title: 10B_M_1775


title: 10B_M_1773

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: strain

tag: Sex

value: male


title: 10B_M_1774


title: 10B_M_1772


title: 10B_M_1797


title: 10B_M_1769


title: 10B_M_1771


title: 10B_M_1766


title: 10B_M_1765


title: 10B_M_1763


title: 10B_M_1760


title: 10B_M_1789


title: 10B_M_1752


title: 10B_M_1755


title: 10B_M_1757


title: 10B_M_1756


title: 10B_M_1780


title: 10B_M_1749


title: 10B_M_1741


title: 10B_M_1746


title: 10B_M_1740


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title: 10B_M_1729


title: 10B_M_1758


title: 10B_M_1728


title: 10B_M_1724


title: 10B_M_1720


title: 10B_M_1723


title: 10B_M_1764


title: 10B_M_1751


title: 10B_M_1722


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title: 10B_M_1709


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title: 10B_M_1699


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title: 10B_M_1692


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title: 10B_M_1572


title: 10B_M_1569


title: 10B_M_1568


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title: 10B_M_1556


title: 10B_M_1559


title: 10B_M_1570


title: 10B_M_1550


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title: 10B_M_1558


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title: 10B_M_1530


title: 10B_M_1529


title: 10B_M_1542


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title: 10B_M_1541


title: 10B_M_1538


title: 10B_M_1536


title: 10B_M_1534


title: 10B_M_1533


title: 10B_M_1527


title: 10B_M_1526


title: 10B_M_1520


title: 10B_M_1519


title: 10B_M_1517


title: 10B_M_1521


title: 10B_M_1512


title: 10B_M_1511


title: 10B_M_1524


title: 10B_M_1510


title: 10B_M_1523


title: 10B_M_1514


title: 9-Input_R1_L002

city: Madison

first: Judith

last: Simcox

state: WI

address: 433 Babcock dr.

department: Biochemistry

institute: University of Wisconsin Madison

data_processing:
FastP for Quality Control and read trimming, version 0.20.0, cmd: $FASTP --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --in1 $Read1File --out1 $Read1OutFile --in2 $Read2File --out2 $Read2OutFile --thread $Threads --html $OutputHTML
bowtie2 version: v2.2.5 , cmd: $BOWTIE2 --sensitive --threads $HALFTHREADS -x $BOWTIE2_REF -1 $inputF_R1 -2 $inputF_R2 -S $sam
macs2 version 2.7.1, cmd: $MACS2 callpeak -f BAMPE --name ${INPUT%.bam} -g $EFF_GENOME_SIZE --qvalue 0.05 -t $PRIMARY_INPUT --bdg --outdir
*treat_pileup.bedgraph =  bedGraph format for treatment/IP sample
*control_lambda.bedgraph = bedGraph format for input sample

source_name: Liver

extract_protocol: RNA was purified from liver using RNeasy mini kit was used (Qiagen, 74106). Samples were submitted to the University of Wisconsin-Madison Biotechnology Center for RNA sequencing. Briefly, RNA size and purity were verified using Qubit<https://products.invitrogen.com/ivgn/product/Q32851?ICID=search-product> RNA HS Assay Kit  (Invitrogen, Carlsbad, California, USA) and Agilent RNA HS chip (Agilent Technologies, Inc., Santa Clara, CA, USA), respectively. Samples were prepared according the TruSeq  Stranded mRNA Library Prep kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were purified using AMPure XP beads (Beckman Coulter, A63880) and sequenced on the NovaSeq 2x150 bp with 30 million reads per sample. Reads were trimmed using trimming software skewer (Jiang et al.2014), filtered for at or near zero expression, and gene expression normalization was carried out by the method of trimmed mean of M-values (TMM). The trimmed single- or paired-end reads are aligned against the selected reference genome sequence using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013). Analysis of differentially expressed genes is performed with a glm using the edgeR package (Robinson, McCarthy, and Smyth 2010).

