title: hf81

city: Albuquerque

first: Raymond

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

description: Raw Reads Per Million - relevantly expressed genes

data_processing:
CAPSOD experimental samples were sequenced without multiplexing on Illumina GAIIx instruments (54-cycle singleton reads).This yielded 13.4 million reads, totaling 718.4 Mbp of sequence, and 9-fold average coverage. Base calling was performed using Illumina Pipeline software v1.4, except for 14 samples performed with v1.3. Approximately 500 million high quality reads were generated per sample.
Sequence quality analysis was performed on the raw data using FastQC version 0.10.1, assessing per-base and overall sequence quality, nucleotide composition, and uncalled bases. Quality trimming and adapter clipping were performed using Trimmomatic version 0.32, trimming trailing bases below Phred quality score of 20 (which corresponds to a 99% base call accuracy rate), and discarding clipped reads shorter than 25 bp. FastQC was used to re-assess the integrity of the clipped reads prior to subsequent mapping and analysis. On average, over 93% of the sequences had a mean Phred base call quality of 20 or higher after trimming. The post-trimming uncalled base rate was 0.09%.
Clipped reads were mapped to the hg19 genome using Tophat version 2.0.7, and assembled with Cufflinks version 2.0.2, all with default parameter settings. The average mapping rate was 77.7%. Read counts for each gene were obtained with HTSeq version 0.5.4, specifically the intersection-nonempty mode of htseq-count. SAM/BAM conversions, sorting, indexing, and marking of PCR duplicates were performed with SAMtools version 0.1.18 and Picard version 1.83.
For variant analysis, sequence data were aligned to the GRCh37.p5 human reference genome using STAR. Read alignments were processed with the Genome Analysis Tool Kit (GATK) version 3.1. Duplicate reads were removed and single nucleotide polymorphisms (SNP) and insertion/deletion (INDEL) discovery and genotyping was performed on all samples individually using the GATK HaplotypeCaller producing a standard variant call format (VCF) . Resulting nuclear variants were hard filtered to keep variants with a Phred scaled quality score of 20 or higher (a measure of quality of DNA sequence). To address issues with varying coverage in the mitochondrial genome, samples were filtered so that only 91 samples with at least 85% of the mitochondrial genome covered by 16 reads or more were included in the final variant analysis. Further, mitochondrial variants were only analyzed if they were identified in 10 reads or more.Variants were annotated with the Rapid Understanding of Nucleotide variant Effect Software (RUNES v1.0). RUNES incorporates data from ENSEMBL’s Variant Effect Predictor software, and produces comparisons to NCBI dbSNP, known disease mutations from the Human Gene Mutation Database , and performs additional in silico prediction of variant consequences using RefSeq and ENSEMBL gene annotations. RUNES categorizes each variant according to American College of Medical Genetics and Genomics recommendations for reporting sequence variation as well as an allele frequency derived from the Children’s Mercy Hospital Center for Pediatric Genomic Medicine Variant Warehouse database.
Genome_build: The Illumina iGenomes UCSC hg19 human reference genome and annotation was used as a reference, downloaded March 2013
Supplementary_files_format_and_content: mRNA sequencing for 129 subjects to an average depth of 13.5 million reads/sample yielded relative levels of transcription of 30,792 genes (of which 18,078 mRNAs were detected in >50% of subjects). Patient values were normalized as reads per million. Expression in less than 50% of the subjects were removed from analysis. A log2(x+1) transformation was performed prior to ANONA analysis

source_name: Whole Blood Cells

extract_protocol:
Whole blood was collected in PAXgene RNA tubes (Qiagen, CA) to stabilize intracellular RNA and subsequently stored at -80°C until use. RNA was prepared using a PaxGene Blood RNA kit (Qiagen) according to the manufacturer’s instructions.
mRNA sequencing libraries were prepared from total RNA using the Illumina mRNA-Seq Sample Prep Kit (Illumina, catalog # RS‐100‐0801), according to manufacturers’ recommend protocols

tag: patient id

tag: sirs outcomes

value: sepsis death

tag: sirs vs sepsis

value: Sepsis


title: hf195

status: Public on Jan 01 2015

type: SRA

middle: J

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: hf120


title: hf270


title: hf6


title: hf301


title: hf287


title: d84


title: Vehicle Rep #2

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The sequenced reads from fastq files were mapped to mm9 using STAR version 2.3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cuffdiff from the Cufflinks suite (Trapnell Nature biotechnology), using upper quartile normalization.
RPKM of all 8 samples were combined into a single file.
Genome_build: mm9

organism: Mus musculus

source_name: Cecal GIST tumor

extract_protocol:
GIST tumors from the cecums of mice were explanted and grounded in 1000 μl Trizol (Invitrogen) using a PowerGen homogenizer (Fisher Scientific), followed by addition of 200 μl chloroform. The samples were then centrifuged at 10,000g for 15 min. The upper phase was mixed with an equal volume of 70% ethanol, and the RNA was further purified using E.Z.N.A total RNA kit (Omega).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Cecal GIST tumor

tag: genotype

value: Kit V558Delta/+; Etv1 flox/flox; Rosa26 CreERT2/CreERT2


title: d194


title: hf40


title: hf274


title: hf231


title: hf295


title: d155


title: hf45


title: hf27


title: hf310


title: hf275


title: hf190


title: HeK4me3 ChIP-Seq

library_source: genomic

data_processing:
The sequenced reads from fastq files were mapped to hg18 using Bowtie v1.
Duplicate reads were discarded
Peaks were called against input DNA (sequencing deposited in GSE22441) using MACS 1.4
Genome_build: hg18

molecule: genomic DNA

source_name: GIST48 Cells

growth_protocol: Cells were grown in log phase using standard tissue culture media.

extract_protocol:
GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with antibody, washed, eluted, reverse cross-linked, and purified.
Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR, and sequenced on Solexa Genome Analyzer.

tag: chip antibody

value: H3K4me3, Abcam, ab8580

value: GIST cell line

tag: cell line


title: d326


title: hf193


title: hf188


title: hf286


title: hf202


title: hf314


title: hf184


title: hf348

value: Uncomplicated sepsis


title: hf203


title: hf210


title: hf216


title: hf102


title: hf128


title: C5-RNAseq

city: beijing

first: Zhenglin

last: Du

address: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

country: China

institute: Beijing Institute of Genomics

data_processing:
Illumina Casava1.7 used for basecalling
Filtered the adaptor sequence and PCR-duplication reads
Aligment by BWA 0.6.2-r126 with maximum 5 mismatch
NCBI Reference Sequence: NC_010717.1
Genome_build: ASM1958v1
Supplementary_files_format_and_content: an EXCEL file including RPKM values for each Sample

organism: Xanthomonas oryzae pv. oryzae

source_name: Bacterial cell

growth_protocol: Xoo strain PXO99 (Philline race 6, P6), PXO86 (Philline race2, P2), and GD1358 (China race 5, C5) were used for this experiment. Cells were grown at 28°C with shaking at 200 rpm in nutrient-rich PSB ) until OD600 equaled 2.0, washed twice, and then immediately transferred into XOM2 for 16hrs.

extract_protocol:
Bacterial cells were washed twice prior to being harvested. Immediately after harvesting, the collected cells were snap-frozen in liquid nitrogen, and stored at -70°C.
The total RNA of each Xoo strain was extracted from each frozen leaf sample using the Trizol kit (Invitrogen, Carlsbad, CA, USA) according to the manufacture’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 16hr cultured in XOM2


title: P2-RNAseq


title: hf83


title: hf107


title: hf126


title: P6-RNAseq


title: hf104


title: hf76


title: hf37


title: hf68


title: hf20


title: hf2


title: d299


title: d315


title: hf225


title: d309


title: d283


title: d246


title: d253


title: d188


title: hf304

value: severe sepsis


title: d68


title: hf296


title: hf97


title: hf236


title: hf213


title: hf194


title: hf217


title: hf159


title: d364


title: hf158


title: hf124


title: siSMYD2.1+BIX-01294

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
Illumina Hiseq2500 for next generation sequencing
Sequence adapters and low quality bases were trimmed, and trimmed fastq data mapping to hg19 genome reference by tophat2. Differential expression gene characterized by using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols


title: siSMYD2.1+Rapamycin


title: siControl+Rapamycin


title: hf99


title: hf33


title: hf57


title: hf11


title: hf86


title: siControl


title: d307


title: siControl+BIX-01294


title: RNAseq_F-shSUZ12_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: mRNA

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilobase pair per million total reads).
Differential gene expression analyses were performed using DEseq.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: Tab-delimited text file of gene RPKM values.

source_name: Human primary fetal live proerythroblasts (ProEs), shSUZ12

growth_protocol: Primary maturing fetal liver erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For RNA-seq analysis using the Illumina HiSeq 2500, 0.1-2 ug of total RNA was processed for library generation using the TruSeq RNA Sample Preparation v2 Kit (Illumina) following the manufacturer's protocol.

value: fetal liver

tag: cell type

value: CD34+ HSPC-derived proerythroblasts

tag: shRNA


title: RNAseq_F-shSUZ12_rep2

description: mRNA


title: d303


title: hf98


title: d39


title: hf10


title: RNAseq_F-shEED_rep2

description: mRNA

source_name: Human primary fetal live proerythroblasts (ProEs), shEED

value: shEED


title: d249


title: siSMYD2.1


title: d38


title: RNAseq_F-shSUZ12_rep1

description: mRNA


title: hf346

value: Septic shock


title: hf330


title: RNAseq_F-shEED_rep1

description: mRNA


title: RNAseq_F-shEZH2_rep2

description: mRNA

source_name: Human primary fetal live proerythroblasts (ProEs), shEZH2


title: RNAseq_F-shEZH2_rep1

description: mRNA


title: hf311


title: hf325


title: RNAseq_F-shEZH1_rep3

description: mRNA

source_name: Human primary fetal live proerythroblasts (ProEs), shEZH1


title: hf258


title: RNAseq_F-shNT_rep3

description: mRNA

source_name: Human primary fetal live proerythroblasts (ProEs), shNT

value: shNT


title: RNAseq_F-shEZH1_rep1

description: mRNA


title: RNAseq_F-shEED_rep3

description: mRNA


title: RNAseq_F-shEZH1_rep2

description: mRNA


title: RNAseq_F-shNT_rep1

description: mRNA


title: RNAseq_F-shNT_rep2

description: mRNA


title: hf241


title: hf244


title: hf207


title: hf230


title: hf240


title: hf201


title: hf319


title: Pu.1_ChIPseq rep2

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using bowtie 0.12.7 with -m 1
Peaks were called using macs2 2.0.10.20130520 with -p 0.1
Genome_build: GRCh37.71

source_name: Dendritic cells

growth_protocol: monocytes were cultured in RPMI 10% FCS supplemented with 2-mercaptoethanol (50 μM), GM-CSF (600 U/ml), and IL-4 (750 U/ml)

extract_protocol:
Chromatine was isolated, fragmented by sonication and immunoprecipitate it with anti PU1 antibody
Libraries were prepared according to Illumina's instructions using the Truseq ChIP-seq protocol.

