title: E22

city: Changhua

first: Shih-Feng

last: Fu

address: No.1, Jin-De Road, Changhua City, 500

country: Taiwan

institute: Department of Biology, National Changhua University

description:
Sample 1
Total small RNA extracted from shoot apex

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw sequences from adaptor sequences, low-quality sequences, low-complexity regions, and sequences shorter than 16nt or longer than 31nt were removed. Unique sequences were retained with count numbers of the individual sequence reads. The unique small RNAs were aligned to known non-coding RNAs downloaded from the Rfam database (http://www.sanger.ac.uk/Software/Rfam) with NCBI BLASTN to discard rRNA, tRNA, snRNA, and snoRNA. To study conserved miRNAs, we used these remained sequences to do BLASTN searches against known plant miRNAs from miRBase v19. Sequences with identical or with less than 2 mismatches to viridiplantae mature miRNAs were considered to be potential conserved miRNAs. The remaining sequences were used to search novel miRNAs in broccoli.
To study novel miRNA candidates, the rest of sRNAs were predicted using psRobot, http://omicslab.genetics.ac.cn/psRobot/index.php. In the absence of the full broccoli genome sequences, we using Brassica rapa (Mustard), BAC-based genome sequence data from GenBank BrGDB154 as a source genome. The matched sequences including the cluster unions and around 200-bp flanking sequences were defined as potential miRNAs. Those sequences are potentially related to a set of acceptable miRNA precursor sequences and the cluster unions are likely to be novel miRNA families. Their secondary structures were predicted by mfold with miRNA precursor sequences. According to the previously described criteria, satisfying all the following rules were considered to be novel miRNAs: (1) A mature sequence localized in one arm of the stem-loop structure and ranging between 19-24 nt was considered; (2) the corresponding miRNA* sequence could be identified; (3) an miRNA/miRNA* duplex exhibited 2-nt 3' overhangs; (4) the pre-miRNA sequence was folded into an appropriate stem-loop hairpin secondary structure; (5) the MFE (minimal folding free energy) of secondary structures was <= -20 kcal/mol; (6) There were no more than 7 nt mismatches in the miRNA:miRNA* duplex.
Genome_build: miRBase v19 and Brassica napus (rape), unigene, DFCI Gene Index (BNGI), version 5,released on 2011_03_18
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample .

organism: Brassica oleracea var. italica

source_name: Broccoli shoot apex from heat-tolerant lines

growth_protocol: Heat tolerant (CNE) and heat sensitive (CNL) plants were grown in growth chambers in long day conditions with 18 h light/ 6 h dark. Seeds were germinated in vermiculite for 7 to 10 days (mostly 10 days) and transplanted to a 9 cm diameter pot (= small pot) or 16.5 cm diameter pot (= big pot) in soil for about 30 days at 22°C. The plants were then transferred to 15°C, 22°C and 27°C in batches for 2 weeks and then extracted the total RNA for analyzing the gene expression at different temperature.

extract_protocol:
Small RNA samples were isolated from apical shoot of CNE and CNL plants using the mirPremier microRNA Isolation Kit (Sigma-Aldrich, St. Louis, MO, USA) following the instruction manual. The small RNA fraction of 18-30 nt in size were purified from 15% denaturing polyacrylamide TBE-Urea gels with SYBR® Safe DNA gel stain (Invitrogen, Cergy Pontoise, France). The size selected small RNA were then sequentially ligated to the 3’ and 5’ adapters using T4 RNA ligase 2 and T4 RNA ligase, respectively (Illumina Inc., San Diego, CA, USA). Reverse transcription was preformed after ligation with adapters, subsequently amplified by PCR as described in the Illumina protocol. The PCR products were purified by separation on and subsequent elution from 10% TBE urea polyacrylamide gel. The libraries from the two samples were sequenced using the Illumina Hiseq2000 that generated single-end reads of 100 nucleotides (YOURGENE BIO SCIENCE Co., New Taipei City, Taiwan).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heat-tolerant broccoli isogenic lines

value: Shoot apex

tag: age

tag: curd-forming capacity

value: high


title: L22

status: Public on Sep 03 2014

type: SRA

description:
Sample 2
Total small  RNA extracted from shoot apex

library_source: transcriptomic

molecule: total RNA

source_name: Broccoli shoot apex from heat-sensitive lines

treatment_protocol: The plants were then transferred to 15°C, 22°C and 27°C in batches for 2 weeks and then extracted the total RNA for analyzing the gene expression at different temperature.

