title: Advanced atherosclerosis, circulating monocyte, replicate 4

description: primary cell

source_name: Blood+Spleen

value: Blood+Spleen

value: monocyte

value: high cholesterol diet for 6 month


title: Advanced atherosclerosis, circulating monocyte, replicate 3

status: Public on Apr 06 2023

type: SRA

city: Freiburg

first: Ingo

last: Hilgendorf

address: Hugstetter Straße 55

department: Department of Cardiology and Angiology

country: Germany

institute: UNIVERSITY HOSPITAL FREIBURG University Heart Center Freiburg-Bad Krozingen

description: primary cell

library_source: transcriptomic

data_processing:
Reads were trimmed to remove adaptors and low quality ends.
Trimmed reads were aligned as pairs to the mouse genome (mm10) using STAR
Primary aligned reads were annotated and quantified as counts of features (exon) using FeatureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including feature counts of each sample

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Cells of interest were directly sorted in RLT lysis buffer with 1% beta-mercaptoethanol. After being further homogenized with QIAshredder (Qiagen), RNA were extracted using Rneasy micro kit (Qiagen).
RNA library were constructed with Ovation SoLo RNA-seq systems (Nugen) and paired-end sequenced using Illumina NextSeq500

treatment_protocol: Aortic macrophages were extracted from collagenase-digested whole aorta. Monocytes were extracted from red blood cell-lysed blood and spleen. Peritoneal macrophages were directly isolated from peritoneal lavage. Pre-processed tissue were subjected to fluorescence-activated cell sorting of monocytes or macrophages.

tag: tissue

tag: cell type

tag: genotype

value: Apoe ko

tag: treatment


title: Advanced atherosclerosis, circulating monocyte, replicate 2

description: primary cell


title: WT_EpiLC_CBX2

city: Dublin

first: Cheng

last: Wang

address: College Green

department: Genetics

country: Ireland

institute: Smurfit Institute of Genetics, Trinity College Dublin

description: no spike in

library_source: genomic

data_processing:
ChIP-seq reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. PCR duplicate reads were removed by Picard.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a). Generally, normalization factor (a) was calculated by a fix number N divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, bigwigs were generated by BamCoverage with extending to 200 bp and RPGC normalization. ChIP-Rx bigwig files  were generated by BamCoverage with  Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Epiblast-like cells (EpiLC)

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were spited and changed medium every 2 days.For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium were changed daily.

extract_protocol: ChIP-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.

treatment_protocol: No treatment/stimulations for this project.

value: ESC-derived epiblast-like cells (EpiLC)

tag: strain

tag: chip antibody

value: CBX2 (Cell Signaling,18687)


title: Advanced atherosclerosis, circulating monocyte, replicate 1

description: primary cell


title: Early atherosclerosis, circulating monocyte, replicate 2

description: primary cell

value: high cholesterol diet for 1 month


title: Early atherosclerosis, circulating monocyte, replicate 3

description: primary cell


title: Advanced atherosclerosis, Aorta macrophage, replicate 3

description: primary cell

source_name: Aorta

value: Aorta

value: macrophage


title: Baseline, circulating monocyte, replicate 2

description: primary cell

value: chow diet


title: Baseline, circulating monocyte, replicate 1

description: primary cell


title: Baseline, circulating monocyte, replicate 4

description: primary cell


title: Early atherosclerosis, Aorta macrophage, replicate 4

description: primary cell


title: Advanced atherosclerosis, Aorta macrophage, replicate 1

description: primary cell


title: Baseline, Aorta macrophage, replicate 3

description: primary cell


title: Early atherosclerosis, circulating monocyte, replicate 1

description: primary cell


title: Early atherosclerosis, circulating monocyte, replicate 4

description: primary cell


title: Baseline, Aorta macrophage, replicate 2

description: primary cell


title: Early atherosclerosis, Aorta macrophage, replicate 2

description: primary cell


title: Baseline, Peritoneum macrophage, replicate 2

description: primary cell

source_name: Peritoneum lavage

value: Peritoneum lavage


title: Baseline, Aorta macrophage, replicate 4

description: primary cell


title: Baseline, Aorta macrophage, replicate 1

description: primary cell


title: Advanced atherosclerosis, Aorta macrophage, replicate 4

description: primary cell


title: ST2ko_F BSSE_QGF_140312

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned to the mouse UCSC mm10 genome using STAR (version 2.7.0c) and setting options for multi-mapping reads to ‘--outFilterMultimapNmax 10 --outSAMmultNmax 1’.
All further analysis was performed within the R/Bioconductor framework. Gene expression was quantified with featureCounts (RSubread package) using extra options `allowMultiOverlap=TRUE, read2pos=5, countMultiMappingReads=TRUE, primaryOnly=TRUE, strandSpecific=2` and relied on gene annotation from Ensembl version 96.
Assembly: mm10
Supplementary files format and content: text file with genes counts per sample. Columns 1-6: "GENEID", "SYMBOL", "DESCRIPTION","GENEBIOTYPE","ENTREZID", "LENGTH". Columns 7-18: counts per sample

source_name: CD8 T Cells

growth_protocol: d0, P14 WT and  P14 ST2-/- cell transfer and LCMV Cl13 high dose infection, analysis d6 p.i.

extract_protocol:
Cells were sorted on a FACSAria II (BectonDickinson), collected directly into Trizol LS (Sigma-Aldrich) and stored at -80°C until RNA extraction. RNA was extracted using the Direct-zolTM RNA MicroPrep kit (Zymo research). RNA from samples  were quality-checked on the Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Pico Chip (Agilent, Cat# 5067-1513) and quantified by Fluorometry using the QuantiFluor RNA System (Cat# E3310, Promega, Madison, WI, USA).
Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the Standard Sensitivity NGS Fragment Analysis Kit (Cat# DNF-473, Advanced Analytical) revealing excellent quality of libraries (average concentration was 63±12 nmol/L and average library size was 317±4 base pairs). Samples were pooled to equal molarity. The pool was quantified by Fluorometry using the QuantiFluor ONE dsDNA System (Cat# E4871, Promega, Madison, WI, USA). Libraries were sequenced Single-reads 76 bases (in addition: 8 bases for index 1 and 8 bases for index 2) using the NextSeq 500 High Output Kit 75-cycles (Illumina, Cat# FC-404-1005) loaded at 2.0pM, and including 1% PhiX.Primary data analysis was performed with the Illumina RTA version 2.11.13. The NextSeq run yielded on average per sample 19.7±1.6 millions pass-filter reads.

treatment_protocol: To assess the impact of IL-33 signals on the CD8 T cell transcriptome on day 6 after LCMV infection we co-transferred 103 MACS-purified (Miltenyi Biotec naïve CD8 T cell isolation kit, mouse) P14 WT and 3x103 MACS-purified P14 ST2-/- cells into WT recipients . P14 WT and P14 ST2ko cells were FACS sorted on day 6 after LCMV infection and processed for RNA seq. Single cell suspensions were prepared by mechanical disruption using a metal mesh. Surface stain was performed at 4°C in the dark for 30 mins. Red blood cell lysis prior to sorting. Cells have been sorted in Trizol-LS.

tag: recipient

value: F


title: WT_F BSSE_QGF_140311

value: WT


title: WT_E BSSE_QGF_140309

value: E


title: Early atherosclerosis, Aorta macrophage, replicate 1

description: primary cell


title: ST2ko_E BSSE_QGF_140310


title: ST2ko_D BSSE_QGF_140308

value: D


title: WT_D BSSE_QGF_140307


title: WT_C BSSE_QGF_140305

value: C


title: ST2ko_C BSSE_QGF_140306


title: Advanced atherosclerosis, Aorta macrophage, replicate 2

description: primary cell


title: Early atherosclerosis, Aorta macrophage, replicate 3

description: primary cell


title: WT_B BSSE_QGF_140303

value: B


title: ST2ko_A BSSE_QGF_140302

value: A


title: RNA_Pcgf24KO_EpiLC_rep2

description: Total RNA was extacted with Qiagen RNeasy mini kit and NEBNext Poly(A) mRNA Magnetic Isolation Module was applied.

data_processing:
RNA-seq reads quality was confirmed by fastqc, then high quality reads aligned to reference mouse transcriptome (Ensembl GRCm38.101) with STAR2.7.1.
The transcriptome aggregated reads counts were combined a metatable for down-streaming analysis. Differentially expressed genes (DE genes) were identified using DESeq2.
Removed the low-expressed genes (BaseMean < 15), the DE genes were counted with cut-off 2 folds change (log2FC> 1 or log2FC <-1) and padj<0.05.
For visualization on the UCSC Genome Browser, bigwigs were generated by BamCoverage with no extend and RPKM normalization.
Assembly: mm10
Supplementary files format and content: RNA-seq counts, data table

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy RNA kit with DNaseI on-column treatment.Prior to starting library preparation, RNA integrity quality was confirmed by RNA ScreenTape with TapeStation (RIN > 9).  Total 1 μg RNA was used for library preparation.
RNA-seq library preparation was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra RNA Library Prep Kit for Illumina (E7770), according to the manufacturer’s protocol.
Illumina NextSeq 500, 75-bp single end

tag: cells

value: Pcgf2/4 KO ESC-derived epiblast-like cells (EpiLC)


title: LID_thyroid-mouse-PAX8-IP

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

country: USA

institute: NIH/NIEHS

data_processing:
Reads were filtered to require on a mean base quality score >20.
Adapter trimming was performed via Cutadapt v1.12 (parameters -a AGATCGGAAGAG -O 5 -q 0), followed by removal of reads less than 30bp in length.
Filtered and trimmed reads were aligned against the mm10 or rn6 reference genome via Bowtie v1.2 with parameter '-m 1'.  For samples with multiple sequencing runs, files were combined with MergeSamFiles (Picard tools v1.110).
Mapped reads were deduplicated via MarkDuplicates.jar (Picard tools v1.110).
Coverage tracks were generated by extending each uniquely-mapped non-duplicate read to the estimated average fragment size of 150bp, depth normalizing to 30 million reads (for histone marks and associated inputs) or 5 million reads (for transcription factors and associated inputs), followed by conversion to bedGraph format with BEDtools v2.24.0 genomeCoverageBed and then to bigWig format with UCSC utility bedGraphToBigWig.
TF peak calls were made by HOMER v4.10.3 with parameters "-style factor", followed by re-sizing to 300bp centered on the called peak midpoint. H3K4me3 peak calls were made by HOMER v4.10.3 with parameters "-region -size 500 -minDist 1000 -L 0".  H3K27me3 peak calls were made by HOMER v4.10.3 with parameters "-region -size 1000 -minDist 2500 -L 0".
Unified peak calls per histone mark were made by collapsing peaks from individual samples via BEDtools v2.24.0 mergeBed.
Assembly: mm10,rn6
Supplementary files format and content: peaks calls in BED format
Supplementary files format and content: depth-normalized coverage tracks in bigWig format

source_name: thyroid

growth_protocol: ChIP was performed with thryoid gland from mice or  rat thyrocyte cell line PCCL3.

