title: ZNF184_eCLIP_Replicate1

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

growth_protocol: 293T cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, cells were crosslinked with UV (254 nm, 400 mJ/cm2). Cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen.

tag: antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog


title: tissue WT input repeat 2

status: Public on Oct 06 2016

type: SRA

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

description: sample name: hj44

library_source: genomic

data_processing:
For the H3K36me2 and H3K36me3 ChIP, there are all with yeast chromatin as spike-in references. All these spike-in samples were aligned to a combined hg19/sacCer3 genome and reads were separated into each organism post-alignment. For the H3.3M36 ChIP, paired-end reads were aligned to the human genome (hg19) using the Bowtie2 software. For the further analysis, the consistent pair reads were used. Sequence reads from RNA-seq samples were aligned to the human genome hg19 and to gene annotations from Refseq gene using TopHat v2.05.
The genome-wide read coverage was calculated by BEDTools and in-house Perl programs.
To identify the genes showing differential occupancy of H3K36me2 and H3K36me3 marks between H3F3B WT or H3F3B K36M mutant cells or tissues, the number of reads in gene body was counted by BEDTools, the corresponding yeast chromation reads were used to do normalization, then DESeq differential read count analysis was performed. For the RNA-seq, Cufflinks v2.0.2 was used to calculate FPKM values of genes. Differential gene expression was analyzed by Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization reads density. For spike-in samples, the scores is the reference-adjusted reads per million (RRPM). For H3.3M36 ChIP, the scores means standard Reads Per Million.

molecule: genomic DNA

organism: Homo sapiens

source_name: tissue

growth_protocol: The immortalized human juvenile costal chondrocyte cell line, T/C 28a2, was cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic solution. T/C 28a2 cells were differentiated in the DMEM medium supplemented with 5% FBS, 1% antibiotic solution, 50 μg/ml ascorbic acid, 10 mM β-glycerol-phosphate, and 1X Insulin-Transferrin-Selenium (ITS) (Invitrogen, Carlsbad, CA) as previously described (3).  Human primary bone cells were generated from surgical waste of bone tissues collected from the patients undergoing elective orthopedic procedures at Mayo Clinic (Rochester, MN) under IRB approved protocol (IRB# 13-005619). Bone tissues were trypsinized overnight, washed thoroughly with PBS, and minced using a scalpel. The minced tissues were incubated in Advanced MEM supplemented with 10% FBS and 1% antibiotic solutionat 37°C and 5% CO2. The primary osteoblasts and osteocytes were plated into new culture dishes and were cultured for 3 passages at which time they become references/control cells for primary human chondroblastomas in ChIP-seq and RNA-seq assays.

extract_protocol:
The frozen tissues were cut and divided into 50 mg aliquots and stored in tubes at -80°C. The frozen tissues were homogenized on ice for 15–30 seconds in 500 μL 1X PBS using a tissue grinder (ACTGene, Piscataway, NJ). Tissue homogenates or cultured cells were cross-linked to final 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktails (Sigma, St. Louis, MO), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 sec on / 30 sec off) using Bioruptor Twin (UCD-400) (Diagenode, Inc., Denville, NJ) and centrifuged at 21,130 x g for 10 min. The cleared supernatant equivalent to 10–20 mg of tissue or 1–2x106 cells was incubated with 2 ug of rabbit polyclonal anti-H3K36me3 antibody (Active Motif, Carlsbad, CA, Cat.# 61101) or 1.5 ug of rabbit monoclonal anti-H3K36me2 antibody (Cell Signaling Technology, Danvers, MA, Cat.#2901) on rocker overnight. After adding 30 μL protein G-magnetic beads (Life technologies, Carlsbad, CA), the reactions were incubated for 3 hours. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH8.0,0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatins were eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA) after the treatment of RNase A and proteinase K.For RNA-seq, total RNA was extracted using the miRNeasy Mini kit (Qiagen, Valencia, CA).
ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN, San Carlos, CA). The ChIP-seq libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN) according to the manufacture’s instruction, and were sequenced on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

tag: cell type

value: primary bone cells (generated from surgical waste of bone tissues)

tag: mutation

value: WT

tag: media

value: frozen tissues

tag: cell cycle stage

value: asynchronization

tag: chip antibody

tag: spike-in

value: yeast reference chromatin


title: ZNF184_input

city: La Jolla

library_source: transcriptomic

molecule: total RNA

tag: cell line


title: 1771013108_H11

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: MouseEmbryoMoleculeCounts.cef

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position. We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC mm10 and UCSC hg19
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell identified by the "Title" field in Samples list. Mitochondrial genes and genes with less than 4 molecules have been omitted. The first two lines of each file are table metadata (see https://github.com/linnarsson-lab/ceftools)

molecule: polyA RNA

organism: Mus musculus

source_name: ventral midbrain

growth_protocol: Wild-type CD1 mice were mated overnight and noon of the day was considered E0.5. Mothers were killed and embryos were dissected out of the uterine horn between the time points E11.5 and E18.5. Adult CD1 animals were dissected at P19 to P27. Human tissue was collected at Addenbrooke’s Hospital (Cambridge, UK) and dissected in HIBERNATE medium (Gibco). Samples were shipped overnight on ice (in HIBERNATE solution) to Sweden. For the embryonic stem cells (hES DA),  iCell DopaNeurons from Cellular Dynamics International (DNC-301030001, lot #6003358) were differentiated following the manufacturer’s recommendations and harvested at day 5 and 21.

extract_protocol:
Human embryo ventral midbrain dissection was performed on ice in neuronal N2 culturing media. 10-17  tissue pieces were collected for each experiment. The tissue pieces were dissociated using the Papain dissociation system (Worthington) following manufacturers recommendations, adjusting incubation time based on tissue piece size to 25-45 mins. Using glass pipettes of increasingly smaller tip diameter, the cell suspension was then filtered with 20um filter (Partec) and cells kept in N2 media, and cells loaded into C1 chips for cell capture.
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C using the “Cell Load (1772x/1773x)” script. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave 3’ fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.

tag: tissue

value: ventral midbrain

tag: Sex

tag: age

tag: strain

tag: inferred cell type

value: mNbDA


title: ZNF184_eCLIP_Replicate2


title: cell line K36M #1 spike-in input repeat 1

description: sample name: hj84

source_name: whole cell

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

value: DMEM


title: cell line K36M #1 k36me3 ChIP-Seq repeat 1

description: sample name: hj68

value: H3K36me3 (Active Motif, catalog# 61101 lot # 32412003)


title: VIM_input


title: cell line WT spike-in input repeat 2

description: sample name: hj130


title: VIM_eCLIP_Replicate2

value: VIM


title: BRD4 siRNA rep1

city: Göttingen

first: Steven

middle: A

last: Johnsen

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

country: Germany

institute: University Medical Center Göttingen

data_processing:
The reads were mapped to the human reference transcriptome (UCSC HG19) using Bowtie2 2.1.0 (Langmead and Salzberg, 2012).
Read counts for each sample and each gene were aggregated using a custom Ruby script.
DESeq (version 1.14.0) was used for the measuring differential expression (Anders and Huber, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample.

source_name: MCF10A normal breast epithelial cells breast cancer cells

growth_protocol: MCF10A (human mammary epithelial) cells were obtained from M. Oren (Weizmann Institute of Science, Israel) and were grown in phenol red-free DMEM/F12 medium supplemented with 5% horse serum, 20 ng/mL epidermal growth factor, 0.1 µg/ml Cholera toxin, 10 µg/mL insulin, 0.5 µg/mL hydrocortisone, 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C under 5% CO2

extract_protocol:
Trizol mediated RNA isolation method was used for harvesting RNA.
500 ng RNA was used for library preparation and libraries were made using the kit TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS–122–2002)

treatment_protocol: After 2 days, the cells were harvested for RNA upon negative control siRNA (siCont), BRD4 siRNA (siBRD4) or JQ1 treatment. 250 nM JQ1 was treated to the cells for 3 days.  JQ1 treated cells were also transfected with negative control siRNA.

value: Human normal breast epithelial cells

tag: passages


title: RNF219_eCLIP_Replicate1


title: BRD4 siRNA rep2


title: VIM_eCLIP_Replicate1


title: JQ1 rep1


title: 1771013108_F05

description: MouseEmbryoMoleculeCounts.cef

value: mRN


title: 1771013108_E08

description: MouseEmbryoMoleculeCounts.cef


title: NUMA_input


title: AIFM_input


title: NUMA_eCLIP_Replicate2


title: Control siRNA rep2


title: 1771013108_E01

description: MouseEmbryoMoleculeCounts.cef

value: mNProg


title: cell line WT spike-in input repeat 1

description: sample name: hj82


title: RANGAP_input


title: RANGAP_eCLIP_Replicate2


title: 1771013108_A05

description: MouseEmbryoMoleculeCounts.cef


title: RANGAP_eCLIP_Replicate1


title: AIFM_eCLIP_Replicate1

value: AIFM


title: 1771013108_B10

description: MouseEmbryoMoleculeCounts.cef


title: RNF219_Input


title: AIFM_eCLIP_Replicate2


title: 1771013013_H01

description: MouseEmbryoMoleculeCounts.cef

value: pooled male and female

value: mUnclassified


title: S17-4_TH17 OX40L treated

city: Houston

first: xiang

last: xiao

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat2
Transcripts FPKM were calculated by Cufflink using Reference Annotation: mm9.gtf from UCSC
Differential gene expression were called by CuffDiff using Reference Annotation: mm9.gtf from UCSC
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: OX40L treated_In vitro Th17

extract_protocol:
For total RNA preparation, 5 million CD4+ T cells cultured under Th17-polarizing conditions were collected for RNA extraction using the miRNAeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD4+ T cell