tag: genotype/variation

value: Heat-sensitive broccoli isogenic lines

tag: tissue

value: low


title: Rho 0 (no mtDNA) 143B

status: Public on Sep 02 2014

city: Philadelphia

first: Douglas

last: Wallace

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

country: USA

institute: The Children's Hospital of Philadelphia

data_processing:
Raw data was mapped with Lifescope 2.5.1
RPKM values were calculated using Partek
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited .txt file reports RPKM value per gene per replicate

organism: Homo sapiens

source_name: Cybrid cell line

growth_protocol: Cell were grown in 75cm2 flasks in DMEM media containing 4.5 g/L (25mM) glucose and 110 mg/L sodium pyruvate (Gibco #10569) supplemented with 50 μg/ml uridine and non-essential amino acids (1:100, Gibco #11140) at 37oC in 95% air, 5 % CO2.

extract_protocol:
Total RNA was extracted with 1ml of Trizol directly applied to the culture dish. Total RNA was depleted of cytosolic rRNA (RiboMinus, Life Technologies #10837-08). RNA was quality checked and quantified on a Bioanalyzer 2100, RNA 6000 Nano kit (Eukaryote Total RNA Nano, Agilent Techonolgies) and Qubit 2.0 fluofometer RNA assay kit (Molecular Probes #Q32852). Five hundred ng of RNA was used for cDNA library preparation using (Ambion, Total RNA-Seq kit #4445374) according to manufacturer's instructions.
Samples were barcoded such that they could be pooled and run on the same sequencing lanes. RNA from all eight experimental groups (transmicotochondrial cybrid cell lines 0, 20, 30, 50, 60, 90 and 100 % 3243G heteroplasmy plus the Rho0 parental cell line) were sequenced on the ABI SOLiD 5500 platform. Barcoded triplicates were sequenced on the same slide in different lanes. All sequencing was performed using paired-end chemistry of 50 (forward) x 35 (reverse) base pairs.

treatment_protocol: Growth media was removed immediately prior to RNA-extraction.

tag: cell line

value: Rho0 parental cell line

tag: confluence

tag: heteroplasmy

value: Rho 0 (no mtDNA) 143B


title: 90% 3243G 143B

value: transmitochondrial cybrid cell line 90


title: 100% 3243G 143B

value: transmitochondrial cybrid cell line 100


title: 60% 3243G 143B

value: transmitochondrial cybrid cell line 60


title: 20% 3243G 143B

value: transmitochondrial cybrid cell line 20


title: 0% 3243G 143B

value: transmitochondrial cybrid cell line 0


title: 30% 3243G 143B

value: transmitochondrial cybrid cell line 30


title: VEC_Input

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Illumina Casava v1.8.2 was used to align the reads. Reads mappable to multiple locations were discarded and at most one read per genomic location (defined by chromosome, start, end and strand) were kept for furthur analysis.
SICER v1.1 was used to call peaks and filter the reads with parameters: W=200, G=200, FDR=1e-3
H3K9ac ChIP-Seq wig files were generated based on the SICER-filtered reads, and rpkm value are used.
Normalized read counts (RPKM) were calculated at promoters (TSS±500bp)
Genome_build: mm9
Supplementary_files_format_and_content: Wig file scores represent RPKM values; wig files for H3K9ac were generated based on SICER-filtered reads and Wig files for input ChIP-Seq were generated based on preprocessed reads.
Supplementary_files_format_and_content: Read counts of H3K9ac are recorded in tab delimited text files; three columns represent gene name (Refseq), read count, and RPKM.