extract_protocol:
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.

value: thyroid

tag: age

value: 1 month

tag: diet

value: Low Iodine Diet (LID, TD.95125, Harlan)

tag: antibody

value: PAX8, Novus Biologicals, NBP1-32440


title: WT_A BSSE_QGF_140301


title: TKO_KO_EpiLC_4C_Tbx3

data_processing:
4C-seq reads quality was confirmed by fastqc, then processed with pipe4C pipeline.
For UCSC genome browser visualization, bigwigs were generated by pipe4C pipeline.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: 4C-seq

extract_protocol:
Circularized chromosome conformation capture (4C) assays were performed using a modified published approach(van de Werken et al., 2012; Wang et al., 2019). Briefly, 10 million detached ESCs or EpiLCs were fixed with 1% final formaldehyde for 10 minutes, and quenched with final 0.125 M glycine. The cells were lysed in the 30 ml lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 0.5% NP-40, 1% Triton, 5 mM EDTA, and  proteinase inhibitors: 2 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1mM PMSF ) with rotation at 4 °C for 45  minutes. Isolated nuclei were then fully digested by restricted enzyme DpnII overnight digestion followed by overnight ligation with 50 U T4 DNA ligase at cool room temperature (18~20  °C) . Ligated circular DNA were purified after de-crosslinking incubation with proteinase K at 65 °C for overnight, followed by further incubation with Rnase A at 37  °C for 1 hour . The purified  DNA was further digested with restricted enzyme NlaIII and then ligated again and purified. The 4C libraries were amplified with the viewpoint-specific primers with inverse PCR using Roche Expand Long Template PCR System. For each viewpoint, at least 8 PCR reaction products were pooled to enhance the library complexity. The 4C PCR products were purified using Qiagen Quick PCR purification Kit. Tbx3 promoter viewpoint primers are AAGGGAAGAAGCTGCAGATC (Reading primer) and TGAAGGGAGCCCCACATG.
4C-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.
Illumina NextSeq 500, 75-bp single end

value: EpiLC

tag: restrict enzyme

value: DpnII-NlaIII


title: J2KO_EpiLC_4C_Tbx3


title: RNA_WT_EpiLC_rep3

value: WT ESC-derived epiblast-like cells (EpiLC)


title: RNA_WT_EpiLC_rep1


title: RNA_WT_EpiLC_rep2


title: 27_QKO_RMTF2_ESC_CBX7

description: 10% human NT2 cells chromatin was used for spike-in.

data_processing:
ChIP-seq reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. PCR duplicate reads were removed by Picard.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a). Generally, normalization factor (a) was calculated by 1 divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, bigwigs were generated by BamCoverage with extending to 200 bp and RPGC normalization. ChIP-Rx bigwig files  were generated by BamCoverage with  Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
ChIP-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.
Illumina NextSeq 500, 75-bp single end

value: QKO+ FLAG-MTF2  ESC-derived epiblast-like cells (EpiLC)

value: CBX7 (Abcam, ab21873)


title: RNA_Pcgf24KO_EpiLC_rep1


title: 23_PclWT_ESC_JARID2

source_name: Mouse Embryonic stem cells (Healy et al 2019)

value: Mouse Embryonic stem cells (ESC)

value: JARID2 (Cell Signaling, D6M9X)


title: 24_QKO_ESC_JARID2

value: PCL1-3&JARID2 QKO Mouse Embryonic stem cells (ESC)


title: 21_QKO_RMTF2_ESC_MTF2

source_name: Mouse Embryonic stem cells (ESC)

value: QKO+ FLAG-MTF2 Mouse Embryonic stem cells (ESC)

value: MTF2 (Peprotech, 16208-1-AP)


title: 25_QKO_RMTF2_ESC_JARID2


title: 22_QKO_RJARID2_ESC_MTF2

value: QKO+ FLAG-JARID2 Mouse Embryonic stem cells (ESC)


title: 26_QKO_RJARID2_ESC_JARID2


title: 20_QKO_ESC_MTF2


title: Baseline, circulating monocyte, replicate 3

description: primary cell

value: Blood+Spleen

value: monocyte

value: Apoe ko

value: chow diet


title: 18_QKO_RJARID2_ESC_H3K27me3

value: H3K27me3 (Cell Signaling, C36B11)


title: 19_PclWT_ESC_MTF2


title: 16_QKO_ESC_H3K27me3


title: ST2ko_B BSSE_QGF_140304

value: B


title: 15_PclWT_ESC_H3K27me3


title: Pcgf24KO_EpiLC_JARID2

value: Pcgf2/4KO ESC-derived epiblast-like cells (EpiLC)


title: Pcgf24WT_EpiLC_JARID2

value: ESC-derived epiblast-like cells (EpiLC)


title: RNA_Pcgf24KO_EpiLC_rep3

value: Pcgf2/4 KO ESC-derived epiblast-like cells (EpiLC)


title: PclQKO_EpiLC_H3K27ac

value: PCL1-3  and JARID2 QKO ESC-derived epiblast-like cells (EpiLC)

value: H3K27ac (Abcam, ab4729)


title: 28_QKO_RJARID2_ESC_CBX7

value: QKO+ FLAG-JARID2  ESC-derived epiblast-like cells (EpiLC)

value: CBX7 (Abcam, ab21873)


title: PclTKO_EpiLC_H3K27ac

value: PCL1-3 TKO ESC-derived epiblast-like cells (EpiLC)


title: PclWT_EpiLC_H3K27ac, 2


title: PclJ2KO_EpiLC_H3K27ac

value: PCL background JARID2 KO ESC-derived epiblast-like cells (EpiLC)


title: J2KO_EpiLC_CBX7

value: JARID2 KO ESC-derived epiblast-like cells (EpiLC)


title: RNA_QKO_EpiLC_rep1

molecule: total RNA

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy RNA kit with DNaseI on-column treatment.Prior to starting library preparation, RNA integrity quality was confirmed by RNA ScreenTape with TapeStation (RIN > 9).  Total 1 μg RNA was used for library preparation.
RNA-seq library preparation was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra RNA Library Prep Kit for Illumina (E7770), according to the manufacturer’s protocol.

value: PCL1-3&JARID2 QKO ESC-derived epiblast-like cells (EpiLC)


title: RNA_QKO_EpiLC_rep3


title: RNA_QKO_EpiLC_rep2


title: RNA_TKO_EpiLC_rep3


title: RNA_TKO_EpiLC_rep1


title: RNA_TKO_ESC_rep3

value: PCL1-3 TKO Mouse Embryonic stem cells (ESC)


title: RNA_QKO_ESC_rep3

value: PCL1-3&JARID2 QKO Mouse Embryonic stem cells (ESC)


title: RNA_TKO_ESC_rep2


title: RNA_TKO_ESC_rep1


title: RNA_PclWT_EpiLC_rep2


title: RNA_PclWT_EpiLC_rep3


title: RNA_PclWT_ESC_rep1

value: Mouse Embryonic stem cells (ESC)


title: RNA_PclWT_ESC_rep2


title: RNA_PclWT_ESC_rep3


title: 17_QKO_RMTF2_ESC_H3K27me3

value: QKO+ FLAG-MTF2 Mouse Embryonic stem cells (ESC)


title: RNA_J2KO_EpiLC_rep1


title: RNA_J2KO_EpiLC_rep3


title: RNA_J2KO_EpiLC_rep2


title: RNA_J2KO_ESC_rep2

source_name: Mouse Embryonic stem cells (Landeira et al., 2015)

value: JARID2 KO Mouse Embryonic stem cells (ESC)


title: PclJ2KO_EpiLC_CBX7


title: J2KO_ESC_CBX7


title: RNA_QKO_ESC_rep2


title: RNA_J2KO_ESC_rep1


title: RNA_J2WT_EpiLC_rep3


title: RNA_J2WT_EpiLC_rep1


title: RNA_TKO_EpiLC_rep2


title: RNA_QKO_ESC_rep1


title: RNA_J2WT_ESC_rep3


title: RNA_J2WT_ESC_rep1


title: 14_QKO_RJ2UIM_SUZ12_ESC

value: SUZ12 (Cell Signaling,D39F6)


title: 11_QKO_SUZ12_ESC


title: RNA_J2WT_ESC_rep2


title: 09_J2_res_FLAG_ESC

value: FLAG-M2 (gift from Dr. Claudio Ciferri)


title: 12_QKO_RPCL2_SUZ12_ESC


title: 10_WT_SUZ12_ESC


title: 13_QKO_RJ2WT_SUZ12_ESC


title: RNA_PclWT_EpiLC_rep1

value: ESC-derived epiblast-like cells (EpiLC)


title: 07_QKO_FLAG_ESC


title: 05_QKO_RSI_SUZ12_ESC


title: 06_QKO_RSIWH_SUZ12_ESC


title: 04_QKO_RWH_SUZ12_ESC


title: 08_MTF2_res_FLAG_ESC


title: 03_QKO_RWT_SUZ12_ESC


title: 02_QKO_SUZ12_ESC


title: QKO_EpiLC_H3K27ac

description: Around 20 ug chromtin was used for ChIP.


title: QKO_ESC_H3K27ac


title: RNA_J2WT_EpiLC_rep2


title: PclWT_EpiLC_H3K27ac


title: 01_WT_SUZ12_ESC


title: PclWT_ESC_H3K27ac


title: RNA_J2KO_ESC_rep3


title: J2KO_ESC_input

description: Drosophila chromatin was used for spike-in.

