title: PBMC Ctrl-3 RNA-seq

first: Vijay

last: Sankaran

address: 1 Blackfan Cr

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the hg19 reference genome using STAR
Gene count abundances were computed using the geneCounts feature in STAR
NA
Genome_build: hg38
Supplementary_files_format_and_content: Per sample raw counts in genes

source_name: bone marrow mononuclear cells

extract_protocol:
RNeasy Micro  kit  (Qiagen)
Nextera  XT  kit  (Illumina)

tag: disease state

value: healthy

value: peripheral blood mononuclear cells


title: Blood_Neutrophil_Untreated_rep3

status: Public on Apr 05 2021

type: SRA

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

description:
Blood Neutrophils from Untreated mice
BN_U3_30024
Partek_DEseq2_Blood_Treated_Untreated.xlsx
Raw_counts_Liver_Blood.xlsx

library_source: transcriptomic

data_processing:
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Alignment with STAR 2.5.3a to the GENCODE  release 16 of the Mus musculus genome (mm10 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheets (xlsx) containint differential expression analysis

molecule: total RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
RNA purification using Rneasy Mini kit (QIAGEN)
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the  manufacturer's protocol (Illumina, San Diego, CA)
Bulk RNAseq

treatment_protocol: Treated sample come from NOD.c3c4 mice treated intravenously with 10 doses of PDC166-coated NPs. Some samples come from mice treated additionally with blocking antibodies against several cytokines.

tag: strain

tag: tissue

value: Blood

tag: cell type

value: Neutrophils

tag: treatment

value: Untreated


title: PBMC Ctrl-2 RNA-seq

city: Boston

state: MA

country: USA

institute: Boston Children's Hospital

organism: Homo sapiens


title: ChIPseq-TM5-DoxNeg-Glis1

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

library_source: genomic

data_processing:
ChIP-seq reads were filtered to retain only those with mean base quality scores at least 20, followed by adapter trimming via Cutadapt v1.12 (parameters -a AGATCGGAAGAG -O 5 -q 0).  Reads less than 30bp after removal of adapter were ignored.  Filtered and trimmed reads were aligned against the hg19 reference genome (excluding haplotype chromosomes) via Bowtie v1.2 with parameter '-m 1'.  Mapped reads were deduplicated via MarkDuplicates.jar (Picard tools v1.110).
For visualization purposes, uniquely-mapped non-duplicate ChIP-seq reads were extended to estimated average fragment length of 150bp.  Alignments were converted to bedGraph format via genomeCoverageBed (Bedtools v2.24.0) then depth normalized to 25M fragments, followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
ChIP-seq peaks were called by HOMER v4.10.3 at FDR e-5 (all other parameters default) for both the DOX- and DOX+ samples.  Peaks for the DOX+ sample were filtered to retain only those meeting the following criteria: (a) did not overlap any peak in the DOX- sample, (b) at least 8x fold change over input signal [equivalent to HOMER parameter F8], and (c) at least 8x fold change over local signal [equivalent to HOMER parameter L8].  Finally, the filtered peaks were re-sized as 200mers centered on the called peak midpoint.
RNA-seq reads were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
RNA-seq counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr" for Gencode V28 gene models.
For visualization purposes, RNA-seq depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Unstranded --outWigNorm None", followed by depth normalization using size factors as reported by DESeq2 then conversion to bigWig format via UCSC utility bedGraphToBigWig.  Each of the 3 RNA-seq datasets were depth-normalized independently.
Genome_build: hg19
Supplementary_files_format_and_content: normalized depth tracks (bigWig), ChIP-seq peaks (BED), and RNA-seq counts-per-gene matrix per dataset (text files)

molecule: genomic DNA

source_name: TM5 cell line

growth_protocol: Cell lines were grown in culture media with cell specific growth factors

extract_protocol:
RNA from cultured HTM and TM5 cells was isolated with aPureLink RNA mini kit  and ChIP-Seq analysis was performed using TM5 cells stably expressing doxycycline (Dox)-inducible GLIS1-HA.  (Illumina).
HTM RNA Sequencing reads were obtained using a NextSeq Sequencing System (Illumina) and TM5 ChIP Sequencing reading was performed with a NextSeq 500 system

treatment_protocol: Cells were infected with Glis1 shRNA and control lentivirus for 48 hours, then RNA was extracted. Doxycyclin inducible stable cells were treated with or without doxycycline and fixed. Then the cells were used for ChIP.

value: Human trabacular meshwork cell line

tag: chip antibody

value: HA antibody; Cell Signaling C29F4


title: RNAseq-TM5_Glis1_DOXpos-rep1


title: PTEN shRNA-2

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

data_processing:
Adapters were trimmed using cutadapt with default parameters
Trimmed reads were aligned to the mouse reference genome, mm10, using STAR and default parameters
Raw read counts per gene were tabulated using HTSeq count and default parameters
Normalization and Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: reads counts

source_name: Murine oviductal cells

growth_protocol: Cells were grown in MTEC media (Russo A, Oncogene, 2018)

extract_protocol:
RNAeasy Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treament

value: control


title: Blood_Neutrophil_Untreated_rep2

description:
Blood Neutrophils from Untreated mice
BN_U2_30023
Partek_DEseq2_Blood_Treated_Untreated.xlsx
Raw_counts_Liver_Blood.xlsx


title: Liver_Neutrophil_Treated_Isotype_rep1

description:
Liver_NeutrLiver Neutrophils from Treated mice with Isotype control Ab
ISO1_34166
Partek_DESeq2_Anti-cytok_Iso.xlsx
Raw_counts_Cytokines.xlsx

source_name: Liver

value: Liver

value: PDC166-NP + Isotype control Ab


title: PBMC II-3 RNA-seq

value: thrombocytopenia


title: PBMC II-2 RNA-seq


title: 2ACO1268: Kidney tissue from mice (1268) with infection followed by a chow with 0.2% adenine

city: Taoyuan

first: Li-Fang

last: Chou

address: 5 Fu-Shing St., Kueishan

department: Department of Medical Research and Development

country: Taiwan

institute: Chang Gung Memorial Hospital, Linkou

description: Chronic leptospira-infected mice with the secondary nephrotoxic injury by adding high-dose adenine in diet

data_processing:
SNP & INDEL calling; Sequencing Reads Filtering: SOAPnuke: version：v1.5.2
Sequenced reads were mapped to Mus_musculus mm10 reference genome using HISAT2 v2.0.4.
To reconstruct transcripts using StringTie v1.0.4, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks v2.2.1) and predict the coding ability of those new transcripts using CPC v0.9-r2
After novel transcript detection, we merge novel coding transcripts with reference  transcripts to get complete reference, then we map clean reads to it using Bowtie2  v2.2.5, then calculate gene expression level for each sample with RSEM v1.2.12
We use DEseq2 algorithms to detect the DEGs

source_name: Kidney

growth_protocol: C57BL/6 female mice aged 7–8 weeks were used for this study. All animal experiments were handled under Animal Biosafety Level 2 conditions and followed all appropriate guidelines for the use of infected animals.

extract_protocol:
Total RNA of kidney tissues was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: C57BL/6 mice were inoculated by using intraperitoneal challenge with L. interrogans. At 28 days after infection, Leptospira-infected mice received a secondary nephrotoxic stimulation by adenine in diet for 14 days.

value: Kidney

value: Mice infected with leptospira at 28 days were subjected to a diet containing 0.2% adenine for 14 days


title: RNAseq-hTM_Glis1_DOXpos-rep2

source_name: Primary TM cells (HTM)

value: Primary human trabacular meshwork cells


title: 2ACO1262: Kidney tissue from mice (1262) with infection followed by a chow with 0.2% adenine


title: RNAseq-hTM_Glis1_DOXpos-rep1


title: PBMC Ctrl-1 RNA-seq


title: PBMC I-2 RNA-seq


title: RNAseq-TM5_Glis1_DOXpos-rep3


title: 2A1244: Kidney tissue from mice (1244) without infection and fed with a chow containing 0.2% adenine

description: Nephrotoxic stimulation by adding high-dose adenine in diet

value: Mice without leptospira infection and fed with a diet containing 0.2% adenine for 14 days


title: RNAseq-TM5_Glis1_DOXpos-rep2


title: RNAseq-TM5_Glis1_DOXneg-rep2


title: RNAseq-hTM_Glis1_shRNA_5-rep1


title: 1ACO1253: Kidney tissue from mice (1253) with infection followed by a chow with 0.1% adenine

description: Chronic leptospira-infected mice with the secondary nephrotoxic injury by adding low-dose adenine in diet

value: Mice infected with leptospira at 28 days were subjected to a diet containing 0.1% adenine for 14 days


title: RNAseq-hTM_Glis1_shRNA_1-rep1


title: RNAseq-hTM_Glis1_shRNA_4-rep1


title: RNAseq-TM5_Glis1_DOXneg-rep1


title: 2A1248: Kidney tissue from mice (1248) without infection and fed with a chow containing 0.2% adenine


title: 2ACO1269: Kidney tissue from mice (1269) with infection followed by a chow with 0.2% adenine


title: RNAseq-TM5_Glis1_DOXneg-rep3


title: RNAseq-hTM_Glis1_DOXneg-rep2


title: 2A1245: Kidney tissue from mice (1245) without infection and fed with a chow containing 0.2% adenine


title: 1A1234: Kidney tissue from mice (1234) without infection and fed with a chow containing 0.1% adenine

description: Nephrotoxic stimulation by adding low-dose adenine in diet

value: Mice without leptospira infection and fed with a diet containing 0.1% adenine for 14 days


