title: EB14_loxp_gDNA_es_eb4

description:
EB_day14_loxp_gDNA_es_eb4
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt

value: Day 14


title: DAP-R Sample_1-C (SI)

status: Public on Aug 07 2020

type: SRA

city: Catania

first: Viviana

last: Cafiso

state: Italy

address: Via Santa Sofia,97

department: Biometec

country: Italy

institute: University of Catania

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads quality has been checked using FastQC v0.11.2
Sequences were trimmed using Trimmomatic 0.32. For Tru-Seq library a minimum base quality 15 over a 4 bases sliding window were required. Only sequences longer than 36 nucleotide were considered. For Short-Insert library a minimum base quality of 15 (Phred scale) and a minimum read lenght of 15 nucleotides were required.
Sequence mapping and quantification was performed using Rockhopper v2.0.2
Genome_build: Staphylococcus aureus NCTC8325 (ASM1342v1)
Supplementary_files_format_and_content: Excel files derived from Rockhopper include for both the DAP-R/DAP-S isogenic couple mRNAs and smallRNAs: Trancription Start, Translation Start, Translation Stop, Transcription Stop, Strand, Name, Synonym, Product, Raw Counts, Normalized Count, RPKM, Expression, pValue and qValue.

molecule: total RNA

organism: Staphylococcus aureus

source_name: DAP-R Staphylococcus aureus_1-C

growth_protocol: The 4 samples were grown in BHI solid culture and incubated over night at 37 °C.

extract_protocol:
A single colony was used to inoculate 7 ml of BHI liquid culture and incubated at 37 °C  for 12h. Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
Sequencing libraries were prepared using the Illumina mRNA-seq sample preparation kit following  the supplier's instructions except that total RNA was not fragmented and double-stranded cDNA was size-selected (100 to 400 bp) to maximize the recovery of small size RNAs. The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified in triplicates with the ABI7900 qPCR instrument using the KAPA Library Quantification Kit, according to the manufacturer’s protocol (KapaBiosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 4 nM were used for sequencing using Illumina Miseq with a A single end stranded library with reads of 50bp. After sequence data generation, raw reads were processed using FastQC v0.11.2 to assess data quality. Reads were then trimmed using Trimmomatic v.0.33.2 to remove sequencing adapters for Single End reads, requiring a minimum base quality of 15 (Phred scale) and a minimum read length of 15 nucleotides. Only trimmed reads were included into downstream analysis.

tag: phenotype

value: Daptomycin resistant S.aureus

tag: infection

value: skin infection

tag: library

value: Short-Insert (SI) Library


title: BilIN of Patient 8 [B8]

type: RNA

city: Heidelberg

first: Stephanie

last: Roessler

address: Im Neuenheimer Feld 224

country: Germany

institute: Heidelberg University Hospital

description: nCounter® Technology

hyb_protocol: miRNAs were  hybridized for 16h at 65°C to a capture/reporter probe pair equipped with a fluorescent barcode

scan_protocol: nCounter Digital Analyzer

data_processing:
nSolver version 3.0
Raw data was normalised according to Nanostring standart procedures. The geometric mean of included negative controls (background subtraction) and positive controls (computing normalisation factor) was calculated in order to diminish differences in hybridization. The expression of every miRNA was then normalised by geometric mean of the top 100 most expressed miRNAs.

label: barcode

organism: Homo sapiens

source_name: BilIN of Patient 8

label_protocol: 100ng total RNA were used as input

growth_protocol: FFPE tissue

extract_protocol: AllPrep DNA/RNA FFPE Kit Qiagen

treatment_protocol: Laser Capture Microdissection

tag: subject id

value: patient 8

tag: subject status

value: patient with distal cholangiocarcinoma

tag: tissue

value: BilIN


title: non-neoplastic biliary epithelia of Patient 9 [N9]

description: nCounter® Technology

value: patient 9

value: non-neoplastic biliary epithelia


title: BrdU_ChIP_G0_100_combined

city: Albuquerque

first: Po-Hsuen

last: Lee

state: NM

address: MSC 08 4660, 1 University of New Mexico

department: Molecular Genetics & Microbiology

country: USA

institute: University of New Mexico Health Science Center

library_source: genomic

data_processing:
All DNA sequencing reads were trimmed of barcode sequences using fastq-multx, with 5 bp removed to account for the barcode.
For BrdU IP-seq analysis, the trimmed data were aligned to the Saccharomyces cerevisiae genome version sacCer3 (GCA_000146045.2) using Bowtie2 and then sorted using Samtools. BrdU IP-seq data analysis was performed as described previously with the following modifications.  For each labeling period, aligned sequences were filtered and sorted into 50-bp nonoverlapping bins using bamCompare from the deepTools package.  Each IP bin was normalized after dividing by its corresponding Input bin to generate the IP/In ratio, which was median-smoothed over a 2000 bp window across all time course experiments.  Two biological replicates were averaged, and to facilitate comparisons between G1 and G0 experiments, the data were scaled to the maximum average G1 signal among the time course points, which was arbitrarily set as “1”. In parallel, BrdU enriched peaks were called using MACS2 (P < 0.01), and origin peaks were identified by their overlap with at least one ARS (autonomously replicating sequence; replication origin) across the samples during the time course experiment in both replicates.  ARS co-ordinates were obtained from the oriDB database.
For Mcm4-Myc ChIP-seq analysis, the trimmed data were aligned to the Saccharomyces cerevisiae genome version sacCer3 (GCA_000146045.2) using BWA.  Aligned sequences from Mcm4 ChIP-seq samples from G1 arrested cells and from G0 cells released into YPD + HU for 90 and 105 min were filtered and binned into 50-bp nonoverlapping bins, and the IP/In ratio was median-smoothed over a 2000 bp window as described above.  Two biological replicates were averaged, and both the G1 and G0 data were scaled to the maximum average G1 signal, set as “1”.  Mcm4-Myc enriched peaks were called using MACS2 (P < 0.01), and origin peaks were identified by their overlap with at least one identified ARS.
Genome_build: Saccharomyces cerevisiae genome version sacCer3 (GCA_000146045.2)
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD medium (1% yeast extract, 2% peptone, 2% dextrose) at 30°C to a density of OD600 = 0.4 and arrested in G1 phase by the addition of alpha-factor (5 μg/mL; United Biochemical Research) at 0, 45, and 90 min for a total incubation time of 135 min. G0 quiescent (Q) cells were isolated by Percoll gradient centrifugation 7 days after culture inoculation. G1 cells were released into YPD + 60 μg/ml pronase + 5 mM CaCl2 + 0.2 M HU, and G0 cells were released into YPD + 0.2 M HU before collected for sequencing.

extract_protocol:
For BrdU IP-seq, genomic DNA was isolated from each pulse-labelled sample by the “smash and grab” protocol (Hoffman, 1987), and 0.2 mg/ml RNase A was added for 30 min at 37C, followed by addition of 0.1 mg/ml of Proteinase K for 30 min at 50C.  DNA was purified with a Qiagen QIAquick PCR purification kit and its concentration was measured by an Invitrogen Qubit 2.0 Fluorometer.  DNA was transferred to a 50 l Covaris microTUBE and sheared to 200 – 250 bp using a Covaris M220 Focused-ultrasonicator (peak power: 75W; duty factor: 10%; cycles per burst: 200; treatment time: 400 sec). For Mcm4 ChIP-seq, twenty-four OD600 units of cells were collected and fixed with 1% formaldehyde for 15 min at room temperature.  Fixation was stopped by the addition of glycine to a final concentration of 125 mM for 5 min and the cells were washed with 50 mM Tris, pH 7.4, followed by centrifugation. Cell pellets were resuspended in 0.6 ml of ice-cold FA lysis buffer (1% Triton X-100, 0.1% sodium deoxycholate, 50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, pH 8.0) supplemented with 1x protease inhibitor cocktail (Millipore-Sigma) and 1 mM of phenylmethylsulfonyl fluoride (PMSF), and then vortexed at highest speed with an equal volume of acid-washed glass beads (Millipore-Sigma) for 25 min at 4°C.  Cell lysates were sonicated using a Branson 250 Sonifier to generate DNA fragments of 200-500 bp.  After centrifugation for 15 min at 17,900 x g, soluble chromatin was collected from the supernatant fraction and protein concentration was determined by a Bradford assay.  Between 1-1.5 mg of chromatin was diluted in 1 ml of FA lysis buffer, and 20 µl was set aside as Input.  Anti-Myc (Millipore-Sigma) or anti-HA (Biolegend) antibodies were added to the remaining chromatin solution and incubation was continued overnight at 4°C  Protein G agarose beads (Invitrogen) were added for 2 h at 4°C, and the beads were then sequentially washed with FA lysis buffer, wash buffer I (1% Triton X-100, 0.1% sodium deoxycholate, 50 mM HEPES-KOH, pH 7.5, 500 mM NaCl, 1 mM EDTA, pH 8.0), wash buffer II (0.5% sodium deoxycholate, 0.5% NP-40, 10 mM Tris, pH 8.0, 250 mM LiCl), and TE, pH 8.0. Immunocomplexes were eluted from beads by incubation with 0.2 ml of elution buffer (1% SDS in TE) for 20 min at 65°C. Immunoprecipitated and Input samples were incubated with pronase solution (2 mg/ml pronase and 10 mM CaCl2) for 2 h at 42°C, followed by reverse crosslinking for 14-16 h at 65°C. DNA was purified with a Qiagen QIAquick PCR purification kit.
For BrdU IP-seq, extracted genomic DNA was transferred to a 50 ml Covaris microTUBE and sheared to 200 – 250 bp using a Covaris M220 Focused-ultrasonicator (peak power: 75W; duty factor: 10%; cycles per burst: 200; treatment time: 400 sec).  One microgram of sheared DNA was end-repaired and ligated to Ion Torrent-compatible barcode adapters (Ion XpressTM Barcode Adapters, Invitrogen) using an Ion Xpress Plus Fragment Library kit (Invitrogen). The adapter-ligated DNA was purified by Agencourt AMPure XP Reagent and DNA concentration was measured by Qubit.  An equal concentration of each pulse-labeled G1 or G0 released DNA sample was pooled for immunoprecipitation (IP) and 20 ng of the mixture was set aside as input (IN) DNA. The pooled DNA was heated for 10 min at 95°C, followed by a snap cooling on ice.  Immunoprecipitation was performed with a 1:250 dilution of anti-BrdU antibody (GE Healthcare, RPN202) for 2h at 4°C, followed by the chromatin immunoprecipitation procedure described above. For Mcm4 ChIP-seq, multiple immunoprecipitation reactions were carried out in order to obtain a total of ~5 mg of immunoprecipitated DNA per sample.  For each sample, 5 mg of DNA was extracted from lysates and processed in parallel as input DNA.  IP and Input DNAs were processed for library preparation, including DNA end-repairing, barcoded adapter ligation, and PCR amplification using Ion Xpress Plus Fragment Library kit (Invitrogen).

tag: cell cycle stage

tag: time point

value: BrdU pulse-labeling 80-100 min post release into HU

tag: antibody

value: Anti-BrdU (GE Healthcare, RPN202)


title: non-neoplastic biliary epithelia of Patient 8 [N8]

description: nCounter® Technology


title: NLX-4 Treatment, replicate 3

city: Jiangsu

first: Jinchi

last: Zhang

state: Nanjing,

address: Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China

department: Co-innovation Center for Sustainable Forestry in Southern China

country: China

institute: Nanjing Forestry University

data_processing:
Raw data produced by Illumina Hiseq 2000 were initially processed to obtain clean data by discarding dirty reads containing adapter, ploy-N, or low-quality bases.
Clean reads were mapped to reference genome (fully assembled genome of strain NLX-4) using SOAP2
Reads per kb per million reads (RPKM) method was used to calculate individual gene expression
The RPKM level data of control and treatment samples were also analyzed using edgeR, limma and Glimma statistical analysis packages to obtain statistically significant differentially expressed genes.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Pseudomonas protegens

source_name: bacteria

growth_protocol: The isolated bacteria were cultured on Alexander Rove agar plates which is composed of 5.0g sucrose, 2.0g Na2HPO4, 0.5g MgSO4·7H2O, 0.005g FeCl3, 0.l g CaCO3, l.0g rock sample, 15.0g agar, 1000mL deionized water). Around 200μL of each dilution (10-4, 10-5, 10-6) was spread onto the surface of Alexander Rove agar plate. The inoculated plates were incubated at 28℃ for 24-72h to isolate individual colonies based on their size, color and morphology. Selected colonies were further purified using standard re-culturing techniques.