value: input


title: J2KO_EpiLC_input


title: J2WT_EpiLC_input


title: QKO_EpiLC_CBX7


title: TKO_EpiLC_CBX7


title: J2WT_ESC_input


title: PclWT_EpiLC_CBX7


title: PclWT_ESC_CBX7


title: QKO_EpiLC_H3K27me3

value: H3K27me3 (Cell Signaling, C36B11)


title: QKO_EpiLC_JARID2

value: JARID2 (Cell Signaling, D6M9X)


title: QKO_ESC_H2AK119ub

value: H2AK119ub (Cell Signaling, D27C4)


title: QKO_ESC_JARID2


title: QKO_EpiLC_H2AK119ub


title: QKO_ESC_H3K27me3


title: QKO_ESC_MTF2

value: MTF2 (Peprotech, 16208-1-AP)


title: ATAC-Seq_LL-ZT20-rep1

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

country: China

institute: National Key Laboratory of Crop Genetic Improvement

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bigWig file by deepTools bamCoverage

organism: Oryza sativa Indica Group

source_name: mature leaf

extract_protocol:
0.5 g-1 g of rice mature leaves cross-linked with 1% formaldehyde were used in each experiment.
Isolated rice nuclei were permeabilised with 0.3% Triton X-100 for 10 min on ice and then prepared for in situ chromatin digestion by Tn5 transposase (VAHTS; cat. no. TD501) for 30 min at 37 °C at 300 rpm. Digested chromatin was purified using a MiniElute kit (QIAGEN; cat. no. 28004), followed by PCR amplification and size selection.

tag: cultivar

value: Minghui 63

tag: protocol

value: constant light (LL)

tag: time-point

value: mature leaf


title: ATAC-Seq_LL-ZT20-rep2


title: QKO_ESC_SUZ12


title: QKO_EpiLC_SUZ12

value: PCL1-3&JARID2 QKO ESC-derived epiblast-like cells (EpiLC)


title: ATAC-Seq_LL-ZT16-rep2


title: TKO_ESC_H2AK119ub

value: PCL1-3 TKO Mouse Embryonic stem cells (ESC)


title: TKO_EpiLC_H3K27me3

value: PCL1-3 TKO ESC-derived epiblast-like cells (EpiLC)


title: ATAC-Seq_LL-ZT12-rep2


title: ATAC-Seq_LL-ZT12-rep1


title: ATAC-Seq_LL-ZT16-rep1


title: TKO_ESC_H3K27me3


title: ATAC-Seq_LL-ZT8-rep2


title: ATAC-Seq_LL-ZT4-rep2


title: TKO_ESC_JARID2


title: TKO_EpiLC_MTF2


title: ATAC-Seq_LL-ZT4-rep1


title: TKO_EpiLC_JARID2


title: ATAC-Seq_LL-ZT8-rep1


title: TKO_ESC_MTF2


title: ATAC-Seq_LL-ZT0-rep1


title: TKO_ESC_SUZ12


title: ATAC-Seq_LL-ZT0-rep2


title: QKO_EpiLC_MTF2


title: TKO_EpiLC_SUZ12


title: Epi_Ovol1

city: Irvine

first: Morgan

last: Dragan

state: CA

address: D288 Medical Sciences I

department: Biological Chemistry

institute: UC Irvine

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.35, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: skin

extract_protocol:
A single cell supsunsion was created from trypsin-islolated epidermis and processed using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads) protocol (CST, ##9003)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Mouse back skin was treated with 5% Imiquimod cream for 6 hours to enrich for Ovol1 expression

value: skin

value: epidermis

value: Ovol1 (Dai et al., 1998)


title: PclWT_ESC_H2AK119ub

value: Mouse Embryonic stem cells (ESC)


title: Epi_IgG


title: Epi_Input

value: Input


title: TKO_EpiLC_H2AK119ub


title: PclWT_EpiLC_H3K27me3

value: ESC-derived epiblast-like cells (EpiLC)


title: PclWT_EpiLC_JARID2


title: PclWT_ESC_H3K27me3


title: PclWT_EpiLC_H2AK119ub


title: Hep3B+ER, input [ChIP-Seq]

city: Perth

first: Zhaoyu

last: Li

state: Western Australia

address: QE II, M block, 225C

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

data_processing:
RNA-seq
Reads were alighed to human genome assembly hg19 and processed using Bowtie2 and Tophat2.
Counts were generated using Cufflinks.
Assembly: GRCh37 (hg19)
Supplementary files format and content: counts.txt
ChIP-Seq reads were aligned to human genome assembly hg19 using bowtie 2.1.0 with default parameters.
Peaks were called by using HOMER v4.2 with "-style histone" to its input and default parameters.
Assembly: GRCh37 (hg19)
Supplementary files format and content: bedgraph

organism: Homo sapiens

source_name: liver

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to ChIP-Seq library preparation kit (NEB).

treatment_protocol: for all HC samples

value: liver

tag: cell line

value: cancer


title: MCF7, input [ChIP-Seq]

source_name: breast

value: breast


title: WT/WT Neural stem cells, Adenovirus-cre treated

city: Durham

first: Khadar

last: Abdi

address: 300 North Duke St.

department: DMPI

institute: Duke University

data_processing:
The primary analytical pipeline for the SC analysis follows the recommended protocols from 10X Genomics. Briefly, we demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files, upon which alignment to the appropriate reference transcriptome, filtering, barcode counting, and UMI counting are performed using the most current version of 10X’s Cell Ranger software. It uses the Chromium cell barcode to generate feature-barcode matrices encompassing all cells captured in each library. The secondary statistical analysis is performed using the R package Seurat, which performs quality control and subsequent analyses on the feature-barcode matrices produced by Cell Ranger. In Seurat, data is first normalized and scaled after basic filtering for minimum gene and cell observance frequency cut-offs. We then closely examine the data and perform further filtering based a range of metrics in attempt to identify and exclude possible multiplets (i.e. instances where more than one cell was present and sequenced in a single emulsified gel bead). The removal of further technical artifacts is performed using regression methods to reduce noise. We perform linear dimensional reduction calculating principal components using the most variably expressed genes in our dataset. Library size and/or the numbers of genes expressed across subsets of cells may necessitate the restriction of cells upon which the variably-expressed genes are selected for inclusion when calculating principal components. The genes underlying the resulting principal components are examined in order to confirm they are not enriched in genes involved in cell division or other standard cellular processes. Significant principal components for downstream analyses are determined through methods mirroring those implemented by Macosko et al, and these principal components will be carried forward for two main purposes: to perform cell clustering and to enhance visualization. Cells will be grouped into an optimal number of clusters for de novo cell type discovery using Seurat’s FindNeighbors() and FindClusters() functions, graph-based clustering approach with visualization of cells being achieved through the use of t-SNE, which reduces the information captured in the selected significant principal components to two dimensions.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files average expression (RPKM) values for each cluster or cell type

source_name: Brain

growth_protocol: Neural stem cells were grown in  proliferation media containing Neural basal media supplmented with B-27, N2, EGF, FGF, penicillin/streptomyocin, and 10% serum.

extract_protocol:
Samples were prepared using the General Sample Preparation protocol from 10× Genomics (10×, Manual Part #CG00053) adapted from published methods
Cells are combined with a master mix that contains reverse transcription reagents. The gel beads carrying the Illumina TruSeq Read 1 sequencing primer, a 16bp 10x barcode, a 12bp unique molecular identifier (UMI) and a poly-dT primer are loaded onto the chip, together with oil for the emulsion reaction. The Chromium Controller partitions the cells into nanoliter-scale gel beads in emulsion (GEMS) within which reverse-transcription occurs. All cDNAs within a GEM, i.e. from one cell, share a common barcode. After the RT reaction, the GEMs are broken and the full length cDNAs cleaned with Silane Dynabeads. cDNAs are then amplified and purified by SPRI beads. After purification, the cDNAs are assayed on an Agilent 4200 TapeStation High Sensitivity D5000 ScreenTape (Santa Clara, CA) for qualitative and quantitative analysis. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size.  Illumina  P5 and P7 sequences (San Diego), a sample index, and TruSeq read 2 primer sequence are added via End Repair, A-tailing, Adaptor Ligation, and PCR.  The final libraries contain P5 and P7 primers used in Illumina bridge amplification. Sequence is generated using paired end sequencing (one end to generate cell specific, barcoded sequence and the other to generate sequence of the expressed poly-A tailed mRNA) on an Illumina sequencing platform at a minimum of 50k reads/cell

treatment_protocol: Both cell lines were treated with adenoviruses expressing cre-recominase and a GFP reporter.

value: Brain

value: Neural stem cells

value: WT

value: Adenovirus-Cre


title: PclWT_ESC_JARID2

value: JARID2 (Cell Signaling, D6M9X)


title: PclWT_ESC_MTF2

value: MTF2 (Peprotech, 16208-1-AP)


title: Hep3B+ER, rep1 [ChIP-Seq]


title: Hep3B+ER, rep2 [ChIP-Seq]


title: PclWT_EpiLC_MTF2


title: PclWT_EpiLC_SUZ12

value: SUZ12 (Cell Signaling,D39F6)


title: MCF7, rep2 [ChIP-Seq]


title: PclWT_ESC_SUZ12


title: MCF7, rep1 [ChIP-Seq]


title: Hep3B+ER, rep2

growth_protocol: all cancer cells were grown to 70-80% confluence in DMEM (Gibco) supplemented with 10% FBS (Hyclone) in 100 mm dishes.

