title: HeLa E2F7_hypoxia

description: ChIP DNA

extract_protocol:
ChIP was performed according the EZ ChIP protocol (Upstate, 17-371) with the following specifications: HeLa cells were seeded at day 1 at a concentration of 7x10^6 cells per 145mm plate. Next day, cells were cultured overnight in hypoxia, or continued to grow under normoxia, and harvested on day 3. For single and double ChIP, 5 145mm plates were used per condition. In vitro crosslinking was performed on a shaker at room temperature (RT) for 10 minutes, using 1% freshly made paraformaldehyde. Crosslinking was quenched for 5 minutes incubation at RT on a shaker. Next, cells were washed twice on ice with PBS (40C, supplemented with protease inhibitors (11873580001, Roche)), and harvested, pelleted and resuspended in 2ml lysis buffer (0.3% SDS, 10mM EDTA, 50mM Tris and protease inhibitors). Sonication (10 cycles of 10 seconds followed by 1 minute incubation on ice) was performed in a FACS tubes using a Soniprep 150 sonicator (MSE). 10µl of sonicated sample was analyzed on gel to check for sonication efficiency. Sonicated lysates were centrifugated (10 minutes, 40C) to remove insoluble components and large DNA fragments. 200µL lysate was used per ChIP sample. The DNA concentration in the sonicated lysate was measure using a Nanodrop to normalize the amount of input DNA between normoxic and hypoxic ChIP samples. Protein G agarose beads (16-266, Milipore) were coated overnight in 0,1% BSA (Sigma, A3294), and 60 µL was used for pre-clear (2h, 40C) and final precipitation of immune complexes (1h, 40C). For single ChIP 5µg and for double ChIP 10µg was used. immunorecipitation were performed overnight at 40C on a rotating platform. In case of double ChIP, eluates were diluted in dilution buffer and incubated with another 10ug of antibody overnight. The following antibodies were used: ChIP grade HIF1α (ab2185, Abcam) E2F7 (sc-66870), E2F1 (sc-193), IgG (2729S; cell signaling). De-crosslinked DNA was purified over a column (Qiagen, 28106) and eluted in 65 µl H2O
immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD/AB sequencer in multiplexed way to produce 50-bp long reads.

value: For hypoxia treatment, cells were incubated in the H35 Hypoxystation (Don Whitley Scientific) at 1% O2 for 16 hours.


title: WT naïve T cells [Tn3_WT]

status: Public on Dec 11 2015

type: SRA

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

country: USA

institute: University of Chicago

description:
Replicate 3
Tn3_WT

library_source: transcriptomic

data_processing:
Reads from all libraries were mapped to the mouse genome (mm9) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq transcripts

molecule: total RNA

organism: Mus musculus

source_name: CD4+CD25-CD62Lhi naïve T cells

extract_protocol:
total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted CD4+CD25-CD62Lhi naïve T cells isolated from indicated mice
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

tag: strain

tag: genotype/variation

value: WT Tg

tag: cell type

value: naive T cells


title: Mouse 7 month astro

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

data_processing:
The FASTQ files were first groomed using the FASTQ groomer and then mapped using TopHat2, which invokes Bowtie as an internal read mapper (Trapnell et al., 2009). The paired end option was selected and human genome version 19 (hg19) was used as the reference genome. We then ran Cufflinks to assemble transcripts and estimate expression level as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) (Trapnell et al., 2010).
Genome_build: Hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse cortex

extract_protocol:
Tissue was dissociated in papain (30units / ml) for 1.5 hours before trituration. Cells were immunopanned on a sequence of plates in the following order: CD45 --> GalC --> GalC --> Thy1 --> HepaCAM. Cells bound to HepaCAM plate were then scraped in Qiazol to harvest RNA
Nugen Ovation V2 kit (7102-32), followed by sonication in the Covaris machine, followed by indexing with NEB Next Ultra kit (E7530L)

tag: age

value: post natal day 210

tag: cell subtype

value: HepaCAM positive cells

value: Astrocyte


title: miR-23 cluster Tg naïve T cells [Tn3_cluster]

description:
Replicate 3
Tn3_cluster

value: cluster Tg


title: WT naïve T cells [Tn2_WT]

description:
Replicate 2
Tn2_WT


title: HeLa HIF1a_hypoxia

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: ChIP DNA

library_source: genomic

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using BWA package
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling. Cisgenome was used for peak-calling from the ChIP-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: peak coordinates file : number_chromosome_start_end_length_fold-enrichment

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The cervical cancer (HeLa) cell line was cultured in DMEM (Invitrogen, 41966-052) supplemented with 10% FBS (Lonza, DE14-802F) and 1% Penicillin/Streptomycin (Lonza, DE17-602E).

extract_protocol:
ChIP was performed according the EZ ChIP protocol (Upstate, 17-371) with the following specifications: HeLa cells were seeded at day 1 at a concentration of 7x10^6 cells per 145mm plate. Next day, cells were cultured overnight in hypoxia, or continued to grow under normoxia, and harvested on day 3. For single and double ChIP, 5 145mm plates were used per condition. In vitro crosslinking was performed on a shaker at room temperature (RT) for 10 minutes, using 1% freshly made paraformaldehyde. Crosslinking was quenched for 5 minutes incubation at RT on a shaker. Next, cells were washed twice on ice with PBS (40C, supplemented with protease inhibitors (11873580001, Roche)), and harvested, pelleted and resuspended in 2ml lysis buffer (0.3% SDS, 10mM EDTA, 50mM Tris and protease inhibitors). Sonication (10 cycles of 10 seconds followed by 1 minute incubation on ice) was performed in a FACS tubes using a Soniprep 150 sonicator (MSE). 10µl of sonicated sample was analyzed on gel to check for sonication efficiency. Sonicated lysates were centrifugated (10 minutes, 40C) to remove insoluble components and large DNA fragments. 200µL lysate was used per ChIP sample. The DNA concentration in the sonicated lysate was measure using a Nanodrop to normalize the amount of input DNA between normoxic and hypoxic ChIP samples. Protein G agarose beads (16-266, Milipore) were coated overnight in 0,1% BSA (Sigma, A3294), and 60 µL was used for pre-clear (2h, 40C) and final precipitation of immune complexes (1h, 40C). For single ChIP 5µg and for double ChIP 10g was used. immunorecipitation were performed overnight at 40C on a rotating platform. In case of double ChIP, eluates were diluted in dilution buffer and incubated with another 10ug of antibody overnight. The following antibodies were used: ChIP grade HIF1α (ab2185, Abcam) E2F7 (sc-66870), E2F1 (sc-193), IgG (2729S; cell signaling). De-crosslinked DNA was purified over a column (Qiagen, 28106) and eluted in 65 µl H2O
immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD/AB sequencer in multiplexed way to produce 50-bp long reads.

tag: cell line

value: HeLa

tag: treatment

tag: antibody

value: HIF1α (ab2185, Abcam)


title: miR-23 cluster DKO naïve T cells [Tn3_DKO]

description:
Replicate 3
Tn3_DKO

value: DKO Tg


title: miR-24 Tg naïve T cells [Tn3_24]

description:
Replicate 3
Tn3_24

value: miR-24 Tg


title: miR-23 cluster Tg naïve T cells [Tn2_cluster]

description:
Replicate 2
Tn2_cluster


title: SK [Exome-seq]

status: Public on Dec 12 2015

city: Doha

first: Najeeb

last: Halabi

address: Education City

country: Qatar

institute: Weill Cornell Medicine in Qatar

description: Processed data file: SK.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina RTA (version 1.17.20).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 27
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Ovarian tumor

extract_protocol:
QIAGEN AllPrep DNA and RNA extraction kit.
SureSelectXT2 Human All Exon V5 (Part No. 5190-6217, Agilent Technologies, Santa Clara, CA).

value: ovarian tumor cell line


title: miR-27 Tg naïve T cells [Tn3_27]

description:
Replicate 3
Tn3_27

value: miR-27 Tg


title: circRNA_identification_RBC

city: Newcastle Upon Tybe

first: Michael

last: Jackson

address: International Centre for Life

country: United Kingdom

institute: Institute of Genetic Medicine

data_processing:
Base calling and demultiplexing were performed using Illumina's CASAVA software
Inner distance metrics computation and quality control analysis were performed using Piccard v 1.85 (http://broadinstitute.github.io/picard/) and FastQC v 0.10 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) respectively
Sequence reads were aligned to the human genome (hg19) using tophat v. 2.0.10 (Trapnell, Pachter, & Salzberg, 2009). RefSeq annotations were supplied using – GTF option along with options: -b2-sensitive, -r, --mate-std-dev, --library-type, as required for each sample. Read counts were generated using HTSEQ v. 0.6.1 (Anders, Pyl, & Huber, 2014), exonic nucleotide sequence coverage data were generated using Bedtools v 2.17 (Quinlan & Hall, 2010). Read count histograms – in bigwig format – were generated using RSeqQC v. 2.4 (Wang, Wang, & Li, 2012).
Identification of circRNA transcripts was perfomed using PTESFinder Pipeline v. 1 . Briefly, this pipeline identifies all RNAseq reads mapping in inverted order and the same orientiation to the same RefSeq entry as putative back-splice exon junction reads, generates exon models of these junctions, and re-maps all reads under analysis to improve mapping efficiency for back-splice exon junction reads with exon junctions close the the read termini. It then eliminates false positives through removal of reads which do not utilise known exon junctions and reads which map equally well or better to the genomic or transcriptome reference (see Methods). Parameters used were: JSpan 10 (to ensure no mismatches within 5bp either side of the back-splice exon junction, PID 0.85 to endure high mapping identity to both exons, and -m 7 to allow mapping to multiple isoforms within Refseq.
Genome_build: HG19
Supplementary_files_format_and_content: Bed file containing all identified circRNA and suitable for UCSC custom track upload.

source_name: Blood

extract_protocol:
Leukocyte depleted Red Blood Cells, from an infection free donor with A+ blood type,  was obtained from the Scottish National Blood Transfusion Service (surplus stock, stored for 27 days post transfusion in red cell storage solution). Leukodepletion filtration reduced white blood cells to <1.85x10E4 per ml, and plasma was removed before resuspension in storage solution. RBCs were pelleted and snap frozen on dry ice prior to RNA extraction using Trizol (Life technologies) and treatment with DNase I (Promega) according to the manufacturer’s instructions. RNA quantitation was performed using the NanoDrop ND-1000 spectrophotometer (NanoDrop) and quality was assessed using the Agilent 2100 Bioanalyser (Agilent Technologies).
400ng of RNA was used in library preparation and sequencing. Library was prepared based on Illumina's guidelines for TruSeq RiboZero stranded mRNA LT sample prep kit, following the alternative fragmentation protocol. Paired-end reads were sequenced using a paired end 100 base pair protocol on an Illumina HiSeq2000.