value: Monocyte-derived denditric cells

value: PU.1 SC-352 from SantaCruz


title: Input DNA rep2


title: hf106


title: hf111


title: RNAseq_F-shEZH2_rep3

description: mRNA


title: Input DNA rep1


title: hf196


title: Pu.1_ChIPseq rep1


title: hf189


title: hf59


title: hf138


title: hf82


title: hf25


title: hf22


title: d387


title: d360


title: hf13


title: d205


title: d37


title: d29


title: d347


title: hf161


title: d25


title: hf292

value: SIRS


title: hf317


title: d284


title: PRE1-Ox/IBH1-Ox 1

city: Jinan

first: Mingyi

last: Bai

state: Shandong

address: 27 Shandananlu

department: Life of Scienec

institute: Shandong University

data_processing:
The sequence reads were mapped to the Arabidopsis genome using Tophat software, and differential gene expression was analyzed using DeSeq software.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana

growth_protocol: Wild type Arabidopsis, 35S:IBH1-myc and 35S:IBH1-myc/35S:PRE1-YFP were grown on half-strength MS medium for 5 days under constant light.

extract_protocol:
Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma)
Libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Ilumina)

tag: ecotype

tag: genotype/variation

value: Seedling


title: IBH1-Ox 2


title: PRE1-Ox/IBH1-Ox 2


title: hf265


title: hf327


title: IBH1-Ox 1


title: Col 1

value: Wild type


title: hf206


title: hf79

value: Sepsis


title: Col 2


title: hf246


title: hf197


title: hf205


title: hf179


title: hf174


title: hf192


title: hf136


title: d366


title: hf101


title: d187


title: hf155


title: d161


title: hf103


title: d91


title: d61


title: T-WGBS for rhesus monkey 8-cell embryos

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

description: tagmentation-based whole genome bisulfite sequencing

data_processing:
After sequencing, adapters were first removed using cutadapt-1.2.1 software (http://code.google.com/p/cutadapt/), only reads with minimally 45 bp length were remained. After removing adapters, low quality reads that contained more than 10% N’s or more than 50% of the sequence with low quality value (quality value <5) per read were filtered out. Read mapping was done on the monkey reference genome (rheMac3) using BS-MAP (version 2.73) alignment software, allowing for maximally 5 mismatches or 1 small insertion or deletion.
After mapping, PCR duplicates were removed using Samtools software. Then, we separated the reads into two categories, depending on whether they are from the top (C changed to T, C-T) and bottom (G changed to A, G-A) strands. By simulating the methylation proportion across each possible read position, the 12 bps from the 3’ ends of C-T reads and the 5’ ends of G-A reads were then removed as which were affected by the 5-methyl-dCTPs incorporated during the gap-repair and strand displacement step.
Methylation level was defined as the fraction of read counts of ‘C’ in the total read counts of both ‘C’ and ‘T’ for each covered C site, and herein average percentage methylation of all cytosine residues for any genomic region covered was computed as the fraction of read counts of ‘C’ in the total read counts of both ‘C’ and ‘T’ for each genomic region. Based on such read fraction, methylated cytosines were called using a binomial distribution as in the method described by Lister et al. (2009), whereby a probability mass function is calculated for each methylation context (CpG, CHG, CHH). The non-conversion rate and sequencing error rate were taken into account, for which the total error rate was determined by unmethylated lambda DNA spike-ins
Genome_build: rheMac3 from UCSC
Supplementary_files_format_and_content: *.txt files contain 8 columns. The format is that: (1)Chromosome ID, (2)Cytosine position, (3)+/- Watson/Crick chain, (4)Type (CG/CHH/CHG), (5)Base pattern, (6)Methylation Ratio, (7)Methylated reads num, (8)Un-methylated reads num.

organism: Macaca mulatta

source_name: 8-cell embryo

extract_protocol:
Cumulus–oocyte complexes were collected from animals by laparoscopic follicular aspiration 32–35 hrs following rhCG administration. Follicular contents were placed in Hepes-buffered Tyrode's albumin lactate pyruvate (TALP) medium containing 0.3% BSA at 37°C. Cumulus-oocyte complexes were exposed to hyaluronidase (0.5 mg/mL, <1 min) in TALP-Hepes to strip of cumulus cells. Oocytes that were mature (MII) at collection were placed in chemically defined, protein-free hamster embryo culture medium-10 (HECM-10) at 37 °C in 5% CO2 until inseminated (within 24 hrs) with capacitated, hyperactivated spermatozoa diluted to a final concentration of 2 × 105 /mL in 50-μL drops of TALP for fertilization. After co-incubation of oocytes and spermatozoa for 12–16 h, oocytes were examined for the presence of two pronuclei and two polar bodies as evidence of fertilization. Then the polar bodies were mechanically dissected using Piezo-Micromanipulator to eliminate the DNA contamination of polar bodies and fertilized ova were washed to remove sperms and then cultured in HECM-10 containing 10% FCS (HyClone Laboratories Inc.) to allow embryo development. Culture medium was replaced every other day. The embryos were collected at constant time point (zygotes,10-20 hrs post fertilization(hpf); 2-cell embryos, 24-30 hpf; 8-cell embryos, 2 days post after fertilization (dpf); morula, 4-5 dpf; ICM, 6-7 dpf. Zona pellucidae of embryos were removed by brief exposure (45-60 s) to 0.5% Pronase in culture medium. For ICMs collection, zona-free blastocysts were exposed to rabbit anti-rhesus spleen serum (Axell Labs, Westbury, NY, USA) (1:5) for 30 min at 37 °C. After extensive washing in ESC derivation medium, embryos were incubated in guinea pig complement (Sigma) (1:5) for an additional 30 min at 37 °C and lysised trophectoderm cells were removed from ICMs by pipetting through a fine pulled glass needle. All samples were carefully washed in PBS-EDTA to remove any contaminants. Total 25 oocytes donor monkeys were used in this study and exception of ICM, all the sperms were derived from same male monkey.
Transposome complexes were first generated by incubating 2.5 µL of 10 µM annealed adaptors with 2.5 µl 100% glycerol and 5 µl Ez-Tn5 transposase (Epicentre) for 30 min at 25°C. Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) and purified by AMPure XP magnetic beads. The purified DNA (~0.5 ng, spiked with 10pg of unmethylated lambda DNA) was then incubated with 4 µL Nextera HMW Buffer (Epicentre-Illumina), nuclease-free water (Ambion) to 16 µL and 4 µL prepared Tn5mC transposomes for 12 min at 55°C followed by purification using 36 µl (1.8X) Agencourt AMPure XP magnetic beads and the DNA was eluted in 14 µL EB buffer. An extension step was then performed by adding 2 µL of 10X Thermopol reaction buffer (NEB), 2 µL 10mM 5-Methylcytosine dNTP Mix (Zymo Research, D1030), 1 µl of Bst DNA Polymerase Large Fragment (NEB, M0275s) to each reaction and incubating for 20 min at 65°C. Each reaction was spiked with 200 ng of sonicated unmethylated lambda DNA (200-400 bp) and then subjected to bisulfite conversion using a Zymo EZ DNA Methylation Kit (D5100) according to recommended protocols with a 14h 50°C dark incubation and 22 µL (2 x11 µL) elution. The purified DNAs were then amplified using 25 µL Kapa 2G Robust Hot Start Ready Mix (Kapa Biosystems), 1 µL 50X Nextera Primer Cocktail (Illumina - compatible) and 1 µL barcoded Illumina-compatible Adaptor 2 (8-bp index) on the thermocycler with the following parameters: 1 min at 95°C; (20 sec at 95°C; 30 sec at 60°C; 45 sec at 72°C) X (10-15) cycles. The prepared libraries were analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified by qPCR and then used for cluster generation and pair-end sequencing with 90 bp reads (PE90) on Illumina Hiseq 2000.

value: embryo

tag: input amount


title: T-WGBS for rhesus monkey morula

source_name: morula


title: hf162


title: T-WGBS for rhesus monkey inner cell mass (ICM) of the blastocysts


title: T-WGBS for rhesus monkey sperm

description: Chemistry ligation based WGBS library construction

source_name: sperm

value: gamete


title: T-WGBS for rhesus monkey zygotes

source_name: zygote


title: T-WGBS for rhesus monkey oocytes

source_name: oocyte


title: LNCaP_DHT_rep2

city: Stanford

first: Xun

last: Lan

state: CA

address: 318 Campus Dr. Room S240

department: Genetics

institute: Stanford University

description: replicate 2

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: four column bed files contains mapped reads information.

source_name: LNCaP cells

growth_protocol: The androgen-dependent prostate cancer cell line LNCaP was obtained from the American Type Culture Collection, and cultured in the RPMI complete medium.

extract_protocol:
For AR ChIP-seq, after treatment with 10 nm DHT or vehicle for 4 h, LNCaP cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-AR antibody. After overnight incubation, 20 ul protein A-agarose was added to pull down the complex. The enriched DNA was purified by QIAquick Purification kit. For MNase-Seq, native chromatin from LNCaP cells were digested with MNase for 10-20 min to generate mainly mononucleosomes. Digestion was stopped by adding EDTA to a final concentration of 50 mM. The chromatin immunoprecipitation was performed using antibodies against different marks. After overnight incubation, 20 ul protein A-agarose was added to pull down the complex. The enriched DNA was purified by QIAquick Purification kit.
The library was generated by using the NEBNext Ultra DNA Library Prep Kit. NEBNext End Prep Enzyme Mix was used for end polishing. Adaptor was ligated with Blunt/TA ligase Master mix at 20°C for 15 minutes. After gel-based size selection, the library was amplified with 16 PCR cycles using NEBNext High Fidelity 2X PCR Master Mix.

treatment_protocol: For hormone responsive experiments, LNCaP cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with 10 nM DHT.

value: LNCaP

tag: cancer

value: Prostate adenocarcinoma

tag: type

value: Androgen-sensitive

value: anti-AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)

tag: agent

value: 10 nm DHT


title: H3K9Me3_rep2

description: replicate 2

value: anti-H3K9me3 (8898) from Abcam (Cambridge, MA)

value: vehicle, control


title: hf100

source_name: Whole Blood Cells

tag: patient id


title: H3K4Me2_090707_s_6

description: replicate 2

value: anti-H3K4me2 (ab7766) from Abcam (Cambridge, MA)


title: H3K9Me3_rep1

description: replicate 1


title: H3K4Me3_090920_s_7

description: replicate 1

value: anti-H3K4me3 (ab8580) from Abcam (Cambridge, MA)


title: H3K4Me1_090920_s_3

description: replicate 2

value: anti-H3K4me1 (ab8895) from Abcam (Cambridge, MA)


title: hf18

tag: sirs outcomes


title: d121

tag: sirs vs sepsis


title: H3K4Me1_090920_s_2

description: replicate 1


title: H3K27Me3_rep2

description: replicate 2

value: anti-H3K27me3 (ab6002) from Abcam (Cambridge, MA)


title: Biofilm treated with carbapenems for 2 hours rep2

city: Cambridge

first: Tsute

state: MA

address: 245 First Street

department: Microbiology

institute: The Forsyth Institute

data_processing:
fastq reads were mapped to K. pneumoniae BAMC 07-18 draft contig sequences
samtools was used to separate mapped reads into forward and reverse complement directions with the linux command "samtools view -h -f16  -S samfile" to generate forward mapped reads and "samtools view -h -F 16  -S $samfile |samtools view -h -F 4 -S - " to genereate reverse mapped reads
Forward and reverse sam files were converted to bam, sorted and indexed using samtools
sorted bam files were converted to WIG files using the samtools command "samtools mpileup -ABQ0 -d10000000 -r chomosomefile  sortedbamfile|cut -f 2,4"
raw read counts (across all nucleotides of each ORF) were generated using a custom PERL script based on the wig files
Genome_build: Draft contig sequence (included) were used as reference for mapping; RAST annotation of draft contigs is also included
Supplementary_files_format_and_content: wig, raw read count and Deseq result files were generated as described above
Supplementary_files_format_and_content: fasta - draft genomic contigs
Supplementary_files_format_and_content: gff - RAST annotation of contig sequences
Supplementary_files_format_and_content: raw read count for DESeq
Supplementary_files_format_and_content: DESeq results

organism: Klebsiella pneumoniae

source_name: Biofilm culture

growth_protocol: K. pneumoniae cultures were grown in Luria-Bertani broth (LB) at 37°C. For biofilm formation, borosilicate glass discs with a diameter of 1.75 mm (Ace Glass Inc, Vineland, NJ, USA) were coated with 10 µg/ml Type I collagen in PBS overnight at 4°C.  K. pneumoniae inoculum, prepared as described above, was suspended in phosphate-buffered saline (PBS; OD600nm of 0.05) and was incubated with the glass discs in a 24-well plate for two hours at room temperature.  Each well contained 1 ml of bacterial suspension and one glass disc. After attachment, the discs were rinsed and 1 ml fresh LB was added to each well.

