AID_V5_Clone1_3-IAA_12h


title: SPT16_AID_V5_Clone1_EtOH_24h


title: Untagged_3-IAA_Rep1_24h


title: SPT16_AID_V5_Clone1_EtOH_6h


title: SPT16_AID_V5_Clone2_EtOH_3h


title: SPT16_AID_V5_Clone1_3-IAA_6h


title: Untagged_3-IAA_Rep2_12h


title: Untagged_3-IAA_Rep2_6h


title: SPT16_AID_V5_Clone1_EtOH_12h


title: Untagged_3-IAA_Rep2_3h


title: SPT16_AID_V5_Clone1_3-IAA_3h


title: Untagged_3-IAA_Rep2_0h


title: Untagged_3-IAA_Rep1_12h


title: Untagged_3-IAA_Rep1_3h


title: Untagged_3-IAA_Rep1_0h


title: Untagged_3-IAA_Rep1_6h


title: S.flexneri tgt∆, tRNATyr

city: Berlin

first: Ann

middle: E.

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

institute: Humboldt-Universität zu Berlin

description:
total RNA
column in processed data file: mm_ratio

data_processing:
Adapter-trimming was performed using Skewer version 0.2.2 and trimming of PCR primers, selection of high-quality reads and sorting of the reads based on the sequence in the degenerate region of the RT-primerwas performed using Bioconductor package ShortRead. Reads were trimmed to the expected size of the transcript using Cutadapt version 3.7.
Alignment to RNA sequences from S. pombe (https://www.pombase.org/) and Shigella flexneri (http://www.ensembl.org/) was achieved using Samtools version 1.12 and Bowtie version 2.2.5. Settings were chosen to allow up to one mismatch in seed with a seed length of 6.
Misincorporation was determined using CoverageAnalyzer.
Assembly: S.pombe genome version ASM294v2.29
Supplementary files format and content: excel-files include position, refbase, coverage, total mismatch ratio (mm_ratio), mismatch ratio of single nucleotides (a_mism, g_mism, t_mism and c_mism) and arrest_ratio.

organism: Shigella flexneri

source_name: RT via RT-KTq I614Y using 25 µM dCTP

growth_protocol: S. pombe strain AEP1 was grown in full medium (YES) with or without 0.1 µM queuine at 30°C. S. flexneri WT and tgt∆ strains were grown in full medium (TSB) at 37°C. Cultures were inoculated at an OD600 of 0.2 and grown to an optical density of 1.

extract_protocol:
Total RNA was isolated from 50 OD of cells. Cells were harvested and after addition of 1 mL of phenol, glass beads and vigorous shaking for 5 min, samples were centrifuged at 20.000 g for 5 min to clear the cell debris. Equal volume of phenol/chloroform/isoamylalcohol was added to the aqueous phase and centrifuged at 20.000 g for 5 min. After mixing the upper phase with an equal volume of chloroform followed by centrifugation at 20.000 g for 5 min, the RNA was precipitated.
Extraction of the RNA was performed as described in the "SAMPLEs" section. 500 ng RNA was hybridized to 500 nM of the respective stemloop-primer with the following thermocycling program: 95 °C for 2 min, 65 °C for 30 sec, ramp down to 4 °C with 5 °C/30 sec. After hybridization and incubation on ice for 1 min, 100 µM of each dNTP and 100 nM RT-KTq I614 DNA polymerase were added. The reverse transcription was carried out in reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% Tween 20) in a total volume of 20 µL. For experiments using decreased dCTP concentrations, 25 µM, 12.5 µM and 6.25 µM dCTP were added to the RT reaction. Following incubation at 55 °C for 1 h and incubation on ice for 10 min, the cDNA was amplified using Taq polymerase. Amplification was performed with 5 µL cDNA in reaction buffer containing 2.5 µM dNTPs, 2 mM MgCl2, 1 x Taq buffer+ KCl and 1.25 U Taq polymerase (Thermo Fisher) in a total volume of 200 µL. Primers binding at the 3’ end contained a barcoded sequence for multiplexing the PCR products. Samples were separated on a 2% agarose gel, and the respective PCR products were gel-purified using the QIAquick Gel Extraktion Kit (Qiagen) according to the manufacturer’s protocol.
Library preparation of amplified tRNAs for deep sequencing was performed using the NEXTflexR qRNA-SeqTM Kit v2 – Set C (Bioo Scientific) according to the manufacturer's protocols.

