title: Input-DNA_MBD


title: UW_ChipSeq_A549_CTCFRep1

status: Public on Oct 19 2012

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwTfbs

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: epithelial cell line derived from a lung carcinoma tissue. (PMID:175022), "This line was initiated in 1972 by D.J. Giard, et al. through explant culture of lung carcinomatous tissue from a 58-year-old caucasian male." - ATCC, newly promoted to tier 2:not in 2011 analysis

tag: cell karyotype

value: cancer

tag: cell lineage

value: endoderm

tag: cell sex

value: M

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labexpid

tag: labversion

tag: replicate


title: UW_ChipSeq_SK-N-MC_InputRep1

source_name: SK-N-MC

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: SK-N-MC

tag: cell organism

tag: cell description

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor, "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: ectoderm

value: F

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.


title: UD-H2AK119Ub_ChIP

city: Augusta

first: Keith

last: robertson

address: 1120 15th street

institute: Georgia Health Sciences University

data_processing:
Novoalign V2.07.00 (-F ILMFQ -r All 10 -o SAM)
MACS 1.4 (-w -f AUTO --call-subpeaks)
DANPOS 0.7.0
Genome_build: hg19
Supplementary_files_format_and_content: All peaks are generated using MACS 1.4 against input.

Each file (except DF-NP.bed and UD-NP.bed) has five columns as following:
1). Chromosome
2). 0-index starting position (inclusive)
3). 0-index end position (exclusive)
4). MACS statistics
5). Peak score

DF-NP.bed and UD-NP.bed have seven columns as following:
1). Chromosome
2). 0-index starting position (inclusive)
3). 0-index end position (exclusive)
4). summit position
5). summit value
6). strand
7). -log(p value)

growth_protocol: NCCIT cells were cultured in McCoy’s 5A medium (Invitrogen) supplemented with 2 mm L-glutamine (Mediatech) and 10% heat-inactivated fetal bovine serum (Hyclone).

extract_protocol: Protein-DNA complexes were isolated with antibodies and libraries were constructed according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Treatment of NCCIT cells with 10 μM all-trans retinoic acid (RA) was performed for up to 7 days

tag: cell type

value: embroynic cancer

tag: cell line

value: NCCIT

tag: cell status

value: differentiated

tag: chip antibody

tag: antibody source

value: Millipore (07-146)


title: DF-H2AK119Ub_ChIP


title: DF-H3K27me3_ChIP

value: Abcam (ab6002)


title: DF-DNMT3B_ChIP


title: DF-DNMT3A_ChIP

value: Santa Cruz (sc-20703)


title: DF-DNMT1_ChIP

value: Santa Cruz (sc-10219)


title: DF-H3K4me3_ChIP

value: Abcam (ab1012)


title: DF-H3K36me3_ChIP

value: Abcam (ab9050)


title: DF-H3K9me3_ChIP

value: Abcam (ab8898)


title: UD-H3K27me3_ChIP

value: undifferentiated


title: DF-NCCIT_MBD

extract_protocol: Enrichment for methylated DNA is essentially based on the MIRA _methylated CpG island recovery assay_ described in {Rauch, 2005 #4114} with the following modifications, using the MethylMagnet mCpG DNA Isolation Kit (RiboMed).  Libraries were constructed according to Illumina's instructions accompanying the DNA Sample Kit _Part# 0801-0303_ and sequenced on the Genome Analyzer following the manufacturer's protocols.


title: UD-H3K36me3_ChIP


title: UD-DNMT1_ChIP


title: UD-DNMT3B_ChIP


title: Input-DNA_ChIP

value: None (input)


title: UD-DNMT3A_ChIP


title: FLAG-Magoh:eIF4AIII  Rep 3 RIPiT-Seq

status: Public on Oct 18 2012

city: Worcester

first: Alper

last: Kucukural

state: MA

address: Lazare Medical Research Building, 870P

department: Biochemistry and Molecular Pharmacology

institute: UMass Medical School

description: Short RNA footprint library from EJC tandem IP.

library_source: transcriptomic

data_processing:
Adapters were removed from short reads using ABI's SOLiD small RNA pipeline (version 0.5.0; custom-fitted with human genomic and exon junction reference sequences).  Colorspace sequences were then converted to sequence space using Ma2Gff conversion tool (version 0.2.06). These gff files were converted to fasta files for further analysis and mapping. Before mapping, abundant non-coding RNAs (rRNAs, snoRNAs etc.) and repetitive sequences (SINEs, LINEs etc.) were filtered out. The rest of the reads were mapped to human genome and exon-junction database using Bowtie (0.12.7; parameters:-p 8 -v 1 -a --strata --best -m 1). The uniquely mapped reads are provided here as bed formats.
Genome_build: hg18
Supplementary_files_format_and_content: bed format alignments generated like in the step above.

molecule: total RNA

source_name: HEK293 cells

growth_protocol: Flp-In TRex-HEK293 cells containing a stable copy of FLAG-tagged EJC proteins routinely were grown in Dulbecco's modified eagle medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin. For generating each EJC footprint library, cells were grown in three 15-cm plates for immunoprecipitation.

extract_protocol:
RIPiT-Seq: Total cell extracts generated by sonication in a buffer containing 300 mM NaCl were used for EJC immunoprecipition. RNA-Seq: PolyA+ RNA was extracted from Flp-In HEK293 cells and base-hydrolyzed. mRNP-Seq: Cleared nuclear extracts from Flp-In HEK293 cells were used to isolate footprints of polyA+ RNPs.
Size-selected RNA fragments were used to generate deep sequencing libraries using the small RNA expression kit (Applied Biosystems) following steps recommended by the manufacturer.

treatment_protocol: Expression of the FLAG-tagged protein was induced with tetracycline for ~16 hr. One hour prior to cell harvesting, cycloheximide (CHX) was added to 100 ug/ml. For formaldehyde crosslinking, cells were resuspended in PBS+CHX+0.1% formaldehyde. After gently mixing the suspension at room temperature for 10 minutes, reactions were quenched with one-tenth volume of quenching buffer (2.5 M Glycine, 25 mM Tris-base).

value: Flp-In 293 T-Rex (Life technologies)

tag: antibody 1

value: anti-FLAG M2 (Sigma A2220)

tag: antibody 1 manufactuer

value: Sigma

tag: antibody 1 catalog #

tag: antibody 2

value: anti-eIF4AIII (2256C1, SantaCruz sc-81263)

tag: antibody 2 manufactuer

tag: antibody 2 catalog #


title: FLAG-Magoh:eIF4AIII  Rep 2 RIPiT-Seq

value: Santa Cruz


title: FLAG-eIF4AIII:Y14 (+ formald) RIPiT-Seq

description: Short RNA footprint library from EJC tandem IP from formaldehyde crosslinked cells.

value: anti-Y14 (4C4; Sigma Y1253)


title: RNA-Seq

description: RNA-Seq library from Flp-In HEK293 cells

data_processing:
In step 1, adapters were removed from short reads using ABI's SOLiD small RNA pipeline (version 0.5.0; custom-fitted with human genomic and exon junction reference sequences).  Colorspace sequences were then converted to sequence space using Ma2Gff conversion tool (version 0.2.06). These gff files were converted to fasta files for further analysis.
In step 2, abundant non-coding RNAs (rRNAs, snoRNAs etc.) and repetitive sequences (SINEs, LINEs etc.) were filtered out. The rest of the reads were mapped to human genome and exon-junction database using Bowtie (0.12.7; parameters:). The uniquely mapped reads are provided here as bed formats.
Genome_build: hg18
Supplementary_files_format_and_content: fastq format reads generated in step 1 above.
Supplementary_files_format_and_content: bed format alignments generated in step 2 above.