extract_protocol:
Biofilm wells were rinsed with LB to remove unattached K. pneumoniae cells and Following 2 or 24 hours of treatment, biofilms were removed from the plates and preserved in RNA protect (QIAgen, Valencia, CA, USA).  RNA was extracted using the RNeasy Mini Kit (QIAgen) according to manufacturer’s instructions.  Samples were then treated twice with TURBO DNase (Ambion, Grand Island, NY, USA) according to manufacturer’s instructions to remove contaminating genomic DNA.  RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and analyzed for quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
2-5ug total RNA was used for strand-specific RNA Sequencing (RNASeq) library preparation. rRNA was depleted from total RNA using the Ribo-Zero Magnetic Kit (Epicentre, Madison, WI, USA).  The directional RNAseq library was developed using the NEXTflex Directional RNA-seq (dUTP based) kit (Bioo Scientific, Austin, TX, USA).  Following purification, mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments went through an end repair process, the addition of a single ‘A’ base, and ligation of the adapters. The products were further purified and enriched with PCR to create the final RNASeq library. Directionality is retained by adding dUTP during the second strand synthesis step and subsequent cleavage of the uridine-containing strand using Uracil DNA Glycosylase. RNASeq libraries were subjected to quantification process, pooled for cBot amplification and subsequent sequencing run with HiSeq 2000 platform (Illumina, San Diego, CA, USA). After the sequencing run, demultiplexing with CASAVA was employed to generate a FASTQ file for each sample.

treatment_protocol: To test the effect of carbapenems on pre-formed biofilms, the discs were first incubated at 37°C for 24 hours after attachment to allow optimal biofilm formation.  The spent media was removed and the discs were incubated for 2 or 24 hours in LB with imipenem (2 µg/ml)

tag: strain

tag: treatment

value: carbapenems

tag: time

value: 2 h


title: LNCaP_CON_rep2

description: replicate 2

tag: chip antibody


title: Biofilm treated with carbapenems for 2 hours rep1


title: Biofilm without carbapenems treatment rep2

value: control


title: T-WGBS for rhesus monkey 2-cell embryos

source_name: 2-cell embryo

tag: tissue


title: Biofilm without carbapenems treatment rep1


title: Biofilm treated with carbapenems for 24 hours rep1


title: H3K4Me3_090920_s_8

description: replicate 2

tag: cell line


title: 101_Day_7_HTKL_1

first: Kim

last: Lewis

address: 360 Huntington Ave

institute: Northeastern University

description: Low-persister

data_processing:
The pool of 48 Illumina RNA-Seq libraries was quantified using qPCR (KAPA Biosystems, USA) and sequenced with 76 base paired-end reads across 4 lanes using an Illumina HiSeq 2000 sequencer (Illumina, USA) running v3 SBS chemistry.
Reads were aligned to the genome of M. tuberculosis H37Rv (RefSeq NC_000962) using BWA (Li, Durbin (2009)) version 5.9.
Gene annotations were obtained from RefSeq and Rfam (Gardner, Daub et al. (2009)).
Fragment coverage of genomic regions corresponding to features such as ORFs and rRNAs was conducted as described (Mandlik, Livny et al. (2011))
Differential expression analysis was conducted using DESeq (Anders, Huber (2010)).
Genome_build: RefSeq NC_000962
Supplementary_files_format_and_content: Normalized reads per gene (txt)

organism: Mycobacterium tuberculosis

source_name: Cell culture

growth_protocol: M. tuberculosis was grown in Middlebrook 7H9 broth at 37°C in a shaking incubator (200 rpm) to exponential phase (optical density at 600 nm of 0.5)

extract_protocol:
1. Cells were resuspended in Trizol (Invitrogen) and lysed by bead beating. 2. Total RNA was extracted with chloroform and preciptated with isopropanol.
Libraries were created by the Broad Technology Labs specialized service facility. Briefly, 48 RNA samples were fragmented, and RNA 3’ ends were tagged with a DNA oligonucleotide containing a sample barcode and a partial 5’ Illumina adapter. Resulting barcoded RNAs were then pooled and subjected to rRNA depletion (Ribo-Zero™ Magnetic Kit (Bacteria); Epicentre, Madison, WI), cDNA synthesis and ligation to a second oligonucleotide containing a partial Illumina 3’ adapter. A second barcode specific to this pool was then added by amplification with full-length barcoded Illumina adapter primers, yielding a single strand-specific sequence-ready pooled RNA-seq library.

treatment_protocol: Exponential phase cultures were challenged with D-cycloserine (125 μg/ml). Samples were taken for RNA extraction at Day 0 (prior to antibiotic) and Day 7 of the challenge. RNA Protect Bacteria Reagent (Qiagen) was added to the samples prior to RNA extraction.

tag: culture

value: Exponential phase culture

tag: cell

value: Whole Cell

tag: experimental day

value: Day 7


title: H3K4Me2_090526_s_2

description: replicate 1

value: LNCaP


title: Biofilm treated with carbapenems for 24 hours rep2


title: 101_Day_7_HTKL_3

description: Low-persister


title: 101_Day_7_HTKL_2

description: Low-persister


title: 102_Day_7_HTKL_1

description: High-persister


title: 102_Day_7_HTKL_3

description: High-persister


title: 98_Day_7_HTKL_3

description: High-persister


title: LNCaP_CON_rep1

description: replicate 1

value: Prostate adenocarcinoma


title: 98_Day_7_HTKL_1

description: High-persister


title: 82_Day_7_HTKL_1

description: High-persister


title: 76_Day_7_HTKL_3

description: Low-persister


title: H3K27Me3_rep1

description: replicate 1

value: Androgen-sensitive


title: 82_Day_7_HTKL_3

description: High-persister


title: 82_Day_7_HTKL_2

description: High-persister


title: 73_Day_7_HTKL_3

description: Low-persister


title: 76_Day_7_HTKL_2

description: Low-persister


title: LNCaP_DHT_rep1

description: replicate 1

value: anti-AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)


title: 73_Day_7_HTKL_2

description: Low-persister


title: 73_Day_7_HTKL_1

description: Low-persister


title: 70_Day_7_HTKL_3

description: Low-persister


title: 70_Day_7_HTKL_2

description: Low-persister


title: 76_Day_7_HTKL_1

description: Low-persister


title: Sample 3

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: 5' polyphosphatase treated

data_processing:
Adapter trimming using Cutadapt v1
fastq to fasta conversion, selection for small RNAs of 15-30nt in length using custom Perl scripts using Perl v5.12.4
fasta collapsed using FastX toolkit fastx_collapser module
Supplementary_files_format_and_content: Fasta header: id_number of reads

organism: Caenorhabditis elegans

source_name: Total RNA whole animal

extract_protocol:
Total RNA extracted using Trisure (BioLine) or Trizol (Invitrogen) according to manufacturer's instructions
Illumina Truseq small RNA according to manufacturer's instructions

tag: developmental stage

tag: sample type

value: Progeny of Orsay infected animals

tag: genotype


title: Sample 2

description: 5' polyphosphatase treated

value: Adult

value: Orsay virus infection


title: 67_Day_7_HTKL_3

description: High-persister


title: 67_Day_7_HTKL_1

description: High-persister


title: Sample 1

description: 5' polyphosphatase treated


title: 102_Day_0_HTKL_3

description: High-persister

value: Day 0


title: 0hCa

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

data_processing:
Basecalls performed using Abi Solid 4+
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50
RNA reads were aligned to the Ca21chr1_C_albicans_SC5314, Ca21chr2_C_albicans_SC5314, Ca21chr3_C_albicans_SC5314, Ca21chr4_C_albicans_SC5314, Ca21chr5_C_albicans_SC5314, Ca21chr6_C_albicans_SC5314, Ca21chr7_C_albicans_SC5314, Ca21chrR_C_albicans_SC5314 (www.candidagenome.org) genome assembly using CLC Genomics Workbench version 4.7.2 with the following configurations…*
Calculate expression levels and discover novel exons using CLC Genomics Workbench version 4.7.2
Genome_build: Ca21chr1_C_albicans_SC5314, Ca21chr2_C_albicans_SC5314, Ca21chr3_C_albicans_SC5314, Ca21chr4_C_albicans_SC5314, Ca21chr5_C_albicans_SC5314, Ca21chr6_C_albicans_SC5314, Ca21chr7_C_albicans_SC5314, Ca21chrR_C_albicans_SC5314 (www.candidagenome.org)
Supplementary_files_format_and_content: fold change

organism: Candida albicans

growth_protocol: PK E6/E7 vaginal epithelial cells  were cultured in Keratinocyte-SFM (GibcoBRL, Eggstein, Germany) supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract, antibiotic/antimycotic solution (Sigma-Aldrich, St. Louis, MA, USA) and 20 mM L-glutamine (Sigma) in a humidiﬁed atmosphere containing 5% CO2 at 37°C.

extract_protocol: RNA quality and quantity measurements were performed on Bioanalyzer (Agilent Technologies) and Qubit (Life Technologies). High quality (RIN >8.5) total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA-Seq Kit (Life Technologies), according to the manufacturer’s instructions. Briefly, 5mg of pooled RNA was DNaseI treated and fragmented using RNaseIII; in case of RNA isolated from PK E6/E7 vaginal epithelial cell – C. albicans co-culture, the eukaryotic ribosomal RNA was depleted prior of fragmentation using RiboMinus Eukaryote Kit for RNA-Seq and RiboMinus Concentration Module (Life Technologies). Next, the 50-200nt RNA fraction was size selected, sequencing adaptors ligated and the templates reverse transcribed using ArrayScript reverse transcriptase. The cDNA library was purified with Qiagen MinElute PCR Purification Kit (Qiagen) and size-selected on a 6% TBE-Urea denaturing polyacrylamide gel. The 150-250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads (Agencourt). Concentration of each library was determined using the SOLID Library TaqMan Quantitation Kit (Life Technologies).

treatment_protocol: 10e5 cells/well of PK E6/E7 vaginal epithelial cells were cultured in 6-well plates for 24 hours in Keratinocyte-SFM (GibcoBRL, Eggstein, Germany) supplemented with 5 ng/ml recombinant epidermal growth factor, 50 µg/ml bovine pituitary extract and 20 mM L-glutamine (Sigma) without antibiotic/antimycotic solution. Fungal cells were then added to the wells with a muliplicity of infection (MOI) of 5:1 in the same medium. Yeast control and control PK E6/E7 cells without fungal cells were harvested at zero time point. Plates were incubated for 3 hours in a humidiﬁed atmosphere containing 5% CO2 at 37°C. Fungal cells switch to filamentous growth spontaneusly in such circumstances. PK E6/E7 cells with hyphae and control hyphae were harvested after 3 hours.

