title: LV_76

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

institute: Auburn University

data_processing:
Illumina Casava software
Sequencing adaptors, low-complexity reads, and reads containing low quality bases were removed in an initial data-filtering step. Reads with a PhredScore lower than 30 were filtered out. Quality control (QC) and read statistics were estimated with FastQC v0.11.8 and MultiQC v1.9 software.
After QC, 31 samples (seven or eight samples per group) remained for further analyses. Reads were mapped to the Bos taurus reference genome (ARS-UCD 1.2) [31] using the STAR aligner v. 2.7.3a. Raw counts per gene were obtained using the –quantMode GeneCounts flag from STAR based on the gene annotation file (release 100, Ensembl). MultiQC, NOISeq, and edgeR software were used to perform the post-mapping quality control.
Based on the edgeR filterByExpr function, genes not expressed or lowly expressed were filtered out. Differential gene expression analysis was carried out using edgeR.
Assembly: Bos taurus ARS-UCD 1.2
Supplementary files format and content: Tab-delimited text files include raw count values for each sample

organism: Bos taurus

extract_protocol:
Total RNA of 31 female fetuses was isolated from the liver tissues using the RNeasy Plus Universal Mini Kit (Qiagen®, Germantown, MA, USA) according to the manufacturer's protocol.
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA). Library preparation and paired-end sequencing with 150-bp reads at a depth of 20 M reads/sample were carried out at Novogene Co. (Nanjing, China).

treatment_protocol: The factors examined included vitamin and mineral supplementation (VTM or NoVTM) and rate of gain (low gain – LG or moderate gain – MG). The treatments were arranged as follows: (1) no vitamin and mineral supplementation and low gain (NoVTM_LG, n = 8); (2) vitamin and mineral supplementation and low gain (VTM_LG, n = 8); (3) no vitamin and mineral supplementation and moderate gain (NoVTM_MG, n = 8), and (4) vitamin and mineral supplementation and moderate gain (VTM_MG, n = 7).

value: Liver


title: 10A_M_1726

status: Public on Apr 14 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: Sex

value: male

tag: strain


title: Col-DC-rep1

type: RNA

city: Pohang

first: Ildoo

last: Hwang

state: Kyungbuk

address: 77 Cheongam-Ro, Hyoja-dong, Nam-gu,

department: Department of Life Sciences

country: South Korea

institute: POSTECH

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.13.0 (R2011b)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col plant, sprayed pathogen

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Wild-type and mutant seeds were germinated on 1/2xB5 medium. Seedlings were planted to soil pot 1 week after germination and grown under short day condition (22℃, 10 hr light/14 hr dark) for 3~4 weeks

extract_protocol: Total RNA from samples was isolated by using Trizol (Invitrogen) according to manufacturer’s instructions

treatment_protocol: In treatment condition(BD), plants were irrigated with 10ml of 30µg/ml b-aminobutyric acid (BABA). In 2 days after BABA treatment, plants were sprayed with 40ml of 5x107 cfu/ml Pseudomonas syringae pathovar tomato (Pst) DC3000 per pot.

tag: genetic background

tag: genotype

value: wild type

tag: treatment

value: sprayed pathogen

tag: tissue

value: plant aerial part


title: LV_67

library_source: transcriptomic

source_name: Liver


title: ChIP-seq.BT549_SLUG-ChIP.shNELFE_input

city: Singapore

first: Zhenhua

last: hu

state: singapore

address: 31 Biopolis drive

country: Singapore

institute: IMCB, A*STAR

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases using Trim_Galore (v0.4.2_dev).
For RNA-seq, cleaned reads were either mapped to the hg19 reference genome, guided by the corresponding gene models. Both reference genomes and gene models were obtained from Illumina iGenome website. Gene expression quantification were carried out by RSEM pipeline. Differential gene expression was called using DESeq2 with default parameters except that normalization was based on ERCC spike-in if included, and that biological replicates were used as covariant.
For ChIP-seq, paired-end raw sequencing reads were trimmed with Trim Galore with parameters: --trim-n --paired (paired-end). Cleaned reads were then mapped to hg19 reference genome obtained from Illumina iGenome website  by Bowtie2 (v.2.2.9) with parameters: -N 1 -L 25 --no-mixed --no-discordant for paired-end and -N 1 -L 25 for single-end sequencing respectively. PCR duplicates were removed using SAMtools (v1.4). Biological replicate alignment files were merged. Bigwig coverage were generated using “bamCompare” function from deepTools package with parameters “-bl mm9-blacklist.bed --ratio subtract -bs 20 –normalizeUsing RPKM -b1 IP.bam -b2 input.bam --extendReads 200” for single-end, and “-bl mm9-blacklist.bed --ratio subtract -bs 20 -p 6 –normalizeUsing RPKM -b1 IP.bam -b2 input.bam –extendReads” for paired-end sequencing, respectively. Blacklist region file “mm9-blacklist.bed” was obtained from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz. Metaplots were generated using “computeMatrix” and “plotProfile” functions from deepTools package with default parameter settings.
Assembly: hg19
Supplementary files format and content: EXCEL file contains DESeq2 differential gene expression analysis results; gene count files by RSEM pipeline ending with ".genes.results"; ChIP-seq signal files, normalized by input and ending with ".bw"

organism: Homo sapiens

growth_protocol: MCF7 and MCF7ras+SS cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin/streptomycin. SUM159 and BT549 cells was maintained in Nutrient Mix F12 (HAM) medium supplemented with 10% (v/v) heat-inactivated FBS and 1% (v/v) penicillin/streptomycin.

extract_protocol:
RNA-seq: Total RNA was extracted using TRI-reagent and purified using the Direct-zol RNA MiniPrep Kit (Zymo). For KAT2B ChIP, MCF7ras+SS cells were harvested and double-crosslinked in suspension with 2mM DSG in PBS for 30 minutes at room temperature, washed with PBS twice and further crosslinked with 1% formaldehyde (FA) in PBS for 15 minutes at room temperature. Crosslinking was quenched by addition of glycine to final concentration of 125mM and incubated at room temperature for 10 min. For all other ChIPs, BT549 and MCF7ras+SS cells were subjected to crosslinking in 1% formaldehyde (FA) in PBS for 15 minutes at room temperature and followed by quenching with 125mM glycine for 10 minutes. Fixed cells were then subjected to standard ChIP lysis protocol to release chromatin. Released chromatin was sonicated to obtain fragments between 100-300bp, pre-cleared and used for IP with antibody-Dynabead complex. Captured fragments were subjected to several rounds of washes before elution with SDS buffer.
RNA-seq: Equal amount of RNA preparations (extracted from equal number of cells) from each sample were subjected to ribosomal RNA depletion using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB Cat# E6310) and library construction using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB Cat# E7760), according to manufacturer’s protocol. ChIP-seq: Eluted DNA and DNA from relevant input materials was purified and made into libraries using NEBNext Ultra II DNA kit (NEB Cat #: E7645). For both RNA-seq and ChIP-seq libraries, average fragment size was determined on Agilent High Sensitivity DNA and D1000 Screentape system (Agilent Cat #:5067-4626, 5067-5582), quantified using Qubit High Sensitivity DNA system (Life Tech Cat# Q32854), and pooled in equimolar. Pooled libraries were sequenced on the Illumina NextSeq or HiSeq platform.

treatment_protocol: For RNA-seq fromBT549, cells were cultured in phenol red-free DMEM supplemented with 5% charcoal stripped FBS and 1% (v/v) penicillin/streptomycin for 72 hours.

tag: cell line

tag: condition

tag: chip antibody


title: 10A_M_1725


title: ChIP-seq.BT549_SLUG-ChIP.scramble_IP_rep2

description: ChIP-seq.BT549_SLUG-ChIP.scramble_rep12.bw; peaks_BT549.scramble_SLUG_rep12_np09.bed

value: SLUG (Cell Signoneling Technology, 9585S)


title: 10A_M_1724


title: LV_48


title: LV_45


title: ChIP-seq.BT549_SLUG-ChIP.scramble_input


title: 10A_M_1723


title: ChIP-seq.BT549_SLUG-ChIP.scramble_IP_rep1


title: Col-BA_sub-rep2

source_name: Col plant, BABA treated

value: BABA treated


title: Col-BA_sub-rep1


title: LV_20


title: 10A_M_1721


title: LV_44


title: 10A_M_1722


title: Col-Ctrl-rep2

source_name: Col plant, control

value: control


title: ChIP-seq.BT549_NELFE-ChIP.scramble_IP_rep2

description: peaks_BT549.scramble_NELFE_rep12_np09.bed

value: NELF-E (Abcam, ab170104)


title: Col-Ctrl-rep1


title: LV_13


title: ChIP-seq.BT549_NELFE-ChIP.scramble_input_rep2


title: LV_65


title: 10A_M_1720


title: 10A_M_1719


title: LV_60


title: 10A_M_1718


title: ChIP-seq.BT549_NELFE-ChIP.scramble_input_rep1


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.shNELFE_DOX_IP_rep1

description: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.shNELFE_DOX_rep12.bw

value: Doxycycline

value: Rnone Polymerase II, CL CTD4H8(Millipore, (CTD4H8) 05-623)


title: LV_59


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.shNELFE_DOX_IP_rep2


title: 10A_M_1717


title: LV_46


title: 10A_M_1716


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.shNELFE_DOX_input


title: LV_41


title: 10A_M_1714


title: 10A_M_1712


title: LV_36


title: LV_29


title: ChIP-seq.BT549_NELFE-ChIP.scramble_IP_rep1


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_DOX_input


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_DOX_IP_rep1

description: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_DOX_rep12.bw


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_Con_IP_rep2

description: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_Con_rep12.bw

value: DMSO


title: 10A_M_1713


title: LV_74


title: 10A_M_1711


title: 10A_M_1710


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_Con_input


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_Con_IP_rep1


title: LV_35


title: ChIP-seq.MCF7Ras_NELFE-ChIP_forGA.DOX_GA_IP_rep2

description: ChIP-seq.MCF7Ras_NELFE-ChIP.DOX_GA_rep12.bw


title: 10A_M_1715


title: ChIP-seq.MCF7Ras_NELFE-ChIP_forGA.DOX_GA_IP_rep1


title: 10A_M_1708


title: ChIP-seq.MCF7Ras_NELFE-ChIP_forGA.DOX_GA_input


title: ChIP-seq.MCF7Ras_NELFE-ChIP_forGA.DOX_DMSO_IP_rep2

description: ChIP-seq.MCF7Ras_NELFE-ChIP.DOX_DMSO_rep12.bw


title: LV_3


title: 10A_M_1705


title: LV_28


title: ChIP-seq.shNELFE_MCF7Ras_RNAPII-ChIP.scramble_DOX_IP_rep2


title: 10A_M_1703


title: ChIP-seq.MCF7Ras_NELFE-ChIP_forGA.DOX_DMSO_IP_rep1


title: LV_22


title: 10A_M_1701


title: LV_68


title: ChIP-seq.MCF7Ras_NELFE-ChIP_forGA.DOX_DMSO_input


title: LV_52


title: Donor 3440, Batch 2, 0mM EtOH, biol rep 4

city: New York

first: Paul

last: Slesinger

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were assessed for quality using FastQC (version 0.11.8) before and after adapter sequence trimming by Cutadapt (version 4.1).
Reads were pseudoaligned using Salmon (version 0.13.1) for estimation of normalized gene expression (TPM, i.e. transcript per million).
Reads were also aligned to the human reference genome (Gencode version 28) and quantified for gene read counts, both in STAR (version 2.5.3a).
For differential gene expression analyses, read counts were modelled in the linear mixed model using batch, sex and donor information as the random effect terms and ethanol-treatment/control as the fixed effect term by the R (version 4.1.0) package "variancePartition" (version 1.28.0).
Assembly: hg38
Supplementary files format and content: "star_gene.tsv" includes reads counts for genes (in rows) across samples (in columns); "salmon_gene.tsv" includes TPM values for genes (in rows) across samples (in columns).

growth_protocol: Doxycycline-inducible transcription factor NGN2 with puromycin selection and rt-TA lentiviruses were used on neural progenitor cells. After dox-induction and antibiotic selection, cells were grown in Neurobasal medium with B27 supplement up to 14 days post-induction, then transitioned to Neurobasal Plus medium.