extract_protocol:
T-RIP-Seq: Total cell extracts generated by sonication in a buffer containing 300 mM NaCl were used for EJC immunoprecipition. RNA-Seq: PolyA+ RNA was extracted from Flp-In HEK293 cells and base-hydrolyzed. mRNP-Seq: Cleared nuclear extracts from Flp-In HEK293 cells were used to isolate footprints of polyA+ RNPs.
Size-selected RNA fragments were used to generate deep sequencing libraries using the small RNA expression kit (Applied Biosystems) following steps recommended by the manufacturer.


title: FLAG-Magoh:eIF4AIII  Rep 1 RIPiT-Seq


title: FLAG-eIF4AIII:Y14 Rep 1 RIPiT-Seq


title: FLAG-eIF4AIII-HMW RIP-Seq

description: Long RNA footprint library from HMW EJCs.


title: FLAG only:Y14 RIPiT-Seq

description: Short RNA footprint library from control tandem IP.


title: FLAG-Magoh:eIF4AIII-long RIPiT-Seq

description: Long RNA footprint library from EJC tandem IP.


title: Rag1-/- proB_IGH_Enriched

city: San Diego

first: Lana

last: Schaffer

address: 10550 North torrey Pines Road

department: DNA Array Core

institute: TSRI

data_processing:
The initial data analysis of 40bp and 100bp RNA-seq was performed using the Genome Analyzer Pipeline Software (Casava 1.8.1) including the image analysis, base calling, and alignment.
The reads were adaptor trimmed using Flicker 3.0, which is an Illumina proprietary early access software.  TopHat (tophat.cbcb.umd.edu), a splice junction mapper for RNA-Seq reads, was used for read alignment to the Mouse genome Build version mm9.
BEDtools v2.13.3 was used to convert the output BAM file to BED12 format.  Reads to Chromosome 12 were extracted and partitioned by plus and minus strand reads.  The junction reads were split and any segments >25bp were retained.  The mapped reads were then sorted and the duplicates with the same start and end positions were removed.  Finally, the BED files were converted to BEDgraph files using the BEDtools function genomeCoverageBed.
The GTF file was created from mm9 (UCSC Genome  table browser)
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

organism: Mus musculus

source_name: Rag1-/- proB_IGH_Enriched; Bone marrow cells isolated from  Rag1-/- mice were enriched for CD19+ pro-B cells with MACS microbeads.  RNA was enriched on an array contain DNA from the Ig loci.

growth_protocol: Bone marrow cells were isolated from 4- to 8-wk-old Rag1-/- mice and were enriched for CD19+ pro-B cells with MACS microbeads. RNA was directly prepared from the ex vivo collected cells.

extract_protocol:
Total RNA was prepared from CD19+ RAG1-/- pro-B cells using Trizol, and was depleted of ribosomal RNA using RiboMinus (Invitrogen) kit.
10 μg of total RNA from freshly isolated Rag1-/- pro-B cells was depleted of ribosomal RNA (rRNA) using RiboMinus (Invitrogen) kit. The depletion was verified using Agilent 2100 Bioanalyser. Approximately 200 ng of Ribo-minus treated total RNA was prepared for Next Generation Sequencing using a slightly modified version of the Illumina protocol (Directional_mRNA-Seq_SamplePrep_Guide_15018460_A.pdf), in which 12 cycles of PCR were performed instead of 15 and standard Truseq adapters and Truseq barcoded primers were used instead of the v1.5 adapters and primers described in the guide. A final size selection was performed using agarose gel to capture a library with insert sizes ranging from 50 – 150 bases in length suitable for 40 base single read sequencing. The library product was purified from agarose using standard oligo purification columns. For the Rag1-/- proB_IGH_Enriched sample, we followed the procedure described above except that we selected insert sizes to be 150-200 bases in length. In addition, after the first round of gel purification, 8 additional cycles of PCR was performed, followed by another gel purification step, then 12 more cycles of PCR followed by Ampure XP bead purification. cDNA was hybridized to arrays using Agilent protocols. After elution of target from the arrays, the sample was PCR amplified for 18 additional cycles (based on Agilent’s protocols). The library was gel purified before loading onto the flow-cell for sequencing the 100bp reads.
Agilent arrays used for target enrichment:  Custom Agilent arrays were made to enrich the total RNA for all RNA hybridizing to the non-repetitive DNA of the immunoglobulin loci.

tag: strain

value: CD19+ pro-B cell

tag: genotype/variation

tag: protocol

value: IGH-enriched


title: UD-H3K9me3_ChIP

value: embroynic cancer

value: NCCIT


title: Chip-Seq input control

city: La Jolla

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court Suite 300

description: Input Control

data_processing:
Data filtering by duplicate read removal.
Mapping with bowtie. Settings  -q -y -a -n 2 -p 8 --best --strata
Filtering for uniquely mapped reads as well as reads mapped to multiple locations within the IgH and LINE repeats.
Binning of reads in 25 bp windows.
Significant bins determined by dynamic windows utilizing Poisson distribution where the null distribution is based upon the the greater of the entire genome, 1kb, 5kb, and 10kb windows as baseline.
Genome_build: mm9
Supplementary_files_format_and_content: YY1.wig - YY1 reads with input control reads subtracted. YY1.peaks.txt - significant peaks at 1e-5 threshold of significance.

source_name: Rag1 -/- pro-B cells

growth_protocol: Bone marrow cells were isolated from 4- to 8-wk-old Rag1−/− mice and were enriched for CD19+ cells with MACS microbeads.

extract_protocol:
B6 Rag1−/− pro-B cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the lysates were sonicated using a Diagenode Biorupter. The chromatin solution was precleared with salmon sperm DNA-protein A agarose beads. The lysate was immunoprecipitated with an antibody against YY1 (abcam, ab 12132 and Santa Cruz Biotechnology, H-414). Immune complexes were isolated with protein A agarose beads.  Following elution, chromatin-antibody complexes and input DNA were reverse crosslinked by heating at 65°C overnight.  The DNA was purified using the Qiagen DNA purification kit.
The sequencing libraries were prepared using 10 ng double-stranded cDNA prepared by ChIP (pull-down and input). ChIP DNA samples ends were repaired using recommended Illumina protocol including T4 DNA polymerase, Klenow Large Fragment, and T4 polynucleotide kinase. DNA products were purified using DNA Clean&Concentrator™-5 Kit (Zymo Research). Next, DNA ends were A-tailed with Klenow (3’→5’ exo-) at 37C for 30 min. DNA products were again purified using the DNA Clean&Concentrator™-5 Kit. Next, Illumina Paired End-adapter oligonucleotides, at 0.33 μM concentration, were ligated to the A-tailed cDNA ends with T4 DNA ligase. DNA products were purified using DNA Clean&Concentrator™-5 Kit. The DNA library products were then separated on a 2% agarose gel and products corresponding to a size of approximately 200-250 bases were removed from the gel and cleaned using the Agencourt SPRI system (Beckman). The DNA material was PCR amplified with Phusion™ Polymerase (Finnzymes) with 0.6 μM PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles. The amplified DNA products were further purified on 2% agarose gel, excised, and isolated again using Zymoclean™Gel DNA recovery kit. The purified DNA library was quantitated using the Qubit quantitation platform (Invitrogen) and sized using the 2100 Bioanalyzer (Agilent). DNA products were then denatured in 0.1N NaOH and diluted to a final concentration of 10 pM before being loaded onto the Illumina paired-end flow-cell for massively parallel sequencing by synthesis on the Illumina GAIIx.

value: pro-B cells

tag: genotype

value: Rag -/-


title: Rag1-/- proB

source_name: Rag1-/- proB; Bone marrow cells isolated from  Rag1-/- mice were enriched for CD19+ pro-B cells with MACS microbeads.