value: 0 h


title: 3hPKCa

value: 3 h

value: exposure to PK E6/E7 vaginal epithelial cells


title: 102_Day_0_HTKL_2

description: High-persister


title: 102_Day_0_HTKL_1

description: High-persister


title: 70_Day_7_HTKL_1

description: Low-persister


title: 98_Day_0_HTKL_2

description: High-persister


title: 98_Day_0_HTKL_1

description: High-persister


title: 101_Day_0_HTKL_1

description: Low-persister


title: 98_Day_0_HTKL_3

description: High-persister


title: 67_Day_7_HTKL_2

description: High-persister


title: 82_Day_0_HTKL_2

description: High-persister


title: 82_Day_0_HTKL_1

description: High-persister


title: 82_Day_0_HTKL_3

description: High-persister


title: Sample 5

description: 5' polyphosphatase treated


title: Sample 4

description: 5' polyphosphatase treated


title: 76_Day_0_HTKL_1

description: Low-persister


title: 76_Day_0_HTKL_2

description: Low-persister


title: 73_Day_0_HTKL_3

description: Low-persister


title: 73_Day_0_HTKL_2

description: Low-persister


title: 73_Day_0_HTKL_1

description: Low-persister


title: 101_Day_0_HTKL_3

description: Low-persister


title: 101_Day_0_HTKL_2

description: Low-persister


title: proband

city: Brisbane

first: Graham

middle: William

last: Magor

state: Queensland

address: 37 Kent St

country: Australia

institute: Mater Research

data_processing:
Base calling was performed within Torrent_Suite version 4.0.1
Sequencing reads were aligned to the human genome (build hg19) using Tophat2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was calculated and differential expression testing between samples was performed with Cuffdiff2 using option --max-bundle-frags 1000000000
Genome_build: hg19
Supplementary_files_format_and_content: comma separated variable file containing FPKM values for each sample

source_name: blood

extract_protocol:
RNA was extracted from the peripheral blood mononuclear cell (PBMC) layer derived by Ficoll-paque extraction from 20 mL of whole blood. In the case of the proband, blood was drawn immediately prior to transfusion to enrich for endogenous nucleated erythroid cells and reticulocytes.
Beginning with 20 µg total RNA, the Ambion GLOBINclear™ kit (#AM1980, Life Technologies) was used to remove human alpha-globin and beta-globin mRNA. Ambion Dynabeads® mRNA DIRECT™ Micro Purification Kit (#61021, Life Technologies) was used to select the polyA+ (mRNA) fraction. ERCC control RNA from the Ambion ERCC RNA Spike-In Mix Kit (#4456740, Life Technologies) was added to estimate the amplification efficiency during library construction. Barcoded RNA-seq libraries were prepared using the Ion Total RNA-Seq Kit v2 (#4475936, Life Technologies) along with the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (#4475485, Life Technologies) for sequencing on the Ion Proton instrument (Life Technologies). Three barcoded libraries were sequenced on a single P1 chip such that approximately 20 million mapped reads were obtained for each sample.

tag: cell type

value: peripheral blood mono-nuclear cells

value: blood


title: 70_Day_0_HTKL_3

description: Low-persister


title: 70_Day_0_HTKL_2

description: Low-persister


title: 67_Day_0_HTKL_1

description: High-persister


title: 67_Day_0_HTKL_2

description: High-persister


title: 67_Day_0_HTKL_3

description: High-persister


title: 3hCa

value: control


title: Mo18w Submerge 72 hr Rep 3

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were preprocessed and then mapped to B73 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each mRNA with trimmed mean of M values (TMM) normalization method. Robinson and Oshlack Genome Biology 2010.
Genome_build: B73 (ZmB73_RefGen_v2)
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is normalized reads counts

organism: Zea mays

source_name: leaf

growth_protocol: Seeds of each genotype were sown directly in soil and grown in greenhouse conditions. Temperature was maintained between 26.7 to 32.2 C during the day and 26.1 to 29.4 C during the night. The relative humidity ranged from 35% to 70%. Supplemental lighting was supplied by 1000-watt metal halide bulbs (Philips Lighting Co., Somerset, NJ, USA) from 0700 to 1800 hrs. Light intensity was measured at approximately 1200 hrs one day prior to submergence with LI-250A light meter and ranged from approximately 378 ± 62.4 μmol m-2 s-1 (LI-COR Biosciences). Pots were irrigated twice a day with approximately 50 ml of water. Half-strength Hoagland solution (50 ml; 50) was applied once the first true leaf was visible to ensure that plants had adequate nutrition throughout the duration of the experiment.

extract_protocol:
RNA was extracted using the TRIzol method and quantified using Nanodrop spectrophotometer. RNA cleanup was performed according to RNeasy MinElute Cleanup kit protocol (Qiagen, Valencia, CA, USA). RNA was eluted with 15 µl RNase-free water after on-column DNase1 treatment using the protocol described by the manufacturer. Prior to library construction, RNA integrity was analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.).
Illumina small RNA library protocol

treatment_protocol: Uniform seedlings (3 seedlings per inbred) were transferred to 416 L tubs at the V2 stage (three leaf stage) for submergence treatment. The water in the tubs was allowed to reach near ambient room temperatures (24-27 C) 24 to 48 h prior to submerging the plants. Plants were arranged in a complete randomized design, and were arranged towards the center to avoid shading by the walls of the tub. Shoot tissue was sampled at 24h and 72h after submergence. Shoot tissue was cut approximately 1 cm above the soil line and snap frozen in liquid nitrogen. This process was completed within 10 seconds.

value: leaf


title: M162w Submerge 72 hr Rep 1


title: B97 Submerge 72 hr Rep 3


title: B97 Submerge 72 hr Rep 2


title: 76_Day_0_HTKL_3

description: Low-persister

value: Exponential phase culture

value: Whole Cell


title: Mo18w Submerge 72 hr Rep 2


title: Mo18w Submerge 72 hr Rep 1


title: B97 Submerge 72 hr Rep 1


title: M162w Submerge 72 hr Rep 3


title: B73 Submerge 72 hr Rep 3


title: B73 Submerge 72 hr Rep 2


title: B73 Submerge 72 hr Rep 1


title: mother


title: father


title: M162w Submerge 24 hr Rep 1


title: 70_Day_0_HTKL_1

description: Low-persister


title: M162w Submerge 24 hr Rep 3


title: M162w Submerge 24 hr Rep 2


title: Mo18w Submerge 24 hr Rep 2


title: Mo18w Submerge 24 hr Rep 3


title: Mo18w Submerge 24 hr Rep 1


title: B97 Submerge 24 hr Rep2


title: B73 Submerge 24 hr Rep 3


title: B97 Submerge 24 hr Rep1


title: M162w Control 24 hr Rep 2


title: Mo18w Control 24 hr Rep 1


title: B73 Submerge 24 hr Rep 2


title: M162w Submerge 72 hr Rep 2


title: M162w Control 24 hr Rep 3


title: M162w Control 24 hr Rep 1


title: B97 Control 24 hr Rep 2


title: Mo18w Control 24 hr Rep 3


title: B97 Control 24 hr Rep 1


title: B73 Control 24 hr Rep 3


title: B73 Control 24 hr Rep 2


title: MT E-L 38

status: Public on Dec 31 2014

city: San Michele all'Adige

first: Laura

last: Costantini

state: Trento

address: Via E. Mach 1

department: Genomics and Biology of Fruit Crops

country: Italy

institute: Fondazione Edmund Mach

data_processing:
Multiplexing and sequencing was done with an Illumina HiSeq 2000 sequencer at Fasteris
Hundred-bp, paired-end sequences were generated. Image analysis, error estimation and base calling were carried out using Illumina Pipeline (version 1.4.5) to generate the sequence data. Indexed primers were used to identify the different reads from different samples in the sequence data. Some low-quality reads were removed using a custom algorithm. Illumina TruSeq adapter sequences were clipped and the remaining reads were considered suitable for further analysis after passing quality control at Fasteris.
Short-read alignment and mapping of all the reads were carried on V1_mRNA version of the 12X draft annotation of the grapevine genome using BWA (Burrows Wheeler Aligner) software with a maximum set of 2 mismatches in the first 32 bp sequences and a maximum of “n” mismatches in total (n from 2 to 9 depending on read length). The mapping results were converted to the standard binary and indexed bam format.
The result of the mapping on V1_mRNA was processed by using the software SAMTOOLS in order to extract for each transcript the number of reads mapping onto it and determine whether they are mapping only on this mRNA (unique) or on multiple mRNAs (repeat). Reads mapping to several positions on the reference with the same “mapping quality” (i.e. number of mismatches and quality of the bases generating the mismatches) were attributed at random to one of them with a “0” mapping quality.
Reads mapped to multiple locations and unmapped reads were excluded from gene expression analysis. Unique reads mapping to V1_mRNA annotated transcripts were summed for each gene model and normalized by million reads (RPM).
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample.

organism: Vitis vinifera

source_name: Ripe berry

value: Ripe berry

value: Mutant

tag: Stage

value: After fertilization

tag: seed content

value: seedless


title: WT E-L 38

value: Wild-type

value: seeded


title: WT E-L 27

source_name: Young berry

value: Young berry


title: WT E-L 15

source_name: Flower

value: Flower

value: Before fertilization


title: MT E-L 15


title: 4d-preterm-NEC

description: Significant intestinal necrotizing enterocolitis (NEC) lesions identified in their intestines neonatally after 4 days.

data_processing:
Genomic DNA of mid-intestines from the same group of piglets was extracted, pooled together, and sequenced by RRBS technology using Illumina HiSeq 2000 sequencer.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 30% 'N's or over 10% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the reference genome using SOAP aligner (Version 2.01).
The uniquely aligned reads that contained MspI enzyme digestion site in the ends were used for further analysis.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Count files include chromosome ID, C sites' coordinate, the number of methylated reads and non-methylated reads, p-value based on Bernoulli distribution.

organism: Sus scrofa

source_name: small intestine, preterm, neonatal 4d, NEC

growth_protocol: Six term pigs were delivered close to full term (115-116 days gestation, by Cesarean section) from two pregnant sows (Large White × Duroc, Askelygaard, Denmark), serving as the 0d-term group. Within 6 hours of birth, these pigs were euthanized (sodium pentobarbitone, 200 mg/kg, intravenous), and mid small intestine was dissected out, snap frozen in liquid nitrogen and stored at -80°C. Under anesthesia, 18 preterm pigs were obtained from five pregnant sows (Large White × Duroc; Askelygaard, Denmark) by Cesarean delivery at 90- 92% (104–107 days) gestation. Six of these pigs were euthanized within 6 hours of birth without any feeding (0d-preterm group). The intestine was also dissected out and frozen at -80°C. The remaining 12 preterm pigs were reared individually in infant incubators (Air-Shields, Hatboro, PN) and fitted with orogastric catheters for PN and oro-gastric feeding tube. The pigs were given PN solution at a rate of 4 mL/(kg × h) on d1 and 6 mL/(kg × h) on d2 as well as minimal enteral nutrition: 24 mL/(kg × d) on d1 and 40 mL/(kg × d) on d2 with infant formula. The PN solution was based on a commercially available product (Kabiven, Fresenius Kabi) and adjusted in nutrient composition to meet the requirement of pigs. On d3, they were transferred to full enteral nutrition (EN) [120 mL/(kg × d)] for two more days before sacrifice. The mid intestine was also dissected out and frozen at -80°C. Detailed feeding protocol was previously described. Pigs were continuously monitored for clinical symptoms of NEC and at tissue collection the severity of NEC-like intestinal lesions was evaluated using scoring system previously described. Six pigs remained healthy at the time of tissue collection on day 4 (4d-preterm) while six other pigs had significant NEC lesions identified in their intestines (4d-preterm-NEC).