value: 6-8 weeks

tag: genotype

value: wild type

tag: culture protocol

value: in the presence of OX40L-TG APCs


title: S17-3_TH17 Ctrl

source_name: Ctrl_In vitro Th17

value: in the presence of WT-APCs


title: 1771013013_E04

description: MouseEmbryoMoleculeCounts.cef

value: ventral midbrain


title: 1771013013_E12

description: MouseEmbryoMoleculeCounts.cef

value: mNbM


title: 4C noPhenotype KCNJ2TSS

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

data_processing:
Library strategy: 4C-Seq
4C-seq reads were cleaned of the primer sequence and mapped to a corresponding reference (GRCh37/hg19 or NCBI37/mm9) using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr11:108500000-115000000 and the human region chr17:67000000-75000000.
To calculate read count profiles the viewpoint and adjacent fragments 1.5 kb up- and downstream were removed. A sliding window of 10 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we obtained the log2 fold change for each window of normalized reads.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bedgraph files of the coverage and the calculated ratios

source_name: human skin fibroblasts

extract_protocol:
4C-seq libraries were generated from microdissected tissues or cells as described previously (van de Werken et al., 2012). DpnII was used as primary, BfaI as secondary restriction enzymes (Csp6I and NlaIII for human samples). For each viewpoint, a total of 1.6 mg of each library was amplified in 8 or 16 PCR reactions, depending on PCR efficiencies. Samples were multiplexed and sequenced with Ilumina Hi-Seq technology. The following primers were used: Sox9-TSS_1 CCACGAAAGTGTGTTTATATTCT   Sox9-TSS_2 TGGCTATTGTTTGTAAATCTCTT  Kcnj2-TSS_1 CGGTGGTGGAGAGAAAGA   Kcnj2-TSS_2 TCACCAAACAACCTCTACAAA  LacZ_1 TCCGACTTCAACTGTAGGG  LacZ_2 GCAGAGCCATCTATTGCTTA  BOR-Sox9tel_1 TTTGACTCCAAGGACCAGA  BOR-Sox9tel_2 TGTGTAAAGGCGGACAGA  Sox9-TAD_1 AACTGGGTATAGTGTGGAGAGA  Sox9-TAD_2 GGACATCAATGGAACATAGC  BOR-Kcnj/Sox9_1 AATGCTGTGGACATCCTG  BOR-Kcnj/Sox9_2 TCCGTCAAGTTCCATGTG  Kcnj-TAD_1 TCTGTGCCAAATGAACTATTCT  Kcnj-TAD_2 AGCACCATCTGTCCTCCTAT  BOR-Kcnjcen_1 AAGAAGAGGGGCTCAAAAT  BOR-Kcnjcen_2 CTGATTGGCATGGGATAGT  SOX9-TSS_1 TCCAAGTGTGTAAGTTTGTCG  SOX9-TSS_2 AATCTCCTGGACCCCTTC  KCNJ2-TSS_1 TTCAGTGAACGTATTTGTTGAA  KCNJ2-TSS_2 GAGCGTTTGATGTTTTACCA
Samples were multiplexed and sequenced with Ilumina Hi-Seq technology using 100bp paired-end or single end reads according to the manufacturer´s protocol.

value: Duplication/ no phenotype

tag: viewpoint


title: 4C noPhenotype SOX9TSS

value: SOX9 TSS


title: 4C noPhenotype Breakpoint

value: Breakpoint


title: 4C WT BorSox9tel

data_processing:
4C-seq reads were cleaned of the primer sequence and mapped to a corresponding reference (GRCh37/hg19 or NCBI37/mm9) using BWA-MEM (v0.7.12-r1044) with default settings.
4C-seq contacts were analyzed in the murine region chr11:108500000-115000000 and the human region chr17:67000000-75000000.
To calculate read count profiles the viewpoint and adjacent fragments 1.5 kb up- and downstream were removed. A sliding window of 10 fragments was chosen to smooth the data and data was normalized to reads per million mapped reads (RPM).
To compare interaction profiles of different samples, we obtained the log2 fold change for each window of normalized reads.
Genome_build: mm9, hg19

Supplementary_files_format_and_content: bedgraph files of the coverage and the calculated ratios

source_name: E12.5 limb buds

value: WT

value: Bor (Sox9 tel)


title: 4C SexRev470kb SOX9TSS

source_name: human ovotestes fibroblasts

value: 46, XX Sex Reversal


title: Control siRNA rep1

value: Human normal breast epithelial cells


title: 4C SexRev470kb KCNJ2TSS


title: 1771013013_C05

description: MouseEmbryoMoleculeCounts.cef


title: 4C WT BorSox9Kcnj

value: Bor (Sox9/Kcnj)


title: 4C SexRev Breakpoint


title: NUMA_eCLIP_Replicate1

tag: antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog


title: 4C DupL Sox9TSS

value: Dup-L

value: Sox9 TSS


title: 4C Ctrl KCNJ2TSS

value: Control

value: KCNJ2 TSS


title: 4C DupL Kcnj2

value: Kcnj2 TSS


title: 4C Cooks SOX9TSS

value: Cooks Syndrome


title: 1771013013_G06

description: MouseEmbryoMoleculeCounts.cef

value: ventral midbrain

value: pooled male and female


title: 4C Cooks KCNJ2TSS


title: 4C DupC Kcnj2TSS

value: Dup-C


title: H3K27ac rep2

description: Cells were crosslinked with 1 % formaldehyde for 10 minutes.

data_processing:
The reads were mapped to the human reference genome (UCSC HG19) using Bowtie (version 1.0.0) (Langmead et al., 2009).
Peak-calling was done by Model based analysis of ChIP-seq (MACS version 1.4.2) (Zhang et al., 2008).
Coverage was normalized on the total number of mapped reads per hundred million.
Input files were previously submitted under the acccession number  GSE65886.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are generated from wiggle files from MACS. Scores represent number of normalized reads per hundred million.

source_name: MCF10A breast

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

tag: cell type

tag: chip-seq antibody

value: H3K27ac , Diagenode pAb-196-050


title: 4C Dup-L LacZ

value: LacZ


title: 1771013013_B11

description: MouseEmbryoMoleculeCounts.cef


title: H3K27ac rep1


title: 1771013013_D02

description: MouseEmbryoMoleculeCounts.cef

value: mNbM


title: BRD4 rep3

value: BRD4 N-terminal antibody kindly provided by Prof. Cheng Ming Chiang (4 µl used)


title: 4C Dup-C Sox9TSS


title: 4C SexRev470kb Breakpoint

value: 46, XX Sex Reversal

value: Breakpoint


title: 4C Ctrl SOX9TSS

value: SOX9 TSS


title: Vehicle_3357

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Division of Cardiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
FASTq files were aligned with Tophat2 and quantified using Cufflinks
Genome_build: rn4
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: ventricle cardiac myocyte

growth_protocol: Cardiomyocytes isolated from the ventricles of neonatal rat hearts were plated on 10cm plastic dishes coated with 0.2% gelatin at a density of 160,000 cells/ml in 12 ml of media.

extract_protocol:
RNA was isolated from NRVMs using the High Pure RNA Isolation Kit (Roche)
NA was submitted to the WITG for library preparation (TruSeq Stranded mRNA Library Prep Kit, Illumina)

treatment_protocol: One day after isolation, NRVMs were treated with control micro RNA mimic or miR-9 mimic (25nM) then 24 hrs after miR treatment, the cells were washed and treated with phenylepherine (10µM) or vehicle. After 48 hours of stimulation, cells were harvested for RNA seq analysis

value: neonatal

tag: treatment

value: vehicle control

value: wildtype


title: BRD4 rep2

value: Human normal breast epithelial cells


title: Vehicle_3359


title: Vehicle_3358


title: PE_3352

value: phenylepherine treatment


title: NRVM_WCE_R1

description: ChIP-Seq whole cell extract (WCE) input control in NRVM

data_processing:
Sequenced reads were aligned to RN4 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: rn4
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

source_name: neonatal rat ventricular myocytes (NRVM)

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin-DNA complexes were isolated with antibody.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: One day after isolation, NRVMs were treated with control micro RNA mimic or miR-9 mimic (25nM) then 24 hrs after miR treatment, the cells were washed and treated with phenylepherine (10µM) or vehicle.  After 48 hours of stimulation, cells were harvested for ChIP seq analysis.

value: NRVM

tag: input

tag: barcode

value: GTGAAA

tag: antibody maker

tag: antibody catalog number


title: NRVM_RNA_POL2_R1

description: ChIP-Seq for RNA Pol II in NRVM

tag: cell line

value: ATGTCA

value: anti RNA Pol II N-term

value: Santa Cruz


title: NRVM_PE_WCE_R1

value: GTGGCC


title: NRVM_PE_MIR9MIMIC_WCE_R1

value: GTTTCG


title: NRVM_PE_POL2_R1

description: ChIP-Seq for RNA Pol II in NRVM

value: phenylepherine

value: CCGTCC


title: 4C WT BorKcnjcen

value: WT

tag: age

value: Bor (Kcnj cen)


title: PE_mir9_3354

value: mir9 mimic


title: PE_mir9_3356

value: neonatal


title: PE_mir9_3355


title: GROseq_LNCaP_TNFa_rep1

status: Public on Oct 05 2016

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Library strategy: GRO-seq
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Peak calling was done using findPeaks tool of HOMER software (V 4.7.2; http://homer.salk.edu/homer/) with default parameters and chromatin input sample as a control . Bed files were done using pos2bed.pl tool.
BedGraph files were done using HOMER software (V 4.7.2; http://homer.salk.edu/homer/) by combining two replicates and normalizing total number of reads to 10 million. GROseq signal is divided between plus- and minus-strand signals in separate files.
Genome_build: hg19
Supplementary_files_format_and_content: Common binding sites of two biological replicates as bed files are provided for ChIP-seq samples where peaks were detected. Signal intensities as tdf files are provided for GRO-seq data (minus and plus-strand signals in separate files) and ChIP-seq samples for which the peak detection was not reliable due to low signal enrichment (androgen receptor in DMSO and TNF-alpha; p65 in DMSO and DHT).

molecule: nuclear RNA

source_name: prostate cancer

growth_protocol: LNCaP cells (from ATCC) were grown in RPMI1640 (Gibco) supplemented with 10 % fetal bovine serum, 1 % penicillin/streptomycin, and 2 mM l-glutamine.