title: Dep_3

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
nAnTi-CAGE
1st run
X31

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads from fastq files were trimmed and mapped to mm10 UCSC genome assembly with bwa aln -n 0.02 -o 1 -e -1 -i 5 -d 10 -l 32 -k 2 -m 2000000 -t 8 -M 3 -O 11 -E 4 -R 30 -q 0, unmapped reads were remapped by using hisat2 (default parameters).
CAGE tag starting site (CTSS), clustering, TPM normalization were perfrmed by applying PomoterPipeline (Arnaud et al., 2016)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited osc file includes CAGE clusters, raw and TPM values for each sample

source_name: soleus muscle

extract_protocol:
Dissected soleus muscles were rapidly frozen in liquid nitrogen. RNA was isolated by RNeasy Fibrous tissue kit (Qiagen).
nAnTi-CAGE protocol by Murata et al., 2014

value: soleus muscle

tag: condition

value: torpor deprivation


title: Post_4

description:
nAnTi-CAGE
1st run
X28

value: recover


title: 1ACO1251: Kidney tissue from mice (1251) with infection followed by a chow with 0.1% adenine


title: RNAseq-hTM_Glis1_DOXneg-rep1


title: RNAseq-hTM_Glis1_shRNA_5-rep2


title: RNAseq-hTM_Glis1_Control-rep1


title: RNAseq-hTM_Control_shRNA-rep3


title: RNAseq-hTM_Control_shRNA-rep2


title: Post_1

description:
nAnTi-CAGE
1st run
X25ab


title: HiT_4

description:
nAnTi-CAGE
1st run
X20

value: high temperature


title: RNAseq-hTM_Control_shRNA-rep1


title: HiT_3

description:
nAnTi-CAGE
1st run
X19


title: RNAseq-hTM_Glis1_Control-rep2


title: Dep_1

description:
nAnTi-CAGE
1st run
X29ab


title: 1A1237: Kidney tissue from mice (1237) without infection and fed with a chow containing 0.1% adenine


title: Dep_4

description:
nAnTi-CAGE
1st run
X32


title: EM1214: Kidney tissue from mice (1214) without infection and fed with a standard chow

description: Control mice

value: Mice without leptospira infection and fed with a standard chow


title: 1ACO1259: Kidney tissue from mice (1259) with infection followed by a chow with 0.1% adenine


title: Pre_2

description:
nAnTi-CAGE
1st run
X14


title: Mid_8

description:
nAnTi-CAGE
1st run
X12a

value: torpor


title: 1A1231: Kidney tissue from mice (1231) without infection and fed with a chow containing 0.1% adenine


title: Dep_2

description:
nAnTi-CAGE
1st run
X30ab


title: Post_3

description:
nAnTi-CAGE
1st run
X27


title: CO1224: Kidney tissue from mice (1224) with infection followed by a standard chow

description: Chronic leptospira-infected mice

value: Mice infected with leptospira at 28 days were subjected to a standard chow


title: WT_ZF_Sperm

city: Salt Lake City

first: Bradley

middle: R

last: Cairns

state: UT

address: 2000 Cir of Hope Dr

department: oncological Sciences

institute: Huntsman Cancer institute/HHMI

data_processing:
Reads were aligned to a merged zv10 (chromosomes were labeled 1-25) and dm6 (chromosomes were labeled 2L, 2R, 3L, 3R, 4D, XD, YD) genome using bwa mem (V 0.7.15-r1140, http://bio-bwa.sourceforge.net/bwa.shtml) using the following options -A 1 -B 4 -E 50 -L 0.
HiCexplorer (V3.3, https://hicexplorer.readthedocs.io/en/latest/) hicBuildMatrix was used to create matrix at 10kb, 25kb, 100kb resolutions, using the option --outBam, to extract valid Hi-C reads.
The bam file from the 25kb built matrices replicates were merged using Samtools merge (V1.8, http://www.htslib.org/doc/samtools-merge.html) and that file was further processed to text file with bamToBed using bedtools (V2.22.1, https://bedtools.readthedocs.io/en/latest/)
Genome_build: zv10 & dm6
Supplementary_files_format_and_content: txt.gz bed file format of all valid pairs used in creating HiC contact matrix. This format is useful for anyone to quickly import into other publicially available HiC contact matrice programs (example:juicer)

organism: Danio rerio

source_name: WT Wik

growth_protocol: Standard zebrafish growth conditions.

extract_protocol:
Embryos were dechorionated with 0.3 mg/ml pronase and then deyolked using deyolking buffer (55 mM NaCl, 3.6 mM KCl, and 1.25 mM NaHCO3). Whole embryos were cross-linked with 1% formaldehyde. Separately, Drosophila S2 spike-in control cells were collected. Washed twice in 1xPBS and cross-linked with 1% formaldehyde. Cell lysis for both was performed on ice with Cell Lysis buffer (10 mM Tris-Cl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630). Drosophila nuclei was spiked into zebrafish embryo nuclei calibrated to represent ~5% of total reads. HiC was performed as origionally described Rao et al., 2014 modified for small cell HIC as described in Diaz et al., 2018.
Samples Ran on Hiseq utilized: library prep was performed using Tn5 tagmentation on DNA according to Picelli, et al. Genome Research 2014 Samples ran on Novaseq utilized: NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240) with NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set, E7600S)

treatment_protocol: Untreated - Embryos Incubated 28C; Drug treatments: 4hrs DMSO treatment - Embryos inc. 28C - 0.1 percent; 4hrs Flavopiridol treatment - Embryos inc. 28C - 1.5 μM;  4hrs SGC-p300 treatment - Embryos inc. 28C - 20 μg/mL

tag: developmental stage

value: Sperm

value: Untreated


title: Post_2

description:
nAnTi-CAGE
1st run
X26ab


title: WT_ZF_Embryos_4hpf_SGC

source_name: WT Tubingen

value: Embryo

value: 4hrs SGC-CBP30 20 µg/nL


title: Mid_7

description:
nAnTi-CAGE
1st run
X11


title: CO1221: Kidney tissue from mice (1221) with infection followed by a standard chow

description: Chronic leptospira-infected mice

value: Kidney


title: Pre_4

description:
nAnTi-CAGE
1st run
X16ab

value: control


title: Aged C57BL6/J mouse(1)_cf-miRNAs

type: RNA

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization and washing were followed by the protocols supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing:
BG subtraction: Signal intensities of each spot were normalized by substitution with a mean intensity of the background signals determined by all the blank spots’ signal intensities of 95% confidence intervals.
Global normalization: Numerical values when corrected so that the median of the signal intensity (sum total) becomes 25.

source_name: mouse plasma

label_protocol: Extracted total RNAs were labeled with Hy5 using a miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: Total RNAs were extracted from plasma by using a Plasma/Serum circulating and exosomal RNA purification mini kit (Norgen) according to the manufacturer’s instructions.

tag: Sex

value: male

tag: age


title: HiT_2

description:
nAnTi-CAGE
1st run
X18


title: Mid_5

description:
nAnTi-CAGE
1st run
X09ab


title: HiT_1

description:
nAnTi-CAGE
1st run
X17


title: Yong C57BL6/J mouse(2)_cf-miRNAs


title: Pre_3

description:
nAnTi-CAGE
1st run
X15b


title: EM1215: Kidney tissue from mice (1215) without infection and fed with a standard chow

description: Control mice


title: Schizont stage duplex RNA-seq rep 1

city: Cambridge

first: Sabah

last: Kadri

state: Massachusetts

address: 7 Cambridge Center

department: Computational Biology

institute: Broad institute

description:
duplex RNA
L1

data_processing:
The paired end reads from the duplex RNA-Seq data were first trimmed to remove any adapter sequences using fastp v0.20.0 (Chen et al. 2018).
Then, STAR v2.5.2 (Dobin et al. 2013) was used to align the trimmed data to the P. falciparum genome (v34) with the parameters --genomeSAindexNbases 11 and  --alignIntronMax 500.
A custom filter was then used to remove low mapping quality (mapping quality =0) and secondary or supplementary alignments.
featurecounts v2.0.0 (Liao et al. 2014) was used to perform gene counting using the latest gene annotations from (Chappell et al. 2020). Reads that mapped to mitochondrial, apicoplast transcripts, rRNAs and tRNAs were removed from this gene expression analysis.
Genome_build: P. falciparum genome (v34)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every mRNA, ncRNA, snoRNA, snRNA gene and every sample

organism: Plasmodium falciparum

source_name: P. falciparum 3D7 cultured in human RBCs

growth_protocol: P. falciparum laboratory adapted parasite line 3D7 was cultured at 2% hematocrit in purified human erythrocytes/RBCs using standard culturing techniques (Trager and Jensen 1976; Duffy and Avery 2018) using RPMI 1640 medium (supplemented with 37.5 mM HEPES, 7 mM D-glucose, 6 mM NaOH, 25 µg of gentamicin sulfate/ml, 2 mM L-glutamine, and 10% Albumax II (Life Technologies) at a pH of 7.2 in a 3% carbon dioxide environment. The asexual blood stage parasite density was calculated routinely using thick blood films. Baseline RBC count was used to calculate the parasitaemia (parasites/µl).

