title: Uninfected_mouse_vagina.rep2

description: control sample

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse (GRCm38) and/or Candida (sc5314) reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: M. musculus (GRCm38), C. albicans (sc5314)
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample


title: Infected_mouse_vagina.rep2

status: Public on Apr 11 2015

type: SRA

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

country: USA

institute: University of Maryland Baltimore

description: infected sample

library_source: transcriptomic

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse (GRCm38) and/or Candida (sc5314) reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: M. musculus (GRCm38), C. albicans (sc5314); Regarding the Candida genome assembly, we used the Candida albican sc5314 assembly 21 from the Candida Genome Database (http://www.candidagenome.org) which is a haploid assembly similar to ?ASM18296v2?.
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse vagina

growth_protocol: C. albicans cells were injected into the vagina of a mouse

extract_protocol:
RNA was isolated from the infected mouse vaginal tissues using the Qiagen Rneasy mini kit (Cat#74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: infection

value: Candida albicans SC5314

tag: tissue

value: Vagina

tag: time point

value: day 3 post innoculation


title: Uninfected_mouse_vagina.rep3

description: control sample

value: day 3 uninfected


title: Limited iron condition 1

city: Porto Alegre

first: Edilena

middle: Reis

last: Sperb

state: RS

address: Bento Gonçalves

department: Genética

country: Brazil

institute: UFRGS

data_processing:
Remove adaptors and trim 15 bp off of the 3'-end.
Comparison and mapping to the P. riograndensis SBR5 genome database located on the Aramis platform (http://aramis.genopar.org/bacteria/PR/) using CLC Genome Workbench 5.5 software.
Library normalization and analysis performed using the RPKM method as described by Mortazavi et al. (2008).
Supplementary_files_format_and_content: *unique.tab: Tab-delimited text files with abundance of unique sequences.
Supplementary_files_format_and_content: *RPKM.txt: Tab-delimited text files with gene-level RPKM values.

organism: Paenibacillus riograndensis SBR5

source_name: bacterial culture, limited iron

growth_protocol: SBR5 grown in KB media.

extract_protocol: Total RNA was extracted from bacterial cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA integrity was verified by electrophoresis on a 1% agarose gel. After the samples were treated with DNase I (Invitrogen), the concentration and purity were determined by spectrophotometer readings at 260 nm and 280 nm using a NanoDrop 2000 (Thermo Scientific). To remove ribosomal RNA, total RNA was processed using a MICROB Express Bacterial mRNA Enrichment Kit (Ambion from Life Technologies), precipitated with ethanol and resuspended in nuclease-free water. cDNA libraries were constructed using a Whole Transcriptome Analysis Kit (Life Technologies) followed by full-scale emulsion PCR according to the supplier’s instructions.

treatment_protocol: SBR5 grown in sufficient or limited iron condition.

tag: strain/background

tag: growth phase

value: stationary

tag: condition

value: limited iron


title: Sufficient iron condition 2

source_name: bacterial culture, sufficient iron

value: sufficient iron


title: Limited iron condition 2


title: TOV21G Ctrl RNAi For Bub3 rep4

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

description: Total RNA with rRNA depleted

data_processing:
Bases are called using Illumina pipeline Casava 1.8.
RNA-seq reads were first mapped to the human genome (hg19) using Tophat2 (Kim et al., 2013). Transcript annotation from Ensembl was used as reference for exon junctions in read mapping.
We then used Cufflinks (Pollier et al., 2013; Trapnell et al., 2012; Trapnell et al., 2010) to assemble un-annotated transcripts. Assembled transcripts from the same cell type were further merged by Cuffmerge (Trapnell et al., 2010).
Finally we used MATS (Park et al., 2013; Shen et al., 2012) to call differential alternative splicing, and the merged transcripts from the previous step were used as transcript annotation in MATS.
Genome_build: hg19

organism: Homo sapiens

source_name: Human Ovarian Cancer Cell Line

growth_protocol: For TOV21G cell (ATCC, CRL-1173) culture, the base medium is a 1:1 mixture of MCDB 105 medium (Sigma-Aldrich, M6395) containing a final concentration of 1.5 g/L sodium bicarbonate and Medium 199 (Sigma-Aldrich, M4530) containing a final concentration of 2.2 g/L sodium bicarbonate.

extract_protocol:
Arcturus picopure RNA isolation kit (Life Technologies, KIT0204) was used to prepare total RNA from cells.
Ribo-Zero™ Gold Kits (Human/Mouse/Rat) (Epicentre, MRZG126) was used to remove both cytoplasmic (nuclear-encoded) rRNA and mitochondrial rRNA from total RNA preparations, and libraries were built using the Illumina TruSeq RNA sample prep kit V2 (Illumina, RS-122-2001).
Libraries were sequenced using an Illumina HiSeq 2000. Single end 100 bp reads were obtained.

treatment_protocol: small molecule treatment or RNAi

tag: treatment

value: Control siRNA transfection for 48 h

tag: cell line


title: TOV21G Ctrl RNAi For Bub3 rep2

description: Total RNA with rRNA depleted


title: TOV21G BuGZ RNAi rep2

description: Total RNA with rRNA depleted

value: BuGZ siRNA transfection for 48 h


title: TOV21G BuGZ RNAi rep1

description: Total RNA with rRNA depleted


title: TOV21G Ctrl RNAi For Bub3 rep1

description: Total RNA with rRNA depleted


title: TOV21G DMSO rep1

description: Total RNA with rRNA depleted

value: DMSO treated for 4 h


title: TOV21G Splicing Inhibitor rep2

description: Total RNA with rRNA depleted

value: pladienolide B treated for 4 h


title: TOV21G Splicing Inhibitor rep1

description: Total RNA with rRNA depleted


title: TOV21G DMSO rep2

description: Total RNA with rRNA depleted


title: TOV21G Ctrl RNAi For Bub3 rep3

description: Total RNA with rRNA depleted


title: TOV21G Bub3 RNAi rep2

description: Total RNA with rRNA depleted

value: Bub3 siRNA transfection for 48 h


title: JUN ChIPseq

status: Public on Apr 12 2015

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

description:
Follow-up JUN ChIPseq
These ChIPseqs were done on a different machine as paired ends, no replicates, sequences combined in a bam file which was used to create the bed file provided, otherwise handled as noted for the other ChIPseqs.

library_source: genomic

data_processing:
Alignment: Sequences were aligned to hg19 using BWA set to default parameters.
Peak-calling: Peaks were called with MACS2 for HG 19, set to default parameters using IgG samples as background control
Replicate consolidation: For TCF21 Ab1 and Ab2 replicates were consolidated to produce one set of peaks per antibody using the IDR pipeline developed by the ENCODE project. For JUN JUND no replicates.
Genome_build: hg19
Supplementary_files_format_and_content: bed files standard format

molecule: genomic DNA

source_name: HCASMC Lonza 0000317155

growth_protocol: Human coronary artery smooth muscle cells were obtained from Lonza and grown as suggested in SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and FBS, but without antibiotics (Lonza, #CC-3182).

extract_protocol:
Ten million HCASMC cells per condition were crosslinked for 10 min with 1% formaldehyde. Cells were lysed for 10 min on ice, and nuclei were then lysed for 10 min on ice. Crosslinked chromatin was sheared for 3x5 min by sonication using a Bioruptor and pre-cleared with 10 µg anti-rabbit IgG pre-immune serum. TCF21 ChIP was performed overnight in IP dilution buffer using anti-TCF21 (Sigma-Aldrich, St. Louis, MA, USA, #HPA013189, Lot. No. R02939 (Ab1) or Abcam, Cambridge, UK, #ab49475, Lot No. 153899 (Ab2)) or anti-rabbit IgG respectively. JUN and JUND ChIP was performed with Santa Cruz Biotechnology sc-1694 and Santa Cruz Biotechnology sc-74 respectively.
After reverse-crosslinking, RNaseA and proteinase K digestion, chromatin was cleaned up using the Qiagen PCR purification kit

tag: cell type

value: coronary artery smooth muscle

tag: chip antibody

value: JUN

tag: chip antibody manufacturer and catalog number

value: Santa Cruz sc-1694


title: TOV21G Bub3 RNAi rep1

description: Total RNA with rRNA depleted


title: HFF Splicing Inhibitor

description: Total RNA with rRNA depleted

source_name: Human Foreskin Fibroblast Cell Line

growth_protocol: The Human Foreskin Fibroblast cells (HFF, from Millipore, Millipore-SCC058) were cultured in FibroGRO LS (low serum) Complete Medium (Millipore, SCMF002). HFFs were changed into fresh medium every other day and passaged using Accutase (Millipore, SCR005) at 1:3 dilution when reaching ~80% of confluency.

value: HFF


title: HFF Ctrl RNAi rep1

description: Total RNA with rRNA depleted


title: HFF BuGZ RNAi rep2

description: Total RNA with rRNA depleted


title: HFF Ctrl RNAi rep2

description: Total RNA with rRNA depleted


title: HFF DMSO

description: Total RNA with rRNA depleted


title: Infected_mouse_vagina.rep3

description: infected sample


title: RNA-seq_57d-3

city: Long Beach

first: Judy

last: Brusslan

address: 1250 Bellflower Blvd

department: Department of Biological Sciences

institute: California State University Long Beach

description: RNA-seq of 57d mature fully-expanded rosette leaf tissue - replicate 3.

data_processing:
RNA-seq library reads were mapped to the TAIR10 reference genome and gene annotation using tophat-2.0.4 (Trapnell et al., 2009) calling bowtie-0.12.8 (Langmead et al., 2009) .
HTSeq (Anders et al., 2014) was used to perform gene counts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file of reads counts (not normalized) per gene (rows) for each sample (columns).

organism: Arabidopsis thaliana

source_name: mature fully-expanded rosette leaf tissue, 57d

growth_protocol: Sunshine LC-1 soil mix, weekly feedings with Gro-Power Liquid 4-8-2. Percival AR-60 growth chamber, 30 micromoles photons m^-2 sec^-1, 20 hours of light 4 hours of dark.

extract_protocol:
Trizol reagent was used for RNA isolation according to manufacturer's instructions, except one additional ethanol precipitation was added to remove residual phenol.
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2-Set A. Three samples were run per lane using multiplexing.

tag: ecotype

value: Columbia (Col-0)

value: predominantly leaf mesophyll

tag: age


title: RNA-seq_57d-2

description: RNA-seq of 57d mature fully-expanded rosette leaf tissue - replicate 2.


title: RNA-seq_42d-1

description: RNA-seq of 42d mature fully-expanded rosette leaf tissue - replicate 1.

source_name: mature fully-expanded rosette leaf tissue, 42d


title: RNA-seq_42d-3

description: RNA-seq of 42d mature fully-expanded rosette leaf tissue - replicate 3.


title: RNA-seq_42d-2

description: RNA-seq of 42d mature fully-expanded rosette leaf tissue - replicate 2.


title: RNA-seq_35d-2

description: RNA-seq of 35d mature fully-expanded rosette leaf tissue - replicate 2.