value: control


title: FLI1 c-Kit

city: Cambridge

first: Rebecca

middle: Louise

last: Hannah

address: Addenbrookes Hospital, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: wildtype

data_processing:
The reads in fastq format were aligned to mm9 using bowtie-0.12.7 (output in SAM format). The SAM files were converted to BED and ELAND formats using in-house scripts - Peaks were calculated from the eland files using the peak finding program MACS-1.4.2 with the following parameters: mfold=10,16 -bw=100 -pvalue=1e-9  -gsize=1870000000
bedGraphs created in-house
Genome_build: mm9
Supplementary_files_format_and_content: Bed and bedGraph – aligned reads and read density profiles

source_name: differentiating murine hematopoietic cells

growth_protocol: A single cell suspension of ES cells was transferred into IVD media (IMDM with 15 % FCS, Pen/Strep, 1 mM glutamine, 0.15 mM MTG, 0.18 mg/ml human transferrin (Roche 652202) and 50 µg/ml ascorbic acid) on 15 cm low adherence bacteriological plates (Sterilin) at a concentration of 2.5 X 104/ml. After 3.25 days embryoid bodies were collected and dissociated by digested with 1 x trypsin/EDTA. The cell suspension was re-suspended in IMDM + 20 % FCS. Flk-1+ (CD309) cells were isolated using a biotinylated Flk-1 antibody (eBioscience 13-5821) used at 5 µl per 107 cells for 10 minutes on ice, followed by 2x wash with MACS buffer (PBS + 5 % BSA and 0.5 mM EDTA). Cells bound by the antibody were then isolated using antibiotin beads and MACS LS columns (Miltenyi Biotec) according to the manufacturers instructions. Purified Flk-1+ve cells were plated in blast media (IMDM supplemented with 10% FCS, Pen/Strep, 1 mM glutamine, 0.45 mM MTG, 0.18 mg/ml human transferrin, 25 µg/ml Ascorbic acid, 20 % D4T conditioned media, 5 µg/L mVEGF (Peprotech), 10 µg/L mIL-6 (Miltenyi Biotec)) at a concentration of 8-10 X103/cm2 on gelatinized tissue culture treated dishes. D4T conditioned media was made by growing confluent D4T cells in fresh IMDM media supplemented with 10 % FCS, Pen/Strep, 1 mM glutamine, 0.15 mM MTG and 50 ng/ml acidic human FGF (R&D Sytems) for 3-4 days. After 2-2.5 days cells were trypsinised, again MACS sorted for Flk-1+ cells as described before and 2x104/ cm2 Flk-1+ cells were plated on gelatin coated tissue culture plates and cultured for 2 days. Hemogenic endothelium media – IMDM supplemented with 10 % FCS, Pen/Strep, 1 mM glutamine, 0.15 mM MTG, 0.18 mg/ml human transferrin, 25 µg/ml Ascorbic acid, Oncostatin 10 µg/ml (R&D Systems 495-MO), basic mFGF 1 µg/ml (Peprotech 450-33), mSCF 10 µg/ml (Peprotech 500-P71).

extract_protocol: Libraries of DNA fragments from chromatin immunoprecipitation were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Qiagen MinElute columns (according to the manufacturer’s guidelines). ‘A’ bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further column clean up to remove excess adaptors, fragments were amplified in an 18-cycle PCR reaction using adapter-specific primers (5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGA*T. The libraries were purified and adapter dimers removed by running the PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 µl of each sample on an Agilent Technologies 2100 Bioanalyser.  Once prepared, DNA libraries were subject to massively parallel DNA sequencing on an Illumina Genome Analyzer.

treatment_protocol: Hemogenic endothelium (HE) cells were treated for an overnight period with 0.3 µl/ml doxycycline to induce the expression of Runx1 (Tet-on system)

value: progenitors

tag: chip antibody vendor

value: santa cruz biotechnology

tag: chip antibody cat. #

tag: chip antibody lot #


title: H3 K9Ac induced (iRunxHE+dox)

description: with induction

tag: cell type

value: hemogenic endothelium

tag: treated with

value: 0.3 µl/ml doxycycline

value: H3 K9Ac

value: Abcam


title: SCL c-Kit

description: wildtype

tag: chip antibody

value: SC


title: YY1 Chip-Seq

description: YY1 Chip-Seq Data

tag: chip antibody 1

tag: chip antibody manufacturer 1

tag: chip antibody catalog # 1

tag: chip antibody 2

tag: chip antibody manufacturer 2

tag: chip antibody catalog # 2


title: H3 K9Ac uninduced (iRunxHE-dox)

description: without induction


title: SCL induced (iRunxHE-dox)

description: with induction

value: SCL


title: FLAG-eIF4AIII:Y14 Rep 2 RIPiT-Seq

value: Flp-In 293 T-Rex (Life technologies)

tag: cell line

tag: antibody 1

value: anti-FLAG M2 (Sigma A2220)

tag: antibody 1 manufactuer

value: Sigma

tag: antibody 1 catalog #

tag: antibody 2

tag: antibody 2 manufactuer

tag: antibody 2 catalog #


title: FLAG only:PHGDH RIPiT-Seq

value: anti-3PGDH (6B2, SantaCruz sc-100317)

value: Santa Cruz


title: RNA Pol II uninduced (iRunxHE-dox)

description: without induction

tag: strain

value: RNA Pol II

tag: chip antibody vendor

tag: chip antibody cat. #

tag: chip antibody lot #


title: CEBPb uninduced (iRunxHE-dox)

description: without induction

tag: cell type

tag: chip antibody

value: CEBPb


title: Nuclear mRNP protection (mRNP-Seq)

description: Short RNA footprint library from nuclear polyA+ RNPs.


title: RUNX Input ES

description: without induction

value: ES cells


title: FLI1 uninduced (iRunxHE-dox)

description: without induction


title: FLI1 induced (iRunxHE+dox)

description: with induction

tag: treated with


title: RUNX uninduced (iRunxHE-dox)

description: without induction

value: Anti-HA


title: SCL uninduced (iRunxHE-dox)

description: without induction


title: RUNX induced (iRunxHE+dox)

description: with induction


title: Footprints from cells infected with HCMV for 72hr, pretreated with cycloheximide, replicate

status: Public on Oct 17 2012

city: San Francisco

first: Noam

last: Ginossar

address: 1700 4th street

institute: UCSF

description:
fp_chx_72hr_s6
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_chx_72hr_s6_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_chx_72hr_s6_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

organism: Human betaherpesvirus 5

source_name: Human fibroblasts infected with HCMV, cycloheximide, 72hr

extract_protocol:
Cells were lysed with 0.5% Triton, and the lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using the acid:phenol extraction method.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

value: Merlin

value: HCMV-infected human foreskin fibroblasts

tag: drug pre-treatment

value: cycloheximide

tag: infection duration


title: Footprints from cells infected with HCMV for 5hr, pretreated with LTM

description:
fp_LTM_05hr_s14
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_LTM_05hr_s14_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_LTM_05hr_s14_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, LTM, 5hr

value: lactimidomycin (LTM)


title: mRNA-seq from cells infected with HCMV for 24hr

description:
mrna_24hr_s1
mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
mrna_24hr_s1_merlin.align.unique.5_prime.merged.minus.wig: NC_006273.2
mrna_24hr_s1_merlin.align.unique.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, 24hr

extract_protocol:
RNA was extracted by lysing cells with Trizol.
Fragmented mRNA was size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.