value: Shigella flexneri 5a M90T

value: tgt{delta}

value: growth in full medium (TSB) at 37°C


title: S.flexneri WT, tRNATyr

value: WT


title: S.flexneri tgt∆, tRNAHis


title: S.flexneri WT, tRNAHis


title: Untagged_3-IAA_Rep2_24h


title: S.flexneri tgt∆, tRNAAsn


title: S.flexneri WT, tRNAAsn


title: S.flexneri tgt∆, tRNAAsp


title: S.flexneri WT, tRNAAsp


title: smn2_rg_lib3_rep3_tot (MPSA)

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

library_source: other

data_processing:
Each barcode was computationally associated with its corresponding 5’ss, and the total number of reads for each 5’ss was tallied: ninc and ntot
A relative splicing ratio was then computed as r = (ninc/ntot)/(Ninc/Ntot), where Ninc and Ntot denote the total number of reads in the inclusion RNA and total RNA samples
Supplementary files format and content: csv files for each sequence context with estimated PSIs per biological replicate
Library strategy: Amplicon sequencing

molecule: other

growth_protocol: HeLa cells were seeded at 5x10^5 cells on 150 mm plates, cultured under 37C 5% CO2 for 24 hrs, applied drug treatment and further cultured for 48 hours.

extract_protocol:
Total RNA was extracted by Trizol following the manufacturer's protocol. Plasmids containing barcode-association were extracted by MaxiPrep using PureLink HiPure Plasmid filter Maxiprep kit (ThermoFisher). Then a fraction of them were applied for Illumina adapter ligation and pair-end sequencing
A second round of amplification of the inclusion and total products added Illumina-compatible ends for sequencing

treatment_protocol: HeLa cells were treated with 100 nM risdiplam, 50 nM branaplam, or solvent DMSO.

value: HeLa

tag: source of cell line

value: CSHL cell line repository

tag: product

value: total


title: smn2_rg_lib3_rep3_in (MPSA)

value: inclusion


title: smn2_rg_lib2_rep2_in (MPSA)


title: smn2_rg_lib3_rep1_in (MPSA)


title: smn2_rg_lib2_rep1_tot (MPSA)


title: smn2_rg_lib3_rep2_in (MPSA)


title: smn2_rg_lib2_rep3_tot (MPSA)


title: smn2_rg_lib3_rep2_tot (MPSA)


title: smn2_rg_lib2_rep2_tot (MPSA)


title: smn2_rg_lib1_rep1_tot (MPSA)


title: smn2_rg_lib1_rep2_in (MPSA)


title: smn2_rg_lib1_rep3_in (MPSA)


title: smn2_rg_lib1_rep1_in (MPSA)


title: smn2_nvs_lib3_rep3_in (MPSA)

value: branaplam


title: smn2_rg_lib2_rep1_in (MPSA)


title: smn2_nvs_lib3_rep3_tot (MPSA)


title: smn2_rg_lib1_rep3_tot (MPSA)


title: smn2_rg_lib1_rep2_tot (MPSA)


title: smn2_nvs_lib3_rep2_tot (MPSA)


title: smn2_nvs_lib3_rep2_in (MPSA)


title: smn2_nvs_lib3_rep1_tot (MPSA)


title: smn2_nvs_lib3_rep1_in (MPSA)


title: smn2_nvs_lib2_rep3_tot (MPSA)


title: smn2_nvs_lib2_rep3_in (MPSA)


title: smn2_nvs_lib2_rep1_tot (MPSA)


title: smn2_nvs_lib2_rep1_in (MPSA)


title: smn2_nvs_lib2_rep2_tot (MPSA)


title: smn2_nvs_lib1_rep3_tot (MPSA)


title: smn2_nvs_lib2_rep2_in (MPSA)


title: smn2_rg_lib2_rep3_in (MPSA)


title: smn2_nvs_lib1_rep3_in (MPSA)


title: smn2_dmso_lib3_rep3_tot (MPSA)

value: DMSO


title: smn2_nvs_lib1_rep1_tot (MPSA)


title: smn2_dmso_lib3_rep3_in (MPSA)