tag: tissue

value: liver

value: 3 months

tag: treatment

value: Cold (4C), 6 hours

tag: chip antibody

value: none (input)


title: 9-Rpb1-CTD_R1_L001


title: 9-Input_R1_L001


title: 9-H3K27-ac_R1_L002


title: 9-HNF4a_R1_L002


title: 9-Rpb1-CTD_R1_L002


title: 9-HNF4a_R1_L001


title: 10B_M_1531


title: 4-Rpb1-CTD_R1_L002

value: RT (25C)  0 hours


title: 4-Input_R1_L002


title: 4-HNF4a_R1_L001


title: 4-HNF4a_R1_L002


title: 4-Rpb1-CTD_R1_L001


title: 4-H3K27-ac_R1_L002


title: 3-Rpb1-CTD_R1_L002


title: 4-H3K27-ac_R1_L001


title: 3-Rpb1-CTD_R1_L001


title: 3-Input_R1_L002


title: 3-Input_R1_L001


title: 3-HNF4a_R1_L002


title: 3-HNF4a_R1_L001


title: 9-H3K27-ac_R1_L001


title: 10-Input_R1_L002


title: 10-Rpb1-CTD_R1_L002


title: 3-H3K27-ac_R1_L002


title: 3-H3K27-ac_R1_L001


title: 4-Input_R1_L001


title: RT6-4_R1_L002

library_source: transcriptomic

molecule: total RNA

value: RT (25C), 6 hours


title: 10-Input_R1_L001


title: 10-HNF4a_R1_L001


title: RT6-1_R1_L002


title: RT24-4_R1_L002

value: RT (25C), 24 hours


title: 10-H3K27-ac_R1_L002


title: RT6-2_R1_L002


title: RT24-3_R1_L002


title: RT24-1_R1_L002


title: RT12-2_R1_L002

value: RT (25C), 12 hours


title: 10-Rpb1-CTD_R1_L001


title: RT12-4_R1_L002


title: RT0-3_R1_L002

value: RT (25C), 0 hours


title: RT0-2_R1_L002


title: RT12-1_R1_L002


title: RT0-4_R1_L002


title: RT0-1_R1_L002


title: RT6-3_R1_L002


title: COLD24-4_R1_L002

value: Cold (4C), 24 hours


title: 10-HNF4a_R1_L002


title: COLD6-4_R1_L002

value: Cold (4C), 6  hours


title: COLD24-3_R1_L002


title: COLD6-2_R1_L002


title: COLD24-2_R1_L002


title: COLD6-1_R1_L002


title: 10-H3K27-ac_R1_L001


title: COLD24-1_R1_L002


title: COLD12-2_R1_L002

value: Cold (4C), 12 hours


title: COLD12-4_R1_L002


title: COLD12-1_R1_L002


title: COLD12-3_R1_L002


title: COLD0-3_R1_L002

value: Cold (4C), 0 hours


title: COLD0-4_R1_L002


title: COLD0-2_R1_L002


title: COLD0-1_R1_L002


title: RT12-3_R1_L002


title: RT24-2_R1_L002


title: COLD6-3_R1_L002


title: 10B_M_992


title: 10B_M_995


title: 10B_M_991


title: 10B_M_997


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title: sc3 G4access Rep2

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

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae (BY4741)

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.

tag: cell type

value: Saccharomyces cerevisiae

tag: cell line

tag: experiment

tag: spike-in reference organism

value: No spike

tag: spike-in cell line

value: untreated

tag: concentration

tag: duration


title: 10A_M_1820

value: male


title: 10A_M_1821


title: 10A_M_1796


title: sc3 G4access Rep1


title: 10A_M_1797


title: 10A_M_1792


title: 10A_M_1795


title: 10A_M_1793


title: 10A_M_1807


title: ddm1_BA_sub_DC_rep2

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

description: bisulfite treated

data_processing:
Image analysis and base calling were performed with the standard Illumina pipeline (Real Time Analysis module 1.8.7 and BCL Converter 1.7.1).
From the total sequenced reads, adaptor sequence trimming and quality filtering were processed by using 'Trimmomatic' (Bolger et al., Bioinformatics,2014)
The following reads were removed for down-stream analysis: multiple match, mismatch >2.
Reads were aligned to the reference genome in TAIR9 using the BSMAP with allowance of two mismatches.
Methylation levels of a C within an aligned read were determined by calculating the ratio of reads that contained a methylated C at the location versus all the reads that covered the location. Each sequence context of methylated C was considered as CG, CHG, or CHH in which H is A, C, or T.
Genome_build: TAIR9
Supplementary_files_format_and_content: tab-delimited BSmap methylation ratio text file.