extract_protocol:
The total RNA of NLX-4 was separately extracted from control group and treated group cultures by using the Trizol method. RNA quality was analyzed on a bioanalyzer (Agilent 2100, Agilent Technologies, USA). Ribosomal RNAs (rRNA) were removed with kit after total RNA was collected from prokaryote. Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primers were used to synthesize the first-strand cDNA.
The second-strand cDNA was synthesized using buffer, dATPs, dGTPs, dCTPs, dUTPs, RNase H and DNA polymerase I respectively after removing dNTPs. Short fragments were purified with QiaQuick® PCR extraction kit and resolved with elution buffer for repairing the end of the strands and adding poly (A). After that, the short fragments were connected with sequencing adapters. Then, the UNG enzyme was used to degrade the second-strand cDNA, and the product was purified by MiniElute® PCR Purification Kit before PCR amplification. The library obtained was sequenced using Illumina HiSeq2000 platform.

treatment_protocol: The culture medium supplemented with 5.0 g L-1 silicate rock sample (sole K+ source) was inoculated with NLX-4 strain and incubated at 30℃ with 180 rpm for time periods ranging from 0, 2, 5, 9, 12, 15, 22, and 30 days respectively. The culture medium was regularly monitored (the above mentioned time periods) for determining the concentration of K+ and Al3+ ions, using inductively coupled plasma-atomic emission spectrometry (ICP-AES, Vista MPX, Varian, USA) as per the protocol reported by Wu, Zhang and Kanicky and Mermet.The NLX-4 cultured in fermentation medium added with 0.3 g L-1 KCl was set as control.

tag: strain

tag: treatment

value: cultured with rock sample 5.0 g L-1 using fermentation medium at 30℃ with 180 rpm for 15 days


title: BrdU_ChIP_G0_85_combined

value: BrdU pulse-labeling 65-85 min post release into HU


title: DAP-S Sample_1-A (SI)

source_name: DAP-S Staphylococcus aureus_1-A

value: Daptomycin sensitive S.aureus


title: EB14_loxp_gDNA_es_eb1

city: Boston

first: Bradley

middle: E

last: Bernstein

state: MA

address: 185 Cambridge Street

department: Pathology

institute: Massachusetts General Hospital

description:
EB_day14_loxp_gDNA_es_eb1
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt

data_processing:
Sequencing RNA libraries, passed through general quality filter such as cluster density, total yield, and per-cycle base quality, were then split by library barcodes using bcl2fastq.
R2 reads were demultiplexed into separate files based on the cell barcode from R1 and mapped to a mouse reference genome (mm9) by Bowtie2. After eliminating reads sharing the same UMI by htseq-count, an accurate molecule count for each gene was generated and converted to the number of UMIs into transcript counts through binomial statistics (CEL-seq2).
Nanopore sequencing reads were converted to fastq files by Guppy (v2.3.5) and then demultiplexed to the each cell based on its matched cell barcode sequence with the highest mapping score by minimap2 with default parameters.
To detect tandem-loxP, different loxP flanking sequences were mapped to the demultiplexed nanopore sequence (minimap2) then assembled into a full tandem-loxP sequence based on their position in the nanopore sequence. Due to the sequencing error, we selected the top 1 combination with additional filter: 1) over 30 reads, 2) outlier from others, 3) full length with upstream and downstream sequence.
To detect the UCI, we first mapped the upstream and downstream of the UCI sequence to nanopore reads by minimap2 then extracted the sequence between M13F and WPRE_M13R_HSV. Due to the sequencing error, we selected the top 1 sequence with additional filter: 1) over 30 reads, 2) outlier from others, 3) represented by the sequence from UCI plasmid.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include UMI count values for each Sample.

organism: Mus musculus

source_name: mESC (Mouse embryoid body at day 0)

growth_protocol:
Mouse v6.5 ESCs were cultured with feeder cells (mouse embryonic fibroblasts (MEF)) in knockout DMEM media supplemented with 15% FBS, and 0.01% Leukemia inhibitory factor (LIF). The media was replenished every day and cells were split every two days.
For differentiation, we detached and dissociated ESCs to single cells. MEFs were further removed by incubating single cell suspensions on a 100mm tissue culture dish for 40 minutes at 37°C. We seeded 1000 cells per well micro-well plate (STEMCELL Technologies) in EB media (mESC media without LIF). For inducible barcoding experiments, we seeded FACS sorted RFP+/GFP-/BFPmid cells. After 4 days of EB differentiation in the micro-well plate, we collected EBs and transferred them to 100mm petri dishes and pursued spontaneous differentiation for another 10 days. EB media was changed every day (micro-well plate) or every other day (petri dish) during EB differentiation.

extract_protocol:
mESC and EBs were dissociated by trypsin to single cells and sorted into 384 well plates. After freeze and thaw for twice, we performed a reverse transcription and second strand synthesis, then pooled samples and ran IVT. For DNA extraction (30%), before pooling, we added unique primers (DNA adapter) involving identical cell barcode with RNA-adapter, targeting dual-barcode region of genomic DNA to each well, and then amplified the region by PCR. For RNA extraction (70%), after 2nd reverse transcription, we amplified RNA fragments by Illumina adapter.
DNA libraries were prepared for sequencing using standard Nanopore protocols.

treatment_protocol: To perturb DNA methylation, we treated EBs with 5-azacytidine or DMSO (100 nM) and replenished them with every media change throughout all days of differentiation.

tag: cell type

value: Embryoid body

tag: media

value: Serum-LIF

tag: differentiation day


title: DAP-R Sample_3-B (TS)

source_name: DAP-R Staphylococcus aureus_3-B

extract_protocol:
RNAs were extracted from the samples after 12h of incubation using the NucleoSpin RNA (Macherey-Nagel, Dueren, Germany) kit following manufacturer’s protocol with minor modifications. Bacterial cell pellets were lysed by bead-beating procedure in the presence of 50 μL Buffer RA1. Then 3.5 μL ß-mercaptoethanol were added and the lysate was filtrate through NucleoSpin Filters (violet rings). RNA binding condition was adjusted by adding 350 μL of ethanol (70%) to the lysate and the RNA was then extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol. The quality of the total RNA was verified using a 2200 TapeStation RNA Screen Tape device (Agilent, Santa Clara, CA, USA) and its concentration ascertained using an ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Bacteria) from 2 microgram of Total RNA, and the depleted RNA was used as input in the Illumina TruseqRNA stranded kit without PolyA-enrichment.
The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified with the ABI9700 qPCR instrument using the KAPA Library Quantification Kit in triplicates, according to the manufacturer’s protocol (Kapa Biosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 2 nM were used for sequencing using Illumina Miseq with a 150 Paired end-Read sequencing module.

value: bloodstream infection

value: Tru-Seq (TS) Library


title: input DNA

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

country: Japan

institute: Kumamoto University

data_processing:
Strand NGS software (Strand Life Sciences)
Peak detection was performed using the MACS algorithm.  The significant enrichment of each signal over input-DNA peaks was determined at a P cut-off value of 10-5.
Genome_build: hg19

source_name: HK-2 cells

growth_protocol: HK-2 HA-TFE3-inducible cell lines which express HA-TFE3 in a doxycycline-dependent manner were cultured with advanced DMEM/F-12 supplemented with 1.5% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol:
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (#9005, Cell Signaling) was utilized for ChIP. Cell cross-linking, chromatin preparation and chromatin immunoprecipitation by anti HA Affinity Matrix (#11815016001, Roche) was performed according to the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: HK-2 HA-TFE3-inducible cells were cultured with or without 0.2 microg/ml of doxycycline for 24hr.

tag: cell line background

tag: genotype/variation

value: HA-TFE3-inducible cells

tag: chip antibody

value: anti-HA antibody (3F10, Roche)


title: BrdU_ChIP_G1_70_combined

value: BrdU pulse-labeling 50-70 min post release into HU


title: DAP-S Sample_3-A (TS)

source_name: DAP-S Staphylococcus aureus_3-A

tag: phenotype


title: BilIN of Patient 5 [B5]

description: nCounter® Technology

source_name: BilIN of Patient 5

value: patient 5


title: invasive dCCA of Patient 5 [T5]

description: nCounter® Technology

source_name: invasive dCCA of Patient 5

value: patient with distal cholangiocarcinoma

value: invasive dCCA


title: BrdU_ChIP_G1_55_combined

value: BrdU pulse-labeling 35-55 min post release into HU


title: EB14_loxp_gDNA_d8_eb7

description:
EB_day14_loxp_gDNA_d8_eb7
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt

value: Day 14


title: non-neoplastic biliary epithelia of Patient 5 [N5]

description: nCounter® Technology

value: non-neoplastic biliary epithelia


title: BrdU_ChIP_G1_40_combined

value: BrdU pulse-labeling 20-40 min post release into HU

value: Anti-BrdU (GE Healthcare, RPN202)


title: DAP-R Sample_1-C (TS)

value: Daptomycin resistant S.aureus

tag: infection

value: skin infection


title: BrdU_ChIP_G0_115_combined

value: BrdU pulse-labeling 95-115 min post release into HU


title: HA-TFE3_1_ChIPSeq


title: EB14_loxp_gDNA_es_eb3

description:
EB_day14_loxp_gDNA_es_eb3
DNA-Seq
384 cells
processed data file: EB_recording_dual_barcode.txt

value: Embryoid body

value: Serum-LIF


title: DAP-S Sample_1-A (TS)

value: Daptomycin sensitive S.aureus

tag: library

value: Tru-Seq (TS) Library


title: BrdU_ChIP_G1_25_combined

value: BrdU pulse-labeling 5-25 min post release into HU


title: K562 [PacBio]

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: PolyA RNA

data_processing:
We employed bcf2fastq (v2.20.0) for converting raw image to sequence information (FASTQ files) and meanwhile demultiplex, allowing two mismatches in index 1 and one mismatch in index 2.
For TIF-Seq2 data, we collapsed all 5’-end or 3’-end sequence reads in each sample according to the indexes. Cutadapt (v1.16) was utilized to trim TIF-seq2 sequencing primer (-AGGTGACCGGCAGGTGT) and Illumina TruSeq adapter (-AGATCGGAAG). After extracting 8 bp of unique molecular identifiers (UMIs) with UMItools (v0.5.4) from the 5’ ends and removing extra A stretches in the 3’ ends caused by poly(A) slippery during PCR amplification, we kept reads over 20 bp for alignment. We used STAR (v2.5.3a) for aligning paired-end reads separately to the human reference genome hg38, supplying Gencode V27 transcript annotation splicing junction as reference annotation. Alignment setting was adjusted as below, --alignIntronMax 200000 --alignEndsType Extend5pOfRead1 --alignSJoverhangMin 10. We then linked paired-end reads and kept the uniquely mapped pairs that are in the same chromosome. Furthermore, a customised script adapted from UMItools was employed to remove PCR duplicates from the leftover reads, allowing 1 bp mismatch in the UMIs and 1 bp shifting in the transcription start sites.
For 3’T-fill sequencing data, we trimmed Illumina TruSeq adapter (-AGATCGGAAG) and extra A stretches in the 3’ ends with cutadapt v1.16. Reads over 20 bp are aligned to hg38 by using STAR v2.5.3a in paired-end mode, supplying Gencode V27 transcript annotation splicing junction as reference annotation with adjusted setting, --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignEndsType Extend5pOfReads12.
A customised python script was employed to extract both boundaries of TIF-Seq2 read pairs and 3’ boundaries of 3’T-fill sequencing data, collapse the boundary tags and calculate the coverage (saved in *boundary.txt and bedGraph files).
For PacBio long-read sequencing data, highly accurate consensus sequences were produced by Pacbio ccs package from sequencing facility. We trimmed the PCR primers from both ends of the reads with cutadapt (v1.16) and extract UMIs with UMItools (v1.0.0), keeping the reads with at least 200 bp in length. Then the reads were aligned to human reference genome using minimap2 (v2.16) with the following setting (-ax splice -uf -C5 -O6,24 -B4). We used UMItools for removing the PCR duplicates with adjusted setting as --method cluster --spliced-is-unique. We further employed BEDTools (v2.27.1) bamToBed function to convert the alignment reads into BED format and a customised script to convert BED format to GFF format.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_boundary.txt: Tab-delimited text files of coverage at transcription boundaries for TIF-Seq2.
Supplementary_files_format_and_content: *.3end.bedGraph: bedGraph files of read coverage at 3' ends for 3T-fill sequencing.
Supplementary_files_format_and_content: K562_target_Pacbio.gff: GFF file of validated cDNA sequence annotation for PacBio long-read sequencing data.