title: smn2_nvs_lib1_rep2_tot (MPSA)


title: smn2_dmso_lib3_rep2_in (MPSA)


title: smn2_dmso_lib3_rep2_tot (MPSA)


title: smn2_dmso_lib3_rep1_tot (MPSA)


title: smn2_nvs_lib1_rep1_in (MPSA)


title: smn2_nvs_lib1_rep2_in (MPSA)


title: smn2_dmso_lib2_rep2_tot (MPSA)


title: smn2_dmso_lib2_rep1_tot (MPSA)


title: smn2_dmso_lib2_rep2_in (MPSA)


title: smn2_dmso_lib2_rep3_tot (MPSA)


title: smn2_dmso_lib2_rep1_in (MPSA)


title: smn2_dmso_lib1_rep3_tot (MPSA)


title: smn2_dmso_lib1_rep3_in (MPSA)


title: smn2_dmso_lib1_rep2_in (MPSA)


title: smn2_dmso_lib1_rep1_tot (MPSA)


title: ikbkap_rg_lib2_rep2_tot (MPSA)


title: smn2_dmso_lib1_rep2_tot (MPSA)


title: ikbkap_rg_lib2_rep2_in (MPSA)


title: smn2_dmso_lib1_rep1_in (MPSA)


title: ikbkap_rg_lib2_rep1_in (MPSA)


title: ikbkap_rg_lib1_rep2_in (MPSA)


title: ikbkap_rg_lib1_rep2_tot (MPSA)


title: ikbkap_rg_lib1_rep1_tot (MPSA)


title: smn2_rg_lib3_rep1_tot (MPSA)


title: ikbkap_rg_lib1_rep1_in (MPSA)


title: smn2_dmso_lib2_rep3_in (MPSA)


title: smn2_dmso_lib3_rep1_in (MPSA)


title: ikbkap_nvssm_lib2_rep2_in (MPSA)


title: ikbkap_nvssm_lib2_rep1_tot (MPSA)


title: ikbkap_dmso_lib2_rep2_tot (MPSA)


title: ikbkap_dmso_lib2_rep2_in (MPSA)


title: ikbkap_nvssm_lib1_rep1_tot (MPSA)


title: ikbkap_nvssm_lib1_rep1_in (MPSA)


title: ikbkap_nvssm_lib2_rep2_tot (MPSA)


title: ikbkap_nvssm_lib2_rep1_in (MPSA)


title: ikbkap_nvssm_lib1_rep2_tot (MPSA)


title: ikbkap_dmso_lib2_rep1_tot (MPSA)


title: ikbkap_dmso_lib2_rep1_in (MPSA)


title: ikbkap_nvssm_lib1_rep2_in (MPSA)


title: ikbkap_dmso_lib1_rep2_in (MPSA)


title: ikbkap_dmso_lib1_rep1_tot (MPSA)


title: ikbkap_rg_lib2_rep1_tot (MPSA)


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid, clone 5

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC.
TrimGalore was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA after which the resulting reads were aligned to the reference genome fasta (genome.fa) using the STAR aligner.
Followup QC on the mapped (bam) files was done using Sambamba, RSeQC and PreSeq.
Read counts were then generated using the Subread FeatureCounts module with the Homo_sapiens.GRCh37.74.gtf file as annotation
Assembly: hg19
Supplementary files format and content: csv file including feature raw counts for all samples

source_name: Liver

growth_protocol: Organoids were cultured in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was isolated using TRIzol Reagent (Thermo Fisher)
RNA libraries were prepared using TruSeq Stranded mRNA polyA kit (Illumina)

value: Liver

value: Human hepatocyte organoid

value: Hepatocyte

value: BAP1 and PRKAR2A mutant

value: Hepatocyte medium


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid cultured in ductal medium, clone 4

value: Ductal medium


title: Wild type human hepatocyte organoid cultured in ductal medium, culture 3

value: Wild type


title: PRKAR2A knock-out human hepatocyte organoid, clone 4

value: PRKAR2A mutant


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid, clone 4


title: ikbkap_dmso_lib1_rep1_in (MPSA)