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions

treatment_protocol: Ethanol exposure began at 21 days post-induction, wither either 2 mM or 17 mM EtOH. EtOH was supplemented daily to account for evaporation.

tag: cell type

value: NGN2-induced neurons

value: WT

value: Control

tag: time

value: Day 28


title: 10A_M_1702


title: 10A_M_1709


title: LV_37


title: Donor 3440, Batch 2, 0mM EtOH, biol rep 3


title: Donor 3440, Batch 2, 0mM EtOH, biol rep 2


title: 10A_M_1698


title: 10A_M_1699


title: 10A_M_1706


title: Donor 3440, Batch 2, 0mM EtOH, biol rep 1


title: LV_24


title: Donor 3440, Batch 2, 2mM EtOH, biol rep 4

value: 7-Day 2mM EtOH Exposure


title: 10A_M_1694


title: LV_23

value: Liver


title: Donor 3440, Batch 2, 2mM EtOH, biol rep 3


title: 10A_M_1693

value: male


title: LV_16


title: LV_15


title: 10A_M_1692


title: Donor 3440, Batch 2, 2mM EtOH, biol rep 1


title: ES JF1XB6 Rep2 2

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

country: France

institute: IGMM

data_processing:
Raw sequencing reads were aligned using Bowtie2 to the human (Hg19), mouse (mm9), drosophila (dm6) and yeast (sacCer3) genomes. Sequence reads that aligned multiple times in the genomes with equal alignment scores, were discarded as well as the duplicate reads with identical coordinates (sequencing depth taken into account) to remove potential sequencing and alignment artifacts. Aligned reads were elongated in silico using the DNA fragment size inferred from paired-reads using an in-house developed R pipeline (PASHA) or using MACS2 which also allows peak calling for G4-ChIP and G4access. MACS2 was run with recommended settings (PMID: 18798982). Bedgraph generated by MACS2 were then converted to wig files (bin10) and scaled using PASHA which uses the sequencing depth. Wiggle files representing average enrichment score every 10bp were generated.
Genome_build: hg19, mm9, dm6, sacCer3
Supplementary_files_format_and_content: bed, wig

source_name: mouse hybrid Embryonic stem cells JB

growth_protocol: Raji and K562 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamine (2 mg/ml) at 37°C and 5% CO2. Haacht cells were grown in DMEM supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) at 37°C and 5% CO2. Hybrid ES cells were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% heat-inactivated fetal bovine serum), penicillin/streptomycin (100 units/mL) and (ESGRO mouse LIF Medium Supplement (1000 units/mL) at 37°C and 5% CO2. S2 cells were cultured in Schneider’s S2 Drosophila medium supplemented with 10% heat-inactivated fetal bovine serum, penicillin/streptomycin (100 units/mL) at 27°C. Yeast S288C (BY4741) haploid cells were grown in YPD (2% glucose) at 30°C.

extract_protocol:
For G4 access: Trypsinized Haacht cells, resuspended S2 cells and suspension of K562, Raji and mouse ESC cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Haacht cells were suspended in 5 mL of permeabilization buffer (150 mM of sucrose, 80 mM Kill, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) and homogenized using a Dounce (40 strokes). For MNase digestion, 5x10^6 cells per titration point were resuspended in 50 μL of prewarmed permeabilization buffer supplemented with 0.2% (v/v) NP40 and incubated 5 minutes at 37ºC. Digestion took place by adding a volume of 500 mL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) to each reaction. Either 3.1, 6.2, 12.5, 25 or 50U MNase (Merck, 10107921001) were added to the MNase reaction buffer and incubated at 37 ºC for 10 min. Digestion was stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. The digestions were incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Trish pH 8) and 1 mL of water. Before DNA purification, digestions were incubated with 5 mL of RNaseq A (Thermofisher, EN0531) at 37 ºC for 2 hours and with 8 mL of proteinase K (Euromoney, 09-0911) at 56 ºC for 2 hours. To verify the performance of the digestion, 125 μL of each sample was cleaned-up using QI quick PCR Purification Kit (QIAGEN, 28106). Digestions were assessed by agarose gel and Bioanalyzer (Fig. 1c). The remaining digestions were purified by phenol-chloroform and ethanol precipitation for subsequent steps.
Yeast S288C were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Pellets from 100mL culture (OD: 0.5) were suspended in 600ul cell breaking buffer (20% glycerol, 100mM Tris pH 7.5), 600µl zirconia beads (0.5mm), 10µl of 100x protease inhibitors (Roche, 06538282001). Beads beating was performed in 1.5mL screw cap tubes in a Bullet Blender (Next advance) for 4 x 3min at a strength of 8 in a cold room. Cell suspensions were recovered by puncturing the bottom of tube (23 gauge syringes) and spined at 170 ruff for 3min into a 5mL Eppendorf tube. Everything was transferred into 1.5mL Eppendorf, then centrifuged for 5min at max speed and the top layers were discarded. Samples were suspended in 300ul of prewarmed NP buffer (50mM NaCl, 10mM Tris pH 7.4, 5mM MgCl2, 1mM CaCl2, 0.2% NP40 (v/v), 0.5mM spermidine (Sigma, S0266-1G), 0.007% B-Mercaptothion (Sigma, M3148-100ML). Digestion took place by adding a volume of 300µL prewarmed NP buffer supplemented with either 60u, 30u, 15u, 7.5u, 3.75, 1.9u, 1u of MNase (Merck 10107921001). Digestions were stopped on ice and by adding 150μL of stop buffer (5% SDS, 50mM EDTA). Before DNA purification, digestions were incubated with 5 µL of RNaseq A (Thermofisher, EN0531) at 37 ºC for 2 hours and with 10 µL of proteinase K (Euromoney, 09-0911) at 56 ºC for 2 hours. Purification was done with two consecutive phenol and one chloroform steps followed by ethanol and linear acrylamide precipitation. Purified DNAs were once again incubated with 5µl RNaseq A (Thermofisher, EN0531) to get rid of persistent RNA contaminations.
The phenol-chloroform purified DNAs were subjected to size selection to remove fragments larger than 100 bp. For that, 1 µg of each digestion product was migrated in a 4-20% polyacrylamide Novant TBE gel (Thermofisher, EC6225BOX) at 100 V for 60 min. The gels were stained with Sober® Gold (Thermofisher, S11494) for 30 min. Fragments according to the size range of 0-100 bp were cut out from the gel and transferred to 0.5-mL Eppendorf tubes, previously punctured in the bottom with a 0.45 µm needle. These tubes were inserted into 1.5-mL tubes and centrifuged 10 min at 15.300 ruff to move the cotted gel through the hole, generating gel beads. To elute the DNA from the beads, 700 μL of water was added and the tubes were incubated overnight at 55 ºC in a thermomixer at 1500 rpm. DNA was purified by transferring the samples (DNA eluate and gel beads) to the top of a 0.22 µm spin filter (Agilent 5185-5990). Spin filters were centrifuged 2 min at 15.300 ruff to recover the DNA eluate. DNA was precipitated with isopropanol and linear acrylamide. Size-selection was verified by Bioanalyzer (Fig. 1c). To assess the optimal MNase titration point in terms of G-quadruplex (G4) forming sequence enrichment, the relative amount of targeted G4s was evaluated by qPCR (Extended Data Fig. 1a). The titration points showing a percentage of mononucleosomal fraction of 30% of the total DNA (excluding subnucleosomal fraction) as quantified using Bioanalyzer chips gave the best qPCR enrichment in targeted G4s after size selection. This observation was further confirmed when sequencing the corresponding libraries.
For Pol II ChIP-seq, fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter.
G4access and ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to standard protocol.

treatment_protocol: For the Pyrido statin experiments, cells were treated with 10 µM pyritization. For DMSO (0.1%), Triptolide (1 µM), KM05283 (100 µM), cells were treated for 2hours.

value: mES hybrid cell; Embryonic stem cell

value: ESC

tag: experiment

tag: spike-in reference organism

value: No spike

tag: spike-in cell line

value: untreated

tag: concentration

tag: duration


title: ES JF1XB6 Rep2 1


title: 10A_M_1690

tag: brain region

tag: age


title: 10A_M_1689

tag: Sex

tag: strain


title: LV_34


title: 10A_M_1696


title: Donor 3440, Batch 2, 17mM EtOH, biol rep 3

tag: genotype

value: 7-Day 17mM EtOH Exposure


title: ES JF1XB6 Rep1 1

tag: treatment


title: ES JF1XB6 Rep1 2


title: 10A_M_1687


title: LV_25

tag: tissue


title: 10A_M_1688


title: Donor 3440, Batch 2, 17mM EtOH, biol rep 1

tag: cell line


title: 10A_M_1686


title: ES B6xJF1 Rep2 1

source_name: mouse hybrid Embryonic stem cells BJ


title: Donor 3440, Batch2, 2mM EtOH, biol rep 2


title: 10A_M_1685


title: ES B6xJF1 Rep1 2


title: 10A_M_1691


title: ES B6xJF1 Rep2 2


title: Donor 3440, Batch 1, 0mM EtOH, biol rep 4


title: Donor 3440, Batch 1, 0mM EtOH, biol rep 2


title: 10A_M_1684


title: Donor 3440, Batch 2, 17mM EtOH, biol rep 4


title: 10A_M_1683


title: Donor 3440, Batch 1, 0mM EtOH, biol rep 1


title: Donor 3440, Batch 2, 17mM EtOH, biol rep 2


title: Donor 3440, Batch 1, 2mM EtOH, biol rep 4


title: Raji rna-seq chRNA untreated rep2

data_processing:
Raw sequencing reads were aligned using Bowtie2 to the human (Hg19), mouse (mm9), drosophila (dm6) and yeast (sacCer3) genomes. Sequence reads that aligned multiple times in the genomes with equal alignment scores, were discarded as well as the duplicate reads with identical coordinates (sequencing depth taken into account) to remove potential sequencing and alignment artifacts. Aligned reads were elongated in silico using the DNA fragment size inferred from paired-reads using an in-house developed R pipeline (PASHA) or using MACS2 which also allows peak calling for G4-ChIP and G4access. MACS2 was run with recommended settings (PMID: 18798982). Bedgraph generated by MACS2 were then converted to wig files (bin10) and scaled using PASHA which uses the sequencing depth. Wiggle files representing average enrichment score every 10bp were generated.
Assembly: hg19, mm9, dm6, sacCer3
Supplementary files format and content: bed, wig

source_name: Raji B cells

growth_protocol: Raji and K562 cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) and glutamin (2 mg/ml) at 37°C and 5% CO2. HaCat cells were grown inDMEM supplemented with 10% fetal calf serum, penicillin/streptomycin (100 units/mL) at 37°C and 5% CO2. Hybrid ES cells were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% heat-inactivated fetal bovine serum), penicillin/streptomycin (100 units/mL) and (ESGRO mouse LIF Medium Supplement (1000 units/mL) at 37°C and 5% CO2. S2 cells were cultured in Schneider’s S2 Drosophila medium  supplemented with 10% heat-inactivated fetal bovine serum, penicillin/streptomycin (100 units/mL) at 27°C. Yeast S288C (BY4741) haploid cells were grown in YPD (2% glucose) at 30°C.