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The cells grow in DMEM medium containing 10% FBS and antibiotics

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: mouse embryonic fibroblasts

tag: passage

value: immortalized by 3T3 protocol

tag: chip antibody

tag: genotype


title: NormalHumanRNA-SeqC

city: New York

first: Peter

last: Sims

state: NEW YORK

address: 3960 Broadway blvd

institute: Columbia Medical Center

description: Poly(A) RNA library

data_processing:
For RNA-Seq: we received fastq files containing demultiplexed, single-end 100 base reads for each sample from the Columbia Sulzberger Genome Center.
Tophat 2 was used to map the reads to the mouse transcriptome
HTSeq to compute read counts for reads that mapped uniquely to the human transcriptome in the total exonic sequence for each gene
Genome_build: hg19

molecule: polyA RNA

source_name: normal brain

extract_protocol:
Standard RNA-Seq library preparation (TruSeq V2 RNA-Seq preparation).
Tumor and normal tissues were homogenized using a glass dounce homogenizer. Lysates were clarified and one half used for poly(A)+ RNA extraction and the other to generate and isolate ribosome-protected RNA fragments.

tag: tissue origin

value: normal brain


title: TumorHumanRNA-SeqA

description: Poly(A) RNA library

source_name: Tumor resection

value: Tumor


title: IGFBP7_LD3_KO

city: Toronto

first: Yutaka

last: Amemiya

state: ON

address: 2075 Bayview Ave.

country: Canada

institute: Sunnybrook Research Institute

data_processing:
Barcoded libraries are loaded into 6 individual flowchip lanes. 5500 Series Genetic Analyzers ICS v1.2.1 software used for color space calling.
.xsq files were converted to .csfasta and .qual files using XSQ_Tools
Paired .csfasta and .qual files  were converted to fastq format to be compatible with the aligner bowtie.
Genesifter v4.0 software with Bowtie WTS PE pipeline was used for the data mapping.
Reads within the fastq file were trimmed of any adaptor/primer sequence and then aligned to the mouse genome reference, mm9, using bowtie (bowtie-0.12.3/bowtie - (colorspace reads and index, allowing up to 2 mismatches)).  Following alignment of reads with bowtie, nucleotide variants were called with SamTools (samtools (0.1.15) pileup and varFilter, defaults setting except –D = 100000).
To identify differentially expressed genes, normalized expression values were calculated per gene by a Reads Per Million mapped reads (RPM) and a Reads Per Kilobase of exon per Million mapped read(RPKM)method.
Genome_build: Mus musculus B37.2
Supplementary_files_format_and_content: wig file and xlsx file include RPM and RPKM value for individual genes

source_name: Mammary gland

extract_protocol:
Breast epithelial cells were isolated from the lactating (day 3) inguinal mammary glands of the WT or Igfbp7-/- (KO) mice and lineage positive (Lin-, CD45+,CD35+, and Ter119+) cells were removed through magnetic cell separation strategy (StemCell Technologies, EasySep negative selection kit).
Total RNA was extracted from the Lin- breast cells using the TRIzol Reagent. Two rounds of Poly(A) RNA selection were carried out by using the MicroPoly(A) Purist kit.
RNA libraries were prepared for sequencing using SOLiD Total RNA-seq Kit

tag: genetic background

value: Mammary gland

tag: Stage

value: lactation day 3

value: IGFBP7 KO


title: IGFBP7_LD3_WT

value: wild type


title: PAR2_ChIP-Seq

city: Montreal

first: Jean-Sebastien

last: Joyal

state: Québec

address: 3175 Cote-Ste-Catherine

department: Paediatrics

institute: CHU Sainte-Justine

data_processing:
Reads are trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters are removed from the reads, and all reads are required to have a length of at least 32 b.p. Trimming and clipping are done using the Trimmomatic software
The filtered reads are aligned to a reference genome hg18. The alignment is done by lane of sequencing using the bwa software. BWA generates a Binary Alignment Map file (.bam). BAM files from different lanes of the same sample are merged into a single global BAM file using the picard software
Wiggle Track Format files are generated from the aligned reads using Homer
Peaks are called using the MACS software. The mfold parameter used in the model building step is estimated from a peak enrichment diagnosis run.
Genome_build: hg18 (NCBI36)
Supplementary_files_format_and_content: File generated by the MACS software including peak calls annotated in the BED file format using ChIP-Seq mini 2.01 suite for hg18 genome build.