organism: Arabidopsis thaliana

source_name: ddm1 BA_sub+DC

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:
Genomic DNA was isolated using DNAzol
Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3’ ends by  Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). Bisulfite treated DNA libraries were amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

treatment_protocol: plants were irrigated with water (Ctrl) or 10ml of 30µg/ml BABA (BA_sub). In 2 days after water or BABA treatment, plants were sprayed with 40ml of 5x10E7 cfu/ml Pseudomonas syringae pathovar tomato DC3000 per pot (DC), (BA_sub+DC).

tag: ecotype

value: plant arial part

tag: genotype

value: ddm1 mutant


title: ddm1_BA_sub_DC_rep3

description: bisulfite treated


title: 10A_M_1787


title: 10A_M_1790


title: ddm1_BA_sub_rep3

description: bisulfite treated

source_name: ddm1 BA_sub


title: ddm1_BA_sub_DC_rep1

description: bisulfite treated


title: 10A_M_1786


title: ddm1_DC_rep2

description: bisulfite treated

source_name: ddm1 DC


title: ddm1_BA_sub_rep2

description: bisulfite treated


title: 10A_M_1785


title: ddm1_ct_rep1

description: bisulfite treated


title: col_BA_sub_DC_rep3

description: bisulfite treated

source_name: Col BA_sub+DC

value: wild type


title: 10A_M_1784


title: ddm1_BA_sub_rep1

description: bisulfite treated


title: col_BA_sub_DC_rep2

description: bisulfite treated


title: 10A_M_1782


title: 10A_M_1794


title: 10A_M_1781


title: 10A_M_1780


title: col_DC_rep3

description: bisulfite treated

source_name: Col DC


title: col_DC_rep2

description: bisulfite treated


title: 10A_M_1778


title: 10A_M_1777


title: ddm1_DC_rep1

description: bisulfite treated


title: col_DC_rep1

description: bisulfite treated


title: col_BA_sub_rep2

description: bisulfite treated

source_name: Col BA_sub


title: ddm1_ct_rep2

description: bisulfite treated


title: col_BA_sub_rep1

description: bisulfite treated


title: 10A_M_1783


title: 10A_M_1798


title: 10A_M_1774


title: col_ct_rep3

description: bisulfite treated

source_name: Col


title: 10A_M_1772


title: 10A_M_1773


title: 10A_M_1776


title: 10A_M_1770


title: 10A_M_1771


title: THP1 cells, CREB1-KD-plus-LPS-3

city: Changsha

first: Nian

last: Wang

state: Hunan

address: No.110 Xiangya Road

country: China

institute: Central south university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts data for each Sample

organism: Homo sapiens

growth_protocol: THP1 monocytes were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using E.Z.N.A.® total RNA kit. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: lipopolysaccharide (100ng/ml) for 3h

value: Human monocytes

value: CREB1 knockdown

value: lipopolysaccharide


title: col_BA_sub_DC_rep1

description: bisulfite treated


title: col_ct_rep1

description: bisulfite treated


title: THP1 cells, CREB1-KD-plus-LPS-2


title: 10A_M_1768


title: 10A_M_1767


title: THP1 cells, CREB1-KD-plus-LPS-1


title: 10A_M_1769


title: 10A_M_1765


title: 10A_M_1766


title: THP1 cells, CREB1-KD-3

value: PBS


title: 10A_M_1775


title: TA muscle, Pairfed, S5

city: Hamilton

first: Dongdong

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

country: Canada

institute: McMaster University

data_processing:
Trim Galore was used to automate quality and adapter trimming as well as quality control.
We quantified the expression of transcripts using RNA-seq data through Salmon.
Salmon’s transcript-level quantifications DESeq2 was applied for detection of differentially expressed genes (DEG).
Supplementary files format and content: mm10
Supplementary files format and content: a csv file include normalized counts for all samples.