extract_protocol: Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

treatment_protocol: Cells were maintained in RPMI 1640 medium with 10% charcoal-stripped for two days to deplete androgens actions and then exposed to vehicle (DMSO), DHT (100 nM 5a-dihydrotestosterone), TNF-alpha (1000 U/ml), or DHT and TNF-alpha for two hours. FOXA1 silencing was done by reverse-transfecting LNCaP cells with siRNAs against FOXA1 or control siRNA (Dharmacon; On-TARGETplus pool or non-targeting pool) with Lipofectamine RNAiMAX transfection reagent. Experiments were performed four days after transfection.

value: LNCaP

tag: treatment 1

value: TNF-alpha (1000 U/ml, 2h)

tag: treatment 2


title: BRD4 rep1

value: Human normal breast epithelial cells

tag: passages

value: BRD4 N-terminal antibody kindly provided by Prof. Cheng Ming Chiang (4 µl used)


title: GROseq_LNCaP_DMSO_rep1

value: DMSO (2h)


title: GROseq_LNCaP_DHT-TNFa_rep2

value: DHT (100nM, 2h) + TNF-alpha (1000U/ml, 2h)


title: PE_3351

value: phenylepherine treatment

tag: genotype

value: wildtype


title: ChIPseq_LNCaP_p65_TNFa_rep1

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Peak calling was done using findPeaks tool of HOMER software (V 4.7.2; http://homer.salk.edu/homer/) with default parameters and chromatin input sample as a control . Bed files were done using pos2bed.pl tool.
BedGraph files were done using HOMER software (V 4.7.2; http://homer.salk.edu/homer/) by combining two replicates and normalizing total number of reads to 10 million. GROseq signal is divided between plus- and minus-strand signals in separate files.
Genome_build: hg19
Supplementary_files_format_and_content: Common binding sites of two biological replicates as bed files are provided for ChIP-seq samples where peaks were detected. Signal intensities as tdf files are provided for GRO-seq data (minus and plus-strand signals in separate files) and ChIP-seq samples for which the peak detection was not reliable due to low signal enrichment (androgen receptor in DMSO and TNF-alpha; p65 in DMSO and DHT).

extract_protocol: Nuclei from approximately 10 million formaldehyde crosslinked (1%; 10min at room temperature) cells were isolated and chromatin was fragmented using sonicator (bioruptor). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and protein-A magnetic beads. DNA fragments were purified and libraries were prepared according to standard Illumina protocol. Samples were sequenced at GeneCore in EMBL (Heidelberg, Germany).

value: anti-p65 (Santa Cruz Biotechnology, sc-372)


title: ChIPseq_LNCaP_p65_DMSO_rep2


title: NRVM_PE_MIR9MIMIC_BRD4_R1

description: ChIP-Seq for BRD4 in NRVM

value: NRVM

value: phenylepherine and mir9mimic

value: AGTTCC

value: anti BRD4

value: Bethyl


title: NRVM_PE_BRD4_R1

description: ChIP-Seq for BRD4 in NRVM

value: phenylepherine

value: AGTCAA


title: ChIPseq_LNCaP_PIAS1_TNFa_rep2

value: anti-PIAS3+PIAS1+PIAS2 (Abcam, ab77231)


title: ChIPseq_LNCaP_input_rep1

value: LNCaP

value: none (input)


title: NRVM_BRD4_R1

description: ChIP-Seq for BRD4 in NRVM

value: CTTGTA


title: ChIPseq_LNCaP_PIAS1_DMSO_rep2


title: ChIPseq_LNCaP_input_rep2


title: ChIPseq_LNCaP_p65_DHT-TNFa_rep1


title: GROseq_LNCaP_DMSO_rep2


title: GROseq_LNCaP_TNFa_rep2

value: TNF-alpha (1000 U/ml, 2h)


title: ChIPseq_LNCaP_PIAS1_TNFa_rep1


title: ChIPseq_LNCaP_FOXA1_DHT_rep2

value: anti-FOXA1 (Abcam, ab23738)


title: ChIPseq_LNCaP_FOXA1_DMSO_rep1

value: DMSO (2h)


title: GROseq_LNCaP_DHT_rep2


title: GROseq_LNCaP_DHT_rep1


title: JQ1 rep2

value: Human normal breast epithelial cells


title: ChIPseq_LNCaP_p65_TNFa_rep2


title: ChIPseq_LNCaP_FOXA1_DHT-TNFa_rep2

value: DHT (100nM, 2h) + TNF-alpha (1000U/ml, 2h)


title: ChIPseq_LNCaP_AR_TNFa_rep1

value: anti-AR (Karvonen et al., 1997)


title: ChIPseq_LNCaP_p65_DHT_rep2

value: anti-p65 (Santa Cruz Biotechnology, sc-372)


title: ChIPseq_LNCaP_AR_DHT_rep1


title: ChIPseq_LNCaP_p65_DHT-TNFa_rep2


title: ChIPseq_LNCaP_p65_DHT_rep1


title: ChIPseq_LNCaP_AR_DHT-TNFa_rep2


title: GROseq_LNCaP_DHT-TNFa_rep1


title: ChIPseq_LNCaP_PIAS1_DHT_rep2


title: ChIPseq_LNCaP_PIAS1_DMSO_rep1


title: ChIPseq_LNCaP-siNON_p65_TNFa_rep2

value: control siRNA transfection


title: ChIPseq_LNCaP_FOXA1_DHT-TNFa_rep1


title: ChIPseq_LNCaP_PIAS1_DHT-TNFa_rep2


title: EPRS shRNA 74 Replicate 3

first: XIANXIAO

last: ZHOU

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

description: Sample 11

data_processing:
The pair-ended sequencing reads were aligned to human genome hg38 using star aligner (version 2.5.0b).
Following read alignment, featureCounts was used to quantify gene expression at the gene level based on GENCODE gene model release 22.
Read counts were further processed and normalized using packages edgeR and limma to obtain normalized and log2 transformed expression levels.
Genome_build: hg38
Supplementary_files_format_and_content: Read counts in tab delimited

source_name: Tam resistant MCF7

growth_protocol: MCF7 TamR cells, obtained from the Rachel Schiff Lab (Houston, TX), were cultured in phenol red-free RPMI media (Life Technologies) with 10% charcoal-stripped fetal bovine serum (FBS) (Sigma), one percent penicillin/streptomycin (Life Technologies), and 100nM 4-hydroxytamoxifen (4-OHT). 4-OHT was withdrawn for functional assays.

extract_protocol:
Seventy-two hours after infection, cells were lysed and total RNA was purified using a Qiagen RNeasy kit according to the manufacturer’s protocol.
RNA was stored at -80°C until submission to the Mount Sinai Genomics Core Facility for ribosomal RNA depletion, cDNA library preparation, and sequencing using paired-end, 100nt reads on an Illumina HiSeq 2000.
Ribosomal RNA depletion

treatment_protocol: For siRNA, cells were reverse-transfected with 20nM siRNA using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s protocol. Media is changed after overnight incubation.  Pre-validated EPRS shRNAs in the pLKO.1 vector were obtained from Sigma. For shRNA lentivirus production, 293T cells were transfected with viral plasmids using Lipofectamine 2000 according to standard protocols. Virus-containing supernatant was collected at 48, 72, 96, and 120 hours after transfection, pooled, and frozen at -80°C to eliminate carry-over 293T cells. For shRNA lentivirus infection of target cells, lentivirus was thawed on ice and concentrated using centrifugal filters (Amicon). ShRNA lentivirus and target cells were simultaneously added to six-well plates, centrifuged at 2250rpm for 30 minutes at room temperature, then incubated at 37°C overnight. Media was changed the next morning and cells were allowed to recover for six to eight hours, after which two μg/mL puromycin was added to select shRNA-expressing cells. Puromycin was reduced to a maintenance dose of one μg/mL after 24-48h. After cells expressing EPRS shRNA vectors being generated, MCF7 TamR cells were infected with control or one of three unique EPRS shRNA sequences.

value: EPRS shRNA 74

tag: phenotype

value: Tamoxifen Resistance


title: ChIPseq_LNCaP_PIAS1_DHT-TNFa_rep1

tag: antibody


title: EPRS shRNA 84 Replicate 3

description: Sample 12

value: EPRS shRNA 84


title: ChIPseq_LNCaP_FOXA1_TNFa_rep2


title: ChIPseq_LNCaP_AR_DHT_rep2


title: EPRS shRNA 73 Replicate 3

description: Sample 10

value: EPRS shRNA 73


title: ChIPseq_LNCaP_p65_DMSO_rep1


title: ChIPseq_LNCaP_FOXA1_TNFa_rep1


title: ChIPseq_LNCaP_FOXA1_DMSO_rep2


title: EPRS shRNA 73 Replicate 2

description: Sample 6


title: ChIPseq_LNCaP_AR_TNFa_rep2


title: EPRS shRNA 73 Replicate 1

description: Sample 2


title: Empty Vector Replicate 3

description: Sample 9

value: Empty Vector


title: ChIPseq_LNCaP_AR_DMSO_rep1


title: ChIPseq_LNCaP-siNON_p65_TNFa_rep1


title: Empty Vector Replicate 2

description: Sample 5


title: ChIPseq_LNCaP-siFOXA1_p65_TNFa_rep2

value: FOXA1 silencing (siRNA transfection)