source_name: mature fully-expanded rosette leaf tissue, 35d


title: HFF Bub3 RNAi rep2

description: Total RNA with rRNA depleted


title: RNA-seq_35d-3

description: RNA-seq of 35d mature fully-expanded rosette leaf tissue - replicate 3.


title: RNA-seq_57d-1

description: RNA-seq of 57d mature fully-expanded rosette leaf tissue - replicate 1.


title: HFF Bub3 RNAi rep1

description: Total RNA with rRNA depleted


title: RNA-seq_35d-1

description: RNA-seq of 35d mature fully-expanded rosette leaf tissue - replicate 1.


title: RNA-seq_29d-3

description: RNA-seq of 29d mature fully-expanded rosette leaf tissue - replicate 3.

source_name: mature fully-expanded rosette leaf tissue, 29d


title: H3K4me3_57d_ChIP

description: H3K4me3 ChIP of 57d mature fully-expanded rosette leaf tissue.

data_processing:
ChIP-seq library reads were mapped to the TAIR10 reference genome using bowtie-0.12.8 (Langmead et al., 2009).
The resultant mapped reads were collapsed to unique start sites and binned within 100bp windows along the genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: BedGraph-formatted files contain ChIP-seq read counts (not normalized) within 100bp.

source_name: mature fully-expanded rosette leaf tissue, 57d, H3K4me3 ChIP

extract_protocol:
Nuclei extraction: Chromatin was fixed by vacuum infiltration with formaldehyde. Frozen tissue was ground in liquid nitrogen, filtered through Miracloth and subject to low speed centrifugation.
Chromatin Immunoprecipitation: Magnetic Dynabeads Protein G were coupled to antibodies and incubated with pre-cleared nuclei that had been sonicated in a BioRupter. Dynabeaks were washed, DNA was eluted and heated to reverse formaldehyde fixation. Histones were digested with proteinase K and DNA was precipitated and quantified using Pico-green.
H3K4me3 ChIP library construction: ChIP DNA was subject to end repair, dA was added to the 3' end, and Illumina adapters were ligated to the dA-tailed DNA. DNA was amplified by PCR and electrophoresed on a TAE gel to separate PCR products from the adaptor dimers. Eluted DNA was quantified using Pico-green. Multiplexing was not used for the H3K4me3 library.
H3K9ac ChIP library construction: The H3K9ac ChIP library used the Illumina TruSeq ChIP Sample Preparation Kit-Set A. Two samples were run per lane using multiplexing.

value: H3K4me3 (Millipore 17-678)


title: H3K9ac_30d_Input

description: H3K9ac input of 30d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 30d, input


title: H3K9ac_42d_Input

description: H3K9ac input of 42d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 42d, input


title: H3K9ac_30d_ChIP

description: H3K9ac ChIP of 30d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 30d, H3K9ac ChIP

value: H3K9ac (Millipore 07-352)


title: H3K9ac_34d_Input

description: H3K9ac input of 34d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 34d, input


title: H3K9ac_42d_ChIP

description: H3K9ac ChIP of 42d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 42d, H3K9ac ChIP


title: H3K4me3_57d_Input

description: H3K4me3 input of 57d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 57d, input


title: RNA-seq_29d-1

description: RNA-seq of 29d mature fully-expanded rosette leaf tissue - replicate 1.


title: H3K4me3_42d_ChIP

description: H3K4me3 ChIP of 42d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 42d, H3K4me3 ChIP


title: H3K4me3_29d_ChIP

description: H3K4me3 ChIP of 29d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 29d, H3K4me3 ChIP


title: H3K4me3_42d_Input

description: H3K4me3 input of 42d mature fully-expanded rosette leaf tissue.


title: RNA-seq_29d-2

description: RNA-seq of 29d mature fully-expanded rosette leaf tissue - replicate 2.


title: H3K4me3_29d_Input

description: H3K4me3 input of 29d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 29d, input


title: H3K9ac_34d_ChIP

description: H3K9ac ChIP of 34d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 34d, H3K9ac ChIP


title: H3K4me3_35d_ChIP

description: H3K4me3 ChIP of 35d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 35d, H3K4me3 ChIP


title: HFF BuGZ RNAi rep1

description: Total RNA with rRNA depleted

source_name: Human Foreskin Fibroblast Cell Line


title: MNase_Spombe

status: Public on Apr 10 2015

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

country: Spain

institute: Instituto de Biología Funcional y Genómica (IBFG)

data_processing:
Alignment: bowtie 0.12.7.
Nucleosome ocupation maps (wig files) were obtained using NUCwave (PMID: 25296770).
Genome_build: S. pombe, ASM294v2.20 assembly(13/08/2013), from Pombase

organism: Schizosaccharomyces pombe

source_name: Mononucleosomal DNA

growth_protocol: Cultures of 200 ml of S. pombe wild type 972h- were grown in rich medium (YES) at 32 ºC up to a A595 = 0.8.

extract_protocol:
Mononucleosomal DNA was isolated as described (de Castro et al. 2012). The amount of Zymolyase  20T used to prepare spheroplasts was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Cell suspensions of the culture of S.pombe were treated with 40 mg of Zymolyase  20T, during 30 minutes at 30 ºC. Spheroplasts were treated with 200 units/ml of micrococcal nuclease at 37 ºC during 45 minutes.  Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina HiSeq 2500 using the paired end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: culture type

value: Asynchronous mitosis

tag: molecule subtype

value: Mononucleosomal DNA


title: 60 min. OGD, mRNA-seq, replicate #2

city: Cork

first: Pavel

middle: V

last: Baranov

state: Co. Cork

address: Western Gateway Building, UCC

department: Biochemistry and Cell Biology

country: Ireland

institute: University College Cork

data_processing:
Initial processing; Cutadapt was used for the removal of the adapter sequence (CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA). The reads were then aligned to rRNA and the introduced “spike-in” (ATGTACACGGAGTCGACCCGCAACGCGA) to remove reads that originated from these sources. Reads were aligned to the rat RefSeq gene catalogue downloaded from NCBI on January 2014 (ftp://ftp.ncbi.nih.gov/refseq/R_norvegicus/mRNA_Prot/) with bowtie. The alignment parameters used where (-a -m 100 -v 2 –norc).
Differential expression analysis; We calculated the number of reads aligning to any of Refseq transcripts originating from the same gene. Ribo-seq reads were assigned to mRNA coordinates based on the inferred location of the A-site. Those of length less than 29 or greater than 35 were discarded. For genes that had transcripts with annotated coding regions we used only ribo-seq reads aligning to them, otherwise those mapped to the entire transcript were included. Some ribo-seq reads were mapped to more than 1 region of a transcript. We assigned them to unique locations based on the following priority order: annotated coding region, 5' leader, 3' UTR. We included ambiguously aligned reads that mapped to less than 4 locations, for these reads the value of aligned reads was reduced by the number of its alignment locations. To reduce the effects of misalignment on a genes estimated level of expression we excluded coordinates corresponding to the three highest density peaks of the ribosome density from each transcript.
Further normalisation to remove the differences due to the total number of mapped reads was carried out. The read counts aligning to a feature in the sample k were multiplied by the rescaling factor x[k]/min(x[i]) where x[k] is the number of all sequence reads aligning to all features within the sample k, and min(x[i]) is the number of all reads aligning to all features in the sample i which has the smallest number of reads. This rescaling was carried out independently for the mRNA-seq and ribo-seq data, however both replicates were normalised together to allow for comparison between replicates.
To identify differentially expressed genes we carried out the Z-score transformation of log ratios in read counts by calculating local Z-scores for the groups of 300 genes clustered based on the lowest signal of their expression mRNA-seq, ribo-seq or both depending on what is being compared. The gene was classified as upregulated if (Z1+Z2)/2 > T and downregulated if (Z1+Z2)/2 < -T, where Z1 and Z2 are Z-scores for the same gene obtained in two replicas and T is the threshold. The threshold T was set based on the desired false discovery rate (FDR). The number of false positives was estimated as the number of genes for which (|Z1|+|Z2|)/2>T when Z1Z2<0. A gene was considered robustly regulated only if it was detected as regulated after exclusion of coordinates corresponding to three highest density peaks of the ribosome density for each of its transcripts.
Genome_build: rat RefSeq gene catalogue downloaded from NCBI (mRNA_Prot/)
Supplementary_files_format_and_content: The tab delimited csv files record the number of mapped reads that aligned to the gene in the RefSeq catalogue after the alignment step. Each row contains the record of a Gene with first 3 columns indicating its Gene symbol, its annotation classification (coding, ncRNA, rRNA,transcript,pseudo,linc) and the number of alignments. Three more columns are used for coding transcripts. These columns indicates the number of alignments to the 5'leader, the acORF and the 3'UTR. The supplmentary_table.xlsx is available on the series record and containsgenes found to differentially regulated as well as records differential gene expression analysis of the dataset.

organism: Rattus norvegicus

extract_protocol:
Detergent lysis was performed in the dish, and after DNAse treatment sample was taken for mRNA isolation. Lysates were subjected to ribosome footprinting by RNAse I treatment. After sucrose density gradient fractionation ribosome-protected fragments were purified from 80S peak fractions. In parallel, mRNA isolated with Oligotex kit (Quiagen) was subjected to alkaline hydrolysis and fragments of the same size as ribosome protected fragments were isolated.
Library preparation was carried out as described in Ingolia et al (2012),Nature Protocols

value: 60 minutes of oxygen and glucose deprivation

tag: rna type

value: “naked” mRNAseq


title: 40 min. OGD, mRNA-seq, replicate #2

value: 40 minutes of oxygen and glucose deprivation


title: 0 min. OGD, mRNA-seq, replicate #2

value: control


title: 40 min. OGD, ribo-seq, replicate #2

value: ribosome protected fragment


title: 60 min. OGD, mRNA-seq, replicate #1


title: 60 min. OGD, ribo-seq, replicate #1


title: 20 min. OGD, mRNA-seq, replicate #2

value: 20 minutes of oxygen and glucose deprivation


title: 20 min. OGD, ribo-seq, replicate #2


title: 60 min. OGD, ribo-seq, replicate #2


title: 0 min. OGD, ribo-seq, replicate #2


title: MN_Soctosporus

data_processing:
genome_build: S. octosporus, SO6 assembly (7/6/2012),  from Broad Institute Schizosaccharomyces group Database
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Matlab “Wavelet Toolbox”, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.

organism: Schizosaccharomyces octosporus

growth_protocol: Cultures of 400 ml of S. octosporus CBS1804 were grown in rich medium (YES) at 32 ºC up to a A595 = 0.8.

extract_protocol:
Mononucleosomal DNA was isolated as described (de Castro et al. 2012). The amount of Zymolyase  20T used to prepare spheroplasts was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Cell suspensions of the culture of S. octosporus were treated with 50 mg of Zymolyase  20T, during 30 minutes at 30 ºC. Spheroplasts were treated with 200 units/ml of micrococcal nuclease at 37 ºC during 45 minutes.  Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina Genome Analyzer IIx using the single-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: H3K4me3_35d_Input

description: H3K4me3 input of 35d mature fully-expanded rosette leaf tissue.