tag: tissue

value: Blood

value: Red Blood Cells (RBC)


title: miR-24 Tg naïve T cells [Tn2_24]

description:
Replicate 2
Tn2_24


title: miR-23 cluster Tg naïve T cells [Tn1_cluster]

description:
Replicate 1
Tn1_cluster


title: miR-27 Tg naïve T cells [Tn1_27]

description:
Replicate 1
Tn1_27


title: miR-23 cluster DKO naïve T cells [Tn1_DKO]

description:
Replicate 1
Tn1_DKO


title: miR-24 Tg naïve T cells [Tn1_24]

description:
Replicate 1
Tn1_24


title: WT naïve T cells [Tn1_WT]

description:
Replicate 1
Tn1_WT


title: Mouse 4 month astro

value: post natal day 120


title: miR-23 Tg naïve T cells [Tn1_23]

description:
Replicate 1
Tn1_23

value: miR-23 Tg


title: PDGFR-Mut2

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins School of Medicine

data_processing:
Basecalls perfromed using Illumina HiSeq Control (HSC) Software and a Illumina HiSeq2500 instrument
We used STAR (Dobin et al., Bioinformatics, 2013) to align RNA-Seq reads onto Ensembl mouse genome GRCm38, release 72. Number of reads mapped to exons was counted by htseq-count (Anders et al., Bioinformatics, 2014). Genes expressed at very low levels were omitted from further analysis.
To generate the stand attribute for alignments containing splice junctions, we used the outSAMstrandField intronMotif program. The spliced alignments without strand definition were removed.
Gene expression differences between wildtype and mutant samples, significance (p-value) and false discovery rate (FDR) were computed using the generalized linear models based EdgeR (Robinson et al., Bioinformatics, 2010).
Genome_build: Ensembl mouse genome GRCm38, release 72
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Retina

extract_protocol:
Retinas were removed and flash frozen with liquid nitrogen.  RNA was harvested using the Qiagen RNeasy extraction protocol.  Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared using standard Iumina protocols.  The PCR amplified library was purified using RNAClean XP magnetic beads (Agencourt, Beverley, MA) and run out on a High Sensitivity DNA Chip (Agilent, Santa Clara, CA) for quality check.

value: Mixed, (primarily CD-1)

value: retina

value: post natal day 0.5

tag: genotype

value: Lhx2 lox/lox; Pdgfr{alpha}-Cre


title: PDGFR-Mut3


title: PDGFR-Mut1


title: PDGFR-WT4

value: Lhx2 lox/lox


title: PDGFR-WT3


title: miR-23 cluster DKO naïve T cells [Tn2_DKO]

description:
Replicate 2
Tn2_DKO

value: naive T cells


title: PDGFR-WT2


title: miR-23 Tg naïve T cells [Tn3_23]

description:
Replicate 3
Tn3_23


title: BCAT2 KO 1

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter trimmed fastq files were generated.
Merged fastq files from lane 1 and lane 2. Fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using mm10 reference genome. BAM files were generated.
FPKM calculation using Cufflinks 2.2.1. Plain text (can be read by excel) files were generated. Both Tophat and Cufflinks used UCSC mm10 gtf file as guided annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: text file includes FPKM values for each sample along with mean, SE, p-value, and q-values from differential gene expression analysis

source_name: gastrocnemius skeletal muscle

growth_protocol: Dams and the weaned mice were maintained on an ad libitum choice diet mice.  They choose between an 18% Protein rodent chow (Teklad 2018 Global 18% Protein Rodent Diet, Harlan, Frederick, MD) and a BCAA-free purified diet (product #510081, Dyets Inc., Bethlehem, PA)

extract_protocol:
Total RNA was extracted as previously described with slight modification (Fertuzinhos S, Li M, Kawasawa YI, Ivic V, Franjic D, Singh D, Crair M, and Sestan N. Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex. Cell Rep 6: 938-950, 2014). Briefly, frozen muscle tissue was pulverized in liquid nitrogen using mortar and pestle, followed by bead mill homogenization (Bullet Blender, Next Advance) using stainless steel beads (Next Advance, cat# SSB14B) and mirVana RNA isolation kit (Life Technologies). Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RIN was confirmed as greater 7 for each sample using Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies). The cDNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Eight libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina). Demultiplexed and quality filtered mRNA-seq reads were then aligned to mouse reference assembly (mm10) using TopHat (v.2.0.9). The uniquely mapped reads were used to calculate the normalized expression level of genes, as fragments per kilobase of exon per million fragments mapped (FPKM), using Cufflinks (v.2.0.2).
The cDNA libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) as per the manufacturer’s instructions. The final product was assessed for its size distribution using Bioanalyzer DNA High Sensitivity Kit (Agilent Technologies) and for its concentration using Kapa library quantification kit (Kapa Biosystems). Six libraries were pooled per HiSeq lane, followed by on-board cluster generation on a Rapid Run single-end flow cell and subsequent 50 cycles sequencing (v3 sequencing kit) according to the manufacturer's instructions (HiSeq 2500, Illumina).

treatment_protocol: When mice were 9-11 weeks old, 4 male WT and 4 KO mice were anesthetized under isoflurane anesthesia (carried with 100% O2) and the gastrocnemius muscle was surgically removed and frozen between two aluminum blocks cooled to the temperature of liquid nitrogen and then stored at -80oC until RNA was isolated. While under continuous anesthesia, the animals were then euthanized by cutting the diaphragm and removing the heart.

value: gastrocnemius skeletal muscle

tag: gender

value: male

tag: body weight (g)

tag: age (wks)

tag: genetic background

value: homozygous for Bcat2tm1.2Clyn allele


title: BCAT2 KO 3


title: BCAT2 KO 2


title: BCAT2 KO 4


title: Wildtype 3

value: wild type


title: Wildtype 4


title: miR-27 Tg naïve T cells [Tn2_27]

description:
Replicate 2
Tn2_27


title: Wildtype 1


title: CB-15_L007

city: Boston

first: Camron

middle: D.

last: Bryant

state: MA

address: 72 E. Concord St. R-604

department: Pharmacology & Experimental Therapeutics

institute: Boston University School of Medicine

description:
Sample run across lanes 7 & 8
CB-15_L007

data_processing:
Samples were run across four lanes (5, 6, 7 & 8) and reads for each sample were generated via the Illumina HiSeq 2500 (~20,000,000 reads per replicate, totalling ~40,000,000 per sample)
Fastq files are quality checked via FastQC (v0.10.1) and possessed Phred quality scores > 30 (i.e. less than 0.1% sequencing error)
Using the FASTX-Trimmer from the FastX-Toolkit (v0.0.13.2) the 51st base was trimmed to enhance read quality and prevent misalignment
Fastq files were utilized in TopHat (v2.0.0)  to align reads to the reference genome (mm10; UCSC Genome Browser).
We computed the read counts per gene using the HTSeq (v0.6.1p1) Python package and edgeR (v2.14), a Bioconductor package for differential gene expression analysis that models read counts using a negative binomial distribution to account for variability in the number of reads via generalized linear models
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: HTseq output for each sample is in the form of a TXT (.txt) file that consists of a list of genes along side respective read counts. EdgeR output is in the form of a CSV file named "EdgeR output FDR0.05" and "EdgeR output FDR0.2".
Supplementary_files_format_and_content: "Tophat script", "Htseq script", "HTseq matrix script", and "edgeR script".

source_name: B6 mouse #8

extract_protocol:
Control (C57BL/6J) and B6.D2 congenic mice at about 50 days of age were decaptitated for brain retrieval. As mentioned before, 3mm strialtal punches (left and right hemispheres) were pooled per mouse, and collected tissue was immediately places into RNAlater (QIAGEN) for 24 hours. After incubation, RNA was extracted via miRNeasy Mini Kit and quality was assessed by Bioanalyzer analysis.
RNA that was deemed high quality was send to the University of Chicago Genomics Core Facility for cDNA library preparation. Libraries were prepared according to Illumina's detailed instructions accompanying the TruSeq® Stranded mRNA LT Kit  (oligo-dT; 50bp single-end reads; Part# RS-122-2101).  The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols

value: Brain

tag: brain area

value: Striatum

value: ~ 50 days


title: CB-15_L008

description:
Sample run across lanes 7 & 8
CB-15_L008


title: CB-13_L007

description:
Sample run across lanes 7 & 8
CB-13_L007

source_name: B6 mouse #7


title: CB-12_L008

description:
Sample run across lanes 7 & 8
CB-12_L008

source_name: B6.D2 congenic mouse #6


title: CB-14_L007

description:
Sample run across lanes 7 & 8
CB-14_L007

source_name: B6.D2 congenic mouse #7


title: CB-16_L007

description:
Sample run across lanes 7 & 8
CB-16_L007

source_name: B6.D2 congenic mouse #8


title: CB-14_L008

description:
Sample run across lanes 7 & 8
CB-14_L008


title: CB-11_L007

description:
Sample run across lanes 7 & 8
CB-11_L007

source_name: B6 mouse #6


title: CB-10_L008

description:
Sample run across lanes 7 & 8
CB-10_L008

source_name: B6.D2 congenic mouse #5


title: CB-11_L008

description:
Sample run across lanes 7 & 8
CB-11_L008


title: CB-9_L008

description:
Sample run across lanes 7 & 8
CB-9_L008

source_name: B6 mouse #5


title: CB-9_L007

description:
Sample run across lanes 7 & 8
CB-9_L007


title: CB-12_L007

description:
Sample run across lanes 7 & 8
CB-12_L007


title: CB-10_L007

description:
Sample run across lanes 7 & 8
CB-10_L007


title: miR-23 Tg naïve T cells [Tn2_23]