source_name: Human embryonic kidney cells

growth_protocol: HEK 293 cells were cultured in DMEM 10% serum

extract_protocol:
Lysates were clarified from sonicated nuclei and PAR2-DNA complexes were isolated with PAR2 antibody. Precipitated ChIP DNA was isolated GFX PCR DNA and Gel Band purifcation kit from Qiagen
TruSeq ChIP Sample Preparation Kits

treatment_protocol: Cells were stimulated with peptide SLGKV

tag: passages


title: Input

first: Juhee

last: Jeong

state: New York

address: 345 E 24th St

department: Basic sciences and Craniofacial development

institute: New York University College of Dentistry

data_processing:
The sequence reads from each sample were aligned to the mouse genome (NCBI Build 37, mm9) using BWA algorithm (Li and Durbin, 2009)
The aligned sequence tags were extended in silico at the 3′-ends into 150-bp fragments, and the histograms of the fragment density along the genome were stored in BAR (Binary Analysis Results) files and visualized using Integrated Genome Browser (IGB) (Nicol et al., 2009)
H3K27ac peaks were identified using SICER peak finding algorithm (Zang et al., 2009) with the following parameters: window size = 200 bp, fragment size = 150 bp, gap size = 600 bp, E value = 1000, false discovery rate = 1E-10
Genome_build: NCBI Build 37, mm9

source_name: Maxillary arch Cells

extract_protocol:
Maxillary arches were dissected from 47 of E11.5 CD-1 wild type embryos in phosphate-buffered saline (PBS), and snap-frozen on dry ice
The tissue was then sent to Active Motif, Inc. (Carlsbad, CA) for HistonePathTM service, which included chromatin preparation, ChIP-seq for H3K27ac, and bioinformatics analysis of the sequencing result to identify H3K27ac-enriched genomic regions (peaks). 20 μg of the maxillary arch chromatin was used for ChIP with a rabbit polyclonal anti-H3K27Ac antibody (Active Motif, cat# AM 39133). Libraries for Illumina sequencing (Hi-Seq) were prepared from ChIP DNA and input chromatin as described (Labhart et al., 2005)

value: Maxillary arch

tag: developmental stage

tag: strain


title: H3K27ac_ChIPSeq

value: H3K27Ac antibody (Active Motif, cat# AM 39133)


title: TumorHumanRNA-SeqB

description: Poly(A) RNA library


title: TumorHumanRiboProfilingA

description: RNA footprint library

data_processing:
For ribosome profiling libraries: basecalls performed using Illumina CASAVA
Samples were demultiplexed and the adapter clipped with fastx_clipper.
Bowtie 2 was used to map rRNA; these were filtered out. Tophat was used to map reads to the mouse transcriptome.
HTSeq was used to compute read counts for reads that mapped uniquely to the  mouse transcriptome in the CDS, 5’-leader (5’-UTR), 3’-UTR, and total exonic sequence for each gene.
Genome_build: hg19

extract_protocol:
Ribosome footpring libraries were prepared by ligating a 3' adapter, reverse transcribing, and circularizing. The circles were then used for PCR amplification of the footprints.
Tumor and normal tissues were homogenized using a glass dounce homogenizer. Lysates were clarified and one half used for poly(A)+ RNA extraction and the other to generate and isolate ribosome-protected RNA fragments.


title: TumorHumanRiboProfilingB

description: RNA footprint library


title: NormalHumanRNA-SeqA

description: Poly(A) RNA library


title: NormalHumanRNA-SeqB

description: Poly(A) RNA library


title: Sj-F

city: Beijing

first: Xianyu

last: Piao

address: Dong Dan San Tiao 9

department: Institute of Pathogen Biology

country: China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Low quality and adapter sequences were removed from the Illumina reads by an in-house Perl script.
High-quality reads were mapped onto the S. japonicum genome of SGST, 17 (http://lifecenter.sgst.cn) by tophat v2.0.4.
Transcript sequences were assembled by Cufflinks v2.0.2. Then Cuffdiff was used to find significant changes of expression.
Functional annotation and classification were analysed by using KEGG and Gene Ontology databases.
Genome_build: S. japonicum genome of SGST, 17 (http://lifecenter.sgst.cn)
Supplementary_files_format_and_content: Sj_Total_Transcriptome