source_name: mature fully-expanded rosette leaf tissue, 35d, input


title: WT1-A_day17

city: New York

first: Betty

last: Chang

state: NY

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

description: fibroblast derived induced pluripotent stem cell

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite
Alignment to hg19 using Tophat release 2.0.9 and Bowtie2 release2.1.0
Differential expression performed with Cufflinks release 2.1.1 and Homo sapiens hg19 reference annotation
Genome_build: hg19
Supplementary_files_format_and_content: MSCtoOB experiment FPKM tables derived from Cufflinks cuffdiff output MSCtoOB_FPKM.txt output tab-delimited file.  See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.

source_name: WT-derived osteoblast

extract_protocol:
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with up to 2 ug of total RNA for the construction of sequencing libraries Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.

treatment_protocol: mesenchymal stem cells were differentiated to osteoblasts by culturing with osteogenic differentiation media: alphaMEM supplemented with 0.1 μM dexamethason, 10mM beta-glycerol phosphate, 200 μM ascorbic acid and 10% fetal bovine serum.

tag: disease/genotype

value: wildtype

tag: source cell type

value: patient-derived iPSCs

tag: cell subtype

value: osteoblast

value: day 17 of osteoblast differentiation treatment


title: WT1-A_day14

source_name: WT-derived MSCs intermediate

value: mesenchymal stem cells (MSCs) intermediate

tag: time point

value: day 14 of osteoblast differentiation treatment


title: WT1-A_day7

value: day 7 of osteoblast differentiation treatment


title: LFS2-B_day17

source_name: LFS-derived osteoblast

value: Li-Fraumeni Syndrome (LFS) patient


title: LFS2-B_day7

source_name: LFS-derived MSCs intermediate


title: 20 min. OGD, ribo-seq, replicate #1


title: LFS2-B_day0

source_name: LFS-derived MSCs

value: mesenchymal stem cells (MSCs)

value: day 0 of osteoblast differentiation treatment


title: LFS1-A_day17


title: 40 min. OGD, ribo-seq, replicate #1


title: LFS2-B_day14


title: 0 min. OGD, ribo-seq, replicate #1


title: 0 min. OGD, mRNA-seq, replicate #1


title: LFS2-D_tumor

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Alignment to hg19 using Tophat release 2.0.9 and Bowtie2 release2.1.0
Differential expression performed with Cufflinks release 2.1.1 and Homo sapiens hg19 reference annotation
Genome_build: hg19
Supplementary_files_format_and_content: WTLFSMSCDerivedTumor.txt output tab-delimited file of gene annotation and FPKM values

source_name: induced pluripotent stem cell derived mesenchymal stem cell

extract_protocol:
Tumors dissected from Nude mice and RNA was isolated using Trizol reagent.
Illumina TruSeq Stranded Total RNA LT with Ribo-Zero Gold Sample Prep Kit was used.

value: tumor tissue isolated from Nude mice

tag: genotype

value: Li-Fraumeni Syndrome patient


title: LFS2-B_tumor


title: LFS1-A_day14


title: 40 min. OGD, mRNA-seq, replicate #1

value: “naked” mRNAseq


title: LFS1-A_day0


title: MN_Sjaponicus

data_processing:
genome_build: S. japonicus, SJ5 assembly (7/6/2012),  from Broad Institute Schizosaccharomyces group Database
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Matlab “Wavelet Toolbox”, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.

organism: Schizosaccharomyces japonicus

growth_protocol: Cultures of 400 ml of S. japonicus var. japonicus ade12- FY53 were grown in rich medium (YES) at 32 ºC up to a A595 = 0.8.

extract_protocol:
Mononucleosomal DNA was isolated as described (de Castro et al. 2012). The amount of Zymolyase  20T used to prepare spheroplasts was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Cell suspensions of the culture of S. japonicus were treated with 12 mg of Zymolyase  20T, during 30 minutes at 30 ºC. Spheroplasts were treated with 200 units/ml of micrococcal nuclease at 37 ºC during 45 minutes.  Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina Genome Analyzer IIx using the single-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

value: S. japonicus var. japonicus ade12- FY53

value: Asynchronous mitosis


title: WT1-A_day0

source_name: WT-derived MSCs


title: 20 min. OGD, mRNA-seq, replicate #1


title: V991w RNAseq replicate

city: Wuhan

first: Qi-Jia

last: Wu

address: Nanhu Avenue

country: China

institute: ABlife. inc

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Verticillium dahliae whole genome using bowtie v0.12.9 with parameters -t -k 2 -v 2 -p 16 --sam --quiet  --solexa-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol of in house. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ASM15067v1, VdLs.17 strain of Verticillium dahliae
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Verticillium dahliae

growth_protocol: Prior to infection, the frozen-stored fungal cells were activated on a potato-dextrose agar plate for 3-4 day, and then was inoculated into Czapek broth on a shaker at 150 rpm,  25℃ for 10-14 days.

extract_protocol:
Total RNAs were extracted using RNAisoTM Plus (TaKaRa) , following manufacture's instruction
The cDNA libraries were prepared from polyadenylated mRNA/ncRNA isolated using oligo-dT beads (NEB) and fragmented by RNase III (NEB). PCR amplification was used to enrich the adapter-attached cDNA library using primers complementary to the ends of the adapters for single-end sequencing (Illumina).


title: JCYL002D

city: Tianjin

first: Yuping

last: Lin

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Illumina Casava_v1.8.0 software used for basecalling. Sequenced reads were trimmed for adaptor sequence.
Sequence reads were assembled and analyzed in CLC Genomics Workbench 6.5 (CLC Bio, Aarhus, Denmark). The Saccharomyces cerevisiae S288C genome was downloaded from RefSeq at the NCBI (http://www.ncbi.nlm.nih.gov/refseq/) including 16 chromosomes and the mitochondrial genome. The genes for N. crassa  b-glucosidase gh1-1 and EGFP-tagged N. crassa cellodextrin transporter cdt-1 were manually annotated and combined with the S. cerevisiae S288C genome as the reference (total size of 12.17 Mb). Expression values were normalized by calculating the reads per kilobase of mRNA exon per million mapped reads (RPKM), and further normalized using the option of “By totals”. To identify differential expression in the cellobiose versus glucose fermentations, an unpaired two-group comparison was used to generate fold-changes and further analyzed for statistical significance by using Baggerley’s test.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Excel file include RPKM values for all the samples and differential expressions in the cellobiose versus glucose fermentations including fold change and FDR p-values.

organism: Saccharomyces cerevisiae

source_name: Cellobiose-grown cells

extract_protocol:
Total RNA was extracted using the RiboPure Yeast kit (Ambion, Austin, TX, USA), according to manufacturer's instructions, except cells were disrupted by bead-beating 3 times for 30 sec, with a 30 sec pause between runs.
4 µg of total RNA were used to prepare the multiplexing libraries with barcodes following the standard instructions of the Illumina TruSeq RNA Sample Prep Kit.

value: Engineered BY4742 containing cellobiose-utilizing pathway

tag: growth condition

value: Anaerobic

tag: carbon source

value: Cellobiose


title: Myoblast-GATA4-ChIP

city: Minneapolis

first: Genomics

last: Center

state: MN

address: 312 Church Street SE

institute: University of Minnesota

data_processing:
Basecalls performed using CASAVA version 1.8.
Following procedures were performed using Galaxy platform.
Identical reads in each data were counted as one read to eliminate PCR duplicates.
Reads were mapped to mouse GRCm38/mm10 genome by bowtie with allowing up to four mismatches.
Peaks were called using MACS in comparison of GATA4- with IgG-ChIP-seq data
Genome_build: mm10
Supplementary_files_format_and_content: BED files were generated using Galaxy.

source_name: Skeletal muscle myoblast

growth_protocol: Satellite cell-derived myoblasts were cultured in growth medium (Ham’s/F10, 20% FBS, 20 ng/ml bFGF) on collagen-coated plate.

extract_protocol:
Myoblasts were fixed with 1% formaldehyde. Extracted protein-DNA complex was fragmented to 200-500 bp then immunoprecipitated with cocktail of anti-GATA4 antibody or control IgG using Protein G Sepharose 4 Fast Flow.
Two-barcoded TruSeq ChIP DNA libraries were prepared as Illumina recommended.
250-300 bp products were subjected to HiSeq 2500 Sequencing System to generate paired-end 150 bp sequence reads.

value: STOCK Myf5tm1Pas/J

tag: culture

value: Growth medium

value: Anti-GATA4 (Santa Cruz, C-20; Santa Cruz, H-112; eBioscience, eBioevan)


title: Myoblast-IgG-ChIP

value: Control IgG (Santa Cruz, sc-2028, sc-3883, sc-3888)


title: JCYL002B

source_name: Glucose-grown cells

value: Glucose


title: JCYL003D


title: JCYL003B


title: V991b RNAseq replicate


title: dcr-1 Embryos RDE-4 Co-IP

status: Public on Apr 09 2015

city: Salt Lake City

first: Joseph

middle: M.

last: Whipple

state: UTAH

address: 15 N Medical Drive East, Rm 4800

department: Department of Biochemistry

institute: University of Utah

description: dsRNA purified from dcr-1(375) embryos worms byco-immunoprecipitation with RDE-4 antibody

data_processing:
All reads were aligned twice to the C. elegans genome: first with Novoalign (Version 2.07.13) using parameters “-r All “–c TGGAATTCTCGGGTGCCAAGG and GATCGTCGGACTGTAGAACTCTGAAC" and then with GNUMAP-bs (Version 3.0.2) using parameters “--lib_type unstrand --read_type rna --per_dist 150 --nt_conv a2i --top_k_hash 10 --map_quality sensitive”.
All alignment files were merged into one alignment file and filtered using the Useq application SamTranscriptomeParser. For GNUMAP alignments, the following command options were used: -a 10000 -n 1 -p -r for unique alignments or -a 10000 -n 1000000 -p -r for unique + repeat alignemnts.  For Novoalign alignments, the following command options were used: -a 120 -n 1 -p -r for unique alignments or -a 120 -n 1000000 -p -r for unique + repeat alignemnts.
Alignment were converted to pileup format using samtools (Version 0.1.19) mpileup with the command options "-A -B".
Pileup files were parsed using the Useq (Version 8.7.9) application RNAEditingPileupParser with the comman options "-v C_elegans_Oct_2010 -t -m"
The USeq application RNAEditingScanSeqs with command options "-t -i" was used to detect editing enriched windows from RNAEditingPileupParser point data
The USeq application EnrichedRegionMaker with command options "-I 0 -s 3-g 1000" generated initial lists of editing-enriched regions. All regions with less than 2 editing-enriched windows were discarded.
Genome_build: WS220/ce10 (October 2010) available from UCSC