description:
Replicate 2
Tn2_23


title: CB-8_L006

description:
Sample run across lanes 5 & 6
CB-8_L006

source_name: B6.D2 congenic mouse #4


title: CB-8_L005

description:
Sample run across lanes 5 & 6
CB-8_L005


title: CB-7_L006

description:
Sample run across lanes 5 & 6
CB-7_L006

source_name: B6 mouse #4


title: CB-7_L005

description:
Sample run across lanes 5 & 6
CB-7_L005


title: Wildtype 2


title: CB-5_L006

description:
Sample run across lanes 5 & 6
CB-5_L006

source_name: B6 mouse #3


title: CB-6_L005

description:
Sample run across lanes 5 & 6
CB-6_L005

source_name: B6.D2 congenic mouse #3


title: CB-5_L005

description:
Sample run across lanes 5 & 6
CB-5_L005


title: CB-16_L008

description:
Sample run across lanes 7 & 8
CB-16_L008


title: CB-6_L006

description:
Sample run across lanes 5 & 6
CB-6_L006


title: CB-13_L008

description:
Sample run across lanes 7 & 8
CB-13_L008


title: CB-4_L005

description:
Sample run across lanes 5 & 6
CB-4_L005

source_name: B6.D2 congenic mouse #2


title: CB-3_L006

description:
Sample run across lanes 5 & 6
CB-3_L006

source_name: B6 mouse #2


title: CB-2_L006

description:
Sample run across lanes 5 & 6
CB-2_L006

source_name: B6.D2 congenic mouse #1


title: CB-2_L005

description:
Sample run across lanes 5 & 6
CB-2_L005


title: CB-1_L005

description:
Sample run across lanes 5 & 6
CB-1_L005

source_name: B6 mouse #1


title: CB-3_L005

description:
Sample run across lanes 5 & 6
CB-3_L005


title: DUX4-V5_V5

city: Columbus

first: Scott

middle: Q

last: Harper

state: Ohio

address: 700 Children's Drive

department: Gene Therapy

institute: Nationwide Children's Hospital

description: human DUX4 (immunoprecipitation)

data_processing:
Peaks were determined using the MACS peak finding algorithm (see Zhang et al., Genome Biology 2008, 9:R137).
The 50-nt sequence reads identified using Illumina's Hi-Seq were mapped to the genome using BWA algorithm with default settings. Only reads that pass Illumina's purity filter, align with no more than two mismatches, and map uniquely to the genome were used in the subsequent analysis. Duplicate reads are removed.
Tags are extended in silico to a length of 150-250 bp. To identify the density of fragments along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin determined. This information is stored as a bigWig file.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files (*.bw) show fragment density for 32-nt bins along the genome. They are in an indexed binary format and can be uploaded to the UCSC browser.

source_name: human immortalized myoblasts

growth_protocol: Human immortalized myoblasts were cultured in media containing DMEM supplemented with 16% Medium 199, 15% fetal bovine serum, 30 ng/ml zinc sulfate, 1.4 µg/ml vitamin B12, 55 ng/ml dexamethasone, 2.5 ng/ml human growth factor, 10 ng/ml fibroblast growth factor, and 20 mM HEPES. Human immortalized myoblasts were transfected plasmids encoding C-terminal epitope tagged DUX4 and Dux using the Human Dermal Fibroblast Nucleofector kit (Amaxa) and fixed 24 hours post-transfection.

extract_protocol:
Cell fixation was performed 24 hours post-transfection by the addition of 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 µg of antibody against V5-tag (Abcam ab15828). Complexes were washed, eluted from the beads with SDS buffer then subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500. Sequences (50 nt reads) were aligned to the human genome (hg19) using the BWA algorithm.

value: unaffected human myoblasts

value: V5-tag (Abcam ab15828)


title: mDux-V5_V5

description: mouse Dux (immunoprecipitation)


title: sip53-2

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

data_processing:
Fragments were mapped to the genome (hg19) using TopHat version V2.0.5
Only fragments with good quality (mean Qphred per read>20), in which both ends uniquely mapped to the genome, were considered
For each gene exonic and intronic signal were calculated; the exonic signal is the sum of all fragments mapped only to exons, and the intronic signal is the sum of all fragments mapped to introns or exon-intron junctions.
Gene models were downloaded from the UCSC Genome Browser (assembly hg19)
The signals from both lanes were summed
The numbers of fragments obtained for each gene in each sample were normalized to the total number of fragments obtained from the corresponding sample
Data was thresholded at 5 (log2 scale) to reduce noise (based on data distribution).
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads for each Sample (log2 scale)

molecule: polyA RNA

extract_protocol:
RNA from MCF10A cells transfected with siControl, siLATS1/2, sip53 or siLATS1/2/p53 was isolated. Two independent batches of cells served as biological replicates
Total RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina). Libraries were evaluated by Qubit and Bioanalyzer. Sequencing libraries were constructed with barcodes to allow multiplexing of 8 samples on one lane

tag: sirna

tag: batch/replicate


title: siLATS1/2/p53-1


title: CB-1_L006

description:
Sample run across lanes 5 & 6
CB-1_L006

tag: strain


title: siLATS1/2/p53-2


title: sip53-1


title: siLATS1/2-2


title: siLATS1/2-1


title: siControl-2

value: siControl


title: CB-4_L006

description:
Sample run across lanes 5 & 6
CB-4_L006


title: Lib130

city: New York

first: Robert

last: Roeder

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequenced reads were mapped to reference genome hg19 using BWA with default settings through GALAXY.
ChIPseq peaks were called by SICER software with parameter settings as W=200,G=400, and FDR=0.001
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using rpkmforgenes.py developed by Sandberg.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each RNA-seq Sample; bedGraph files were generated for each ChIP-Seq sample.

source_name: THP1, pLKO.1 control

extract_protocol: ChIP-seq libraries were constructed with 5 to 10 ng immunoprecipitated DNA. Samples were sequenced on HiSeq 2000 by following the manufactor's protocols. RNA libraries were prepared for sequencing using strand-specific protocols

tag: genotype/variation

value: wild type (control)

tag: chip antibody

value: Pol II (ser-5p)  (Abcam, ab5131)


title: Lib131

source_name: THP1, pLKO.1-PAF1 shRNA #1

value: PAF1 knockdown


title: siControl-1


title: Lib106

growth_protocol: The human AML cell line THP1 and the human ALL cell line CCRF-CEM were grown in RPMI-160 medium supplemented with 10% FBS and 2% Penicillin/Streptomycin.

extract_protocol:
For ChIP assays, normally, cells were fixed with 0.4% (v/v) formaldehyde at room temperature for 10 min. For improving the ChIP efficiency of non-DNA binding factors, double fixation was used. For double fixation with EGS (Pierce, Cat. no. 21565) and formaldehyde, cells were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For double fixation with DMA (Pierce, Cat. no. 20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hour, and subsequently with 0.4% formaldehyde at room temperature for 10 min. After two washes with PBS, fixed cells were resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH7.4) at the concentration of 40 million/ml, and chromatin was disrupted by sonication to the size range of 100 to 500 bp. Antibodies were diluted in RIPA-0.3, and bound to Dynabeads protein A (Life Technologies, cat. no. 10002D) by incubating at 4 °C for 3 hours. The bead-antibody complexes were washed with RIPA-0.3 twice, and then incubated with sonicated chromatin at 4 °C overnight. The second day, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 0.25 M LiCl, 0.25% NP-40, and 0,25% NaDOC, pH7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, and 1% SDS, pH7.4) supplemented with 10 µg/ml RNase A for elution and RNA digestion, and incubated at 55 °C for 1 hour. Afterwards, proteinase K was added to the final concentration of 100 µg/ml, and 30 min later, the temperature of incubation was increased to 65 °C for decrosslinking.  After decrosslinking for 4–6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205). RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) or Quick-RNA MiniPrep Kit (Zymo, R1054) by following the manufacturer’s protocol (Qiagen, cat. no. 74134).
ChIP-seq libraries were constructed with 5 to 10 ng immunoprecipitated DNA. RNA-seq libraries were prepared by following a previously published strand-specific protocol. Samples were sequenced on HiSeq 2000 or 2500 by following the manufacturer's protocols.

treatment_protocol: For knockdown experiments with lentiviral shRNAs, TRC control or gene-specific shRNA was transduced into cells by spin infection. Around 15 hours after transduction, cells were washed with PBS twice, and re-suspended in fresh medium. Puromycin (2 μg/ml, final conc.) was added to the culture medium 24 hours later. Cells were harvested for ChIP or RNA extraction 3 days after puromycin selection. For flavopiridol (Sigma, cat. no. F3055) treatment of THP1 cells, flavopiridol was solubilized in DMSO and added to culture medium at 1 μM (final conc.). Meanwhile, an equal volume of DMSO was added to control cells. After 1 more hour in culture, cells were fixed for ChIP.

tag: cell type

value: human acute monocytic leukemia (AML) cell line

value: pMY56 (control)

value: vector control

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #

tag: fixation

value: EGS+ FA


title: Lib72

tag: cell line

tag: treatment

value: Flavopiridol

value: Pol II

value: Santa Cruz


title: Lib81


title: Lib78

value: DMSO


title: Lib109

value: pMY136 (PAF1 shRNA #1)


title: Lib108


title: Lib70


title: DUX4-V5_Input

description: human DUX4 (input)

tag: antibody


title: Lib22


title: Lib19


title: Lib20


title: mDux-V5_Input

description: mouse Dux (input)


title: PAF1KD-1-THP1 RNAseq


title: Lib16


title: PAF1KD-2-THP1 RNAseq


title: Control-1-THP1 RNAseq


title: Control-2-THP1 RNAseq


title: HPT.BAHD1.ChIPSeq.R2.b.Input

city: Jouy-en-Josas

first: Helene

last: Bierne

address: Domaine de Vilvert, bat 442, INRA Micalis

department: Micalis Institute

country: France

institute: INRAE - University PARIS SACLAY

description: control

data_processing:
Basecalls performed using CASAVA version 1.8
reads were filtered with custom Python scripts
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie with default parameters, clonal reads were removed
enriched regions were selected with CCAT (v3.0) using individual replicates of ChIP vs Input with the following parameters: fragmentSize =150, slidingWinSize= 1000, movingStep=50, isStrandSensitiveMode = 0, minCount =4 (R1), 8 (R2), outputNum =10000, randomSeed = 123456, minScore =5.0 (R1) (fold change criteria) bootstrapPass =50.
reads were assigned to genomic windows of 400 bp using Repitools
counts were normalized with edgeR per effective library size
regions selected with CCAT were used to subset the table of library size normalized counts per genomic window
a generalized linear model was run with edgeR with time and IP as confounding factors
Genome_build: hg19 (female)
Supplementary_files_format_and_content: bedGraph files, library size normalized counts per 400 bp genomic window

source_name: HEK293 cells

growth_protocol: Stable HEK293-HPT-BAHD1 and control HEK293-HPT-blue cells were generated as described (Lebreton et al. Science 2011, PMID: 21252314). Stable pool of transfectants having undergone integration of HPT-expressing plasmids at the single FRT locus were grown under 5% CO2 atmosphere, in DMEM supplemented with 10% (v/v) Fetal Calf Serum (FCS) and Penicillin/Streptomycin (0.1 mg/ml each), 100 mg/ml hygromycin to maintain the integration and 15 μg/ml of Blasticidin in order to select for the maintenance of Tet repressor expression. Cellular amplification was performed in 2-liter spinner flasks (3 flasks containing 1L of the same medium per condition and replicate) as thoroughly described (Derivery et al. Methods Enzymol. 2010, PMID: 21036256) for one week.