extract_protocol:
For G4 access:  Trypsinized HaCaT cells, resuspended S2 cells and suspension of K562, Raji and mouse ESC cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). HaCaT cells were suspended in 5 mL of permeabilization buffer (150 mM of sucrose, 80 mM KCl, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) and homogenized using a dounce (40 strokes). For MNAse digestion, 5x106 cells per titration point were resuspended in 50 μL of prewarmed permeabilization buffer supplemented with 0.2% (v/v) NP40 and incubated 5 minutes at 37ºC. Digestion took place by adding a volume of 500 mL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) to each reaction. Either 3.1, 6.2, 12.5, 25 or 50U MNase (Merck, 10107921001) were added to the MNase reaction buffer and incubated at 37 ºC for 10 min. Digestion was stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. The digestions were incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Tris.HCl pH 8) and 1 mL of water. Before DNA purification, digestions were incubated with 5 mL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 8 mL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours. To verify the performance of the digestion, 125 μL of each sample was cleaned-up using QIAquick PCR Purification Kit (QIAGEN, 28106). Digestions were assessed by agarose gel and Bioanalyzer (Fig. 1c). The remaining digestions were purified by phenol-chloroform and ethanol precipitation for subsequent steps.  Yeast S288C were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Pellets from 100mL culture (OD: 0.5) were suspended in 600ul cell breaking buffer (20% glycerol, 100mM Tris pH 7.5), 600µl zirconia beads (0.5mm), 10µl of 100x protease inhibitors (Roche, 06538282001). Beads beating was performed in 1.5mL screw cap tubes in a Bullet Blender (Next advance) for 4 x 3min at a strength of 8 in a cold room. Cell suspensions were recovered by puncturing the bottom of tube (23 gauge syringes) and spinned at 170 rcf for 3min into a 5mL Eppendorf tube. Everything was transferred into 1.5mL Eppendorf, then centrifuged for 5min at max speed and the top layers were discarded. Samples were suspended in 300ul of prewarmed NP buffer (50mM NaCl, 10mM Tris pH 7.4, 5mM MgCl2, 1mM CaCl2, 0.2% NP40 (v/v), 0.5mM spermidine (Sigma, S0266-1G), 0.007% B-Mercaptoethanol (Sigma, M3148-100ML). Digestion took place by adding a volume of 300µL prewarmed NP buffer supplemented with either 60u, 30u, 15u, 7.5u, 3.75, 1.9u, 1u of MNase (Merck 10107921001). Digestions were stopped on ice and by adding 150μL of stop buffer (5% SDS, 50mM EDTA). Before DNA purification, digestions were incubated with 5 µL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 10 µL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours. Purification was done with two consecutive phenol and one chloroform steps followed by ethanol and linear acrylamide precipitation. Purified DNAs were once again incubated with 5µl RNAse A (ThermoFisher, EN0531) to get rid of persistent RNA contaminations.     The phenol-chloroform purified DNAs were subjected to size selection to remove fragments larger than 100 bp. For that, 1 µg of each digestion product was migrated in a 4-20% polyacrylamide NovexTM TBE gel (ThermoFisher, EC6225BOX) at 100 V for 60 min. The gels were stained with Syber® Gold (ThermoFisher, S11494) for 30 min. Fragments according to the size range of 0-100 bp were cut out from the gel and transferred to 0.5-mL Eppendorf tubes, previously punctured in the bottom with a 0.45 µm needle. These tubes were inserted into 1.5-mL tubes and centrifuged 10 min at 15.300 rcf to move the cutted gel through the hole, generating gel beads. To elute the DNA from the beads, 700 μL of water was added and the tubes were incubated overnight at 55 ºC in a thermomixer at 1500 rpm. DNA was purified by transferring the samples (DNA eluate and gel beads) to the top of a 0.22 µm spin filter (Agilent 5185-5990). Spin filters were centrifuged 2 min at 15.300 rcf to recover the DNA eluate. DNA was precipitated with isopropanol and linear acrylamide. Size-selection was verified by Bioanalyzer (Fig. 1c). To assess the optimal MNase titration point in terms of G-quadruplex (G4) forming sequence enrichment, the relative amount of targeted G4s was evaluated by qPCR (Extended Data Fig. 1a). The titration points showing a percentage of mononucleosomal fraction of 30% of the total DNA (excluding subnucleosomal fraction) as quantified using Bioanalyzer chips gave the best qPCR enrichment in targeted G4s after size selection. This observation was further confirmed when sequencing the corresponding libraries.    For Pol II ChIP-seq, fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter; Chromatin associated RNAs (ChrRNAs) were isolated from 2x107 Raji cells as described previously (Nojima et al., 2015) followed by TurboDNase treatment. Purified RNAs were quantified by Qubit and quality was assessed using RNA Pico Assay kit with Bioanalyzer (Agilent Technologies, USA). chrRNA were then subjected to library preparation using True-seq stranded total RNA library prep gold kit (Ref#220599) from Illumina using 1 µg of chrRNA, 15 cycles of amplification and following manufacturer instructions (including ribo-depletion).
G4access and ChIP-seq librairies were prepared usingNEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to standard protocol. RNA-seq were prepared using True-seq stranded total RNA library prep gold kit according to standard protocol.

treatment_protocol: For the Pyridostatin experiments, cells were treated with 10 µM pyridistatin.   For DMSO (0,1%), Triptolide (1 µM), KM05283 (100 µM), cells were treated for 2hours.

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

value: chrRNA-seq

value: ERCC


title: Raji rna-seq chRNA untreated rep1


title: 10A_M_1682


title: 10A_M_1681


title: Raji PolII T0 PDS2

value: ChIP-seq

tag: spike-in reference organisme

value: Drosophila melanogaster

value: Total PolII (N20 - sc899 - Santa Cruz Biotechnology)


title: 10A_M_1680


title: Donor 3440, Batch 1, 2mM EtOH, biol rep 3

value: NGN2-induced neurons

value: WT

value: Day 28


title: Raji PolII T0 PDS1

tag: chip antibody


title: Donor 3440, Batch 1, 2mM EtOH, biol rep 2

tag: cell type

value: 7-Day 2mM EtOH Exposure


title: Donor 3440, Batch 1, 0mM EtOH, biol rep 3

value: Control

tag: time


title: Raji Mnase-seq Untreated rep2

tag: experiment

value: MNase-Seq


title: 10A_M_1679

value: male


title: Donor 3440, Batch 1, 2mM EtOH, biol rep 1


title: Donor 3440, Batch 1, 17mM EtOH, biol rep 4


title: 10A_M_1676


title: 10A_M_1677


title: Raji Mnase-seq Untreated rep1

value: untreated


title: Donor 3440, Batch 1, 17mM EtOH, biol rep 3

value: 7-Day 17mM EtOH Exposure


title: 10A_M_1675


title: 10A_M_1673


title: BCP52

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

country: China

institute: Guangxi Medicla University

data_processing:
RNA-seq analysis was carried out by Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).
The quality control of the raw sequencing data, including the purity and quantity of RNA and RNA integrity number (RIN) values, was appraised by adopting FastQC software.
After pretreatment using Fastp software, the filtered data were compared with the human reference genome (HG19) using HISAT2 (Pertea et al., 2016) and StringTie software (Pertea et al., 2015) with the default mapping parameters before merged the data by Cufflinks software (Ghosh and Chan, 2016).
The genes complyed with adjusted p < 0.05 and |fold change|> 2 were considered to be the differential genes (DEGs)
The differentially expressed genes were annotated based on the Gene Ontology (GO) database and the outcome was described by GOplot.
Supplementary files format and content: The excel file includes the RPKM value for each Sample

source_name: Bladder non-tumor tissue

extract_protocol:
Total RNA  was extracted with Trizol reagent (Life Technologies Corporation, Carlsbad, CA, USA).
RNA-seq library was constructed in line with the instruction of the Illumina TruSeq RNA Sample Preparation Kit (Illumina)

value: Bladder non-tumor tissue


title: Donor 3440, Batch 1, 17mM EtOH, biol rep 1


title: BCP51


title: 10A_M_1672


title: BCP50


title: Donor 9429, Batch 2, 0mM EtOH, biol rep 4


title: BCP49


title: meningioma_cell_differentiated

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

data_processing:
Sequencing data base-calling, demultiplexing, alignment to mouse genome and transcript quantification were performed by Cell Ranger v6.0.2 (10x Genomics)
Assembly: GRCh38.p13
Supplementary files format and content: Processed data file consist of the three standard  cell ranger output file named barcodes, features and matrix that can be found  in the folder  …/outs/filtered_feature_bc_matrix

molecule: polyA RNA

source_name: primary culture derived from human menigioma specimens (M69, M71)

growth_protocol: Meningioma tissues were obtained within 2h after surgery, dissected into two portions and processed for RNA isolation and cell culture. For cell culture, tissue was mechanically dissociated, filtered through a 70μm cell strainer (Corning), washed in PBS and cultured in DMEM-F12 (EuroClone), 10% fetal bovine serum (FBS, Gibco), 2mM L-glutamine (EuroClone), 1% penicillin/streptomycin (EuroClone), for up to 1 week1. Successful subconfluent cultures giving origin to living cell monolayers (p0) were detached using TrypLE Express (Gibco) and divided into flasks containing either the same FBS-enriched medium (differentiated cells, named PD-Mg- S) or in a stem-permissive medium composed of FBS-free DMEM-F12/ Neurobasal (1:1, Gibco), 2mM Lglutamine, 1% penicillin/streptomycin, B27 supplement (Gibco), 20 ng/ml bFGF and 20 ng/ml EGF (Miltenyi Biotec). Under these conditions cells grew as floating aggregates/spheroids, therefore, to obtain more experimentally manageable cultures, plates/flasks were coated with 1:200 growth factor-reduced Matrigel™ (Corning) allowing monolayer cell growth.

extract_protocol:
Single-cell suspensions were washed twice in PBS-EDTA to reduce ambient RNA contamination and avoid cell aggregation. Both cell populations from the two meningiomas (one male, M71 and one female, M69) were pooled. and a total of 6000 cells from each pool was used for emulsion partitioning using Chromium Controller (10x Genomics).
Sequencing libraries were generated using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Dual Index (10x Genomics). Libraries were controlled for correct size using High Sensitivity D1000 ScreenTape System (Agilent). Libraries were then pooled and quantified by real-time PCR using PhiX Control v3 (Illumina) as a reference.