source_name: chronic myeloid leukemia cells

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 1% pen/strep (Life Technologies) at 37 °C with 5% CO2 in a humidified atmosphere.

extract_protocol:
RNA was extracted with Trizol and Direct-zol RNA kit from Zymo Research.
PacBio: Selected cDNA were PCR amplified using gene specific primers with containing following common sequences: GTGACTGGAGTTCAGACGTGTNNNNNNNN and ACACTCTTTCCCTACACGAC. PCR products were purified and pooled. Pooled PCR products were used for library generation using SMRTbell™ Template Prep Kit 1.0‐SPv3 and sequenced on PacBio Sequel system.

treatment_protocol: K562 cells (3 X 10e5 cells/mL) were exposed to 1µM Imatinib for 24 hours and corresponding DMSO treated control cells were used for TIFseq library preparation, 3’T fill library preparation and PacBio target sequencing.

tag: cell line

value: Chronic myeloid leukemia cells


title: BilIN of Patient 3 [B3]

description: nCounter® Technology

source_name: BilIN of Patient 3

tag: subject id

value: patient 3

tag: subject status

value: BilIN


title: non-neoplastic biliary epithelia of Patient 3 [N3]

description: nCounter® Technology

value: patient with distal cholangiocarcinoma

tag: tissue


title: J1.TSA_ChIP.Input

status: Public on Aug 06 2020

city: Oxford

first: Skirmantas

last: Kriaucionis

address: Old Road Campus Research Building, Roosevelt Drive, Headington

country: United Kingdom

institute: Ludwig Cancer Research Oxford

description: Input control for ChIP, cells were crosslinked using 1% formaldehyde for 10 min

data_processing:
ChIP-seq reads were aligned to the mm10 genome build using bowtie2 (v2.2.5.0) with the options --no-mixed and --no-discordant. Reads with multiple alignments (sam tag "XS:" present) and fragments mapping to a custom “blacklist” of artificially high regions of the genome (derived from ENCODE, https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded. Samtools (v1.3) was used for sorting and indexing bam files, and removing duplicates. All alignment files for the same transcription factor ChIP, along with the corresponding input controls, were randomly down-sampled (Picard Tools v1.105 DownsampleSam) so as to retain an equivalent number of alignments in all samples (ChIP or Input). Enriched regions were identified using the ‘dpeak’ peak-calling algorithm of DANPOS v2.2.2 (Chen et al., 2013) with the options –m, –kd 250, -kw 150 and –p 1e-100. For each condition, peaks were called from 3 biological replicate ChIP-seq samples with input control used as background. For calling peaks in GABPA ChIP-seq data, peak intervals were further filtered as described in the manuscript. To produce genome coverage files, alignments from biological replicate samples were first merged (Samtools v.13) then bigWig files were generated using the Deeptools (v2.4.2) function 'bamCoverage' with the option -e and -bs 2.
Genome_build: mm10
Supplementary_files_format_and _content: BigWig files representing genome read coverage for merged biological replicates. Reads were extended to fragment size.

source_name: Embryonic Stem Cells

growth_protocol: Mouse embryonic stem cells were grown on 0.1% gelatin-coated dishes in DMEM complemented with 10% FBS, 2 mM L-glutamine, 1% non-essential amino acids, 1% penicillin-streptomycin, 10 ng/ml leukaemia inhibitory factor and 0.1 mM beta-mercaptoethanol (Sigma) at 37 °C at 5% CO2.

extract_protocol:
Chromatin was prepared from 1 x 108 mouse ES cells grown to 70-90% confluency. Cells were crosslinked at room temperature for either 10 min in 1% methanol-free formaldehyde (Thermo Scientific) or 2 mM disuccinimidyl glutarate (DSG) for 1 hour followed by 10 min with 1% formaldehyde (see "description"). Crosslinking reactions were quenched by the addition of glycine to a concentration of 200 mM. Chromatin was prepared at 4 °C by rotating the cells in 10 ml buffer LB1 (50 mM HEPES KOH pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton x-100, with 1x cOmpleteTM EDTA-free Protease Inhibitor Cocktail (Roche)), 10 ml buffer LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, with 1x cOmpleteTM EDTA-free Protease Inhibitor Cocktail) and 1 ml buffer LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1x cOmpleteTM EDTA-free Protease Inhibitor Cocktail). Chromatin was sheared in a 1 ml milliTUBE with AFA Fiber (Covaris) using a Covaris S220 AFA ultrasonicator (set at 150 W Peak Incident Power, 8% Duty Factor, 200 Cycles/Burst) for 30 min. Following sonication, the sheared chromatin was spun at 15,000 x g for 20 min and the soluble fraction collected and aliquoted.  Immunoprecipitation (IP) was performed using the sheared chromatin from approximately 1 x 107 cells in Chromatin Dilution Buffer (16.7 mM Tris pH 8.1, 167 mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, freshly complemented with 1x cOmpleteTM EDTA-free Protease Inhibitor Cocktail). Following a 30 min preclear using 50 µl blocked Protein A or G agarose beads (Roche), the chromatin was incubated with 5 µg antibody overnight at 4 °C. Immune complexes were captured with blocked Protein A or G agarose beads by incubation for 4 h with rotation and then washed with the following buffers: Low Salt Buffer (20 mM Tris pH8.1, 150 mM NaCl, 0.2% SDS, 1% Triton X-100, 5 mM EDTA, and 5% w/v sucrose), High Salt Buffer (50 mM HEPES pH 7.5, 500 mM NaCl, 0.1% deoxycholic acid, 1% Triton X-100 and 1 mM EDTA), Lithium Chloride Buffer (10 mM Tris pH 8.0, 250 mM LiCl, 0.5% deoxycholic acid, 0.5% NP-40 and 1 mM EDTA) and twice with TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Captured chromatin was eluted in 125 µl elution buffer (1% SDS and 0.1 M NaHCO3) by shaking vigorously for 30 min at room temperature and then subjected to reverse crosslinking by incubating at 65 °C overnight in the presence of 200 mM NaCl. Input controls consisted of 50 µl (5%) samples of pre-cleared chromatin that were reverse crosslinked and purified as described for the IP samples. After incubation with 0.5 µg RNase A (1 h at 37 °C) and 20 µg Proteinase K (1 h at 45 °C), DNA was purified using the QIAquick PCR Purification kit (Qiagen).
Automated library preparation was performed on 5 ng input material using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and in-house single indexing primers. Equivalent amounts of individual libraries were pooled together. Paired-end sequencing was performed using a HiSeq4000 75 bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of >30 million reads per sample.

treatment_protocol: Wild type or DNMT.TKO mouse ESCs were treated with 5 ng/µl Trichostatin A or control 0.0033% DMSO for 36 h

tag: genotype

value: wild type

value: 5 ng/µl Trichostatin A for 36 h


title: J1_IGG1_G3A1

description: ChIP-seq using mouse isotype control antibody, cells were crosslinked using 1% formaldehyde for 10 min

value: Mouse G3A1 IgG1 (Cell Signalling Technologies, 5415, lot 9)


title: HA-TFE3_2_ChIPSeq

value: HA-TFE3-inducible cells

value: anti-HA antibody (3F10, Roche)


title: TKO.Unt_ChIP.Input

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO


title: J1.Unt_ChIP.Input


title: control sample (PA01)

city: Guangzhou

first: Jianhe

last: Wang

state: guangdong

address: wushan road

institute: Integrative Microbiology Research Centre, South China Agricultural University

hyb_protocol: Target hybridization, washing and staining were performed in in the Affymetrix Fluidics Station 450 following the manufacturer’s instructions.

scan_protocol: GeneChip arrays were scanned with an Affymetrix probe array scanner 3000 in the BSF Microarray Service of A-Star.

data_processing: The data were normalized using RMA method.

label: biotin

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PAO1

label_protocol: cDNA was synthesized from total RNA samples by using random primers (Invitrogen). SuperScript II (Invitrogen) and biotin-ddUTP were used to label the products according to the protocol from Affymetrix.

growth_protocol: PAO1 cells were cultured in LB medium supplemented with NTA with or without addition of 30μM of ALA at 37°C with shaking for 4 h.

extract_protocol: Total RNA were isolated from fresh bacterial cultures using the RNeasy mini kit according to the manufacturer’s instructions (Qiagen), and digested with DNase I (Promega) to remove contaminating genomic DNA and PCR with the RNA was performed to ensure the absence of contaminating DNA.NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: PAO1 cells were cultured in LB medium supplemented with NTA with or without addition of 30μM of ALA .

value: without ALA treatment


title: J1.Unt_DSG_ChIP.Input

description: Input control for ChIP, cells were crosslinked in two steps using 2mM disuccinimidyl glutarate for 1 h then 1% formaldehyde for 10 min


title: TKO.Unt_DSG_ChIP.Input


title: 30 μM ALA treated PAO1

department: Integrative Microbiology Research Centre,

value: with ALA treatment


title: invasive dCCA of Patient 3 [T3]

description: nCounter® Technology

source_name: invasive dCCA of Patient 3

value: invasive dCCA


title: TKO.TSA_ChIP.Input


title: J1_IGG

description: ChIP-seq using rabbit isotype control antibody, cells were crosslinked using 1% formaldehyde for 10 min

value: Normal Rabbit IgG (Cell Signalling Technologies, 2729, lot 7)


title: iHep_4a3_2_Hnf4a_input

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.6.2) with the option (aln -t 6).
peak finding algorithm MACS (v2.1.0) with the option (-g mm -p 0.00001).
The bedgraph files were obtained from the bam files using Bedtools (v2.16.2), then converted into the bw files.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files contain the positions of the peaks that were obtained when normalizing the reads of the ChIP-Seq to the input. The bw files converted from the bedgraph files contain depth of reads.

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were prepared from 13.5 days post coitum embryos. iHep cells were generated and maintained following the previously described protocol (Sekiya and Suzuki, 2011).

extract_protocol:
Sonicated DNA from cells was pulled down with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in iHep cells.

tag: transfection

value: infected with Foxa3, Hnf4alpha

tag: Stage

value: iHep

tag: antibody

value: none (input)


title: TKO.TSA_YY1_REP2

description:
anti-YY1 ChIP-seq, cells were crosslinked in two steps using 2mM disuccinimidyl glutarate for 1 h then 1% formaldehyde for 10 min
YY1_TKO.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

tag: strain

tag: treatment

tag: replicate

value: 2 of 3

value: YY1 (Santa Cruz, sc-1703, lot F0415)


title: TKO.Unt_YY1_REP2

description:
anti-YY1 ChIP-seq, cells were crosslinked in two steps using 2mM disuccinimidyl glutarate for 1 h then 1% formaldehyde for 10 min
YY1_TKO.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: TKO.Unt_YY1_REP3

value: 3 of 3


title: iHep_4a3_2_Hnf4a


title: J1.TSA_YY1_REP2

description:
anti-YY1 ChIP-seq, cells were crosslinked in two steps using 2mM disuccinimidyl glutarate for 1 h then 1% formaldehyde for 10 min
YY1_J1.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: 48hr_4a3 del2_S5PS2P

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.6.2) with the option (aln -t 6).
The bedgraph files were obtained from the bam files using Bedtools (v2.16.2), then converted into the bw files.
Genome_build: mm9
Supplementary_files_format_and_content: The bw files converted from the bedgraph files contain depth of reads.

growth_protocol: Mouse embryonic fibroblasts (MEFs) were prepared from 13.5 days post coitum embryos. iHep cells were generated and maintained following the previously described protocol (Sekiya and Suzuki, 2011). Hepatocytes were isolated from 10-week-old adult mouse livers by two-step collagenase digestion (Seglen, 1979).