source_name: tibialis anterior (TA) muscle

extract_protocol:
Tissues were homogenized and lysed in TRIzol reagent. After centrifuged, the supernatant (aqueous phase) was applied to the RNeasy kit (Qiagen, ID: 74106) for subsequent total RNA extraction and purification according to its protocols.
RNA libraries for RNA-seq were prepared using the NEBNext® Ultra™ II Directional RNA Library kit following manufacturer's protocols.

treatment_protocol: Mice were placed on a NASH diet and housing condition (~29°C) at 8-weeks of age. Prior to treatment, mice were randomized and separated into different treatment groups matched on body weight and composition, and single-housed. Recombinant GDF15 (Novo Nordisk, NNC no. 0247-0000-0001, dissolved in synthetic buffer with 5 mM Acetate, 240 mM propylene glycol, and 0.007% polysorbate 20) was delivered by subcutaneous injection at 1-2 h post to light cycle in the morning (0700-0900) at 0.3, 1 and/or 5 nmol/kg once daily. The individual dosage was calculated by body weight of one day before. Pair-fed animals received the same amount of food as ingested by the corresponding GDF15-treated groups the day before.

value: tibialis anterior (TA) muscle

tag: mice background

value: WT

value: PairFed


title: col_BA_sub_rep3

description: bisulfite treated


title: TA muscle, Pairfed, S6


title: 10A_M_1764

tag: brain region


title: col_ct_rep2

description: bisulfite treated


title: THP1 cells, CREB1-KD-2


title: 10A_M_1791

tag: age


title: TA muscle, Pairfed, S4


title: 10A_M_1763

tag: strain


title: THP1 cells, CREB1-KD-1


title: HeLa_CRISPR_ESRRB_3

city: Xi'an

first: Qinshu

last: Li

address: No.277, West Yanyan Road

institute: Xi'an Jiaotong University

data_processing:
Data filtering   The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification   Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis  Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation  To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cervix

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

extract_protocol:
RNA was harvested using TRIzol for the construction of sequencing libraries.
1.Sample QC. 2. mRNA isolation. 3. mRNA Fragmentation. 4. cDNA synthesis. 5. End Repair, Add A and Adaptor Ligation. 6. PCR. 7. Library QC. 8. Circularization 9. Sequencing

treatment_protocol: Transfection of pSpCas9-2A-GFP plasmid and pSpCas9-2A-GFP-sgEsrrb plasmid into HeLa cells, respectively.

value: cervix

value: HeLa

value: Human cervical cancer cells

value: ESRRB knockout

value: Transfection of pSpCas9-2A-GFP-sgEsrrb plasmid


title: HeLa_CRISPR_ESRRB_2


title: HeLa_CRISPR_ESRRB_1


title: 10A_M_1762

tag: Sex


title: TA muscle, Pairfed, S2

tag: tissue


title: TA muscle, Pairfed, S3

tag: treatment


title: 10A_M_1759


title: THP1 cells, LPS-3h-3


title: HeLa_CRISPR_Ctrl_3

value: Transfection of pSpCas9-2A-GFP plasmid


title: HeLa_CRISPR_Ctrl_2


title: 10A_M_1758

value: male


title: THP1 cells, LPS-3h-2


title: THP1 cells, LPS-3h-1


title: TA muscle, GDF15, S6


title: TA muscle, GDF15, S5


title: HeLa_CRISPR_Ctrl_1


title: THP1 cells, Control-3


title: TA muscle, GDF15, S4


title: 10A_M_1757


title: 10A_M_1756


title: NK_NCT503_3

last: Liu

address: Xiangya road 87#

department: Department of Dermatology

institute: Xiangya Hospital, Central South University

data_processing:
Sequencing data filtering：This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution);2) Remove reads whose N content is greater than 5%;3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).The filtered "Clean Reads" are saved in FASTQ format.
After getting clean reads, we used HISAT to align the clean reads to the reference genome.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result.
Assembly: hg38
Supplementary files format and content: FPKM values for each Sample