title: Wild type human hepatocyte organoid, culture 3


title: Wild type human hepatocyte organoid, culture 4


title: DNAJB1-PRKACAfusion human hepatocyte organoid, clone 5

value: DNAJB1-PRKACA fusion


title: DNAJB1-PRKACAfusion human hepatocyte organoid, clone 4


title: BAP1 knock-out human hepatocyte organoid, clone 4

value: BAP1 mutant


title: BAP1 knock-out human hepatocyte organoid, clone 5


title: Wild type human hepatocyte organoid cultured in ductal medium, culture 1


title: Wild type human hepatocyte organoid, culture 2


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid cultured in ductal medium, clone 3


title: DNAJB1-PRKACAfusion human hepatocyte organoid, clone 2


title: Wild type human hepatocyte organoid, culture 1


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid, clone 2


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid, clone 1


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid, clone 3


title: Wild type human hepatocyte organoid cultured in ductal medium, culture 2


title: ikbkap_dmso_lib1_rep2_tot (MPSA)


title: BAP1 knock-out human hepatocyte organoid, clone 3


title: Wild type human hepatocyte organoid cultured in ductal medium, culture 4


title: DNAJB1-PRKACAfusion human hepatocyte organoid, clone 1


title: PRKAR2A knock-out human hepatocyte organoid, clone 2


title: PRKAR2A knock-out human hepatocyte organoid, clone 1


title: BAP1 knock-out human hepatocyte organoid, clone 2


title: tumor brain, CAPS+

description: brain_tumor_astair_CpG.filtered.bedGraph.gz

source_name: brain

extract_protocol:
The genomic DNA of human normal brain and glioblastoma samples were obtained from the Amsbio
Genomic DNA was spiked with 0.5% of CpG-methylated lambda DNA and 0.25% of unmodified 2 kb spike-in control. DNA samples were fragmented by Covaris M220 and size-selected to 300–500 bp with 0.55–0.85× Ampure XP beads according to the manufacturer’s protocol. The sonicated DNA was additionally spiked with 0.05% of 144 mer spike-in after size-selection with Ampure XP beads. End-repair and A-tailing reaction and ligation of NEBNext Adaptor for Illumina were prepared with KAPA HyperPrep Kit according to the manufacturer’s protocol. The uracil in the loop of NEBNext Adaptor was removed by adding 6  ml of USER Enzyme (New England Biolabs) to the ligation reaction and incubating at 37 °C for 45 min. The reaction was purified with 0.8× Ampure XP beads by washing twice with 80% acetonitrile/water (v/v).

value: brain

tag: Sex

value: female

tag: disease

value: glioblastoma


title: BAP1 knock-out human hepatocyte organoid, clone 1

tag: treatment


title: normal brain, CAPS+

description: brain_healthy_astair_CpG.filtered.bedGraph.gz

value: male

value: normal


title: DNAJB1-PRKACAfusion human hepatocyte organoid, clone 3

tag: cell line


title: Reg_HA_U3

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

institute: University of British Columbia

description:
Unstimulated
Reg_HA_U3

data_processing:
Trimming was performed with TRIMMOMATIC v0.36.
The reads were aligned to the GRCh38 reference genome (release 102) with BOWTIE2 v2.2.6.
In order to represent the real Tn5 transposase binding sites of 9bp, the coordinates of the reads were shifted by 4bp for the plus strand and by 5bp for the minus strand, using Deeptools v3.0.1. The former was also used to remove ENCODE’s blacklisted regions (signal artefact regions) and convert Bam files to BEDPE forma
MACS2 was used to identify significant peaks. Diffbind v2.10.0 R package was used to generate the count matrix of Tn5 insertion site numbers for each consensus peak (peaks that were present in all samples for each condition).
Differentially accessibility regions (DARs) were identified between conditions within each cell type and controlling for the effect of sex, using DESeq2 v1.30.0 R package. DARs were annotated with their closest feature and different transcription binding motifs identified with HOMER v4.8.0.
Assembly: GRCh38 reference genome (release 102)
Supplementary files format and content: Conv. Excel File. Counts normalized relative to library size in Differentially Accessible Regions between HA_unstim vs. 19unstim.
Supplementary files format and content: Reg. Excel File. Counts normalized relative to library size in Differentially Accessible Regions between HA_unstim vs. 19unstim.