organism: Schistosoma japonicum

source_name: worm

extract_protocol:
Total RNA from the parasites was purified with Trizol reagent and contaminating gemomic DNA was removed by the RNase-Free DNase Set. Polyadenylated RNA  were isolated from total RNA.
The mRNA was interrupted into short fragments by adding fragmentation buffer as described (Illumina RNA-seq kit, part no. 1004898). Taking these short fragments as templates, random hexamer primers were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified and double strand cDNAs were end-repaired according to manufacturer-recommended protocols (https://icom.illumina.com/), and then were connected with Illumina adapters (Illumina RNA-seq kit, part no. 1004898). The fragments were first amplified by PCR. Purified cDNA fragments were pooled and indexed and were loaded onto one lane of an Illumina GA IIX flow cell. Pair-end 75 sequencing cycles were carried out.

tag: gender

value: female

value: 42 day mature adult parasite


title: 50% 3243G 143B

value: transmitochondrial cybrid cell line 50


title: Sj-M

value: male


title: NormalHumanRiboProfilingC

description: RNA footprint library


title: NormalHumanRiboProfilingB

description: RNA footprint library


title: NormalHumanRiboProfilingA

description: RNA footprint library


title: H3K27M_2_WingDiscs

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

description:
Ribosomal RNA-depleted total RNA.
Replicate 2

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8.
Reads were aligned to the Drosophila genome (UCSC dm3) and to gene annotations from Ensembl 74 using TopHat v2.0.9 (Trapnell et al., 2009), allowing uniquely mapping reads only and allowing up to two mismatches.
UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: Release 5 (UCSC dm3)
Supplementary_files_format_and_content: bigWig files; http://genome.ucsc.edu/goldenPath/help/bigWig.html

organism: Drosophila melanogaster

source_name: Wing discs, late third instar larvae, H3.3K27M-FLAG-HA

growth_protocol: Flies were raised at 29 degrees Celsius. Wing imaginal discs were dissected from late third instar larvae.

extract_protocol:
80-95 wing imaginal discs were dissected at room temperature in PBS and quickly transferred immediately to ice before snap freezing in liquid nitrogen. Discs were ground in RLT buffer and purified with RNeasy (Qiagen). RNA was then DNased and re-purified with RNeasy.
2 µg of total RNA was depleted of ribosomal RNA with the Ribo Zero kit (Epicentre #MRZG12324) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina #RS-122-2001).

treatment_protocol: Flag-HA tagged WT H3.3 and Flag-HA tagged H3.3K27M were expressed under the control of T80-Gal4 (Bloomington 1878).

value: wing imaginal discs

value: late third instar larvae


title: H3K27M_1_WingDiscs

description:
Ribosomal RNA-depleted total RNA.
Replicate 1


title: WT_2_WingDiscs

source_name: Wing discs, late third instar larvae, H3.3WT-FLAG-HA

value: wild type (T80-GAL4/UAS-H3.3WT-FLAG-HA)


title: WT_1_WingDiscs


title: Gata3-deleted DN2 sample #2

city: Pasadena

first: Ellen

last: Rothenberg

state: CA

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

description: Acutely Gata3 deleted DN2

data_processing:
Alignment was done using Tophat (v.2.0.6). command: tophat -p 7 --no-novel-juncs --library-type fr-unstranded -G Mus_musculus.NCBIM37.66.gtf
Abundance measurements were done using Cufflinks (v.2.1.1).   cufflinks (fpkm) command: cuffdiff -p7 --dispersion-method blind --library-type fr-unstranded --no-effective-length-correction --library-norm-method quartile -u -b mm9.fa --emit-count-tables Mus_musculus.NCBIM37.66.gtf
Genome_build: UCSC mm9, NCBI37
Supplementary_files_format_and_content: tab-delimited files with fpkm generated from Cufflinks

source_name: Pro-T cells

growth_protocol: Cells from the indicated genotypes of mice were obtained from fetal liver at day 13.5-14 of gestation.  Cells were grown on OP9-DL1 stromal monolayers with 5 ng/ml Flt3L and 5 ng/ml IL-7 for 4 days.