extract_protocol:
Total RNA was isolated from cells or tissues with TRIpure Reagent (Bio Teke, China)
1) mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA (For total RNA extracted from human whole blood, globin mRNA are depleted ); 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB; 6) Sequencing on DNBSEQ platform

value: NK cells


title: 10A_M_1755


title: TA muscle, GDF15, S3


title: THP1 cells, Control-2


title: THP1 cells, Control-1


title: 10A_M_1754


title: NK_NCT503_1


title: Input_NT2_16hour_retinoic_acid_rep2

city: BOSTON

first: MITZI

middle: I

last: KURODA

state: MA

address: 77 Ave Louis Pasteur NRB 168

department: Genetics

institute: Brigham & Women's Hospital / Harvard Medical School

description: Input for BRD4-NUT in differentiated Ntera-2 cells after 16 hr retinoic acid treatment

data_processing:
ChIP-seq reads were aligned to the UCSC hg19 genome using Bowtie 2/2.3.4.3. Only uniquely mapping reads with at most two mismatches were retained.
Smoothed enrichment profiles were generated with the bandwidth of 5 kb. Bigwig files were generated using deeptools (version 3.0.2) with the parameters--RPGC--smoothLength 5000. To visualize ChIP-seq signal at individual genomic regions, we used the Integrative Genomics Viewer (IGV; https://software.broadinstitute.org/software/igv/).
Peak enrichment for BRD4-NUT was identified using the HOMER package (Heinz et al. 2010). Briefly, BAM files were converted into tag directories and peaks were called using findPeaks program with the parameters -region -size 20000 -minDist 200000 -F 2 -L 2 -C 2. Peaks greater than 96 kb was used as a minimal size cutoff for megadomain detection. Bedtools intersect (version 1.9) (Quinlan et al. 2010) was used to identify common and differential peaks. Heatmaps for BRD4-NUT occupancy was scaled to average megadomain size of 180kb region summing RPGC-normalized counts from 10 bp bins spanning ± 100 kb from peak start and end site and visualized with the deeptools plotHeatmap function (Ramírez et al. 2014). Heatmaps was plotted to visualize the score distributions of the BRD4-NUT enrichment associated with genomic regions specified in the BED files with peaks from HUES64 or dME cell
Assembly: hg19
Supplementary files format and content: bigWig, braod peak files

source_name: Cell state-dependent chromatin targeting in NUT carcinoma

growth_protocol: HUES64 cells were maintained on matrigel (Corning) in mTeSR1 media (Stemcell Technologies). Cells were routinely passaged as clumps after dissociation with 10uM EDTA for 3 minutes as needed. For mesoderm formation, single hESC cells were plated at a density of approximately 5x105 per each well of a 6 well plate in the presence of ROCK inhibitor and exposed to commercially available mesoderm induction media (Stemcell Technologies 05221).   NTERA-2 (NT2) cells were maintained in Dulbecco's modified Eagle's medium (high glucose) containing 10% fetal bovine serum (FBS), 2 mM L-alanyl-L-glutamine (AG), 25 mM HEPES buffer (pH7.3), 1X minimum essential medium non-essential amino acids, 56 µM β-mercaptoethanol (β-ME). For differentiation with retinoic acid, NT2 cells were plated at 2.7×104cells/cm2 in Opti-MEM I (Invitrogen; Carlsbad, CA) containing 4% FBS, 2 mM L-alanyl-L-glutamine (AG), 56 µM β-mercaptoethanol (β-ME) and 10 µM all-trans retinoic acid.

extract_protocol:
Formaldehyde cross-linked chromatin for ChIP-seq experiments with antibodies against were prepared from 5 × 107 transient transfected cells of each HUES64, HUEs64 derived mesoderm, Ntera-2 and Ntera-2 derived differentiated cells as described in Alekseyenko et al. 2015. ChIP-seq was performed using anti-NUT (15 ul per IP; Cell Signaling, catalog no. 3625).ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015).
ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015).