title: ChIPseq_LNCaP-siFOXA1_p65_TNFa_rep1

value: LNCaP


title: lung_N3_oxBS

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

country: China

institute: Sun Yat-sen University

description: library strategy: oxBS-Seq

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned by BSmooth bisulfite alignment pipeline (version 0.7.1) as previously described in detail. Briefly, reads were aligned by Bowtie2 (version 2.0.1) against human genome (hg19) as well as the lambda phage genome.
After alignment, methylation measurements for each CpG were extracted from aligned reads. We filtered out measurements with mapping quality < 20 or nucleotide base quality on cytosine position < 10 and we also removed measurements from the 5’ most 10 nucleotides of both mates.
5hmC regions for both normal and tumor groups in each tissue, which actually were DMRs between oxBS-Seq and corresponding BS-Seq libraries were identified using bsseq package in Bsmooth.
Only CpGs with at least coverage of 10 in at least 3 samples within each group were included in our analysis. Smooth window of 70 CpGs or 1 kb, and t-statistic cutoff of -2, 2 and at least 2 CpGs in each hmC region were used in our analysis. After obtaining 5hmC regions, CpGs within 5hmC regions were considered as hydroxymethycytosines (5hmC sites).
Genome_build: hg19
Supplementary_files_format_and_content: text file, methylated read count and total read count at each CpG site and each sample

extract_protocol:
DNA was extracted with DNeasy Blood & Tissue Kit (Qiagen)
4 μg genomic DNA plus spike-in 20 ng hydroxmethylated lambda phage and non-methylated E. coli DNA control (Zymo) in 150 μl water was sheared into ~10 kb fragments using g-Tube (Covaris) following manufacturer’s instructions. And sheared DNA was cleaned up using GeneJET PCR Purification Kit (Thermo Scientific) with a modified protocol (Protocol 03, TrueMethyl Preparation of High Molecular Weight gDNA, http://www.cambridge-epigenetix.com/en_US/resources/application-notes). Then oxidative bisulfite (oxBS) and only bisulfite (BS) converted DNA templates were generated using TrueMethyl 24 Kit (Cambridge Epigenetix) for each sample according to manufacturer’s instructions. Last, oxBS and BS converted DNA were used to construct oxBS-Seq and corresponding BS-Seq libraries using EpiGnome Methyl-Seq Kit (Epicentre) following manufacturer’s instructions.

tag: tissue

value: lung

tag: tumor stage

value: normal


title: lung_T3_BS

value: tumor


title: lung_T2_oxBS

description: library strategy: oxBS-Seq


title: lung_N2_BS


title: lung_T2_BS


title: lung_T1_oxBS

description: library strategy: oxBS-Seq


title: lung_N1_BS


title: lung_T1_BS


title: liver_T4_oxBS

description: library strategy: oxBS-Seq

value: liver


title: ChIPseq_LNCaP_FOXA1_DHT_rep1

value: anti-FOXA1 (Abcam, ab23738)


title: ChIPseq_LNCaP_AR_DMSO_rep2

value: DMSO (2h)


title: EPRS shRNA 74 Replicate 2

description: Sample 7


title: Empty Vector Replicate 1

description: Sample 1


title: EPRS shRNA 84 Replicate 1

description: Sample 4


title: EPRS shRNA 84 Replicate 2

description: Sample 8


title: lung_N2_oxBS

description: library strategy: oxBS-Seq


title: ChIPseq_LNCaP_PIAS1_DHT_rep1

value: anti-PIAS3+PIAS1+PIAS2 (Abcam, ab77231)


title: EPRS shRNA 74 Replicate 1

description: Sample 3


title: liver_T2_BS


title: liver_T1_oxBS

description: library strategy: oxBS-Seq


title: lung_T3_oxBS

description: library strategy: oxBS-Seq


title: liver_T3_BS


title: liver_N2_BS


title: lung_N3_BS


title: lung_N1_oxBS

description: library strategy: oxBS-Seq


title: liver_N1_oxBS

description: library strategy: oxBS-Seq


title: liver_T4_BS


title: lung_N2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned against human genome (hg19) by OSA (version 2.0.1) with default parameters. After alignment, only uniquely aligned reads were kept for further analysis.
Reads count for each gene of all samples were estimated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and then were used to identify differentially expressed (DE) genes using DESeq package. Genes with adjusted p-value < 0.01 and fold-change > 2 between A38-41 and A38-5 were considered as DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: text file, raw read counts of each gene for all samples

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to manufacturer’s manual.


title: lung_T1


title: liver_N4_oxBS

description: library strategy: oxBS-Seq


title: liver_T3_oxBS

description: library strategy: oxBS-Seq


title: liver_T1


title: liver_N2


title: liver_N1


title: E18.5 Mouse Salivary Gland Replicate 2

city: Buffalo

first: Satrajit

last: Sinha

address: 701 Ellicott Street

department: Department of Biochemistry

institute: State University of New York at Buffalo

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) with TopHat2 (v2.0.13),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm9 build were quantified with featureCounts 66, which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.10.1) was used to normalize the read counts and derive FPKM values.
Supplementary_files_format_and_content: Comma separated files containing DESeq2 Median Normalized FPKM values for individual biological samples

source_name: Embryonic Mouse Salivary Gland

extract_protocol:
RNA was harvested from dissected submandibular glands using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain

value: salivary gland

tag: developmental stage

value: embryo


title: 12 week old Mouse Salivary Gland Replicate 2

source_name: Adult Mouse Salivary Gland

value: 12 week old

value: adult


title: E16.5 Mouse Salivary Gland Replicate 2


title: E16.5 Mouse Salivary Gland Replicate 1


title: liver_N3_oxBS

description: library strategy: oxBS-Seq


title: liver_N3_BS


title: liver_N2_oxBS

description: library strategy: oxBS-Seq


title: liver_T2_oxBS

description: library strategy: oxBS-Seq


title: Extracted RNA from Lgr5+ cells replicate 1

city: Utrecht

first: Kay

last: Wiebrands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
To calculate log2 fold-changes, a pseudo count of one was added to the RPM-normalized values
Genome_build: mm10
Supplementary_files_format_and_content: RPM_counts.csv: Processed data for the DCS cells and Lgr5 cells of the 2 biological replicates. Tab separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Transcript counts are normalized per sample to Reads Per Million (RPM). Column name indicates the sample type, DCS for Deep Crypt Secretory cell, Lgr5 for Lgr5-positive cell and 1 and 2 for the different biological replicates. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Colon

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 6ug glycogen (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing

tag: cell type


title: Extracted RNA from Reg4+ DCS cells replicate 2

value: Reg4+ DCS


title: E18.5 Mouse Salivary Gland Replicate 1


title: liver_T1_BS


title: liver_N1_BS


title: lung_T3


title: lung_N3


title: lung_T2


title: shUSP21

city: Shanghai

first: Liu

last: Zhenping

address: 1239 Si Ping Road

institute: Tongji University

data_processing:
Basecalls performed using Illumina CASAVA v1.8.2 at Personalbio-Shanghai (sequencing service provider).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Personalbio-Shanghai (sequencing service provider).
RNA-seq reads for each sample were aligned to the mouse refseq using Tophat version 2.0.14 with parameters –p 8 respectively.
Fragments Per Kilobase of transcript per Million mapped reads(FPKM) were caculated by using Cufflinks v2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: mouse embryonic stem cell

growth_protocol: E14 cells were maintained feeder free on gelatin-coated plastics in mES media (DMEM with 15% FBS (Gibco 10099), 2mM GlutaMAX, 0.1mM non-essential amino acids (NEAA), 0.1mM β-mercaptoethanol, 100 U/ml penicillin and 100 µg/ml streptomycin) supplemented with 1000 U/ml LIF and passaged every 3 days.

extract_protocol:
Total RNA was extracted from each sample using Trizol reagent (TaKaRa) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at Shanghai Personal Biotechnology Co., Ltd..

treatment_protocol: E14 cells were transfected with control or USP21 shRNA. Cells were harveated after 3 days knockdown.

value: USP21 knockdown

value: E14 stem cell line derived from 19/Ola mouse


title: Flag-USP21.fastq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations:bowtie -v 2 -m1
Peaks were called using macs version 1.4.2 with the default parameters plus -p 1e-4.
Genome_build: mm9
Supplementary_files_format_and_content: bed

growth_protocol: E14 cells were maintained feeder free on gelatin-coated plastics in mES media (DMEM with 15% FBS, 2 mM GlutaMAX, 0.1 mM non-essential amino acids (NEAA), 0.1 mM β-mercaptoethanol, 100 U/ml penicillin and 100 µg/ml streptomycin supplemented with 1000 U/ml LIF and passaged every 3 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
5-10 ng of ChIP DNA was used for generation of libraries for deep-sequencing using the NEXTflex™ ChIP-Seq Kit. Briefly, the DNA was end-repaired following adding an A-base to the end-repaired DNA fragments. Illumina adaptors (regular or multiplex) were ligated to the ChIP DNA fragments and 100-300 bp of size fractions were excised from 2% agarose gel. Adaptor-modified fragments library prep was validated in Bioanalyzer for quantity and size before putting into sequencing (The Beijing Genomics Institute, BGI).

value: mouse embryonic stem cells E14

tag: chip-antibody

value: Flag(Sigma,  F3165)


title: liver_N4_BS


title: lung_N1


title: liver_T3


title: liver_N3


title: liver_T2


title: Neutrophil_treated_PMA_and_PAD4i_5h.rep2

city: Palo Alto

first: Xingqi

last: Chen

address: 269 Campus Drive

institute: Stanford University

description: human neutrophl from healthy donor +PMA 5h +PAD4 inhibitor with fixation on slide  with Atto-590 Tn5 after imaging

data_processing:
library strategy: ATAC-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets fromm the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand

source_name: human neutrophl from healthy donor

growth_protocol: ATCC cell lines (GM12878, HT1080) were purchesed from ATCC and maintained in standerd protocol according to the instruction, human neutrophils were purfied from healthy volunteer according to the Stanford IRB protocol and maintained in RPMI-HEPES (10 mM) during 30nM PMA (Phorbol myristate acetate ) and PAD4 inhibitor (200 μM Cl-amidine ) treatment.

extract_protocol:
50K cells were used for ATAC-seq lib in both fixed (1% formaldehyde 10mins at RT ) and unfixed samples. After imaging, ~50K cells were used for ATAC-seq library construction
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit and using custom-made Tn5 transposase ( where Atto-590 labled adaptor)

tag: subject status/id

value: healthy donor

value: human neutrophl from healthy donor  +PMA 5h+PAD4 inhibitor rep2

tag: stimulated with

value: PMA 5h+PAD4 inhibitor

tag: genotype/variation


title: Neutrophil_treated_PMA_and_PAD4i_5h.rep1

treatment_protocol: human neutrophils were purfied from healthy volunteer according to the Stanford IRB protocol and maintained in RPMI-HEPES (10 mM) during 30nM PMA (Phorbol myristate acetate ) and PAD4 inhibitor (200 μM Cl-amidine ) treatment.