treatment_protocol: No treatement was performed

tag: sample id

value: M69 female, M71 male

tag: culture condition

value: Foetal Bovine Serum containing medium


title: meningioma_stem_cell

value: EGF/FGF containing medium


title: Donor 9429, Batch 2, 0mM EtOH, biol rep 2


title: BCP48


title: 10A_M_1670


title: 10A_M_1671


title: 10A_M_1669


title: Donor 9429, Batch 2, 0mM EtOH, biol rep 1


title: Donor 9429, Batch 2, 2mM EtOH, biol rep 4


title: 10A_M_1666


title: BCP45


title: Donor 9429, Batch 2, 2mM EtOH, biol rep 3


title: Donor 3440, Batch 1, 17mM EtOH, biol rep 2


title: 10A_M_1665


title: BCP44


title: Donor 9429, Batch2, 2mM EtOH, biol rep 2


title: Donor 9429, Batch 2, 0mM EtOH, biol rep 3


title: BCP43


title: Donor 9429, Batch 2, 17mM EtOH, biol rep 4


title: 10A_M_1662


title: Donor 9429, Batch 2, 2mM EtOH, biol rep 1


title: 10A_M_1661


title: 10A_M_1664


title: BCP42


title: Donor 9429, Batch 2, 17mM EtOH, biol rep 3


title: 10A_M_1659


title: BCP40


title: BCP47


title: 10A_M_1667


title: 10A_M_1657


title: Donor 9429, Batch 2, 17mM EtOH, biol rep 2


title: BCP46


title: BCP39


title: Donor 9429, Batch 2, 17mM EtOH, biol rep 1


title: 10A_M_1656


title: 10A_M_1655


title: Donor 9429, Batch 1, 0mM EtOH, biol rep 4


title: BCP38


title: BCP37


title: Donor 9429, Batch 1, 0mM EtOH, biol rep 3


title: Donor 9429, Batch 1, 0mM EtOH, biol rep 2


title: BCP36


title: 10A_M_1652


title: Donor 9429, Batch 1, 2mM EtOH, biol rep 4


title: BCP35


title: 10A_M_1651


title: BCP41


title: 10A_M_1650


title: Donor 9429, Batch 1, 2mM EtOH, biol rep 3


title: Donor 9429, Batch 1, 2mM EtOH, biol rep 2


title: BCP33


title: BCP32


title: 10A_M_1648


title: Donor 9429, Batch 1, 2mM EtOH, biol rep 1


title: Donor 9429, Batch 1, 0mM EtOH, biol rep 1


title: 10A_M_1649


title: BCP34


title: Donor 9429, Batch 1, 17mM EtOH, biol rep 4


title: BCP31


title: BCP30


title: Donor 9429, Batch 1, 17mM EtOH, biol rep 3


title: 10A_M_1646


title: 10A_M_1647


title: BCP29


title: 10A_M_1653


title: LV_18

value: Liver


title: 10A_M_1645


title: Donor 9429, Batch 1, 17mM EtOH, biol rep 2


title: BCP28


title: 10A_M_1643


title: Donor 9429, Batch 1, 17mM EtOH, biol rep 1


title: BCP27


title: Donor BJ, Batch 2, 0mM EtOH, biol rep 4

source_name: BJ

value: BJ


title: BCP26


title: 10A_M_1641


title: 10A_M_1640


title: Donor BJ, Batch 2, 0mM EtOH, biol rep 3


title: BCP23


title: Donor BJ, Batch 2, 0mM EtOH, biol rep 2


title: BCP24


title: 10A_M_1639


title: BCP22


title: LV_43


title: 10A_M_1638


title: 10A_M_1637


title: Donor BJ, Batch 2, 2mM EtOH, biol rep 4


title: BCP21


title: BCP20


title: Donor BJ, Batch 2, 2mM EtOH, biol rep 3


title: BCP19


title: 10A_M_1633


title: Donor BJ, Batch2, 2mM EtOH, biol rep 2


title: BCP18


title: Donor BJ, Batch 2, 17mM EtOH, biol rep 4


title: LV_31


title: Donor BJ, Batch 2, 2mM EtOH, biol rep 1


title: BCP17


title: 10A_M_1630


title: BCP15


title: 10A_M_1629


title: Donor BJ, Batch 2, 17mM EtOH, biol rep 3


title: Donor BJ, Batch 2, 0mM EtOH, biol rep 1


title: Donor BJ, Batch 2, 17mM EtOH, biol rep 1


title: BCP2


title: 10A_M_1628


title: 10A_M_1634


title: BCA52

source_name: Bladder tumor tissue

value: Bladder tumor tissue


title: Donor BJ, Batch 1, 0mM EtOH, biol rep 4


title: Donor BJ, Batch 1, 0mM EtOH, biol rep 3


title: 10A_M_1626


title: BCA49


title: 10A_M_1625


title: 10A_M_1624


title: Donor BJ, Batch 1, 0mM EtOH, biol rep 2


title: Donor BJ, Batch 1, 0mM EtOH, biol rep 1


title: 10A_M_1632


title: 10A_M_1631


title: BCA47


title: BCA50


title: 10A_M_1623


title: BCP13


title: Donor BJ, Batch 2, 17mM EtOH, biol rep 2


title: Donor BJ, Batch 1, 2mM EtOH, biol rep 4


title: Donor BJ, Batch 1, 2mM EtOH, biol rep 3


title: BCA45


title: 10A_M_1620


title: 10A_M_1619


title: Donor BJ, Batch 1, 2mM EtOH, biol rep 2


title: BCA44


title: BCA43


title: Donor BJ, Batch 1, 2mM EtOH, biol rep 1


title: 10A_M_1627


title: BCA42


title: Donor BJ, Batch 1, 17mM EtOH, biol rep 4


title: 10A_M_1617


title: 10A_M_1618


title: Donor BJ, Batch 1, 17mM EtOH, biol rep 2


title: 10A_M_1615


title: BCA48


title: Donor BJ, Batch 1, 17mM EtOH, biol rep 3


title: Donor BJ, Batch 1, 17mM EtOH, biol rep 1


title: 10A_M_1614


title: BCA40


title: BCA38


title: 10A_M_1613


title: Donor 12455, 0mM EtOH, biol rep 4


title: BCA37


title: BCA36


title: 10A_M_1611


title: Donor 12455, 0mM EtOH, biol rep 2


title: 10A_M_1610


title: 10A_M_1612


title: Donor 12455, 0mM EtOH, biol rep 3


title: BCA35


title: Donor 12455, 0mM EtOH, biol rep 1


title: BCA34


title: 10A_M_1609


title: LentiAS 2 [Hi-C]

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

data_processing:
Contact matrices were generated on the Rnor6.0/rn6 version of the Rattus norvegicus genome assembly  (https://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz) using HiC-Pro (https://github.com/nservant/HiC-Pro).
Contact matrix .matrix files are in standard triple sparse format (https://nservant.github.io/HiC-Pro/RESULTS.html), which has three columns: The first two columns show the indices of the interacting chromosomal locations (see below for description); the third column shows the read count
The genomic coordinates of each index in the first two columns of the .matrix files can be found in the matching .bed files.
When necessary,  .hic files were prepared from the .matrix files (and their corresponding .bed files) using the hicdc2hic routine of the HiCDCPlus Bioconductor package.
Genome build: Rn6 (Rnor_6.0)

organism: Rattus norvegicus

source_name: Primary rat Schwann cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 4 μM forskolin, 5 ng/ml heregulin-β1 and antibiotics, in surface modified 75cc Primaria flasks. Cells were fed every other day and passaged at 80% confluence.

extract_protocol: HiC was performed using the Arima-HiC kit. As per their protocol, we tested the amount of input sample beforehand and we used 2 million cells per each independent sample. We did QC on samples in every recommended step. Sonication was performed using the Covaris s220 instrument to a fragment size of 300-400bp (Settings: Power: 5, Duty Factor: 10%, Cycles per Burst: 200, and Time: 60 sec per process). We used KAPA Hyper Prep Kit to generate libraries. The primers used for indexing were obtained from Illumina, and the libraries were quantified and QC was done using the KAPA Library Quantification Kit. Libraries were sequenced by GENEWIZ using the Illumina HiSeq 2500 system to acquire 150 bp paired-end sequence reads, reaching 300M reads for each sample based on total usable reads >20Kb.

treatment_protocol: Overexpression of the Egr2-AS-RNA (and the backbone virus control carrying GFP) was performed with a lentiviral construct at a concentration of 2UFC/cell, with polybrene at a 1:1500 concentration, for 48 hours. The virus generation was described in detail in previous work (Martinez-Moreno et al., 2017). The plasmid to generate the lentivirus was deposited to Addgene and is available to order (#177737).

value: sciatic nerve

value: Schwann cells

value: infected/treated with virus that will overexpress the Egr2-AS-RNA


title: BCA41


title: LentiAS 1 [Hi-C]


title: LentiGFP 2 [Hi-C]

value: infected/treated with control virus


title: BCA30


title: 10A_M_1608


title: BCA32


title: 10A_M_1607


title: 10A_M_1606


title: Donor 12455, 2mM EtOH, biol rep 3

value: NGN2-induced neurons

value: WT

value: 7-Day 2mM EtOH Exposure

value: Day 28


title: Donor 12455, 2mM EtOH, biol rep 1


title: BCA29


title: Donor 12455, 2mM EtOH, biol rep 2


title: Donor 12455, 2mM EtOH, biol rep 4


title: Donor 12455, 17mM EtOH, biol rep 3


title: BCA28


title: 10A_M_1604

value: male


title: Donor 12455, 17mM EtOH, biol rep 4

value: 7-Day 17mM EtOH Exposure


title: 10A_M_1605


title: 10A_M_1603


title: BCA33


title: 10A_M_1602


title: Donor 12455, 17mM EtOH, biol rep 1


title: BCA27


title: Donor 12455, 17mM EtOH, biol rep 2


title: LentiGFP 2 [ATAC-seq]

description: ATAC DNA

data_processing:
FASTQ files of sequencing reads for each sample provided by GENEWIZ were aligned to the RGSC6.0/rn6 Rattus norvegicus reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz) using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads with a mapping quality of 30 or better were retained for analysis. Duplicate reads were remove with Picard (https://github.com/broadinstitute/picard).
ATAC peaks were detected with MACS2 (https://pypi.org/project/MACS2/). Peaks with a -log10qvalue at peak summit of 5 or greater were retained for further analysis.
Gene promoters were defined as the regions from -1500 to +500 nucleotides with respect to the annotated Transcription Start Sites in RefSeq, as extracted from the refGene.txt file (http://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/refGene.txt.gz).
ATAC peaks mapping to promoters were detected with the intersectBed routine of bedtools (https://bedtools.readthedocs.io/en/latest/), using the peaks coordinates and the promoter coordinates as inputs.
ATAC read mapping to peaks or promoter regions were counted and summarized with featureCounts (https://doi.org/10.1093/bioinformatics/btt656).
Assembly: Rn6 (Rnor_6.0)
Supplementary files format and content: narrowPeak files

extract_protocol: For each biological replicate, 100,000 cells were used to prepare ATACseq libraries following a modified protocol from Kaestner’s lab (Ackermann et al., 2016). After the transposition reaction, using the Nextera DNA Library Prep Kit, DNA was isolated using a MinElute Reaction Cleanup Kit. To make the libraries, we used the NEBNext High-Fidelity 2X PCR Master Mix. Primers (universal and indexing) used are listed in Table 1. For multiplexing, we used the same universal primers for every sample, and every sample had their unique indexing primer. Quality control (QC) of the libraries was performed before sequencing using KAPA Library Quantification Kit for Illumina Platforms.


title: LentiAS 2 [ATAC-seq]

description: ATAC DNA


title: LentiGFP 1 [Hi-C]


title: LentiAS 2 [RNA-seq]

data_processing:
FASTQ files of sequencing reads for each sample provided by GENEWIZ were aligned to the RGSC6.0/rn6 Rattus norvegicus reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz) using GSNAP (https://doi.org/10.1093/bioinformatics/btq057). Reads with a mapping quality of 30 or better were retained for analysis.
Read summarization was done with featureCounts (https://doi.org/10.1093/bioinformatics/btt656) using the RefSeq annotation of the rn6 genome extracted from the refGene.txt file (http://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/refGene.txt.gz).
Assembly: Rn6 (Rnor_6.0)
Supplementary files format and content: LentiAS.rnaseq.counts.txt: Tab-delimited text file includes counts.