source_name: Peripheral blood

growth_protocol: Naïve Tregs were flow-sorted as live CD4+CD127loCD25hi CD45RA+CD62Lhi cells and naïve CD4+ Tconvs cells were sorted as live CD4+ CD45RA+CD62Lhi. Cells were resuspended at 1x106 cells/ml in XH media (X-Vivo 15 (Lonza) with 5% human serum, 1% penicillin/streptavidin, 1% glutamine and phenol red) containing 300U IL2/ml (Proleukin) and were stimulated with a 3 bead : 1 cell ratio of Dynabead. On day 2 and 3, cells were transduced with a retrovirus containing a non-tonic signaling CAR (non-TS-CAR; CD19) or a TS one (HA CAR). At day 7, cells were collected and live CAR+ were flow sorted  and resuspended at 0.5x106 cells/ml in XH media containing 300U IL2/ml for an addition 3 days for conventional T cells and 4 days for Tregs. Then, we removed the beads and rested them for an additional 24 hours.

extract_protocol:
50,000 cells were pelleted then lysed to isolate nuclei. For tagmentation, supernatants were removed and nuclei were resuspended in 50uL of Tn5 transposition mix (100nM Tn5 (Illumina, 20034197), 0.01% digitonin, 0.1% Tween-20 in 1x TD Buffer (Illumina, 20034197), and incubated at 37°C for 30 minutes in a thermomixer while shaking at 700 rpm. Tagmented DNA was purified using a Qiagen Min-Elute PCR clean-up Kit (Qiagen, 28004) and PCR amplified for 8-13 cycles using Q5 High-Fidelity DNA polymerase (NEB, M0491S) with primers containing Illumina Nextera adaptors for library generation.
The libraries were then size selected (described in (76)) with SPRISelect Beads (Beckman-Coulter, Cat# B23318), and concentrations were measured by a Qubit fluorometer using the Qubit dsDNA HS Assay kit (Life Technologies, Q32851) followed by bioanalyzer verification. Libraries were sequenced on the NextSeq 2000 platform (paired-end, 50 bp read lengths).

treatment_protocol: transduced with a non-TS CAR (CD19) or a TS one (HA)

value: Peripheral blood

value: naive CD4+ regulatory T cells

tag: donor number

value: TS-CAR (HA)

tag: biological replicate


title: PRKAR2A knock-out human hepatocyte organoid, clone 3

value: Liver

value: Human hepatocyte organoid


title: Reg_C2_HA_U11

description:
Unstimulated
Reg_C2_HA_U11


title: Reg_C3_HA_U15

description:
Unstimulated
Reg_C3_HA_U15


title: Reg_HA_U7

description:
Unstimulated
Reg_HA_U7


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid cultured in ductal medium, clone 1

value: Hepatocyte

value: BAP1 and PRKAR2A mutant


title: Reg_C2_19_U9

description:
Unstimulated
Reg_C2_19_U9

value: non-TS CAR (CD19)


title: Reg_19_U5

description:
Unstimulated
Reg_19_U5


title: Reg_C3_19_U13

description:
Unstimulated
Reg_C3_19_U13


title: Conv_C3_HA_U7

description:
Unstimulated
Conv_C3_HA_U7

value: naive CD4+ conventional T cells


title: BAP1 and PRKAR2A knock-out human hepatocyte organoid cultured in ductal medium, clone 2

value: Ductal medium


title: Conv_C2_HA_U3

description:
Unstimulated
Conv_C2_HA_U3


title: Conv_C3_19_U5

description:
Unstimulated
Conv_C3_19_U5


title: Conv_C2_19_U1

description:
Unstimulated
Conv_C2_19_U1


title: Conv_19_U13

description:
Unstimulated
Conv_19_U13


title: Conv_19_U9

description:
Unstimulated
Conv_19_U9


title: ST_AN_SLI-171

city: Boston

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

data_processing:
Read library quality was assessed using FastQC and multiQC
Illumina adapters were removed and leading and trailing low quality bases (below quality 30) were trimmed using trimmomatic
Reads less than 36 bases long after trimming were dropped.
Genome and Annotation (GTF) were from GENCODE v38.  Trimmed reads were then aligned directly to the contiguous splice graphs built from the hg38 human reference genome with STAR.
Used HTSeq counts for quantification
Genome_build: hg38
Supplementary_files_format_and_content: comma separated gene counts file