Supplementary_files_format_and_content: GNUMAP_Unique_EERs.bed; BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - # of editing-enriched windows in EER, Column 6 - Strand
GNUMAP_Unique_and_Repeat_EERs.bed; BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - # of editing-enriched windows in EER, Column 6 - Strand
Novoalign_Unique_EERs.bed; BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - # of editing-enriched windows in EER, Column 6 - Strand
Novoalign_Unique_and_Repeat_EERs.bed; BED format, Column 1 - Chromosome, Column 2 - Start Coordinate, Column 3 - Stop Coordinate, Column 4 - EER Name, Column 5 - # of editing-enriched windows in EER, Column 6 - Strand
GNUMAP_Unique_and_Repeat_Editing_Minus.bw; bigWig format, minus strand track displaying RNA editing sites
GNUMAP_Unique_and_Repeat_Editing_Plus.bw; bigWig format, plus strand track displaying RNA editing sites
GNUMAP_Unique_Editing_Minus.bw; bigWig format, minus strand track displaying RNA editing sites
GNUMAP_Unique_Editing_Plus.bw; bigWig format, plus strand track displaying RNA editing sites
Novoalign_Unique_and_Repeat_Editing_Minus.bw; bigWig format, minus strand track displaying RNA editing sites
Novoalign_Unique_and_Repeat_Editing_Plus.bw; bigWig format, plus strand track displaying RNA editing sites
Novoalign_Unique_Editing_Minus.bw; bigWig format, minus strand track displaying RNA editing sites
Novoalign_Unique_Editing_Plus.bw; bigWig format, plus strand track displaying RNA editing sites

organism: Caenorhabditis elegans

source_name: Embryos

growth_protocol: Embryos were harvested by hypochorite treatment from gravid adults grown in liquid culture at 20°C.

extract_protocol:
Embryo extracts were prepared by douncing. Extracts were incubated with anti-RDE-4 polyclonal antibody at 4°C. Antibody/dsRNA complexes were purified on protein A/G agarose and dsRNA isolated by Trizol extraction followed by Turbo DNAse treatment.
RNAs were fragmented to and average size of 150-200 nt prior to library preparation. cDNA libraries were generated using the Illumina TruSeq small RNA preparation kit according to manufacturer's protocol, with the exception that a final concentration of 10% DMSO was added to the reverse transcriptase reaction.

tag: developmental stage

value: Embryos

tag: tissue

tag: ip antibody

value: Rabbit polyclonal antibody raised against C. elegans RDE-4

tag: ip antibody vendor

value: Covance


title: V991w RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Verticillium dahliae whole genome using bowtie v0.12.9 with parameters -t -k 2 -v 2 -p 16 --sam --quiet  --solexa-quals --chunkmbs 256 --sam-nohead --sam-nosq --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol of in house. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ASM15067v1, VdLs.17 strain of Verticillium dahliae
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...


title: JCYL001D


title: Cumulus cells

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

country: France

institute: INSERM

description: Human cumulus cells was mechanically separated from mature oocytes and lysed for RNA extraction

data_processing:
Illumina Casava software used for basecalling.
Raw sequence reads were filtered, mapped to the reference human genome using the CRAC software and annotated according to the ENSEMBL Genome Browser (Ensembl API version 66).
Supplementary_files_format_and_content: Tab-delimited text files include count of each sequence
genome build: hg19

source_name: follicular cells

extract_protocol:
The RNeasy Micro Kit (Qiagen) was used to isolate total and small RNAs from cumulus cells or MII mature oocytes.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: cell type

value: Cumulus cells

tag: maturation stage

value: Mature (MII)


title: Oocytes

description: Human MII mature oocytes lysed for RNA extraction

source_name: germinal cells

value: Oocytes


title: B6xKI_H3K4me3_Input_sample_2

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
H3K4me3_BxKI_merge_ChIP.BedGraph.gz
H3K4me3_BxKI_merge_e-5_peaks.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph and peak files were generated from MACS with p-value e-5. BvH_DiffBind.counts.csv.gz contains the normalized read counts and log fold change for all H3K4me3 peaks exported from R package DiffBind

source_name: spermatocytes

growth_protocol: Crude isolation of germ cells was conducted from male mice at 12 days post-partum (dpp). For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

tag: age

value: 12 days post-partum

tag: strain background

tag: prdm9 allele

tag: ChIP

value: input

tag: antibody manufacturer

tag: antibody catalog number

tag: antibody lot/batch#


title: N2 Mixed Stage J2 IP

description: dsRNA purified from N2 mixed stage worms by immunoprecipitation with the J2 dsRNA antibody

source_name: Mixed Stage

growth_protocol: Mixed stage worm were grown in liquid culture at 20°C.

extract_protocol:
Total RNA was isolated from mixed stage worms by Trizol extraction and treated with Turbo DNAse. 40 μg of Total RNA was depleted of rRNA using the RiboMinus kit and incubated with J2 dsRNA antibody overnight at 4°C. J2/dsRNA complexes were purified on protein A/G agaorse and RNA isolated by Trizol extraction.
RNAs were fragmented to and average size of 150-200 nt prior to library preparation. cDNA libraries were generated using the Illumina TruSeq small RNA preparation kit according to manufacturer's protocol, with the exception that a final concentration of 10% DMSO was added to the reverse transcriptase reaction.

tag: strain

value: wild-type (N2)

value: Mixed Stage

value: Whole worm

value: J2 dsRNA antibody

value: English & Scientific Consulting

tag: ip antibody cat./lot#


title: N2 Embryos RDE-4 Co-IP

description: dsRNA purified from N2 embryos worms byco-immunoprecipitation with RDE-4 antibody


title: dcr-1 Mixed Stage J2 IP

description: dsRNA purified from dcr-1(mg375) mixed stage worms by immunoprecipitation with the J2 dsRNA antibody


title: B6xKI_H3K4me3_ChIP_sample_2

value: Millipore/EMD


title: V991b RNAseq


title: JCYL001B

value: Engineered BY4742 containing cellobiose-utilizing pathway

tag: growth condition

value: Anaerobic

tag: carbon source


title: N2 Embryos DCR-1 Co-IP

description: dsRNA purified from N2 embryos worms byco-immunoprecipitation with DCR-1 antibody

extract_protocol:
Embryo extracts were prepared by douncing. Extracts were incubated with anti-DCR-1 polyclonal antibody at 4°C. Antibody/dsRNA complexes were purified on protein A/G agarose and dsRNA isolated by Trizol extraction followed by Turbo DNAse treatment.
RNAs were fragmented to and average size of 150-200 nt prior to library preparation. cDNA libraries were generated using the Illumina TruSeq small RNA preparation kit according to manufacturer's protocol, with the exception that a final concentration of 10% DMSO was added to the reverse transcriptase reaction.

tag: developmental stage

value: Embryos

value: Rabbit polyclonal antibody raised against C. elegans DCR-1


title: B6xKI_H3K4me3_ChIP_sample_1


title: dcr-1 Embryos DCR-1 Co-IP

description: dsRNA purified from dcr-1(375) embryos worms byco-immunoprecipitation with DCR-1 antibody

tag: tissue

value: Covance


title: LFS1-A_day7

tag: disease/genotype

value: Li-Fraumeni Syndrome (LFS) patient

tag: source cell type

value: patient-derived iPSCs

tag: cell subtype

value: mesenchymal stem cells (MSCs) intermediate

tag: time point

value: day 7 of osteoblast differentiation treatment


title: MN_Scerevisiae

data_processing:
genome_build: S. cerevisae strain S288C, R64-1-1 assembly (3/2/2011), from Saccharomyces Genome Database
Alignment: bowtie 0.12.7
The smoothed signal generated by using the multilevel 1-D biorthogonal wavelet decomposition/reconstruction tool implemented in the Matlab “Wavelet Toolbox”, is used to calculate the average spacing between boundary peaks for individual nucleosomes.
The resulting combined profile was wavelet-smoothed to generate the final nucleosome positioning profile.

organism: Saccharomyces cerevisiae W303

source_name: Mononucleosomal DNA

growth_protocol: S. cerevisiae W303-1a was grown in 200 ml of rich medium (YEPD) at 30 ºC up to a density of 107 cells/ml.

extract_protocol:
Mononucleosomal DNA was isolated as described (de Castro et al. 2012). The amount of Zymolyase  20T used to prepare spheroplasts was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Cells of S. cerevisiae were treated with 5 mg of Zymolyase 20T during 10 minutes at 30 ºC. Permeabilized cells were treated with 45 units/ml of micrococcal nuclease at 37 ºC during 10 minutes. Mononucleosomal DNA was recovered from 1.5% agarose gelsl.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture type

value: Asynchronous mitosis


title: B6xKI_H3K4me3_Input_sample_1

tag: age

value: 12 days post-partum

tag: strain background

value: input


title: G5-CMP2 [RRBS]

city: Houston

first: Ronald

last: Depinho

address: 1400 Pressler St

institute: University of Texas MD Anderson Cancer Center

description: Methylation data from telomere dysfunctional  mice

data_processing:
bisulphite-treated DNA was aligned to UCSC Genome Browser mm10 reference genome using Bowtie
methylation called using Bismark v0.7.11
methylation profile analysis conducted using methylKit (Akalin, A. et al. methylKit: a comprehensive R package for the analysis of genome-wide   DNA methylation profiles. Genome biology 13, R87, doi:10.1186/gb-2012-13-10-r87   (2012))
Genome_build: mm10
Supplementary_files_format_and_content: excel files containing the hyper- and hypo methylated regions of G0 & G5 CMP

source_name: CMP from telomere dysfunctional  mice

extract_protocol:
Genomic DNA was extracted from sorted CMP populations isolated from 3 pools of G0 or 2 pools of G5 mice using UltraPure Phenol:Chloroform:Isoamyl Alcohol according to manufacturer’s instructions (Life Technologies). 14,000 to 30,000 cells were available for each sample, resulting in a minimum of 45ng of DNA
Gu, H. et al. Preparation of reduced representation bisulfite sequencing libraries for   genome-scale DNA methylation profiling. Nature Protocol 6, 468-481,   doi:10.1038/nprot.2010 (2011)

value: mainly C576BL/6

tag: genotype/variation

value: mouse with short telomeres

value: G5 TERTER/ER

value: bone marrow

tag: cell type

value: FACs sorted cells common myeloid progenitor (CMP) cells


title: H3K27ac_DP

city: Marseille - cedex 09

first: Aurélien

last: Griffon

address: 163, Avenue de Luminy - case 928

institute: TAGC - Inserm U1090

data_processing:
Libraries for TCF1, HEB and the DNaseI were sequenced sequenced on 5500 SOLiD System (Life technologies), according to manufacturer’s instructions. Libraries for H3K9me3 and H3K27ac were sequenced sequenced on HighSeq 2000 (Illumina), according to manufacturer’s instructions.
The different lanes were combined for each sample.
Reads were mapped to the mouse genome (mm9) using Bfast tool (v0.7.0). Only reads that have a best scoring alignment were used.
Reads were elongated to the fragment size  estimated by the HOMER tool (v6.1) and converted to wig format using a binning window of 50bp. Wiggle files were then normalized by the number of mapped reads in the samples.
Peak-calling was performed using the HOMER tool (v6.1) with default settings (FDR: 0.001; local and input fold enrichment: 4.0).
Genome_build: mm9
Supplementary_files_format_and_content: Fixed-step 50bp wiggle files were generated using a developed in-house tool.
Supplementary_files_format_and_content: BED files were generated using the HOMER tool (v6.1).