title: mRNA-seq from cells infected with HCMV for 5hr

description:
mrna_05hr_s1
mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
mrna_05hr_s1_merlin.align.unique.5_prime.merged.minus.wig: NC_006273.2
mrna_05hr_s1_merlin.align.unique.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, 5hr


title: mRNA-seq from cells infected with HCMV for 5hr, replicate

description:
mrna_05hr_s11
mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
mrna_05hr_s11_merlin.align.unique.5_prime.merged.minus.wig: NC_006273.2
mrna_05hr_s11_merlin.align.unique.5_prime.merged.plus.wig: NC_006273.2


title: mRNA-seq from cells infected with HCMV for 72hr, replicate

description:
mrna_72hr_s11
mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
mrna_72hr_s11_merlin.align.unique.5_prime.merged.minus.wig: NC_006273.2
mrna_72hr_s11_merlin.align.unique.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, 72hr


title: mRNA-seq from cells infected with HCMV for 72hr

description:
mrna_72hr_s1
mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
mrna_72hr_s1_merlin.align.unique.5_prime.merged.minus.wig: NC_006273.2
mrna_72hr_s1_merlin.align.unique.5_prime.merged.plus.wig: NC_006273.2


title: Footprints from cells infected with HCMV for 5hr, no drug pretreatment

description:
fp_nodrug_05hr_s4
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_nodrug_05hr_s4_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_nodrug_05hr_s4_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, none, 5hr


title: mRNA-seq from cells infected with HCMV for 24hr, replicate

description:
mrna_24hr_s11
mRNA

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
mrna_24hr_s11_merlin.align.unique.5_prime.merged.minus.wig: NC_006273.2
mrna_24hr_s11_merlin.align.unique.5_prime.merged.plus.wig: NC_006273.2


title: Footprints from cells infected with HCMV for 72hr, no drug pretreatment

description:
fp_nogrug_72hr_s4
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_nodrug_72hr_s4_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_nodrug_72hr_s4_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, none, 72hr


title: Footprints from cells infected with HCMV for 5hr, pretreated with Harringtonine

description:
fp_harr_05hr_s3
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_harr_05hr_s3_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_harr_05hr_s3_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, Harringtonine, 5hr

value: Harringtonine


title: Footprints from cells infected with HCMV for 72hr, pretreated with cycloheximide

description:
fp_chx_72hr_s1
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_chx_72hr_s1_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_chx_72hr_s1_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2


title: Footprints from cells infected with HCMV for 5hr, pretreated with cycloheximide

description:
fp_chx_05hr_s1
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_chx_05hr_s1_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_chx_05hr_s1_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, cycloheximide, 5hr


title: Footprints from cells infected with HCMV for 24hr, pretreated with cycloheximide

description:
fp_chx_24hr_s1
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_chx_24hr_s1_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_chx_24hr_s1_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, cycloheximide, 24hr


title: nrpe1 ChIP

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

description: AGO4 antibody is a rabbit polyclonal antibody raised against the C-terminal chunk of AGO4 (aa 573-924) and affinity-purified (PMID: 19377477).

data_processing:
In essence, all reads were pre-processed and mapped to the Arabidopsis genome using a pipeline as previously described (Zheng, Q., PLoS Genet. 2010) with slight modifications. First, all raw reads were aligned to the Illumina Genomic DNA 3'-adaptor sequence using cross-match program from Phrap package and those with ≥10 nts of alignment at the 3'-end with ≤10% mismaches were subsequently trimmed at the insert/adaptor junctions. Reads without detectable 3'-adaptors were also kept un-changed for subsequent processing. Then both trimmed and untrimmed reads were reduced to non-redundant (NR) tags by collapsing reads with identical sequences, to save processing time and space requirements. The clone-number for each NR-tag was also recorded for subsequent analysis. The trimmed and untrimmed NR-tags/reads were mapped to Arabidopsis thaliana genome (TAIR9 assembly) independently using the Bowtie, allowing ≤6% of seed mismatches (34 nt seeds), ≤8% of total mismatches and all valid alignments are reported. A subsequent parsing step was implemented to enforce these restraints, as well as to require insert lengths of ≥15 nt or ≥30 nt for the trimmed and untrimmed reads, respectively. It is of importance that the actual "insert length" for untrimmed reads was determined according to their alignments, by implementing a one-dimensional dynamic programming algorithm that could identify the most possible insert-fragment length based on output from Bowtie. Finally, we filtered only "best-stratum" alignments that contain ≤4% more mismatches compared to the best-hits for any given read. At last, all mapped trimmed and untrimmed reads (NR-tags) were combined and their mapping and clone-number information was recorded.  Alignment input file for CSAR peak calling, using weighted clone-number for NR-tags were provided as processed data.
Genome Build:
nrpe1_chip_NR_TAIR9_CSAR.txt: TAIR9

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana nrpe1 (nrpd1b-11) and ago4 (ago4-1 (Zilberman, D., Science 2003) introgressed into the Col-0 background) were described previously (Onodera, Y., Cell 2005; Wierzbicki, A.T., Nat. Genet. 2009). Plants were cultivated at 22C under long day conditions (16 h day, 8 h night).

extract_protocol: ChIP was performed as described (Rowley, M.J., PLoS Genet. 2011) with slight modifications. 3 g of 2-3 week old seedling tissue was harvested and crosslinked with 0.5% formaldehyde for 2 min followed by 8 min vacuum infiltration. Glycine was added to 80 mM and vacuum reapplied for 1 min then 4 min. Crosslinked tissue was rinsed with water and frozen in liquid nitrogen. Nuclei were extracted by grinding frozen tissue into powder using a mortar and pestle, suspended in 25 ml of Honda Buffer (20 mM HEPES-KOH pH 7.4, 0.44 M sucrose, 1.25% ficoll, 2.5% Dextran T40, 10 mM MgCl2, 0.5% Triton X-100, 5 mM DTT, 1 mM PMSF, 1% plant protease inhibitors (Sigma)), filtered through two layers of Miracloth and centrifuged at 2000 x g for 15 min. Nuclear pellets were washed three times with 1 ml of Honda buffer, resuspended in Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF, 1% Plant Protease Inhibitors) and DNA was fragmented to the average size of 250 bp by 8 pulses of sonication each 10 seconds long with 1 minute pauses in between pulses using Fisher Scientific 100 Sonic Dismembrator at power setting 1. After centrifugation at 16,000 x g for 10 min, the supernatant was diluted 10-fold with 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl. 50 ul Dynabeads Protein A (Invitrogen) and the appropriate antibody were added and samples were incubated for 8 h at 4 C on a rotating mixer. Bead-antibody complexes were washed 5 times, 5 min each, with binding/washing buffer (150 mM NaCl, 20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 1 mM PMSF and twice for 5 min each with TE. Samples for ChIP-seq were eluted with RIP elution buffer (100 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) for 20 min at 65C and were digested with 20 μg of proteinase K (Invitrogen) overnight at 60C. An equal volume of phenol/chloroform/isoamyl alcohol pH 6.7 25:24:1 was added to extract DNA, followed by addition of an equal volume of chloroform/isoamyl alcohol 24:1 and subsequent precipitation by addition of 2 volumes 100% EtOH, 0.1 volume 3 M Sodium Acetate and 4 ul Glycoblue (Ambion). Precipitated samples were washed once with 70% EtOH and resuspended in 30 ul TE. All ChIP-seq libraries were prepared according to the Illumina ChIP-seq library preparation protocol.

tag: background ecotype

tag: genotype/variation

value: nrpe1 mutant

tag: tissue

value: 2-3 week old seedling

value: AGO4 antibody


title: ago4 input

data_processing:
In essence, all reads were pre-processed and mapped to the Arabidopsis genome using a pipeline as previously described (Zheng, Q., PLoS Genet. 2010) with slight modifications. First, all raw reads were aligned to the Illumina Genomic DNA 3'-adaptor sequence using cross-match program from Phrap package and those with ≥10 nts of alignment at the 3'-end with ≤10% mismaches were subsequently trimmed at the insert/adaptor junctions. Reads without detectable 3'-adaptors were also kept un-changed for subsequent processing. Then both trimmed and untrimmed reads were reduced to non-redundant (NR) tags by collapsing reads with identical sequences, to save processing time and space requirements. The clone-number for each NR-tag was also recorded for subsequent analysis. The trimmed and untrimmed NR-tags/reads were mapped to Arabidopsis thaliana genome (TAIR9 assembly) independently using the Bowtie, allowing ≤6% of seed mismatches (34 nt seeds), ≤8% of total mismatches and all valid alignments are reported. A subsequent parsing step was implemented to enforce these restraints, as well as to require insert lengths of ≥15 nt or ≥30 nt for the trimmed and untrimmed reads, respectively. It is of importance that the actual "insert length" for untrimmed reads was determined according to their alignments, by implementing a one-dimensional dynamic programming algorithm that could identify the most possible insert-fragment length based on output from Bowtie. Finally, we filtered only "best-stratum" alignments that contain ≤4% more mismatches compared to the best-hits for any given read. At last, all mapped trimmed and untrimmed reads (NR-tags) were combined and their mapping and clone-number information was recorded.  Alignment input file for CSAR peak calling, using weighted clone-number for NR-tags were provided as processed data.
Genome Build:
ago4_input_NR_TAIR9_CSAR.txt: TAIR9