extract_protocol:
For ChIP-seq expreriments, sonicated DNA from cells was pulled down with antibody. For FAIRE-seq, experiments, DNA fragments were extracted with phenol/chloroform from sonicated chromatins.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in MEF, iHep cells, or primary hepatocytes. FAIRE-seq expreriments were carried out following standard procedures in iHep cells.

value: infected with Foxa3 del2 muntat fused with x3Ty1-tag, Hnf4alpha


title: 48hr_4a3 del2_input


title: TKO.TSA_YY1_REP1

value: 1 of 3


title: 14_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim mCherry-Fc

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: RNA expression value derived from Expression Console software; core- gene or -exon analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console v4.0 using default analysis settings for RNA analyses  for  gene default and exon default .CHP files.

source_name: Ba/F3 (DSMZ no.: ACC 300)

label_protocol: 150 ng total RNAwas amplified using the  WT Expression Kit and the WT Terminal Labeling Kit (Thermofisher, Darmstadt, Germany).

growth_protocol: All cells were grown at 37°C with 5% CO2 in a water saturated atmosphere in Dulbecco’s modified Eagle’s Medium (DMEM) high glucose culture medium (GIBCO®, Life Technologies, Darmstadt, Germany) with 10% fetal calf serum (GIBCO®, Life Technologies, Darmstadt, Germany) and 60 mg/l penicillin and 100 mg/l streptomycin (Genaxxon Bioscience GmbH, Ulm, Germany). Murine Ba/F3/gp130 cells were obtained from Immunex (Seattle, WA, USA) and grown in the presence of Hyper-IL-6, a fusion protein of IL-6 and soluble IL-6 receptor. 0.2% (10 ng/ml) of conditioned medium from a stable clone of CHO-K1 cells secreting Hyper-IL-6 in the supernatant (stock solution approximately 5 μg/ml as determined by ELISA) were used to maintain Ba/F3/gp130 cells and derivates thereof.

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: Ba/F3/gp130 cells were washed 4 times with PBS to remove cytokines and starved in serum-free DMEM for 4 h. Cells were stimulated for 2 h (or indicated if other time points) with 100 ng/ml of purified protein, harvested, frozen in liquid nitrogen and then lysed.

tag: cell type

value: interleukin-3 or Hyper-Interleukin-6 dependent pro-B cellline

value: mCherry-Fc (n100 ng/ml)


title: TKO_IGG1_G3A1

value: Mouse G3A1 IgG1 (Cell Signalling Technologies, 5415, lot 9)


title: 15_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim mCherry-Fc


title: TKO_IGG


title: TKO.TSA_YY1_REP3

value: 5 ng/µl Trichostatin A for 36 h


title: TKO.Unt_YY1_REP1

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO


title: J1.TSA_YY1_REP1

value: wild type


title: J1.TSA_YY1_REP3


title: iHep_4a3_DA1_input

value: infected with Foxa1, Hnf4alpha


title: iHep_4a3_DA1


title: TKO.TSA_SP1_REP3

description:
anti-SP1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
SP1_TKO.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: TKO.Unt_SP1_REP3

description:
anti-SP1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
SP1_TKO.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

value: SP1 (Santa Cruz, sc-17824, lot G0114)


title: iHep_4a3_2_Foxa3

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.6.2) with the option (aln -t 6).
peak finding algorithm MACS (v2.1.0) with the option (-g mm -p 0.00001).
The bedgraph files were obtained from the bam files using Bedtools (v2.16.2), then converted into the bw files.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files contain the positions of the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input. The bw files converted from the bedgraph files contain depth of reads.

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in iHep cells or hepatocytes.


title: iHep_4a3_2_Foxa3_input


title: J1.Unt_YY1_REP3

description:
anti-YY1 ChIP-seq, cells were crosslinked in two steps using 2mM disuccinimidyl glutarate for 1 h then 1% formaldehyde for 10 min
YY1_J1.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: J1.Unt_YY1_REP2


title: J1.TSA_SP1_REP3

description:
anti-SP1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
SP1_J1.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: 48hr_4a3_del2_input

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in iHep cells or MEFs 48 hours after transfection with retroviruses.

value: infected with Foxa3 del2 mutant fused with x3Ty1-tag, Hnf4alpha


title: TKO.Unt_SP1_REP2


title: TKO.TSA_SP1_REP2


title: J1.Unt_SP1_REP3

description:
anti-SP1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
SP1_J1.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: J1.Unt_YY1_REP1


title: J1.TSA_SP1_REP2


title: 9_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim mCherry-Fc


title: TKO.TSA_SP1_REP1


title: 13_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim mCherry-Fc


title: 14_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim w_o

value: untreated


title: 8_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim mCherry-Fc


title: 10_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim mCherry-Fc


title: 13_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim w_o


title: MEF with Hnf4a (Day30) none (input)

description: MEF with Hnf4a (Day30)

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in MEFs.

value: infected with Hnf4alpha

value: MEF


title: 12_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim w_o


title: J1.Unt_SP1_REP2

value: 2 of 3


title: BEEC.83

city: Wilrijk

first: Veerle

last: Van Hoeck

state: Antwerp

address: Campus Drie Eiken, Universiteitsplein 1

department: Department of Veterinary Sciences

country: Belgium

institute: University of Antwerp

description: 2x 100BP paired end reads

data_processing:
Transcriptome analysis was performed in Galaxy (https://usegalaxy.org).
Quality control was performed by FastQC (version 0.71).
Paired reads were mapped to the Bos taurus reference genome (UMD 3.1) using HISAT2 (version 2.1.0), after which the counts per gene model was performed with FeatureCounts (version 1.6.2).
Expression values were normalized, and global and pairwise statistics were performed using DESeq2 (version 1.18.1) using false discovery rate (FDR)-corrected P values.
Ensemble reference IDs were used
Genome_build: Bos taurus UMD 3.1
Supplementary_files_format_and_content: Excel file includes normalized counts for all samples

organism: Bos taurus

source_name: Bovine Endometrial Epithelial Cells

growth_protocol: Bovine endometrial epithelial cells (bEECs) were harvested from Bos taurus beef cows post mortem. The uterine horn ipsilateral to the ovary containing the corpus haemorrhagicum was opened longitudinally at the mesometrial insertion and the endometrial luminal surface was carefully scraped with sterile glass slides. Cells collected from  four uteri were pooled. Primary cells were plated into T25 culture flasks and maintained in humidified atmosphere of 5% CO2 at 38.5°C. The cell culture medium consisted of DMEM/F-12 phenol red-free medium (Gibco, Thermo Fisher Scientific) supplemented with 10% FBS (Sigma-Aldrich), 2% Penicillin/Streptomycin, and 1% Fungizone. Cells were subcultured until passage two, when bEECs were cryopreserved. Subculture three–bEECs were thawed as needed and assigned to co-culture experiments.

extract_protocol:
Total RNA isolation was carried out using PicoPure RNA Isolation Kit (Thermo Fisher). Briefly, bEEC samples were subjected to cell lysis in 500 µL of Extraction Buffer for 30 min at 42 ºC. Lysates were loaded into pre-conditioned purification columns and processed as per manufacturer’s instructions. Membranes were subjected to on-column DNase (RNase-Free DNase Set; Qiagen) treatment at room temperature for 15 min according to the standard protocol. After subsequent washing steps, the membrane-bound RNA was eluted in 16 µL of the Elution Buffer provided. Total RNA yield and integrity were assessed using RNA 6000 Nano Lab-chips (Agilent Genomics, Dublin, Ireland) on a Bioanalyzer 2100 (Agilent Genomics). Absorbance ratios (28S/18S) and RNA integrity values ranged between 2.0 to 2.6, and 8.5 to 10.0, respectively. The isolated RNA samples were stored at –80°C until RNA sequencing.
Poly-A containing mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces using divalent cations under elevated temperature. First-strand cDNA was synthetized using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis using DNA Polymerase I and RNase H. The synthesized cDNA was subjected to end-repair and 3’ adenylation. Adapters were ligated to the ends of 3’ adenylated cDNA fragments. cDNA fragments with adapters from previous step were amplified by PCR. The resultant PCR products were purified with Agencourt AMPure XP Beads (Beckman Coulter, Beverly, MA, US), and dissolved in buffer EB. Double stranded PCR products were heat denatured and circularized by the splint oligo sequence. Single stranded circular DNAs (ssCir DNA) were used for PE100 strand-specific library construction and validation on the Bioanalyzer 2100 (Agilent Genomics). The library was amplified with phi29 and DNA nanoballs (DNBs) were generated with ssCir DNA by rolling circle replication (RCR) to intensify the fluorescent signals during the sequencing process. The DNBs were load into the patterned nanoarray and pair-end reads of 100 bp were read on the BGISEQ-500 (Cambridge, MA, US) platform for subsequent data analysis.

treatment_protocol: In vitro produced, day-5.5 morulae were selected under the stereomicroscope and transferred in groups of 15±1 to a 96-well plate (ClearView, IncuCyte®) containing 90% confluent, untreated bEEC monolayers according to the treatments: (i) Control Embryos: morulae without bEECs; (ii) Contact+: morulae juxtapositioned to bEEC monolayers; (iii) Contact⎼: morulae placed on cell culture transwells, without contact with bEECs; or (iv) Control bEEC: bEECs in the absence of embryos. In each replicate, all experimental conditions were conducted in a single 96-well and received transwells. The experiment was performed in six replicates, with two to four wells of each treatment per replicate. Embryos were transferred using mouth-controlled, fine pore glass capillaries to minimize the volume of media transferred to the wells. Embryos–bEECs co-cultures (for all the experimental conditions) were conducted in 150 µL of synthetic oviductal fluid (SOF) medium supplemented with 5% of fetal bovine serum (FBS), in humidified atmosphere of 5% CO2 at 38.5°C. After 48 h of co-culture, embryos and bEEC monolayers were evaluated and harvested.

value: Endometrium

value: Bovine Endometrial Epithelial Cells

value: Control bEEC

tag: passage


title: J1.TSA_SP1_REP1

value: 1 of 3

tag: chip antibody


title: MEF with Foxa3 (Day30) Foxa3

description: MEF with Foxa3 (Day30)

value: infected with Foxa3


title: BEEC.104

description: 2x 100BP paired end reads


title: TKO.TSA_NRF1_REP3

description:
anti-NRF1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
NRF1_TKO.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

value: 3 of 3


title: BEEC.24

description: 2x 100BP paired end reads


title: TKO.Unt_SP1_REP1


title: 48hr_4a3_del2_Foxa3_del2-x3Ty1

value: iHep


title: MEF with Foxa2 (Day30) none (input)

description: MEF with Foxa2 (Day30)

value: infected with Foxa2

value: none (input)


title: J1.Unt_SP1_REP1

value: wild type


title: BEEC.103

description: 2x 100BP paired end reads


title: BEEC.84

description: 2x 100BP paired end reads


title: BEEC.Embryos.Contact.97

description: 2x 100BP paired end reads

value: Contact+


title: MEF with Foxa3 (Day30) none (input)

description: MEF with Foxa3 (Day30)


title: MEF with Hnf4a (Day30) Hnf4alpha

description: MEF with Hnf4a (Day30)


title: TKO.Unt_NRF1_REP3

description:
anti-NRF1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
NRF1_TKO.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO


title: MEF with Foxa1 (Day30) none (input)

description: MEF with Foxa1 (Day30)

value: infected with Foxa1


title: MEF with Foxa2 (Day30) Foxa2

description: MEF with Foxa2 (Day30)


title: MEF with Foxa1 (Day30) Foxa1

description: MEF with Foxa1 (Day30)


title: BEEC.Embryos.Contact.28

description: 2x 100BP paired end reads


title: MEF with Hnf4a (Day2) Hnf4alpha

description: MEF with Hnf4a (Day2)


title: BEEC.Embryos.Contact.108

description: 2x 100BP paired end reads


title: BEEC.Embryos.Contact.107

description: 2x 100BP paired end reads


title: TKO.TSA_NRF1_REP2

value: 5 ng/µl Trichostatin A for 36 h


title: MEF with Foxa3 (Day2) none (input)

description: MEF with Foxa3 (Day2)


title: J1.Unt_NRF1_REP3

description:
anti-NRF1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
NRF1_J1.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: MEF with Hnf4a (Day2) none (input)