extract_protocol:
P. falciparum parasites were isolated after saponin lysis and washed with incomplete medium (without Albumax). The RNA from each stage were isolated by the Trizol (Thermofisher) method followed by Turbo DNAse (Thermofisher) treatment. Total RNA was then subjected to two rounds of rRNA depletion with custom biotinylated oligos designed against P.falciparum’s rRNAs (Suppl. Table 1). Briefly, 500 pmol of biotinylated capture probes were used in a binding buffer containing 10 mM Tris-Cl pH 7.4, 3 mM MgCl2, 300 mM NaCl and 0.5% Igepal-CA 630. The hybridization reaction was prepared on ice in the presence of 50 ug of total RNA in each tube and 2ul of RNase inhibitor. The oligo probe and total RNA mixture was heated at 70 °C for 5 minutes followed by gradually reducing the heat until the oligonucleotides have reached room temperature. Finally, rRNA bound oligos were separated by Streptavidin conjugated magnetic Dynabeads M-280 (Invitrogen) followed by ethanol precipitation of rRNA depleted total RNAs. Next, RNA samples were treated with a single-strand specific ribonuclease, RNase One (Promega) (5 units per ug of RNA), according to the manufacturer’s instructions. After nuclease treatment, each RNA sample was fragmented with Fragmentation Reagents (Ambion) and then end corrected with T4PNK (Thermofisher). The RNA went through phenol-chloroform extraction and ethanol precipitation before using them for RNA-seq library preparation.
P. falciparum duplex RNA sequencing libraries were prepared from the three developmental stages: ring, trophozoite and schizont (see results section for details). Two independent sets of libraries were prepared (2 replicates for each developmental stage). The sequencing library was constructed using the Small RNA Sequencing Kit v3 (Illumina, San Diego, CA) as per manufacturer’s instructions.
Library quality was checked by Bioanalyzer and then pair-end sequencing was done on two different Illumina high-throughput sequencing platforms, HiSeq2500 for RNA-seq-1 (Otogenetics Corp., Atlanta, GA) and NextSeq500 for RNA-seq-2 (ACGT Inc, Germantown, MD) (Table-1).

treatment_protocol: P.falciparum Infected Red Blood Cells (iRBCs) were treated with a pre-warm aliquot of 5% D-sorbitol in RPMI at 37°C to attain synchronized parasite cultures in order to isolate homogeneous stages of parasites. Multiple sorbitol treatments were administered to achieve >90% synchrony of parasites. Parasites were collected from the three different developmental stages (ring, trophozoite and schizont) after stringent synchronizations.

tag: Stage

value: Schizont

tag: collection

value: 30-42 hours post-invasion of parasite in human RBCs


title: Pre_1

description:
nAnTi-CAGE
1st run
X13


title: Fed_3

description:
nAnTi-CAGE
1st run
X07b

value: starvation


title: wt_UV2hr A3

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Library strategy: CPD-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A3 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Background values dipyrimidine sequences were generated in WIG file using custom perl script
Genome_build: SacCer3
Supplementary_files_format_and_content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences and including background value of 0.0 at nucleotides associated with dipyrimidines with no mapped sequencing reads. A sequencing read count was  assigned to each nucleotide in the lesion-containing dipyrimidine sequence.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 5 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 3 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. After UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at 2 hours after UV irradiation (2hr). Cells were spun down and kept at -80˚C until genomic DNA isolation.

tag: genotype

value: Wild-type

value: UV irradiated 125 J/m2

tag: repair time

value: 2 hr


title: wt_NoUV A1


title: EM1213: Kidney tissue from mice (1213) without infection and fed with a standard chow

description: Control mice


title: wt_UV0hr A2

value: 0 hr


title: Fed_1

description:
nAnTi-CAGE
1st run
X05a

value: soleus muscle


title: Aged C57BL6/J mouse(2)_cf-miRNAs


title: CO1223: Kidney tissue from mice (1223) with infection followed by a standard chow

description: Chronic leptospira-infected mice


title: WT_ZF_Embryos_2.25hpf_LD


title: E15.5 microglia from stressed CD1 embryos

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: # FACS sorted cells: 9,055 cells; Loaded: ~6,000 cells on 10X: Recovered: 1,467 cells

data_processing:
All raw FASTQs reads were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics Cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.4 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells were excluded from the overall experiment. Gene expression was log normalized. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. Expression of marker genes across cell clusters identified by graph based clustering was used to define cluster identity.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

molecule: polyA RNA

source_name: E15.5 microglia (stress) hypothalamic/thalamic region

extract_protocol:
E15.5 brains were dissected from one wild-type control CD1 dam (n = 10 brains, hypothalamic/thalamic tissue pooled) and one stressed CD1 dam (n = 5 brains, hypothalamic/thalamic tissue pooled) in cold Hank’s Buffered Salt Solution (HBSS; Life Technologies) on ice, where the hypothalamic/thalamic region was micro-dissected out and then placed in our live-cell media (DMEM, F12, GlutaMAX, FBS, HS, N2, B27 mixture) and chopped into smaller pieces using a blade while on ice. The cell suspension was then run through 70 µm cell filter and centrifuged at 300 x g. for 5 min at 4 degrees. Liberated single cells were re-suspended in 500 µL  of our live-cell media, and stained with 3 µL of Cd11b-PE and 3 µL of Cd45-FITC for 45 min at 4 degrees on a shaker in the dark. The staining cell suspension was then washed in 10mL of HBSS + 5% FBS on ice, spun at 1200rpm ( ~300 x g in a table-top centriduge) for 5 min at 4 degrees. The cells were resuspended in 300 µL of HBSS + 5% FBS and filtered through a 70 µm cell filter. For FACS purification, a stringent initial forward and side scatter gates were used to exclude debris, and cell doublets. Cd11b-PE / Cd45-FITC double positive cells were purified (10-12 min total length for each run) and collected in 100% FBS. The cells were then spun at 300 x g for 5 min at 4 degrees to achieve a final volume of ~40-50 µL to be used for 10X.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 10X Gene expression solution (using Chip B) as per the manufacturer’s protocol. In brief, single cells were FACS sorted into 100% FBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using D1000 ScreenTape System. Next Generation Sequencing was done using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~100,000 reads/cell. We recovered 1,156 cells from E15.5 control tissue (pooled) and 1,467 cells from E15.5 stressed tissue (pooled), with an estimated doublet rate of ~3-4%.

treatment_protocol: wild-type CD1 microglia were extracted from the hypothalamic/thalamic region of E15.5 embryos OR stressed CD1 microglia (pregnant dams stressed - placed in 4 degree for 30 min each day between E11.5 - E15.5 (5 days) during pregnancy) were extracted from the hypothalamic/thalamic region of E15.5 embryos

tag: transgenic strain

value: CD1 - N/A

tag: background

tag: facs strategy

value: Cd11b-PE / Cd45-FIT

tag: stress

value: pregnant dams exposed to a mild cold stress over 5 days

value: E15.5 microglia


title: Fed_4

description:
nAnTi-CAGE
1st run
X08

tag: tissue

tag: strain


title: Mid_4

description:
nAnTi-CAGE
1st run
X04

value: torpor


title: elf1_NoUV A1

tag: treatment


title: elf1_UV0hr A2


title: Mid_6

description:
nAnTi-CAGE
1st run
X10ab


title: Mid_2

description:
nAnTi-CAGE
1st run
X02


title: Mid_1

description:
nAnTi-CAGE
1st run
X01b


title: Ring stage duplex RNA-seq rep 1

description:
duplex RNA
E1

value: Ring

value: 2-12 hours post-invasion of parasite in human RBCs


title: Fed_2

description:
nAnTi-CAGE
1st run
X06


title: WT_ZF_Embryos_2.25hpf_ED

value: Embryo

value: Untreated


title: 4hpf_Rad21

data_processing:
Fastq files were aligned to Zv10 using Novocraft novoalign (version 2.8) with the following parameters: -r Random -o SAM.
SAM files were converted to BAM format and sorted with Samtools. Bam files for technical replicates were merged using Samtools merge.
For single-end ChIP-seq, fragment sizes were first checked using Macs2 predicted and bam2wig.pl (Biotoolbox, https://github.com/tjparnell/biotoolbox  ) for IP and corresponding input bam files. The Multi-Replica Macs ChIPSeq Wrapper (version 9, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq) was then run with options: --species zebrafish --size M --nodup --cutoff 2 --tdep N, where M represents the predicted fragment size, and N represents the lowest observed sequencing depth in millions.
Genome_build: zv10
Supplementary_files_format_and_content: narrowPeak and bigWig files. The narrowPeak files are the identified peaks of enrichment at a threshold of q-value 0.01. The bigWig files are log2-scaled Fold Enrichment of ChIP signal over Input signal

extract_protocol:
Briefly, approximately 200-300 embryos were dechorionated with pronase and deyolked with deyolking buffer (55mM NaCL, 1.8mM KCl, 1.25mM Sodium Biocarbonate). Zebrafish cells were fixed using formaldehyde and stopped with 0.2M  glycine. Cells were snap frozen with liquid nitrogen and stored at -80C. Approximately 1000 embryos were used for the 4hpf Chip-seq was fragmented to a size range of 200–700bp with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with antibody.  Protein A‐sepharose was used to pull‐down the antibody–chromatin complexes which were then washed and eluted. After cross‐link reversal (5 hours, 65C) and proteinase K digestion, immunoprecipitated DNA was extracted with phenol‐chloroform, ethanol precipitated, and treated with RNase.
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240) with NEBNext Multiplex Oligos for Illumina (E7335L)

treatment_protocol: untreated

tag: chip antibody

value: Rad21 (Cohesin)


title: elf1_UV2hr A3


title: Trophozoite stage duplex RNA-seq rep 1

description:
duplex RNA
M1

value: Trophozoite

value: 18-26 hours post-invasion of parasite in human RBCs


title: Post_7

description:
nAnTi-CAGE
2nd run
CNhi10976_NoIndex_L004_R1_001.fastq.GCG

value: recover


title: Mid_3

description:
nAnTi-CAGE
1st run
X03


title: MBT_ATAC-seq_rep1

description:
11766X3_150911_D00550_0290_AC7JV1ANXX_5
11766X4_150911_D00550_0290_AC7JV1ANXX_5

data_processing:
Fastq files were aligned to Zv10 using novoalign (version 3.8) with the following parameters: -r Random -o SAM.
SAM files were converted to BAM format and sorted with Samtools. Bam files for technical replicates were merged using Samtools merge.
Bam files were processed using Multi-Replica Macs ChIPSeq Wrapper (version 12, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq) with the following parameters: --species zebrafish --pe --min 30 --max 120 --nodup --cutoff 2 --tdep N, where N represents the lowest observed sequencing depth in millions. The fragment sizes were set to be subnucleosomal to allow for identification of transcription factor binding. The log2 fold enrichment bigwig files were used for generating heatmaps and metaplots.
Genome_build: zv10
Supplementary_files_format_and_content: narrowPeak and bigWig files. The narrowPeak files are the identified peaks of enrichment at a threshold of q-value 0.01. The bigWig files are log2-scaled Fold Enrichment of ChIP signal over Input signal

extract_protocol:
Approximately 300 embryos/tube of a 4hpf embryo was lysed with TN5 Lysis buffer (10mM Tris-CL, pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Igepal CA 630 + 1% protease inhibitor). Nuclei was isolated by removing. Chorion, yolk and cell membrane by physical disruption utilizing a 3mL syringe/20G needle while kept on ice. Nuclei was washed 2 times at room temperature for 10mins with nuclei wash buffer (50mM Tris-HCL pH 8.0, 100mM NaCl, 10mM EDTA + 1% protease inhibitor).
The ATAC-seq library was made using Nextera DNA Flex Library Prep Kit (illumina, 20018704) was followed according to kit specifications.  Proper sizing of tagmentation was determined by DNA acrylamide gels utilizing Typhoon imager (GE Healthcare) for each lot of enzyme used.