source_name: ago4_input DNA

value: ago4 mutant


title: Footprints from cells infected with HCMV for 72hr, pretreated with LTM

description:
fp_LTM_72hr_s14
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_LTM_72hr_s14_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_LTM_72hr_s14_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, LTM, 72hr


title: UD-H3K4me3_ChIP

data_processing:
Novoalign V2.07.00 (-F ILMFQ -r All 10 -o SAM)
MACS 1.4 (-w -f AUTO --call-subpeaks)
DANPOS 0.7.0
Genome_build: hg19
Supplementary_files_format_and_content: All peaks are generated using MACS 1.4 against input.

Each file (except DF-NP.bed and UD-NP.bed) has five columns as following:
1). Chromosome
2). 0-index starting position (inclusive)
3). 0-index end position (exclusive)
4). MACS statistics
5). Peak score

DF-NP.bed and UD-NP.bed have seven columns as following:
1). Chromosome
2). 0-index starting position (inclusive)
3). 0-index end position (exclusive)
4). summit position
5). summit value
6). strand
7). -log(p value)

value: embroynic cancer

tag: cell line

value: NCCIT

tag: cell status

value: undifferentiated

tag: antibody source

value: Abcam (ab1012)


title: LCLBACD3, small RNA sequencing

status: Public on Oct 16 2012

city: Durham

middle: L

last: Skalsky

state: NC

address: 430 CARL, Research Dr.

institute: Duke University

description:
Small RNA sequencing.
Small RNAs, 18-24 nt.
5' barcode: GCCTA
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT

data_processing:
Mapping Reads: The reads from Ago2 PAR-CLIP deep sequencing libraries were stripped of the 3' adapter sequence and 5' barcode using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads that were less than 13 nt in length or contained an ambiguous nucleotide were discarded. The remaining reads were aligned to the human genome (hg19), with up to 2 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009). Mapped locations were only reported for those with the minimum number of observed mismatches for each read. All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location. After subtraction, only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis. The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1 (Hubbard et al., 2007). If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3'UTR, coding sequence, 5'UTR, intron, non-coding RNA, intergenic.
Defining microRNA interaction sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained ≥5 reads with conversions at two or more locations. Separate kernel density estimates were calculated across all positions based on read counts both with and without T to C conversions, as long as there was a minimum read depth of 5 at a position to ensure a robust density estimate. Clusters (*.bed files) were defined as regions for which the conversion density was greater than the non-conversion density for at least 5 consecutive nucleotides, and extended until the group read depth fell below 5. Following filtering (see supplemental methods in PMID 22291592), clusters were scored by a cross-linking index (CLI) = log2(1+T to C conversion events for all reads within a cluster). PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer .
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated for the PAR-CLIP experiments.
Supplementary_files_format_and_content: TAB files were generated for the small RNA sequencing experiments using the fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Barcodes and adapter sequences have been removed and reads were collapsed into unique reads. Column 1: Sequence; Column 2: ReadCount.

source_name: EBV+ LCL

growth_protocol: Established lymphoblastoid cell lines (LCLs) were infected with EBV B95-8 (EF3D-AGO2 and LCL35) or an EBV B95-8 BACmid (BAC) and were analyzed three to five months post-infection. LCLs (EF3D-AGO2, LCL35, SDLCL, LCL-BAC, LCL-BAC-D1, LCL-BAC-D3) were maintained in RPMI 1640 medium supplemented with 15% FBS and 10 μg/mL gentamicin (GIBCO). EF3D-AGO2 cells stably expressing FLAG/HA-tagged Ago2 were generated by transducing the LCL EF3D with pMIGw-FLAG/HA-Ago2-GFP and FAC-sorting for GFP-expressing cells post-transduction. LCL-BAC-D1 (mutationally inactivated for miR-BHRF1-1 expression) and LCL-BAC-D3 (mutationally inactivated for miR-BHRF1-3 expression) were infected with EBV miRNA-mutant viruses described in Feederle et al., 2011 (PMID 21752900), and were generated from the same donor as LCL-BAC.

extract_protocol: Total RNA was size-fractionated on 15% TBE-Urea PAGE and small RNAs corresponding to 18-24 nt were carried through a cDNA library preparation protocol described in Hafner et al., 2008 (PMID 18158127).

value: EBV B95-8-infected lymphoblastoid cells


title: SDLCL, small RNA sequencing

description:
Small RNA sequencing.
Small RNAs, 18-24 nt.
5' barcode: TTGGC
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT

value: SDLCL


title: LCLBACD3, Ago2 PAR-CLIP

description:
Ago2 PAR-CLIP
Ago2 ribonucleoprotein complexes.
PAR-CLIPed sites as determined by PARalyzer.
5' barcode: GCCTA
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT

data_processing:
Library strategy: PAR-CLIP
Mapping Reads: The reads from Ago2 PAR-CLIP deep sequencing libraries were stripped of the 3' adapter sequence and 5' barcode using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads that were less than 13 nt in length or contained an ambiguous nucleotide were discarded. The remaining reads were aligned to the human genome (hg19), with up to 2 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009). Mapped locations were only reported for those with the minimum number of observed mismatches for each read. All T to C mismatches between the RNA fragment and the genome were subtracted from the mismatch count for each mapped location. After subtraction, only reads that mapped to a single genomic location at the minimum number of mismatches were used for further analysis. The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL v57 database 1 (Hubbard et al., 2007). If a read mapped to a location representing multiple categories, it was reported to belong to the category based on the following order of preference: 3'UTR, coding sequence, 5'UTR, intron, non-coding RNA, intergenic.
Defining microRNA interaction sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained ≥5 reads with conversions at two or more locations. Separate kernel density estimates were calculated across all positions based on read counts both with and without T to C conversions, as long as there was a minimum read depth of 5 at a position to ensure a robust density estimate. Clusters (*.bed files) were defined as regions for which the conversion density was greater than the non-conversion density for at least 5 consecutive nucleotides, and extended until the group read depth fell below 5. Following filtering (see supplemental methods in PMID 22291592), clusters were scored by a cross-linking index (CLI) = log2(1+T to C conversion events for all reads within a cluster). PARalyzer is available at http://www.genome.duke.edu/labs/ohler/research/PARalyzer .
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated for the PAR-CLIP experiments.
Supplementary_files_format_and_content: TAB files were generated for the small RNA sequencing experiments using the fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Barcodes and adapter sequences have been removed and reads were collapsed into unique reads. Column 1: Sequence; Column 2: ReadCount.

extract_protocol: The pellets of cells crosslinked with UV 365 nm were resuspended in NP40 lysis buffer and incubated on ice for 10 min. The cell lysate was cleared by centrifugation at 13,000g. RNase T1 (Fermentas) was added to the cleared cell lysates and the reaction mixture was incubated at 22ºC for 15 min and subsequently cooled for 5 min on ice before addition of antibody-conjugated magnetic beads. The recovered RNA was carried through a cDNA library preparation protocol originally described for cloning of small regulatory RNAs (Hafner et al., 2008 (PMID 18158127)). The first step, 3' adapter ligation, was carried out as described on a 20 ul scale using 10.5 ul of the recovered RNA. UV 365 nm crosslinked sample RNAs were ligated to Illumina sequencing adapter sets and reversed transcribed to cDNA. Following PCR amplification of the cDNA, products were gel-extracted and sequenced on the Illumina GAIIX sequence analyzer.