description: MEF with Hnf4a (Day2)

value: infected with Hnf4alpha


title: J1.TSA_NRF1_REP3

description:
anti-NRF1 ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
NRF1_J1.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: BEEC.Embryos.No.Contact.90

description: 2x 100BP paired end reads

value: Contact⎼


title: TKO.Unt_NRF1_REP2

value: 2 of 3


title: MEF with Foxa3 (Day2) Foxa3

description: MEF with Foxa3 (Day2)

value: MEF


title: 13_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim GFP-mCherry

value: interleukin-3 or Hyper-Interleukin-6 dependent pro-B cellline

value: GFP-mCherry (100 ng/ml)


title: 11_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim w_o

value: untreated


title: 14_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim GFP-mCherry


title: 7_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim w_o


title: J1.Unt_NRF1_REP2


title: J1.TSA_NRF1_REP2


title: BEEC.Embryos.No.Contact.89

description: 2x 100BP paired end reads

value: Endometrium

value: Bovine Endometrial Epithelial Cells


title: BEEC.Embryos.Contact.87

description: 2x 100BP paired end reads


title: 9_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim w_o


title: 11_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim GFP-mCherry


title: 7_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim GFP-mCherry


title: 9_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim GFP-mCherry


title: BEEC.Embryos.No.Contact.30

description: 2x 100BP paired end reads


title: 4_IL-10R2/IL-22Rα1 stim w_o


title: 5_IL-10R2/IL-22Rα1 stim w_o


title: MEF with Foxa2 (Day2) none (input)

description: MEF with Foxa2 (Day2)


title: TKO.TSA_NRF1_REP1

value: 1 of 3


title: BEEC.Embryos.No.Contact.110

description: 2x 100BP paired end reads


title: MEF with Foxa2 (Day2) Foxa2

description: MEF with Foxa2 (Day2)

value: infected with Foxa2


title: TKO.Unt_NRF1_REP1


title: BEEC.Embryos.No.Contact.109

description: 2x 100BP paired end reads


title: MEF with Foxa1 (Day2) none (input)

description: MEF with Foxa1 (Day2)

value: none (input)


title: MEF with Foxa1 (Day2) Foxa1

description: MEF with Foxa1 (Day2)


title: J1.TSA_NRF1_REP1

value: wild type


title: J1.Unt_NRF1_REP1


title: fdl1_coleoptile_tips_rep3

city: Piscataway

first: Andrea

last: Gallavotti

state: NJ

address: 190 Frelinghysen Rd.

department: Waksman Institute of Microbiology

institute: Rutgers University

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence using trimmomatic, then mapped to ZmB73v3 whole genome using Tophat v2.1.1
Differentially expressed genes were identified using cuffdiff
Genome_build: ZmB73v3.31

organism: Zea mays

source_name: 3-4 mm maize W22 growth chamber-grown (at 28°C) fdl1 mutant coleoptile tips

extract_protocol:
samples were snap frozen in liquid nitrogen and total RNA was extracted using RNeasy kit (Qiagen) with DNAse treatment
Stranded Illumina mRNA sequencing libraries were generated using TruSeq (Illumina)

treatment_protocol: 3-4 mm maize W22 growth chamber-grown ( at 28°C ) coleoptile tips were harvested. fdl1 samples included coleoptile tips with normal appearance

tag: background

value: fdl1/Zmmyb94 mutant

value: coleoptile tips


title: fdl1_coleoptile_tips_rep2


title: 48hr_4a3_del2_2

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.7.12) with the option (mem -t 6 -M)
Fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using Tigar (v2) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen)
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: Retrovirus was produced following standard procedures, following transfection of pGCDNsam retroviral backbones containing the respective cDNAs (available from us via Addgene). Media was changed 8 hours after transfection and viral supernatant collected after another 24 and 48 hours.

value: infected with Foxa3 del2 mutant, Hnf4alpha

value: iHep


title: fdl1_coleoptile_tips_rep1


title: TKO.TSA_RNA_REP2

description:
RNA-seq using ribo-RNA depleted total RNA
RNAseq_Read_Count_Table.txt

data_processing:
RNA-seq reads were aligned to the mm10 genome build using TopHat (v2.0.13) with the --library-type option fr-firststrand, --mate-inner-dist set to 100 and coverage based searching for junctions disabled. FeatureCounts (v1.4.5-p1)  was used to count aligned RNA-seq reads that mapped to the exons of annotated genes (UCSC). Read counting was strand specific (option -s set to 2). Reads with a mapping quality below 1 were excluded. Differential analysis was performed using the R package edgeR (v3.22.3) with raw read counts supplied as input. Genes with a low level of expression in all samples were filtered out using a counts-per-million threshold of 1. The generalized linear model likelihood test was used to determine differential expression between multiple groups of biological replicate samples. Genes or transcripts were considered as significantly differentially expressed if they had a p-value < 10-5 after adjusting for multiple comparisons using the Benjamini and Hochberg procedure.
Genome_build: mm10
Supplementary_files_format_and _content: Tab-delimited matrix containing raw strand-specific read counts for all genes and all RNA-seq samples. Counts were obtained using FeatureCounts v1.4.5-p1 with options -p, -s 2, -t "exon", and -Q 1.

extract_protocol:
Total RNA was isolated from mES cells using the TRI Reagent (Sigma) following the protocol provided by the manufacturer. Contaminating genomic DNA was removed by incubating 10 µg RNA with 10 U DNaseI (Thermo Scientific) in Reaction Buffer for 30 min at 37 °C. The reaction was stopped by adding 10 µl of 50 mM EDTA after which RNA was extracted using a phenol-choloroform purification and ethanol precipitation.
Total RNA was depleted of ribosomal RNA using Ribo-Zero rRNA Removal Kit (Epicentre/Illumina, Human/Mouse/Rat) and library preparation was completed using NEBNext® Ultra Directional RNA Library Prep Kit for Illumina® (New England Biolabs), both following manufacturer’s instructions. Libraries were amplified (12 cycles) on a Tetrad (Bio-Rad). Equivalent amounts of individual libraries were pooled together. Paired end sequencing was performed using a Hiseq2000 51 bp platform (v3 SBS chemistry), generating a raw read count of >40 million reads per sample.

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: 5 ng/µl Trichostatin A for 36 h

value: 2 of 2


title: TKO.TSA_MAX_REP3

description:
anti-MAX ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
MAX_TKO.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

value: 3 of 3

value: MAX (Santa Cruz, sc-197, lot B2414)


title: wildtype_coleoptile_tips_rep3

source_name: 3-4 mm maize W22 growth chamber-grown (at 28°C) coleoptile tips

value: wildtype


title: TKO.DMSO_RNA_REP2

value: control DMSO treatment


title: 3_IL-10R2/IL-22Rα1 stim w_o

value: interleukin-3 or Hyper-Interleukin-6 dependent pro-B cellline

value: untreated


title: 2_IL-10R2/IL-22Rα1 stim w_o


title: wildtype_coleoptile_tips_rep2


title: 5_IL-10R2/IL-22Rα1 stim IL-22


title: 48hr_4a3_del2_1


title: iHep_4a2_2_Hnf4a_R242

value: infected with Foxa2, Hnf4alpha


title: 3_IL-10R2/IL-22Rα1 stim IL-22


title: 2_IL-10R2/IL-22Rα1 stim IL-22


title: iHep_4a2_2_input_R242


title: J1.Unt_MAX_REP3

description:
anti-MAX ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
MAX_J1.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: J1.TSA_MAX_REP3

description:
anti-MAX ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
MAX_J1.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: J1.TSA_RNA_REP2


title: 1_IL-10R2/IL-22Rα1 stim IL-22


title: wildtype_coleoptile_tips_rep1


title: iHep_4a1_2_input_R225

value: infected with Foxa1, Hnf4alpha


title: J1.DMSO_RNA_REP2


title: TKO.TSA_MAX_REP2

value: 2 of 3


title: TKO.Unt_MAX_REP2

description:
anti-MAX ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
MAX_TKO.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: TKO.TSA_RNA_REP1

value: 1 of 2


title: EEDKO_input

city: Nijmegen

first: Gert

middle: Jan

last: Veenstra

state: Not US or Canada

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: Input of EED KO supplemented with drosophila spike In

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads from this study and from Perino et al, Nat. Gen (2018) were trimmed to 42bp with fastx_trimmer (version 0.0.13.2), and in case of paired-end sequencing only read_1 was used for analysis
All fastq files were mapped using bwa (version 0.7.10-r789), filtered to retain only uniquely mapping reads using mapping quality of 30 and samtools (version 1.7, flag -F 1024)
Peaks were called with MACS2-2.7 with qvalue 0.0001 using --call-summits for transcription factors and --broad for H3K27me3. Only peaks independently called in both replicates were used for downstream analysis
High-confidence peaks for each mark were obtained by merging peaks called in both replicates and overlapping by at least 50% of their length, and combined to obtain the list of all PRC2 peaks.
Coverage files in bigWig format were created using bam2bw (https://bitbucket.org/simonvh/bam2bw/) with the -e auto and -c parameters
Clustering was performed with fluff v3.0.2  https://fluff.readthedocs.io/en/latest/ using the -g option to detect dynamics
Samples supplemented with Drosophila chromatin were mapped on a combined mm10-dm6 genome, filtered to remove multimappers and duplicates. The resulting bam files were split according to the species of origin and dm6 reads were used to calculate a per-sample scaling factor relative to the less deeply sequenced sample. ChIPseq were first normalized based on the number of spike-in reads to obtain the number of reads per million of spike-in reads, and further normalized to account for the potentially varying starting amount of spike-in in different samples.
Genome_build: mm10
Supplementary_files_format_and_content: Coverage files in bigWig format, high-confidence PRC2 peaks and clustered peaks, normalized bam files for spike-in ChIP

source_name: embryonic stem cells with Drosophila chromatin spike in

growth_protocol: mESC were grown in serum+LIF medium as described in Marks, H. et al. (doi:10.1016/j.cell.2012.03.026)

extract_protocol:
Chromatin extraction and ChIP were performed as described in Kloet, S. L. et al. (doi:10.1038/nsmb.3248 ). For spike-in ChIP 50ng of sonicated Drosophila chromatin was added to each sample prior to IP
Five ng/sample of ChIP were prepared for sequencing with the Kapa Hyper-prep Kit (Kapa Biosystems) using NEXTflex adapters (Bio Scientific) and amplified with ten cycles of PCR. Libraries were size-selected to obtain 300bp fragments using E-gel (Invitrogen) and sequenced on an Illumina NextSeq machine to obtain 75bp reads

treatment_protocol: Where indicated ESCs were treated with 10 µM EED226 for 4 days to inhibit EED function. Full knockout of Ring1b was induced through treatment with Tamoxifen (OHT) for 2 days. For H2AK119u depletion cells were incubated in medium containing 5uM of MG132 for 6 hours

value: EEDKO

value: Eed KO


title: iHep_4a1_2_Hnf4a_R225


title: EEDKO_Ezh2

description: ChIP for Ezh2 in EED KO supplemented with drosophila spike In

value: Diagenode C15410039, lot 003  + Active Motif 61686, lot 00419007


title: TKO.Unt_MAX_REP3


title: TKO.DMSO_RNA_REP1


title: MEF_1_H3K9ac_R102

extract_protocol:
For ChIP-seq expreriments, sonicated DNA from cells was pulled down with antibody. For FAIRE-seq, experiments, DNA fragments were extracted with phenol/chloroform from sonicated chromatins.
Libraries were prepared according to Illumina's instructions.
ChIP-Seq, FAIRE-Seq


title: J1.TSA_MAX_REP2

value: wild type


title: J1.TSA_RNA_REP1


title: J1.Unt_MAX_REP2


title: E14226_input

description: Input of E14+EED226  supplemented with drosophila spike In

value: WT

value: EED 226


title: E14226_Ezh2

description: ChIP for Ezh2 in E14+EED226  supplemented with drosophila spike In


title: MEF_1_H3K27me3_R102


title: J1.DMSO_RNA_REP1


title: E14_input

description: Input of E14  supplemented with drosophila spike In


title: E14_Ezh2

description: ChIP for Ezh2 in E14  supplemented with drosophila spike In


title: iHep_4a3_3_S5PS2P_R170

value: infected with Foxa3, Hnf4alpha

value: iHep

value: Pol2 Ser2P/5P


title: iHep_4a3_3_S5P_R170

value: Pol2 Ser5P


title: TKO.Unt_MAX_REP1

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: 1 of 3

value: MAX (Santa Cruz, sc-197, lot B2414)


title: J1.TSA_MAX_REP1

value: 5 ng/µl Trichostatin A for 36 h


title: J1.Unt_MAX_REP1


title: iHep_4a3_3_input_R170_R172

value: none (input)


title: iHep_4a3_3_input_R242


title: MEF_1_input_R102


title: R1AB_FCS_Ezh2_A.mapUnique

description:
ChIP for Ezh2 in R1AB cells treated with tamoxifen
processed data file:
R1AB_FCS_Ezh2.mapUnique.bw