extract_protocol: For each biological replicate, total RNA was isolated from 1 million Rat Schwann cells. 2 micrograms of RNA were submitted to GENEWIZ, used to generate libraries and sequencing on the Illumina HiSeq 2500 in a 50 bp paired-end run.


title: BCA26


title: BCA25


title: LentiAS 1 [ATAC-seq]

description: ATAC DNA


title: BCA24


title: 10A_M_1601


title: 10A_M_1600


title: 10A_M_1622


title: LentiAS 1 [RNA-seq]


title: LentiGFP 2 [RNA-seq]


title: Sublibrary 6, scRNAseq

city: Raleigh

first: Thomas

last: Rudibaugh

state: North Carolina

address: 840 Main Campus Dr, Partners II Room 3700

institute: North Carolina State University

description:
50,000 reads/cell
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz

library_source: transcriptomic single cell

data_processing:
A splici (spliced + intron) index was created using salmon (v1.7.0) using human GENCODE v39 and hg38 human reference genome.
Sequences were mapped to the splici indexed using salmon and quantified using alevin fry (v0.5.0). Seurat (v4.1.1) was used to filter, process, and analyze gene expression matrices.
The eight sequenced sublibraries were merged into a single Seurat object and reads not matching sample barcodes within a hamming distance of 1 were filtered out. QC filtering was performed removing cells that did not meet the following criteria: Count_RNA > 2000, nFeature_RNA > 1000, mitochondrial percentage < 10%, resulting in 43,844 high-quality cells for analysis.
SCTransform was then used to normalize for read depth across cells, scale the data, and find variable features. Mitochondrial mapping percentage was regressed out during normalization to remove this confounding source of variation.
Principle component analysis (PCA) was performed and an ElboxPlot was generated to determine the number of informative dimensions (50).
Assembly: hg38
Supplementary files format and content: matrix.mtx.gz; Matrix of gene expressions
Supplementary files format and content: barcodes.tsv.gz; features.tsv.gz

source_name: H1 cell line (NIH 0043)

extract_protocol:
To obtain a single cell dissociation, the papain dissociation kit was used according to the manufacturer’s protocols (Worthington). Briefly, 2-3 organoids were initially broken into smaller pieces using a sterile razer before dissociation in papain solution. The cells were broken up further by gently pipetting using a 1000µL pipette.
Barcoding and library preparation of single cell suspensions was performed according to the manufacturer’s protocols (SplitBio). The cells were fixed and lysed, before multiple rounds of barcoding and cell measurements were employed to ensure the cells were in a uniform single cell suspension and each cell was given a unique barcode.

value: H1 cell line (NIH 0043)

value: hESC

tag: condition

value: H1-derived cultures (2-D, 3-D)

value: dopamine, cocaine, morphine, untreated


title: Sublibrary 7, scRNAseq


title: Sublibrary 8, scRNAseq


title: 10A_M_1599


title: BCA23


title: BCA22


title: Sublibrary 5, scRNAseq


title: BCA21


title: LentiGFP 1 [RNA-seq]


title: Expanded regulatory T cells 3

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Reads were aligned using STAR v2.6.1c (GRCh38 Ensembl 98). The reads per gene were counted using FeatureCount of the R v3.6.1 package Subread v2.0.1. Differential gene expression was conducted using DESeq v1.24.0.
Assembly: hg38
Supplementary files format and content: raw read counts in comma separated format
Supplementary files format and content: DeSeq2 normalized read counts in comma separated format

source_name: Regulatory T cells

growth_protocol: The regulatory T cells (Tregs) used in this study were produced according to our previously published GMP-compliant Treg expansion protocol and were subjected to the implemented lot-release criteria to finally fulfill the criteria of the Investigational Medical Product (IMP). Non-expanded Tregs were directly cryopreserved after CD25-enrichment and stored in liquid nitrogen identical to the IMP-Tregs after ex vivo expansion.

extract_protocol:
mRNA of non-expanded and IMP-Tregs was isolated with the NucleoSpin RNA Kit for RNA isolation (Machery Nagel).
RNA libraries were prepared for sequencing using the Illumina protocol.

value: Regulatory T cells

value: Expanded for 21 days


title: LentiGFP 1 [ATAC-seq]

description: ATAC DNA


title: 10A_M_1597


title: Sublibrary 4, scRNAseq


title: Sublibrary 3, scRNAseq


title: 10A_M_1598


title: Expanded regulatory T cells 1


title: Sublibrary 2, scRNAseq


title: 10A_M_1593


title: BCA19

value: Bladder tumor tissue


title: Expanded regulatory T cells 2


title: BCA20


title: 10A_M_1596


title: BCA18


title: 10A_M_1592


title: Sublibrary 1, scRNAseq


title: Non-expanded regulatory T cells 2

value: Non-expanded


title: BCA17


title: 10A_M_1591


title: RNA-seq, SUM159, WT, rep2

description: RNA-seq.xlsx

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases using Trim_Galore (v0.4.2_dev).
For RNA-seq, cleaned reads were either mapped to  hg19 reference genome, guided by gene models. Both reference genomes and gene models were obtained from Illumina iGenome website. Gene expression quantification were carried out by RSEM pipeline. Differential gene expression was called using DESeq2 with default parameters.
For ChIP-seq,reads were trimmed to remove the adapter sequences and low quality bases using Trim_Galore (v0.4.2_dev). Cleaned reads were then mapped to hg19 reference genome obtained from Illumina iGenome website  by Bowtie2 (v.2.2.9) with parameters: -N 1 -L 25 --no-mixed --no-discordant. PCR duplicates and reads with low mapping quality (MAPQ < 10) were removed using SAMtools (v1.4). Biological replicate alignment files were merged. Bigwig coverage were generated using “bamCompare” function from deepTools package with parameters: -bl hg19-blacklist.v2.bed --ratio subtract -bs 20 -p 16 –normalizeUsing RPKM -b1 IP.bam -b2 input.bam –extendReads. “hg19-blacklist.v2.bed” was obtained from https://github.com/Boyle-Lab/Blacklist/tree/master/lists/hg19-blacklist.v2.bed.gz.
Genome_build: hg19
Supplementary_files_format_and_content: gene count files by RSEM pipeline end with ".genes.results"; DESeq2 result is in RNA-seq.xlsx.gz; ChIP-seq called peaks file end with ".bed"; ChIP-seq signal files normalized by input end with ".bw"

source_name: SUM159, WT

growth_protocol: MCF7 and MCF7ras+SS cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin/streptomycin. SUM159 cells was maintained in Nutrient Mix F12 (HAM) medium supplemented with 10% (v/v) heat-inactivated FBS and 1% (v/v) penicillin/streptomycin.

extract_protocol:
RNA-seq: Total RNA was extracted using TRI-reagent and purified using the Direct-zol RNA MiniPrep Kit (Zymo). For KAT2B ChIP, MCF7ras+SS cells were harvested and double-crosslinked in suspension with 2mM DSG in PBS for 30 minutes at room temperature, washed with PBS twice and further crosslinked with 1% formaldehyde (FA) in PBS for 15 minutes at room temperature. Crosslinking was quenched by addition of glycine to final concentration of 125mM and incubated at room temperature for 10 min. For all other ChIPs, MCF7ras+SS cells were subjected to crosslinking in 1% formaldehyde (FA) in PBS for 15 minutes at room temperature and followed by quenching with 125mM glycine for 10 minutes. Fixed cells were then subjected to standard ChIP lysis protocol to release chromatin. Released chromatin was sonicated to obtain fragments between 100-300bp, pre-cleared and used for IP with antibody-Dynabead complex. Captured fragments were subjected to several rounds of washes before elution with SDS buffer.
RNA-seq: Equal amount of RNA preparations (extracted from equal number of cells) from each sample were subjected to ribosomal RNA depletion using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB Cat# E6310) and library construction using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB Cat# E7760), according to manufacturer’s protocol. ChIP-seq: Eluted DNA and DNA from relevant input materials was purified and made into libraries using NEBNext Ultra II DNA kit (NEB Cat #: E7645). For both RNA-seq and ChIP-seq libraries, average fragment size was determined on Agilent High Sensitivity DNA and D1000 Screentape system (Agilent Cat #:5067-4626, 5067-5582), quantified using Qubit High Sensitivity DNA system (Life Tech Cat# Q32854), and pooled in equimolar. Pooled libraries were sequenced on the Illumina HiSeq platform.

treatment_protocol: For RNA-seq from MCF7, cells were cultured in phenol red-free DMEM supplemented with 5% charcoal stripped FBS and 1% (v/v) penicillin/streptomycin for 72 hours. For RNA-seq from MCF7ras+SS, cells were transduced with scrambled/NELF-E shRNA or transfected with scrambled/KAT2B siRNA and then treated with 1μg/ml of Doxycycline or vehicle DMSO for 72 hours. For RNA-seq from Garcinol (GA)-treated MCF7ras+SS cells, cells were treated with 16μM GA and 1μg/ml of Doxycycline or vehicle DMSO for 72 hours.

value: Wildtype


title: 10A_M_1590


title: RNA-seq, SUM159, WT, rep1

description: RNA-seq.xlsx


title: Non-expanded regulatory T cells 1


title: Cell, human OC-like cells 16

city: Perth

first: Sarah

last: Rashid

state: WA

address: Nedlands

department: School of Biomedical Sciences

country: Australia

institute: The Univeristy of Western Australia

data_processing:
Illumina bc12fastq 2.20.0.422 was used to produce primary sequence data
Cleaned reads were aligned agaist Homo sapiens genome (build version hg38)
Star aligner v.2.5.3a was used to map reads to genomic sequences
FeatureCounts v1.5.3 was used to summarise raw counts at the gene level
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw read counts for each sample

source_name: OC-like cells

extract_protocol:
AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA libraries for RNAseq were prepared using the TruSeq stranded RNA sample preparation protocol.