source_name: Double Positive thymocytes

extract_protocol:
After purification, cross-linked nuclei from DP thymocytes or P5424 cells, were sonicated using a Misonix 4000 (Misonix Inc) sonicator for 7 cycles (30 seconds on, 30 seconds off, amplitude 40). After the addition of Triton X-100 to a final concentration of 1%, debris were removed through centrifugation at 20.000g and 4°C for 20 minutes. Extracts were incubated overnight at 4°C on a rotating wheel with antibodies bound to protein G Dynabeads (Life technologies). Beads were washed 5 times in RIPA buffer (50 mM Hepes pH 7.6, 500mM LiCl, 1 mM EDTA pH 8, 1% NP-40, 0.7% Na-Deoxycholate), once in TE+ (10 mM Tris pH 8, 1 mM EDTA pH 8, 50 mM NaCl) and once in TE (10 mM Tris pH 8, 1 mM EDTA pH 8). Immunoprecipitated chromatin was recovered from the beads with two subsequent elution steps at 65°C for 15 and 10 minutes in elution buffer (NaHCO3 100 mM, 1% SDS). The two eluates were combined and incubated at 65°C overnight (13-15 hours) for crosslink reversal in presence of proteinase K. DNA was purified using QIAquick PCR purification kit (Qiagen). Antibodies used for ChIP were the following: TCF1 (cell signaling, 2203), HEB (Santa cruz, sc-357X), H3K9me3 (Abcam, ab8898), H3K27ac (Abcam, ab4729).  At least 1 ng of ChIP was used for library preparation.
Libraries for the TCF1 and HEB ChIPs in DP thymocytes were prepared according to the SOLiD ChIP-Seq protocol and sequenced on 5500 SOLiD System (Life technologies), according to manufacturer’s instructions. Libraries for ChIPs against H3K9me3 and H3K27ac in DP thymocytes were prepared according to Illumina ChIP-Seq protocol and sequenced on a HighSeq 2000 (Illumina) according to manufacturer’s instructions.

value: Double Positive thymocytes

value: 4-6 weeks

tag: chip antibody


title: G5-CMP1 [RRBS]


title: DNaseI_DP

description: DNase I digestion and high-throughput sequencing were performed on intact nuclei from DP thymocytes following published method2. Briefly, nuclei were extracted using NP-40 in an isotonic buffer. The NP-40 detergent was removed and the nuclei were incubated for 3 min at 37 °C with limiting concentrations of the DNA endonuclease, DNase I (Sigma-Aldrich) supplemented with Ca2+ and Mg2+. The digestion was stopped with EDTA and the samples were treated with proteinase K. The small double-hit fragments (<500bp) were recovered by high resolution agarose gel electrophoresis followed by gel purification. DNase I hypersensitive sites were sequenced on a 5500 SOLiD System.


title: G0-CMP3 [RRBS]

description: Methylation data from normal mice

source_name: CMP from normal mice

value: normal mice

value: G0 TERTER/+


title: G0-CMP1 [RRBS]

description: Methylation data from normal mice


title: ADR-H3-T45

city: Seoul

first: Hong-Duk

last: Youn

address: Daehak-ro Jonno-gu

department: Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads for each sample were aligned to the human genome (GRCh37/hg19)  using Bowtie v.2.1.0  with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: mammary gland/breast

growth_protocol: MCF10A cells were cultured in DMEM-F12 media, supplemented with 5% (v/v) FBS, L-glutamine, antibiotics, insulin (20 μg/ml, Sigma), cholera toxin (0.1 μg/ml, Listbiological Labs), hydrocortisone (1 μg/ml, Sigma) and hEGF (0.02 μg/ml, PeproTech).

extract_protocol:
Nuclear pellets were washed and resuspended in 1× micrococcal nuclease reaction buffer [10 mM Tris–Cl (pH 7.9), 5 mM CaCl2, 0.5 mM DTT] and the chromatin was digested with micrococcal nuclease (New England Biolabs). The digestion was stopped with EDTA. Histone-DNA complexes were isolated with antibody.
DNA fragments were ligated to a pair of adaptors for sequencing on an Illumina Hiseq-2000. The ligation products were size-fractionated to obtain 200–300-bp fragments on a 2% agarose gel and PCR-amplified for 18 cycles. Each library was diluted to 8 pM for 76 cycles of single-read sequencing on the Illumina Hiseq-2000 following the manufacturer's recommended protocol.

tag: cell line

value: epithelial

tag: cell lineage

value: ectoderm

tag: treatment

value: adriamycin

value: anti-phosphorylated H3-T45


title: DMSO-H3-T45

value: DMSO


title: TCF1_DP

tag: strain


title: G0-CMP2 [RRBS]

description: Methylation data from normal mice


title: ADR-H3K36me3

value: adiramycin


title: KPC1 rep2- run2

city: Haifa

first: Aaron

last: Ciechanover

state: Haifa

address: Efron Street, Bat Galim, POB 9649

department: Faculty of Medicine, Cancer and Vascular Biology Research Center

country: Israel

institute: Technion-Israel Institute of Technology

description:
Sample 12
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

data_processing:
both analysis: RNA was analyzed using Illumina HiSeq 2500. The number of reads was between 25,949,993 and 39,809,768 per sample
RNASeq analysis mapped to the human genome:
The reads were mapped to the human genome (GRCh37) using Tophat version 2.0.9 , Up to 3 mismatches were allowed per read, with up to 3 mismatches per segment.The-b2-sensitive parameter was set.
Only uniquely mapped reads were counted in the analysis, using the HTSeq-count package version 0.5.3p3 with ‘intersection-nonempty’ mode
The counts normalization and the differential expression analysis were done using the DESeq2 package version 1.2.8
The reads were mapped  both to the human and mouse genomes (builds GRCh37.64 and NCBIM37.64, respectively) using Bowtie2 version 2.2.2 with the parameters-sensitive - k 5.
Using an in house written Perl script, we determined for each read whether it was mapped to both, one, or neither of the genomes. We used only reads that were uniquely mapped to the mouse genome.
Gene expression values were determined using the Cufflinks software version 2.2.1  by the "cuffnorm" command.
Genome_build: GRCh37 for the human trascripts analysis. GRCh37.64 (human) and NCBIM37.64 (murine) builds were used in the murine trascripts analysis
Supplementary_files_format_and_content: final_results_U87_run1+run2.xlsx: RNASeq analysis mapped to the human genome. A differential expression table for U87-MG samples that contains the following columns: Gene name and chromosomal position for each gene ,  Base mean – mean of the normalized counts across all samples. For each pair of samples:  Log2Fold change – log2 of the fold change between the pair of samples. For comparisons where samples of one conditions are zeroes and the other conditions’ are low (average < 1), the fold change that is calculated by DESeq2 is very high due to division by zero. In such cases the fold change is set to “NA_zeros’.  p-value - The p value for rejecting the null hypothesis ’mean ==meanB’.  padj - The Benjamini & Hochberg adjusted p values (multiple testing correction).  Flag – can be either of the following:    Tested – the statistical test was conducted, the log2 fold change and the adjusted p-value are   informative.  Low count – indicates that either the gene was filtered due to low expression (in such case the adjusted p-value will be 'NA'), or none of the samples in that comparison received  5 counts or more.  Outlier:X – this gene was not tested for differential expression in this  comparison since it is an outlier in sample X. The p-value and adjusted p-value are 'NA' in this case.  All zero – the counts of this gene is 0 in all samples. Such genes are not tested for differential expression. Significant - can be either "yes" or "no", it is “yes” if the adjusted p-value (padj) is < 0.05
Supplementary_files_format_and_content: genes.fpkm_tracking:  RNASeq analysis mapped to the murine genome to identify the host immune cell signeture. Contains gene expression values. To identify the cell type origin of the murine reads,  gene expression of each sample was compared with the characteristic gene expression of murine immune cell types obtained   from the Immunological Genome Project (ImmGen)

source_name: KPC1 - run2

extract_protocol:
Following 21 days, mRNA from U87-MG xenografts was isolated using an RNA purification kit (NucleoSpin® Kit for RNA purification, was from Macherey-Nagel)
Total mRNA was analyzed using Illumina HiSeq 2500. Standard Illumina protocols were used to prepare the RNA libraries.

treatment_protocol: Exponentially growing U87-MG cells were stably transfected with an empty vector (V0) or vectors coding for Myc-KPC1 or Flag-p50. Cells were dissociated with trypsin, washed with PBS, and brought to a concentration of 50×106 cells/ml. Cell suspension (5×106/0.1 ml) was inoculated subcutaneously at the right flank of 7-weeks old male Balb/C nude mice (n=7).

value: U87-MG glioblastoma human cells

tag: transfected with

value: vectors coding for Myc-KPC1

tag: xenografts host mice

value: 7-wks old male Balb/C nude mice

tag: tumor stage

value: 21 days old xenografts


title: KPC1 rep1- run2

description:
Sample 11
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx


title: HEB_DP

value: HEB


title: V0 (control) rep2- run2

description:
Sample 9
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

source_name: V0 (control) - run2

value: empty vector (V0)


title: ADR-POLII-ser2

value: anti-phosphorylated RNA Pol II-S2


title: CapStarr-seq 3T3

description: CapStarr-seq

data_processing:
Libraries were sequenced on ION 318 Chip v2 (Life Technologies) using the Ion PGM Sequencing 400 kit (Life Technologies), according to manufacturer’s instructions.
Reads were mapped to the mouse genome (mm9) using the Ion PGM pipeline.
Reads were elongated to the mean fragment size  estimated by the HOMER tool (v6.1) and converted to wig format using a binning window of 50bp.
Wiggle files were then normalized by the number of mapped reads in the samples.
Genome_build: mm9
Supplementary_files_format_and_content: Fixed-step 50bp wiggle files were generated using a developed in-house tool.