extract_protocol:
Total cell RNA from sorted populations (250,000 +/- 50,000 cells/sample) was extracted using Qiagen RNeasy DNA/RNA preparation kit
RNA-seq libraries were made after poly(A) selection of mRNA using the NEBNeXT poly(A) isolation module (E7490). Isolated mRNA was used to generate the library using the NEBNeXT Ultra RNA library preparation kit (E7530) reagents (New England Biolabs) following standard procedures

treatment_protocol: Cells were then harvested from OP9-DL1 monolayers, infected with indicated retroviral vectors for 4 hr, returned to OP9-DL1 monolayers overnight and sorted after ~18 hr further culture to purify DN2 (CD44+ c-Kit+ CD25+) cells that were either YFP+ or GFP+, except for sample 2 sorted as DN2 only.

value: In vitro differentiated DN2 cells

tag: viral transduction

value: retroviral Cre infected


title: Control empty vector-treated Gata3(f/f) sample

description: Gata3-floxed control without Cre

value: empty (GFP) retroviral infected


title: Gata3-deleted DN2 sample #1

description: Acutely Gata3 deleted DN2


title: Control Cre-treated B6 DN2 sample

description: B6 control (+/- cre)

value: retroviral Cre infected (about 50%; 50% uninfected)


title: CVL125 Ancestral sample bisulfite

status: Public on Sep 01 2014

city: Zürich

first: Christian

last: Heichinger

state: Zürich

address: Zollikerstrasse 107

department: Institute of Plant Biology

country: Switzerland

institute: Zürich University

description: DNA methylome of 25-day-old plants which did not undergo selection

data_processing:
SOCS V1.0 Alignment (Ondov et. al 2010, Bioinformatics, Volume 26, Issue 15, pages 1901-2), using recombinant genomes between Cvi/Ler Ecotypes
SOCS V1.0  Alignment gives the methylation statistics as number methylated and unmethylated cytosines per genomic position
Filter out positions which are covered by at least 4 and less than 50 reads
Apply Fisher's exact test to identify differentially methylated positions between the test samples (S2 samples) and the reference samples (A2 sample) for each genotype (_DMC4 Processed Data Files)
Genome_build: Arabidopsis TAIR10

organism: Arabidopsis thaliana

source_name: CVL125 Ancestral sample

growth_protocol: Sterilized seeds were initially sown on MA agar plates and stratified at 4°C for three days to ensure synchronised germination. After 12 days seedlings of CVL39 and CVL125 were transferred to pots in a general soil mix and grown under long-day conditions (23°C, 16 h light, 8 h dark). On day 25 the above ground parts of one individual were harvested in an Eppendorf tube containing glass beads and flash frozen in liquid nitrogen for DNA extraction.

extract_protocol: Using four micrograms of genomic DNA, a SOLIDTM fragment library for bisulfite genomic methylation profiling was prepared according to the manufacturer’s instructions Life technologiesTM with the following modifications. Both the P1-A and the P2-A adaptors consisted of 5-methyl-cytosines instead of cytosine, which ensures amplification of both the sense and antisense strands during emulsion PCR and avoids loss of unique molecules. After adaptor ligation and nick-translation, 500 ng of DNA was subjected to bisulfite conversion.

treatment_protocol: Library prepared DNA was subjected to bisulfite treatment to convert unmethylated cytosines to thymines for bisulfite sequencing.

value: Recombinant inbred line CVL125

value: Whole above ground plant

tag: age

value: 25 days


title: CVL125 Selected sample D1 bisulfite

description: DNA methylome of 25-day-old plants which experienced 5 generations of selection and 2 generations without selection