value: OC-like cells

value: OC differentiation media


title: BCA15


title: 10A_M_1587

source_name: C57BL/6J Male P56 Mouse Brain


title: Cell, human OC-like cells 15


title: Non-expanded regulatory T cells 3


title: 10A_M_1586


title: RNA-seq, SUM159, NELFEKO, rep1

description: RNA-seq.xlsx

source_name: SUM159, NELFEKO

value: NELFEKO


title: BCA13


title: BCA12


title: BCA14


title: 10A_M_1585


title: Cell, human OC-like cells 12


title: RNA-seq, siKAT2B_MCF7Ras, siKAT2B_DOX, rep1

description: RNA-seq.xlsx

source_name: siKAT2B_MCF7Ras, siKAT2B_DOX

value: transfected with KAT2B siRNA

value: Doxycycline


title: 10A_M_1584


title: RNA-seq, siKAT2B_MCF7Ras, siKAT2B_DOX, rep2

description: RNA-seq.xlsx


title: Cell, human OC-like cells 13


title: BCA11


title: 10A_M_1583


title: Cell, human OC-like cells 11


title: 10A_M_1582


title: RNA-seq, siKAT2B_MCF7Ras, scramble_DOX, rep1

description: RNA-seq.xlsx

source_name: siKAT2B_MCF7Ras, scramble_DOX

value: transfected with scrambled siRNA


title: BCA16


title: Cell, human OC-like cells 10


title: BCA9


title: RNA-seq, shNELFE_MCF7Ras, shNELFE_DOX, rep2

description: RNA-seq.xlsx

source_name: shNELFE_MCF7Ras, shNELFE_DOX

value: transduced with NELF-E shRNA


title: 10A_M_1581

value: male


title: Cell, human OC-like cells 9


title: RNA-seq, SUM159, NELFEKO, rep2

description: RNA-seq.xlsx


title: Cell, human OC-like cells 14


title: BCA8


title: RNA-seq, shNELFE_MCF7Ras, shNELFE_DOX, rep1

description: RNA-seq.xlsx


title: BCA7


title: BCA6


title: RNA-seq, siKAT2B_MCF7Ras, scramble_DOX, rep2

description: RNA-seq.xlsx


title: RNA-seq, shNELFE_MCF7Ras, shNELFE_Con, rep2

description: RNA-seq.xlsx

source_name: shNELFE_MCF7Ras, shNELFE_Con

value: DMSO vehicle


title: RNA-seq, shNELFE_MCF7Ras, shNELFE_Con, rep1

description: RNA-seq.xlsx


title: BCA10


title: Cell, human PBMC 8

source_name: PBMC

value: PBMC

value: Control media


title: BCA4


title: 10A_M_1577


title: 10A_M_1579


title: Cell, human PBMC 5


title: Cell, human PBMC 6


title: Cell, human PBMC 7


title: RNA-seq, shNELFE_MCF7Ras, scramble_DOX, rep2

description: RNA-seq.xlsx

source_name: shNELFE_MCF7Ras, scramble_DOX

value: transduced with scrambled shRNA


title: BCA5


title: RNA-seq, shNELFE_MCF7Ras, scramble_DOX, rep1

description: RNA-seq.xlsx


title: BCA3


title: Cell, human PBMC 4


title: 10A_M_1575


title: Cell, human PBMC 3


title: RNA-seq, shNELFE_MCF7Ras, scramble_Con, rep2

description: RNA-seq.xlsx

source_name: shNELFE_MCF7Ras, scramble_Con


title: RNA-seq, shNELFE_MCF7Ras, scramble_Con, rep1

description: RNA-seq.xlsx


title: Cell, human PBMC 2


title: 10A_M_1574


title: 10A_M_1578


title: BCA2


title: BCA1


title: 10A_M_1580


title: 10A_M_1573


title: 10A_M_1576


title: 10A_M_1572


title: RNA-seq, MCF7, WT, rep2

description: RNA-seq.xlsx

source_name: MCF7, WT

value: WT


title: 10A_M_1571


title: Cell, human PBMC 1


title: RNA-seq, MCF7, WT, rep1

description: RNA-seq.xlsx


title: 10A_M_1569


title: RNA-seq, MCF7Ras, GA_DOX, rep2

description: RNA-seq.xlsx

source_name: MCF7Ras, GA_DOX

value: Garcinol + Doxycycline


title: U251, control, rep1

city: GuangZhou

first: Waiyip

last: Liang

address: Guangzhou Higher Education Mega Centre, Panyu District, Guangzhou

institute: South China of Technology

data_processing:
The expression abundance was measured in transcripts per million (TPM), which is independent of the mean expressed transcript length and is comparable across samples.
Expression correlation was characterized by Pearson's correlation coefficient between TPM of all transcripts.
Differentially expressed genes (DEGs) were identified through Cufflinks-Cuffdiff pipelines. Only genes with adjusted p-value < 0.05 were considered as DEGs and used for further analysis.
Clustering of genes was implemented using the software program Cluster. The functional annotation tool DAVID was used for Gene Ontology (GO) enrichment.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: U251, control

growth_protocol: NPC cells were cultured in N2B27 medium (50% DMEM/F12, 50% neurobasal, 0.5× N2, 0.5× B27, 1% Glutamax, 1% NEAA, 5 μg/mL insulin and 1 μg/mL heparin plus 5 μM SB431542 and 5 μM dorsomorphin.

extract_protocol:
NPC cells, NPC-KRASG13D, U251-GSC, and U118MG-GSC were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U118-MG and U251 cells were labelled with CD133/2 antibody kit, and the CD133+ cells were sorted and analyzed by flow cytometry.

value: glioma cell

value: no treatment


title: RNA-seq, MCF7Ras, GA_DOX, rep1

description: RNA-seq.xlsx

value: Wildtype


title: U251-GSC, CD133+

value: glioma stem cell

value: CD133+ cells were sorted


title: U251, control, rep2


title: PC3 + TOP2A inhibitor ICRF-193_rep3

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

description: log2FoldChange_TOP2Ai_vs_DMSO_PC3_RNAseq.xlsx

data_processing:
Fastaq files were aligned to the hg38 genome assembly using Bowtie2 (version 2.3.4.3) with default parameters
for RNA SEQ, reads were aligned to the reference genome (ensembl version 82) with Subread (i.e. subjunc, version 1.4.6-p4; 50) allowing up to 16 alignments per read (options: –trim5 10 –trim3 15 -n 20 -m 5 -B 16 -H –allJunctions). Count tables were generated with Rcount 51 with an allocation distance of 100 bp for calculating the weights of the reads with multiple alignments, considering the strand information, and a minimal number of 5 hits. For each gene, exon coverage was calculated using a custom pipeline and then normalized in reads per kilobase per million (RPKM) (Mortazavi et al., 2008), the method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: PC3 cells (prostate cancer bone metastasis)

growth_protocol: The PC3 cell line was purchased from the American Type Culture Collection. PC3 cells were cultured in RPMI 1640 medium and Ham's F12 medium (1:1; Gibco) containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). 2.5x106 cells were seeded in 150 mm tissue culture dishes (TPP®) and cultured for 2 to 3 days. All cells were regularly tested for mycoplasma contamination.

extract_protocol:
Total RNA from three independent dishes of PC3 cells treated with DMSO, OG-L002 or ICRF-193 were purified with TRIzol reagent (Life Technologies). In order to remove DNA contaminants, the samples were treated with 1U DNaseI (Thermo Scientific) for 1h at 37°C and the RNA samples were re-purified using TRIzol. The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany).
The TruSeq RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were poly A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA). The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq SR Cluster Kit HS4000 (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT. Sequencing was performed on the NovaSeq 6000 single end 100 bp using the TruSeq SBS Kit HS4000 (Illumina, Inc, California, USA).

treatment_protocol: Cells were treated for 48 hours with 10uM of the KDM1 inhibitor OG-L002 or with the TOP2A inhibitor ICRF-193; control cells were treated with DMSO.

tag: antibody

value: 10uM ICRF-193 for 48h


title: RNA-seq, MCF7Ras, DMSO_DOX, rep2

description: RNA-seq.xlsx

source_name: MCF7Ras, DMSO_DOX


title: PC3 + TOP2A inhibitor ICRF-193_rep2

value: PC3 cells (prostate cancer bone metastasis)


title: PC3 + TOP2A inhibitor ICRF-193_rep1


title: PC3 + KDM1 inhibitor OG-L002_rep3

description: log2FoldChange_KDM1Ai_vs_DMSO_PC3_RNAseq.xlsx

value: 10uM OG-L002 for 48h


title: U118MG-GSC, CD133+


title: 10A_M_1567

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: RNA-seq, MCF7Ras, DMSO_DOX, rep1

description: RNA-seq.xlsx

value: Doxycycline


title: U118MG, control

source_name: U118MG, control


title: PC3 + DMSO_rep3

value: DMSO for 48h


title: 10A_M_1568

tag: age

value: male


title: PC3 + KDM1 inhibitor OG-L002_rep2


title: 10A_M_1565

tag: Sex


title: 10A_M_1563

tag: strain


title: PC3 + KDM1 inhibitor OG-L002_rep1


title: RNA-seq, MCF7, NELFEKO, rep2

description: RNA-seq.xlsx

source_name: MCF7, NELFEKO

value: NELFEKO

tag: genotype

value: NELFE KO


title: ChIP-seq, shNELFE_MCF7Ras_SLUG-ChIP, shNELFE_DOX_IP, rep1

description: ChIP-seq.shNELFE_MCF7Ras_SLUG-ChIP.shNELFE_DOX_rep12.bw; peaks_MCF7Ras.shNELFE_DOX_SLUG_rep12_np09.bed

value: transduced with NELF-E shRNA

tag: treatment

value: SLUG (Cell Signaling Technology, 9585S)


title: 10A_M_1564


title: NPC cells, control, rep1

source_name: NPC cells, control

value: Human neural stem cells (H1 cells)