source_name: 3T3 cell line

extract_protocol:
Genomic DNA from C57bl6 mouse thymus was sheared by sonication (Diagenode pico) and DNA fragments between 330 bp and 430 bp were size-selected on a 1.2% high resolution agarose gel (Sigma-Aldrich) and purified using Qiaquick gel extraction kit (Qiagen). Ion Torrent adapters were ligated to 8 µg of size-selected DNA fragments using Ion Plus Fragment Library Kit (Life Technologies) following manufacturer’s instructions except for the final PCR amplification. Forty PCR reactions (98°C for 2 minutes; followed by ten cycles of 98°C for 20s, 65°C for 15s, 72°C for 15s) with 2µL of adaptor ligated DNA were performed using KAPA Hifi Hot Start Ready Mix (KAPA Biosystems) and primers (fw: TAGAGCATGCACCGGAACCATCTCATCCCTG*C*G*T*G and rw: GGCCGAATTCGTCGAAACCACTACGCCTCCGC*T*T*T*C, * indicates phosphorothioates bonds) which add a specific 15 nucleotides extension to both adapters for directional cloning using recombination (In Fusion HD, Clontech). The forty PCR reactions were pooled and purified with Agencourt AMPureXP DNA beads (Ratio beads/PCR 1.2; Beckman Coulter). For target enrichment, a home-designed oligonucleotide microarray covering the 7,542 CRMs defined above was constructed using the SureSelect technology (Agilent) and the eArray tool (https://earray.chem.agilent.com/earray/). The genomic library was hybridized on the microarray as outlined in the Agilent SureSelect DNA Capture Array protocol (Agilent). Briefly, an hybridization mixture with 10 μg of PCR along with Blocking oligo 1 (TAGAGCATGCACCGGAACCATCTCATCCCTG*C*G*T*G), Blocking oligo 2 (GGCCGAATTCGTCGAAACCACTACGCCTCCGC*T*T*T*C), Blocking oligo 3 (CACGCAGGGATGAGATGGTTCCGGTGCATGC*T*C*T*A), Blocking oligo 4 (GAAAGCGGAGGCGTAGTGGTTTCGACGAATTC*G*G*C*C), was denatured at 95°C for 3 minutes followed by transfer to 37°C for 30 minutes. The hybridization mixture was dispensed onto the center of a gasket slide and the oligonucleotide array was placed with the active side contacting the hybridization mixture. The resulting sandwich was incubated at 65°C for 65 hours on a rotisserie in an Agilent hybridization oven. Following hybridization, the slide-gasket sandwich was disassembled and the µarray was washed, following manufacturer’s instructions. Slides were dried and 490 μL of nuclease-free water were added to a new gasket slide and the dried µarray was placed atop as described earlier, creating a fresh slide-gasket sandwich. The slide-gasket sandwich was incubated at 95°C 10 minutes on a rotisserie in an Agilent hybridization oven. After heat denaturation, the eluate was recovered with a 1-ml 30G syringe. The eluted DNA was purified with Agencourt AMPureXP DNA beads (Ratio beads/PCR 1.8) and eluted in 80 µL. Twenty independent 25 µL PCR (98°C for 2 minutes; followed by 20 cycles of 98°C for 20s, 65°C for 15s, 72°C for 15s) reactions with 4 µL of captured DNA were performed using KAPA Hifi Hot Start Ready Mix and primers (fw: TAGAGCATGCACCGGAACCATCTCATCCCTG*C*G*T*G and rw: GGCCGAATTCGTCGAAACCACTACGCCTCCGC*T*T*T*C). PCR reactions were pooled, purified with Agencourt AMPureXP DNA beads (Ratio beads/PCR 1.8) and eluted in 200 µL H2O. The mammalian STARR-Seq screening vector has been previously described. The screening vector was linearized by a 6 hours digestion with AgeI-HF and SalI-HF (New England Biolabs), followed by agarose gel electrophoresis, QIAquick gel extraction (Qiagen) and a clean-up with Qiagen Minelute PCR purification Kit (Qiagen). The purified PCR products were recombined (Clontech In-Fusion HD) with the screening vector (Qiagen) in a total of ten 10 µL reactions. The recombination reactions were pooled, purified with Agencourt AMPureXP DNA beads and eluted in 29 µL. Thirteen aliquots (20 µL each) of MegaX DH10B Electrocompetent Bacteria (Life technologies) were transformed with 2 µL of DNA each, according to the manufacturer’s recommendation. After one hour recovery at 37°C, transformations were pooled and transferred to 2 L of LBAMP medium and grown overnight. An aliquot of the transformation was plated on LBAMP to estimate the number of cloned fragments. Finally, the plasmid library was extracted using Qiagen Plasmid Plus Mega Kit (Qiagen). Transfection of library (5µg/1x10^6 cells) was performed using Neon Transfection System (Life technologies). A total of 30x10^6 cells were transfected per experiment. 25x10^6 cells were used for RNA purification and 5x10^6 for DNA purification. P5424 cells were transfected with 1600v-20ms-1 pulse and 3T3 with 1400v-20ms-2 pulses. Cells were transferred to complete growth medium and incubated for 24 hours before RNA and DNA isolation. Total RNA was extracted using RNeasy miniprep kit (Qiagen) with the on-column DNaseI treatment. The PolyA RNA fraction was isolated using µMACS mRNA isolation kit (Miltenyi) following manufacturer’s instructions. PolyA RNA was treated with Ambion turboDNase (Ambion) and purified with RNeasy Minelute kit (Qiagen). Finally, mRNA was quantified with Qubit RNA HS Kit (Life technologies). Plasmid DNA was extracted from 5x10^6 cells using a QIAGEN plasmid plus mini kit (Qiagen), following manufacturer’s instructions. 1st strand cDNA synthesis was performed with superscript III (Life technologies) using a reporter-RNA specific primer (CAAACTCATCAATGTATCTTATCATG) and 0.2 to 0.3 µg of polyA RNA per reaction for a total of 10 reactions. After reverse transcription, 1 µL of RNaseH was added (37°C, 1h). cDNA was purified with QIAquick PCR purification kit and concentration was determined with Qubit ssDNA Kit (Life technologies).
cDNA was amplified by a 2-step nested PCR using the KAPA Hifi Hot Start Ready Mix. In the first PCR (98°C for 2 minutes; followed by 15 cycles of 98°C for 20s, 65°C for 20s, 72°C for 30s), 5 ng of cDNA per reaction were amplified using 2 reporter-specific primers (fw: GGGCCAGCTGTTGGGGTG*T*C*C*A*C and rw: CTTATCATGTCTGCTCGA*A*G*C), one of which spans the splice junction of the synthetic intron, in a total of 10 reactions. To remove any residual contamination of plasmid or cDNA, PCR products were purified on gel using QIAquick gel extraction Kit (Qiagen) followed by a clean-up with QIAquick minelute PCR purification kit (Qiagen). To generate the Ion Torrent libraries, the purified PCR was used as template for the second PCR (5 ng/PCR, for a total of 10 PCR; 98°C for 2 minutes; followed by 10 cycles of 98°C for 20s, 65°C for 20s, 72°C for 30s) with the KAPA Hifi Hot Start Ready Mix and Ion Torrent library amplification primer mix (Life technologies, T_PCR_A: CCA TCT CAT CCC TGC GTG TC and P1amp: CCA CTA CGC CTC CGC TTT CCT CTC TAT G). To generate the INPUT control, ten reactions with 5 ng of reporter constructs (library) per reaction were amplified using the same conditions as above, at the exception of the forward primer in the 1st PCR (fw: GGGCCAGCTGTTGGGGTG*A*G*T*A*C). To assess change in library composition caused by electroporation, 10 reactions with 5 ng per reaction of reporter constructs isolated from transfected cells were amplified as described above. The emulsion PCRs were performed with 25 µL of Starr-Seq libraries (10 pM) using the Ion PGM Template OT2 400 kit and the ONE TOUCH 2 system (Life Technologies), according to manufacturer’s instructions. Template-positive Ion Sphere Particles were enriched using the Ion PGM Enrichment Beads (Life Technologies), according to manufacturer’s instructions.


title: CapStarr-seq P5424 replicate 1

description: CapStarr-seq

source_name: P5424 cell line


title: input DNA_ChIPseq

city: Cincinnati

first: Mark

last: Rochman

state: OH

address: 3333 Burnett Ave

department: Allergy and Immunology

institute: CCHMC

description: ChIPseq

data_processing:
For ChIPseq Fastq files from Illumina pipeline were aligned by bowtie version 1.0.0 with maximum one allowed error in a sequence and number of hits was not more then one. MACS2 version  2.0.10.20130712 were used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less then 0.2.
To visualize the data it were uploaded to UCSC genome browser and fragment coverage were used with estimated fragment size from MACS2 output.
To produce list of differentially enriched regions Manorm algorithm was applied. The normalized log(2) ratio of read density between two samples (M) was calculated and used as a quantitative measure of differential binding in each peak region between two samples, with peak regions associated with larger absolute M values exhibiting greater differences in binding.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files for RNAseq are DESeq output from comparing each time point of IL-13 treatment with control untreated sample. These files also includes RPKM values. When two sample were processed they were combined in one group for analysis. File designated "Control_2hr_6hr.fastq" is common for  2 hr and 6 hr time points. ChIPseq files are Manorm output comparing IL-13-treated cells to control untreated sample.

source_name: esophagus

growth_protocol: TE-7 cells were grown in RPMI medium supplemented with 5% FCS

extract_protocol:
For ChIP cells were fixed with 0.8% formaldehyde for 8 min at RT and DNA was processed and sonicated according to the protocol from Covaris using Covaris S220 sonicator.
RNA and DNA libraries for single read sequencing were prepared for using standard Illumina protocols

treatment_protocol: Cells were treated with IL-13 at 100ng/ml for 2 hr, 6 hr and 24 hr for RNA-sequencing and for 6 hr for ChIP-sequencing

value: esophageal epithelial

value: none (input)


title: Plasmid library after transfection

description: Plasmid library after transfection; plasmid DNA


title: CapStarr-seq P5424 replicate 2

description: CapStarr-seq


title: V0 (control) rep3- run2

description:
Sample 10
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx


title: V0 (control) rep1- run2

description:
Sample 8
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx


title: IL-13 H3K27Ac_ChIPseq

description: ChIPseq

value: ab4729 (Abcam)


title: H3K9me3_DP

value: Double Positive thymocytes

value: 4-6 weeks


title: p50 rep2- run1

description:
Sample 7
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

source_name: p50 - run1

value: vectors coding for Flag-p50


title: RNA-seq from IMR90

city: Cambridge

first: Xiaowei

last: Zhuang

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

data_processing:
Gene models were constructed using cufflinks 2.1.1 and the human genome (v18)
Genome_build: Gencode 18
Supplementary_files_format_and_content: Output of cufflinks

molecule: polyA RNA

source_name: Human primary fibroblasts

growth_protocol: Cells were grown in Eagle's Minimum Essential Medium at 37C and 5% CO on glass slides for 48 hours

extract_protocol:
Total RNA was extracted using the Zymo Quick RNA Miniprep, polyA RNA was selected using the NEB poly(A) mRNA magnetic isolation module
Libraries were contstructed using the NEBNext Ultra Directional Kit according to manufacturer's instructions

tag: passages

value: fibroblast


title: SIP2

city: Shanghai

first: Panfeng

last: Zhao

address: 800 Dongchuan RD. Minhang District

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by Trimmomatic (version 0.32), then mapped to Solanum lycopersicum whole genome (ITAG2.4) using tophat v2 2.0.10 with parameters -g 1 -I 5000 --no-novel-juncs
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Solanum lycopersicum (ITAG2.4)
Supplementary_files_format_and_content: xls files include RPKM values for each Sample

organism: Solanum chilense

source_name: Styles

extract_protocol:
styles  were collected, immediately frozen in liquid nitrogen, and  RNA was harvested using RNAprep pure Plant Kit (TIANGEN, China).  Illumina TruSeqTM RNA Sample Prep Kit  was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: styles