source_name: CVL125 Selected sample

tag: tissue


title: CVL39 Selected sample D6 bisulfite

source_name: CVL39 Selected sample

value: Recombinant inbred line CVL39


title: CVL125 Selected sample D6 bisulfite


title: CVL125 Selected sample D5 bisulfite


title: CVL39 Ancestral sample bisulfite

source_name: CVL39 Ancestral sample


title: CVL39 Selected sample D1 bisulfite


title: CVL39 Selected sample D5 bisulfite


title: NGS CVL39 S3_D5_86

description: Whole genome sequence 25-day-old plant -  selected line

data_processing:
For image analysis and base calling, we used the Illumina® RTA and CASAVA software version 1.8.2.
Reads were mapped to the recombinant CVL39 genome reference sequence with bowtie 2 using default settings.
Single nucleotide polymorphisms were determined by using the unified genotyper of the Genome Analysis Toolkit (GATK version 2.1.6)
To identify SNP positions between the two ancestral and seven selected CVL39 samples we used tools implemented in PoPoolation 2
The two results files given are the input file for the Fisher Exact Test in popoolation 2 (sync.txt) consisting of all SNP positions with allele frequencies (format A:T:C:G:N:del) identified by CASAVA and the output file (fet.txt), which contains -log10(P-values) of pairwise ancestral (A2) and seleted (D1,D5,D6) comparisons.
Genome_build: Arabidopsis TAIR10

source_name: Whole above ground plant tissue 25 days after sowing

growth_protocol: Sterilized seeds were initially sown on MA agar plates and stratified at 4°C for three days to ensure synchronised germination. After 12 days seedlings  were transferred to pots in a general soil mix and grown under long-day conditions (23°C, 16 h light, 8 h dark). On day 25 the above ground parts of one individual were harvested in an Eppendorf tube containing glass beads and flash frozen in liquid nitrogen for DNA extraction.

extract_protocol:
Genomic DNA was extracted from whole-plant tissue of individual 25-day-old plants with the Qiagen DNeasy kit (Qiagen).
The Low Sample (LS) protocol and reagents as described in the Illumina® TruSeq® DNA Sample Preparation Guide p55ff (Illumina Part # 15026486 Rev. C July 2012) was followed to prepare paired-end genomic sequencing libraries from 500 – 1000 ng genomic DNA. Sequencing was performed on an Illumina Highseq 2000 instrument. For the majority of samples, two libraries were sequenced independently (4 raw files given).

tag: sample


title: NGS CVL39 S3_D5_68


title: NGS CVL39 S3_D5_57


title: Frontal lobe

city: Copenhagen

first: Mads

last: Bak

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description: Clontech polyA+ RNA (cat.# 636165)

data_processing:
Reads were trimmed for adapter sequence and aligned to hg18 using Bowtie version 0.12.7. Alignment files of replicate sequencing runs were merged and converted to BED format.
Duplicate reads were removed from the final BED files.
Genome_build: hg18
Supplementary_files_format_and_content: bed files containing positions and strand of aligned reads

source_name: Frontal lobe

extract_protocol:
Commercially prepared polyA RNA.
300 ng poly(A) RNA was reverse transcribed using a random hexamer modified with an adapter-sequence at the 3' end. Second strand cDNA was generated using Rnase H and DNA polymerase I. The resulting double stranded cDNA was end polished and 3' A overhangs were added. Sequencing adapter were ligated to the doublestranded cDNA and the library was amplified by 16 cycles of PCR.

value: Adult

value: Brain

tag: tissue region

value: Frontal lobe


title: Hippocampus

description: Clontech polyA+ RNA (cat.# 636134)

source_name: Hippocampus

value: Hippocampus


title: NGS CVL39 S3_D1_43


title: NGS CVL39 S3_D1_42


title: NGS CVL39 A3_2

description: Whole genome sequence 25-day-old plant - ancestral line


title: NGS CVL39 A3_1


title: strain9_x_strain160-Total_RNA

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
base calling: Casava1.8
read alignment, RNA-seq data: TopHat 2.0.8
read alignment, ChIP-seq data: Bowtie 0.12.7
bedgraph track generation: custom-written python script
Genome_build: droVir2
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million)

organism: Drosophila virilis

extract_protocol: RNA was extracted from 30 flies using standard ribosol RNA extraction. Samples were then rRNA depleted using Ribozero Kit, and DNAse treated prior to library preparation and sequencing.