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads from this study and from Perino et al, Nat. Gen (2018) were trimmed to 42bp with fastx_trimmer (version 0.0.13.2), and in case of paired-end sequencing only read_1 was used for analysis to ensure maximum comparability
All fastq files were mapped using bwa (version 0.7.10-r789), filtered to retain only uniquely mapping reads using mapping quality of 30 and samtools (version 1.7, flag -F 1024)
Peaks were called with MACS2-2.7 with qvalue 0.0001 using --call-summits for transcription factors and --broad for H3K27me3. Only peaks independently called in both replicates were used for downstream analysis
High-confidence peaks for each mark were obtained by merging peaks called in both replicates and overlapping by at least 50% of their length, and combined to obtain the list of all PRC2 peaks.
Coverage files in bigWig format were created using bam2bw (https://bitbucket.org/simonvh/bam2bw/) with the -e auto and -c parameters
Clustering was performed with fluff v3.0.2  https://fluff.readthedocs.io/en/latest/ using the -g option to detect dynamics
Samples supplemented with Drosophila chromatin were mapped on a combined mm10-dm6 genome, filtered to remove multimappers and duplicates. The resulting bam files were split according to the species of origin and dm6 reads were used to calculate a per-sample scaling factor relative to the less deeply sequenced sample. ChIPseq were first normalized based on the number of spike-in reads to obtain the number of reads per million of spike-in reads, and further normalized to account for the potentially varying starting amount of spike-in in different samples.
Genome_build: mm10
Supplementary_files_format_and_content: Coverage files in bigWig format, high-confidence PRC2 peaks and clustered peaks, normalized bam files for spike-in ChIP

source_name: embryonic stem cells

extract_protocol:
Chromatin extraction and ChIP were performed as described in Kloet, S. L. et al. (doi:10.1038/nsmb.3248 )
Five ng/sample of ChIP were prepared for sequencing with the Kapa Hyper-prep Kit (Kapa Biosystems) using NEXTflex adapters (Bio Scientific) and amplified with ten cycles of PCR. Libraries were size-selected to obtain 300bp fragments using E-gel (Invitrogen) and sequenced on an Illumina NextSeq 500 machine to obtain 75bp reads

value: Ring1a-/-;RIng1bfl/fl; ER-Cre

value: Tamoxifen

value: Diagenode C15410039, lot 003


title: TKO.TSA_GABPA_REP3

description:
anti-GABPA ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
GABPA_TKO.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

value: 3 of 3

value: GABPA (Santa Cruz, sc-22810, lot D0715)


title: iHep_4a3_3_H3K9ac_R172


title: R1AB_FCS_Ezh2.mapUnique


title: R1AB_FCS_226_Mtf2_B.mapUnique

description:
ChIP for Mtf22 in R1AB cells treated with Eed226 and tamoxifen
processed data file:
R1AB_FCS_226_Mtf2.mapUnique.bw

value: EED 226 + Tamoxifen

value: Aviva System Biology ARP34292, lot QC49692-42166


title: iHep_4a3_3_H3K27me3_R172


title: TKO.Unt_GABPA_REP3

description:
anti-GABPA ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
GABPA_TKO.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: J1.TSA_GABPA_REP3

description:
anti-GABPA ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
GABPA_J1.TSA_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw

value: wild type


title: TKO.TSA_MAX_REP1


title: J1.Unt_GABPA_REP3

description:
anti-GABPA ChIP-seq, cells were crosslinked using 1% formaldehyde for 10 min
GABPA_J1.DMSO_MERGED_sorted_rmdup_filtered.uniqReads.DS.bw


title: R1AB_FCS_226_Mtf2.mapUnique


title: TKO.TSA_GABPA_REP2

value: 2 of 3


title: R1AB_FCS_226_Mtf2_A.mapUnique


title: TKO.Unt_GABPA_REP2


title: iHep_4a2_1_input_R242

value: infected with Foxa2, Hnf4alpha

value: iHep


title: iHep_4a2_1_input_R157_R159


title: R1AB_FCS_Ezh2_B.mapUnique


title: R1AB_FCS_226_Jarid2.mapUnique

description:
ChIP for Jarid2 in R1AB cells treated with Eed226 and tamoxifen
processed data file:
R1AB_FCS_226_Jarid2.mapUnique.bw

value: Novus Biologicals NB100-2214, Lot E2


title: R1AB_FCS_226_Jarid2_A.mapUnique


title: J1.TSA_GABPA_REP2


title: R1AB_FCS_226_Ezh2_B.mapUnique

description:
ChIP for Ezh2 in R1AB cells treated with Eed226 and tamoxifen
processed data file:
R1AB_FCS_226_Ezh2.mapUnique.bw


title: iHep_4a2_1_FAIRE_R242


title: TKO.TSA_GABPA_REP1

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO


title: J1.Unt_GABPA_REP2


title: R1AB_FCS_226_Ezh2_A.mapUnique


title: iHep_4a1_1_input_R225

value: infected with Foxa1, Hnf4alpha


title: iHep_4a1_1_input_R157


title: iHep_4a3_3_FAIRE_R242

value: infected with Foxa3, Hnf4alpha


title: J1.TSA_GABPA_REP1

value: 5 ng/µl Trichostatin A for 36 h

value: 1 of 3


title: TKO.Unt_GABPA_REP1


title: R1AB_FCS_226_Ezh2.mapUnique

value: Ring1a-/-;RIng1bfl/fl; ER-Cre


title: R1AB_FCS_226_Jarid2_B.mapUnique


title: Mtf2GT_FCS_Jarid2.mapUnique

description:
ChIP for Jarid2 in Mtf2GT/GT cells from Perino et al 2018
processed data file:
Mtf2GT_FCS_Jarid2.mapUnique.bw
GSM3021210
GSM3021211

value: Gene trapping cassette disrupting Mtf2 CDS


title: iHep_4a1_1_H3K9ac_R157


title: Mtf2GT_FCS_H3K27me3.mapUnique

description:
ChIP for H3K27me3 in Mtf2GT/GT cells from Perino et al 2018
processed data file:
Mtf2GT_FCS_H3K27me3.mapUnique.bw
GSM2472751
GSM2472752


title: iHep_4a1_1_H3K27me3_R157


title: iHep_4a2_1_H3K9ac_R157


title: TKO.TSA_ATAC.Input_REP4

description:
Tn5 tagmented naked genomic DNA control
TKO.TSA_Input_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw

data_processing:
ATAC-seq reads were trimmed using cutadapt (v1.16) to remove 3' adapter sequences and short reads (<30bp) then aligned to the concatenated mm10 + galGal4 genome using bowtie2 (v2.2.5.0) with the options --no-mixed and --no-discordant. Reads that aligned to the exogenous galGal4 genome (mapping to chromosomes whose names have the prefix "galGal4_"), reads with multiple alignments (sam tag "XS:" present) and fragments mapping to a custom “blacklist” of artificially high regions of the genome (derived from ENCODE, https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded. Samtools (v1.3) was used for sorting and indexing bam files, and removing duplicates. Alignment files were randomly down-sampled (Picard Tools v1.105 "DownsampleSam") so as to retain an equivalent number of alignments in all samples. To produce genome coverage files, alignments from biological replicate samples were first merged (Samtools v.13) then bigWig files were generated using the Deeptools (v2.4.2) function 'bamCoverage' with the option -bs set to 2. Enriched regions were identified using the ‘dpeak’ peak-calling algorithm of DANPOS v2.2.2 (Chen et al., 2013) with the options –m, –kd 250, -kw 150 and –p 1e-60. For each condition, peaks were called from 4 biological replicate ATAC-seq samples with the corresponding 4 Tn5 control samples used as background.
Genome_build: mm10.galGal4.fa
Supplementary_files_format_and _content: BigWig files representing genome read coverage for merged biological replicates.

extract_protocol:
Assay for Transposase Accessible Chromatin (ATAC)-seq experiments were carried out by adapting the protocol published by (Buenrostro et al., 2015). To allow for calibration of the ATAC-seq signal between different samples, 5 x 105 chicken DF-1 cells were spiked-in with 5 x 106 mouse ES cells from each experimental condition.  Cell mixtures were lysed in 1 ml of Lysis Buffer (50 mM KCl, 10 mM MgSO4.7H2O, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF and 3 mM DTT) by incubating at room-temperature for 1 min followed by the two washes in 1 ml ice-cold RSB Buffer (10 mM NaCl, 10 mM Tris (pH 7.4), 3 mM MgCl2).   ATAC reactions were performed in 50 µl reactions in the presence of Tn5 reaction buffer (10 mM TAPS, 5 mM MgCl2 and 10% dimethylformamide), 5 x 104 nuclei (resuspended in H2O) and 2 µl of 12 µM Tn5 transposase (produced in house following a protocol by Picelli et al, 2014) for 30 min at 37 °C. DNA was purified using the QiaQuick MinElute columns (Qiagen) following manufacturer’s instructions.   Input samples were prepared by subjecting genomic DNA that had been isolated from each sample prior to the ATAC reaction to Tn5 tagmentation in reactions containing 5 ng genomic DNA, 1 µl of Tn5 and incubated at 55 °C for 7 min.
ATAC-seq libraries were prepared by PCR amplification using custom made Illumina barcodes in the NEBNext Ultra II Q5 2x PCR Master Mix with 6-12 cycles. PCR amplicons were purified and size selected using home-made SPRI beads (Rohland and Reich 2012) in two rounds (1:0.6 then 1:1.4 DNA:beads ratio). ATAC-seq libraries were quantified using the NEBNext Library Quant Kit and pooled prior to sequencing on an Illumina HiSeq4000 instrument to generate 75 bp paired-end reads.