value: human neutrophl from healthy donor +PMA 5h+PAD4 inhibitor rep1

value: with fixation on slide  with Atto-590 Tn5 after imaging


title: Neutrophil_donor2_PMA_5h

description: human neutrophl from healthy donor 2 +PMA 5h with fixation on slide  with Atto-590 Tn5 after imaging

source_name: human neutrophl from healthy donor 2

value: healthy donor 2

value: PMA 5h


title: Postnatal Day 5 Mouse Salivary Gland Replicate 1

source_name: Neonatal Mouse Salivary Gland

value: Postnatal Day 5

value: neonatal


title: 4 week old Mouse Salivary Gland Replicate 2

value: salivary gland

value: 4 week old


title: Neutrophil_donor1_PMA_3h

description: human neutrophl from healthy donor 1+PMA 3h with fixation on slide  with Atto-590 Tn5 after imaging

source_name: human neutrophl from healthy donor 1

value: healthy donor 1

value: PMA 3h


title: 4 week old Mouse Salivary Gland Replicate 1

value: adult


title: ChIPseq_LNCaP_AR_DHT-TNFa_rep1

tag: cell line

value: LNCaP

value: DHT (100nM, 2h) + TNF-alpha (1000U/ml, 2h)

value: anti-AR (Karvonen et al., 1997)


title: 12 week old Mouse Salivary Gland Replicate 1

tag: age

value: 12 week old


title: Extracted RNA from Lgr5+ cells replicate 2


title: E14.5 Mouse Salivary Gland Replicate 2

value: embryo


title: E14.5 Mouse Salivary Gland Replicate 1


title: Neutrophil_control_donor1

description: human neutrophl from healthy donor 1 with fixation on slide  with Atto-590 Tn5 after imaging

value: human neutrophl from healthy donor 1

value: none (control)


title: Neutrophil_control_donor2

description: human neutrophl from healthy donor 2 with fixation on slide  with Atto-590 Tn5 after imaging

value: human neutrophl from healthy donor 2


title: Extracted RNA from Reg4+ DCS cells replicate 1

value: Reg4+ DCS


title: Neutrophil_donor1_PMA_5h

description: human neutrophl from healthy donor 1+PMA 5h with fixation on slide  with Atto-590 Tn5 after imaging

value: PMA 5h


title: HT1080_fixed_rep1

description: ATCC Cell line HT1080 with fixation #1

source_name: ATCC Cell line HT1080

value: ATCC Cell line HT1080

value: with fixation #1


title: E14.5 Mouse Salivary Gland Replicate 3

value: salivary gland


title: DroKO

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

country: South Korea

institute: Chonnam National University Medical School

data_processing:
The FASTQ sequences were trimmed to remove the nucleotides with low quality. The nucleotides from 2nd to 37th position were used for further processing.
The trimmed sequences were aligned into the human reference genome (GRCh37/hg19) using Bowtie2 (Langmead and Salzberg, 2012).
Among the aligned reads, those with perfect match into human genome were selected, and converted into bedGraph files.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph files to visualize the aligned reads in the genome browser

source_name: HCT116 cell line

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies). 10 µg of RNA was used to enrich mRNAs with poly(A) tails using oligo(dT) Dynabeads (Life Technologies).
The sequencing libraries were made using TruSeq Stranded Total RNA Library Prep Kit (Illumina). The quality of the libraries was verified by Agilent 2100 Bioanalyzer (Agilent).

tag: ko status

value: knockout of DROSHA


title: WT

value: wild type


title: Input-USP21.fastq

value: mouse embryonic stem cells E14


title: GM12878_home_made_Atto_Tn5_rep1

description: ATCC Cell line GM12878 with Atto-590 Tn5#1

source_name: ATCC Cell line GM12878

value: ATCC Cell line GM12878

value: with Atto-590 Tn5#1


title: GM12878_home_made_Atto_Tn5_rep2

description: ATCC Cell line GM12878 with Atto-590 Tn5#2

value: with Atto-590 Tn5#2


title: GM12878_Illumina_Tn5_rep2

description: ATCC Cell line GM12878 with Illumina Nextera Tn5 #2

value: with Illumina Nextera Tn5 #2


title: GM12878_Illumina_Tn5_rep1

description: ATCC Cell line GM12878 with Illumina Nextera Tn5 #1

value: with Illumina Nextera Tn5 #1


title: RYBPfl/fl.YAF2KO_nucRNA_OHT_rep3

city: London

first: Hamish

middle: W

last: King

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

description:
Processed data file: mESC_RYBPfl.YAF2-KO_NucRNA_96hrTAM_MERGED_FORWARD.bw
Processed data file: mESC_RYBPfl.YAF2-KO_NucRNA_96hrTAM_MERGED_REVERSE.bw
Processed data file: RYBPfl.DESeq2.Output.txt

data_processing:
RNA-seq reads were initially aligned against the rRNA genomic sequence (GenBank: BK000964.3) using bowtie2 to filter out rRNA fragments, prior to alignment using the STAR RNA-seq aligner (Dobin et al., 2012). To improve mapping of nascent, intronic sequences, reads which failed to map using STAR were aligned against the genome using bowtie2.
Biological triplicate read counts were determined using custom scripts for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered on size (>200bp), gene body and TSS mappability, unique TSS and TTS, so as to remove poorly mappable and highly similar transcripts.
The final set of 20,634 genes were used for differential analysis using DESeq2 (Love et al., 2014), with default settings and a significance threshold of padj < 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Stranded bigWig files representing genome coverage for merged biological triplicates.
Supplementary_files_format_and_content: DESeq2 results table.

source_name: Embryonic stem cells, Tamoxifen-treated, nuclear RNA-seq

growth_protocol: RYBPfl/fl;YAF2-/- mouse embryonic stem cells were maintained in DMEM supplemented with 15% FBS, 10 ng/mL leukemia-inhibiting factor (LIF), penicillin/streptomycin, beta-mercaptoethanol, l-glutamine and non-essential amino-acids, on 0.1% gelatin-coated dishes.

extract_protocol:
1 x 10^7 Rybpfl/fl;Yaf2-/- cells with or without tamoxifen were resuspended in 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF, 3 mM DTT) for 1 min at room temperature to isolate nuclei. Nuclei were centrifuged at 1,000 x g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer. Nuclei were then resuspended in 1mL of TriZOL reagent (Thermo Scientific) according to the manufacturer's protocol. Nuclear RNA was treated with the TURBO DNA-free Kit (Thermo Scientific) and depleted for rRNA using the RiboMinus kit and protocol (Thermo Scientific).
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA-seq kit (NEB) and libraries were sequenced on the Illumina NextSeq 500 with 40bp paired-end reads.

treatment_protocol: Cells were treated with 800nM 4-hydroxytamoxifen (OHT) for 96 hours prior to cell harvest.

value: RYBPfl/fl;YAF2-/- ES cells

tag: treatment

value: tamoxifen

tag: biological replicate


title: RYBPfl/fl.YAF2KO_nucRNA_UNT_rep3

description:
Processed data file: mESC_RYBPfl.YAF2-KO_NucRNA_UNT_MERGED_FORWARD.bw
Processed data file: mESC_RYBPfl.YAF2-KO_NucRNA_UNT_MERGED_REVERSE.bw
Processed data file: RYBPfl.DESeq2.Output.txt

source_name: Embryonic stem cells, Untreated control, nuclear RNA-seq


title: Postnatal Day 5 Mouse Salivary Gland Replicate 2

value: Postnatal Day 5

value: neonatal


title: shCon

tag: genotype

value: Normal

value: E14 stem cell line derived from 19/Ola mouse


title: RYBPfl/fl.YAF2KO_nucRNA_UNT_rep1


title: Neutrophil_donor2_PMA_3h

description: human neutrophl from healthy donor 2 +PMA 3h with fixation on slide  with Atto-590 Tn5 after imaging

value: healthy donor 2

value: PMA 3h


title: AR Early G1 Input

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

data_processing:
alignment to hg18 genome with bowtie
peak calling with MACS1.4 with a 10E-8 p-value cutoff
Genome_build: hg18
Supplementary_files_format_and_content: BED file with called peaks

source_name: LNCaP Cell Line

growth_protocol: LNCaP cells were cultured in hormone proficient media unless otherwise indicated.

extract_protocol:
ChIP was performed as previously described by Schmidt et al 2009
Illumina library prep kit was utilyzed according to manufacturer's instructions

treatment_protocol: Cells were treated with indicated drug 24 hours prior to harvest, and 10nM DHT 3 hours prior to harvest, with the exception of G0 control which was treated with CDT for 72 hours and EtOH 3 hours prior to harvest

value: LNCaP

tag: cell cycle arrest treatment

value: treated for 24 hours with 0.5μM PD-0332991 +3 hour 10nm DHT

tag: dht treatment

tag: chip antibody

value: none (input)


title: RYBPfl/fl.YAF2KO_Input_OHT_rep1

description: Processed data file: mESC_RYBPfl.YAF2-KO_Input_96hrTAM_DownsampledMERGED.MACS.bw

data_processing:
Paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the "--no-mixed" and "--no-discordant" options, and non-uniquely mapping reads were discarded. PCR duplicates were removed using samtools and biological replicates were randomly downsampled to contain the same number of reads prior to being merged together.
Peaks were identified using MACS2 (--broad) for individual replicates, which were then combined. Only peaks identified in all biological triplicates were used.
Genome coverage tracks were made using the pileup function of MACS2 and visualised using the UCSC genome browser.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files representing genome coverage for merged biological triplicates.