tag: mating system

value: self-incompatibility

tag: time

value: 24-h self-pollination (P)


title: NP2810

city: Pirassununga

first: Mario

last: Binelli

state: SP

address: Rua Duque de Caxias Norte, 255

department: department of animal reproduction

institute: University of Sao Paulo (USP)

data_processing:
CASAVA v1.8.2
The paired end (PE) reads were filtered using the Seqyclean v1.4.13  package (https://bitbucket.org/izhbannikov/seqyclean) which removed all reads with a mean quality under 26 and removed the primer and vector contaminants using the UniVec database (http://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/).
The reads were mapped using the local alignment with Bowtie2 v2.1.0 against the masked Bos taurus genome masked assembly (Bos taurus  UMD3.1) and read counts were obtained using  HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
The differential expression analysis of the RNA-Seq data was performed with package  DESEq2 v1.12.1, from R. The normalized counts were then obtained for each annotated gene.
After normalization, the log2foldchange was obtained through a general linear model approach, the significance test was followed by the FDR-Benjamini-Hochberg correction for multiple tests.
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: P_vs_NP.txt reports abundance measurements

organism: Bos indicus

extract_protocol:
Total RNA was extracted from frozen biopsy samples using the AlLrep® DNA/RNA/Protein Mini kit (No. 80004, Qiagen), as recommended by manufacturer’s instructions. cDNA was generated by a routine RNA library preparation TruSeq protocol developed by Illumina Technologies (San Diego, CA) using 1 μg of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Therefore, beef cows were synchronized and artificially inseminated at detected estrus. Six days after AI, jugular blood samples and a biopsy from the uterine horn contralateral to the ovary containing the corpus luteum were collected. Based on pregnancy outcome on day 30, samples were retrospectively allocated to the following groups: Pregnant and Non-Pregnant.

tag: developmental stage

value: multiparous cows

tag: health status

value: Healthy

tag: breed

value: Nelore

tag: pregnancy status

value: Non-Pregnant

value: endometrial biopsy


title: IL-13 H3K9Ac_ChIPseq

description: ChIPseq

tag: cell type

value: ab10812 (Abcam)


title: ADR-POLII-ser5

value: epithelial

value: ectoderm

value: adiramycin

tag: chip antibody

value: anti-phosphorylated RNA Pol II-S5


title: Input

description: Plasmid library; plasmid DNA

source_name: Thymus

value: thymus


title: p50 rep1- run1

description:
Sample 6
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

value: U87-MG glioblastoma human cells

value: 7-wks old male Balb/C nude mice

value: 21 days old xenografts


title: SIP1

value: styles


title: NP856


title: SIUP3

value: self-incompatibility

value: 24-h unpollination (UP)


title: IL-13 H3K4me3_ChIPseq

description: ChIPseq

tag: cell line

value: esophageal epithelial

value: ab8580 (Abcam)


title: control H3K27Ac_ChIPseq

description: ChIPseq

value: ab4729 (Abcam)


title: KPC1 rep2- run1

description:
Sample 5
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

source_name: KPC1 - run1

value: vectors coding for Myc-KPC1


title: control H3K9Ac_ChIPseq

description: ChIPseq


title: KPC1 rep1- run1

description:
Sample 4
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx


title: SIP3

value: 24-h self-pollination (P)


title: P617

value: multiparous cows

value: Healthy

value: Nelore

tag: status

value: Pregnant

value: endometrial biopsy


title: SIUP2


title: SIUP1


title: control H3K4me3_ChIPseq

description: ChIPseq


title: V0 (control) rep2- run1

description:
Sample 2
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

source_name: V0 (control) - run1

value: empty vector (V0)


title: IL-13 24hr_RNAseq

description: RNAseq

data_processing:
For RNAseq Fastq files from Illumina pipeline were aligned by tophat version 2.0.9 with –T –G parameters. The -T parameter is used to align reads to the human transcriptome only and -G parameter is used to provide transcriptome annotation.
To estimate difference between treated and untreated experiments DESeq package were used (for experiments without replicates blind method was forced).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files for RNAseq are DESeq output from comparing each time point of IL-13 treatment with control untreated sample. These files also includes RPKM values. When two sample were processed they were combined in one group for analysis. File designated "Control_2hr_6hr.fastq" is common for  2 hr and 6 hr time points. ChIPseq files are Manorm output comparing IL-13-treated cells to control untreated sample.

extract_protocol:
RNA was harvested using Trizol reagent and isolated by RNeasy kit with on-column DNaseI treatment.
RNA and DNA libraries for single read sequencing were prepared for using standard Illumina protocols


title: NP238

value: Non-Pregnant


title: NP2541


title: SCP2

organism: Solanum pimpinellifolium

value: self-compatibility


title: IL-13 6hr_RNAseq

description: RNAseq


title: P2396


title: V0 (control) rep1- run1

description:
Sample 1
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

value: U87-MG glioblastoma human cells

value: 7-wks old male Balb/C nude mice

value: 21 days old xenografts


title: SCP1

value: styles


title: anti-MIWI CLIP-Seq, MIWI targets

city: Beijing

first: Jiao

last: Yuan

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

description: This Sample represents the MIWI targets from CLIP-Seq of round spermatids using anti-MIWI antibody.

data_processing:
For each read, the first 4 random index sequences were removed and appended to the read name. The resulting read was 36 nt in length.
The 3'-adaptor sequence (CTCGTATGCCGTCTTCTGCTTG) was trimmed and short reads (< 16 nt) were filtered out.
Reads were then mapped to the mouse genome (mm9) using Bowtie37 with parameters: “-l25 -n2 -k101 -m100 -e200 --best --strata --sam --phred33-quals”. Mapped reads with ≤ 1 mismatch were chosen for downstream analysis.
Reads with lengths of 25-33 nt were classified as piRNAs, and longer reads are considered as MIWI targets.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: mergepi.DuplicateMerged.fa: NR-seq information for piRNAs, including raw counts.
Supplementary_files_format_and_content: merge36.DuplicateMerged.fa: NR-seq information for MIWI targets, including raw counts.

source_name: round spermatids

extract_protocol:
Isolated round spermatids from adult C57BL/6J mice were UV-irradiated (254 nm) at 400 mj in a 15-cm plate before immunoprecipitation using a highly specific anti-MIWI antibody (generated in the lab and reported in PMIDs 24787618 and 12062093). Immunoprecipitated RNA-protein complexes were digested with micrococcal nuclease, labeled with [g-32P]-ATP (PerkinElmer) by T4 PNK (Fermentas), and isolated by SDS-PAGE, from which [32P]-labeled RNA-protein bands were cut for extracting RNAs for linker ligation, PCR amplification, and deep sequencing.
Libraries were prepared according to Illumina's instructions.

tag: strain/background

value: round spermatids

tag: antibody

value: anti-MIWI


title: anti-MIWI CLIP-Seq, piRNAs

description: This Sample represents the piRNAs from CLIP-Seq of round spermatids using anti-MIWI antibody.


title: P1753


title: abo4

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Arabidopsis thaliana (tair10) whole genome using tophat v2.0.12 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (tair10).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: Arabidopsis seeds were surface-sterilized and placed on MS (Murashige and Skoog) agar medium. After they were kept for 3 days at 4°C, the plates were transferred to a growth chamber with 16-h-light and 8-h-dark at 22°C for 14 days.

extract_protocol:
Seeding tissues was ground into fine powder in liquid nitrogen; Total RNA was isolated with Trizol reagent (Invitrogen) and treated with DNase I; The mRNA was enriched  using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

value: Col

tag: genotype

value: seedling

tag: age

value: 14-day old


title: SCUP1

value: 24-h unpollination (UP)


title: control 24 hr_RNAseq

description: RNAseq

value: esophageal epithelial


title: NP638

value: multiparous cows

value: Healthy

value: Nelore


title: SCUP3


title: P1631

value: Pregnant

value: endometrial biopsy


title: V0 (control) rep3- run1

description:
Sample 3
processed data file: genes.fpkm_tracking, final_results_U87_run1+run2.xlsx

tag: transfected with

value: empty vector (V0)

tag: xenografts host mice

tag: tumor stage


title: control 6hr_RNAseq

description: RNAseq


title: control 2hr_RNAseq

description: RNAseq


title: P904

tag: tissue


title: mms19-1


title: P1541

tag: developmental stage


title: SCP3

tag: mating system

value: self-compatibility

tag: time

value: 24-h self-pollination (P)


title: Fibroblasts newborn male P4

status: Public on Apr 08 2015

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using Bowtie2 v2.1.0 to mm10. Data were conversed and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 2x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Supplementary_files_format_and_content: Excel file containing read counts after normalization by DESeq2

organism: Callithrix jacchus

source_name: Primary skin fibroblasts

extract_protocol:
RNA was isolated using Trizol Reagent according to instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

value: P4 (animal 3d)

value: Primary skin fibroblasts


title: Fibroblasts adult male P3

value: P3 (animal 3J, 2M)


title: Fibroblasts adult male P4

value: P4 (animal 1J, 2M)


title: Fibroblasts adult male P1

value: P1 (animal 1d)


title: cjes001 P94

source_name: Embryonic stem cells

value: Embryonic stem cells


title: cjes001 P91


title: IL-13 2hr_RNAseq

description: RNAseq


title: cjes001 P96


title: Fibroblasts adult male P6

value: P6 (animal 1J, 5M)


title: Fibroblasts newborn male P2

value: P2 (animal 2d)


title: cjes001 P83


title: iPSC1 P24

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: iPSC1 P22


title: SCUP2

value: styles

value: 24-h unpollination (UP)


title: R3D1B rep 3

city: College Station

first: Zach

last: Adelman

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

data_processing:
FASTX_clipper: Adapters were removed from ends of reads using FASTX_clipper toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Bowtie1 mapping: Bowtie1 (-v 0 -m 1) (http://bowtie-bio.sourceforge.net/index.shtml) was used to map sequences to a Aedes aegypti transcript reference file
Cleaning up mapped files: A custom Linux pipeline(Haac et al.) was used to remove reads <18nt and >30nt
Counting reads: A custom Linux pipeline(Haac et al.) was used to count reads mapping at sizes 21-24
Merging Count tables: Counts data was merged from all samples into one file
EdgeR analysis: The 21-24 counts table was analyzed in EdgeR (Robinson et al, 2010)
Genome_build: The transcript reference file was taken from Vectorbase() adding all the Aedes aegypti transposon sequences and dsRNA sequences
Supplementary_files_format_and_content: tab delimited text file containing the counts data for 21-24 data

organism: Aedes aegypti

source_name: Aag2 cell line

growth_protocol: Aag2 cells were maintained at 28 degrees C in Schneider's Drosophilamedium (Lonza BioWhittaker, Basel, Switzerland) supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% L-glutamine