value: Ntera-2 derived differentiated cells

value: human embryonal carcinoma cell line

tag: chip antibody

value: none (input)


title: Input_NT2_16hour_retinoic_acid_rep1

tag: cell type


title: NK_NCT503_2

tag: cell line


title: 10A_M_1753


title: NK_L_Ser_3

value: L-serine


title: TA muscle, GDF15, S1


title: NK_L_Ser_2


title: TA muscle, Vehicle, S4

value: Vehicle


title: Input_NT2_4hour_retinoic_acid_rep2

description: Input for BRD4-NUT in differentiated Ntera-2 cells after 4hr retinoic acid treatment


title: 10A_M_1752


title: 10A_M_1751


title: Input_NT2_4hour_retinoic_acid_rep1


title: Input_NT2_0hour_rep2

description: Input for BRD4-NUT in Ntera-2 cells


title: NK_Vehicle_3


title: 10A_M_1750


title: TA muscle, Vehicle, S3


title: 10A_M_1749


title: Input_NT2_0hour_rep1

description: Input for BRD4-NUT in Ntera-2 cells


title: TA muscle, Vehicle, S1


title: NK_Vehicle_2


title: TA muscle, GDF15, S2


title: TA muscle, Vehicle, S2


title: NK_Vehicle_1


title: 10A_M_1748


title: Input_BRD4-NUT_dME_replicate2

description: Input for BRD4-NUT in HUES64 derived dME

value: HUES64 derived dME

value: differentiated cells


title: Liver, PairFed, S6

data_processing:
Trim Galore was used to automate quality and adapter trimming as well as quality control.
We quantified the expression of transcripts using RNA-seq data through Salmon.
Salmon’s transcript-level quantifications DESeq2 was applied for detection of differentially expressed genes (DEG).
Supplementary files format and content: mm10
Supplementary files format and content: a csv file include counts for all samples.

value: Liver

value: WT


title: Liver, PairFed, S5

value: PairFed


title: Input_BRD4-NUT_HUES64_replicate2

description: Input for BRD4-NUT in HUES64

value: Human embryonic stem cell line


title: TA muscle, Vehicle, S5

value: tibialis anterior (TA) muscle


title: TTX_3

city: Nijmegen

first: Sofia

last: Puvogel

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: RadboudUMC

description:
Multiple_samples_count_matrix_human
Multiple_samples_count_matrix_rat

data_processing:
Mapping : STAR/2.7.8a
Quantification : RSEM/1.3.0
Genome : GRCh38+Rnor6.0
Annotation : gencode39+ensembl104

organism:
Homo sapiens
Rattus norvegicus

source_name: hiPSCs-derived neurons/primary culture of rat astrocytes

growth_protocol: Co-cultures of iPSC-derived neurons and rat astrocytes were cultured in neurobasal medium supplemented with B-27, GlutaMAX, Primocin, NT-3, BDNF and doxycycline in humidified atmosphere with 5% CO2 at 37°C until DIV 49

extract_protocol:
Quick-RNA Microprep kit (Zymo Research, R1051) according to manufacturer’s instructions.
The RNASeq libraries are prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) starting from 500 ng of total RNA

treatment_protocol: DIV 49 co-cultures were treated with 1 uM TTX for 48 hours

value: iPSCs

value: neuron+astrocyte

value: TTX

tag: time

value: Days in vitro 49


title: Liver, PairFed, S4


title: Input_BRD4-NUT_HUES64_replicate1

description: Input for BRD4-NUT in HUES64


title: NK_L_Ser_1

value: NK cells


title: 10A_M_1746

value: male


title: TTX_1

value: hiPSCs-derived neurons/primary culture of rat astrocytes


title: Input_BRD4-NUT_dME_replicate1

value: none (input)


title: Liver, PairFed, S3


title: 10A_M_1745


title: Veh_3

value: vehicle


title: IP_NT2_16hour_retinoic_acid_rep2

description: ChIP-seq for BRD4-NUT in differentiated Ntera-2 cells after 16 hr retinoic acid treatment

value: Ntera-2 derived differentiated cells

value: human embryonal carcinoma cell line

value: NUT (C52B1) Rabbit mAb#3625


title: 10A_M_1744


title: Veh_2


title: Liver, PairFed, S1

value: Liver


title: IP_NT2_16hour_retinoic_acid_rep1


title: 10A_M_1741


title: Veh_1

value: WT


title: 10A_M_1747


title: IP_NT2_4hour_retinoic_acid_rep2

description: ChIP-seq for BRD4-NUT in differentiated Ntera-2 cells after 4hr retinoic acid treatment