extract_protocol:
For each sample, total DNA was prepared by proteinase K/phenol extraction and examined by agarose gel electrophoresis. Four pools of intestinal genomic DNA were extracted from the four groups of piglets and they were used for RRBS library construction as previously described.
Briefly, four micrograms of genomic DNA was digested with 100U of MspI enzymes (NEB) in 100 μl reactions at 37°C overnight. After purification, the digested products were progressed by blunt-ending, dATP addition and methylated-adapter ligation. Two ranges of 160-240bp and 240-340bp fractions were excised from a 2% agarose gel, respectively. Then bisulfite conversion was conducted by ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO) following the manufacturer's instructions. The converted DNAs were amplified using JumpStartTM Taq DNA Polymerase (Sigma) by 11-13 cycles (11 cycles for 160-240 bp and 13 cycles for 240-340 bp) of 94°C for 30 sec, 58°C for 30 sec, 72°C for 30 sec. RRBS libraries were then analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified by PCR.

tag: breed

value: Large White X Duroc

value: mid small intestine

value: preterm (104-107 days gestation), neonatal 4 days

tag: disease status

value: significant intestinal necrotizing enterocolitis (NEC) lesions


title: 0d-term

description: Full term (115-116 days gestation, by  Cesarean section)

source_name: small intestine, term, 0d

value: full term (115-116 days gestation)


title: 4d-preterm

description: Healthy at the time of tissue collect neonatally after 4 days.

source_name: small intestine, preterm, neonatal 4d, healthy

value: healthy


title: CON

first: Kang

last: Kang

state: Guangdong

address: Nanhai Road No. 3688

department: College of life science

institute: Shenzhen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and Removed too small and polyA.
The processed sequenced reads were mapped to the T.reesei genome using Mireap 2.0.
Genome_build: Trichoderma_reeseiV2.allmasked.gz (http://genome.jgi-psf.org/Trire2/Trire2.download.ftp.html)

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: The T.reesei QM9414 mycelium was added into the basal medium supplemented with 3% Avicel at 28℃ for 96 h as cellulase inducible sample (IN). The same amount of mycelium was added into 50 ml of the basal medium supplemented with 2% glucose for 72 h, which served as a non-induction control (CON).

extract_protocol:
The total RNAs of T. reesei CON and IN mycelium were extracted using the mirVana PARIS Kit (Ambion) according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mycelia

tag: growth condition

value: non-induced


title: 0d-preterm

description: 6 hours of birth without any feeding.

source_name: small intestine, preterm, 0d

value: preterm (104-107 days gestation)


title: IN

value: cellulase induced


title: B73 Submerge 24 hr Rep 1

value: leaf


title: Mo18w Control 24 hr Rep 2


title: B97 Control 24 hr Rep 3


title: wheat_4_3

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were quality trimmed using trimmomatic v0.30 with parameters: ILLUMINACLIP:adapters.txt:2:30:10 LEADING:17 SLIDINGWINDOW:5:15
Reads were mapped using STAR version 2.3.0e with parameters --outFilterMultimapScoreRange 0 --alignIntronMax 25000 --outFilterMismatchNmax 4 --outFilterMatchNminOverLread 0.9
Transcripts were identified using Cufflinks version 2.1.1 with parameters --max-intron-length 25000 --min-intron-length 21 --frag-bias-correct reference.fasta --GTF-guide annotation.gtf --multi-read-correct
Differential expressoin analysis was performed with Cuffdiff version 2.1.1 --frag-bias-correct reference.fasta --multi-read-correct

organism: Triticum aestivum

source_name: leaf, 4 ºC

growth_protocol: Wheat plants were grown in two growth chambers under either 23℃ or 4℃ day/night temperature regime with a 16-hour photoperiod and light intensity of 120 μmol m-2 s-1

extract_protocol:
Total RNA were extracted from wheat tissues grown at 23ºC and 4ºC using Qiagen Rneasy Plant Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols, Truseq V2

treatment_protocol: 2 weeks cold

tag: lipid phenotype

value: 18:3 lipid phenotype

tag: weeks

value: 4 weeks


title: wheat_4_1

tag: tissue


title: Rex rabbit, back skin, 42 days, chinchilla color(C)

city: Yangzhou

first: Lizhi

last: Qin

state: Jiangsu

address: No.48 Wenhui East Road

department: College of Animal Science and Technology

institute: Yangzhou University

description: Gene expression about back skin of chinchilla Rex rabbit in 42 days

data_processing:
The library was sequenced using IlluminaHiSeqTM 2000 (Illumina, USA)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to the rabbit genome in the Ensembl database.
If the alignment results passed the QC assessment, the samples were then subjected to downstream analysis, including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation, and SNP detection.
The level of gene expression was calculated as RPKM (reads per kilobase transcriptome per million mapped reads), differentially expressed Genes (DEGs) were identified using an FDR≤0.001 (false discovery rate no greater than 0.05)
Cluster v3.0 and javaTreeview v1.1.1 were used forExpression pattern analysis of DEGs. Gene Ontology functional analysis was based on GO::TermFinder. KEGG (major public pathway-related database) is used in our pipeline to perform pathway enrichment analysis of DEGs for  further understand genes biological functions.
Genome_build: The rabbit genome in the Ensembl database
Supplementary_files_format_and_content: Tables include RPKM values, coverage for each Sample.

organism: Oryctolagus cuniculus

source_name: Back skin

growth_protocol: The three Rex rabbits used for this study were purchased from Yuyao Xinnong Rabbit Co., Ltd. (Zhejiang, China). These animals were healthy, were born in the same nest by one mother, and were raised under the same conditions for 42 days (at the first molt) to minimize the impact of genetic background and environment on fur color.

extract_protocol:
Total RNA was extracted from the back skin of the Rex rabbits using TRIzol reagent (Invitrogen, USA). A Qubit fluorometer (Invitrogen, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., USA) were used to determine the quality and quantity of the RNA. The mRNA was enriched using oligo (dT) magnetic beads, then fragmented into short fragments (approximately 200-700 nt) using fragmentation buffer (Invitrogen, USA). Double-stranded cDNA product was synthetized and purified .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For anesthesia, 5 ml 0.5% sodium pentobarbital solution was injected into the ear vein of the rabbits. After anesthesia, a 1-cm2 skin tissue sample was obtained from the backs of the animals, placed immediately in liquid nitrogen, and preserved at –80°C until use. An iodine solution was smeared on the resultant lesion to prevent bacterial infection.

tag: age (days)

value: 42 days

tag: phenotype

value: chinchilla color(C)


title: Rex rabbit, back skin, 42 days, white color(W)

description: Gene expression about back skin of white Rex rabbit in 42 days

value: white color(W)


title: Rex rabbit, back skin, 42 days, black color(B)

description: Gene expression about back skin of black Rex rabbit in 42 days

value: black color(B)


title: B73 Control 24 hr Rep 1


title: MT E-L 27

value: Young berry

value: Mutant

value: After fertilization

value: seedless


title: B97 Submerge 24 hr Rep3


title: wheat_23_2

source_name: leaf, 23 ºC

value: 2 weeks


title: wheat_23_1


title: mock TO cells

city: Oslo

first: Hetron

last: Munang’andu

state: Oslo

address: Ullevålsveien 72

department: Basic Sciences and Aquatic Medicine

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Basecalls performed using CASAVA software
Clean reads were obtained after removal of adaptor sequences, and removal of reads having greater than 10% of unknown bases as well as removal of reads with low quality bases (base with quality value ≤ 5) greater than 50% in a read. Once a library of clean reads was prepared, the reads were then used for transcriptome de novo assembly using the Trinity prorgam (http://trinityrnaseq.sourceforge.net/). Thereafter, we used BlastX (version 2.2.23) alignment against four public protein databases; NCBI non-redundat (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups (COG) at e-value<0.00001.
The mapped read counts for each gene were normalized for RNA length and for the total read number in each lane using the reads per kilobase per million (RPKM) method, which facilitates comparison of the number of transcript levels generated between samples. The cutoff value for determining gene transcriptional activity was based on 95% confidence interval for all RPKM values for each gene. We used a rigorous algorithm to identify differentially expressed genes (DEGs) based on comparing the exposed with unexposed group to generate the DEGs.
Genome_build: denovo assembly
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

organism: Salmo salar

source_name: TO cells

growth_protocol: TO-cells were propagated at 20°C in HMEM (Eagle’s minimal essential medium [MEM] with Hanks’ balanced salt solution [BSS]) supplemented with L-glutamine, MEM nonessential amino acids, gentamicin sulfate, and 10% FBS.

extract_protocol:
Total RNA was isolated using the RNeasy mini Kit (Qiagen, Hilden, Germany) with on-column DNase treatment according to the manufacturer’s instructions.
Equal quantities of total RNA from triplicates of the type I IFN treated, SAV-3 infected and mock-TO-cells were mixed to prepare the pooled RNA sample for RNA-Seq. Total RNA samples were treated with DNase I to degrade any possible DNA contamination. Then the mRNA was enriched using oligo(dT) magnetic beads. The mRNA was fragmented into short fragments (about 200 bp) by mixing with the fragmentation buffer. Thereafter, the first strand of cDNA was synthesized using random hexamer-primer. A buffer containing dNTPs, RNase H and DNA polymerase I was added to synthesize the second strand. The double strand cDNA was purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments and the fragments were enriched by PCR amplification. During quality check (QC step), Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System (Biorad.com) were used to qualify and quantify the sample library. Thereafter, library products were ready for RNA-sequencing using Illumina HiSeqTM 2000, BGI-Hong Kong.

treatment_protocol: One batch of TO-cells was treated with 500 ng/ml of Atlantic salmon Type I IFN in triplicates and another was infected with SAV-3 at MOI 1 when the cells were 80% confluent. Thereafter, both the type I IFN treated and SAV-3 infected cells were incubated at 15°C in maintenance media using HMEM growth media supplemented with 2% FBS. The mock group was only treated with maintenance media.

tag: cell line

value: TO

value: head kidney leukocytes

tag: passage

tag: treatment

value: treated with growth medium


title: wheat_4_2


title: type I IFN treated TO cells

value: treated with type I IFN


title: SAV-3 infected TO cells

value: infected with SAV-3


title: MCF10A_RS_SC_R5

city: Manchester

first: Ged

last: Brady

address: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Rd

department: Clinical and Experimental Pharmacology

institute: Caner Research UK Manchester Institute

description: Amplified cDNA from single cell

data_processing:
50mer single-ended strand specific RNA-seq data were generated using a SOLID 5500 sequencing machine and aligned to human genome hg19 using SHRIMP2.
Filtering; reads that aligned to multiple loci were discarded
Normalisation; For each sample, reads were positioned relative to annotated genes from ENSEMBL version 70, using the annmap database and Bioconductor package(4), and the number of reads hitting exonic regions was counted for each gene. These data were then used to identify differentially expressed (DE) genes using the Bioconductor package EdgeR(10) (FDR < 0.05; absolute fold change > 2; exact test method(11)). A MCF10A vs. MCF7 gene list was produced.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM in exonic regions of all protein coding genes which has at least one read in one of 10 samples (Ensembl HS70)

source_name: MCF10A single cell

growth_protocol: The human epithelial cell lines MCF7 and MCF10A were grown in DMEM (Gibco, Paisley, Scotland) supplemented with 10% heat-inactivated FCS, 2.5% HEPES buffer (pH 7.2), 0.1% β-mercaptoethanol and 2mM L-glutamine (all from Sigma, UK). Both cell lines were maintained in a 5% CO2 humidified incubator at 37°C and were routinely tested for the presence of mycoplasma.