value: WT

value: Generation of NPCs from H1 cells


title: NPC cells, control, rep4


title: RNA-seq, MCF7, NELFEKO, rep1

description: RNA-seq.xlsx


title: 10A_M_1560

source_name: C57BL/6J Male P56 Mouse Brain


title: NPC-KRAS G13D cells, rep3

source_name: NPC-KRAS G13D cells

value: KRASG13D mutation


title: ChIP-seq, shNELFE_DOX_inputFor_RNAPII_AND_SLUG, rep2


title: ChIP-seq, shNELFE_MCF7Ras_SLUG-ChIP, shNELFE_DOX_IP, rep2


title: PC3 + DMSO_rep1


title: NPC-KRAS G13D cells, rep4


title: 10A_M_1562


title: Raji TSA mnase rep3

description: Treated with 2 µM Trichostatin A for 24 hours

source_name: Raji B cells

extract_protocol:
For G4 access:  Trypsinized HaCaT cells, resuspended S2 cells and suspension of K562, Raji and mouse ESC cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). HaCaT cells were suspended in 5 mL of permeabilization buffer (150 mM of sucrose, 80 mM KCl, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) and homogenized using a dounce (40 strokes). For MNAse digestion, 5x106 cells per titration point were resuspended in 50 μL of prewarmed permeabilization buffer supplemented with 0.2% (v/v) NP40 and incubated 5 minutes at 37ºC. Digestion took place by adding a volume of 500 mL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) to each reaction. Either 3.1, 6.2, 12.5, 25 or 50U MNase (Merck, 10107921001) were added to the MNase reaction buffer and incubated at 37 ºC for 10 min. Digestion was stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. The digestions were incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Tris.HCl pH 8) and 1 mL of water. Before DNA purification, digestions were incubated with 5 mL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 8 mL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours. To verify the performance of the digestion, 125 μL of each sample was cleaned-up using QIAquick PCR Purification Kit (QIAGEN, 28106). Digestions were assessed by agarose gel and Bioanalyzer (Fig. 1c). The remaining digestions were purified by phenol-chloroform and ethanol precipitation for subsequent steps.  Yeast S288C were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Pellets from 100mL culture (OD: 0.5) were suspended in 600ul cell breaking buffer (20% glycerol, 100mM Tris pH 7.5), 600µl zirconia beads (0.5mm), 10µl of 100x protease inhibitors (Roche, 06538282001). Beads beating was performed in 1.5mL screw cap tubes in a Bullet Blender (Next advance) for 4 x 3min at a strength of 8 in a cold room. Cell suspensions were recovered by puncturing the bottom of tube (23 gauge syringes) and spinned at 170 rcf for 3min into a 5mL Eppendorf tube. Everything was transferred into 1.5mL Eppendorf, then centrifuged for 5min at max speed and the top layers were discarded. Samples were suspended in 300ul of prewarmed NP buffer (50mM NaCl, 10mM Tris pH 7.4, 5mM MgCl2, 1mM CaCl2, 0.2% NP40 (v/v), 0.5mM spermidine (Sigma, S0266-1G), 0.007% B-Mercaptoethanol (Sigma, M3148-100ML). Digestion took place by adding a volume of 300µL prewarmed NP buffer supplemented with either 60u, 30u, 15u, 7.5u, 3.75, 1.9u, 1u of MNase (Merck 10107921001). Digestions were stopped on ice and by adding 150μL of stop buffer (5% SDS, 50mM EDTA). Before DNA purification, digestions were incubated with 5 µL of RNAse A (ThermoFisher, EN0531) at 37 ºC for 2 hours and with 10 µL of proteinase K (Euromedex, 09-0911) at 56 ºC for 2 hours. Purification was done with two consecutive phenol and one chloroform steps followed by ethanol and linear acrylamide precipitation. Purified DNAs were once again incubated with 5µl RNAse A (ThermoFisher, EN0531) to get rid of persistent RNA contaminations.     The phenol-chloroform purified DNAs were subjected to size selection to remove fragments larger than 100 bp. For that, 1 µg of each digestion product was migrated in a 4-20% polyacrylamide NovexTM TBE gel (ThermoFisher, EC6225BOX) at 100 V for 60 min. The gels were stained with Syber® Gold (ThermoFisher, S11494) for 30 min. Fragments according to the size range of 0-100 bp were cut out from the gel and transferred to 0.5-mL Eppendorf tubes, previously punctured in the bottom with a 0.45 µm needle. These tubes were inserted into 1.5-mL tubes and centrifuged 10 min at 15.300 rcf to move the cutted gel through the hole, generating gel beads. To elute the DNA from the beads, 700 μL of water was added and the tubes were incubated overnight at 55 ºC in a thermomixer at 1500 rpm. DNA was purified by transferring the samples (DNA eluate and gel beads) to the top of a 0.22 µm spin filter (Agilent 5185-5990). Spin filters were centrifuged 2 min at 15.300 rcf to recover the DNA eluate. DNA was precipitated with isopropanol and linear acrylamide. Size-selection was verified by Bioanalyzer (Fig. 1c). To assess the optimal MNase titration point in terms of G-quadruplex (G4) forming sequence enrichment, the relative amount of targeted G4s was evaluated by qPCR (Extended Data Fig. 1a). The titration points showing a percentage of mononucleosomal fraction of 30% of the total DNA (excluding subnucleosomal fraction) as quantified using Bioanalyzer chips gave the best qPCR enrichment in targeted G4s after size selection. This observation was further confirmed when sequencing the corresponding libraries.    For Pol II ChIP-seq, fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter;
G4access and ChIP-seq librairies were prepared usingNEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to standard protocol.

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

value: Drosophila melanogaster

tag: spike-in cell line

value: Trichostatin A

tag: concentration

value: 2 uM Trichostatin A

tag: duration

value: 24 hours


title: 10A_M_1561


title: ChIP-seq, shNELFE_MCF7Ras_SLUG-ChIP, scramble_DOX_IP, rep2

description: ChIP-seq.shNELFE_MCF7Ras_SLUG-ChIP.scramble_DOX_rep12.bw; peaks_MCF7Ras.scramble_DOX_SLUG_rep12_np09.bed

tag: cell line

value: transduced with scrambled shRNA

value: Doxycycline

tag: chip antibody


title: NPC cells, control, rep3

tag: cell type


title: NPC-KRAS G13D cells, rep2


title: NPC cells, control, rep2


title: 10A_M_1556

value: male


title: ChIP-seq, shNELFE_MCF7Ras_SLUG-ChIP, scramble_DOX_IP, rep1


title: Raji TSA mnase rep1

tag: experiment

tag: spike-in reference organisme


title: ChIP-seq, shNELFE_MCF7Ras_SLUG-ChIP, shNELFE_DOX_input, rep1


title: Raji TSA G4access rep2


title: single-cell RNA seq data of PBMC from patient MS72

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v3.1.0 (10X Genomics), according to the manufacturer’s instructions. Briefly, subsequent read alignments and transcript counting were done individually for each sample using the cellranger count pipeline with standard parameters. The cellranger aggr pipeline was used to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format

extract_protocol:
CSF samples were centrifuged for 5 min at 400 g and resuspended in 40 µl of X-Vivo 15 medium. 6 µl were used for counting in a Fuchs-Rosenthal chamber. The maximum of CSF cells used was 10,000 cells and if less than 10,000 cells were available, all cells were used. To carry out scRNA-seq with blood samples, gradient centrifugation was performed with blood using Lymphoprep (Stemcell). The cells in the interphase were extracted and washed  in 10 ml of X-Vivo 15 media. After manual cell counting (Fuchs-Rosenthal chamber), we used up to 10,000 cells for subsequent steps (see Table S1 for details).
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (both from 10X Genomics). Sample processing and library preparation were performed according to the manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out commercially on an Illumina Nextseq500 with 26-8-0-57 read setup.

tag: tissue

value: blood leukocytes

tag: diagnosis

value: RRMS

value: alemtuzumab


title: PC3 + DMSO_rep2

value: PC3 cells (prostate cancer bone metastasis)

tag: antibody

value: DMSO for 48h


title: Raji DMSO control TSA mnase rep3

description: Treated with 0,1% DMSO for 24 hours

value: DMSO

value: 0,1% DMSO


title: single-cell RNA seq data of CSF from patient MS27

source_name: CSF

value: CSF leukocytes


title: NPC-KRAS G13D cells, rep1

value: Human neural stem cells (H1 cells)

value: KRASG13D mutation

value: Generation of NPCs from H1 cells


title: 10A_M_1558

tag: brain region


title: ChIP-seq, MCF7Ras_NELFE-ChIP, DOX_IP, rep2

description: ChIP-seq.MCF7Ras_NELFE-ChIP.DOX_rep12.bw; peaks_MCF7Ras.scramble_DOX_NELFE_rep12_np09.bed

source_name: MCF7Ras_NELFE-ChIP, DOX_IP

tag: condition

value: NELF-E (Abcam, ab170104)


title: single-cell RNA seq data of PBMC from patient MS27


title: ChIP-seq, scramble_DOX_inputFor_NELFErep2_AND_SLUG, rep2


title: Raji TSA G4access rep3

value: B lymphocyte

value: Burkitt's lymphoma

value: Raji

value: Drosophila melanogaster

value: Trichostatin A

value: 2 uM Trichostatin A


title: 10A_M_1551

tag: age

tag: Sex

value: male


title: Raji PolII Triptolide Rep2

description: Treated with 1 uM Triptolide for 2hours

value: B lymphocyte; Burkitt's lymphoma

value: ChIP-seq

tag: spike-in reference organism

value: Total PolII (F12 - sc-55492 - Santa Cruz Biotechnology)

value: Triptolide

value: 1 uM Triptolide

value: 2 hours


title: Raji DMSO control TSA mnase rep2

description: Treated with 0,1% DMSO for 24 hours

tag: strain

tag: treatment

value: DMSO

value: 0,1% DMSO

value: 24 hours


title: Raji TSA mnase rep2

tag: spike-in cell line

tag: concentration


title: single-cell RNA seq data of CSF from patient MS72

value: CSF leukocytes

value: RRMS

value: alemtuzumab


title: Raji PolII Triptolide Rep1

description: Treated with 1 uM Triptolide for 2hours

tag: cell line

value: Raji

tag: duration


title: 10A_M_1554


title: ChIP-seq, scramble_DOX_inputFor_NELFErep2_AND_SLUG, rep1

tag: genotype

value: transduced with scrambled shRNA

value: Doxycycline

tag: chip antibody


title: 10A_M_1552


title: 10A_M_1549


title: ChIP-seq, MCF7Ras_NELFE-ChIP, DOX_IP, rep1

value: NELF-E (Abcam, ab170104)


title: ChIP-seq, MCF7Ras_NELFE-ChIP, Con_IP, rep1

description: ChIP-seq.MCF7Ras_NELFE-ChIP.Con_rep12.bw; peaks_MCF7Ras.scramble_Con_NELFE_rep12_np09.bed

source_name: MCF7Ras_NELFE-ChIP, Con_IP

value: DMSO vehicle


title: Raji PolII KM Rep2

description: Treated with 100 uM KM05283 for 2hours

tag: cell type

value: B lymphocyte; Burkitt's lymphoma

tag: experiment

value: Drosophila melanogaster


title: 10A_M_1550

value: male


title: 10A_M_1559


title: ChIP-seq, MCF7Ras_NELFE-ChIP, DOX_input, rep1

source_name: MCF7Ras_NELFE-ChIP, DOX_input


title: 10A_M_1546


title: Raji DMSO control TSA G4access rep3

description: Treated with 0,1% DMSO for 24 hours

value: B lymphocyte

value: Burkitt's lymphoma

tag: spike-in reference organisme


title: 10A_M_1545


title: ChIP-seq, MCF7Ras_NELFE-ChIP, Con_input, rep2

source_name: MCF7Ras_NELFE-ChIP, Con_input


title: Raji DMSO control TSA G4access rep1

description: Treated with 0,1% DMSO for 24 hours


title: Raji DMSO control TSA G4access rep2

description: Treated with 0,1% DMSO for 24 hours


title: ChIP-seq, MCF7Ras_NELFE-ChIP, Con_IP, rep2


title: 10A_M_1543


title: Raji TSA G4access rep1

value: Trichostatin A

value: 2 uM Trichostatin A


title: Raji PolII DMSO Rep1

description: Treated with 0.1% DMSO for 2hours

value: ChIP-seq

value: Total PolII (F12 - sc-55492 - Santa Cruz Biotechnology)

value: DMSO

value: 0.1% DMSO

value: 2 hours


title: Raji PolII KM Rep1

description: Treated with 100 uM KM05283 for 2hours

value: Raji


title: Raji DMSO control TSA mnase rep1

description: Treated with 0,1% DMSO for 24 hours

value: 0,1% DMSO

value: 24 hours


title: Raji PolII DMSO Rep2

description: Treated with 0.1% DMSO for 2hours


title: 10A_M_1542


title: ChIP-seq, MCF7Ras_NELFE-ChIP, Con_input, rep1

value: transduced with scrambled shRNA


title: Hela H9 siWRN Rep2

description: Treated with 20nM siWRN for 72h

source_name: Hela H9  cells

value: Cervical cells

value: Cervical adenocarcinoma

value: Hela H9

value: untreated


title: Hela H9 siWRN Rep1

description: Treated with 20nM siWRN for 72h

value: Drosophila melanogaster


title: Raji G4access Triptolide Rep2

description: Treated with 1 uM Triptolide for 2hours

value: B lymphocyte; Burkitt's lymphoma

value: No spike

value: Triptolide

value: 1 uM Triptolide


title: 10A_M_1541

value: male


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, DOX_IP, rep2

description: ChIP-seq.MCF7Ras_KAT2B-ChIP.DOX_rep12.bw; peaks_MCF7Ras.DOX_KAT2B_rep12_np09.bed

source_name: MCF7Ras_KAT2B-ChIP, DOX_IP

value: wildtype

value: Doxycycline

value: PCAF/KAT2B (Cell Signaling Technology, 3378S)