source_name: Embryonic stem cells, Tamoxifen treated, sonicated control

extract_protocol:
Cells were fixed for 1 hr in 2 mM EGS, followed by 15 min in 1% formaldehyde. Reactions were quenched by the addition of glycine to a final concentration of 125 µM. After cell lysis and chromatin extraction, chromatin was sonicated using a BioRuptor sonicator (Diagenode), followed by centrifugation at 16,000 x g for 20 min at 4°C, and the supernatant was taken for immunoprecipitation. Immunoprecipitations were performed overnight at 4°C using chromatin corresponding to 5 x 10^6 cells and were carried out in a total volume of 1 ml using approximately 3 µg of antibody. Antibody-bound chromatin was isolated on protein A agarose beads (RepliGen, Waltham, CA) or protein A magnetic Dynabeads (Invitrogen, Carlsbad, CA). Beads were washed with low salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl buffer (0.25 M LiCl, 1% NP40, 1% Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and TE buffer (x2) (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). To prepare ChIP-seq material, ChIP DNA was eluted, and cross-links reversed at 65°C in the presence of 200 mM NaCl where required. Samples were then treated with RNase and proteinase K before being purified with ChIP DNA Clean & Concentrator™ kit (Zymo, Irvine, CA).
Libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit, with 8-10 PCR cycles. Libraries were purified using AMPure XP cleanup, and quantified by qPCR using KAPA Library Quantitation Standards (KAPA Biosystems). Libraries were sequenced as 40bp paired-end reads on Illumina NextSeq 500 platform.


title: RYBPfl/fl.YAF2KO_Input_UNT_rep1

description: Processed data file: mESC_RYBPfl.YAF2-KO_Input_UNT_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Untreated control, sonicated control


title: RYBPfl/fl.YAF2KO_Input_UNT_rep2


title: Neutrophil_donor2_PMA_1h

description: human neutrophl from healthy donor 2 +PMA 1h with fixation on slide  with Atto-590 Tn5 after imaging

value: PMA 1h


title: Neutrophil_donor1_PMA_1h

description: human neutrophl from healthy donor 1+PMA 1h with fixation on slide  with Atto-590 Tn5 after imaging

value: healthy donor 1


title: RYBPfl/fl.YAF2KO_Input_OHT_rep3


title: HT1080_home_made_atto_on_slide_after_imaging.rep2

description: ATCC Cell line HT1080 with fixation on slide  with Atto-590 Tn5 after imaging #2

value: ATCC Cell line HT1080


title: AR Late S ChIP-Seq

value: treated for 24 hours with 1mM hydroxyurea +3 hour 10nm DHT


title: HT1080_Illumina_on_slide_rep2

description: ATCC Cell line HT1080 with fixation on slide Illumina Tn5 #2

value: with fixation on slide Illumina Tn5 #2


title: HT1080_fixed_rep2

description: ATCC Cell line HT1080 with fixation #2

value: with fixation #2


title: HT1080_Illumina_on_slide_rep1

description: ATCC Cell line HT1080 with fixation on slide Illumina Tn5 #1

value: with fixation on slide Illumina Tn5 #1


title: HT1080_unfixed.rep2

description: ATCC Cell line HT1080 without fixation#2

value: without fixation#2


title: LN AR G0 ChIP-Seq

value: 72 hour CDT + 3 hour EtOH


title: RYBPfl/fl.YAF2KO_nucRNA_OHT_rep1

value: RYBPfl/fl;YAF2-/- ES cells

value: tamoxifen


title: HT1080_unfixed.rep1

description: ATCC Cell line HT1080 without fixation#1

value: without fixation#1


title: AR G2/M Input

value: 2μg/mL aphidicolin for 15 hours, followed by washout and treatment with 50ng/mL nocodozole for 9 hours +3 hour 10nm DHT


title: RYBPfl/fl.YAF2KO_nucRNA_UNT_rep2


title: HT1080_home_made_atto_on_slide_after_imaging.rep1

description: ATCC Cell line HT1080 with fixation on slide  with Atto-590 Tn5 after imaging #1


title: RYBPfl/fl.YAF2KO_SUZ12_UNT_rep2

description: Processed data file: mESC_RYBPfl.YAF2-KO_SUZ12_UNT_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Untreated control, SUZ12 ChIP

value: SUZ12 (Cell Signaling, D39F6)


title: AR Late S Input

value: LNCaP


title: AR Early S Input

value: treated for 24 hours with 2μg/mL aphidicolin +3 hour 10nm DHT


title: AR Early G1 ChIP-Seq

value: treated for 24 hours with 0.5μM PD-0332991 +3 hour 10nm DHT


title: AR Late G1 Input

value: treated for 24 hours with 5μg/mL roscovitine + 3 hour DHT

value: none (input)


title: RYBPfl/fl.YAF2KO_SUZ12_UNT_rep1


title: OU14_48h

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Blumeria graminis f. sp. hordei DH14 (BluGen genome assembly, version 3.0) using tophat v2.0.10 with parameters -a 10  -g 10 -r 160 --mate-std-dev 160
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
SNP calling was performed against the genome of Blumeria graminis f. sp. hordei DH14 (BluGen genome assembly, version 3.0) using samtools mpileup (version 0.1.19) with options -A -u -D -d 2000 and converted to vcf format using bcftools with options -bvcg
Genome_build: Blumeria graminis fsp. hordeii (Bgh) DH14, BluGen (http://www.blugen.org/) genome assembly version 3.0
Supplementary_files_format_and_content: tab-delimited text file including raw read counts per gene per sample; vcf file including transcriptome variant information for all isolates

organism: Blumeria hordei

source_name: Blumeria graminis f. sp. hordei_OU14

extract_protocol:
RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacurer's instruction, including an on-column DNA digestion.
RNA-seq libraries were prepared from total RNA by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

tag: isolate

tag: time

tag: host tissue

value: barley leaf epidermal peels


title: OU14_16h


title: RYBPfl/fl.YAF2KO_RING1B_OHT_rep2

description: Processed data file: mESC_RYBPfl.YAF2-KO_RING1B_96hrTAM_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Tamoxifen treated, RING1B ChIP

tag: cell type

value: RING1B (Cell Signaling, D22F2)


title: Will_48h

source_name: Blumeria graminis f. sp. hordei_Will

value: Will


title: RYBPfl/fl.YAF2KO_Input_OHT_rep2


title: AR G0 Input


title: RYBPfl/fl.YAF2KO_Input_UNT_rep3


title: AR Early S ChIP-Seq


title: RYBPfl/fl.YAF2KO_SUZ12_OHT_rep3

description: Processed data file: mESC_RYBPfl.YAF2-KO_SUZ12_96hrTAM_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Tamoxifen treated, SUZ12 ChIP


title: AR G2/M ChIP-Seq


title: AR Late G1 ChIP-Seq


title: Will_16h


title: RYBPfl/fl.YAF2KO_SUZ12_OHT_rep2


title: RYBPfl/fl.YAF2KO_SUZ12_OHT_rep1


title: RYBPfl/fl.YAF2KO_RING1B_UNT_rep2

description: Processed data file: mESC_RYBPfl.YAF2-KO_RING1B_UNT_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Untreated control, RING1B ChIP


title: B103_16h

source_name: Blumeria graminis f. sp. hordei_B103


title: RYBPfl/fl.YAF2KO_SUZ12_UNT_rep3


title: RACE1_48h

source_name: Blumeria graminis f. sp. hordei_RACE1


title: RYBPfl/fl.YAF2KO_RYBP_OHT_rep3

description: Processed data file: mESC_RYBPfl.YAF2-KO_RYBP_96hrTAM_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Tamoxifen treated, RYBP ChIP

value: RYBP (Millipore, AB3637)


title: Aby_16h

source_name: Blumeria graminis f. sp. hordei_Art

value: Art


title: RYBPfl/fl.YAF2KO_RYBP_OHT_rep2


title: RACE1_16h


title: RYBPfl/fl.YAF2KO_RING1B_OHT_rep1


title: RYBPfl/fl.YAF2KO_RING1B_OHT_rep3


title: RYBPfl/fl.YAF2KO_RING1B_UNT_rep3


title: Aby_48h

source_name: Blumeria graminis f. sp. hordei_Aby

value: Aby


title: B103_48h


title: RYBPfl/fl.YAF2KO_RING1B_UNT_rep1


title: A6_16h

source_name: Blumeria graminis f. sp. hordei_A6

value: barley leaves


title: RYBPfl/fl.YAF2KO_NativeInput_OHT_rep3

description:
Calibrated ChIP-seq using spiked-in Drosophila melangaster S2 cells.
Processed data file: mESC_RYBPfl.YAF2-KO_NativeInput_96hrTAM_mm10.NormalisedMERGED.MACS2.bw

data_processing:
ChIP-seq experiments which contained a spike-in genome (D. melanogaster) were aligned against a concatenated genome of the two genome sequences (mm10+dm6) using bowtie2 (Langmead and Salzberg, 2012) with the "--no-mixed" and "--no-discordant" options, and reads which mapped more than once were discarded. PCR duplicates were removed using samtools.
Spiking an identical concentration of D. melanogaster cells into our quantitative ChIP-seq experiments allows for calibration of each sample for IP efficiency and total mouse cell number. When comparing ChIP-seq for untreated and OHT-treated cell lines using an internal calibration, the number of mm10 reads were randomly downsampled to reflect the total number of dm6 reads in that sample. Furthermore, to adjust for variation in the dm6/mm10 ratio between biological replicates, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in each sample's input DNA.
Genome coverage tracks were made using the pileup function of MACS2 and visualised using the UCSC genome browser.
H2AK119ub1 peaks were identified using the dpeak function of DANPOS2 (-q 40 –kw 750 –kd 1500, height_logP > 100) (Chen et al., 2013) and peaks closer than 5 kb were merged.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files representing genome coverage for merged biological triplicates.