treatment_protocol: For UV crosslinking, ~4 L of cells were cultured in R-15 containing 100 microMolar 4-thiouridine overnight and collected by centrifugation. Cells were washed once with ice-cold PBS and irradiated on ice at UV 365 nm in a Stratalinker 2400 (Stratagene). Cross-linked cells were collected by centrifugation at 500×g for 5 min.

tag: photoactivatable ribonucleoside analog and crosslinking wavelength

value: 4-thiouridine / 365 nm

tag: antibody

value: Anti-Ago2 (clone 9E8)

tag: antibody vendor, catalog#

value: Millipore, 04-642

tag: immunoprecipitated protein


title: EF3DAGO2, small RNA sequencing


title: LCL35, small RNA sequencing

description:
Small RNA sequencing.
Small RNAs, 18-24 nt.
5' barcode: TCAAG
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT


title: Col-0 ChIP

data_processing:
In essence, all reads were pre-processed and mapped to the Arabidopsis genome using a pipeline as previously described (Zheng, Q., PLoS Genet. 2010) with slight modifications. First, all raw reads were aligned to the Illumina Genomic DNA 3'-adaptor sequence using cross-match program from Phrap package and those with ≥10 nts of alignment at the 3'-end with ≤10% mismaches were subsequently trimmed at the insert/adaptor junctions. Reads without detectable 3'-adaptors were also kept un-changed for subsequent processing. Then both trimmed and untrimmed reads were reduced to non-redundant (NR) tags by collapsing reads with identical sequences, to save processing time and space requirements. The clone-number for each NR-tag was also recorded for subsequent analysis. The trimmed and untrimmed NR-tags/reads were mapped to Arabidopsis thaliana genome (TAIR9 assembly) independently using the Bowtie, allowing ≤6% of seed mismatches (34 nt seeds), ≤8% of total mismatches and all valid alignments are reported. A subsequent parsing step was implemented to enforce these restraints, as well as to require insert lengths of ≥15 nt or ≥30 nt for the trimmed and untrimmed reads, respectively. It is of importance that the actual "insert length" for untrimmed reads was determined according to their alignments, by implementing a one-dimensional dynamic programming algorithm that could identify the most possible insert-fragment length based on output from Bowtie. Finally, we filtered only "best-stratum" alignments that contain ≤4% more mismatches compared to the best-hits for any given read. At last, all mapped trimmed and untrimmed reads (NR-tags) were combined and their mapping and clone-number information was recorded.  Alignment input file for CSAR peak calling, using weighted clone-number for NR-tags were provided as processed data.
Genome Build:
col0_chip_NR_TAIR9_CSAR.txt: TAIR9

value: Wild type


title: Col-0 input

data_processing:
In essence, all reads were pre-processed and mapped to the Arabidopsis genome using a pipeline as previously described (Zheng, Q., PLoS Genet. 2010) with slight modifications. First, all raw reads were aligned to the Illumina Genomic DNA 3'-adaptor sequence using cross-match program from Phrap package and those with ≥10 nts of alignment at the 3'-end with ≤10% mismaches were subsequently trimmed at the insert/adaptor junctions. Reads without detectable 3'-adaptors were also kept un-changed for subsequent processing. Then both trimmed and untrimmed reads were reduced to non-redundant (NR) tags by collapsing reads with identical sequences, to save processing time and space requirements. The clone-number for each NR-tag was also recorded for subsequent analysis. The trimmed and untrimmed NR-tags/reads were mapped to Arabidopsis thaliana genome (TAIR9 assembly) independently using the Bowtie, allowing ≤6% of seed mismatches (34 nt seeds), ≤8% of total mismatches and all valid alignments are reported. A subsequent parsing step was implemented to enforce these restraints, as well as to require insert lengths of ≥15 nt or ≥30 nt for the trimmed and untrimmed reads, respectively. It is of importance that the actual "insert length" for untrimmed reads was determined according to their alignments, by implementing a one-dimensional dynamic programming algorithm that could identify the most possible insert-fragment length based on output from Bowtie. Finally, we filtered only "best-stratum" alignments that contain ≤4% more mismatches compared to the best-hits for any given read. At last, all mapped trimmed and untrimmed reads (NR-tags) were combined and their mapping and clone-number information was recorded.  Alignment input file for CSAR peak calling, using weighted clone-number for NR-tags were provided as processed data.
Genome Build:
col0_input_NR_TAIR9_CSAR.txt: TAIR9

source_name: WT_input DNA


title: ago4 ChIP

data_processing:
In essence, all reads were pre-processed and mapped to the Arabidopsis genome using a pipeline as previously described (Zheng, Q., PLoS Genet. 2010) with slight modifications. First, all raw reads were aligned to the Illumina Genomic DNA 3'-adaptor sequence using cross-match program from Phrap package and those with ≥10 nts of alignment at the 3'-end with ≤10% mismaches were subsequently trimmed at the insert/adaptor junctions. Reads without detectable 3'-adaptors were also kept un-changed for subsequent processing. Then both trimmed and untrimmed reads were reduced to non-redundant (NR) tags by collapsing reads with identical sequences, to save processing time and space requirements. The clone-number for each NR-tag was also recorded for subsequent analysis. The trimmed and untrimmed NR-tags/reads were mapped to Arabidopsis thaliana genome (TAIR9 assembly) independently using the Bowtie, allowing ≤6% of seed mismatches (34 nt seeds), ≤8% of total mismatches and all valid alignments are reported. A subsequent parsing step was implemented to enforce these restraints, as well as to require insert lengths of ≥15 nt or ≥30 nt for the trimmed and untrimmed reads, respectively. It is of importance that the actual "insert length" for untrimmed reads was determined according to their alignments, by implementing a one-dimensional dynamic programming algorithm that could identify the most possible insert-fragment length based on output from Bowtie. Finally, we filtered only "best-stratum" alignments that contain ≤4% more mismatches compared to the best-hits for any given read. At last, all mapped trimmed and untrimmed reads (NR-tags) were combined and their mapping and clone-number information was recorded.  Alignment input file for CSAR peak calling, using weighted clone-number for NR-tags were provided as processed data.
Genome Build:
ago4_chip_NR_TAIR9_CSAR.txt: TAIR9


title: LCLBACD1, Ago2 PAR-CLIP


title: LCLBAC, Ago2 PAR-CLIP

description:
Ago2 PAR-CLIP
Ago2 ribonucleoprotein complexes.
PAR-CLIPed sites as determined by PARalyzer.
5' barcode: TTGGC
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT

value: LCL-BAC


title: Footprints from cells infected with HCMV for 72hr, pretreated with Harringtonine

description:
fp_harr_72hr_s3
Ribosome-protected mRNA.