title: E15.5 microglia from CD1 embryos

description: # FACS sorted cells: 8,834 cells; Loaded: ~6,000 cells on 10X: Recovered: 1,156 cells

source_name: E15.5 microglia (wild-type) hypothalamic/thalamic region

value: control

tag: cell type


title: 4hpf_input

value: none (input)


title: CB-MK#1

first: Keiichi

last: Tozawa

address: 35 Shinanomachi

institute: Keio University School of Medicine

description: Gene expression data from Cord blood stem cell derived megakaryocytes.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The raw data were normalized by MAS5 algorithm.

label: biotin

label_protocol: Affymetrix standard protocol

extract_protocol: Trizol


title: MBT_input


title: Post_6

description:
nAnTi-CAGE
2nd run
CNhi10976_NoIndex_L004_R1_001.fastq.AGT

tag: condition


title: BiSulfite-seq HEMnDP2 UVR3

city: Philadelphia

first: Sarah

last: Alp

state: PA

address: 3307 N Broad Street

department: Fels Institute

institute: Temple University

data_processing:
Adapter sequences were removed using TrimGalore.
Bismark bisulfite read mapper and methylation caller was used to align to the hg19 genome and enumerate methylated and unmethylated CpG sites.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-deliminated text file. The columns of the file are: chrBase, chromosome , base, strand, coverage, freqC (number of methylated reads), freqT (number of unmethylated reads)

growth_protocol: HEMn-DP cells were cultured in Medium 254 (Gibco) supplemented with human melanocyte growth supplement (Gibco) and phorbol 12-myristate acetate (200nM).

extract_protocol:
Cells were pelleted and lysed in 2% SDS, 25 mM EDTA; proteins were percipitated by the addition of 10M ammonium acetate and removed by centrifugation. DNA was precipitated by the addition of isopropanol and washed twice with 70% ethanol. The DNA pellet was dissolved in TE (Tris 10 nM, EDTA 1mM). High molecular DNA was recovered by immobilization on 0.4x AMPure XP beads (Agencourt) prior to methylation analysis.
One microgram of genomic DNA was digested with MspI restriction enzyme for 1 h at 37°C.  3' end filling and dA tailing was performed by 15 units of Klenow Fragment (3'>5' exonuclease deficient; NEB) with nucleotide mix ( 0.4 mM final concentration of each dCTP, dGTP, dATP).
Libraries were prepared by ligation of NEBNext methylated adapters  at a 10:1 adapter to fragment ratio using T4 DNA ligase (NEB) at 16°C overnight. Hairpin loops of the adapters were cleaved with USER enzyme at 37°C for 15 m. Ligated DNA was dual-size selected using AMPure XP beads for fragments between 150 to 350 bp range. Adapter-ligated DNA fragments were bisulfite converted using Qiagen's EPITECT kit (Qiagen). Bisulfite treated DNA fragments were indexed with NEBNext Index  i7 primers (NEB). Libraries were amplified for 17 cycles and cleaned with AMPureXP beads prior to sequencing. Libraries were were pooled to 10 nM and spiked with 25% phiX to ensure sequence diversity.

treatment_protocol: Cells were plated in biological triplicate 2 days before UVR exposure.  Cells were at 80% confluence at time of treatment. Cells were washed with DPBS and covered with Saran wrap for UVR exposure.  Two TL-20 lamps emitting a broad spectrum waveband  (35% UVA and 65% UVB) were used.  Cells received a total dose of 175 J/m2 over 90 s at a rate of 1.94 W/m2. The majority of the cells survive this exposure.  Cells were cultured for one month after UVR treatment before detecting changes in DNA methylation.

tag: cell line

value: UVRc


title: Yong C57BL6/J mouse(1)_cf-miRNAs

tag: Sex

value: male


title: Mid_13

description:
nAnTi-CAGE
2nd run
CNhi10976_NoIndex_L004_R1_001.fastq.ACC

value: soleus muscle


title: MBT_polii

description:
11294X7_141223_D00550_0217_AC62APANXX_4
11294X8_141223_D00550_0217_AC62APANXX_4

tag: developmental stage

value: RNA pol II (8WG16/Covance cat# MMS-126R)


title: Mid_10

description:
nAnTi-CAGE
2nd run
CNhi10975_NoIndex_L003_R1_001.fastq.TAC


title: BiSulfite-seq HEMnDP2 UVR1

value: UVRa


title: WT_ZF_Embryos_4hpf_FLAV

value: 4hrs flavopiridol 1.5 µM


title: Post_5

description:
nAnTi-CAGE
2nd run
CNhi10976_NoIndex_L004_R1_001.fastq.CAC


title: MBT_ATAC-seq_rep2

description:
11916X3_151021_D00550_0297_AC7HL4ANXX_5
11916X4_151021_D00550_0297_AC7HL4ANXX_5
11916X3_151021_D00550_0297_AC7HL4ANXX_6


title: BiSulfite-seq HEMnDP2 control1

value: Control


title: BiSulfite-seq HEMnDP2 control2


title: Pre_5

description:
nAnTi-CAGE
2nd run
CNhi10975_NoIndex_L003_R1_001.fastq.CAC


title: WT_ZF_Embryos_5.3hpf


title: BiSulfite-seq HEMnDP2 UVR2

value: UVRb


title: BiSulfite-seq HEMnDP2 control3


title: Mid_9

description:
nAnTi-CAGE
2nd run
CNhi10975_NoIndex_L003_R1_001.fastq.GCG

value: torpor


title: SK-LMS-1_H3K27me3 H4KO ChIP [N2_S1]

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

description:
N2_S1
Facultative heterochromatin evaluation in HDAC4KO cells

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
Peaks were called using HOMER for HDAC4 ChIP (“factor” mode) and using MACS2 version 2.1.0 for H3K27ac and H3K27me3 (“sharp” mode and “broad” mode, respectively), q<0.05
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated by the deepTools python suite command ‘bamCoverage’. Output files represent  the genomic coverage associated with each ChIP-seq experiment, expressed as reads per bin. Bins are short consecutive counting windows of size n=50nt. Data normalized as Reads Per Kilobase per Million mapped reads (RPKM).

growth_protocol: SK-LMS-1 cells (HDAC4KO/HDAC4-ER) were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine and penicillin–streptomycin (Euroclone, Milan, Italy). For each ChIP, 3.2*10^6 cells were used.

extract_protocol:
Lysates were obtained with a two-step protocol (nuclei were obtained with an hypotonic buffer (20mM TRIS-HCl pH8; 85 mM KCl; 0.5% NP-40), and nuclear membrane was lysed with Lysis buffer (10mM TRIS pH7.5; 1% NP-40, 0.5% Na-deossicholate; 0.1% SDS); then lysates were clarified from sonicated nuclei (30', medium power, Bioruptor Diagenode) and histone-DNA complexes were isolated with protein A/antibodies: 2μg of anti-H3K27ac (Abcam ab177178) , 3μg  of anti-H3K27me3 (Abcam ab6002), 4μg of anti-HDAC4 (Paroni et al, 2004) antibodies or control IgG. Washes were performed in LOW SALT IMMUNE COMPLEX WASH BUFFER (0.1% SDS, 1% TRITON, 20mM Tris-HCl pH8, 150 mM NaCl), HIGH SALT WASH BUFFER (0.1% SDS, 1% TRITON, 2mM EDTA, 20mM Tris-HCl pH8, 500 mM NaCl), LiCl Immune Complex Wash Buffer (0.25M LiCl, 1% NP40, 0.2% Na-deossicolato, 1mM EDTA, 10Mm Tris-HCl pH8) and TE. RNA was digested with RNAseA (2μg). DNA was de-crosslinked and purified with Zymo DNA columns.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 ng of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were seeded in 200 mm plate three days before the ChIP. 36h before the ChIP, HDAC4-ER induction was removed (in KO samples) or mantained (in WT samples). At the moment of the ChIP, cross-linking was performed for 15' with 1% formaldeyde (Fisher Scientific, Schwerte, Germany) and then blocked with 125 mM Glycine (Sigma-Aldrich, Darmstadt, Germany).