extract_protocol:
RNA isolation from these cancer cells was performed using TRIzol™ Reagent (Invitrogen) and Rneasy kit (Qiagen) according to manufacturer’s protocol.
Libraries were generated using Truseq RNA stranded polyA (Illumina)

treatment_protocol: for all HCR samples


title: J2KO_ESC_H2AK119ub

value: JARID2 KO Mouse Embryonic stem cells (ESC)

value: H2AK119ub (Cell Signaling, D27C4)


title: Ppm1k flox/flox neural stem cells, Adenovirus-cre treated

value: Ppm1k flox/flox


title: J2KO_EpiLC_H3K27me3

value: JARID2 KO ESC-derived epiblast-like cells (EpiLC)

value: H3K27me3 (Cell Signaling, C36B11)


title: Hep3B+ER, rep1


title: J2KO_ESC_H3K27me3


title: Hep3B, rep1


title: MCF7△ESR1, rep2


title: J2KO_EpiLC_JARID2


title: J2KO_ESC_MTF2


title: J2KO_EpiLC_MTF2


title: MCF7△ESR1, rep1


title: MCF7, rep1


title: J2KO_ESC_JARID2


title: J2WT_EpiLC_H2AK119ub


title: CB-SKNAS-TR-MYCN-120h-Tet1

city: Berlin

first: Steffen

last: Fuchs

address: Augustenburger Platz 1

department: Pediatric Oncology

institute: Charité - Universitätsmedizin Berlin

data_processing:
Reads were aligned to GRCh38 using the GENCODE (v30) annotation and the STAR aligner (v2.7.1a) with the following non-standard parameters --sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --outSAMattributes NH NM MD AS XS nM HI.
Feature counting  was done using featureCounts (v1.5.1) with the following non-standard parameters when counting at the gene level -t exon -g gene_id -C -M --fraction -p -O -Q 4 -J
Genome_build: GRCh38 using the GENCODE (v30)
Supplementary_files_format_and_content: Table reporting unque mapping read counts

source_name: Neuroblastoma cell line

growth_protocol: SK-N-AS neuroblastoma cells stably transfected with a tetracycline-inducible MYCN expression system were generated with the tetracycline repressor (TR) system (pcDNA™6TR, Invitrogen). Single clones were maintained by adding 500 µg/ml G418-BC (Merck) and 5µg/ml Blasticidin (ThermoFisher Scientific) as selection antibiotic to the culturing medium.

extract_protocol:
Cells were harvested and RNA was isolated with Trizol.
Depletion of ribosomal RNA was performed by enzymatic digestion. The ribodepletion was validated by qRT-PCR and a depletion of 95-99% was regularly reached. The ribodepleted RNA was used for generation of total RNA sequencing libraries with the TrueSeq Stranded mRNA kit (Illumina San Diego, USA) according to the manufacturer. The final libraries were stored at -20°C until sequencing. Libraries were sequenced on a HiSeq4000 (Illumina, San Diego, USA) with a paired-end read length of 2 × 150 nucleotides. On average 100 Mio read pairs were generated per sample.

treatment_protocol: Induction of MYCN expression by addition of tetracyclin to the growth medium for 5d. Induction of MYCN was confirmed by qRT-PCR and Western Blot.

tag: cancer type

value: Neuroblastoma

tag: knockdown

value: Induction

value: SK-N-AS


title: CB-SKNAS-TR-MYCN-120h-Tet2


title: CB-SKNAS-TR-MYCN-120h-Tet3


title: CB-SKNAS-TR-MYCN-120h-ETOH3

value: Control


title: J2KO_ESC_SUZ12

tag: cell type


title: J2WT_ESC_H2AK119ub

value: Mouse Embryonic stem cells (ESC)


title: J2WT_ESC_H3K27me3


title: J2WT_EpiLC_JARID2

value: ESC-derived epiblast-like cells (EpiLC)


title: J2WT_EpiLC_H3K27me3


title: J2KO_EpiLC_SUZ12


title: Lin-neg

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

data_processing:
10x cell ranger analysis for short read analysis:
Cluster analysis with the Seurat software
Genome_build: hg38
Supplementary_files_format_and_content: cell_ranger diff_expr_cluster_matrix, Seurat_scRNA_object

source_name: bone marrow

growth_protocol: cells collected from discarded bone marrow filter bags

extract_protocol:
ficoll gradient, negative magnetic selection for progenitor cells (Stemcell technologies)
scRNA libraries were prepared  using 10x droplet based single cell technology

tag: tissue

value: lineage negative cells


title: CB-SKNAS-TR-MYCN-120h-ETOH2


title: CB-SKNAS-TR-MYCN-120h-ETOH1


title: J2KO_EpiLC_H2AK119ub


title: MCF7, rep2

value: breast

value: cancer

tag: genotype

tag: treatment


title: J2WT_ESC_MTF2

tag: strain

tag: chip antibody


title: J2WT_EpiLC_MTF2


title: total BM

value: bone marrow


title: CB-IMR5-KHSRP_si3-R01-R3

data_processing:
Reads were aligned to GRCh38 using the GENCODE (v30) annotation and the STAR aligner (v2.7.1a) with the following non-standard parameters --sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --outSAMattributes NH NM MD AS XS nM HI.
Feature counting  was done using featureCounts (v1.5.1) with the following non-standard parameters when counting at the gene level -t exon -g gene_id -C -M --fraction -p -s 2 -O -B -Q 4 and the following non-standard parameters when counting at the exon level -t exon -f -J -g gene_id -C -M --fraction -p -s 2 -O -B -Q 4.
Genome_build: GRCh38 using the GENCODE (v30)
Supplementary_files_format_and_content: Table reporting the read counts

growth_protocol: IMR-05 cells were routinely cultured with RPMI medium supplemented with 10% FCS, 1% penicillin and streptomycin

extract_protocol:
Cells were harvested and RNA was isolated with Trizol.
Total RNA was used for generation of mRNA sequencing libraries with the TrueSeq Stranded mRNA kit (Illumina San Diego, USA) according to the manufacturer. The final libraries were stored at -20°C until sequencing. Libraries were sequenced on a HiSeq4000 (Illumina, San Diego, USA) with a paired-end read length of 2 × 100 nucleotides. On average 50 Mio read pairs were generated per sample.

treatment_protocol: Knockdown with 2 different siRNAs and scrambled control was performed by lipofection for 3 days.

value: SiRNA 3


title: J2WT_EpiLC_SUZ12

value: SUZ12 (Cell Signaling,D39F6)


title: CB-IMR5-KHSRP_si3-R01-R2


title: J2WT_ESC_JARID2

value: JARID2 (Cell Signaling, D6M9X)


title: CB-IMR5-KHSRP_si3-R01-R1


title: J2WT_ESC_SUZ12


title: Pooled Input

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

description: Pooled Input

data_processing:
The data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore.
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Differential regions were determined using the diffReps software using the G-test with significance achieved for a fold change exceeding 1.5 and an FDR-adjusted q-value < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq tracks represented normalized to reads per million mapped in  TDF format

source_name: Mouse lung

extract_protocol:
Frozen lung tissue was pulverized, followed by cross-linking of proteins to DNA with 37% formaldehyde, and then incubation with 10X glycine to stop the reaction. Cross-linked tissue was homogenized, and centrifuged at 1,500 rpm for 5 min at 4°C. The cell pellet was resuspended with cell lysis buffer (PBS with 0.5 mM EDTA and 0.05% Triton X-100), incubated on ice for 15 min, followed by centrifiugation at 5,000 rpm for 5 min at 4°C. The cell pellet was then resuspended with nuclear lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl at pH 8.1) and incubated on ice for 10 min. Chromatin was sonicated with a bioruptor (Diagenode, Denville, NJ) to obtain fragment sizes of 100-300 bp for ChIP-seq. ChIP was performed by incubating sheared chromatin with Magna ChIPTM Protein A+G magnetic beads, and antibodies against H3K27ac overnight at 4°.The next day, the beads were washed with low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl) high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), lithium chloride wash buffer (0.25 M LiCl, 1% IGEPAL CA630, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8), and TE buffer (20 mM Tris-HCl pH 8 and 1 mM EDTA) for 5 minutes each at 4°. Immunoprecipitated DNA was recovered from the beads by incubation with ChIP elution buffer (1% SDS, 1 mM EDTA, 50 mM NaHCO3, and 50 mM Tris-HCl pH 8) and proteinase K for 2 hours at 62° with shaking, followed by incubation at 95° for 10 minutes. DNA was purified using the QIAquick PCR Purification kit (Qiagen) and DNA concetration was measured using a NanoDrop spectrophotometer (Thermo Scientific).
Sequencing libraries were prepared using the NexFlex Bioo Kit Option 2 protocol using 1.7-10 ng of DNA per sample.

treatment_protocol: Mouse pups were exposed to hyperoxia (95% O2),  within 12 h of birth for 5 days.  Neonatal mice are at the saccular stage of lung development during this period, which is equivalent to 26-36 weeks in human neonates. This leads to a pronounced arrest of lung development and is similar to the disease phenotype seen in human neonates with BPD.  Mice were euthanized on P7, and P21 (after recovery in room air) as most of postnatal lung development in mice is completed by this age.  Lung tissue was harvested on post-natal day 7 and on PND21. Tissue was snap-frozen in liquid nitrogen for downstream epigenomic analyses.

value: Pooled Tissue


title: CB-IMR5-KHSRP_si1-R01-R3

value: SiRNA 1


title: CB-IMR5-KHSRP_si1-R01-R2


title: Female Room Air PND7

description: Female Room Air PND7

value: H3K27ac (Abcam, Ab4729)

value: Room Air

tag: gender

value: female


title: CB-IMR5-KHSRP_si1-R01-R1

value: Neuroblastoma


title: Male Hyperoxia PND7

description: Male Hyperoxia PND7

value: Hyperoxia

value: male


title: Male Room Air PND7

description: Male Room Air PND7


title: Female Room Air PND21

description: Female Room Air PND21


title: Female Hyperoxia PND21

description: Female Hyperoxia PND21


title: CB-IMR5-circARID1A_scr6-R01-R3

treatment_protocol: Knockdown by siRNA and scrambled control was performed by lipofection for 4 days.

value: Scramble


title: CB-IMR5-circARID1A_si6-R01-R2

value: SiRNA


title: CB-IMR5-circARID1A_si6-R01-R3


title: Male Room Air PND21

description: Male Room Air PND21


title: CB-IMR5-KHSRP_scr-R01-R3


title: CB-IMR5-KHSRP_scr-R01-R1


title: CB-IMR5-KHSRP_scr-R01-R2


title: CB-IMR5-circARID1A_scr6-R01-R2


title: HARPE on DPR - replicate 2 in Drosophila (in vitro)

city: La Jolla

first: Torrey

middle: E.