extract_protocol:
Preparation of solubilized chromatin fractions from these cells (Fritsch et al. Mol. Cell 2010, PMID: 20129054) and tandem affinity purification (Lebreton et al. Science 2011, PMID: 21252314) were performed as previously described. Only the eluates from the first affinity column were used for DNA extraction. DNA was purified by two extractions with equal volumes of phenol:chloroform:isoamy lalcohol (25:24:1, pH=8), starting from 10 µL of the input samples diluted in 200 µL water, or 200 µL of eluates. Phenol was eliminated with one extraction with chloroform, then DNA was precipitated by addition of 900 µL of ethanol, 100 µL of ammonium acetate 7.5 M and 0.2 µL of glycogen (20 µg/µL) to each aqueous phase, incubation at -80°C for 30 min and centrifugation at 4°C, 20,000  ´ g for 15 min. The pellet was washed once in 100 µL of ethanol, then resuspended in 50 µL of pure water for inputs, 25 µL for eluates. 2 independent experiments were performed (R1 and R2)
The library construction was performed by Fasteris according to the Illumina guidelines, with the following steps: 3’ A addition; Ligation of adapters; Gel purification to isolate fragments of specified inserts size; PCR amplification to generate the DNA Colonies Template Library, library purification; Library quantification and dilution at 10 nM. Library Quality Control, done by titration run on the HiSeq. Independent libraries were produced for R1 and R2. The DNA Colony Template library was sequenced as single reads of 50 bp. Sequencing was multiplexed at 3 libraries per channel. For the HPT-BAHD1 ChIP sample, the R2 library was sequenced twice (R2.a and R2.b).

treatment_protocol: To induce the production of the HPT-BAHD1 fusion, tetracycline was added to cell culture media 30 h before cell recovery at a final concentration of 11 µg/ml. Tetracyclin was also added to the cultures of the control HEK293-HPT-blue cells.

value: embryonic semi-differentiated kidney cells

tag: sequencing time

tag: fraction

value: input DNA


title: HPT.Blue.ChIPSeq.R2.ChIP

description: control

value: mock IP


title: HPT.BAHD1.ChIPSeq.R2.b.ChIP

description: DNA occupancy of BAHD1

value: ChIP

value: anti-protein C mouse monoclonal antibody, clone HPC4 (11814508001, Roche)


title: HPT.Blue.ChIPSeq.R1.ChIP

description: control


title: HPT.BAHD1.ChIPSeq.R2.a.ChIP

description: DNA occupancy of BAHD1


title: Lib107


title: HPT.BAHD1.ChIPSeq.R1.ChIP

description: DNA occupancy of BAHD1


title: HEK-BAHD1

description: methylated DNA

data_processing:
Basecalls performed using CASAVA version 1.8
data were filtered with BGI programs, Low-quality reads include two types, and the read which could be accord with anyone of the two types will be removed: (1) The ratio of N in whole read was over 10%; (2) The ratio of base whose quality was less than 20 was over 10%.
SOAP aligner mapping as described in Li Y, Zhu J, Tian G, Li N, Li Q, et al. (2010) The DNA Methylome of Human Peripheral Blood Mononuclear Cells. PLoS Biol 8(11): e1000533.
cout: methylation information of cytosines in whole genome wide
Genome_build: hg19
Supplementary_files_format_and_content: cout (BGI); each line contains: Chromosome ID 2.Position 3. strand 4. Cytosine pattern (CG/CHH/CHG) 5. Cytosine sequence context 6. Copynumber 7. Methyl-reads num 8. Non-methyl-reads num 9. Binomial distribution expected values

growth_protocol: Cells were grown at 37°C, in a humidified 10% CO2 incubator, in Dulbecco's modified Eagle's medium with GlutaMAX (Gibco) supplied with 10%FBS (Gibco) and 200 ug/ml Hygromycin B (10687-010-Invitrogen).

extract_protocol:
High molecular weight genomic DNA was isolated using the conventional proteinase K/organic extraction method. DNA was reduced into 100-300 bp fragments by sonication and treated with DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adapters. Samples underwent bisulfite treatment with the ZYMO EZ DNA Methylation-Gold kit.
Desalted, size-selected, PCR amplified fragments were size-selected and qualified libraries were selected for Illumina sequencing according to BGI tech protocol.

treatment_protocol: HEK-BAHD1 were generated by integration of a single copy of the BAHD1 cDNA under the control of the human cytomegalovirus (CMV) immediate-early enhancer/promoter in the HEK293 genome. In the isogenic control line (HEK293-CT), the β-galactosidase DNA sequence was inserted in place of BAHD1, albeit out-of-frame to avoid translation into protein.

value: embryonic semi-differentiated kidley cells

value: overexpressing BAHD1 constituively


title: HEK293-CT

description: methylated DNA


title: Lib34

value: human acute monocytic leukemia (AML) cell line

value: wild type (control)


title: HEK293-CT MeDIP R1

description: methylated DNA

data_processing:
Basecalls performed using CASAVA version 1.8
reads were filtered with custom Python scripts
MeDIP-seq reads were aligned to the hg19 genome assembly using MAQ with default parameters
reads were assigned to genomic windows of 300 bp using MEDIPS
counts were normalized with edgeR per effective library size
Genome_build: hg19
Supplementary_files_format_and_content: WIG files, library size normalized counts per 300 bp genomic window

extract_protocol:
DNA was isolated using the conventional proteinase K/organic extraction method and sheard to obtain 100 to 500bp fragments. Fragments were size selected and purified by separating on agarose gel followed by gel-purification using gel-extraction kit (Qiagen)
the fragments were subjected for library preparation using Illumina paired-end sample preparation kit, using manufactures protocol.

value: control

tag: sample type

value: MeDIP enrichment


title: HEK-BAHD1 Input R2

description: DNA

value: over-expressing the BAHD1 gene

value: genomic background


title: HEK293-CT Input R2

description: DNA


title: HEK293-CT MeDIP R2

description: methylated DNA


title: in vitro WT 01 h R2

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description: total RNA after rRNA depletion

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: in vitro infection model

growth_protocol: To mimic the early stages of the infection of a host cell in vitro, the indicated Salmonella strains were grown in LB overnight, diluted 1:100 in LB and grown to an OD600 of 2.0 (i.e. a condition under which SPI-1 is highly induced).

extract_protocol:
miRvana kit for total RNA (Ambion)
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 s each). Then, RNAs <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). This was followed by a dephosphorylation with Antarctic Phosphatase (AP, NEB) and re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB). Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis.

treatment_protocol: Cells were washed twice with PBS and once with SPI-2 medium, diluted 1:50 in pre-warmed SPI-2 medium 24 (defined as t0) and grown further in SPI-2 medium in Erlenmeyer flasks for the indicated time periods.

tag: infection agent

value: Salmonella Typhimurium SL1344


title: HEK-BAHD1 MeDIP R1

description: methylated DNA


title: HEK293-CT Input R1

description: DNA


title: HEK-BAHD1 Input R1

description: DNA


title: HEK-BAHD1 MeDIP R2

description: methylated DNA


title: in vitro WT 01 h R3

description: total RNA after rRNA depletion


title: in vitro WT 00 h R2

description: total RNA after rRNA depletion


title: in vitro ΔpinT 01 h R3

description: total RNA after rRNA depletion


title: in vitro WT 00 h R1

description: total RNA after rRNA depletion


title: in vitro ΔpinT 01 h R2

description: total RNA after rRNA depletion


title: in vitro ΔpinT 01 h R1

description: total RNA after rRNA depletion


title: in vitro ΔpinT 00 h R3

description: total RNA after rRNA depletion


title: in vitro WT 01 h R1

description: total RNA after rRNA depletion


title: in vitro ΔpinT 00 h R2

description: total RNA after rRNA depletion


title: in vitro ComppinT 01 h R2

description: total RNA after rRNA depletion


title: in vitro ΔpinT 00 h R1

description: total RNA after rRNA depletion


title: in vitro ComppinT 00 h R3

description: total RNA after rRNA depletion


title: in vitro ComppinT 01 h R3

description: total RNA after rRNA depletion


title: in vitro ComppinT 00 h R2

description: total RNA after rRNA depletion


title: HPT.BAHD1.ChIPSeq.R1.Input

description: control


title: in vitro ComppinT 00 h R1

description: total RNA after rRNA depletion


title: in vitro WT 00 h R3

description: total RNA after rRNA depletion


title: Control larvae 0Hr replicate3

city: Gainesville

first: Pablo

middle: Emiliano

last: Canton

state: Florida

address: Natural Area Dr.

department: Entomology and Nematology

institute: University of Florida

data_processing:
Reads were checked for quality with FastQC utility and trimmed to 72 bp if necessary to remove adapter and low quality ends using Fastx trimmer
Reads were aligned to Aedes aegypti transcripts v 3.2 with TopHat2  v2.0.12 in Transcriptome mode with the following parameters: -N 2 -r 150 --mate-std-dev 50
Reads counts were summarized using HTSeq-Count v0.5.4p5 with the following parameters: -m intersection-nonempty -s no -t gene -i gene_id using Aaegl3.2 basefeatures.gtf
A count table for all samples was derived from HTSeq-Count outputs
Differential expression predictions were determined with EdgeR  v3.6.8 and DESeq2 v1.4.5, both in GLM mode using treatment tim and biological replicate in model design.
Genome_build: AaegL3.2
Supplementary_files_format_and_content: For each sample, data files contain tab separated gene ID, as identified in Vectorbase Database, counts summarized by HTSeq-Count, and normalized abundance from DEseq2 and EdgeR.