tag: spike-in

value: 10:1 with Chiken DF-1 cells

value: 4 of 4


title: J1.Unt_GABPA_REP1

value: GABPA (Santa Cruz, sc-22810, lot D0715)


title: Mtf2GT_FCS_226_Ring1b_B.mapUnique

description:
ChIP for Ring1b in E4 cells treated with Eed226
processed data file:
Mtf2GT_FCS_226_Ring1b.mapUnique.bw

value: EED 226


title: iHep_4a1_1_FAIRE_R225


title: TKO.DMSO_ATAC.Input_REP4

description:
Tn5 tagmented naked genomic DNA control
TKO.DMSO_Input_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw

value: control DMSO treatment


title: iHep_4a2_1_H3K27me3_R159


title: Mtf2GT_FCS_Ezh2.mapUnique

description:
ChIP for Ezh2 in Mtf2GT/GT cells from Perino et al 2018
processed data file:
Mtf2GT_FCS_Ezh2.mapUnique.bw
GSM2472749
GSM2472750

value: Diagenode C15410039, lot 003


title: J1.TSA_ATAC.Input_REP4

description:
Tn5 tagmented naked genomic DNA control
J1.TSA_Input_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw

value: wild type


title: Hep_3_S5PS2P_R159

source_name: hepatocytes obtained from adult mouse livers

value: Pol2 Ser2P/5P


title: Mtf2GT_FCS_226_Ring1b_A.mapUnique


title: Hep_3_S5P_R159

value: Pol2 Ser5P


title: Mtf2GT_FCS_226_Ring1b.mapUnique


title: TKO.TSA_ATAC.Input_REP3

value: 3 of 4


title: iHep_4a3_CA2_input

value: infected with Hnf4alpha, Foxa3 containing CTD of Foxa2

value: iHep

value: none (input)


title: Mtf2GT_FCS_226_MG132_Ezh2_B.mapUnique

description:
ChIP for Ezh2 in E4 cells treated with Eed226 and MG132
processed data file:
Mtf2GT_FCS_226_MG132_Ezh2.mapUnique.bw


title: TKO.DMSO_ATAC.Input_REP3

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO


title: J1.TSA_ATAC.Input_REP3

value: 5 ng/µl Trichostatin A for 36 h


title: Mtf2GT_FCS_226_MG132_Ezh2.mapUnique


title: J1.DMSO_ATAC.Input_REP4

description:
Tn5 tagmented naked genomic DNA control
J1.DMSO_Input_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw


title: iHep_4a3_CA1_input

value: infected with Hnf4alpha, Foxa3 containing CTD of Foxa1


title: Mtf2GT_FCS_226_MG132_Ezh2_A.mapUnique

value: Gene trapping cassette disrupting Mtf2 CDS


title: iHep_4a3_NA2_input

value: infected with Hnf4alpha, Foxa3 containing NTD of Foxa2


title: Mtf2GT_FCS_226_Jarid2_B.mapUnique

description:
ChIP for Jarid2 in E4 cells treated with Eed226
processed data file:
Mtf2GT_FCS_226_Jarid2.mapUnique.bw

value: Novus Biologicals NB100-2214, Lot E2


title: iHep_4a3_NA1_input

value: infected with Hnf4alpha, Foxa3 containing NTD of Foxa1


title: J1.DMSO_ATAC.Input_REP3

value: 10:1 with Chiken DF-1 cells


title: Hep_3_input_R159


title: TKO.TSA_ATAC.Input_REP2

value: 2 of 4


title: iHep_4a2_CA3_input

value: infected with Hnf4alpha, Foxa2 containing CTD of Foxa3


title: Mtf2GT_FCS_226_Jarid2_A.mapUnique

value: EED 226


title: iHep_4a2_NA3_input

value: infected with Hnf4alpha, Foxa2 containing NTD of Foxa3


title: Mtf2GT_FCS_226_Jarid2.mapUnique


title: Mtf2GT_FCS_226_Ezh2_B.mapUnique

description:
ChIP for Ezh2 in E4 cells treated with Eed226
processed data file:
Mtf2GT_FCS_226_Ezh2.mapUnique.bw

value: Diagenode C15410039, lot 003


title: 12_mCherryVHHIL-10R2/GFPVHHIL-22Rα1 stim GFP-mCherry

description: RNA expression value derived from Expression Console software; core- gene or -exon analysis

value: interleukin-3 or Hyper-Interleukin-6 dependent pro-B cellline

value: GFP-mCherry (100 ng/ml)


title: iHep_4a1_CA3_input

value: infected with Hnf4alpha, Foxa1 containing CTD of Foxa3

value: iHep


title: Mtf2GT_FCS_226_Ezh2_A.mapUnique


title: TKO.DMSO_ATAC.Input_REP2

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: control DMSO treatment


title: Mtf2GT_FCS_226_Ezh2.mapUnique


title: TKO.TSA_ATAC.Input_REP1

value: 5 ng/µl Trichostatin A for 36 h

value: 1 of 4


title: J1.DMSO_ATAC.Input_REP2

value: wild type


title: iHep_4a3_CA1

value: infected with Hnf4alpha, Foxa3 containing CTD of Foxa1


title: TKO.DMSO_ATAC.Input_REP1


title: EEDKO_FCS_Mtf2.mapUnique

description:
ChIP for Mtf2 in EEDKO cells from Perino et al 2018
processed data file:
EEDKO_FCS_Mtf2.mapUnique.bw
GSM3021214

value: EEDKO

value: Eed KO

value: Aviva System Biology ARP34292, lot QC49692-42166


title: J1.TSA_ATAC.Input_REP1

value: 10:1 with Chiken DF-1 cells


title: iHep_4a3_NA2

value: infected with Hnf4alpha, Foxa3 containing NTD of Foxa2


title: E4_FCS_Mtf2.mapUnique

description:
ChIP for Mtf2 in E4 cells from Perino et al 2018
processed data file:
E4_FCS_Mtf2.mapUnique.bw
GSM3021212
GSM3021213

value: Jarid2 KO


title: iHep_4a3_NA1

value: infected with Hnf4alpha, Foxa3 containing NTD of Foxa1


title: E4_FCS_H3K27me3_B.mapUnique

description:
ChIP for H3K27me3 in E4 cells
processed data file:
E4_FCS_H3K27me3.mapUnique.bw


title: TKO.TSA_ATAC_REP4

description:
ATAC-seq
TKO.TSA_ATAC_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw

value: 4 of 4


title: E4_FCS_H3K27me3_A.mapUnique


title: J1.TSA_ATAC.Input_REP2

value: 2 of 4


title: iHep_4a1_NA3_input

value: infected with Hnf4alpha, Foxa1 containing NTD of Foxa3

value: none (input)


title: iHep_4a2_CA3

value: infected with Hnf4alpha, Foxa2 containing CTD of Foxa3

value: iHep


title: TKO.DMSO_ATAC_REP4

description:
ATAC-seq
TKO.DMSO_ATAC_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: control DMSO treatment


title: E4_FCS_H3K27me3.mapUnique


title: E4_FCS_Ezh2_B.mapUnique

description:
ChIP for Ezh2 in E4 cells
processed data file:
E4_FCS_Ezh2.mapUnique.bw

value: Diagenode C15410039, lot 003


title: J1.TSA_ATAC_REP4

description:
ATAC-seq
J1.TSA_ATAC_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw

value: wild type

value: 5 ng/µl Trichostatin A for 36 h


title: E4_FCS_Ezh2_A.mapUnique


title: iHep_4a3_CA2

value: infected with Hnf4alpha, Foxa3 containing CTD of Foxa2


title: iHep_4a1_NA3


title: E4_FCS_Ezh2.mapUnique


title: J1.DMSO_ATAC_REP4

description:
ATAC-seq
J1.DMSO_ATAC_MERGED_mm10.UniqMapped_sorted_rmdup_filtered_LibDepth.DS.bw


title: TKO.DMSO_ATAC_REP3

value: 3 of 4


title: TKO.TSA_ATAC_REP3

value: 10:1 with Chiken DF-1 cells


title: iHep_4a2_NA3

value: infected with Hnf4alpha, Foxa2 containing NTD of Foxa3


title: iHep_4a1_CA3

value: infected with Hnf4alpha, Foxa1 containing CTD of Foxa3


title: E4_FCS_226_Ring1b.mapUnique

description:
ChIP for Ring1b in E4 cells treated with Eed226
processed data file:
E4_FCS_226_Ring1b.mapUnique.bw

value: Jarid2 KO

value: EED 226


title: Hep_4_EGS_input_R176

value: hepatocytes obtained from adult mouse livers


title: J1.TSA_ATAC_REP3


title: J1.DMSO_ATAC.Input_REP1

value: 1 of 4


title: Hep_4_EGS_Foxa3_R176


title: E4_FCS_226_Mtf2_B.mapUnique

description:
ChIP for Mtf2 in E4 cells treated with Eed226
processed data file:
E4_FCS_226_Mtf2.mapUnique.bw

value: Aviva System Biology ARP34292, lot QC49692-42166


title: Hep_4_EGS_Foxa2_R176


title: J1.DMSO_ATAC_REP3


title: Hep_4_EGS_Foxa1_R176


title: E4_FCS_226_Mtf2_A.mapUnique


title: TKO.TSA_ATAC_REP2

value: 2 of 4


title: iHep_4a3_b2_EGS_flag_R156

value: mouse embryonic fibroblasts

value: infected with Foxa3, Hnf4alpha

value: iHep

value: Flag


title: E4_FCS_226_Mtf2.mapUnique


title: E4_FCS_226_Ezh2_B.mapUnique

description:
ChIP for Ezh2 in E4 cells treated with Eed226
processed data file:
E4_FCS_226_Ezh2.mapUnique.bw

value: Diagenode C15410039, lot 003


title: TKO.DMSO_ATAC_REP2

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: control DMSO treatment


title: iHep_4a3_3_EGS_input_R170

value: none (input)


title: J1.TSA_ATAC_REP2

value: wild type

value: 5 ng/µl Trichostatin A for 36 h

value: 10:1 with Chiken DF-1 cells


title: J1.DMSO_ATAC_REP2


title: E14_FCS_Ring1b_B.mapUnique

description:
ChIP for Ring1b in E14 cells
processed data file:
E14_FCS_Ring1b.mapUnique.bw

value: WT


title: iHep_4a2_3_EGS_flag_R170

value: infected with Foxa2, Hnf4alpha


title: iHep_4a2_2_Foxa2_R215


title: iHep_4a3_1_EGS_input_R156


title: iHep_4a3_1_EGS_Foxa3_R156


title: TKO.DMSO_ATAC_REP1


title: iHep_4a2_2_EGS_input_164


title: TKO.TSA_ATAC_REP1


title: iHep_4a3_3_EGS_Foxa3_R170


title: iHep_4a2_2_input_R215


title: iHep_4a2_1_EGS_input_R164


title: E14_FCS_Ring1b_A.mapUnique


title: TKO.DMSO_Nat.ChIP.Input_REP2

description: Input control for native ChIP-seq

data_processing:
ChIP-seq reads were aligned to the concatenated mm10 + galGal4 genome using bowtie2 (v2.2.5.0) with the options --no-mixed and --no-discordant. Reads that had multiple alignments (sam tag "XS:" present) were discarded and duplicate reads were removed using Samtools v1.3. Alignments were split by species based on chromosome names: in the mm10.galGal4.fa genome build, chromosome names have the prefix "mm10_" or "galGal4_". The number of reads mapping to the mm10 or galGal4 genome were counted and used to calculate the ratio of galGal4 to mm10 reads for both IP and inputs samples. To adjust for the variation in mouse cells used for the four conditions from a single experiment, the number of galGal4 reads in the input samples were randomly down-sampled (Picard Tools v1.105 "DownsampleSam") so that the resulting mm10:galGal4 ratio in the four input samples was equal. To generate bigWig coverage files calibrated to the exogenous spike-in, we first randomly down-sampled BAM files containing the mm10 alignments for a particular sample based on the number of reads mapping to the galGal4 genome for that sample (in a manner which results in an equal mm10:galGal4 reads ratio in all samples). BigWig files were subsequently created using the Deeptools (Ramirez et al., 2016) function ‘bamCoverage’ with the options -e and -bs 2. Enriched regions were identified using the MACS2 function ‘callpeak’ (v2.0.10, Zhang et al., 2008) with the genome size set to 1.87 x 109. Peak calling was performed independently for each biological replicate using all uniquely mapped mm10 reads. Regions identified as enriched in more than one sample from any condition were kept for downstream analyses.
Genome_build: mm10.galGal4.fa
Supplementary_files_format_and _content: BigWig files representing genome coverage calibrated to the exogenous spike-in. Reads were extended to fragment size.