last: Rhyne

email: terhyne@ucsd.edu, jkadonaga@ucsd.edu

state: California

address: 9500 Gilman Dr.

department: Biological Sciences

institute: UCSD

description:
reporter RNA and plasmid DNA
Raw DNA files were previously submitted (GSE139635). Raw RNA files are provided here.

data_processing:
Single-read sequences (SR75) were required to perfectly match the 10 nt sequences immediately upstream and downstream of the randomized region, which had to be exactly 19 nt. All reads that matched this pattern were deemed usable and trimmed for sequences outside of the randomized region.
When present, highly abundant reads in the randomized box that correspond to the original promoter sequence or to invariant sequences from other constructs were discarded, as they likely originated from inaccurate indexing of other multiplexed samples.
DNA and cDNA read counts were then computed for each variant.
For the DNA datasets, we used only sequences with a minimum read count of 0.75 reads per million (RPM) so that low confidence variants would not be included in the analysis. RNA (cDNA) dataset sequences were then matched to the corresponding DNA dataset, which was used as a reference. Transcription strength was then defined as RNA tag count (in RPMs) divided by DNA tag count (in RPMs).
Assembly: hg19 (HeLa cells), dm3 (S2 cells), dm6 (Drosophila embryos)
Supplementary files format and content: Two txt files (HARPE rep1 and rep2) containing the sequence of each DPR variant and its DNA read count, RNA read count, DNA read count in RPM, RNA read count in RPM, and transcription strength (“score”).
Supplementary files format and content: Three bed files containing the positions of human focused TSSs (identified in HeLa cells) and Drosophila focused TSSs (identified in embryos and S2 cells) with their human and Drosophila DPR scores according to SVRh and SVRd, respectively.
Supplementary files format and content: One model file containing the Drosophila DPR (in vitro) SVR model.
Supplementary files format and content: One updated Rscript for use of the SVR models.
Library strategy: HARPE (high-throughput analysis of randomized promoter elements)

organism: Drosophila melanogaster

source_name: embryonic nuclear extract

extract_protocol:
The HARPE procedure and data processing was performed for the DPR as described in Vo ngoc et. al (2020), with the exception that the in vitro transcription reactions were carried out with Drosophila nuclear extracts by the method of Wampler et al. (1990). A brief summary is as follows. The HARPE plasmid library was subjected to in vitro transcription (six standard reactions, 300 ng DNA each) with Drosophila extracts for 30 minutes. The transcription was performed independently two times to ensure reproducibility of the data. The combined RNA transcripts from the six reactions were extracted with Trizol™ LS (Thermo Fisher Scientific) and the contaminating plasmid DNA was removed with the TURBO DNA-free™ Kit (Thermo Fisher Scientific). After ethanol precipitation, the RNA was subjected to reverse transcription with SuperScript™ III Reverse Transcriptase (Thermo Fisher Scientific) and treatment with RNase H (New England Biolabs). The cDNA was extracted with phenol-chloroform-isoamyl alcohol, precipitated with ethanol, and size-selected on a 6% polyacrylamide-8M urea gel with radiolabeled size markers. The HARPE plasmid DNAs and the size-selected cDNAs were used as templates to generate DNA amplicons for Illumina sequencing by using custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequence corresponding to nucleotides +1 to +16 (relative to the +1 TSS) of the SCP1m promoter cassette. Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (New England Biolabs), which match the Illumina Read2-primer sequence present on the HARPE plasmid and corresponding cDNA. NGS PCR amplicons were size-selected on native 6% polyacrylamide gels prior to Illumina sequencing.
As described above, the HARPE plasmid DNAs and the size-selected cDNAs were used as templates to generate DNA amplicons for Illumina sequencing by using custom forward oligonucleotides containing the Illumina P5 and Read1-primer sequences preceding the sequence corresponding to nucleotides +1 to +16 (relative to the +1 TSS) of the SCP1m promoter cassette. Reverse primers were selected from the NEBNext® Multiplex Oligos for Illumina® kits (NEB), which match the Illumina Read2-primer sequence present on the HARPE plasmid and corresponding cDNA. NGS PCR amplicons were size-selected on native 6% polyacrylamide gels prior to Illumina sequencing.

value: embryonic nuclear extract

value: Canton-S


title: CB-IMR5-circARID1A_scr6-R01-R1


title: Male Hyperoxia PND21

description: Male Hyperoxia PND21


title: Infected, scRNAseq

city: Madison

first: Anna

last: Huttenlocher

state: WI

address: 1550 Linden Drive

department: Pediatrics

institute: University of Wisconsin School of Medicine and Public Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were processed by cellranger-6.1.2 (10x Genomics) for demultiplexing, barcoded processing, and gene counting.
Assembly: zv11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Descaled cells

extract_protocol:
Euthanized adult zebrafish were briefly dunked in room temperature phosphate-buffered saline (PBS, Gibco 14190-144) and then placed in a 60mm Petri Dish (Fisher FB0875713A) containing 8 milliliters of room temperature PBS. One (gloved) hand was used to hold the fish in place by firmly grasping the head, and the second hand was used to scrape rostrally along the body of the fish with an angled dissecting knife (Fine Science Tools 10056-12) to descale. This was done under a dissecting microscope and scale loss was visually monitored. Scales at the base of the caudal, dorsal, and anal fins typically had to be individually removed by plucking with thin-tip tweezers (Dumont). PBS from the Petri Dish was then washed over the scaled fish for approximately 30 seconds with a transfer pipette (Fisher 13-711-7M) to promote cells entering the suspension, and the buffer was then passed through a 40-micron filter. This cell suspension was then mixed 1:1 with cell isolation media (L-15, penicillin-streptomycin, and 2% FBS) in a 15 mL falcon tube, washed, resuspended in 500 uL of ACK lysis buffer for 90 seconds to lyse red blood cells, and washed once more with cell isolation media.
Library was performed according to the manufacter’s instructions (Chromium Single Cell Gene Expression Solution 3’ v2, 10x Genomics).

value: Descaled cells

value: infected


title: Female Hyperoxia PND7

description: Female Hyperoxia PND7


title: LPS-Xf-48H-S-1

city: Davis

first: Mélanie

last: Massonnet

address: 2105 Robert Mondavi Institute-North Building

department: Viticulture and Enology

institute: University of California, Davis

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 1

data_processing:
Adapter contamination removal and quality trimming of raw reads was done using Trimmomatic v.0.36 with the options LEADING:3 TRAILING:3 SLIDINGWINDOW:10:20 CROP:100 MINLEN:36.
Bowtie2 v.2.3.4.1 was used to map the processed reads onto the predicted protein-coding sequences of V. vinifera ‘PN40024’ (version V1 from http://genomes.cribi.unipd.it/grape/) with parameters: -q -end-to-end -sensitive -no-unal.
Counts of uniquely mapped reads (mapping quality Q > 30) were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91.
Assembly: Predicted transcriptome of V. vinifera ‘PN40024’ (version V1 from http://genomes.cribi.unipd.it/grape/)
Supplementary files format and content: grape_raw_counts.txt : tab delimited text file, raw read counts determined by mapping the trimmed sequencing reads

organism: Vitis vinifera

source_name: petioles

growth_protocol: The experiment was conducted on potted Vitis Vinifera cv. ‘Cabernet Sauvignon’ plants propagated from cuttings. Plants were arranged in a completely randomized design and were grown under greenhouse conditions. Optimal water and nutrients were provided on a consistent basis. X. fastidiosa subsp. fastidiosa was grown on PD3 solid medium for 5 days at 28°C for grapevine inoculations and LPS extraction.

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Vitis vinifera ‘Cabernet sauvignon’ were inoculated with 40 μL of lipopolysaccharides from Xylella fastidiosa subsp. fastidiosa (50 μg/mL) and challenged with 40 μL of X. fastidiosa in 1X PBS (108 CFU/mL) 4 hours later using the needle-inoculation method. For the control plants, grapevines were inoculated with either LPS and 1X PBS, H2O and X. fastidiosa, or H2O and 1X PBS. Grapevines were randomized in the greenhouse. Petioles were harvested at 4 h, 24 h, and 48 h post-X. fastidiosa challenge from the point of inoculation and 20 nodes above the point of inoculation. Grapevines were randomized in the greenhouse. Petioles were harvested at 4 h, 24 h, and 48 h post-X. fastidiosa challenge from the point of inoculation and 20 nodes above the point of inoculation. For each treatment and time point, the petioles of three plant replicates were pooled to build one biological replicate for a total of three biological replicates.

value: petioles

value: Cabernet Sauvignon

value: Primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa

tag: time

value: 48 hpi

tag: location

value: 20 nodes above the point of inoculation


title: LPS-Xf-24H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 3

value: 24 hpi


title: HARPE on DPR - replicate 1 in Drosophila (in vitro)


title: Control, scRNAseq

description: 10x Genomics

value: control


title: met1-3_methyltransferase_mutants_MNase_rep2

city: Ann Arbor

first: Shriya

last: Sethuraman

state: MI

address: 5164 Biological Sciences Building, 1105 N. University Ave.