organism: Aedes aegypti

source_name: intestine

growth_protocol: Mosquito larvae were reared in controlled temperature and humidity, fed with yeast diet, until 4th instar

extract_protocol:
Total RNA was isolated by TRIzol reagent, treated with DNAseI, and purified by RNeasy columns
PolyA RNA cDNA library was prepared with Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Larvae were fed with a LC50 of purified Cry11Aa toxin crystals starting at same hour for each replicate. At 0,3,6,9 or 12 hours, dead and dying larvae were discarded and all others dissected to extract intestinal tissue

tag: developmental stage

value: 4th instar

tag: breed

value: IBT-UNAM

tag: tissue

value: intestine

tag: timepoint

value: 0 hr


title: lem2_met-2_set-25_2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
All paired-end ChIP-seq data (2x50bp) were mapped to the c.elegans genome (ce6) with the R package QuasR (http://www.bioconductor.org/packages/3.1/bioc/html/QuasR.html) using the included aligner bowtie [1] allowing only for uniquely mapping read pairs. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6")" which instructs bowtie to align using the parameters "--fr -m 1 --best --strata --maxins 500 --phred33-quals". Read density along the genome was calculated by tiling the genome into 200kb windows (non-overlapping) and counting the number of sequence fragments within each window [lem2_win200k_rawCounts.txt]. The command used to create the window count table was qCount(proj,regions,useRead="first"). This instructs QuasR to position each read at the middle of its respective fragment (determined by the two reads) and to only consider the first read (on any strand) for quantification in order to avoid double counting. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of mapped reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 1 (y=log2(x+1)) [lem2_win200k_normalized.txt].
Genome_build: ce6
Supplementary_files_format_and_content: lem2_win200k_rawCounts.txt
Supplementary_files_format_and_content: lem2_win200k_normalized.txt

organism: Caenorhabditis elegans

source_name: Early embryo extracts

growth_protocol: Wild-type, met-2 set-25 and cec-4 mutant strains were grown in parallel and in two independent biological replicas. For each strain, 400,000 L1 worms were grown synchronously in 500 ml S-medium containing HB101 E. coli strain, as food source, under continuous agitation (180 rpm) at 20ºC until gravid adults with early embryos were observed (between 60-65 hours depending on strain). Embryonic progeny was harvested using hypochlorite treatment

extract_protocol:
LEM-2 ChIP was performed as described in (Ikegami et al., 2010) with anti-LEM-2 (Novus Biologicals #48540002)
Libraries were prepared from chromatin IP (1.7 -7.4 ng) and input (10 ng) samples using the NEBNext ultra DNA library prep kit for Illumina (NEB # 7370) and the NEBNext Multiplex Oligos for Illumina (NEB # E7335), according to the manufacturer’s recommendations. No size selection was performed during sample preparation and the libraries were indexed and amplified using 15 PCR cycles, using the recommended conditions. After a final cleanup with Agencourt AmPure XP beads (Beckman # A63881), the library size distribution and concentrations were determined using a BioAnalyzer 2100 (Agilent technologies) and Qubit (Invitrogen) instrument, respectively. The final pools were prepared by mixing equimolar amounts of all individual indexed libraries and then sequenced on a HiSeq 2500 (Illumina) in Rapid mode (Paired-End 50).

treatment_protocol: Embryos were cross-linked with 2.16% formaldehyde in M9 buffer for 30 minutes at room temperature, washed twice with M9 and once with FA buffer (50mM HEPES-KOH pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 150mM NaCl)

value: early embryo

tag: strain

tag: genotype/variation

value: met-2 set-25_delta_delta

value: anti-LEM-2 (Novus Biologicals, catalog #48540002, lot# T01872A01)


title: lem2_cec-4_2

tag: chip antibody


title: lem2_met-2_set-25_1


title: lem2_cec-4_1


title: Control larvae 12Hr replicate3

value: 12 hr


title: Control larvae 0Hr replicate2


title: Control larvae 12Hr replicate2


title: Input_cec-4_2


title: lem2_wild-type_1

value: wild-type


title: Cry11Aa LC50 9Hr replicate 4

value: 9 hr


title: Control larvae 0Hr replicate1


title: lem2_wild-type_2


title: Cry11Aa LC50 6Hr replicate 4

value: 6 hr


title: Cry11Aa LC50 9Hr replicate 3


title: Cry11Aa LC50 12Hr replicate 3


title: Cry11Aa LC50 3Hr replicate 4

value: 3 hr


title: Cry11Aa LC50 6Hr replicate 3


title: Control larvae 12Hr replicate1


title: Cry11Aa LC50 3Hr replicate 3


title: in vitro ComppinT 01 h R1

description: total RNA after rRNA depletion


title: Input_met-2_set-25_1


title: Cry11Aa LC50 0Hr replicate 3


title: Cry11Aa LC50 9Hr replicate 2


title: Cry11Aa LC50 12Hr replicate 2


title: Input_met-2_set-25_2


title: Cry11Aa LC50 12Hr replicate 4


title: Input_wild-type_2


title: Cry11Aa LC50 0Hr replicate 4


title: RAW264.7 WT 04 h replicate 2

description:
total RNA after RNA depletion
RAW264.7:WT:04_h:R2

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1; human: hg19, GRCh37; mouse Gencode M2; GRCm38.p2; pig: Sscrofa10.2
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

organism:
Mus musculus
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: cell culture infection model

growth_protocol: HeLa-S3 cells were cultured according the guidelines provided by the ENCODE consortium (http://genome.ucsc.edu/encode/protocols/cell/human/Stam_15_protocols.pdf). Cells were grown in DMEM (Gibco) supplemented with 10% fetal calf serum (FCS; Biochrom), 2 mM L-glutamine (Gibco) and 1 mM sodium pyruvate (Gibco) in T-75 flasks (Corning) in a 5% CO2, humidified atmosphere at 37°C.  All further cell lines used in this study (THP-1, CaCo-2, AGS, HEK, MEF and RAW264.7) were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.  For the differentiation of bone marrow derived macrophages the marrow of femur and tibia was isolated from 8-12 week old female C57BL/6 wild-type mice and stored in RPMI supplemented with 10% FCS. The cell suspension was centrifuged for 5 min at 250 g and the leukocyte pellet was resuspended in differentiation medium consisting of X-vivo-15 medium (Lonza) supplemented with 10% FCS and 10% L929 conditioned DMEM medium (same composition as above). Cells were cultured for 3 days at 3*106 cells per 10 mL in a T-75 flask. At day 3 another 3 mL of differentiation medium were added and cells were further cultured until day 5. Successful macrophage differentiation was validated by microscopy on day 5 upon which the cells were disattached using a rubber scraper (Sarstedt) and seeded into 6-well plates at 105 cells per well in fresh differentiation medium. Infection was carried out on day 7 as described below.

treatment_protocol: Infection samples: In vitro infection was carried out following the protocol of (Schulte et al., 2011) with the indicated Salmonella Typhimurium (SL1344) strain in 6-well format. At the indicated time point post-infection, cells were fixed with RNAlater (Qiagen) and sorted for invaded (GFP+) and non-infected (GFP-) host cells using a FACSAria III device (BD). Total RNA from the sorted cells was extracted following the miRvana protocol (Ambion). "0 h" refers to RNA extracted from mixed lysates of extracellular Salmonella and host cells.

tag: organism

value: mixed sample:mouse cell line RAW264.7 and Salmonella Typhimurium SL1344


title: Input_cec-4_1


title: RAW264.7 WT 24 h replicate 2

description:
total RNA after RNA depletion
RAW264.7:WT:24_h:R2


title: 3D4 31 mock 01 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:mock:01_h:R3

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Pig: Sscrofa10.2; Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

organism:
Sus scrofa
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: Host cells were cultured according the guidelines provided by the ENCODE consortium (http://genome.ucsc.edu/encode/protocols/cell/human/Stam_15_protocols.pdf). Cells were grown in DMEM (Gibco) supplemented with 10% fetal calf serum (FCS; Biochrom), 2 mM L-glutamine (Gibco) and 1 mM sodium pyruvate (Gibco) in T-75 flasks (Corning) in a 5% CO2, humidified atmosphere at 37°C.  All further cell lines used in this study (THP-1, CaCo-2, AGS, HEK, MEF and RAW264.7) were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.For the differentiation of bone marrow derived macrophages the marrow of femur and tibia was isolated from 8-12 week old female C57BL/6 wild-type mice and stored in RPMI supplemented with 10% FCS. The cell suspension was centrifuged for 5 min at 250 g and the leukocyte pellet was resuspended in differentiation medium consisting of X-vivo-15 medium (Lonza) supplemented with 10% FCS and 10% L929 conditioned DMEM medium (same composition as above). Cells were cultured for 3 days at 3*106 cells per 10 mL in a T-75 flask. At day 3 another 3 mL of differentiation medium were added and cells were further cultured until day 5. Successful macrophage differentiation was validated by microscopy on day 5 upon which the cells were disattached using a rubber scraper (Sarstedt) and seeded into 6-well plates at 105 cells per well in fresh differentiation medium. Infection was carried out on day 7 as described below.

tag: pig cell line

value: mixed sample:pig cell line 3D4/31 and Salmonella Typhimurium SL1344


title: MEF WT 00 h replicate 2

description:
total RNA after RNA depletion
MEF:WT:00_h:R2

value: MEF

value: mixed sample:mouse cell line MEF and Salmonella Typhimurium SL1344


title: MEF WT 20 h replicate 2

description:
total RNA after RNA depletion
MEF:WT:20_h:R2

value: Salmonella Typhimurium SL1344


title: 4 h mock replicate 3

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Human: hg19/GRCh37; Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

organism:
Homo sapiens
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: HeLa-S3 cells were cultured according the guidelines provided by the ENCODE consortium (http://genome.ucsc.edu/encode/protocols/cell/human/Stam_15_protocols.pdf). Cells were grown in DMEM (Gibco) supplemented with 10% fetal calf serum (FCS; Biochrom), 2 mM L-glutamine (Gibco) and 1 mM sodium pyruvate (Gibco) in T-75 flasks (Corning) in a 5% CO2, humidified atmosphere at 37°C.  All further cell lines used in this study (THP-1, CaCo-2, AGS, HEK, MEF and RAW264.7) were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.For the differentiation of bone marrow derived macrophages the marrow of femur and tibia was isolated from 8-12 week old female C57BL/6 wild-type mice and stored in RPMI supplemented with 10% FCS. The cell suspension was centrifuged for 5 min at 250 g and the leukocyte pellet was resuspended in differentiation medium consisting of X-vivo-15 medium (Lonza) supplemented with 10% FCS and 10% L929 conditioned DMEM medium (same composition as above). Cells were cultured for 3 days at 3*106 cells per 10 mL in a T-75 flask. At day 3 another 3 mL of differentiation medium were added and cells were further cultured until day 5. Successful macrophage differentiation was validated by microscopy on day 5 upon which the cells were disattached using a rubber scraper (Sarstedt) and seeded into 6-well plates at 105 cells per well in fresh differentiation medium. Infection was carried out on day 7 as described below.