title: 10A_M_1740


title: TTX_2


title: IP_NT2_4hour_retinoic_acid_rep1


title: Liver, GDF15, S5


title: 10A_M_1739


title: IP_NT2_0hour_rep2

description: ChIP-seq for BRD4-NUT in Ntera-2 cells


title: 10A_M_1738


title: Liver, GDF15, S3


title: Liver, GDF15, S4


title: IP_NT2_0hour_rep1

description: ChIP-seq for BRD4-NUT in Ntera-2 cells


title: IP_BRD4-NUT_dME_replicate2

description: ChIP-seq for BRD4-NUT in HUES64 derived dME

value: HUES64 derived dME

value: differentiated cells


title: 10A_M_1737


title: Liver, PairFed, S2

value: PairFed


title: 10A_M_1736


title: IP_BRD4-NUT_dME_replicate1


title: 10A_M_1742


title: Liver, GDF15, S1


title: Liver, GDF15, S6


title: 10A_M_1735


title: IP_BRD4-NUT_HUES64_replicate2

description: ChIP-seq for BRD4-NUT in HUES64

value: Human embryonic stem cell line


title: IP_BRD4-NUT_HUES64_replicate1

description: ChIP-seq for BRD4-NUT in HUES64


title: 10A_M_1734


title: Liver, Vehicle, S6

value: Vehicle


title: ES B6xJF1 Rep1 1

source_name: mouse hybrid Embryonic stem cells BJ

value: mES hybrid cell; Embryonic stem cell

value: ESC

tag: experiment

tag: spike-in reference organism

value: No spike

value: untreated


title: Liver, Vehicle, S5


title: 10A_M_1733

value: male


title: Liver, Vehicle, S4


title: Liver, Vehicle, S3


title: 10A_M_1732


title: 10A_M_1731


title: Liver, GDF15, S2


title: RNA-seq.BT549.WT_rep2

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"

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: condition


title: Liver, Vehicle, S2


title: RNA-seq.BT549.WT_rep1


title: ddm1-DC-rep2

type: RNA

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

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

source_name: ddm1 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

value: sprayed pathogen

value: plant aerial part


title: ddm1-BA_sub-rep1

source_name: ddm1 plant, BABA treated

value: BABA treated


title: ddm1-BA_sub+DC-rep1

source_name: ddm1 plant, sprayed pathogen after BABA treatment

value: sprayed pathogen after BABA treatment


title: Liver, Vehicle, S1

source_name: Liver


title: RNA-seq.BT549.shNELFE_rep1

value: shNELFE


title: ddm1-BA_sub-rep2


title: ddm1-Ctrl-rep1

source_name: ddm1 plant, control

value: control


title: ddm1-BA_sub+DC-rep2


title: ddm1-Ctrl-rep2


title: ddm1-DC-rep1


title: RNA-seq.BT549.shNELFE_rep2


title: dm6 G4access Rep2

organism: Drosophila melanogaster

source_name: Schneider 2 cells

value: Schneider 2 cells; Macrophage-like

tag: spike-in cell line

tag: concentration

tag: duration


title: 10A_M_1729

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: 10A_M_1728

tag: age


title: 10A_M_1727

tag: strain


title: dm6 G4access Rep1


title: ChIP-seq.BT549_SLUG-ChIP.shNELFE_IP_rep2

description: ChIP-seq.BT549_SLUG-ChIP.shNELFE_rep12.bw

value: SLUG (Cell Signoneling Technology, 9585S)


title: ChIP-seq.BT549_SLUG-ChIP.shNELFE_IP_rep1


title: 10A_M_1730

tag: Sex


title: col-BA_sub+DC-rep2

source_name: Col plant, sprayed pathogen after BABA treatment

tag: genotype

value: wild type

tag: tissue


title: col-BA_sub+DC-rep1

tag: treatment


title: Col-DC-rep2

source_name: Col plant, sprayed pathogen