department: Bioinformatics

institute: University of Michigan

description:
processed data file:
met13_MNase_readCount_met1_CG_DMR.csv
met13_MNase_readCount_met1_CHG_DMR.csv
met13_MNase_readCount_met1_CHH_DMR.csv

data_processing:
library strategy: Mnase-H3-ChIP-Seq
The fastq reads were mapped using Bowtie2.
The mapped reads were deduplicated using PICARD and filtered by fragment length between 120-170 bp and MAPQ value >=2.
Differential nucleosomes were identified using DANPOS2.
The WGBS reads were mapped using Bismark allowing no mismatches. The methylation information was extracted using bismark_methylation_extractor
DMRs were identified using methylKit R package.
Genome_build: TAIR10
Supplementary_files_format_and_content:
PolV_stabilized_nucleosomes.bed: the locations of the identified Pol V stabilized nucleosomes
SWI3B_stabilized_nucleosomes.bed: the locations of the identified SWI3B stabilized nucleosomes
PolV_stabilized_Col-0_methylation.csv: the Col-0 average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
PolV_stabilized_nrpe1_methylation.csv: the nrpe1 average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
PolV_stabilized_swi3b_methylation.csv: the swi3b average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
SWI3B_stabilized_Col-0_methylation.csv: the Col-0 average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
SWI3B_stabilized_nrpe1_methylation.csv: the nrpe1 average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
SWI3B_stabilized_swi3b_methylation.csv: the swi3b average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
Col-0_MNase_readCount_drm2_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CG-DMRs
Col-0_MNase_readCount_drm2_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CHG-DMRs
Col-0_MNase_readCount_drm2_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CHH-DMRs
Col-0_MNase_readCount_met1_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CG-DMRs
Col-0_MNase_readCount_met1_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CHG-DMRs
Col-0_MNase_readCount_met1_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CHH-DMRs
Col-0_MNase_readCount_cmt3_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CG-DMRs
Col-0_MNase_readCount_cmt3_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHG-DMRs
Col-0_MNase_readCount_cmt3_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHH-DMRs
drm2_MNase_readCount_drm2_CG_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CG-DMRs
drm2_MNase_readCount_drm2_CHG_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CHG-DMRs
drm2_MNase_readCount_drm2_CHH_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CHH-DMRs
met13_MNase_readCount_met1_CG_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CG-DMRs
met13_MNase_readCount_met1_CHG_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CHG-DMRs
met13_MNase_readCount_met1_CHH_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CHH-DMRs
cmt3_MNase_readCount_cmt3_CG_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CG-DMRs
cmt3_MNase_readCount_cmt3_CHG_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHG-DMRs
cmt3_MNase_readCount_cmt3_CHH_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHH-DMRs

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana plants were grown at 22ºC under white fluorescent light in 16h/8h day/dark cycle for 3.5 weeks

extract_protocol:
Mnase samples: Mature leaf tissues from the 3.5-week old plants were digested with Micrococcal Nuclease. MNase-digested chromatin was immunoprecipitated with anti-histone H3 antibody.
WGBS samples: Genomic DNA was extracted from 3.5-week old Arabidopsis leaves using Dneasy Plant Mini Kit.
The Mnase-ChIP-seq samples were sequenced by 50 bp paired-end sequencing. The DNA extracted for WGBS were processed with bisulfite treatment followed by 100 bp paired-end sequencing.

tag: ecotype background

value: Columbia

tag: genotype/variation

tag: developmental stage/tissue

value: 3.5 week old leaves

value: anti-histone H3 antibody


title: LPS-Xf-48H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 3

tag: cultivar


title: CB-IMR5-circARID1A_si6-R01-R1

value: Neuroblastoma


title: LPS-Xf-48H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 2


title: LPS-Xf-24H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 2


title: Hep3B, rep2

value: liver

value: cancer


title: drm2_methyltransferase_mutants_MNase_rep2

description:
processed data file:
drm2_MNase_readCount_drm2_CG_DMR.csv
drm2_MNase_readCount_drm2_CHG_DMR.csv
drm2_MNase_readCount_drm2_CHH_DMR.csv


title: LPS-Xf-24H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 1


title: Col-0_methyltransferase_mutants_MNase_rep2

description:
processed data file:
Col-0_MNase_readCount_drm2_CG_DMR.csv
Col-0_MNase_readCount_drm2_CHG_DMR.csv
Col-0_MNase_readCount_drm2_CHH_DMR.csv
Col-0_MNase_readCount_met1_CG_DMR.csv
Col-0_MNase_readCount_met1_CHG_DMR.csv
Col-0_MNase_readCount_met1_CHH_DMR.csv
Col-0_MNase_readCount_cmt3_CG_DMR.csv
Col-0_MNase_readCount_cmt3_CHG_DMR.csv
Col-0_MNase_readCount_cmt3_CHH_DMR.csv

value: Col-0 (wild-type)


title: cmt3_methyltransferase_mutants_MNase_rep2

description:
processed data file:
cmt3_MNase_readCount_cmt3_CG_DMR.csv
cmt3_MNase_readCount_cmt3_CHG_DMR.csv
cmt3_MNase_readCount_cmt3_CHH_DMR.csv


title: DiseaseCALXC_S12

city: Lisbon

first: Rita

last: Rosado-Ramos

address: Lisbon

country: Portugal

institute: Nova Medical School

description: 1x75 bp

data_processing:
Adapter contamination and low-quality and ambiguous nucleotides were trimmed from the remaining reads. The overall quality assessment of each corrected data set was carried out using FastQC
Single-end reads from the NextSeq500 were mapped against the de novo assemblies with Bowtie2
n/a
n/a
n/a
Assembly: Saccharomyces cerevisiae (S288C) was used as the reference genome (BioProject accession no. PRJNA128).
Supplementary files format and content: AvsAG.csv: aSyn vs aSyn + genipin
Supplementary files format and content: CvsA.csv: control vs aSyn
Supplementary files format and content: CvsG.csv: control vs control + genipin

organism: Saccharomyces cerevisiae

source_name: aSyn + genipin C

extract_protocol:
Total RNA was extracted using E.Z.N.A.® Yeast RNA Kit according to manufacturer instructions using yeast cells expressing αSyn-GFP or the control vector for 6 h, incubated or not with 10 uM of genipin.
RNA quality control, library preparation and sequencing was conducted by the Genomic Unit at Instituto Gulbenkian da Ciência, Oeiras, Portugal. cDNA and the libraries were obtained using SmartSeq2 protocol as previously described. cDNA and library quality was verified using the DNA 1000 Assay Chip on the AATI Fragment Analyzer (Agilent, Santa Clara, USA).

value: whole cells

value: yeast cells

value: W303 MAT a; can1-100 his3-11 15 leu2-3 112 GAL1pr-SNCA(WT)-GFP::TRP1 GAL1pr-SNCA(WT)-GFP::URA3 ade2-1

value: 6h of plasmid expression aSyn + 10 uM genipin


title: DiseaseC_S9

description: 1x75 bp

source_name: aSyn C

value: 6h of plasmid expression aSyn


title: LPS-Xf-48H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 3

value: petioles

value: Cabernet Sauvignon

value: Primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa

value: Point of inoculation


title: LPS-Xf-4H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 3

value: 4 hpi

value: 20 nodes above the point of inoculation


title: LPS-Xf-4H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 2


title: DiseaseCALXA_S10

description: 1x75 bp

source_name: aSyn + genipin A


title: LPS-Xf-48H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 2

value: 48 hpi


title: LPS-Xf-48H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 1


title: DiseaseB_S8

description: 1x75 bp

source_name: aSyn B


title: LPS-Xf-24H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 3

value: 24 hpi


title: ControlCALXC_S18

description: 1x75 bp

source_name: Control + genipin C

value: 6h of plasmid expression control + 10 uM genipin


title: ControlCALXB_S17

description: 1x75 bp

source_name: Control + genipin B


title: DiseaseA_S7

description: 1x75 bp

source_name: aSyn A


title: ControlCALXA_S16

description: 1x75 bp

source_name: Control + genipin A


title: ControlC_S15

description: 1x75 bp

source_name: Control C

value: 6h of plasmid expression control


title: ControlB_S14

description: 1x75 bp

source_name: Control B


title: ControlA_S13

description: 1x75 bp

source_name: Control A


title: LPS-Xf-4H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 1


title: LPS-PBS-48H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 48 hours post-inoculation, biological replicate 3

value: Primed with lipopolysaccharide and inoculated with PBS


title: LPS-Xf-4H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 1


title: LPS-PBS-48H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 48 hours post-inoculation, biological replicate 2


title: LPS-Xf-24H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 1


title: LPS-Xf-4H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 3


title: LPS-PBS-24H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 24 hours post-inoculation, biological replicate 3


title: LPS-Xf-24H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 2


title: LPS-Xf-4H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 2


title: LPS-PBS-48H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 48 hours post-inoculation, biological replicate 3


title: LPS-PBS-4H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 4 hours post-inoculation, biological replicate 3


title: LPS-PBS-4H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 4 hours post-inoculation, biological replicate 2


title: LPS-PBS-24H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 24 hours post-inoculation, biological replicate 1


title: LPS-PBS-48H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 48 hours post-inoculation, biological replicate 1


title: LPS-PBS-4H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 4 hours post-inoculation, biological replicate 1


title: LPS-PBS-24H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 24 hours post-inoculation, biological replicate 2


title: LPS-PBS-48H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 48 hours post-inoculation, biological replicate 1


title: LPS-PBS-24H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 24 hours post-inoculation, biological replicate 3


title: LPS-PBS-4H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 4 hours post-inoculation, biological replicate 3


title: LPS-PBS-4H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 4 hours post-inoculation, biological replicate 1


title: H2O-Xf-48H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 2

value: Primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa


title: H2O-Xf-48H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 3


title: LPS-PBS-24H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 24 hours post-inoculation, biological replicate 2


title: H2O-Xf-48H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 1


title: H2O-Xf-24H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 2


title: LPS-PBS-48H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 48 hours post-inoculation, biological replicate 2


title: LPS-PBS-24H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 24 hours post-inoculation, biological replicate 1


title: H2O-Xf-24H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 3


title: DiseaseCALXB_S11

description: 1x75 bp

source_name: aSyn + genipin B

value: whole cells


title: LPS-PBS-4H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with lipopolysaccharide and inoculated with PBS at 4 hours post-inoculation, biological replicate 2


title: H2O-Xf-24H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 1


title: H2O-Xf-48H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 3


title: H2O-Xf-4H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 1


title: H2O-Xf-4H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 2


title: H2O-Xf-48H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 1


title: H2O-Xf-24H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 2


title: H2O-Xf-24H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 3


title: H2O-PBS-24H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 24 hours post-inoculation, biological replicate 3

value: Primed with water and inoculated with PBS


title: H2O-PBS-48H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 48 hours post-inoculation, biological replicate 2


title: H2O-Xf-48H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 48 hours post-inoculation, biological replicate 2


title: H2O-PBS-48H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 48 hours post-inoculation, biological replicate 3


title: H2O-Xf-24H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 24 hours post-inoculation, biological replicate 1


title: H2O-Xf-4H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 1


title: H2O-PBS-48H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 48 hours post-inoculation, biological replicate 1