title: Hela H9 siNT Rep2

description: Treated with 20nM siNT for 72h


title: Raji G4access Triptolide Rep1

description: Treated with 1 uM Triptolide for 2hours

value: Raji

value: 2 hours


title: 10A_M_1540


title: Hela H9 siNT Rep1

description: Treated with 20nM siNT for 72h


title: Raji G4access Rep2


title: 10A_M_1539


title: Hela H9 siDHX36 Rep2

description: Treated with 20nM siDHX36 for 72h


title: 10A_M_1538


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, DOX_IP, rep1


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, DOX_input, rep1

source_name: MCF7Ras_KAT2B-ChIP, DOX_input


title: Raji G4access Rep1


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, DOX_input, rep2


title: 10A_M_1537


title: Hela H9 siDHX36 Rep1

description: Treated with 20nM siDHX36 for 72h


title: Raji G4access PDS 60min Rep2

description: Treated with 10 uM Pyridostatin for 60minutes

value: Pyridostatin

value: 10 uM Pyridostatin

value: 60 minutes


title: Raji G4access PDS 60min Rep1


title: P9

city: Chicago

first: Ruli

last: Gao

state: Illinois

address: 303 East Superior

department: Department of Biochemistry and molecular genetics

institute: Northwestern University

data_processing:
Adapter sequences and low-quality reads were trimmed from the raw sequencing reads using Trim_Galore
Alignment to the reference genome was done using STAR
Read counts and gene expression values were calculated using RSEM
Assembly: GRCh38
Supplementary files format and content: A tab-delimited text file including count values for each Sample

source_name: ATC cell line

extract_protocol:
Whole-cell RNA extraction was performed according to the manufacturer’s instructions (Fisher TR 118–100ML)
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease state

value: anaplastic thyroid cancer

tag: tissue source

value: ATC cell line

value: anaplastic thyroid cancer tumor cell


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, Con_IP, rep1

description: ChIP-seq.MCF7Ras_KAT2B-ChIP.Con_rep12.bw; peaks_MCF7Ras.Con_KAT2B_rep12_np09.bed

source_name: MCF7Ras_KAT2B-ChIP, Con_IP

tag: condition

value: DMSO vehicle


title: P8

value: untreated


title: Raji G4access PDS 30min Rep2

description: Treated with 10 uM Pyridostatin for 30minutes

extract_protocol:
For G4 access: Trypsinized Haacht cells, resuspended S2 cells and suspension of K562, Raji and mouse ESC cells were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Haacht cells were suspended in 5 mL of permeabilization buffer (150 mM of sucrose, 80 mM Kill, 5 mM KH2PO4, 5 mM MgCl2, 0.5 mM CaCl2 and 35 mM HEPES pH 7.4) and homogenized using a Dounce (40 strokes). For MNase digestion, 5x10^6 cells per titration point were resuspended in 50 μL of prewarmed permeabilization buffer supplemented with 0.2% (v/v) NP40 and incubated 5 minutes at 37ºC. Digestion took place by adding a volume of 500 mL of prewarmed MNase reaction buffer (150 mM sucrose, 50 mM Tris-HCl pH 8, 50 mM NaCl and 2 mM CaCl2) to each reaction. Either 3.1, 6.2, 12.5, 25 or 50U MNase (Merck, 10107921001) were added to the MNase reaction buffer and incubated at 37 ºC for 10 min. Digestion was stopped on ice and by adding 11 μL of 500 mM EDTA to each reaction. The digestions were incubated 10 minutes on ice with 550 μL of SDS lysis buffer (1% (v/v) SDS, 10 mM EDTA and 50 mM Trish pH 8) and 1 mL of water. Before DNA purification, digestions were incubated with 5 mL of RNaseq A (Thermofisher, EN0531) at 37 ºC for 2 hours and with 8 mL of proteinase K (Euromoney, 09-0911) at 56 ºC for 2 hours. To verify the performance of the digestion, 125 μL of each sample was cleaned-up using QI quick PCR Purification Kit (QIAGEN, 28106). Digestions were assessed by agarose gel and Bioanalyzer (Fig. 1c). The remaining digestions were purified by phenol-chloroform and ethanol precipitation for subsequent steps.
Yeast S288C were pelleted and rinsed twice in phosphate-buffered saline buffer (PBS). Pellets from 100mL culture (OD: 0.5) were suspended in 600ul cell breaking buffer (20% glycerol, 100mM Tris pH 7.5), 600µl zirconia beads (0.5mm), 10µl of 100x protease inhibitors (Roche, 06538282001). Beads beating was performed in 1.5mL screw cap tubes in a Bullet Blender (Next advance) for 4 x 3min at a strength of 8 in a cold room. Cell suspensions were recovered by puncturing the bottom of tube (23 gauge syringes) and spined at 170 ruff for 3min into a 5mL Eppendorf tube. Everything was transferred into 1.5mL Eppendorf, then centrifuged for 5min at max speed and the top layers were discarded. Samples were suspended in 300ul of prewarmed NP buffer (50mM NaCl, 10mM Tris pH 7.4, 5mM MgCl2, 1mM CaCl2, 0.2% NP40 (v/v), 0.5mM spermidine (Sigma, S0266-1G), 0.007% B-Mercaptothion (Sigma, M3148-100ML). Digestion took place by adding a volume of 300µL prewarmed NP buffer supplemented with either 60u, 30u, 15u, 7.5u, 3.75, 1.9u, 1u of MNase (Merck 10107921001). Digestions were stopped on ice and by adding 150μL of stop buffer (5% SDS, 50mM EDTA). Before DNA purification, digestions were incubated with 5 µL of RNaseq A (Thermofisher, EN0531) at 37 ºC for 2 hours and with 10 µL of proteinase K (Euromoney, 09-0911) at 56 ºC for 2 hours. Purification was done with two consecutive phenol and one chloroform steps followed by ethanol and linear acrylamide precipitation. Purified DNAs were once again incubated with 5µl RNaseq A (Thermofisher, EN0531) to get rid of persistent RNA contaminations.
The phenol-chloroform purified DNAs were subjected to size selection to remove fragments larger than 100 bp. For that, 1 µg of each digestion product was migrated in a 4-20% polyacrylamide Novant TBE gel (Thermofisher, EC6225BOX) at 100 V for 60 min. The gels were stained with Sober® Gold (Thermofisher, S11494) for 30 min. Fragments according to the size range of 0-100 bp were cut out from the gel and transferred to 0.5-mL Eppendorf tubes, previously punctured in the bottom with a 0.45 µm needle. These tubes were inserted into 1.5-mL tubes and centrifuged 10 min at 15.300 ruff to move the cotted gel through the hole, generating gel beads. To elute the DNA from the beads, 700 μL of water was added and the tubes were incubated overnight at 55 ºC in a thermomixer at 1500 rpm. DNA was purified by transferring the samples (DNA eluate and gel beads) to the top of a 0.22 µm spin filter (Agilent 5185-5990). Spin filters were centrifuged 2 min at 15.300 ruff to recover the DNA eluate. DNA was precipitated with isopropanol and linear acrylamide. Size-selection was verified by Bioanalyzer (Fig. 1c). To assess the optimal MNase titration point in terms of G-quadruplex (G4) forming sequence enrichment, the relative amount of targeted G4s was evaluated by qPCR (Extended Data Fig. 1a). The titration points showing a percentage of mononucleosomal fraction of 30% of the total DNA (excluding subnucleosomal fraction) as quantified using Bioanalyzer chips gave the best qPCR enrichment in targeted G4s after size selection. This observation was further confirmed when sequencing the corresponding libraries.
For Pol II ChIP-seq, fifty million cells were used to perform each Pol II ChIP-seq experiments. Cells were crosslinked for 10 min at 20°C with the crosslinking solution (10 mM NaCl, 0.1 mM EDTA pH 8, 0.05 mM EGTA pH 8, 5 mM HEPES pH 7.8 and 1% formaldehyde). The reaction was stopped by adding glycine at a final concentration of 250 mM. After 5 min of formaldehyde quenching, cells were washed twice with cold PBS and resuspended in cold 2.5L LB1 (50 mM HEPES pH 7.5, 140 mM NaCl,1 mM EDTA pH 8, 10% glycerol, 0.75% NP-40, 0.25% Triton X-100) at 4°C for 20 min on a rotating wheel. Nuclei were pelleted down by spinning at 1350 rcf in a refrigerated centrifuge and washed in 2.5L LB2 (200 mM NaCl, 1 mM EDTA pH 8, 0.5 mM EGTA pH 8, 10 mM Tris pH 8) for 10 min at 4°C on a rotating wheel followed by centrifugation to collect nuclei. Nuclei were then resuspended in 1L LB3 (1 mM EDTA pH 8, 0.5 mM EGTA pH8, 10 mM Tris pH8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using Bioruptor Pico (Diagenode) in 15L tubes for 20 cycles of 30 s ON and 30 s OFF pulses in 4°C bath. All buffers (LB1, LB2 and LB3) were complemented with EDTA free Protease inhibitor cocktail (Roche), 0.2 mM PMSF and 1 µg/L Pepstatin just before use. After sonication, Triton X-100 was added to a final concentration of 1% followed by centrifugation at 20000 rcf and 4°C for 10 min to remove particulate matter.
G4access and ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to standard protocol.

value: B lymphocyte; Burkitt's lymphoma

value: No spike

value: 30 minutes


title: 10A_M_1533

tag: brain region

tag: age

value: male


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, Con_input, rep1

source_name: MCF7Ras_KAT2B-ChIP, Con_input

value: wildtype


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, Con_input, rep2


title: 10A_M_1536

tag: Sex


title: P7


title: Raji G4access PDS 30min Rep1

tag: spike-in reference organism


title: 10A_M_1532

tag: strain


title: P6

tag: treatment

value: 3 months of  atezolizumab/vemuafenib/cobimetinib


title: HaCaT G4access Rep2

source_name: HaCaT cells

value: Keratinocyte; Immortal keratinocyte cell

value: HaCaT

tag: spike-in cell line

tag: concentration


title: Raji G4access PDS 24h Rep2

description: Treated with 10 uM Pyridostatin for 24hours

tag: cell line

value: Raji

tag: duration

value: 24 hours


title: 10A_M_1531


title: P5

value: dabrafenib/trametinib for 1 year


title: HaCaT G4access Rep1

tag: chip antibody


title: Raji G4access PDS 24h Rep1

tag: cell type

value: Pyridostatin

value: 10 uM Pyridostatin


title: P4

value: anaplastic thyroid cancer

value: ATC cell line


title: ChIP-seq, MCF7Ras_KAT2B-ChIP, Con_IP, rep2

tag: genotype

value: DMSO vehicle

value: PCAF/KAT2B (Cell Signaling Technology, 3378S)


title: P3

value: anaplastic thyroid cancer tumor cell

value: untreated


title: MCT-week3-4 [M_430_4]

city: 咸阳

first: yangfan

last: jia

state: 陕西

address: 中国陕西省杨凌区

institute: 西北农林科技大学

data_processing:
Cleaned raw data were aligned to the rat reference genome (NCBI: GCA_000001895.4) using Hisat2 (v2.0.5). FeatureCounts (v2.0.3) was used to count the reads numbers mapped to each gene.
Genes showing an adjusted P value < 0.05 and |log2 (fold change) | > log2 (1.5) identified by the DESeq2 R package (1.32.0) were assigned as differential expressed genes. Data processing and visualization using Tidyverse R Package (1.3.1).
Assembly: GCA_000001895.4
Supplementary files format and content: counts

source_name: lung

growth_protocol: Male SD rats were treated with PBS buffer or monocrotaline for one to three weeks. Then the lung tissues were harvested for total RNA extraction and library preparation.

extract_protocol:
RNA was harvested using Trizol (TaKara).
RNA libraries for RNA-seq were prepared using the Next UltraTM Directional RNA Library Prep Kit for Illumina (NEB, MA, USA)following manufacturer's protocols.

tag: tissue

value: lung

value: SD

value: WT

value: MCT (50mg/kg), 21days