tag: human cell line

value: HeLa-S3 (ATCC CCL-2.2)

value: mixed sample:human cell line HeLa-S3 and Salmonella Typhimurium SL1344


title: Input_wild-type_1


title: RAW264.7 WT 00 h replicate 2

description:
total RNA after RNA depletion
RAW264.7:WT:00_h:R2

tag: cell line


title: 3D4 31 mock 01 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:mock:01_h:R2


title: 3D4 31 mock 01 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:mock:01_h:R1


title: MEF WT 04 h replicate 2

description:
total RNA after RNA depletion
MEF:WT:04_h:R2


title: 16 h mock replicate 3


title: L929 WT 06 h replicate 2

description:
total RNA after RNA depletion
L929:WT:06_h:R2

value: mixed sample:mouse cell line L929 and Salmonella Typhimurium SL1344


title: L929 WT 06 h replicate 1

description:
total RNA after RNA depletion
L929:WT:06_h:R1


title: 4 h WT replicate 3


title: 3D4 31 WT 16 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:WT:16_h:R2


title: L929 WT 01 h replicate 1

description:
total RNA after RNA depletion
L929:WT:01_h:R1


title: RAW264.7 WT 04 h replicate 1

description:
total RNA after RNA depletion
RAW264.7:WT:04_h:R1


title: 16 h WT replicate 3


title: L929 WT 01 h replicate 2

description:
total RNA after RNA depletion
L929:WT:01_h:R2


title: 0 h WT replicate 3


title: L929 WT 00 h replicate 2

description:
total RNA after RNA depletion
L929:WT:00_h:R2


title: 3D4 31 WT 16 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:WT:16_h:R1


title: RAW264.7 WT 00 h replicate 1

description:
total RNA after RNA depletion
RAW264.7:WT:00_h:R1


title: 16 h ΔyrlA/B replicate 3


title: 3D4 31 WT 06 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:WT:06_h:R3


title: L929 WT 00 h replicate 1

description:
total RNA after RNA depletion
L929:WT:00_h:R1


title: MEF WT 20 h replicate 1

description:
total RNA after RNA depletion
MEF:WT:20_h:R1


title: 4 h ΔyrlA/B replicate 3


title: MEF WT 04 h replicate 1

description:
total RNA after RNA depletion
MEF:WT:04_h:R1


title: 0 h ΔyrlA/B replicate 3


title: BMDM WT 20 h replicate 2

description:
total RNA after RNA depletion
BMDM:WT:20_h:R2

value: BMDM

value: mixed sample:mouse cell line BMDM and Salmonella Typhimurium SL1344


title: 3D4 31 WT 16 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:WT:16_h:R3


title: BMDM WT 06 h replicate 2

description:
total RNA after RNA depletion
BMDM:WT:06_h:R2


title: RAW264.7 WT 24 h replicate 1

description:
total RNA after RNA depletion
RAW264.7:WT:24_h:R1


title: BMDM WT 06 h replicate 1

description:
total RNA after RNA depletion
BMDM:WT:06_h:R1


title: MEF WT 00 h replicate 1

description:
total RNA after RNA depletion
MEF:WT:00_h:R1


title: 3D4 31 WT 06 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:WT:06_h:R1


title: 0 h ΔryhB/ΔisrE replicate 3


title: BMDM WT 02 h replicate 1

description:
total RNA after RNA depletion
BMDM:WT:02_h:R1


title: 3D4 31 WT 02 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:WT:02_h:R2


title: BMDM WT 02 h replicate 2

description:
total RNA after RNA depletion
BMDM:WT:02_h:R2


title: 3D4 31 WT 02 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:WT:02_h:R3


title: 16 h ΔomrA/B replicate 3


title: 3D4 31 WT 06 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:WT:06_h:R2


title: 16 h ΔryhB/ΔisrE replicate 3


title: 3D4 31 WT 01 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:WT:01_h:R3


title: 4 h ΔryhB/ΔisrE replicate 3


title: 3D4 31 WT 02 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:WT:02_h:R1


title: BMDM WT 00 h replicate 1

description:
total RNA after RNA depletion
BMDM:WT:00_h:R1


title: BMDM WT 00 h replicate 2

description:
total RNA after RNA depletion
BMDM:WT:00_h:R2


title: THP-1 with PMA WT 24 h replicate 1

description:
total RNA after RNA depletion
THP-1_with_PMA:WT:24_h:R1

value: THP-1 (-PMA)

value: mixed sample:human cell line THP-1 (-PMA)and Salmonella Typhimurium SL1344


title: 4 h ΔomrA/B replicate 3


title: 3D4 31 WT 01 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:WT:01_h:R2


title: 0 h ΔomrA/B replicate 3


title: THP-1 with PMA WT 04 h replicate 1

description:
total RNA after RNA depletion
THP-1_with_PMA:WT:04_h:R1


title: BMDM WT 20 h replicate 1

description:
total RNA after RNA depletion
BMDM:WT:20_h:R1


title: THP-1 with PMA WT 00 h replicate 1

description:
total RNA after RNA depletion
THP-1_with_PMA:WT:00_h:R1


title: THP-1 with PMA WT 24 h replicate 2

description:
total RNA after RNA depletion
THP-1_with_PMA:WT:24_h:R2


title: 3D4 31 WT 00 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:WT:00_h:R3


title: THP-1 with PMA WT 00 h replicate 2

description:
total RNA after RNA depletion
THP-1_with_PMA:WT:00_h:R2


title: HEK WT 04 h replicate 1

description:
total RNA after RNA depletion
HEK:WT:04_h:R1

value: HEK 293

value: mixed sample:human cell line HEK 293 and Salmonella Typhimurium SL1344


title: THP-1 with PMA WT 04 h replicate 2

description:
total RNA after RNA depletion
THP-1_with_PMA:WT:04_h:R2


title: HEK WT 24 h replicate 1

description:
total RNA after RNA depletion
HEK:WT:24_h:R1


title: THP-1 without PMA WT 04 h replicate 2

description:
total RNA after RNA depletion
THP-1_without_PMA:WT:04_h:R2


title: THP-1 without PMA WT 24 h replicate 2

description:
total RNA after RNA depletion
THP-1_without_PMA:WT:24_h:R2


title: AGS WT 24 h replicate 1

description:
total RNA after RNA depletion
AGS:WT:24_h:R1

value: AGS

value: mixed sample:human cell line AGS and Salmonella Typhimurium SL1344


title: 3D4 31 WT 00 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:WT:00_h:R1


title: HEK WT 00 h replicate 1

description:
total RNA after RNA depletion
HEK:WT:00_h:R1


title: AGS WT 04 h replicate 1

description:
total RNA after RNA depletion
AGS:WT:04_h:R1


title: THP-1 without PMA WT 00 h replicate 2

description:
total RNA after RNA depletion
THP-1_without_PMA:WT:00_h:R2


title: AGS WT 00 h replicate 1

description:
total RNA after RNA depletion
AGS:WT:00_h:R1


title: 3D4 31 ΔpinT 16 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:16_h:R3


title: LoVo WT 20 h replicate 2

description:
total RNA after RNA depletion
LoVo:WT:20_h:R2

value: LoVo

value: mixed sample:human cell line LoVo and Salmonella Typhimurium SL1344


title: 3D4 31 ΔpinT 16 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:16_h:R1

value: mixed sample:pig cell line 3D4/31 and Salmonella Typhimurium SL1344


title: 3D4 31 ΔpinT 06 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:06_h:R3


title: LoVo WT 20 h replicate 1

description:
total RNA after RNA depletion
LoVo:WT:20_h:R1


title: SPI-2 (in vitro) pinT vector 5 min ara replicate 2

description: in_vitro:SPI-2_STnc440_vector:05_min_ara:R2

extract_protocol:
miRvana for total RNA (Ambion)
miRvana kit for total RNA (Ambion) or TRIzol (Invitrogen) as indicated
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 s each). Then, RNAs <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). This was followed by a dephosphorylation with Antarctic Phosphatase (AP, NEB) and re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB). Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis.

value: Salmonella typhimurium SL1344

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: 3D4 31 ΔpinT 06 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:06_h:R2

value: Salmonella Typhimurium SL1344


title: LoVo WT 02 h replicate 2

description:
total RNA after RNA depletion
LoVo:WT:02_h:R2


title: SPI-2 (in vitro) empty vector 5 min ara replicate 2

description: in_vitro:SPI-2_empty_vector:05_min_ara:R2

value: HeLa-S3 (ATCC CCL-2.2)


title: 3D4 31 WT 01 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:WT:01_h:R1


title: SPI-2 (in vitro) pinT vector 5 min ara replicate 1

description: in_vitro:SPI-2_STnc440_vector:05_min_ara:R1


title: 3D4 31 ΔpinT 06 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:06_h:R1


title: 3D4 31 WT 00 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:WT:00_h:R2


title: LoVo WT 02 h replicate 1

description:
total RNA after RNA depletion
LoVo:WT:02_h:R1


title: 16 h mock replicate 2

value: mixed sample:human cell line HeLa-S3 and Salmonella Typhimurium SL1344


title: 3D4 31 ΔpinT 02 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:02_h:R3


title: 3D4 31 ΔpinT 16 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:16_h:R2


title: 3D4 31 ΔpinT 02 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:02_h:R2


title: 16 h mock replicate 1


title: SPI-1 pinT vector 5 min ara replicate 2

description: in_vitro:SPI-1_STnc440_vector:05_min_ara:R2


title: 3D4 31 ΔpinT 02 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:02_h:R1


title: LoVo WT 00 h replicate 1

description:
total RNA after RNA depletion
LoVo:WT:00_h:R1


title: SPI-1 empty vector 5 min ara replicate 2

description: in_vitro:SPI-1_empty_vector:05_min_ara:R2


title: 4 h mock replicate 2


title: 4 h mock replicate 1


title: 3D4 31 ΔpinT 01 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:01_h:R3


title: HT29 WT 20 h replicate 2

description:
total RNA after RNA depletion
HT29:WT:20_h:R2

value: mixed sample:human cell line HT29 and Salmonella Typhimurium SL1344


title: SPI-1 pinT vector 5 min ara replicate 1

description: in_vitro:SPI-1_STnc440_vector:05_min_ara:R1


title: 3D4 31 ΔpinT 01 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:01_h:R2


title: SPI-1 empty vector 5 min ara replicate 1

description: in_vitro:SPI-1_empty_vector:05_min_ara:R1


title: HT29 WT 02 h replicate 2

description:
total RNA after RNA depletion
HT29:WT:02_h:R2


title: 16 h WT replicate 2


title: 3D4 31 ΔpinT 01 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:01_h:R1