source_name: Embryonic stem cells with Drosophila spike-in, Tamoxifen treated, MNase-digested chromatin control

extract_protocol:
A native ChIP protocol combined with a calibrated ChIP-seq approach was employed, as previously described (Hu et al., 2015; Bonhoure et al., 2014; Orlando et al., 2014). To achieve this, 1.25 x 10^7 Drosophila melanogaster S2 cells were spiked in to 5 x 10^7 Rybpfl/fl;Yaf2-/- mouse embryonic stem cells with or without OHT treatment. Nuclei were then isolated with RSB buffer (10 mM Tris-HCl (pH 8.), 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% NP-40 and 5 mM N-ethylmaleimide, followed by MNase digestion for 5 min with 150 U MNase (Fermentas, Waltham, MA) in 1 ml RSB supplemented with 0.25 M sucrose, 3 mM CaCl2 and 10 mM N-ethylmaleimide. Digestions were stopped with EDTA, before nuclei were pelleted by centrifugation at 1500 x g and the soluble S1 fraction collected. Pelleted nuclei were then resuspended in 300 µl nucleosome release buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 0.2 mM EDTA, 10 mM N-ethylmaleimide), incubated at 4°C for 1 hr with gentle rotation, and then gently passed through a 27G syringe needle five times. Following centrifugation to pellet the insoluble material, the soluble S2 fraction was collected and combined with the S1 fraction. Immunoprecipitations were performed overnight at 4°C using chromatin corresponding to 5 x 10^6 cells. Antibody-bound chromatin was isolated on protein A agarose beads (RepliGen, Waltham, CA) or protein A magnetic Dynabeads (Invitrogen, Carlsbad, CA). Native histone ChIPs were washed four times with native ChIP wash buffer (20 mM Tris-HCl (pH 7.5), 2 mM EDTA, 125 mM NaCl and 0.1% Triton), followed by a final TE buffer wash. Samples were then treated with RNase and proteinase K before being purified with ChIP DNA Clean & Concentrator™ kit (Zymo, Irvine, CA). For calibrated ChIP-seq experiments, an input control was prepared for each individual sample, to allow the quantitation of spike-in consistency.
Libraries were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit, with 8-10 PCR cycles. Libraries were purified using AMPure XP cleanup, and quantified by qPCR using KAPA Library Quantitation Standards (KAPA Biosystems). Libraries were sequenced as 40bp paired-end reads on Illumina NextSeq 500 platform.

tag: spiked-in organism

value: Drosophila melanogaster

value: RYBPfl/fl;YAF2-/- ES cells


title: CC148_16h

source_name: Blumeria graminis f. sp. hordei_CC148


title: RYBPfl/fl.YAF2KO_RYBP_UNT_rep1

description: Processed data file: mESC_RYBPfl.YAF2-KO_RYBP_UNT_DownsampledMERGED.MACS.bw

source_name: Embryonic stem cells, Untreated control, RYBP ChIP


title: RYBPfl/fl.YAF2KO_RYBP_OHT_rep1

value: tamoxifen


title: Untreated

city: Bloomington

first: Stephen

middle: D

last: Bell

state: IN

address: Simon Hall MSB

department: MCB

institute: Indiana University

description:
Archaea
Processed data file: RPKM.txt

data_processing:
Aligned to NC_002754 (Sulfolobus solfataricus P2) using Genious 6.1.7.
Read count quantitation using SeqMonk.
Genome_build: NC_002754.1 (ASM700v1)
Supplementary_files_format_and_content: RPKM.txt: Tab-delimited text file includes RPKMs for each sample.

organism: Saccharolobus solfataricus

source_name: Sulfolobus solfataricus, untreated

extract_protocol:
RNA prepped by acid-phenol method.
Wellcome Trust Centre for Human Genetics.

treatment_protocol: Mid-log cells grown with or without 5 mM HU for 4 hours.

tag: strain/background


title: Art_16h


title: HK2

city: Corvallis

first: Brett

middle: Lewis

last: Mellbye

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

description: Sample 6

data_processing:
The mRNA-Seq reads were analyzed using the CLC Main Workbench (CLC bio, Aarhus, DK).
The module for empirical analysis of differential gene expression (DGE) was used as described (Robinson and Smyth 2008) with default values of the software and normalized to reads per kilobase per million (RPKM).
Significant DGE for two-group comparisons was determined for all possible but non-reciprocal pair-wise comparisons (P-value threshold <= 0.05).
The fold change in mRNA abundance indicates the difference between the number of mRNA transcripts in the control and treatment groups. If the relative abundance of a transcript in the control was smaller than in the treatment, the number was given a positive value; conversely, if the transcript count was larger in the control than in the treatment group, the number was given a negative value.
Genome_build: N. winogradskyi: NC_007406.1
Supplementary_files_format_and_content: Microsoft Excel software; data; matrix processed data, CLC data output

organism: Nitrobacter winogradskyi

source_name: QS-proficient_bacterial cells

growth_protocol: N. winogradskyi cells were grown in batch culture in 100 mL 60 mM NO2- medium with shaking.

extract_protocol:
Cells were collected by centrifuging, lysed by sonication, and total RNA was extracted with a Qiagen Rneasy Kit. Ribosomal RNA was depleted with a MICROBExpress Bacterial mRNA enrichment kit.
An Illumina-targeted RNA Expression Kit and at least 200 ng of RNA containing less than 5% rRNA were used to prepare mRNA-Seq libraries.
The libraries were sequenced (150mer paired-end) on a HISEq 3000 Sequencer (Illumina, San Diego, CA) at the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University. mRNA-Seq.

treatment_protocol: The quorum-sensing-deficient reference treatment (A) was accomplished by addition of purified, recombinant AiiA lactonase. The quorum-sensing-proficient treatment (HK) was accomplished by addition of heat-denatured AiiA lactonase.

tag: strain

tag: sample group

tag: treated with

value: heat-denatured AiiA lactonase


title: HK1

description: Sample 5


title: RYBPfl/fl.YAF2KO_H3K27me3_OHT_rep3

description:
Calibrated ChIP-seq using spiked-in Drosophila melangaster S2 cells.
Processed data file: mESC_RYBPfl.YAF2-KO_H3K27me3_96hrTAM_mm10.NormalisedMERGED.MACS2.bw

source_name: Embryonic stem cells with Drosophila spike-in, Tamoxifen treated, H3K27me3 ChIP

value: H3K27me3 (rabbit polyclonal generated in-house)


title: RYBPfl/fl.YAF2KO_RYBP_UNT_rep3


title: RYBPfl/fl.YAF2KO_H3K27me3_OHT_rep2


title: A4

description: Sample 4

source_name: QS-deficient reference_bacterial cells

value: quorum-sensing-deficient reference treatment (A)

value: purified, recombinant AiiA lactonase


title: CC66_48h

source_name: Blumeria graminis f. sp. hordei_CC66


title: RYBPfl/fl.YAF2KO_RYBP_UNT_rep2


title: CC148_48h


title: A3

description: Sample 3


title: RYBPfl/fl.YAF2KO_NativeInput_OHT_rep2


title: Art_48h


title: 5 mM HU

description:
Archaea
Processed data file: RPKM.txt

source_name: Sulfolobus solfataricus, HU treated

value: 5 mM HU


title: CC88_48h

source_name: Blumeria graminis f. sp. hordei_CC88


title: CC88_16h


title: RYBPfl/fl.YAF2KO_H3K27me3_UNT_rep3

description:
Calibrated ChIP-seq using spiked-in Drosophila melangaster S2 cells.
Processed data file: mESC_RYBPfl.YAF2-KO_H3K27me3_UNT_mm10.NormalisedMERGED.MACS2.bw

source_name: Embryonic stem cells with Drosophila spike-in, Untreated control, H3K27me3 ChIP


title: RYBPfl/fl.YAF2KO_NativeInput_OHT_rep1


title: CC52_48h

source_name: Blumeria graminis f. sp. hordei_CC52


title: CC52_16h


title: A2

description: Sample 2


title: 63.5_48h

source_name: Blumeria graminis f. sp. hordei_63,5


title: RYBPfl/fl.YAF2KO_NativeInput_UNT_rep3

description:
Calibrated ChIP-seq using spiked-in Drosophila melangaster S2 cells.
Processed data file: mESC_RYBPfl.YAF2-KO_NativeInput_UNT_mm10.NormalisedMERGED.MACS2.bw

source_name: Embryonic stem cells with Drosophila spike-in, Untreated control, MNase-digested chromatin control


title: RYBPfl/fl.YAF2KO_H3K27me3_UNT_rep1


title: CC107_48h

source_name: Blumeria graminis f. sp. hordei_CC107


title: A6_48h


title: 63.5_16h


title: NCI_16h

source_name: Blumeria graminis f. sp. hordei_NCI

value: NCI


title: NCI_48h


title: HK3

description: Sample 7


title: RYBPfl/fl.YAF2KO_NativeInput_UNT_rep2


title: CC107_16h


title: RYBPfl/fl.YAF2KO_NativeInput_UNT_rep1


title: K1_48h

source_name: Blumeria graminis f. sp. hordei_K1


title: RYBPfl/fl.YAF2KO_nucRNA_OHT_rep2

description:
Processed data file: mESC_RYBPfl.YAF2-KO_NucRNA_96hrTAM_MERGED_FORWARD.bw
Processed data file: mESC_RYBPfl.YAF2-KO_NucRNA_96hrTAM_MERGED_REVERSE.bw
Processed data file: RYBPfl.DESeq2.Output.txt

source_name: Embryonic stem cells, Tamoxifen-treated, nuclear RNA-seq


title: RYBPfl/fl.YAF2KO_H2AK119ub1_UNT_rep1

description:
Calibrated ChIP-seq using spiked-in Drosophila melangaster S2 cells.
Processed data file: mESC_RYBPfl.YAF2-KO_H2AUb1_UNT_mm10.NormalisedMERGED.MACS2.bw

source_name: Embryonic stem cells with Drosophila spike-in, Untreated control, H2AK119ub1 ChIP

value: H2AK119ub1 (Cell Signaling, D27C4)


title: CEL-Seq_39

status: Public on Oct 04 2016

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description:
Negative Control containing only ERCC
counts_batch2.txt

data_processing:
Base calling and quality scoring: Real-Time Analysis v1.18.61
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the in-built mm10 annotation.
Count data from two batches were combined and batch effects removed using removeBatchEffect from limma
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise generalised linear models (McCarthy et al NAR 2012) were fitted to summarise the values from replicates samples using functionality from the edgeR package (version 3.22.0, Smyth, 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID and the number of reads mapping to that gene from each sample.