title: H2O-Xf-4H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 3


title: H2O-Xf-4H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 2


title: H2O-PBS-4H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 4 hours post-inoculation, biological replicate 3


title: H2O-PBS-24H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 24 hours post-inoculation, biological replicate 2


title: H2O-PBS-24H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 24 hours post-inoculation, biological replicate 1


title: H2O-PBS-4H-S-2

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 4 hours post-inoculation, biological replicate 2


title: H2O-PBS-24H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 24 hours post-inoculation, biological replicate 3


title: H2O-PBS-4H-S-1

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with PBS at 4 hours post-inoculation, biological replicate 1


title: H2O-PBS-24H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 24 hours post-inoculation, biological replicate 1


title: H2O-PBS-48H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 48 hours post-inoculation, biological replicate 2


title: H2O-PBS-48H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 48 hours post-inoculation, biological replicate 3


title: H2O-PBS-48H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 48 hours post-inoculation, biological replicate 1


title: H2O-PBS-24H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 24 hours post-inoculation, biological replicate 2


title: H2O-PBS-4H-P-3

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 4 hours post-inoculation, biological replicate 3


title: H2O-Xf-4H-S-3

description: Cabernet Sauvignon petioles from 20 nodes above the point of inoculation primed with water and inoculated with Xylella fastidiosa subsp. fastidiosa at 4 hours post-inoculation, biological replicate 3


title: H2O-PBS-4H-P-1

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 4 hours post-inoculation, biological replicate 1


title: H2O-PBS-4H-P-2

description: Cabernet Sauvignon petioles from the point of inoculation primed with water and inoculated with PBS at 4 hours post-inoculation, biological replicate 2


title: LNCaP-V16A, androgen deprived, biological replicate 1

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

data_processing:
Sequence quality was assessed with FastQC (v0.11.8) (38), and FASTQ files from multiple lanes corresponding to the same samples were merged.
Reads were trimmed for quality with TrimGalore! (v0.6.2) (39) using Cutadapt (v2.3) (40).
Trimmed read pairs were used to quantify transcripts with Kallisto (v0.45.1) (41) against the GRCh38 transcriptome reference index (Ensembl v94) with the following command: kallisto quant -b 100 -t 8 --pseudobam -i {index} {sample_R1} {sample_R2}.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files and h5 files include the coefficient of each sample

source_name: Prostate

growth_protocol: Cells were cultured in RPMI media (with or without phenol red)

extract_protocol:
RNA was extracted using the RNeasy plus mini kit (Qiagen, #74136), with 1μg of RNA used to make the library.
First ribosomal RNA depletion using Ribo-Zero Gold rRNA Removal kit (Illumina), then RNA libraries were prepared by the Princess Margaret Genomic Centre (PMGC).
RNA -seq,  the RNA libraries were sent for 75 bp paired-end sequencing on an Illumina NextSeq 550 at a target depth of 60M read pairs per sample.

value: Prostate

value: epithelial

value: WT

value: Androgen deprivation


title: LNCaP-LT1, Long term hypoxic, biological replicate 3

value: LNCaP-CH

value: Exposure to 1% oxygen, >144 hours


title: LNCaP-LT1, Long term hypoxic, biological replicate 1


title: LNCaP-LT1, Long term hypoxic, biological replicate 2


title: LNCaP, parental line, biological replicate 3

value: LNCaP clone FGC


title: LNCaP, parental line, biological replicate 2


title: LNCaP, parental line, biological replicate 1


title: LID_thyroid-mouse-NKX21-input

description: input for NKX2.1 ChIP

data_processing:
Reads were filtered to require on a mean base quality score >20.
Adapter trimming was performed via Cutadapt v1.12 (parameters -a AGATCGGAAGAG -O 5 -q 0), followed by removal of reads less than 30bp in length.
Filtered and trimmed reads were aligned against the mm10 or rn6 reference genome via Bowtie v1.2 with parameter '-m 1'.  For samples with multiple sequencing runs, files were combined with MergeSamFiles (Picard tools v1.110).
Mapped reads were deduplicated via MarkDuplicates.jar (Picard tools v1.110).
Coverage tracks were generated by extending each uniquely-mapped non-duplicate read to the estimated average fragment size of 150bp, depth normalizing to 30 million reads (for histone marks and associated inputs) or 5 million reads (for transcription factors and associated inputs), followed by conversion to bedGraph format with BEDtools v2.24.0 genomeCoverageBed and then to bigWig format with UCSC utility bedGraphToBigWig.
TF peak calls were made by HOMER v4.10.3 with parameters "-style factor", followed by re-sizing to 300bp centered on the called peak midpoint. H3K4me3 peak calls were made by HOMER v4.10.3 with parameters "-region -size 500 -minDist 1000 -L 0".  H3K27me3 peak calls were made by HOMER v4.10.3 with parameters "-region -size 1000 -minDist 2500 -L 0".
Unified peak calls per histone mark were made by collapsing peaks from individual samples via BEDtools v2.24.0 mergeBed.
Assembly: mm10,rn6
Supplementary files format and content: peaks calls in BED format
Supplementary files format and content: depth-normalized coverage tracks in bigWig format

source_name: thyroid

extract_protocol:
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.

value: thyroid

tag: age

value: 1 month

tag: diet

value: Low Iodine Diet (LID, TD.95125, Harlan)


title: LID_thyroid-mouse-PAX8-input

description: input for PAX8 ChIP


title: IHH cells, shANGPTL3 rep1

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institue for Medical Research

data_processing:
Trimmomatic (phred >= 30)
START (GRCh38)
HTseq (union, CRCh38)

growth_protocol: IHHs immortalized by SV40 large T-Antigen (IHH, ATCC® PTA-5565TM) were cultured in Williams E medium (Gibco by Life Technologies, 22551-022) with added 10%(v/v) fetal bovine serum (FBS), 0.2 mg/ml glutamine, 100 μg/ml streptomycin and 100 U/ml penicillin.

extract_protocol:
RNA was extracted using RNeasy® Mini Kit (Qiagen, 74,104) according to manufacturer's protocol.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to generate cDNA libraries.

treatment_protocol:
The cells were transduced with MISSION™ shRNA Lentiviral Vector particles (TRCN0000242782, Sigma Aldrich) targeting ANGPTL3 (NM_014495.2) or with a non-targeting shRNA (SHCOO2, Sigma Aldrich) [MOI (multiplicity of infection) 1].
Transduced cells were selected with 5 μg/ml puromycin and cultured further in the above medium containing puromycin. 4h before collecting cells, the medium was changed into fresh growth medium without puromycin.

tag: cell line

value: immortalized human hepatocyte

value: ANGPTL3 knock-down (shANGPTL3)

value: shRNA Lentiviral Vector (TRCN0000242782, SigmaAldrich) targeting ANGPTL3 (NM_014495.2)


title: IHH cells, shNT (control) rep4

value: WT (shNT)

value: shshRNA (SHCOO2, Sigma Aldrich)


title: IHH cells, shANGPTL3 rep3


title: IHH cells, shANGPTL3 rep4


title: IHH cells, shANGPTL3 rep2


title: IHH cells, shNT (control) rep1


title: IHH cells, shNT (control) rep2


title: Liver tissue sample  [410RD]

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Ductular reaction cells: 410RD

data_processing:
FASTQ files were trimmed with Quality Score method
Torrent Suite Software v 5.2 was used for basecalling, alignment, and mapping validated reads to HG19 transcriptome and AmpliSeq specific bed files.
Assembly: Genome_build: hg19
Supplementary files format and content: read counts RNA-seq

source_name: Liver tissue

growth_protocol: Liver cell populations (Hepatocytes, hepatobiliary cells and ductular reaction cells) were isolated by laser capture microdissection as previously described in Aguilar-Bravo et al, Hepatology 2019

extract_protocol: RNA-Seq analysis was performed using 1-10ng of RNA per sample. For each sample, libraries were created using the AmpliSeq Transcriptome Human Gene Expression Kit (ThermoFisher Scientific, ref. A26325) and the User Guide MAN0010743 (Revision C.0) with minor modifications.

value: Ductular reaction cells


title: IHH cells, shNT (control) rep3


title: Liver tissue sample  [408RD]

description: Ductular reaction cells: 408RD


title: Liver tissue sample  [410HB]

description: Hepatobiliary cells: 410HB

value: Hepatobiliary cells


title: Liver tissue sample  [408HB]

description: Hepatobiliary cells: 408HB


title: Liver tissue sample  [408HC]

description: Hepatocyte: 408HC

value: Hepatocyte


title: Liver tissue sample  [129RD]

description: Ductular reaction cells: 129RD


title: PCCL3-rat-NKX21-input

description: input for NKX2.1 ChIP

organism: Rattus norvegicus

source_name: thyrocyte cell line PCCL3

value: thyrocyte cell line PCCL3


title: PCCL3-rat-GLIS3-IP

tag: antibody

value: HA, Cell Signaling #3724


title: PCCL3-rat-NKX21-IP

value: NKX2.1 Abcam, ab76013


title: Liver tissue sample [129HB]

description: Hepatobiliary cells: 129HB

tag: cell type


title: LNCaP-V16A, androgen deprived, biological replicate 2

tag: tissue

value: Prostate

value: epithelial

value: WT

value: Androgen deprivation


title: Liver tissue sample  [129HC]

description: Hepatocyte: 129HC


title: PCCL3-rat-FOXE1-IP

value: FOXE1, Biopat, PA02000


title: PCCL3-rat-G_F-input

description: input for GLIS3 and FOXE1 ChIPs


title: ps-vec..ph-bZIP9_Col..h-B_o2

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

department: Biology

institute: New York University

description: double DAP-seq empty vector control; no peaks expected

data_processing:
library strategy: DAP-seq
Base calling was done with RTA 2.4.11 and FASTQ files were generated by Picard tools IlluminaBasecallsToFastq v2.17.11.
Raw reads were trimmed using TrimGalore 0.6.6 wrapper for Cutadapt 3.1 with the following parameter: "-q 20".
Trimmed reads were aligned by bowtie2 version 2.3.2 with default parameters against the Arabidopsis thaliana genome assembly TAIR10. Aligned reads were filtered by MAPQ score of at least 30.
Peak calling was done by the GEM peak caller version 3.3 with the default read distribution, Arabidopsis thaliana genome TAIR10 nuclear chromosome sequences, and parameters "--f SAM ---t 1 --k_min 5 --k_max 14 --k_seqs 2000 --k_neg_dinu_shuffle --outNP --outBED --outMEME --outJASPAR --outHOMER --print_bound_seqs --print_aligned_seqs".  Peaks were called for each replicate individually or by merging the two replicates using GEM's multi-replicate mode, with samples from experiments of empty vector pIXHALO and/or pIXSBP as control (indicated by the "control sample" characteristics of the sample).
Assembly: TAIR10
Supplementary files format and content: Binding events determined by GEM and GPS (part of GEM) in narrowPeak format.