title: 16 h WT replicate 1


title: 4 h WT replicate 2


title: HT29 WT 02 h replicate 1

description:
total RNA after RNA depletion
HT29:WT:02_h:R1


title: HT29 WT 00 h replicate 2

description:
total RNA after RNA depletion
HT29:WT:00_h:R2


title: 3D4 31 ΔpinT 00 h replicate 2

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:00_h:R2


title: SPI-2 (in vitro) empty vector 5 min ara replicate 1

description: in_vitro:SPI-2_empty_vector:05_min_ara:R1


title: LoVo WT 00 h replicate 2

description:
total RNA after RNA depletion
LoVo:WT:00_h:R2


title: 4 h WT replicate 1


title: 3D4 31 ΔpinT 00 h replicate 1

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:00_h:R1


title: 0 h WT replicate 2


title: HEK WT 24 h replicate 2

description:
total RNA after RNA depletion
HEK:WT:24_h:R2


title: HT29 WT 00 h replicate 1

description:
total RNA after RNA depletion
HT29:WT:00_h:R1


title: 0 h WT replicate 1


title: IPEC-J2 WT 20 h replicate 2

description:
total RNA after RNA depletion
IPEC-J2:WT:20_h:R2

value: mixed sample:pig cell line IPEC-J2 and Salmonella Typhimurium SL1344


title: IPEC-J2 WT 20 h replicate 1

description:
total RNA after RNA depletion
IPEC-J2:WT:20_h:R1


title: HEK WT 04 h replicate 2

description:
total RNA after RNA depletion
HEK:WT:04_h:R2


title: HEK WT 00 h replicate 2

description:
total RNA after RNA depletion
HEK:WT:00_h:R2


title: 16 h ΔyrlA/B replicate 2


title: HT29 WT 20 h replicate 1

description:
total RNA after RNA depletion
HT29:WT:20_h:R1


title: 16 h ΔyrlA/B replicate 1


title: IPEC-J2 WT 02 h replicate 1

description:
total RNA after RNA depletion
IPEC-J2:WT:02_h:R1


title: CaCo-2 WT 24 h replicate 2

description:
total RNA after RNA depletion
CaCo-2:WT:24_h:R2

value: mixed sample:human cell line CaCo-2 and Salmonella Typhimurium SL1344


title: 4 h ΔyrlA/B replicate 2


title: CaCo-2 WT 24 h replicate 1

description:
total RNA after RNA depletion
CaCo-2:WT:24_h:R1


title: IPEC-J2 WT 02 h replicate 2

description:
total RNA after RNA depletion
IPEC-J2:WT:02_h:R2


title: IPEC-J2 WT 00 h replicate 2

description:
total RNA after RNA depletion
IPEC-J2:WT:00_h:R2


title: 3D4 31 ΔpinT 00 h replicate 3

description:
total RNA after rRNA depletion
3D4_31:DeltapinT:00_h:R3


title: IPEC-J2 WT 00 h replicate 1

description:
total RNA after RNA depletion
IPEC-J2:WT:00_h:R1


title: CaCo-2 WT 04 h replicate 1

description:
total RNA after RNA depletion
CaCo-2:WT:04_h:R1


title: CaCo-2 WT 04 h replicate 2

description:
total RNA after RNA depletion
CaCo-2:WT:04_h:R2


title: 3D4/31 WT 16 h replicate 3

description:
total RNA after RNA depletion
3D4_31:WT:16_h:R3


title: 0 h ΔyrlA/B replicate 1


title: CaCo-2 WT 00 h replicate 2

description:
total RNA after RNA depletion
CaCo-2:WT:00_h:R2


title: 4 h ΔyrlA/B replicate 1


title: Mock 24 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:mock:24_h:R3

extract_protocol:
miRvana kit for total RNA (Ambion) or TRIzol (Invitrogen) as indicated
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 s each). Then, RNAs <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). This was followed by a dephosphorylation with Antarctic Phosphatase (AP, NEB) and re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB). Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis.

value: human cell line HeLa-S3


title: 16 h ΔryhB/ΔisrE replicate 2


title: 3D4/31 WT 16 h replicate 2

description:
total RNA after RNA depletion
3D4_31:WT:16_h:R2


title: CaCo-2 WT 00 h replicate 1

description:
total RNA after RNA depletion
CaCo-2:WT:00_h:R1


title: 0 h ΔyrlA/B replicate 2


title: 3D4/31 WT 16 h replicate 1

description:
total RNA after RNA depletion
3D4_31:WT:16_h:R1


title: 16 h ΔryhB/ΔisrE replicate 1


title: Mock 24 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:mock:24_h:R2


title: Mock 24 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:mock:24_h:R1


title: 4 h ΔryhB/ΔisrE replicate 2


title: 3D4/31 WT 06 h replicate 3

description:
total RNA after RNA depletion
3D4_31:WT:06_h:R3


title: Mock 16 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:mock:16_h:R3


title: AGS WT 24 h replicate 2

description:
total RNA after RNA depletion
AGS:WT:24_h:R2


title: AGS WT 04 h replicate 2

description:
total RNA after RNA depletion
AGS:WT:04_h:R2


title: 3D4/31 WT 06 h replicate 2

description:
total RNA after RNA depletion
3D4_31:WT:06_h:R2


title: 4 h ΔryhB/ΔisrE replicate 1


title: Mock 16 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:mock:16_h:R2


title: 3D4/31 WT 06 h replicate 1

description:
total RNA after RNA depletion
3D4_31:WT:06_h:R1


title: 0 h ΔryhB/ΔisrE replicate 2


title: 3D4/31 WT 02 h replicate 3

description:
total RNA after RNA depletion
3D4_31:WT:02_h:R3


title: Wild-type infection 24 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:WT:24_h:R3


title: 0 h ΔryhB/ΔisrE replicate 1


title: 3D4/31 WT 02 h replicate 2

description:
total RNA after RNA depletion
3D4_31:WT:02_h:R2


title: Mock 8 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:mock:08_h:R3


title: 16 h ΔomrA/B replicate 2


title: Mock 8 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:mock:08_h:R2


title: 3D4/31 WT 02 h replicate 1

description:
total RNA after RNA depletion
3D4_31:WT:02_h:R1


title: Wild-type infection 24 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:WT:24_h:R1


title: 16 h ΔomrA/B replicate 1


title: 3D4/31 WT 01 h replicate 3

description:
total RNA after RNA depletion
3D4_31:WT:01_h:R3


title: 4 h ΔomrA/B replicate 2


title: Mock 8 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:mock:08_h:R1


title: Wild-type infection 16 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:WT:16_h:R3


title: 3D4/31 WT 01 h replicate 2

description:
total RNA after RNA depletion
3D4_31:WT:01_h:R2


title: Mock 4 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:mock:04_h:R3


title: AGS WT 00 h replicate 2

description:
total RNA after RNA depletion
AGS:WT:00_h:R2


title: Mock 4 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:mock:04_h:R2


title: Mock 16 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:mock:16_h:R1


title: Mock 4 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:mock:04_h:R1


title: 0 h ΔomrA/B replicate 2


title: 3D4/31 WT 00 h replicate 3

description:
total RNA after RNA depletion
3D4_31:WT:00_h:R3


title: Wild-type infection 8 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:WT:08_h:R3


title: 0 h ΔomrA/B replicate 1


title: 3D4/31 WT 01 h replicate 1

description:
total RNA after RNA depletion
3D4_31:WT:01_h:R1


title: Mock 2 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:mock:02_h:R3


title: Wild-type infection 24 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:WT:24_h:R2


title: 3D4/31 WT 00 h replicate 2

description:
total RNA after RNA depletion
3D4_31:WT:00_h:R2


title: Wild-type infection 8 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:WT:08_h:R2


title: Mock 2 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:mock:02_h:R2


title: Wild-type infection 8 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:WT:08_h:R1


title: THP-1 without PMA WT 24 h replicate 1

description:
total RNA after RNA depletion
THP-1_without_PMA:WT:24_h:R1

value: THP-1 (-PMA)

value: mixed sample:human cell line THP-1 (-PMA)and Salmonella Typhimurium SL1344


title: THP-1 without PMA WT 04 h replicate 1

description:
total RNA after RNA depletion
THP-1_without_PMA:WT:04_h:R1


title: Mock 2 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:mock:02_h:R1


title: THP-1 without PMA WT 00 h replicate 1

description:
total RNA after RNA depletion
THP-1_without_PMA:WT:00_h:R1


title: Wild-type infection 16 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:WT:16_h:R2


title: Wild-type infection 4 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:WT:04_h:R2


title: 4 h ΔomrA/B replicate 1


title: 16 h pinT* replicate 2


title: input DNA

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 rue d'Ulm

department: Inserm U830, Genetics and biology of cancers

institute: Institut Curie

data_processing:
reads alignment BWA
normalized density construction HMCan-diff
Genome_build: hg19
Supplementary_files_format_and_content: bigwig  normalized chip-seq density

source_name: A549 cell line

growth_protocol: A549 cells were grown in RPMI 1640 medium complemented with 10% of fetal calf serum, Glutamax plus extra D-glucose and sodium pyruvate.

extract_protocol:
Chromatin preparation and ChIP were performed with Ideal ChIP-seq kit for histones according to the supplier's protocol (Diagenode )
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® ChIP sample Preparation Kit (Part# IP-202-1012 or IP-202-1024). Briefly, Input and ChIP DNA (5–10 ng) were size-selected using Agencourt® SPRI®select beads to get fragments between 100 to 300 bp. Size-selected DNA was blunt-ended and phosphorylated. A single 'A' nucleotide was added to the 3' ends of the fragments before ligation to an adapter bearing  a single 'T' base overhang. The ligation products were purified and PCR-amplified (11 cycles) to enrich for fragments that have adapters on both ends. Libraries were then measured and qualified before cluster generation. Fragments presented with a size around 450 bp (insert plus adaptor, index and PCR primer sequences). Libraries were sequenced on the HiSeq 2500 system following manufacturer's protocols (Rapid Run, Single Read 100 bp).

tag: cell type

value: lung carcinoma


title: 25yo whole cortex

data_processing:
The FASTQ files were first groomed using the FASTQ groomer and then mapped using TopHat2, which invokes Bowtie as an internal read mapper (Trapnell et al., 2009). The paired end option was selected and human genome version 19 (hg19) was used as the reference genome. We then ran Cufflinks to assemble transcripts and estimate expression level as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) (Trapnell et al., 2010).
Genome_build: Hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Adult temporal lobe

extract_protocol:
Tissue was dissociated in papain (30units / ml) for 1.5 hours before trituration. Cells were immunopanned on a sequence of plates in the following order: CD45 --> GalC --> GalC --> Thy1 --> HepaCAM. Cells bound to HepaCAM plate were then scraped in Qiazol to harvest RNA
Nugen Ovation V2 kit (7102-32), followed by sonication in the Covaris machine, followed by indexing with NEB Next Ultra kit (E7530L)

tag: age

value: 25 years old

tag: cell subtype

value: Whole cortex


title: Wild-type infection 4 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:WT:04_h:R1


title: 63yo whole cortex

value: 63 years old


title: Wild-type infection 2 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:WT:02_h:R3


title: H3K27me3_ChIPSeq

value: H3K27me3 C15410069 (Rabbit polyclonal, ChIP-seq grade,Diagenode)


title: 16 h pinT* replicate 1


title: HeLa_CTCF

city: Farmington

first: Oscar

middle: J.