value: Leiomyosarcoma cells

tag: passages

value: below 40

tag: genotype/variation

value: H3K27me3 (Abcam ab6002)


title: BRXL2 rep2

city: Taipei

first: Chin-Min

middle: Kimmy

last: Ho

address: No. 128 Sec2 Academia Rd

department: IPMB

institute: Academia Sinica

data_processing:
Sequenced reads were trimmed for adaptor sequence then mapped to Arabiopsis_thaliana.TAIR10.16 with Bowtie2
Read number were generated by
Genome_build: Arabiopsis_thaliana.TAIR10.16
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample ...

organism: Arabidopsis thaliana

source_name: Ture leaves

growth_protocol: Seeds were placed on 1/2 MS plate. After cold teatment for 2 days, plants were grown on 22 degree 16/8 long day condition.

extract_protocol:
~ 20,000 sorted cells were used for total RNA extraction using RNeasy Micro Kit (QIAGEN). 20 ng total RNA with RIN (Agilent bioanalyzer) larger then 8 from each sample was subjected to mRNA isolation (NuGen-Ovation® RNA-Seq System V2) and cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: Columbia

value: Ture leaves

tag: age

value: 9 days post germination

tag: genotype


title: Pre_6

description:
nAnTi-CAGE
2nd run
CNhi10975_NoIndex_L003_R1_001.fastq.AGT

value: control


title: myrBRX rep2


title: WT_ZF_Embryos_4hpf

value: Embryo

value: Untreated


title: ASCL-MK#3

description: Gene expression data from adipose tissue derived megakaryocytes.

source_name: Adipose tissue derived megakaryocytes

value: Adipose tissue derived megakaryocytes


title: SK-LMS-1_H3K27me3 WT ChIP [N1_S10]

description:
N1_S10
Facultative heterochromatin evaluation in wt cells

value: wild type


title: ASCL-MK#2


title: IP2

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description: single cell RNA

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) and potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. After initial clustering, contaminating cell populations were removed. Matrices were log normalized to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for tumor ECs

source_name: PBS treated tumor ECs from implanted breast tumour model

extract_protocol:
FACS sorted endothelial cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Next GEM Single cell 3' v3 Reagent Kit (10X genomics), cDNA libraries were constructed

value: tumor endothelial cells

tag: sorting

value: FACS sorted

value: Adult

value: PBS injected CD31+ tumor EC


title: BRX rep2


title: IS2

description: single cell RNA

source_name: cGAMP treated tumor ECs from implanted breast tumour model

value: cGAMP injected CD31+ tumor EC


title: Mid_11

description:
nAnTi-CAGE
2nd run
CNhi10975_NoIndex_L003_R1_001.fastq.ACG

value: soleus muscle

value: torpor


title: ASCL-MK#1


title: myrBRX rep1


title: CB-MK#2

source_name: Cord blood stem cell derived megakaryocytes


title: IS1

description: single cell RNA


title: SK-LMS-1_H3K27ac H4KO ChIP [G_S14]

description:
G_S14
Open chromatin evaluation in HDAC4KO cells

value: Leiomyosarcoma cells

value: below 40

value: H3K27ac (Abcam ab177178)


title: BRX rep1

value: Columbia

value: Ture leaves


title: BRXL2 rep1

value: 9 days post germination


title: SK-LMS-1_HDAC4 WT ChIP [Br_S11]

description:
Br_S11
HDAC4 bound regions


title: Mid_12

description:
nAnTi-CAGE
2nd run
CNhi10975_NoIndex_L003_R1_001.fastq.GCT


title: TMMp 10X Genomics pool 2

city: Stanford

first: Dominique

last: Bergmann

state: CA

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
Data processing steps and methods used are included in the manuscript. Otherwise, note that the raw data for the "ATML1p 10X Genomics pool 1" sample were re-generated using bamtofastq (https://support.10xgenomics.com/docs/bamtofastq).
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed files include compiled TPM values and FACS outputs for Smart-seq2 scRNA-seq datasets. Cell Ranger outputs are included for the 10X Genomics datasets.

source_name: true leaves

extract_protocol: 10X Genomics 3' v3 chemistry

value: 10 days post-germination

tag: transgene

tag: pool


title: SK-LMS-1_H3K27ac WT ChIP [Cr_S12]

description:
Cr_S12
Open chromatin evaluation in wt cells


title: WT_ZF_Embryos_4hpf_DMSO

tag: tissue

value: Embryo

value: 4hrs DMSO 1%


title: TMMp 10X Genomics pool 3


title: SK-LMS-1_Input H4KO [Lr_S17]

description:
Lr_S17
Input

value: Input


title: MP2

description: single cell RNA

source_name: PBS treated tumor ECs from MMTV-PyMT model

value: tumor endothelial cells

tag: strain


title: MS1

description: single cell RNA

source_name: cGAMP treated tumor ECs from MMTV-PyMT model

value: FACS sorted

tag: treatment


title: SK-LMS-1_Input WT [I_S16]

description:
I_S16
Input

value: wild type

tag: chip antibody


title: TMMp 10X Genomics pool 1


title: ATML1p 10X Genomics pool 1

extract_protocol: 10X Genomics 3' v2 chemistry


title: IP1

description: single cell RNA

tag: cell type

value: Adult

value: PBS injected CD31+ tumor EC


title: MP1

description: single cell RNA


title: Mouse Fetal liver cells (WT), 30 hours, treated with DRB for 3 hours

status: Public on Apr 04 2021

city: Oxford

first: Jelena

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

country: United Kingdom

institute: Oxford University

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFL_DRB_3h

data_processing:
All the below steps except normalisation were done with CCseqBasic tool, or its predecessors ( http://userweb.molbiol.ox.ac.uk/public/telenius/CCseqBasicManual/ )
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser.pl)
Removal of ploidy regions and off target capture (custom scripts)
Counting reads per dpnII fragment (CCanalyser.pl)
Normalising the counts to 100 000 reported interacting fragments for each capture site, combining all capture sites to a single file (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: Normalised read counts per dpnII fragment, custom format : chr:str-stp \t count \t count \t count .. etc (one column per capture site)

source_name: Erythroid cells

growth_protocol: Disaggregated mouse foetal liver cells were cultured for 6-7 days to expand the progenitor population.

extract_protocol:
Erythroblasts grow in suspension.
NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for generation of the 3C libraries: cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in MilliQ dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an ethanol precipitation and a wash with 70% ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next sample preparation reagent kits, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using the Illumina MiSeq (150bp paired end reads). The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage). Oligonucleotide capture technology was then used to pull down the restricion fragments containing the promoters of the genes of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.

treatment_protocol: The cultures were depleted of Ter119+ve cells then sorted for CD44 and cell size. Cells were then sampled after 0h and 30h in differentiation medium. BrdU was added for the last 16/17 hours of culture.

value: Disaggregated mouse foetal liver cells

tag: genes analysed

value: WT

value: DRB


title: Mouse Fetal liver cells (WT), 30 hours, treated with DMSO for 3 hours

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFL_DMSO

value: DMSO


title: Mouse Fetal liver cells (WT), 30 hours, harvested prior to treatment

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFL_Ctrl

value: untreated


title: MS2

description: single cell RNA

value: cGAMP injected CD31+ tumor EC


title: Mouse Fetal liver cells, MiSeq, 0 hour, biol rep 3, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 0h, Hba1/2 MiSeq, repl 3
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

data_processing:
All the below steps except normalisation were done with CCseqBasic tool, or its predecessors ( http://userweb.molbiol.ox.ac.uk/public/telenius/CCseqBasicManual/ ).
Trim_galore (to remove sequencing adaptors).
FLASH (to reconstruct paired end reads into single reads where possible).
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl).
Alignment to the genome (Bowtie -m 2) maintaining strict read order.
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser.pl).
Removal of ploidy regions and off target capture (custom scripts).
Counting reads per dpnII fragment (CCanalyser.pl).
Normalising the counts to 100 000 reported interacting fragments for each capture site, combining all capture sites to a single file (custom scripts).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.gfc.out.txt: Tab-delimited text files; Normalised read counts per dpnII fragment, custom format : chr:str-stp \t count \t count \t count .. etc (one column per capture site).

growth_protocol:
Disaggregated mouse foetal liver cells were cultured for 6-7 days to expand the progenitor population.
Primary erythroblasts were grown ex vivo in suspension.

extract_protocol: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for generation of the 3C libraries: cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate-buffered saline; resuspended in cold lysis buffer (Tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in MilliQ dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of Triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNase (Roche). Phenol/Chloroform extraction was then performed followed by an ethanol precipitation and a wash with 70% ethanol. Digestion efficiencies were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life Technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing, DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation were performed using the NEB Next sample preparation reagent kits, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible, 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using the Illumina MiSeq (150bp paired end reads). The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage). Oligonucleotide capture technology was then used to pull down the restriction fragments containing the promoters of the genes of interest and their interacting partners, which were subsequently identified by high throughput sequencing. The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.

tag: strain/background

tag: time of differentiation

value: 0 hour


title: Mouse Fetal liver cells, MiSeq, 30 hours, biol rep 3, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 30h, Hba1/2 MiSeq, repl 3
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: 30 hours


title: Mouse Fetal liver cells, MiSeq, 30 hours, biol rep 1, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 30h, Hba1/2 MiSeq, repl 1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse Fetal liver cells, MiSeq, 0 hour, biol rep 2, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 0h, Hba1/2 MiSeq, repl 2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: H49-Desiccation stress-Input-Rep1

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.1
ChIP-seq reads were aligned to the rice genome assembly MSU v7.0 using Bowtie2
For peak calling, MACS2 software (v2.1.1.20160309) was used
Genome_build: Rice genome MSUv7.0 (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/)
Supplementary_files_format_and_content: tab delimited text files showing the posiiton of the peaks

organism: Oryza sativa

source_name: Seedlings

growth_protocol: Seedlings were grown in hydroponics in a culture room maintained at 28 ± 1 ºC.