extract_protocol:
RNA (1ng-25pg) or cell lysates in CLS were adjusted to 6.75ml volume and RNA-amplified using the EpiStem RNA-Amp Kit according to the manufacturers protocols (EpiStem, Manchester, UK). Briefly the samples underwent oligo-dT priming and 5’ capping prior to x35 cycles of PCR amplification using the conditions 90ºC 30 sec, 42ºC 2 min and 72ºC 6 min. Following amplification all samples were purified using a MoBio UltraClean® PCR Clean-Up Kit (Carlsbad, CA, USA) and quantified on a NanoDrop spectrophotometer. To ensure all cDNA generated using the Epistem RNA Amp kit was double stranded one cycle of re-amplification was performed.
A library was then prepared using 1ug of the dsDNA in the Life Technologies 5500 SOLiD Fragment Library Core Kit (Life Tech, Paisley, UK) according to the manufacturer's instructions. The libraries were quantified using the Life Technologies SOLiD Library Taqman Quantitation kit (Life Tech, Paisley, UK) and Emulsion PCR was performed using the Life Technologies SOLiD EZ Bead System (Life Tech, Paisley, UK). 50bp single read sequencing was carried out on the Life Technologies 5500XL SOLiD System (Life Tech, Paisley, UK).


title: MCF10A_RS_SC_R2

description: Amplified cDNA from single cell


title: RCIC3

description: Amplified cDNA from volume equivalent to 10 cells

data_processing:
50mer single-ended strand specific RNA-seq data were generated using a SOLID 5500 sequencing machine and aligned to human genome hg19 using SHRIMP2.
Filtering; reads that aligned to multiple loci were discarded
Normalisation; For each sample, reads were positioned relative to annotated genes from ENSEMBL version 70, using the annmap database and Bioconductor package(4), and the number of reads hitting exonic regions was counted for each gene. These data were then used to identify differentially expressed (DE) genes using the Bioconductor package EdgeR(10) (FDR < 0.05; absolute fold change > 2; exact test method(11)). Three gene lists were produced: TT vs. MCIC, TT vs. RCIC, and MCIC vs. RCIC samples.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM in exonic regions of all protein coding genes which has at least one read in one of 10 samples (Ensembl HS70)

source_name: patient-derived non-small cell lung cancer xenograft resident cancer initiating cells

growth_protocol: Patient derived xenografts (PDX) were established from lung cancer primary tumors and expanded as previously described (Moro et al. 2012). Briefly, after approval from the Internal Review and the Ethics Boards of the Fondazione IRCCS Istituto Nazionale Tumori, samples of primary non-small cell lung cancer (NSCLC) were obtained from patients undergoing surgical resection. Each sample was cut in small pieces (25-30 mm3) and implanted subcutaneously using a trocar gauge in the flank of female SCID mice. PDXs were then expanded in vivo through successive rounds of transplantation from donor to recipient mice.

extract_protocol:
To obtain single cell suspension, PDXs were mechanically and then enzymatically digested in a solution of collagenase IV (5mg/ml) and DNAse (100U/ml) (Sigma-Aldrich) in DMEM/F12 (Lonza) for 1h at 37 °C. Partially digested tissue was filtered through a 100µm cell strainer (BD Falcon) and red blood cells were removed by Lysing Buffer 1X (BD Bioscience).  Single cell suspensions from dissociated NSCLC-PDXs were washed and incubated in staining solution 1% BSA and 2mM EDTA with specific antibodies at appropriate dilutions for 30 min at 4 °C: PE anti-human CD133/1, FITC anti-human CD326 (EpCAM) (Miltenyi Biotech), APC anti-human CD187 (CXCR4) (BD Pharmingen), Alexa Fluor® 488 anti-human HLA-ABC (BD Pharmingen) , PerCP-eFluor 710 anti-mouse MHC class I (e-Bioscience). Prior to sorting, cells were resuspended to a final concentration of 10x106 cells/ml in Hepes Buffered Saline (HBS) (Lonza) + 0.1% B27 Supplements (Gibco) and 7-AAD viability staining solution (1:10) (e-Bioscience) for dead cells exclusion.  PDX-cells were sorted with FACSAria (Becton Dickinson) into a chilled 96-well plate (Corning Incorporated). For sorting of different CSC fractions, an initial gate excluding doublets, dead cells and mouse MHC class I+ cells was set.  Then, within the gate of human viable CD133+ cells, the fraction of EpCAM+ and CXCR4+EpCAM- cells were identified and sorted.  Total tumor population was isolated based on human HLA-ABC+ expression. For each cell fraction, 300 cells were directly sorted in 30 μl of CLS (Complete Lysis Solution) per well and within 1h approximately 100 cells/10 μl were transferred into 0.5 ml tubes and stored to -80 0C.  To ensure all cDNA generated using the Epistem RNA Amp kit was double stranded one cycle of re-amplification was performed.
RNA (1ng-25pg) or cell lysates in CLS were adjusted to 6.75ml volume and RNA-amplified using the EpiStem RNA-Amp Kit according to the manufacturers protocols (EpiStem, Manchester, UK). Briefly the samples underwent oligo-dT priming and 5’ capping prior to x35 cycles of PCR amplification using the conditions 90ºC 30 sec, 42ºC 2 min and 72ºC 6 min. Following amplification all samples were purified using a MoBio UltraClean® PCR Clean-Up Kit (Carlsbad, CA, USA) and quantified on a NanoDrop spectrophotometer.


title: MCF7_RS_SC_R1

description: Amplified cDNA from single cell

source_name: MCF7 single cell


title: MCF10A_RS_SC_R1

description: Amplified cDNA from single cell


title: MCF10A_RS_SC_R4

description: Amplified cDNA from single cell


title: MCF7_RS_SC_R5

description: Amplified cDNA from single cell


title: MCF7_RS_SC_R4

description: Amplified cDNA from single cell


title: wheat_23_3

value: leaf


title: RCIC2

value: patient-derived non-small cell lung cancer xenograft resident cancer initiating cells


title: MCIC4

source_name: patient-derived non-small cell lung cancer xenograft metastasis associated cancer initiating cells


title: RCIC1


title: RCIC4


title: MCIC2

value: patient-derived non-small cell lung cancer xenograft metastasis associated cancer initiating cells


title: MCIC3


title: MCIC1


title: TT3

source_name: patient-derived non-small cell lung cancer xenograft total tumour


title: TT4

value: patient-derived non-small cell lung cancer xenograft total tumour


title: TT1


title: mRNA_none_16hr

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Sequenced reads were filtered for low-quality sequence, trimmed for adaptor sequence, trimmed 3' ends of the resulting reads for which PHRED quality scores were lower than 20 using Cutadapt v.1.0, and then mapped to NCBI build 5.3 using TopHat v2.0.5 with parameters -p 16 --bowtie-n --b2-sensitive --mate-inner-dist 70 --mate-std-dev 90 --no-coverage-search --library-type fr-unstranded --no-novel-juncs.
After removing duplicate reads, the read counts (count per million) for each gene were calculated using HTSeq
Raw read counts were normalized by Trimmed Mean of M-value (TMM) normalization method using edgeR package
Genome_build: NCBI build 5.3
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: midgut of Control flies

extract_protocol:
Total RNA was extracted from Each of midguts using the Qiagen RNeasy mini kit (Qiagen). Poly(A) mRNA isolation from total RNA (5 µg) and fragmentation were performed using the Illumina Truseq RNA Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina True-seq RNA sample prep kit v2, according to the manufacturer’s protocol.

value: midgut

tag: time

value: 16 hrs


title: mRNA_none_2hr

value: 2 hrs


title: mRNA_uracil_16hr

source_name: midgut of uracil-treated flies

value: uracil


title: TT2

organism: Homo sapiens


title: MCF10A_RS_SC_R3

description: Amplified cDNA from single cell


title: MCF7_RS_SC_R3

description: Amplified cDNA from single cell


title: mRNA JHDM2-KD-None-16hr

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Sequenced reads were filtered for low-quality sequence, trimmed for adaptor sequence, trimmed 3' ends of the resulting reads for which PHRED quality scores were lower than 20 using Cutadapt v.1.0, and then mapped to UCSC drosophila genome dm3 using TopHat v2.0.5 with parameters -p 16 --bowtie-n --b2-sensitive --mate-inner-dist 70 --mate-std-dev 90 --no-coverage-search --library-type fr-unstranded --no-novel-juncs.
After removing duplicate reads, the FPKM values for each gene were calculated using Cufflinks v.2.0.2
Genome_build: UCSC dm3
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: midgut of JHDM2 Knockdown flies

tag: knockdown

tag: infection

tag: days after treatment

value: 16hrs None


title: mRNA_uracil_2hr


title: mRNA JHDM2-KD-None-4hr

value: 4hrs None


title: 98_Day_7_HTKL_2

city: Boston

description: High-persister

source_name: Cell culture

tag: culture

value: Exponential phase culture

tag: cell

value: Whole Cell

tag: experimental day

value: Day 7


title: MCF7_RS_SC_R2

description: Amplified cDNA from single cell


title: 2032T_MBDCap-Seq

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

institute: Garvan Institute of Medical Research

description: MBDCap-Seq

data_processing:
Sequenced reads were aligned to hg18 genome assembly using bowtie. Reads with more than three mismatches and reads mapping to multiple positions were removed. Finally, multiple reads mapping to exactly the same genomic coordinate were eliminated and only one read was retained for downstream analysis.
For each MBDCap-Seq sample, fragment length was estimated using HOMER software, sequenced tags were shifted to the middle of estimated fragment lenght and the number of sequenced tags overlapping SssI regions was computed.
Genome_build: hg18
Supplementary_files_format_and_content: Text files contain genomic coordinates of SssI regions and  the number of overlapping sequenced tags.

source_name: Human tumour breast tissue

growth_protocol: DNA was extracted from cells microdissected from human tissue samples representing normal breast and tumor breast tissue.

extract_protocol:
The MethylMinerTM Methylated DNA Enrichment Kit (Invitrogen) was used to isolate methylated DNA from 500 ng – 1 μg of genomic FFPET DNA.
10ng DNA of MBDCap enriched DNA was prepared for Ilumina sequencing using the Illumina ChIP-Seq DNA sample prep kit (IP-102-1001) according to the manufacturer’s instructions.  The library preparation was analyzed on Agilent High Sensitivity DNA 1000 Chip.