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen), small RNAs were size selected by PAGE
illumina TruSeq small RNA sample preparation kit

treatment_protocol: Aag2 cells were transfected in 6well plates using the Effectene (Qiagen, Germantown, MC) with 2.5ug dsRNA created with Replicator RNAi kit (Thermo Scientific, Waltham,MA)

tag: sample type


title: R3D1B rep 2


title: R3D1B rep 1


title: R3D1 rep 2


title: Col

value: Col

value: wildtype

value: seedling

value: 14-day old


title: iPSC1 P19

tag: cell type


title: R3D1 rep 1


title: R2D2 rep 3


title: iPSC1 P18


title: R2D2 rep 1


title: GFP rep 1

value: GFP


title: Passage 2

city: New York

first: Nicholas

middle: S

last: Heaton

address: One Gustave L Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: A pool of mutants was made (input), and then by passaging the resulting mutant viruses we select for viable mutants in passage 1 and passage 2.

data_processing:
Custom script for extracting reads with transposon inserts
Map reads with and without inserts to the measles virus genome using Bowtie
Produce statistics and visualization with samtools and bedtools
Genome_build: AF266290.1 [For technical reasons, the sequence "TAG" was added after nucleotide 1685 and there are some point mutations in our clone relative    to the deposited sequence.  The exact reference sequence is linked to  the Series record as supplementary file MeV_Reference_Genome.txt.]
Supplementary_files_format_and_content: normalized counts

organism: Measles morbillivirus

source_name: A549 Cells, passage 2

extract_protocol:
Total RNA was collected via trizol extraction and RT-PCR was performed with viral specific primers
TruSeq DNA sample Preparation Kit (Illumina) as per the manufacturer’s instructions.
Samples were sequenced via 100nt single-end run on a HiSeq 2000

tag: infection

value: Mutant libraries were rescued and passaged on A549 cells

tag: passage


title: Passage 1

source_name: A549 Cells, passage 1


title: GFP rep 2

tag: cell line


title: Smad2_Dome_Drug

first: Julien

last: Dubrulle

address: 16 Divinity Ave

department: MCB

data_processing:
All sequence reads were aligned using Bowtie 4.2.1 version
Genome_build: Zv9
Supplementary_files_format_and_content: A tiled data file (TDF) file (.tdf) is a binary file that contains data that has been preprocessed for faster display in IGV.

organism: Danio rerio

source_name: embryonic cells

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: embryonic stage

tag: experimental conditions

value: SB505124 treated embryos


title: FoxH1_Dome_Squint

value: Squint injected embryos

tag: antibody


title: FoxH1_Dome_WT

value: WT


title: Smad2_Dome_Squint


title: Input_control_DNA_macrophage

city: Oxford

last: O'Callaghan

state: Oxfordshire

address: Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Base calls were generated using a Illumina basecaller bcl2fastq, version 1.8.4
Reads were mapped to the UCSC hg19 reference genome (with a canonical haplotype) using STAMPY v1.021 with default parameters.
Mapped reads were filtered in SAMTOOLS based on a minimum MAPQ score of 15.
For subsequent data analysis paired end files were converted to single end by retaining one read of each proper pair and all improperly paired reads and reads from ENCODE blacklisted sites were removed.
Peak calling was performed using MACS1.4.2 (with background input control DNA) on pooled replicates and dynamic enhancer sites were identified with Diffreps V1.55 (window 500bp, step 50bp, two biological replicates, negative binomial based statistical test, FDR 2.5%).
Genome_build: UCSC hg19 (Canonical haplotype)
Supplementary_files_format_and_content: MACS files are in BED format and comprise peaks that identify enhancers sites (and promoters). Diffreps output is in tab delimited text file output and comprises dynamic enhancer sites (and promoters).

organism: Homo sapiens

source_name: Macrophage-control

growth_protocol: CD14 positive monocytes were isolated by positive selection from peripheral blood from healthy volunteers. Monocytes were cultured for 7 days with 50ng/ml macrophage colony stimulating factor to generate macrophages.

extract_protocol:
H3K27ac enriched genomic DNA and input control DNA (no antibody) was extracted using the Invitrogen Magnify Kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA) with rabbit polyclonal anti-H3K27ac (ab4729, Abcam, Cambridge, MA).
Libraries were generated from gel-purified ~200bp DNA fragments. After adapter ligation and PCR-based amplification, samples were multiplexed into one lane of the Illumina HiSeq platform to generate paired end 50bp reads (Illumina, San Diego, CA).

treatment_protocol: After 7 days of culture cells were treated for 48 hours with either oxLDL (50mcg/ml, Copper oxidized, endotoxin-free) or control buffer which lacked oxLDL

tag: treatment

value: Control buffer

tag: gender

value: male

value: Macrophage

tag: chip antibody

value: none (input)


title: PU.1-Eng expressing DN2 cells #2

city: Los Angeles

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

description: PU.1-Eng - 2

data_processing:
Sequence reads from each sample were trimmed to remove the adapter sequences and the resulting 50 bp reads were mapped to the NCBI37/mm9 mouse genome assembly
Alignment was done using Tophat (v.2.0.6). command: tophat --no-novel-juncs --library-type fr-unstranded -G Mus_musculus.NCBIM37.66.gtf
Abundance measurements were done using Cufflinks (v.2.1.1). cufflinks (fpkm) command: cuffdiff --dispersion-method blind --library-type fr-unstranded --no-effective-length-correction --library-norm-method quartile -u -b mm9.fa --emit-count-tables Mus_musculus.NCBIM37.66.gtf
Genome_build: UCSC mm9, NCBI37
Supplementary_files_format_and_content: Tab-delimited files with fpkm values generated from Cufflinks

organism: Mus musculus

source_name: fetal liver progenitor derived DN2 cells

growth_protocol: Fetal liver progenitors from e14.5 mouse embryos were cultured on OP9-DL1 stromal cells with IL-7 and Flt3L (5 ng/ml each) for 4 days to obtain early DN stage cells.

extract_protocol:
Sorted cells were lysed in the TRIzol reagent (Invitrogen) and total RNA was extracted as per the manufacturer’s protocol. polyA+ mRNA was isolated using the Dynabeads mRNA purification kit (Invitrogen) and used to generate RNAseq libraries using the NEBNeXT Ultra RNA library preparation kit (E7530) reagents (New England Biolabs) following standard procedures.
polyA+ mRNA was isolated by two rounds of selection with Dynabeads (Invitrogen), fragmented to an average size of 200 bp by Mg2+ mediated hydrolysis and used to synthesize cDNA by random priming. The cDNA was end-repaired, the blunt ends were phosphorylated and Illumina adapters were ligated to the fragments. ~300 bp cDNA fragments were then purified by gel electrophoresis and SPRI (Agencourt AMPure XP catalog #A63880) beads were used to remove shorter fragments (<100 bp). The cDNA was then PCR amplified for 15 cycles and the resulting DNA fragments were purified once again with SPRI beads and sequenced on the Illumina HiSeq 2000 sequencer following the manufacturer's protocol.

treatment_protocol: Fetal liver derived DN cells were harvested from OP9-DL1 co-cultures and infected with retroviruses carrying the indicated constructs. Cells were returned to fresh OP9-DL1 monolayers after 4 hours of infection and GFP+ c-Kit+ CD44+ CD25+ DN2 cells were sorted after ~ 18 hours of culture.

tag: strain

value: In-vitro differentiated DN2 cells

tag: retroviral transduction

value: Retroviral vector expressing PU.1-Eng construct


title: Input

source_name: A549 Cells, input

value: Mutant library before passaging

value: before passaging


title: H3K27ac_Macrophage-oxLDL_251

description:
processed data file: macs_H3K27ac_foam_cell_peaks.bed
processed data file: diffreps_H3K27ac.txt

source_name: Macrophage-oxLDL

value: rabbit polyclonal anti-H3K27ac (ab4729, Abcam)


title: Smad2_Dome_WT


title: PU.1-ETS expressing DN2 cells #2

description: PU.1-ETS - 2

value: Retroviral vector expressing PU.1-ETS construct


title: H3K27ac_Macrophage-oxLDL_249


title: H3K27ac_Macrophage-control_252

description:
processed data file: macs_H3K27ac_macrophage_peaks.bed
processed data file: diffreps_H3K27ac.txt


title: H3K27ac_Macrophage-control_250


title: R3D1 rep 3


title: Control vector infected DN2 cells #2

description: Empty vector control - 2

value: Retroviral vector backbone without insert


title: R2D2 rep 2


title: FAIRE_seq_Macrophage-oxLDL_205

description:
processed data file: fseq_foam_cells.bed
processed data file: FAIRE_diffreps_FDR2.5.txt
processed data file: dynamic_FAIRE_hotspots.bed

data_processing:
Base calls were generated using a standard Illumina HiSeq pipeline using Bustard 1.9.3
Reads were mapped to the UCSC genome browser hg19 reference genome (with a canonical haplotype) using STAMPY v1.021 with default parameters.
Mapped reads were filtered in SAMTOOLS based on a minimum MAPQ score of 15.
For subsequent data analysis paired end files were converted to single end by retaining one read of each proper pair and all improperly paired reads and reads from ENCODE blacklisted sites were removed.
Peak calling was performed using FSEQ on pooled replicates (V1.84, default parameters, peaks merged if within 140bp (fragment size) and removed if < 50bp or >5kb in width. The top 100k peaks were retained) and dynamic FAIRE-seq sites were identified on pooled biological replicates using Diffreps V1.55 (200bp windows, 20bp step, G-test, FDR < 2.5%)
Genome_build: UCSC hg19 (Canonical haplotype)
Supplementary_files_format_and_content: FSEQ files are in BED format and comprise peaks that identify open chromatin sites [column headers are: Chromosome, start, end, peak_signal, peak_width]. Diffreps output is in tab delimited text file output and comprises 13,516 dynamic chromatin sites. Dynamic FAIRE hotspots are in BED format and comprise hotspots of dynamic chromatin identified by Diffreps with p value < 0.05

growth_protocol: CD14 positive monocytes were isolated by positive selection from 50ml of peripheral blood from healthy volunteers. Monocytes were cultured for 7 days with 50ng/ml macrophage colony stimulating factor to generate macrophages.

extract_protocol:
FAIRE enriched genomic DNA was extracted using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).
Libraries were generated from gel-purified ~200bp DNA fragments (actual fragment size median 151bp +-39 median absolute deviation (MAD) for samples numbered 279, 280, 277, 278 and 141+-32 MAD for samples 205, 207). After adapter ligation and PCR-based amplification, samples were sequenced on the Illumina HiSeq platform to generated paired end 50bp reads (Illumina, San Diego, CA). Samples were multiplexed across 2 lanes.


title: PU.1-Eng expressing DN2 cells #1

description: PU.1-Eng - 1


title: FAIRE_seq_Macrophage-oxLDL_278

value: female


title: PU.1-ETS expressing DN2 cells #1

description: PU.1-ETS - 1


title: FAIRE-seq_Macrophage-control_207

description:
processed data file: fseq_macrophages.bed
processed data file: FAIRE_diffreps_FDR2.5.txt
processed data file: dynamic_FAIRE_hotspots.bed


title: GFP rep 3

value: GFP


title: FoxH1_Dome_Drug


title: FAIRE-seq_Macrophage-control_280


title: FAIRE-seq_Macrophage-control_279