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. DNA-protein complexes were pulled down using protein A Dynabeads from Invitrogen and anti-OsHOX24p antibody.
Libraries were prepared using ChIP-Seq Sample Prep kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Control and dessication treatments were given to wild-type and OsHOX24 over-expression transgenic rice seedlings. For dessication, seedlings were kept on dry filter paper and for control, reverse osmosis water was used.


title: H49-Desiccation stress-Input-Rep2


title: H49-Desiccation stress-ChIP-Rep1

value: anti-OsHOX24 antibody


title: WT-Desiccation stress-Input-Rep2


title: WT-Desiccation stress-Input-Rep1


title: Mouse Fetal liver cells, MiSeq, 30 hours, biol rep 2, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 30h, Hba1/2 MiSeq, repl 2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse Fetal liver cells, MiSeq, 0 hour, biol rep1, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 0h, Hba1/2 MiSeq, repl 1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: WT-Desiccation stress-ChIP-Rep1


title: WT-Desiccation stress-ChIP-Rep2


title: H49-Control-Input-Rep2


title: E10.5 Otocysts, Tbx2/3cDKO vs control, rep4

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per non-control probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

source_name: control 4

label_protocol: Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Life Technologies) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Otocysts were mechanically dissected from E10.5 embryos.

value: NMRI

tag: gender

value: male

tag: developmental stage

value: Otocyst

source_name: Tbx2/3cDKO 4


title: WT-Control-Input-Rep2


title: H49-Control-Input-Rep1


title: H49-Control-ChIP-Rep2


title: E10.5 Otocysts, Tbx2/3cDKO vs control, rep1

source_name: control 1

value: female

source_name: Tbx2/3cDKO 1


title: E10.5 Otocysts, Tbx2/3cDKO vs control, rep2

source_name: control 2

source_name: Tbx2/3cDKO 2


title: WT-Control-ChIP-Rep2


title: M5_S13

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome and transcriptome using STAR 2.6.1d, and normalized
Lognormal with shrinkage mean value were calculated using Gene-specific analysis by Partek flow (Partek Inc., USA).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: Gli1-CreER;Arid1a fl/fl_Incisor

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
The proximal region of the incisor was collected for RNA isolation with an RNeasy Micro Kit (QIAGEN).
The quality of RNA samples was evaluated using an Agilent 2100 Bioanalyzer and all samples used for sequencing had RNA integrity (RIN) numbers >9.0. cDNA library preparation and sequencing were performed by DNA Link, Inc. Single-end reads with 75 cycles were performed on NextSeq500 for three pairs of samples.

treatment_protocol: Tamoxifen was dissolved in corn oil  at 20 mg/ml and injected intraperitoneally at a dosage of 1.5mg/10g body weight daily for 3 consecutive days at the age of 1 month old.

tag: strain background

value: Gli1-CreER;Arid1a fl/fl

value: 6-week old

value: Incisor


title: WT-Control-Input-Rep1


title: H49-Desiccation stress-ChIP-Rep2


title: H49-Control-ChIP-Rep1


title: M4_S12


title: M2_S10


title: C6_S6

source_name: Arid1a fl/fl_Incisor

value: Arid1a fl/fl


title: GA-M4_S9

source_name: molar

extract_protocol:
The apical region of the first mandibular molar was collected for RNA isolation with an RNeasy Micro Kit (QIAGEN).
The quality of RNA samples was evaluated using an Agilent 2100 Bioanalyzer and all samples used for sequencing had RNA integrity (RIN) numbers >9.0. cDNA library preparation and sequencing were performed by DNA Link, Inc. Single-end reads with 75 cycles were performed on NextSeq500 for three pairs of samples.

treatment_protocol: Tamoxifen was dissolved in corn oil  at 20 mg/ml and injected intraperitoneally at a dosage of 1.5mg/10g body weight at PN3.5.

value: molar


title: 895-GA-M3_S8


title: C2_S2


title: C1_S1


title: GA-M5_S10


title: GA-C5_S5


title: E10.5 Otocysts, Tbx2/3cDKO vs control, rep3

source_name: control 3

source_name: Tbx2/3cDKO 3


title: GA-C3_S3


title: ldl1ldl2_rep_2_DAU

city: Busan

first: Ho Won

last: Jung

address: 37 Nakdong-Daero 550beon-gil, Saha-gu

department: Molecular Genetics

institute: Dong-A University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome to separate paired sequenced reads and unpaired sequenced reads to the reference using Trimmomatic-0.33 with parameters PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Fragments Per Kilobase of exon per Million reads mapped (FPKM) were calculated using a protocol from Cole Trapnell et al.
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene in a sample

source_name: Leaf

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 (Col-0) and ldl1ldl2 mutant plants (Col-0 background), were grown in potting mixture, in an environmentally controlled growth chamber (21±1 °C, 50~60 % relative humidity, 12 h day and 12 h night).

extract_protocol:
Leaves of plans were removed, and tota RNA was extracted using a combination of TriZol ® reagent, and a Qiagen RNeasy kit. Both the quantity and quality of total RNA were examined using a 2100 bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaf

value: 3-week-old plants after sowing

value: ldl1 ldl2 double mutant


title: GA-C2_S2


title: Arid1b_S2

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC v0.11.8
Bowtie2 v2.2.5 was used to align the sequencing reads to the mm10 mouse genome.
All unique alignments (MAPQ>=10) were further filtered by Picard MarkDuplicates v2.21.4 to remove duplicates.
ChIP-Seq peaks were called by MACS2  v2.1.1 (callpeak -g ‘mm’, --format BAMPE) for each library with a stringent statistical criterion (p-value < 1e-5).
Genome_build: mm10
Supplementary_files_format_and_content: NARROWPEAK File; Arid1b_S2_vs_input_S3_peaks

growth_protocol: Primary DPCs, collected from the apical portion of first mandibular molars from wild type mice at PN3.5-PN7.5 were cultured in a-mem medium with 10% FBS.

extract_protocol:
The SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads; Cell Signaling Technology 9005) was used for this process.
Libraries were prepared according to Illumina's instructions.

value: dental mesenchyme cell

value: Arid1b (Cell Signaling, 92964)


title: ldl1ldl2_rep_1_DAU


title: WT_rep_1_DAU

value: wild type


title: Mouse fetal liver cells (WT), NextSeq, 30 hour, biol rep3 Captured from: Hba1, Hba2 HS39.5

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFLwt_30h_rep3

value: Disaggregated mouse foetal liver cells

value: 30 hours

tag: genotype/variation

value: WT


title: WT-Control-ChIP-Rep1

value: anti-OsHOX24 antibody


title: Mouse fetal liver cells (WT), NextSeq, 30 hour, biol rep1 Captured from: Hba1, Hba2 HS39.5

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFLwt_30h_rep1


title: Mouse fetal liver cells (KO), NextSeq, 30 hour, biol rep2 Captured from: Hba1, Hba2 HS39.5

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFLko_30h_rep2

value: KO:alpha globin genes regulatory regions R1 and R2 deleted


title: Mouse Fetal liver cells, biol rep 2, techn rep 2, Captured from: FISH probes EX,E,A,C,CX

description:
MFL 30h FISH probes, repl2.2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: input_S3


title: Mouse fetal liver cells (KO), NextSeq, 30 hour, biol rep1 Captured from: Hba1, Hba2 HS39.5

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFLko_30h_rep1


title: Mouse fetal liver cells (KO), NextSeq, 30 hour, biol rep3 Captured from: Hba1, Hba2 HS39.5

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFLko_30h_rep3


title: Mouse Fetal liver cells, biol rep 3, techn rep 2, Captured from: FISH probes EX,E,A,C,CX

description:
MFL 30h FISH probes, repl3.2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse embryonic stem cells, biol rep 3, techn rep 2, Captured from: FISH probes EX,E,A,C,CX

description:
mES FISH probes, repl3.2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

source_name: E14 embryonic stem cells

tag: cell line

value: Embryonic stem cell line


title: Mouse fetal liver cells (WT), NextSeq, 30 hour, biol rep2 Captured from: Hba1, Hba2 HS39.5

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
MFLwt_30h_rep2


title: Mouse Fetal liver cells, biol rep 1, techn rep 2, Captured from: FISH probes EX,E,A,C,CX

description:
MFL 30h FISH probes, repl1.2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Gonadal fat pads of control mice, biological rep3

city: Shenzhen

first: Li-Feng

last: Sun

address: University Town, Nanshan District

institute: Peking University Shenzhen Graduate School

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip MTA1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Gonadal fat pads from control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All the mice were housed in plastic cages containing shavings as bedding material and were exposed to 12-h light/dark cycles at a constant temperature (22 °C) and humidity (50%), with access to food and water ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 25-day-old C57BL/6J female mice were selected. Mice in the DHT group were implanted with silicone capsules containing 5 mg of DHT powder to mimic the hyperandrogenic state of PCOS patients. Control mice were implanted with empty capsules.The mice were euthanized ~60 days after implantation. Ovaries and gonadal fat pads were isolated. These tissues were transferred to a basket, rinsed with PBS and placed on ice in the Trizol solution.

value: gonadal fat

value: control


title: BMDM_24h_both_rep2

city: Berkeley

first: Greg

last: Timblin

department: MCB

institute: UC Berkeley

data_processing:
Unmanipulated reads were aligned to the mouse geneome (mm10) using STAR, producing SAM files.
SAM files were converted to tag directories using HOMER.
For reporting, HOMER was used to calculate nomalized reads per gene (reads per kilobase per million mapped reads, or RPKM).
For differential expression analysis, HOMER was used to count raw reads per gene. The raw read counts were used as input to DESeq2 or EdgeR to call differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: six xlsx spreadsheets containing: 1),2) RPKM values for each gene 3)-6) differential expression analysis outputs

growth_protocol: Bone marrow-derived macrophages (BMDMs) were prepared by flushing leg bones from 8-week-old female C57BL/6J mice (Jackson), filtering cells through a 40mm filter, RBC lysis, and plating in DMEM (Corning 10-013-CV) supplemented with 10% FBS (HyClone SH30071.03), pen/strep (Gibco), and 20ng/mL murine M-CSF (Shenandoah) in 15cm non-TC treated Petri dishes. Media was refreshed every 3 days. On day 7, cells were harvested by scraping and plated in TC-treated 24 well plates at 7.5x104 cells per well in 1mL of media.