extract_protocol:
Chicken DF-1 and mouse ES cells were harvested by trypsinisation. For each experimental condition, 5 x 106 chicken DF-1 cells were added to 5 x 107 mESCs. Cell mixtures were pelleted and resuspended in 1 ml ice-cold RSB Buffer (10 mM NaCl, 10 mM Tris (pH 8.0), 3 mM MgCl2). Chromatin was fragmented by adding 200 units of Micrococcal Nuclease (MNase, Fermentas) and incubating at 37 °C for 5 min. The reaction was stopped by the addition of 8 µl of 0.5 M EDTA and spun at 2348 x g for 5 min at 4 °C. The supernatant containing soluble nucleosomes was collected (S1 fraction). Nucleosomes in the remaining insoluble fraction were extracted by rotating in 300 µl Nucleosome Release Buffer (10 mM Tris pH 7.5, 10 mM NaCl, 0.2 mM EDTA, with 1x cOmpleteTM EDTA-free Protease Inhibitor Cocktail (Roche) and 10 mM sodium butyrate) for 1 h at 4 °C followed by the passing through a 25G needle five times. The supernatant was collected as described above and pooled with the S1 chromatin fraction.   Immunoprecipitations were set up with 100 µl solubilised chromatin and 3 µg of an anti-acetylated histone H3 antibody in a total of 1 ml Native ChIP Incubation Buffer (10 mM Tris pH 7.5, 70 mM NaCl, 2 mM MgCl2, 2 mM EDTA and 0.1% Triton X-100, 1x cOmpleteTM EDTA-free Protease Inhibitor Cocktail and 10 mM sodium butyrate) and rotated overnight at 4 °C. Immune complexes were captured using 20 µl Protein A agarose beads (Roche, previously saturated with 1 mg/ml BSA and 1 mg/ml yeast tRNA) for 1 hour at 4°C with rotation, washed four times with Native ChIP Wash Buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once in TE buffer (10 mM Tris HCl pH 8.0, 1 mM EDTA) and subsequently eluted in 100 µl elution buffer (1% SDS, 0.1 M NaHCO3) by vigorous shaking for 30 min at room temperature. DNA was purified using the ZymoResearch ChIP DNA clean and concentrator kit (Zymo Research) following the manufacturer’s instructions. For input samples, DNA was purified from 100 µl of solubilised chromatin using the same DNA purification procedure.
Automated library preparation was performed on 5 ng input material using the Apollo prep system (Wafergen, PrepX ILMN 32i, 96 sample kit) and standard Illumina multiplexing adapters following manufacturer’s protocol up to pre-PCR amplification. Libraries were PCR amplified (18 cycles) on a Tetrad (Bio-Rad) using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) and in-house single indexing primers. Equivalent amounts of individual libraries were pooled together. Paired-end sequencing was performed using a HiSeq4000 75 bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit), generating a raw read count of >30 million reads per sample.

value: 2 of 2


title: J1.TSA_ATAC_REP1

value: 1 of 4


title: E14_FCS_Jarid2.mapUnique

description:
ChIP for Jarid2 in E14 cells from Perino et al 2018
processed data file:
E14_FCS_Jarid2.mapUnique.bw
GSM3021208
GSM3021209

value: Novus Biologicals NB100-2214, Lot E2


title: J1.DMSO_ATAC_REP1


title: E14_FCS_Input.mapUnique

description:
Input gDNA for reference from Perino et al 2018
processed data file:
E14_FCS_Input.mapUnique.bw
GSM2472755


title: TKO.TSA_Nat.ChIP.Input_REP2

description: Input control for native ChIP-seq


title: J1.TSA_Nat.ChIP.Input_REP2

description: Input control for native ChIP-seq


title: E4_FCS_226_Ezh2_A.mapUnique

value: Jarid2 KO

value: EED 226


title: E14_FCS_H3K4me3.mapUnique

description:
ChIP for H3K4me3 in E14 cells from Perino et al 2018
processed data file:
E14_FCS_H3K4me3.mapUnique.bw
GSM2472745
GSM2472746

value: Abicam Ab858, lot GR240214-4


title: E4_FCS_226_Ezh2.mapUnique


title: J1.DMSO_Nat.ChIP.Input_REP2

description: Input control for native ChIP-seq


title: E14_FCS_Ring1b.mapUnique


title: E14_FCS_Mtf2.mapUnique

description:
ChIP for Mtf2 in E14 cells from Perino et al 2018
processed data file:
E14_FCS_Mtf2.mapUnique.bw
GSM2472747
GSM2472748

value: Aviva System Biology ARP34292, lot QC49692-42166


title: iHep_4a2_2_EGS_Foxa2_164

value: mouse embryonic fibroblasts

value: iHep


title: iHep_4a2_1_EGS_Foxa2_R164


title: TKO.TSA_Nat.ChIP.Input_REP1

description: Input control for native ChIP-seq

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: 1 of 2


title: E14_FCS_226_Ring1b_B.mapUnique

description:
ChIP for Ring1b in E14 cells treated with Eed226
processed data file:
E14_FCS_226_Ring1b.mapUnique.bw


title: TKO.DMSO_Nat.ChIP.Input_REP1

description: Input control for native ChIP-seq

value: control DMSO treatment


title: E14_FCS_226_Ring1b_A.mapUnique


title: J1.TSA_Nat.ChIP.Input_REP1

description: Input control for native ChIP-seq

value: wild type


title: E14_FCS_226_Mtf2_A.mapUnique

description:
ChIP for Mtf2 in E14 cells treated with Eed226
processed data file:
E14_FCS_226_Mtf2.mapUnique.bw


title: J1.DMSO_Nat.ChIP.Input_REP1

description: Input control for native ChIP-seq


title: iHep_4a1_2_Foxa1_R225

value: infected with Foxa1, Hnf4alpha


title: E14_FCS_226_Ring1b.mapUnique


title: iHep_4a1_2_EGS_input_R170

value: none (input)


title: TKO.TSA_H3ac_REP2

description: acetyl-H3 native ChIP-seq

value: 5 ng/µl Trichostatin A for 36 h

value: 10:1 with Chiken DF-1 cells

value: pan-acetyl H3 (Millipore, 06-599, lot 2768436)


title: E14_FCS_226_Jarid2_B.mapUnique

description:
ChIP for Jarid2 in E14 cells treated with Eed226
processed data file:
E14_FCS_226_Jarid2.mapUnique.bw

value: WT


title: TKO.DMSO_H3ac_REP2

description: acetyl-H3 native ChIP-seq

value: 2 of 2


title: iHep_4a1_2_input_R225.


title: iHep_4a3_3_input_R170

value: infected with Foxa3, Hnf4alpha


title: iHep_4a3_3_Hnf4a_R170


title: J1.DMSO_H3ac_REP2

description: acetyl-H3 native ChIP-seq


title: E14_FCS_H3K27me3.mapUnique

description:
ChIP for H3K27me3 in E14 cells from Perino et al 2018
processed data file:
E14_FCS_H3K27me3.mapUnique.bw
GSM2472743
GSM2472744


title: TKO.TSA_H3ac_REP1

description: acetyl-H3 native ChIP-seq


title: E14_FCS_226_Jarid2_A.mapUnique

value: EED 226

value: Novus Biologicals NB100-2214, Lot E2


title: iHep_4a3_3_Foxa3_R170


title: E14_FCS_Ezh2.mapUnique

description:
ChIP for Ezh2 in E14 cells from Perino et al 2018
processed data file:
E14_FCS_Ezh2.mapUnique.bw
GSM2472741
GSM2472742

value: Diagenode C15410039, lot 003


title: E14_FCS_226_Jarid2.mapUnique


title: iHep_4a1_2_EGS_Foxa1_R170

value: mouse embryonic fibroblasts


title: E14_FCS_226_Mtf2_B.mapUnique

value: Aviva System Biology ARP34292, lot QC49692-42166


title: iHep_4a1_1_EGS_input_R164

value: iHep


title: J1.TSA_H3ac_REP2

description: acetyl-H3 native ChIP-seq


title: E14_FCS_226_Mtf2.mapUnique


title: TKO.DMSO_H3ac_REP1

description: acetyl-H3 native ChIP-seq

value: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/- TKO

value: 1 of 2


title: E14_FCS_226_Ezh2_B.mapUnique

description:
ChIP for Ezh2 in E14 cells treated with Eed226
processed data file:
E14_FCS_226_Ezh2.mapUnique.bw


title: J1.TSA_H3ac_REP1

description: acetyl-H3 native ChIP-seq

value: wild type


title: J1.DMSO_H3ac_REP1

description: acetyl-H3 native ChIP-seq

value: control DMSO treatment


title: iHep_4a2_1_input_R215.

value: infected with Foxa2, Hnf4alpha

value: none (input)


title: iHep_4a2_1_Hnf4a_R242


title: E14_FCS_226_Ezh2_A.mapUnique


title: iHep_4a1_1_Hnf4a_R225

value: infected with Foxa1, Hnf4alpha


title: iHep_4a1_1_input_R225.


title: grass-fed2

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

institute: Northwest A&F University

data_processing:
To merge the sequencing data for same individual.
Raw reads were processed by removing adapters and low quality reads, and using FastQC (Version 0.11.5) to perform qualify control.
For RNA-seq, reads after filtered were mapped to Bos taurus reference genome (ARS-UCD1.2) using Hisat2-2.1.0
Genome_build: Bos taurus reference genome (ARS-UCD1.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (G1 for grass-fed and  G2 for grain-fed)

source_name: liver

extract_protocol:
Total RNA was extracted and purified from liver samples using the RNAeasy® Plus Mini Kit (Qiagen, Valencia, CA) according to the manual instruction.
The cDNA libraries were built using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: After post-weaning, Wyu Angus cattle were raised by two method: grass-fed (mainly including alfalfa, hay or grass pasture) and grain-fed (mainly including corn silage, shelled corn, soybean and minerals, etc)

tag: breed

value: Wyu Angus

value: liver

tag: diet

value: grass

tag: age

value: 21 months old


title: iHep_4a2_1_Foxa2_R215


title: iHep_4a1_1_Foxa1_R225


title: MoeN_01

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
 Total RNA was extracted from three replicates of dorsophila ovaries of given genotype with TRI Reagent (Millipore-Sigma) according to the manufacturer protocol. The RNA-seq library was prepared by using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced with the HiSEq 2500 sequencing platform (performed at the NYUAD Sequencing Center). All of the subsequent analysis, including quality trimming, was executed using the BioSAILs workflow execution system. The raw reads were quality trimmed using Trimmomatic (version 0.36) to trim low quality bases, systematic base calling errors, as well sequencing adapter contamination. FastQC was used to assess the quality of the sequenced reads pre/post quality trimming. Only the reads that passed quality trimming were retained for downstream analysis. The quality trimmed RNAseq reads were aligned to the Drosophila_melanogaster BDGP6 release 81 (ENSEMBL genomes) using HISAT2 (version 2.0.4). The resulting SAM alignment files for each sequenced sample were then converted to BAM format and sorted by coordinate using SAMtools (version 0.1.19). The BAM alignment files were processed using HTseq-count using the reference annotation file to produce raw counts for each sample. The raw counts were then analyzed using the online analysis portal NASQAR (http://nasqar.abudhabi.nyu.edu/) in order to merge, normalize and identify differentially expressed genes. Differentially expressed genes by at least 2-fold (log2(FC)≥1 and adjusted p-value of <0.05 for upregulated genes and log2(FC)≤-1 and adjusted p-value of <0.05 for downregulated genes) between each genotype were subjected to Gene Ontology (GO) enrichment using DAVID Bioinformatics (https://david.ncifcrf.gov/). Venn diagram was produced by Bioinformatics & Evolutionary Genomics platform (http://bioinformatics.psb.ugent.be/webtools/Venn/).
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Fly strains were maintained and crosses were carried out on standard cornmeal, yeast, sucrose Drosophila medium at 25°C.

extract_protocol:
TRIzol was used to isolate total RNA
The RNA-seq library was prepared by using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced with the HiSEq 2500 sequencing platform (performed at the NYUAD Sequencing Center).

treatment_protocol: The total RNA-seq preparation was performed from three replicates of 3-day-old fly ovaries of 10 females/genotype (moe[G0415]/w[1118], moe[NES]/w[1118] and moe[NES]/moe[G0415]) (by using the Trizol method as described in (Kristó et al. 2017).

value: ovaries

value: 3 days


title: MoeN_03


title: MoeN_02


title: MoeGMoeN_03

value: mutant (moe[G0415]/moe[NES])


title: grass-fed1


title: MoeGMoeN_02


title: iHep_4a2_1_input_R242.

value: mouse embryonic fibroblasts


title: 48hr_4a3_1_input_R209.

value: infected with Foxa3, Hnf4alpha

value: 48hr after transfection


title: 48hr_4a3_1_Hnf4a_R209


title: MoeGMoeN_01


title: MoeG_03

value: heterozygous null (w[1118]moe[G0415])


title: E14_FCS_226_Ezh2.mapUnique

tag: cell line

value: WT

value: EED 226

value: Diagenode C15410039, lot 003


title: grain-fed2

tag: tissue

value: grain

value: 14 months old


title: 48hr_4a2_1_input_R209

value: infected with Foxa2, Hnf4alpha

value: none (input)


title: MoeG_01

tag: genotype


title: MoeG_02


title: grain-fed1

value: Wyu Angus

value: liver


title: 48hr_4a2_1_Hnf4a_R209

tag: transfection


title: 48hr_4a2_1_Foxa2_R209

tag: Stage


title: 48hr_4a3_1_Foxa3_R209

tag: antibody