source_name: rosette leaf

growth_protocol: Arabidopsis thaliana reference accession Col-0 CS70000 was grown in 16h light/8h dark cycle for three weeks. Leaf materials was collected between 9am and 11am.

extract_protocol:
Genomic DNA extracted method and DAP-seq experiment was performed as described in Li et al., 2022 (Li M., Huang SS.C. DNA Affinity Purification Sequencing (DAP-Seq) for Mapping Genome-Wide Transcription Factor Binding Sites in Plants. In: Bilichak A., Laurie J.D. (eds) Accelerated Breeding of Cereal Crops. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1526-3_15) and Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factorbinding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055).  The DAP-seq DNA library was prepared from fragmented genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  In DAP-seq, a protein expression construct containing HALO-tagged transcription factors are translated by in vitro (rabbit reticulocyte) expression system in single DAP experiment to form homodimers. In double DAP-seq, one construct containing Halo-tagged transcription factor and one containing SBP-tagged transcription factor were co-expressed by in vitro  (rabbit reticulocyte) expression system to form heterodimers. The affinity-tagged proteins are immobilized on the Halo ligand magnetic beads.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The DNA fragments bound to in vitro expressed proteins (homodimers or heterodimers) were eluted from affinity beads, PCR amplified with a full-length indexed TruSeq primer and directly sequenced on Illumina NextSeq 500.

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior to genomic DNA isolation.

tag: protein complex

value: ps-pIXSBP

tag: protein2 gene id tair

tag: protein1 family

value: control

tag: protein2 family

value: bZIP

tag: protein1 affinity tag

value: SBP

tag: protein2 affinity tag

value: HALO

tag: dna affinity purification tag

tag: expression system

value: rabbit reticulocyte lysate

tag: protein source

value: Arabidopsis thaliana

tag: dna source

tag: replicate code

tag: replicate

tag: control sample 1

tag: control sample 2


title: LID_thyroid-mouse-NKX21-IP

city: Research Triangle Park

first: Hong Soon

last: Kang

address: 111 T.W. Alexander Dr.

institute: NIH/NIEHS

value: thyroid

tag: age

value: 1 month

tag: strain

tag: genotype

tag: diet

value: Low Iodine Diet (LID, TD.95125, Harlan)

tag: antibody


title: NSPCs, Control 3, 24h

city: Guangzhou

first: Li

last: Xu

address: TianHe road 600#

institute: the third affiliated hospital of SYSU

data_processing: Comparative gene expression profiling analysis of RNA-seq data for PTN groups and control groups.

source_name: neural stem progenitor cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 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.

tag: cell line

value: neural stem progenitor cells

tag: cell type

tag: treatment

value: PBS

tag: time


title: NSPCs, Control 2, 24h


title: ps-vec..ph-bZIP9_Col..h-B_o1

tag: cultivar

tag: protein complex

tag: protein2 gene id tair

tag: protein1 family

tag: protein2 family

tag: protein1 affinity tag

tag: protein2 affinity tag

tag: dna affinity purification tag


title: ps-vec..ph-bZIP63_Col..h-B_r2

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B_r2-nuc1_GPS_events.narrowPeak

tag: expression system

tag: protein source

tag: dna source

tag: replicate code

tag: replicate

tag: control sample 1

tag: control sample 2


title: ps-vec..ph-bZIP63_Col..h-B_r1

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B_r1-nuc1_GPS_events.narrowPeak


title: ps-vec..ph-bZIP63_Col..h-B_q2

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak


title: NSPCs, PTN 3, 24h

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: PTN


title: ps-vec..ph-bZIP63_Col..h-B_q1

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP63_Col..h-B_q1-nuc1_GPS_events.narrowPeak

tag: cultivar

tag: protein complex

tag: protein2 gene id tair


title: ps-vec..ph-bZIP25_Col..h-B_o1

tag: protein1 family

tag: protein2 family

tag: protein1 affinity tag


title: NSPCs, PTN 1, 24h

tag: time


title: Liver tissue sample  [377RD]

description: Ductular reaction cells: 377RD

value: Ductular reaction cells


title: ps-vec..ph-bZIP25_Col..h-B_o2

tag: protein2 affinity tag

tag: dna affinity purification tag

tag: expression system

tag: protein source


title: NSPCs, PTN 2, 24h

value: WT


title: ChIP-seq IgG single-end

city: Ottawa

first: Marjorie

last: Brand

address: 501 Smyth Road

institute: Ottawa Hospital Research Institute

description: ChIP-seq using mouse IgG for the pulldown (control for the SATB2 pulldown) - single-end

data_processing:
Data was mapped using bowtie2, and peaks were called for ChIP-seq using combined MACS2 peak calling with q-value cutoff of 0.05. Gene Ontology (GO) term annotation was performed using GREAT v3.0.0 available online from the Bejerano lab at Stanford University.
Data was mapped using bowtie2, and peaks were called for ChIP-seq using combined MACS2 peak calling with q-value cutoff of 0.05.
For RNA-seq, data was mapped to reference mm10 genome using TopHat2. Transcripts were identified using CuffLinks. Differential expression was calculated using CuffDiff.

source_name: muscle myoblast

growth_protocol: Cells of the immortalized mouse cell line, C2C12, were grown on non-collagen coated cell culture plates in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (growth medium). When confluent, cells were differentiated in DMEM supplemented with 2% horse serum and 1% penicillin/streptomycin (differentiation medium).

extract_protocol:
Twenty million cells per time point were used for each ChIP sample. Cells were fixed for 10 min using 1% formaldehyde in DMEM. Cell fixation was quenched by removing the fixation solution, rinsing the plates with PBS, and then pouring a solution of 0.125 M glycine in PBS onto the cells and incubating for 5 min. Subsequently, plates were washed 2× with PBS and then cells were scraped from the plates, pelleted, and stored at -80 °C until used.  Given that SATB2 is a nuclear matrix attachment protein, it required an alternative protocol for chromatin shearing than standard preparations. First, a commercial hypotonic solution (Active Motif) was used to lyse cellular membranes but retain intact nuclear membranes. We subsequently performed additional lysis using a hand held glass Dounce homogenizer. After centrifugation, the supernatant was discarded and the pelleted nuclei were treated with Active Motif’s Pro-enzymatic Digestion Nuclear Extraction Solution. After incubation at 37 °C for 5 min, we supplemented the reaction with 1 U micrococcal nuclease (New England Biolabs) and allowed it to incubate for 10 min. We then supplemented the reaction with SDS to a final volume 2% SDS-chromatin solution. We proceeded to the second stage of shearing using sonication via a Covaris M220 Focused-Ultrasonicator instrument, setting the parameters to produce sheared DNA of 200 bp. After sonication, we performed a final centrifugation at 16 000 × g at 4 °C for 20 min and collected the supernatant containing the sheared chromatin.   We performed immunoprecipitations with 5 μg 1°Ab (Target: SATB2, Abcam, positive control: RNA pol II, Active Motif, negative control: mouse IgG, Santa Cruz) using magnetic beads (Active Motif) diluted in commercial ChIP-buffer (Active Motif) overnight at 4 °C. Captured chromatin was isolated using magnetic stands to pulldown the beads. Bound DNA was subsequently eluted with commercial elution, reverse cross-linking, protein digestion, and RNA digestion solutions (Active Motif). The resulting samples of DNA were further purified using phenol:chloroform extraction procedures. Final DNA was quantified using a NanoDrop spectrophotometer, with a 25 μL final   volume having concentrations of 75–100 ng/μL.
For genome-wide analysis, immunoprecipitated DNA was amplified and 75 bp single read sequencing was performed on an Illumina HiSeq 2500 at the Next-Generation  Sequencing Facility at The Centre for Applied Genomics in The Hospital for Sick Children (Toronto, Ontario, Canada).

value: C2C12 muscle myoblasts

tag: strain


title: ps-vec..ph-bZIP11_Col..h-B_q

description:
merged replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP11_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP11_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP11_Col..h-B_q-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP11_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: dna source

tag: replicate code

value: q

tag: replicate

tag: control sample 1

tag: control sample 2


title: ps-vec..ph-bZIP2_Col..h-B_q

description:
merged replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP2_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP2_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP2_Col..h-B_q-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP2_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: cultivar

value: ps-pIXSBP


title: ps-bZIP9..ph-vec_Col..h-B_q

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP9..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP9..ph-vec_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: protein complex

value: ph-pIXHALO

tag: protein1 gene id tair

value: control


title: ps-vec..ph-bZIP1_Col..h-B_q

description:
merged replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP1_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP1_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP1_Col..h-B_q-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP1_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: protein2 gene id tair

tag: protein1 family

value: bZIP

value: SBP


title: ps-vec..ph-bZIP10_Col..h-B_o1

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak

tag: protein2 family

tag: protein1 affinity tag

value: HALO

value: rabbit reticulocyte lysate


title: C2C12 Cells SATB2 ChIP-seq 3

description: ChIP-seq using mouse SATB2 for the pulldown

tag: cell type


title: ps-bZIP63..ph-vec_Col..h-B_q

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP63..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP63..ph-vec_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: protein2 affinity tag

tag: dna affinity purification tag

value: Arabidopsis thaliana


title: ps-bZIP53..ph-vec_Col..h-B_o

tag: expression system

tag: protein source

value: o


title: ps-vec..ph-bZIP44_Col..h-B_q

description:
merged replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP44_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP44_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP44_Col..h-B_q-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP44_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: dna source