extract_protocol:
Cells were directly lysed in 300mL Trizol (Invitrogen) and total RNA isolated with Direct-zol RNA Miniprep kit (Zymo).
mRNA was isolated from total RNA and converted into sequencing libraries using mRNA HyperPrep kit (KAPA/Roche) and custom Illumina-compatible unique dual index (UDI) adaptors (IDT) according to manufacture’s instructions. Libraries were PCR amplified, quantified with Illumina Library qPCR quantification kit (KAPA/Roche), and pooled for sequencing on HiSeq4000 (Illumina).

treatment_protocol: BMDMs were treated with vehicle controls, LPS alone (100ng/mL stock in PBS, 1:1000 for 100ng/mL final), 4-OHE1 alone (5mM stock in EtOH, 1:1000 for 5mM final), or both in combination for 6 or 24 hours.

tag: Sex

value: female

value: 24h both

value: bone marrow-derived macrophage (BMDM)


title: Mouse Fetal liver cells, biol rep 3, techn rep 1, Captured from: FISH probes EX,E,A,C,CX

description:
MFL 30h FISH probes, repl3.1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: BMDM_24h_both_rep3


title: Gonadal fat pads of control mice, biological rep1

description: Gene expression data


title: Gonadal fat pads of control mice, biological rep2

description: Gene expression data


title: Ovaries of control mice, biological rep2

description: Gene expression data

source_name: Ovaries from control

value: ovary


title: WT_rep_2_DAU

value: Leaf

tag: age

value: 3-week-old plants after sowing

tag: genotype


title: Gonadal fat pads of DHT-treated mice, biological rep2

description: Gene expression data

source_name: Gonadal fat pads from DHT-treated mice

value: DHT-treated


title: Ovaries of DHT-treated mice, biological rep1

description: Gene expression data

source_name: Ovaries from DHT-treated mice


title: Gonadal fat pads of DHT-treated mice, biological rep3

description: Gene expression data


title: Ovaries of control mice, biological rep1

description: Gene expression data


title: Ovaries of control mice, biological rep3

description: Gene expression data


title: Gonadal fat pads of DHT-treated mice, biological rep1

description: Gene expression data


title: Mouse Fetal liver cells, biol rep 2, techn rep 1,  Captured from: FISH probes EX,E,A,C,CX

description:
MFL 30h FISH probes, repl2.1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

source_name: Erythroid cells


title: Ovaries of DHT-treated mice, biological rep2

description: Gene expression data


title: Mouse Fetal liver cells, biol rep 1, techn rep 1, Captured from: FISH probes EX,E,A,C,CX

description:
MFL 30h FISH probes, repl1.1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse embryonic stem cells, biol rep 2, techn rep 1, Captured from: FISH probes EX,E,A,C,CX

description:
mES FISH probes, repl2.1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: BMDM_24h_both_rep1


title: BMDM_24h_LPS_rep3

value: 24h LPS


title: BMDM_24h_4OHE1_rep2


title: BMDM_24h_4OHE1_rep3


title: BMDM_24h_LPS_rep2


title: Mouse embryonic stem cells, biol rep 3, techn rep 1, Captured from: FISH probes EX,E,A,C,CX

description:
mES FISH probes, repl3.1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: BMDM_24h_LPS_rep1


title: BMDM_24h_4OHE1_rep1


title: Mouse embryonic stem cells, biol rep 1, techn rep 1, Captured from: FISH probes EX,E,A,C,CX

description:
mES FISH probes, repl1.1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: BMDM_24h_ctlr_rep3

value: 24h control


title: Mouse Fetal liver cells, NextSeq, 30 hours, biol rep 3, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 30h, Hba1/2 NextSeq, repl 3
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: Disaggregated mouse foetal liver cells


title: Mouse Fetal liver cells, NextSeq, 30 hours, biol rep 1, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 30h, Hba1/2 NextSeq, repl 1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: 30 hours


title: BMDM_6h_both_rep2

value: 6h both


title: BMDM_24h_ctlr_rep1


title: Mouse Fetal liver cells, NextSeq, 30 hours, biol rep 2, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 30h, Hba1/2 NextSeq, repl 2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: WT


title: Mouse Fetal liver cells, NextSeq, 0 hour, biol rep 2, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 0h, Hba1/2 NextSeq, repl 2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: 0 hour


title: BMDM_6h_both_rep1


title: Mouse Fetal liver cells, NextSeq, 0 hour, biol rep 1, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 0h, Hba1/2 NextSeq, repl 1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse Fetal liver cells, biol rep 3, Captured from: R1, R2

description:
MFL 30h R1/R2, repl3
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: 0 hours


title: BMDM_6h_4OHE1_rep2

value: 6h 4-OHE1


title: BMDM_6h_4OHE1_rep3


title: BMDM_6h_both_rep3


title: Mouse Fetal liver cells, NextSeq, 0 hour, biol rep 3, Captured from: HS39.5, Hba-1, Hba-2

description:
MFL 0h, Hba1/2 NextSeq, repl 3
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse embryonic stem cells, biol rep 3, Captured from: R1, R2

description:
mES R1/R2, repl3
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: Embryonic stem cell line


title: BMDM_6h_LPS_rep2

value: female

value: 6h LPS


title: Mouse embryonic stem cells, biol rep 2, Captured from: R1, R2

description:
mES R1/R2, repl2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse embryonic stem cells, biol rep1, Captured from: R1, R2

description:
mES R1/R2, repl1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: Mouse Fetal liver cells (AMKO), Captured from: R1, R2

description:
AMKO MFL 30h, R1/R2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: KO:alpha globin genes (Hba1, Hba2) deleted


title: BMDM_6h_LPS_rep1

value: bone marrow-derived macrophage (BMDM)


title: Mouse Fetal liver cells, biol rep 2, Captured from: R1, R2

description:
MFL 30h R1/R2, repl2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.


title: BMDM_6h_LPS_rep3


title: Input KO-cells - Rep2

city: Munich

first: Maxim

last: Barenboim

address: Koelner Platz 1

department: Department of Pediatrics

institute: TECHNICAL UNIVERSITY OF MUNICH

data_processing:
Basecalls was performed with Real-Time Analysis (RTA) software Ver.2. Demultiplexing was performed with bcl2fastq Conversion Software.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.3.4 with the default configuration
Data were filtered using the following parameters: only unique reads were allowed with 2 mismatches, all duplicate reads were removed.
peaks were called using macs2 version 2.1.1 with the following setting: fdr=0.01 for Myc IP and fdr=0.05 for MondoA IP
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and bedGraph files were generated using Deeptools bamcoverage, bamCompare
Supplementary_files_format_and_content: peak text files, bigWig

source_name: Input KO

growth_protocol: Nalm6 cells were grown in RPMI medium containing 10% FCS and 1% penicillin/streptomycin

extract_protocol:
Cells were treated with 1% formaldehyde for 9 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA), 6% of murine spike-in were added, and DNA was fragmented to a size <300 bp using a Branson sonifier. Chromatin was immunoprecipitated with 10-15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
NEBNext® Ultra II DNA Library Prep with Sample Purification Beads®. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Sample Purification Beads. DNA fragments were amplified by 18 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical).

treatment_protocol: no treatment

value: B cell precursor leukemia

value: Human Pre-B Cell Line Nalm6

value: CRISPR/Cas9 MondoA knockout

value: MondoA-KO


title: BMDM_6h_ctlr_rep2

value: 6h control


title: BMDM_24h_ctlr_rep2

value: 24h control


title: BMDM_6h_ctlr_rep1


title: Input WT-cells - Rep1

source_name: Input WT

value: CRISPR/Cas9 control

value: MondoA-WT


title: Input KO-cells - Rep1


title: BMDM_6h_ctlr_rep3


title: MondoA-IP from KO-cells - Rep1

source_name: MondoA-IP from KO

value: MLXIP Rabbit Polyclonal antibody 13614-1-AP (Lot:00042515)


title: 768_T_H3K27ac_Chip-seq

city: Hong Kong

first: Alfred Sze-Lok

last: Cheng

address: Rm 405A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
bowtie2 v2.2.9 for alignment
Reads were trimmed 10-bp from the front and the back to produce 80-bp. Only reads with mapQ >10 and with duplicates removed by rmdup were used for subsequent analysis.
MACS2 v2.1.0 for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files (fold change over control or signal p-value) were generated from bedGraph files with UCSC tools (bedClip, bed-Graph-ToBigWig)

source_name: Tumor tissue from NAFLD-HCC patient

extract_protocol:
Tissues were directly crosslinked with 1% formaldehyde and the reaction was stopped by glycine at room temperature (RT). Fixed tissues were lysed with SDS-Lysis buffer containing proteinase inhibitor. The lysates were fragmented into 200-300bp by Bioruptor (Diagenode, Denville, New Jersey, USA).
ChIP-graded anti-H3K27ac antibody (39133, Active Motif, 1:500) or control normal Rabbit IgG (2729, Cell Signaling Technology, 1:500) were conjugated with magnetic beads (Magna ChIP™ Protein A+G Magnetic Beads, Life Technologies) by rotation in cold room (4°C) for 1 hour. Meanwhile, the cell lysates were incubated with magnetic beads and rotated in cold room (4°C) for 1 hour, to remove endogenous antibodies. Cell lysates were then incubated with magnetic beads-conjugated antibodies and rotated in cold room (4°C) for 12-16 hours. After washing and reversed crosslinking, the immunoprecipitated DNA were purified by purification kit (Qiagen). Whole-genome amplification was performed using the WGA4 kit (Sigma-Aldrich) and BpmI-WGA primers and digested with BpmI (New England Biolab) before the NEBNext ChIP-seq library prep reagent set (New England Biolab). Each library was sequenced to an average depth of 20 to 30 million raw reads on HiSeq4000 using 100-bp pair-end reads.