tag: tissue type

value: Triple negative breast cancer (TNBCs)


title: mRNA Control-None-4hr

value: control


title: mRNA JHDM2-KD-Ecc15-16hr

value: 16hrs post-infection with Ecc15


title: mRNA JHDM2-KD-Ecc15-4hr

value: 4hrs post-infection with Ecc15


title: mRNA Control-Ecc15-4hr


title: mRNA Control-Ecc15-16hr


title: 4488T_MBDCap-Seq

description: MBDCap-Seq


title: mRNA Control-None-16hr


title: 3050T_MBDCap-Seq

description: MBDCap-Seq


title: 12627T_MBDCap-Seq

description: MBDCap-Seq


title: 214T_MBDCap-Seq

description: MBDCap-Seq


title: 2532T_MBDCap-Seq

description: MBDCap-Seq


title: 19328T_MBDCap-Seq

description: MBDCap-Seq


title: 2319T_MBDCap-Seq

description: MBDCap-Seq


title: 8948T_MBDCap-Seq

description: MBDCap-Seq


title: 1138T_MBDCap-Seq

description: MBDCap-Seq


title: 14906T_MBDCap-Seq

description: MBDCap-Seq


title: 19038T_MBDCap-Seq

description: MBDCap-Seq


title: 102_Day_7_HTKL_2

description: High-persister


title: 2850T_MBDCap-Seq

description: MBDCap-Seq


title: 4537T_MBDCap-Seq

description: MBDCap-Seq


title: 7700T_MBDCap-Seq

description: MBDCap-Seq


title: 14906N_MBDCap-Seq

description: MBDCap-Seq

source_name: Human normal breast tissue

value: matched normal tissue


title: 2850N_MBDCap-Seq

description: MBDCap-Seq


title: SssI_MBDCap-Seq

description: MBDCap-Seq

source_name: Human blood tissue

value: blood

value: SssI treated


title: 20578T_MBDCap-Seq

description: MBDCap-Seq


title: 16693T_MBDCap-Seq

description: MBDCap-Seq


title: 23622T_MBDCap-Seq

description: MBDCap-Seq


title: 16693N_MBDCap-Seq

description: MBDCap-Seq


title: 17420T_MBDCap-Seq

description: MBDCap-Seq


title: L8Female

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Sequenced reads were mapped to the rn4 whole genome using bowtie2 v2.0.2 with local alignment.
Data was preprocessed and analysed in the R environment (2.15.2) loading DESeq and biomaRt packages. Normalisation, estimation of dispersions and testing for differentially expressed genes based on a test assuming negative binomial data distribution was computed via DESeq.
Genome_build: rn4
Supplementary_files_format_and_content: Counts.txt files include normalized abundance measurements. Counts were divided by the size factor allowing for relative library size correction.

organism: Rattus norvegicus

source_name: liver, female

growth_protocol: Animals were kept in the animal facility of Charles River Laboratories under conventional housing conditions (22°C,55 % humidity, and 12 h day/night cycle) and were given free access to water and rat chow.

extract_protocol:
Livers were extracted post mortem, conserved in RNAlater®, and transported to our laboratory in Germany. RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Without treatment.

tag: strain/background

value: liver

tag: Sex

value: female

tag: developmental stage

value: adult

tag: age

value: 16 weeks

value: obese


title: L6Male

source_name: liver, male

tag: tissue

value: male


title: L9Female

tag: phenotype


title: L5Male


title: L3Male


title: L13Female


title: L2Male


title: L1Male


title: 23622N_MBDCap-Seq

description: MBDCap-Seq


title: L12Female


title: L10Female


title: 20578N_MBDCap-Seq

description: MBDCap-Seq


title: Hermaphrodite flower replicate 1

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

description: herm.txt.gz

data_processing:
Reads with low scored nucleotids < 20 were removed.
3' adapters were removed and the small RNA sequences were extracted from the raw reads.
5' adapters were removed from the processed small RNA sequences.
The reads with at least 18nt were maintained in the final results.
The reads of the Male flower replicate 1 and Male flower replicate 2 were combined. The reads of the Female flower replicate 1, Female flower replicate 2 and Female flower replicate 3 were combined.
The unique sequences and their counts were calculated from the extracted sequences.
Supplementary_files_format_and_content: unique sequence and count

organism: Carica papaya

source_name: hermaphrodite flower

extract_protocol:
The plants were grown in Hawaii.
Total RNA was isolated from selected tissues using TRIzol reagent and small RNA libraries were generated by following Solexa protoco (18-28nt). The 3' adapters for all libraries are TCGTATGCCGTCTTCTGCTTG. There is a 5' barcode of CA in Male flower replicate 1 and Male flower replicate 2. There is a 5' barcode of GT for Female flower replicate 1, Female flower replicate 2 and Female flower replicate 3. There is a 5' barcode of TG for Hermaphrodite flower replicate 1.

value: hermaphrodite flower


title: Female flower replicate 2

description:
The processed reads of Female flower replicate 1, Female flower replicate 2 and Female flower replicate 3 are combined to form the processed data file.
female.txt.gz

source_name: female flower

value: female flower


title: Male flower replicate 2

description:
The processed reads of Male flower replicate 1 and Male flower replicate 2 are combined to form the processed data file.
male.txt.gz

source_name: male flower

value: male flower


title: Male flower replicate 1


title: 4i WIS2 hESC (Fig. S7) rep2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Low quality bases (q < 20) from the 3' end and adapter sequences were removed with the TrimGalore wrapper scripts (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Reads were mapped to the human (GRCh37/hg19) reference genome with Tophat 2.0.12 (http://ccb.jhu.edu/software/tophat)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Processed data files contain read counts per RefSeq transcripts generated by using the HTSeq 0.6.1 python package (http://www-huber.embl.de/users/anders/HTSeq)

source_name: Human embryonic stem cell cultured in 4i condition

extract_protocol: Total RNA was extracted using DirectZol RNA mini-prep. Libraries were prepared by the INCPM unit in the Weizmann Institute of Science according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit v2 (RS-122-2001).

tag: cell type

tag: protocol

value: Unsorted

tag: gender

value: Male


title: Conventional WIS2 hESC (Fig. S7) rep1

source_name: Human embryonic stem cell cultured in conventional condition


title: Female flower replicate 3


title: L7Female


title: 17420N_MBDCap-Seq

description: MBDCap-Seq


title: Mo-DC mRNA rep 1

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

description:
mRNA
C DC

data_processing:
Basecalls performed using CASAVA version 1.7
Data analysis consisted of a filtering step to eliminate reads consisting mono- and di-nucleotide repeats followed by the identification of exact unique matches using fetchGWI [Iseli C, Ambrosini G, Bucher P, Jongeneel CV (2007) Indexing strategies for rapid searches of short words in genome sequences. PLoS One 2: e579].
Megablast was used to recover unmatched reads (http://www.ncbi.nlm.nih.gov/blast/html/megablast.html). Paired information was used to generate alignments of each read on the genomic region where hits were found by previous steps using SIBsim4 http://sibsim4.sourceforge.net/. Alignments were analyzed using Tromer [Steijger T, Abril JF, Engstrom PG, Kokocinski F, Akerman M, et al. (2013) Assessment of  transcript reconstruction methods for RNA-seq. Nat Methods 10: 1177-1184].
Counts for DC0904 and DC0907 were pooled for subsequent analysis. The sample name for these reads is listed as DC_normal in the processed data file
Counts for DCLPS0910 and DCLPS0913 were pooled for subsequent analysis. The sample name for these reads is listed as DC_treated in the processed data file
Genome_build: hg19
Supplementary_files_format_and_content: Raw count data are provided in tab-delimited format

source_name: Mo-DC mRNA rep 1

extract_protocol:
Nascent RNA: nuclei were isolated and lysed, the resulting chromatine was pelleted by centrifugation. Primary RNA was extracted using acid water-saturated hot phenol extraction
Total RNA was extracted using Trizol reagent (Life Technologies)
TruSeq library preparation protocol

treatment_protocol: 1 hour LPS (25ng/ml)

value: Monocyte-derived denditric cells


title: Mo-DC 1h LPS mRNA rep 1

description:
mRNA
C DC LPS

source_name: Mo-DC 1h LPS mRNA rep 1


title: 4i WIS2 hESC (Fig. S7) rep1

value: Human embryonic stem cell cultured in 4i condition


title: Mo-DC 1h LPS nascent RNA rep 2

description:
Nascent/primary RNA
A DC LPS
mRNA-seq sample preparation protocol (PE-102-1002-Paired-end kit)

source_name: Mo-DC 1h LPS nascent RNA rep 2


title: L4Male


title: Mo-DC 1h LPS nascent RNA rep 1.1

description:
Nascent/primary RNA
DCLPS
mRNA-seq sample preparation protocol (PE-102-1002-Paired-end kit)

source_name: Mo-DC 1h LPS nascent RNA rep 1.1


title: Mo-DC nascent RNA rep 2

description:
Nascent/primary RNA
A DC
mRNA-seq sample preparation protocol (PE-102-1002-Paired-end kit)

source_name: Mo-DC nascent RNA rep 2


title: Mo-DC nascent RNA rep 1.2

description:
Nascent/primary RNA
DC
mRNA-seq sample preparation protocol (PE-102-1002-Paired-end kit)

source_name: Mo-DC nascent RNA rep 1.2


title: Mo-DC nascent RNA rep 1.1

source_name: Mo-DC nascent RNA rep 1.1


title: Mo-DC 1h LPS nascent RNA rep 1.2

source_name: Mo-DC 1h LPS nascent RNA rep 1.2


title: Female flower replicate 1


title: Conventional WIS2 hESC (Fig. S7) rep2

value: Human embryonic stem cell cultured in conventional condition


title: TT2_H3K9me3_1,000c

city: Vancouver

first: Matthew

middle: C

last: Lorincz

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: index: ACCCAG

data_processing:
Alignment (ChIP-seq): Sequence reads were mapped to mm9 (NCBI 37) using BWA (Li and Durbin 2009) and default parameters.
Wigs (ChIP-seq): Reads having identical coordinates were collapsed into a single read and reads with mapQ >=5 passed to FindPeaks 3.1 (Fejes et al., 2008) for  visualization.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized values were obtained by claculating the reads per kilobase per million reads (RPKM) at the indicated genomic regions. For RNA-seq, the RPKM values were generated for the exonic regions only.

organism: Mus musculus

extract_protocol:
For ChIP, cells were sorted directly in nuclear isolation buffer containing RNAse inhibitor and protease inhibitor cocktail. For RNA-seq libraries, RNA was extracted using TriReagent, and dsCDNA was synthesized using Superscript III and Klenow fragment, respectively. For ChIP-seq libraries, DNA was extracted from immunoprecipitated DNA-protein complexes using phenol:chloroform:isoamyl alcohol 25:24:1.
Adaptor ligation based library construction for paired-end Illumina sequencing.

tag: strain

value: C57BL/6 x CBA

value: embryonic stem cells

tag: dev. stage

value: blastocyst (ICM)

tag: genotype

value: wildtype

tag: antibody

value: H3K9me3 (Active Motif #39161)


title: TT2_H3K9me3_1,000b

description: index: AACCCC


title: TT2_H3K27me3_10,000

description: index: AACTTG

value: H3K27me3 (Diagenode pAb-069-050)


title: TT2_1,000_RNAseq

description:
index: AACCCC
rRNA depleted

data_processing:
Alignment (RNA-seq): Sequence reads were aligned to the mouse reference genome mm9 (NCBI 37) using BWA (Li and Durbin 2009), with annotated exon-exon junctions compiled from Ensembl, RefSeq and UCSC gene annotation sources, as described (Morin et al., 2010; Shah et al., 2009). Sequence reads that could be uniquely assigned a position in the transcript resource (exon-exon junctions) were computationally repositioned to the genomic mm9 coordinates and a single merged bam file (Li et al., 2009) generated for downstream analyses.
Wigs (RNA-seq): The Samtools pileup utility (Li et al., 2009) and FindPeaks 3.1 (Fejes et al., 2008) was used to generate data tracks for visualization (wig and bigWig (Kent et al., 2010)) in the UCSC browser. Repbase (Jurka et al., 2005), a comprehensive database of repetitive elements, was used for alignment of reads to repetitive elements.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized values were obtained by claculating the reads per kilobase per million reads (RPKM) at the indicated genomic regions. For RNA-seq, the RPKM values were generated for the exonic regions only.