source_name: CTRL

extract_protocol:
Bone marrow cells were flushed and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted directly into 384 well-plate containing lysis buffer.
3' biased mRNA libraries were prepared according to the CEL-Seq protocol (Hashimshony et al., 2012) with the following deviations: 1) all column clean-ups were exchanged for AmpPure XP magnetic bead  (Beckman Coulter) clean-ups; 2) aRNA underwent TurboDNase I (NEB) tretment proir to fragmentation; 3) fragmentation was done using the Covaris system 4) Phosphatase and PNK treatment were omitted

value: CTRL

tag: initial sequence

value: AGCCAGAG

value: Control

tag: batch


title: CEL-Seq_38

value: GCTTGGAG


title: RYBPfl/fl.YAF2KO_H3K27me3_OHT_rep1

tag: treatment


title: CEL-Seq_36

source_name: WT

value: TAGGTTCA

value: WT


title: HK4

description: Sample 8

source_name: QS-proficient_bacterial cells


title: CC66_16h

value: barley leaves


title: CEL-Seq_33

value: ILCP

value: CTAACTCA


title: CEL-Seq_29

value: CILP

value: CTAACCGC

value: TCF


title: CEL-Seq_34

description:
Technical Replicate of CEL-Seq_6
counts_batch2.txt

value: CLP

value: GCTTGTCA


title: CC1_48h

source_name: Blumeria graminis f. sp. hordei_CC1


title: CEL-Seq_24

value: ATGTGTCA


title: RYBPfl/fl.YAF2KO_H3K27me3_UNT_rep2

value: Drosophila melanogaster

value: RYBPfl/fl;YAF2-/- ES cells

value: H3K27me3 (rabbit polyclonal generated in-house)

tag: biological replicate


title: A1

description: Sample 1

source_name: QS-deficient reference_bacterial cells

value: quorum-sensing-deficient reference treatment (A)

value: purified, recombinant AiiA lactonase


title: CEL-Seq_21

value: TCACATCA

tag: genotype


title: CEL-Seq_22

value: CGTGTTCA


title: RYBPfl/fl.YAF2KO_H2AK119ub1_OHT_rep3

description:
Calibrated ChIP-seq using spiked-in Drosophila melangaster S2 cells.
Processed data file: mESC_RYBPfl.YAF2-KO_H2AUb1_96hrTAM_mm10.NormalisedMERGED.MACS2.bw

source_name: Embryonic stem cells with Drosophila spike-in, Tamoxifen treated, H2AK119ub1 ChIP

value: tamoxifen

value: H2AK119ub1 (Cell Signaling, D27C4)


title: RYBPfl/fl.YAF2KO_H2AK119ub1_OHT_rep2


title: CEL-Seq_18

description:
Unused due to unsuccessful knockout
counts_batch2.txt

source_name: Nfil

value: CGTGTCGC

value: Nfil


title: RYBPfl/fl.YAF2KO_H2AK119ub1_OHT_rep1


title: RYBPfl/fl.YAF2KO_H2AK119ub1_UNT_rep3


title: CC1_16h

value: barley leaves


title: RYBPfl/fl.YAF2KO_H2AK119ub1_UNT_rep2


title: K1_16h


title: CEL-Seq_37

value: CTRL

value: CTAACGAG

value: Control


title: CEL-Seq_12

value: TGATGTCC

value: WT


title: CEL-Seq_40

value: TAGGTGAG


title: CEL-Seq_11

value: ACGACTCC


title: CEL-Seq_35

description:
Technical Replicate of CEL-Seq_7
counts_batch2.txt

value: CILP

value: AGCCATCA


title: CEL-Seq_10

value: GTCGTTCC


title: CEL-Seq_8

value: TGATGATC


title: CEL-Seq_31

value: CLP

value: AGCCACGC


title: CEL-Seq_7

value: ACGACATC


title: CEL-Seq_30

value: GCTTGCGC

value: TCF


title: CEL-Seq_28

value: ATGTGGAG


title: CEL-Seq_32

value: TAGGTCGC


title: CEL-Seq_6

value: GTCGTATC


title: CEL-Seq_25

value: TCACAGAG


title: CEL-Seq_26

value: CGTGTGAG


title: CEL-Seq_1

value: CATCACGC

value: WT


title: CEL-Seq_2

description:
Unused due to being outlier
counts_batch2.txt

value: GTCGTCGC


title: CEL-Seq_4

value: TGATGCGC


title: CEL-Seq_20

value: CILP

value: ATGTGCGC


title: CEL-Seq_19

value: GACACCGC


title: CEL-Seq_23

value: GACACTCA


title: CEL-Seq_27

value: GACACGAG


title: Donor D31, live sorted cells, library 5

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

institute: Single Cell Discoveries

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: hg19
Supplementary_files_format_and_content: cellsystems_dataset_4donors.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the originating donor (D*) and the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: human pancreas

extract_protocol:
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by an automated version of the previously described Cel-Seq2 technique. Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.

tag: tissue

value: pancreas


title: Donor D31, live sorted cells, library 6


title: CEL-Seq_9

value: CLP

value: CATCATCC


title: Donor D31, live sorted cells, library 7


title: Donor D31, live sorted cells, library 3


title: Donor D31, live sorted cells, library 2


title: CEL-Seq_17

value: TCACACGC

value: Nfil


title: CEL-Seq_16

value: TGATGGAA


title: Donor D31, live sorted cells, library 4


title: CEL-Seq_14

value: GTCGTGAA


title: Donor D30, live sorted cells, library 8


title: Donor D30, live sorted cells, library 7


title: Donor D30, live sorted cells, library 5


title: CEL-Seq_13

value: CATCAGAA


title: Donor D30, live sorted cells, library 1


title: Donor D30, live sorted cells, library 6


title: Donor D29, live sorted cells, library 8


title: Donor D29, live sorted cells, library 7


title: CEL-Seq_15

value: ACGACGAA


title: CEL-Seq_3

value: ILCP

value: ACGACCGC

value: WT


title: Donor D31, live sorted cells, library 8


title: Donor D31, live sorted cells, library 1


title: Donor D30, live sorted cells, library 4


title: Donor D29, live sorted cells, library 2


title: Donor D28, live sorted cells, library 7


title: CEL-Seq_5

value: CATCAATC


title: Donor D28, live sorted cells, library 4


title: Donor D28, live sorted cells, library 2


title: Donor D28, live sorted cells, library 1


title: Donor D30, live sorted cells, library 2


title: Donor D30, live sorted cells, library 3


title: Donor D28, live sorted cells, library 8


title: Donor D29, live sorted cells, library 3


title: Donor D29, live sorted cells, library 5


title: Donor D28, live sorted cells, library 6


title: Donor D29, live sorted cells, library 1


title: Donor D29, live sorted cells, library 4


title: DIF_STAT3_A

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

institute: University of Stuttgart

description: processed data file: Merged_DIF_STAT3.bigwig

data_processing:
The FASTQ files were mapped to the human reference genome (assembly hg19) using BOWTIE2 with very-sensitive presets in end-to-end mode on Galaxy Platform (version 2.2.6). The resulting BAM files of ChIPs were deduplicated with RmDup Samtools (Galaxy version 2.0). The corresponding BAM files of the replicates were merged within condition. The merged BAM files were normalized to fragments (reads) per kilobase per million (RPKM) using the bamCoverage tool on Deeptools Galaxy (version 1.1.4) with minimum mapping quality (MAPQ) set to 10 and with removal of duplicates (--ignoreDuplicates).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig represent the normalized RPKM values of ChIP-seq signal

growth_protocol:
Human fetal osteoblasts (hFOB) were maintained as previously described (Harris et al., 1995). In short, cells were maintained at 34⁰C in 5% CO2-atmosphere incubator in phenol red-free high-glucose Dulbecco’s modified Eagle’s media (DMEM/F12, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich).
L3.6 cells were maintained in Minimum Essential Media (MEM, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich) as previously described (Herreros-Villanueva et al., 2013).

extract_protocol:
The ChIP was performed with 20 min crosslinking in 1 % formaldehyde in PBS. Following chromatin shearing , 1-2µg antibody was used for immunoprecipitation overnight. The immunocomplexes were incubated 2 additional hours with protein A sepharose beads and subjected to washes. After reversing the cross-linking, the DNA was isolated by standart phenol-chloroform-isoamyl extraction procedure.
ChIP-Seq libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions.

treatment_protocol: For induction of osteoblastic differentiation, the confluent cells were treated with differentiation cocktail as described previously (Karpiuk et al., 2012) and shifted to 39⁰C incubator.The undifferentiated cells were incubated with DMSO for 24 hr and then harvested. For differentiated state, cells were preatreated with JQ1 (250nM) or equal volume of DMSO one hour before the induction of differentiation. The media was refreshed every 48 hr with subsequent addition of inhibitor. The cells were differentiated for 5 days.

tag: immortalization type

value: SV40 large T antigen immortalized

value: human Fetal Osteoblasts (hFOB)

tag: protocol

value: differentiated for 5 days into osteoblastic lineage

value: Santa Cruz, sc-482, C-20


title: Donor D28, live sorted cells, library 3

value: pancreas


title: L3.6_INPUT_B

description: processed data file: Merged_l3.6_INPUT.bigwig

value: L3.6 pancreatic cancer cells

tag: chip antibody


title: DIF_JUND_B

description: processed data file: Merged_DIF_JUND.bigwig

value: Santa Cruz, sc-74,329


title: L3.6_BRD4_B

description: processed data file: Merged_L3.6_BRD4.bigwig

value: N-terminal BRD4 antibody, Wu et al., 2006


title: L3.6_BRD4_A


title: L3.6_INPUT_A