treatment_protocol: HCC patients with a clinical background of no HBV and/or HCV infection, no history of alcoholic liver who underwent hepatectomy at the Prince of Wales Hospital (Hong Kong) were included in this study. The specimens were processed immediately after surgery and snap-frozen in liquid nitrogen for epigenomic analyses.

value: AJCC 3

value: Tumor tissue


title: BMDM_6h_4OHE1_rep1

value: 6h 4-OHE1


title: 741_T_H3K27ac_Chip-seq


title: MYC-IP from KO-cells - Rep1

source_name: MYC-IP from KO

value: Recombinant Anti-c-Myc antibody [Y69] - BSA and Azide free (ab168727) (Lot:GR3224130-10)


title: Mouse Fetal liver cells (WT), Captured from: R1,R2

description:
WT MFL 30h, R1/R2
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: WT

value: Disaggregated mouse foetal liver cells

value: 30 hours


title: 741_NT_H3K27ac_Chip-seq

source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient

value: Adjacent non-tumor liver tissue


title: 768_NT_H3K27ac_Chip-seq


title: Input WT-cells - Rep2

value: B cell precursor leukemia


title: 705_NT_H3K27ac_Chip-seq


title: MYC-IP from WT-cells - Rep1

source_name: MYC-IP from WT

value: Human Pre-B Cell Line Nalm6


title: 796_T_H3K27ac_Chip-seq

value: AJCC 1


title: 796_NT_H3K27ac_Chip-seq


title: BMDM_H3K27ac_2OHE1_LPS_ChIP

description:
H3K27ac CHIP
KSGT004L

data_processing:
Unmanipulated reads were aligned to the mouse geneome (mm9) using STAR, producing SAM files.
SAM files were converted to tag directories using HOMER, and HOMER makeUCSCfile was used to create input-normalized bedGraph files.
HOMER findPeaks was used to call peaks/regions in each sample relative to input.
HOMER getDifferentialPeaks was used to identify peaks/regions with significantly increased read density induced by LPS. HOMER getDifferentialPeaks was then used to quantify the percentage of LPS-induced peaks/regions that were significantly reduced in read density in hydroxyestrogen-pretreated, LPS stimulated samples.
HOMER annotatePeaks.pl was used to make histograms showing read density at LPS-induced peaks/regions across the 3 conditions for both p65 and H3K27ac ChIP-seqs.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files of input-normalized ChIP-seq read density for viewing as UCSC genome browser tracks.

source_name: bone marrow-derived macrophage

growth_protocol: Bone marrow-derived macrophages (BMDMs) were prepared by flushing leg bones from multiple 8-week-old female C57BL/6N mice (Charles River), filtering pooled cells through a 40mm filter, RBC lysis, and plating in phenol red-free DMEM (Corning 17-205-CV) supplemented with 10% charcoal-stripped FBS (HyClone SH30068.03), pen/strep (Gibco), and 20ng/mL murine M-CSF (Shenandoah) in 15cm non-TC treated Petri dishes (3 dishes per mouse). Media was refreshed every 3 days. On day 7, cells (approximately 1.0x10^7 per dish) were used in ChIP-seq experiments.

extract_protocol:
Cells were washed 2x with PBS and fixed with 0.67mg/mL DSG (Thermo Fisher) in PBS for 30 minutes at room temperature with shaking, followed by addition of paraformaldehyde (Electron Microscopy Sciences) to 1% and an additional 15 minutes of room temperature fixation. Fixation was quenched by adding glycine to 125mM and shaking 10 minutes, after which fixed cells were scraped, pooling three independent 15cm plates per ChIP condition (approximately 3.0x10^7 cells per ChIP). Cell pellets were washed 2x with PBS, resuspended in 1.5mL ice cold ChIP RIPA buffer (20mM Tris HCl pH 8.0, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% Triton X-100) with protease inhibitors (Roche), and sonicated with metal probe adaptor using Bioruptor (Diagenode) for 60 minutes (continuous cycles of 20 seconds ON/40 seconds OFF, “medium” setting). Samples were spun 20 minutes at maximum speed at 4ºC in a benchtop centrifuge to remove insoluble material, and supernatant containing soluble sheared chromatin transferred to new tube, saving 1% volume for input library preparation. Immunoprecipitation was performed overnight at 4ºC with 2mg of primary antibody (p65: Santa Cruz sc-372, H3K27ac: Abcam ab4729), or corresponding species-appropriate IgG control antibody (GenScript), conjugated to Protein A Dynabeads (Invitrogen). The next day, beads were captured with magnet on ice and washed with ice cold wash buffer II (20mM Tris HCl pH 8.0, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.5% NaDOC) 3 times, wash buffer III (10mM Tris HCl pH 8.0, 250mM LiCl, 2mM EDTA, 1% NP-40, 0.5% NaDOC) 3 times, and TE with 50mM NaCl two times, all supplemented with protease inhibitors. Beads with antibody-target-DNA complexes were then resuspended in 200mL elution buffer (50mM Tris HCl pH 8.0, 10mM EDTA, 1% SDS) for 30 minutes at 37ºC to elute immunoprecipitated complexes. 200mL eluent was collected, 10mL of 5M NaCl added, and DNA-protein crosslinks reversed overnight at 65ºC. Next day, samples were treated with RNAse A (Thermo Fisher) for 1 hour at 37ºC, Proteinase K (NEB) for 1 hour at 50ºC, and DNA fragments recovered with Zymo ChIP DNA Clean & Concentrator kit.
Sequencing libraries were prepared from both input chromatin, and chromatin recovered from immunoprecipitations, using in-house protocol. Briefly, DNA was blunted, A-tailed, and ligated to Illumina-compatible NEXTFlex sequencing adaptors (Bioo). Libraries were PCR amplified, gel size selected, quantified, pooled, and sequenced on an Illumina HiSeq2500.

treatment_protocol: Cells were pretreated 1 hour with EtOH vehicle control (1:100) or indicated hydroxyestrogen (1mM stocks used at 1:1000 for 1mM final concentration). Cells were then treated with PBS vehicle control (1:1000) or LPS (100ng/mL stock in PBS, 1:1000 for 100ng/mL final) for 30 minutes before fixation and processing for ChIP.

value: female

value: bone marrow-derived macrophage (BMDM)

value: 2OHE1 LPS


title: MYC-IP from KO-cells - Rep2

value: CRISPR/Cas9 MondoA knockout

value: MondoA-KO


title: BMDM_H3K27ac_EtOH_ChIP

description:
H3K27ac CHIP
KSGT004J

value: EtOH


title: 717_T_H3K27ac_Chip-seq


title: 754_T_H3K27ac_Chip-seq


title: MYC-IP from WT-cells - Rep2

value: CRISPR/Cas9 control

value: MondoA-WT


title: 717_NT_H3K27ac_Chip-seq


title: Mouse Fetal liver cells, biol rep 1, Captured from: R1, R2

description:
MFL 30h R1/R2, repl1
Next-generation Capture-C products : 3C library preparation followed by double oligonucleotide capture.

value: 0 hours


title: Ovaries of DHT-treated mice, biological rep3

description: Gene expression data

value: ovary

value: DHT-treated


title: BMDM_H3K27ac_2OHE1_LPS_input

description:
input H3K27ac CHIP
KSGT004R


title: BMDM_p65_2OHE2_LPS_ChIP

description:
p65 ChIP ChIP
KSGT002F

value: 2OHE2 LPS


title: 705_T_H3K27ac_Chip-seq

value: AJCC 3

value: Tumor tissue


title: BMDM_H3K27ac_EtOH_LPS_input

description:
input H3K27ac CHIP
KSGT004Q

value: EtOH LPS


title: BMDM_H3K27ac_EtOH_input

description:
input H3K27ac CHIP
KSGT004P


title: BMDM_p65_EtOH_LPS_ChIP

description:
p65 ChIP ChIP
KSGT002E


title: MondoA-IP from WT-cells - Rep1

source_name: MondoA-IP from WT

value: B cell precursor leukemia

value: Human Pre-B Cell Line Nalm6

value: MLXIP Rabbit Polyclonal antibody 13614-1-AP (Lot:00042515)


title: 707_T_H3K27ac_Chip-seq


title: BMDM_p65_2OHE2_LPS_input

description:
input p65 ChIP
KSGT002C

value: female

value: bone marrow-derived macrophage (BMDM)


title: 715_NT_H3K27ac_Chip-seq

value: Adjacent non-tumor liver tissue


title: 707_NT_H3K27ac_Chip-seq


title: BMDM_p65_EtOH_LPS_input

description:
input p65 ChIP
KSGT002B


title: BMDM_H3K27ac_EtOH_LPS_ChIP

description:
H3K27ac CHIP
KSGT004K


title: BMDM_p65_EtOH_input

description:
input p65 ChIP
KSGT002A


title: 678_T_H3K27ac_Chip-seq

value: AJCC 1


title: BMDM_p65_EtOH_ChIP

description:
p65 ChIP ChIP
KSGT002D

value: EtOH


title: 715_T_H3K27ac_Chip-seq


title: 678_NT_H3K27ac_Chip-seq


title: 651_T_H3K27ac_Chip-seq


title: 754_NT_H3K27ac_Chip-seq