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v0.12.7 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded.
All remaining reads were aligned to the HCMV virus genome (NC_006273.2).
Still-unaligned reads were aligned to 200bp sequences that spanned splice junctions.
Wig files were then generated by summing the numbers of reads obtained from each position in the viral genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: NC_006273.2
Supplementary_files_format_and_content: fp*.minus.wig: Wiggle file presenting the footprints reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: fp*.plus.wig: Wiggle file presenting the footprints reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.minus.wig: Wiggle file presenting the mRNA reads that aligned to the minus strand of the HCMV genome.
Supplementary_files_format_and_content: mrna*.plus.wig: Wiggle file presenting the mRNA reads that aligned to the plus strand of the HCMV genome.
Supplementary_files_format_and_content: 'GSE41605_merlin_final_orfs.bed.gz', which is linked to the Series record as a supplementary file, includes the 751 ORFs of HCMV that were identified in this study.
Genome Build:
fp_harr_72hr_s3_merlin.align.unique.p_offset.5_prime.merged.minus.wig: NC_006273.2
fp_harr_72hr_s3_merlin.align.unique.p_offset.5_prime.merged.plus.wig: NC_006273.2

source_name: Human fibroblasts infected with HCMV, Harringtonine, 72hr

tag: strain

value: Merlin

value: HCMV-infected human foreskin fibroblasts


title: LNCaP Cells RNA-seq

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

description: cDNA, first strand of synthesis

data_processing:
The adapter sequence ATCTCGTATGCCGTCTTCTGCTTG was removed with the program cutadapt.
Reads were mapped with TopHat 1.2.0. Only uniquely mapping reads were allowed. The mapped reads were then assembled into transcripts with Cufflinks 1.1.0. Default parameters were kept, except that ENSEMBL release 54 for hg18 was used as a reference transcript annotation. Novel transcripts were not assembled.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Read coverage of genomic positions, per 1 million bases mapped.

source_name: LNCaP

growth_protocol: Cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum.

extract_protocol: RNA was extracted from cell lines using Trizol reagent (Invitrogen) according to the manufacturer’s protocol and the integrity confirmed using an Agilent Bioanalyzer. To make a sequencing library, both Illumina mRNA-Seq Sample Prep Kit (#RS-100-0801) and Small RNA Sample Prep Kit Illumina (# FC-102-1009) were used.

value: LNCaP


title: Transcription Start Site Sequencing of PrEC Cells

description: 5' cap-selected single-stranded cDNA

data_processing:
Nine bases were removed from the 5' end of every read, as these are of the multiplexing barcode. Two bases were removed from the 3' end of every read, as these sometimes belonged to the adapter.
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. After mapping, only the first base position of each read was used, and the number of bases per 1 million bases mapped was calculated for each genomic position.

source_name: PrEC

growth_protocol:
Cells were grown at 37ºC with 5% CO2 in PREGM media (Cambrex).
See SAMPLES section.

extract_protocol: DeepCAGE was performed by the service provider GeneWorks (www.geneworks.com.au)

value: PrEC


title: Transcription Start Site Sequencing of LNCaP Cells

description: 5' cap-selected single-stranded cDNA

growth_protocol:
Cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum.
See SAMPLES section.


title: LNCaP Cells Input gDNA-seq

data_processing:
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed. When more than one read mapped to the same genomic position, only one read was kept at that position.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Counts across the whole genome in windows 20 bases wide, per 1 million mapped reads.

extract_protocol: ~ 1 x 106 cells, in a 10cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1mg/ml aprotinin and 1mg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30ml H2O. The DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.


title: LCLBAC, small RNA sequencing


title: LNCaP Cells H3K27me3 ChIP-seq

data_processing:
Read files of technical replicates were pooled.
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed. When more than one read mapped to the same genomic position, only one read was kept at that position.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Counts across the whole genome in windows 20 bases wide, per 1 million mapped reads.

extract_protocol: ~ 1 x 106 cells, in a 10cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1mg/ml aprotinin and 1mg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibody specific for histone 3 lysine 27 trimethylation (Millipore #07-449). 10 ml of antibody was used. No antibody controls were also included, and no precipitation was observed by quantitative Real-Time PCR analysis. The antibody/protein complexes were collected by Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30ml H2O. The ChIP DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Santa Cruz


title: nrpe1 input

data_processing:
In essence, all reads were pre-processed and mapped to the Arabidopsis genome using a pipeline as previously described (Zheng, Q., PLoS Genet. 2010) with slight modifications. First, all raw reads were aligned to the Illumina Genomic DNA 3'-adaptor sequence using cross-match program from Phrap package and those with ≥10 nts of alignment at the 3'-end with ≤10% mismaches were subsequently trimmed at the insert/adaptor junctions. Reads without detectable 3'-adaptors were also kept un-changed for subsequent processing. Then both trimmed and untrimmed reads were reduced to non-redundant (NR) tags by collapsing reads with identical sequences, to save processing time and space requirements. The clone-number for each NR-tag was also recorded for subsequent analysis. The trimmed and untrimmed NR-tags/reads were mapped to Arabidopsis thaliana genome (TAIR9 assembly) independently using the Bowtie, allowing ≤6% of seed mismatches (34 nt seeds), ≤8% of total mismatches and all valid alignments are reported. A subsequent parsing step was implemented to enforce these restraints, as well as to require insert lengths of ≥15 nt or ≥30 nt for the trimmed and untrimmed reads, respectively. It is of importance that the actual "insert length" for untrimmed reads was determined according to their alignments, by implementing a one-dimensional dynamic programming algorithm that could identify the most possible insert-fragment length based on output from Bowtie. Finally, we filtered only "best-stratum" alignments that contain ≤4% more mismatches compared to the best-hits for any given read. At last, all mapped trimmed and untrimmed reads (NR-tags) were combined and their mapping and clone-number information was recorded.  Alignment input file for CSAR peak calling, using weighted clone-number for NR-tags were provided as processed data.
Genome Build:
nrpe1_input_NR_TAIR9_CSAR.txt: TAIR9

source_name: nrpe1_input DNA

value: nrpe1 mutant

value: 2-3 week old seedling


title: PrEC Cells RNA-seq

description: cDNA, first strand of synthesis

growth_protocol: Cells were grown at 37ºC with 5% CO2 in PREGM media (Cambrex).


title: LCL35, Ago2 PAR-CLIP

description:
Ago2 PAR-CLIP
Ago2 ribonucleoprotein complexes.
PAR-CLIPed sites as determined by PARalyzer.
5' barcode: TCAAG
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT

tag: cell type


title: EF3DAGO2, Ago2-FLAG PAR-CLIP

description:
Ago2-FLAG PAR-CLIP
Ago2 ribonucleoprotein complexes.
PAR-CLIPed sites as determined by PARalyzer.
5' barcode: TTGGC
3' adapter (Illumina): TCGTATGCCGTCTTCTGCTTGT

value: anti-Flag M2

value: Sigma, F1804


title: LNCaP Cells H3K4me3 ChIP-seq

extract_protocol: ~ 1 x 106 cells, in a 10cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1mg/ml aprotinin and 1mg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibody specific for histone 3 lysine 4 trimethylation (Abcam #ab8580). 10 ml of antibody was used. No antibody controls were also included, and no precipitation was observed by quantitative Real-Time PCR analysis. The antibody/protein complexes were collected by Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30ml H2O. The ChIP DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.

tag: chip antibody

value: Abcam


title: PrEC Cells H3K27me3 ChIP-seq


title: PrEC Cells Input gDNA-seq


title: PrEC Cells H3K4me3 ChIP-seq


title: H3K27me3-ShPhf19_ChIPSeq

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

description: Chromatin IP against H3K27me3 in cells depleted of Phf19 (shPhf19)

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: text file containing peak coordinates

growth_protocol: Wild-type (E14Tg2A) ES cells were cultured feeder-free in plates coated with 0.1% of gelatin in Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone), and leukemia inhibitory factor (LIF).

extract_protocol:
ESCs were trypsinized and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 0.125 M glycine for 5 min. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 14 min in a Bioruptor. ChIP-Seq experiments were performed as previously described (Morey et al, Cell Stem Cell. 2012, 10: 47-62). Immunoprecipitated DNA was eluted, reverse crosslinked and purified using Qiagen columns.
It was performed using the NEBNext DNA Sample Prep Reagents Set 1

value: embryonic stem cells

value: H3K27me3 - Millipore, #07450


title: Suz12_ChIPSeq

description: Chromatin IP against Suz12

value: wild type


title: HeLa-siLuc (RNA-seq)

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Reads were mapped, measured and quantifed by cufflinks v2.0.0, tophat v2.0.0 and bowtie v2.0.0-beta5 with --library-type fr-secondstrand and other default options. The gene annotations for cufflinks were retrieved from Illumina iGenome repository as of Sep 11, 2011.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and log2 fold changes between samples

molecule: polyA RNA

source_name: Cervical cancer cells transfected with siRNA against luciferase two times over a 5 day period.