title: TT2_panH3_1,000a

description: index: CAACTA

value: pan-H3 (Sigma I8140)


title: TT2_H3K4me3_5,000

description: index: TGAATG

value: H3K4me3 (Abcam ab1012)


title: TT2_H3K27me3_1,000

description: index: CGATGT

value: male


title: TT2_H3K27me3_100,000

description: index: AGCGCT


title: TT2_H3K4me3_100,000

description: index: CAACTA


title: TT2_panH3_1,000b

description: index: CTATAC


title: TT2_H3K9me3_10,000

description: index: CTAGCT


title: TT2_H3K9me3_1,000a

description: index: AGTTCC


title: TT2_H3K9me3_100,000

description: index: ACCCAG


title: TT2_H3K9me3_1million

description: index: CCAACA


title: Crygc-mutant-4W-SSCs-WGBS

city: Beijing

first: Xiaoying

last: Fan

state: Beijing

address: 5 Yiheyuan Road

department: College of Life Sciences

institute: Peking University

description: whole genome bisulfite sequencing

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
reads were aligned to the mouse refference genome (mm9) using BWA software
DNA methylation level on each imprinting locus was estimated.
Genome_build: mm9
Supplementary_files_format_and_content: DNA methylation level on each C genomewide

source_name: mouse spermatogenic stem cell

growth_protocol: cells were grown on the mouse embryonic fibroblast feeder cells and cultured with the modified SSC medium.

extract_protocol:
mouse SSC gDNA was extracted with DNeasy Blood & Tissue Kit (QIAGEN) following the manual instructions
the extracted gDNA was fragmentated physically to 250-300bp and then directly for library construction following illumina's Truseq protocol. for WGBS libraries, do the bisulfite conversion after ligated with illumina adaptors and then do library amplification.

treatment_protocol: The pX330-mcherry plasmids harbouring corresponding sgRNA and oligo DNA were transfected into SSCs with Amaxa Cell Line Nucleofector Kit L (Lonza) using Amaxa Nucleofector according to the manufacturer’s instruction manual.

value: BALB/c

tag: passage

value: spermatogenic stem cell (SSC)

tag: cell status

value: Crygc mutant


title: CT26 spheroids p1 rep2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

data_processing:
fastq files were aligned using STAR version 2.3.0
exon-level counts were generarated using python script provided as part of DEXSeq package version 1.6.0 using UCSC annotation for mm9 mouse genome build
gene-level counts were generated collapsing exon-level counts using geneCountsTable function from DEXSeq 1.6.0
gene-level differential expression was assessed using DESeq2 version 1.0.19
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file encompassing gene-level raw counts for the 4 experiments

source_name: cell line CT26

growth_protocol: The adherent CT26 epithelial cells were cultured in DMEM supplemented with 20% FCS (GIBCO, Grand Island, NY). Single CT26 cells were plated in ultra low attachment flasks (Corning Life Sciences, Chorges, France) at 6 x 104 viable cells/ml in serum-free DMEM-F12 medium (Cambrex BioScience, Venviers, Belgium) supplemented with 20 ng/ml basic fibroblast growth factor (bFGF), 20 ng/ml epidermal growth factor (EGF), 5 Î¼g/ml insulin, and 0.4% bovine serum albumin (BSA), all from Sigma-Aldrich (St. Louis, MO). Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days.

extract_protocol:
Total RNA extraction was done with Rneasy QIAGEN kit following manufacturer instruction. Quality of RNA was evaluated by Bioanalyser and quantified with Nanodrop.
Libraries construction and indexing was done using Illumina TrueSeq unstranded Illumina kit following manufacturer instructions using 1 microgram of total RNA.

value: spheroids p1

tag: cell line

tag: disease status

value: colon carcinoma


title: CT26 spheroids p1 rep1


title: TUBO mammospheres p1 rep1

source_name: cell line TUBO

growth_protocol: The adherent TUBO epithelial cells were cultured in DMEM supplemented with 20% FCS (GIBCO, Grand Island, NY). Single TUBO cells were plated in ultra low attachment flasks (Corning Life Sciences, Chorges, France) at 6 x 104 viable cells/ml in serum-free DMEM-F12 medium (Cambrex BioScience, Venviers, Belgium) supplemented with 20 ng/ml basic fibroblast growth factor (bFGF), 20 ng/ml epidermal growth factor (EGF), 5 Î¼g/ml insulin, and 0.4% bovine serum albumin (BSA), all from Sigma-Aldrich (St. Louis, MO). Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days.

value: mammospheres p1

value: TUBO

value: breast cancer


title: CT26 epithelial bulk rep2

value: epithelial bulk


title: TUBO epithelial bulk rep2


title: TUBO epithelial bulk rep1


title: CT26 epithelial bulk rep1


title: B16 epithelial bulk rep2

source_name: cell line B16

growth_protocol: The adherent B16 epithelial cells were cultured in DMEM supplemented with 20% FCS (GIBCO, Grand Island, NY). Single B16 cells were plated in ultra low attachment flasks (Corning Life Sciences, Chorges, France) at 6 x 10^4 viable cells/ml in serum-free DMEM-F12 medium (Cambrex BioScience, Venviers, Belgium) supplemented with 20 ng/ml basic fibroblast growth factor (bFGF), 20 ng/ml epidermal growth factor (EGF), 5 µg/ml insulin, and 0.4% bovine serum albumin (BSA), all from Sigma-Aldrich (St. Louis, MO). Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days.

value: melanoma


title: B16 mammospheres p1 rep1


title: B16 mammospheres p1 rep2


title: TT2_H3K4me3_10,000

description: index: CCAACA

value: C57BL/6 x CBA

value: embryonic stem cells

value: blastocyst (ICM)


title: B16 epithelial bulk rep1


title: Mutant2

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

country: France

institute: INSERM

description: Sample 4

data_processing:
Basecalls were done with Illumina's software and CASAVA 1.8.1
Reads were aligned on the mm9 mouse whole genome using TopHat 1.4.0 with default parameters on the usegalaxy.org platform. Subsequent bam files were used to compute reads counts per gene using HTSeq-count script with the following options : unstranded, intersection-nonempty, counting on exons using gene_id as the grouping value and the mm9 UCSC gtf file as a reference.
Read counts were used to compute differentially expressed genes using the R package DESeq2 with genotypes as a variable (replicates of 2 wild-type and 2 mutant mice).
Genome_build: mm9
Supplementary_files_format_and_content: TRamiAmhCre_Data.txt is a matrix presenting for each sample the raw number of reads for every gene (output from HTSeq-count) which served as input for gene differential expression analysis.

source_name: Mouse testis

growth_protocol: Mouse were obtained by crosses between AmhCre mice and TRαAMI heterozygous mice and raised in a conventional animal house.

extract_protocol: Cells were lyzed and total RNA was extracted using a commercial kit. PolyA RNA were then enriched by oligo-dT purification. Libraries were constructed according to Illumina dedicated protocols for single-end sequencing of 100bp reads.

value: C57BL/6J dominant background

value: whole testes

value: Post-natal day 3

tag: genotype/variation

value: Dominant-negative TR_alpha_1 receptor


title: Wild-type1

description: Sample 1

value: Wild-type TR_alpha_1 receptor


title: TUBO mammospheres p1 rep2


title: Line-HDR1-SC-8-WGBS

description:
whole genome bisulfite sequencing
Line-HDR1-SC-8-WGBS_index10
Line-HDR1-SC-8-WGBS_index11

value: BALB/c

value: spermatogenic stem cell (SSC)

value: CRISPR rescued


title: Wild-type2

description: Sample 2


title: ESC_chromatin

city: Singapore

first: Benson

last: Chen

address: 60 Biopolis Street, Genome, #04-01

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

description: original REDseq protocol

data_processing:
library strategy: RED-seq (deep sequencing analysis of Restriction Enzyme Digestion)
Basecalls performed using CASAVA version 1.8.2
Barcode sequences were trimmed and RED-seq reads were aligned to the mm9 genome assembly using Bowtie allowing at most one mismatch in every alignment.
For multimappers, only one alignment was chosen randomly by the -M 1 parameter setting.
Assignment of aligned sequences to individual restriction enzyme cut sites (REs) and differential cut analysis were performed using the Bioconductor package REDseq.
The ChIPpeakAnno package was used to annotate the differentially cut sites to the nearest genes.
Genome_build: mm9
Supplementary_files_format_and_content: The assigned reads for each restriction enzyme site are in bedGraph format (*.bedGraph).

source_name: Mouse embryonic stem cells

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol:
One million cells were used to construct RED-seq libraries. Cells were washed, pelleted, and resuspended in Swelling buffer (10mM Tris pH8.0, 85mM KCl, 0.5% NP-40, 10mM MgCl2) with 100 units of Sau96I (NEB) and incubated in a thermomixer (Eppendroff) at 37°C for 1 hour, shaking at 900 rpm. Digestion was terminated by adding 40μl of 10% SDS and 20μl of 0.5M EDTA and the chromatin was treated with proteinase K (Ambion) overnight at 55°C. Digested DNA was purified using Phenol/Chloroform/Isoamyl alcohol extractions and precipitated at -80°C for 1 hour.
Digested DNA samples were end-repaired and A-tailed according to Illumina's instructions., and ligated with biotinylated and barcoded adaptors. DNA was purified using Zymo Research DNA clean and concentrate columns following each enzyme reaction. The biotin-adaptor ligated DNA was sonicated in a Covaris sonicator (S220) to generate DNA peak fragments of 200 bp, on average. The sonicated DNA samples were then end-repaired, A-tailed, and ligated with non-biotinylated adaptors. The ligation samples were loaded on 2% agarose gel and DNA was purified within a size range of roughly 200-350 bp in length. Gel-purified DNA was diluted to 250μl with streptavidin binding buffer (20mM HEPES pH 7.6, 500mM NaCl, 1mM EDTA, 0.02% NP-40) and incubated with 30μl of pre-washed streptavidin magnetic beads (NEB) at room temperature for 1 hour. After magnetic separation, the supernatants were removed, and the beads were washed additional three times with streptavidin binding buffer. DNA was eluted from streptavidin magnetic beads by adding 20 μl of 0.1X TE and heating at 60°C for 3 minutes. The elution was repeated three times. The adaptor-ligated material was then PCR amplified with Phusion polymerase (NEB) using 16 cycles of PCR and its concentration was determined using a NanoDrop (Thermo).

treatment_protocol: In one 10 cm2 dish, 1X10^6 cells were infected with 2.5 ug of esiRNA. After 12-15 hours, the media was replaced and cells were cultured until 5 days post-transfection.

value: wild type

value: Mouse embryonic stem cells

tag: material for redseq

value: chromatin DNA


title: ESC_DNA

description: original REDseq protocol

value: naked DNA


title: Mutant1

description: Sample 3