last: Luo

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

description:
Combined
ChIA-PET

data_processing:
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the human reference genome (hg19) using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
ChIP-nexus sequencing raw reads (including the fixed and random barcodes) were first reduced for PCR redundancy, and then the fixed and random barcodes (read positions 1-9) were trimmed. The remaining sequences were aligned to human genome assembly hg19 by bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.
The sequence alignment results were used as input to MACE (v1.2) (Wang et al., 2014) to identify RAD21 and SMC3 occupancy borders (footprints).
genome build: hg19
processed data files format and content: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET cluster. For ChIP-nexus, the processed data is the MACE processed genome coverage profile in bigwig format.

growth_protocol: GM12878 and HeLa cells (ATCC®) were cultured following manufacture’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 300 bp by sonication. The anti-PolII monoclonal antibody 8WG16 (Covance, MMS-126R) and anti-CTCF antibody (Abcam, ab70303) were used to enrich PolII and CTCF-bound chromatin fragments, respectively.
ChIP DNA on beads was used for ChIA-PET library preparation. After performing the end-repair and A-tailing using T4 DNA polymerase (NEB) and Klenow enzyme, the ChIP DNA ends were proximity-ligated by the single biotinylated bridge-linker with the 3' nucleotide T over-hanging on both strands. Proximity ligation DNA was reverse cross-linked and fragmented and added sequencing adaptors simultaneously by using Tn5 transposase (Nextera kit, Illumina). DNA fragments contained the bridge-linker at ligation junctions were captured by Streptividin beads, and used as templates for PCR amplification. These DNA products were then subjected to size-selection and paired-end sequencing (2×150 bp) using Illumina Hi-Seq 2500.

treatment_protocol: Approximately 100-200 million cells were harvested and fixed by 30 ml of 1.5 mM EGS (ethylene glycol bis[succinimidylsuccinate]) in PBS buffer for 45 minutes at room temperature. Next, formaldehyde was added to final concentration of 1% to cross-link the cells for another 20 minutes at room temperature and then neutralized by using glycine. The cross-linked cells were lysed by cell lysis buffer and nuclear lysis buffer.

tag: factor

value: CTCF

tag: antibody

value: anti-CTCF antibody (Abcam, ab70303)


title: 45yo whole cortex

value: 45 years old


title: GM12878_RNAPII

description:
Combined
ChIA-PET

value: RNAPII

value: anti-PolII monoclonal antibody 8WG16 (Covance, MMS-126R)


title: Wild-type infection 2 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:WT:02_h:R2

value: HeLa-S3 (ATCC CCL-2.2)

tag: infection agent

value: Salmonella Typhimurium SL1344

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: Wild-type infection 2 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:WT:02_h:R1


title: 13yo ctx endo

value: 13 years old

value: BSL bound cells

value: Endothelial


title: GM12878_CTCF

description:
Combined
ChIA-PET


title: 3D4/31 WT 00 h replicate 1

description:
total RNA after RNA depletion
3D4_31:WT:00_h:R1

value: mixed sample:pig cell line 3D4/31 and Salmonella Typhimurium SL1344


title: 47 yo ctx endo

value: 47 years old


title: 16 h wildtype replicate 2

value: Salmonella typhimurium SL1344


title: Wild-type infection 0 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:WT:00_h:R3


title: Wild-type infection 4 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:WT:04_h:R3


title: 16 h wildtype replicate 1


title: 63 yo ctx myeloid

value: CD45 positive cells

value: Myeloid


title: 53yo whole cortex

value: 53 years old

value: Whole cortex


title: HEK-BAHD1 WGBS (replicate 2)

description:
bisulfte converted DNA
genome-wide methylated and non-methylated read counts

data_processing:
Qualified libraries were selected for Illumina sequencing by BGI tech. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were filtered by custom BGI scripts. Low-quality reads include two types, and reads of the two types were removed: (1) when the ratio of N in whole read was over 10%; (2) when the ratio of base whose quality was less than 20 was over 10%. Observed cytosines on the forward read of each read pair were in silico replaced by thymines, and observed guanines on the reverse read of each read pair were in silico replaced by adenines. The “alignment form” reads were then mapped to the “alignment form” reference genome by SOAP aligner. Every hit with a single placement with minimum numbers of mismatches and a clear strand assignment was defined as unambiguous alignment (uniquely mapped reads) and was used for methyl-cytosine ascertainment. Only the uniquely mapped reads were used to estimate the copy numbers of the local region. Genomic bases with a copy number larger than 1.5 were not used to call methylcytosines and not used in any subsequent analysis to avoid errors caused by misalignment.
Genome_build: hg19
Supplementary_files_format_and_content: chromosome-specific text files including coordinates of CpG positions and counts of methylated reads and coverage at each position.

source_name: modified HEK293

extract_protocol: Isolated DNA was reduced into 100-300 bp fragments by sonication and treated with DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adapters. Samples underwent bisulfite treatment with the ZYMO EZ DNA Methylation-Gold kit, with 99.6% bisulfite conversion rate. Desalted, size-selected, PCR amplified fragments were size-selected again.

treatment_protocol: EZ DNA Methylation-Gold bisulfite conversion kit (Zymo Research, USA)

value: modified HEK293 cell overexpressing BAHD1


title: Lib185

value: CCRF-CEM

value: human acute lymphocytic leukemia (ALL) cell line

tag: fixation

value: DMA + FA


title: 51yo ctx myeloid

value: 51 years old


title: Wild-type infection 0 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:WT:00_h:R2

value: HeLa-S3 (ATCC CCL-2.2)

value: Salmonella Typhimurium SL1344


title: 16 h mock infection replicate 2

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: Wild-type infection 0 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:WT:00_h:R1


title: 16 h pinT replicate 2


title: 16 h mock infection replicate 1


title: 45yo ctx myeloid

value: 45 years old


title: Lib181

value: human acute monocytic leukemia (AML) cell line

tag: treatment

value: pMY136 (PAF1 shRNA #1)

value: PAF1 knockdown

tag: chip antibody vendor

value: LSBio

tag: chip antibody cat. #


title: ΔpinT infection 24 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:24_h:R3

value: Salmonella Typhimurium SL1344 delta-pinT


title: SPI-2 (in vivo) pinT vector 5 min ara replicate 2

description: HeLa-S3:SPI-2_STnc440_vector:05_min_ara:R2

value: Salmonella typhimurium SL1344


title: 16 h pinT replicate 1


title: Lib180

value: pMY56 (control)

value: vector control


title: Lib177

value: pMY137 (PAF1 shRNA #2)

value: Pol II

value: Santa Cruz

value: EGS+ FA


title: ΔpinT infection 24 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:24_h:R2


title: ΔpinT infection 24 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:24_h:R1


title: 47yo ctx oligo

value: 47 years old

value: O4 positive cells

value: Oligodendrocyte


title: 63yo ctx B oligo

value: 63 years old

value: GalC positive cells


title: Lib176

value: CCRF-CEM

value: human acute lymphocytic leukemia (ALL) cell line


title: ΔpinT infection 16 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:16_h:R3

value: HeLa-S3 (ATCC CCL-2.2)

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: SPI-2 (in vivo) pinT vector 5 min ara replicate 1

description: HeLa-S3:SPI-2_STnc440_vector:05_min_ara:R1


title: SPI-2 (in vivo) empty vector 5 min ara replicate 1

description: HeLa-S3:SPI-2_empty_vector:05_min_ara:R1


title: 63yo ctx A oligo


title: ΔpinT infection 16 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:16_h:R2

value: Salmonella Typhimurium SL1344 delta-pinT


title: Lib174

value: Bethyl


title: 25yo ctx neuron

value: 25 years old

value: Thy1 positive cells

value: Neuron


title: 22yo ctx oligo

value: 22 years old


title: 53yo B Hippocampus astro

source_name: Hippocampus

value: 53 years old

value: HepaCAM positive cells

value: Astrocyte


title: 24 h WT GFP+ replicate 3

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Human: hg19/GRCh37; Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

extract_protocol:
miRvana for total RNA (Ambion)
miRvana kit for total RNA (Ambion) or TRIzol (Invitrogen) as indicated
cDNA libraries for Illumina sequencing were generated by Vertis Biotechnology AG, Freising-Weihenstephan, Germany (http://www.vertisbiotech.com/). A minimal amount of ~100 ng of total RNA was required for cDNA library preparation. DNase I-treated total RNA samples were first sheared via ultra-sound sonication (4 pulses of 30 s at 4°C each) to generate on average ~200-400 bp fragmentation products. Then, fragments <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). As an internal quality control for this pilot experiment, spike-in RNA (sequence of spike: 5’-AAAUCCGUUCGUACGGGCCC-3’; was 5’-monophosphorylated and gel-purified) was added to a final concentration of 0.5%. The samples were then poly(A)-tailed using poly(A) polymerase and the 5’triphosphate (and eukaryotic cap) structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (NEB). The resulting cDNA was PCR-amplified to about 20-30 ng/µL using a high fidelity DNA polymerase (barcode sequences for multiplexing were part of the 3’primers). The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Agilent Technologies).

value: Salmonella typhimurium SL1344


title: SPI-2 (in vivo) empty vector 5 min ara replicate 2

description: HeLa-S3:SPI-2_empty_vector:05_min_ara:R2


title: Lib153

value: human acute monocytic leukemia (AML) cell line

value: pMY201 (CDK9 shRNA #1)

value: PAF1 knockdown

value: Pol II

value: Santa Cruz

value: EGS+ FA


title: 24 h mock GFP- replicate 3

value: HeLa-S3 (ATCC CCL-2.2)

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: ΔpinT infection 8 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:08_h:R3

value: Salmonella Typhimurium SL1344 delta-pinT


title: Lib146

source_name: THP1 ChIP-seq

value: DMA + FA


title: 53yo A Hippocampus astro


title: ΔpinT infection 16 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:16_h:R1


title: 24 h WT GFP- replicate 3


title: 63yo ctx 3 oligo

value: 63 years old

value: O4 positive cells

value: Oligodendrocyte