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: To prepare mRNA libraries, mRNAs were purified from total RNAs using Dynabeads mRNA Purification Kit (Invitrogen, 61011). Purified mRNAs were fragmented by RNA Fragmentation Reagents (Ambion, AM8740). After fragmentation, phosphate group at 3′ end was removed by Antarctic phosphatase (NEB, M0289L), and RNAs were 5′ phosphorylated by T4 PNK (NEB). Directional and multiplexed mRNA libraries were generated using TruSeq Small RNA Sample Preparation Kit (Illumina, RS-200–0012). The mRNA libraries were sequenced using Illumina HiSeq 2000.

treatment_protocol: HeLa cells were transfected with 42nM of siLuciferase or 14nM of each siTUT7, 4, and 2 using Lipofectamine 2000 (Invitrogen). Transfection was performed two times over a 4~5 day period to enhance knockdown efficiency.

value: HeLa

tag: sirna

value: siLuc

tag: treatment

value: transfected with 42nM of siLuciferase


title: H83M2 Male (HMM2)

city: Columbia

first: Lin

last: Sun

state: MO

address: 311 Tucker Hall

department: Biological Sciences

institute: University of Missouri

description:
H83M2 Male (HMM)
This sample is one of three biological replicates (HMM1, HMM2, HMM3)

data_processing:
We used TopHat to map the RNA-Seq reads of each replicate of each sample to the Drosophila melanogaster genome (dm3) in the UCSC genome browser  in conjunction with the RefSeq genome reference annotation (RefSeq Assembly ID: GCF_000001215.2).
The threshold of mismatch was set to 2. Overall, ~80% of reads of each replicate were mapped to the genome
The reads that were mapped to a unique location on the genome were used to calculate the RNA counts of the genes. We used both our in-house tool (MULTICOM) and a public tool (HTseq)to calculate read counts of the genes in a replicate according to the genome mapping outputs and the RefSeq genome reference annotation.
The counts of the genes in a replicate calculated by MULTICOM or HTseq were normalized by dividing them by the total number of uniquely mapped reads in the replicate
Genome_build: Release 5
Supplementary_files_format_and_content: .txt files with aligned reads and normalized reads for each genes

organism: Drosophila melanogaster

source_name: adult flies

growth_protocol: The ectopically expressed MSL2 females were obtained using a P-element msl2 construct with a mini-white transformation marker, [(w+) H83M2-6I] (Kelley et al., 1995). The global expression pattern of these females (y w; (w+) H83M2-6I/+; +/+), normal females (y w; +/+; TM3/+) and males (y w; +/+; TM3/+) were obtained by mRNA-sequencing and analyzed by comparing the ratio distributions to each other

extract_protocol:
Total RNA was isolated using TRIZOL Reagent (Invitrogen) and  High-throughput sequencing services were performed at the University of Missouri DNA Core Facility
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq RNA sample preparation kit (#RS-930-2001).

value: ectopically expressed MSL2 protein

tag: gender

value: male

tag: biological replicate


title: H83M2 Female (HMF2)

description:
H83M2 Female (HMF)
This sample is one of three biological replicates (HMF1, HMF2, HMF3)

tag: genotype/variation

value: female


title: Phf19-Repl2_ChIPSeq(Hi)

description: Chromatin IP against Phf19_replica2

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: text file containing peak coordinates (binding sites were defined as those sites (ChIP-seq peaks) present in both replicas)

tag: cell line

value: Phf19 - OpenBiosystems, costum made


title: H83M2 Male (HMM1)


title: MUT XX MEF

status: Public on Oct 15 2012

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

data_processing:
solexa1.3 basecalling
mapping to genome with bowtie -m 1
conversion of sam/bam files to bigwig using bamToGBrowse.pl (http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.14/bin/bamToGBrowse.pl)
Genome_build: mm9

source_name: smcHD1-/- female embryonic fibroblast cell line

growth_protocol: Standard culture conditions including 5% CO2, 37oC, 5% fetal calf serum, penicillin and streptomycin in DMEM culture media.  For ES cell growth cells were maintained with 10% fetal calf serum and supplemented with LIF

extract_protocol: genomic DNA was isolated using a standard protocol after RNase and proteinase K treatment, it was then sonicated to between 200-600 bp, before 20-30 ug was fractionated using a MBD column.  Unmethylated DNA was eluted with 0.715 M NaCl and methylated DNA with 1M NaCl.  Efficient fractionation was confirmed by PCR analysis of fractions for known methylated and unmethylated loci.  Methylated DNA was then pooled, concentrated, desalted in a 30K filter and precipitated.  Samples were resuspended in 20 microlitres of H20 and submitted for sequencing after quality was confirmed using picogreen.  Each sample isolation and MBD-seq was performed.

treatment_protocol: MEF cell lines were untreated.  ES cell differentiation followed the standard embryoid body method.

value: MEF


title: Phf19-Repl1_ChIPSeq(Hi)

description: Chromatin IP against Phf19_replica1


title: WT XX MEF

source_name: wild type female embryonic fibroblast cell line


title: Control Female (CF3)

description:
Control Female (CF)
This sample is one of three biological replicates (CF1,CF2, CF3)

value: Control


title: Control Female (CF1)


title: Control Female (CF2)


title: Control Male (CM2)

description:
Control Male (CM)
This sample is one of three biological replicates (CM1, CM2, CM3)


title: H83M2 Female (HMF1)


title: Control Male (CM3)


title: Control Male (CM1)


title: LCLBACD1, small RNA sequencing

value: EBV B95-8-infected lymphoblastoid cells


title: PrEC Cells CTCF ChIP-seq

extract_protocol: ~ 1 x 106 cells, in a 10cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1mg/ml aprotinin and 1mg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibody specific for CTCF (Millipore #07-729). 10 ml of antibody was used. No antibody controls were also included, and no precipitation was observed by quantitative Real-Time PCR analysis. The antibody/protein complexes were collected by Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30ml H2O. The ChIP DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.

value: PrEC

value: CTCF

value: Millipore


title: IgG_ChIPSeq(Hi)

description: Chromatin IP against IgG (control sample for Phf19 experiment; peaks not provided)

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: control sample for Phf19 experiment; peaks not provided

value: IgG; Abcam, #46540


title: MUT XY MEF

source_name: smcHD1-/- male embryonic fibroblast cell line


title: WT XY MEF

source_name: wild type male embryonic fibroblast cell line


title: H83M2 Male (HMM3)


title: PGK_2

source_name: wild type female embryonic stem cell line paired end 2

value: PGK


title: HeLa-siGFP-1

description: small RNA

data_processing: All small RNA sequences except low-quality reads are provided with the number of reads for each unique sequence. Illumina SRA v1.5 3' adapter sequences are trimmed using half-open Smith-Waterman algorithm (score parameters: 2 for match, -2 for mismatch, -3 for linear gap penalty).

source_name: Cervical cancer cells transfected with siRNA against GFP.

extract_protocol: To prepare small RNA cDNA libraries, total RNAs were separated on 15% urea-PAGE and 17~30nt RNAs were gel-purified. Size fractionized RNAs were ligated with 3' adapter using T4 RNA ligase2 trucated form (NEB). 3’ adaptor-ligated mixture was hybridized with RT primer (NEB v1.5). After RT primer hybridization, RT primer hybridized mixture was ligated with 5' adapter using T4 RNA ligase1 (NEB). The ligation products were reverse transcribed using superscript II (Invitrogen) and the cDNA was PCR-amplified with Phusion DNA polymerase (NEB).

treatment_protocol: HeLa cells were transfected with 42nM of siLuciferase or 14nM of each siTUT7, 4, and 2 or GFP using Lipofectamine 2000 (Invitrogen). Transfection was performed two times over a 4~5 day period to enhance knockdown efficiency.

tag: transfection

value: siGFP


title: IgG_ChIPSeq

description: Chromatin IP against IgG (control sample; peaks not provided)

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: control sample; peaks not provided

value: embryonic stem cells

value: wild type