source_name: prefrontal cortex (BA9)

extract_protocol: RNA isolation protocol by BU core

value: prefrontal cortex (BA9)

tag: rin

tag: apoe


title: ST_AN_K-954


title: ST_AN_K-931


title: ST_AN_K-930


title: ST_AN_K-903


title: ST_AN_K-892


title: ST_AN_K-880


title: ST_AN_K-877


title: ST_AN_K-876


title: ST_AN_K-887


title: ST_AN_K-875


title: ST_AN_K-837


title: ST_AN_K-853


title: ST_AN_K-845


title: ST_AN_K-847


title: ST_AN_K-844


title: Conv_HA_U11

description:
Unstimulated
Conv_HA_U11


title: ST_AN_K-833


title: ST_AN_K-828


title: ST_AN_K-818


title: ST_AN_SLI-177


title: ST_AN_K-812


title: ST_AN_K-795


title: ST_AN_K-794


title: ST_AN_K-780


title: ST_AN_K-775


title: ST_AN_K-814


title: ST_AN_K-806


title: ST_AN_K-772


title: ST_AN_K-756


title: ST_AN_K-758


title: ST_AN_K-755


title: ST_AN_K-879


title: ST_AN_K-743


title: ST_AN_K-872


title: ST_AN_K-826


title: ST_AN_K-735


title: ST_AN_K-750


title: ST_AN_K-742


title: ST_AN_K-729


title: ST_AN_K-726


title: ST_AN_K-712


title: ST_AN_K-711


title: ST_AN_K-703


title: ST_AN_K-706


title: ST_AN_K-696


title: ST_AN_K-805


title: ST_AN_K-774


title: ST_AN_K-763


title: ST_AN_K-691


title: ST_AN_K-690


title: ST_AN_K-673


title: ST_AN_K-670


title: ST_AN_K-688


title: ST_AN_K-757


title: ST_AN_K-625


title: ST_AN_K-669


title: ST_AN_K-620


title: ST_AN_K-666


title: ST_AN_K-653


title: ST_AN_K-665


title: ST_AN_K-617


title: ST_AN_K-622


title: ST_AN_K-611


title: ST_AN_K-606


title: ST_AN_K-594


title: ST_AN_K-601


title: ST_AN_K-700


title: ST_AN_K-591


title: ST_AN_K-610


title: ST_AN_K-695


title: ST_AN_K-587


title: ST_AN_K-580


title: ST_AN_K-571


title: ST_AN_K-579


title: ST_AN_K-589


title: ST_AN_K-578


title: ST_AN_K-570


title: ST_AN_K-562


title: ST_AN_K-560


title: ST_AN_K-554


title: ST_AN_K-551


title: ST_AN_K-548


title: ST_AN_K-553


title: ST_AN_K-547


title: ST_AN_K-540


title: ST_AN_K-536


title: ST_AN_K-543


title: ST_AN_K-505


title: ST_AN_K-489


title: ST_AN_K-522


title: ST_AN_K-513


title: ST_AN_K-483


title: ST_AN_K-464


title: ST_AN_K-461


title: ST_AN_K-487


title: ST_AN_K-460


title: ST_AN_K-458


title: ST_AN_K-467


title: ST_AN_K-432


title: ST_AN_K-419


title: ST_AN_K-559


title: ST_AN_K-437


title: ST_AN_K-408


title: ST_AN_K-545


title: ST_AN_K-402


title: ST_AN_K-429


title: ST_AN_K-393


title: ST_AN_K-389


title: ST_AN_K-378


title: ST_AN_K-459


title: ST_AN_K-375


title: ST_AN_K-370


title: ST_AN_K-366


title: ST_AN_K-377


title: ST_AN_K-368


title: ST_AN_K-367


title: ST_AN_K-364


title: ST_AN_K-362


title: ST_AN_K-353


title: ST_AN_K-352


title: ST_AN_K-356


title: ST_AN_K-349


title: ST_AN_K-348


title: ST_AN_K-341


title: ST_AN_K-335


title: ST_AN_K-340


title: ST_AN_K-327


title: ST_AN_K-316


title: ST_AN_K-330


title: ST_AN_K-322


title: ST_AN_K-310


title: ST_AN_K-334


title: ST_AN_K-312