value: Strain9 x Strain160


title: strain9-Total_RNA


title: strain9_x_strain160-Input-Rep2

extract_protocol:
Flies were put on yeast for 2-3 days and 100 ovaries per IP condition were dissected. Ovaries were fixed for 10 min at RT using 1% paraformaldehyde (PFA) followed by 5 min quenching at RT by directly adding glycine (final concentration 25mM) and 3 washes in PBS. Ovaries were slightly dounced in Farnham Buffer (5mM HEPES pH8.0; 85mM KCl; 0.5% NP-40/Igepal; NaCl Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM), palleted, followed by strong douncing in RIPA Buffer (20mM Tris pH7.4; 150mM; 1% NP-40/Igepal; 0.5% Sodium Deoxycholate; 0.1% SDS; Protease Inhibitor Cocktail; NaF 10mM; Na3VO4 0.2mM) prior to sonication using a Bioruptor from Diagenode on medium power for 20 cycles (30sec ON, 30sec OFF). Samples were then centrifuged, supernatant collected and pre-cleared for 2h at 4ºC using Dynabeads Protein G (Invitrogen). Antibodies were conjugated to Dynabeads Protein G for 2h at 4ºC. A sample of 5% of the pre-cleared supernatant was saved as input control fraction and the rest was incubated with the antibody-conjugated beads for 2h at 4ºC. The beads were washed 5 times at 4ºC using LiCl IP Buffer (10mM Tris ph7.5; 500mM LiCL; 1% NP-40/Igepal; 1% Sodium Deoxycholate), once with TE. Samples were digested in Proteinase K Buffer (200mM Tris ph7.4; 25mM EDTA; 300mM NaCL; 2% SDS) with 100µg of proteinase K. Samples for 3h at 55ºC and revers-crosslinked overnight at 65ºC. DNA was extracted following standard phenol-chloroform extraction and concentration was measured by Qubit.
Libraries were generated following Illumina's DNA Sample Prep Kit protocol

tag: chip-antibody

value: none, sonicated input


title: strain160_x_strain9_Total_RNA

value: Strain160 x Strain9


title: strain9_x_strain160-H3K9me3-Rep1


title: strain160-Total_RNA


title: strain9_x_strain160-H3K9me3-Rep2


title: Temporal lobe

description: Clontech polyA+ RNA (cat.# 636168)

source_name: Temporal lobe

value: Temporal lobe


title: strain9-Pol2-Rep2


title: strain9_x_strain160-Input-Rep1


title: NGS CVL39 S3_D6_23


title: strain9-Input-Rep2


title: strain9-Pol2-Rep1


title: NGS CVL39 S3_D6_79


title: strain160_x_strain9-Input-Rep2


title: strain9-H3K9me3-Rep2


title: strain9-Input-Rep1


title: strain160_x_strain9-H3K9me3-Rep1


title: strain160_x_strain9-H3K9me3-Rep2


title: strain160-Input-Rep1


title: strain160-Pol2-Rep1


title: strain160-Input-Rep2


title: Chimera_F19b2

city: Portland

first: Branden

last: Tarlow

state: OR

address: 3181 SW Sam Jackson Park Road

department: Pediatrics

institute: Oregon Health & Science University

data_processing:
Base calling performed by CASAVA
Alignment was performed with Bowtie version 0.12.7 set to allow no mismatches.  I trimmed the first 4 bases from each read and aligned to the next 44 bases.  Only tags with unique alignments were counted.
Tags counts were compiled into a matrix using custom R-scripts
Genome_build: A custom transcriptome of 42 NCBI Refseq genes was used
Supplementary_files_format_and_content: tab-delimited text files include unique mapped reads for each sample and gene

organism:
Homo sapiens
Mus musculus

source_name: Humanized mouse liver

extract_protocol:
Liver were homogenized in trizol.  The aqueous layer was alcohol precipitated and cleaned up on Qiagen Rneasy Mini columns with on column DNAse digestion
2ug total RNA was prepared with the Illumina Truseq RNA sample prep kit v2

value: Liver tissue

tag: injury


title: Chimera_F19b3


title: Chimera_DDC_3567

source_name: Humanized mouse liver + DDC injury

value: ddc


title: Chimera_DDC_1794


title: Chimera_DDC_1431


title: Chimera_30012


title: strain160_x_strain9-Input-Rep1


title: strain9-H3K9me3-Rep1


title: U3-RAP-RNA-FA-140503

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

description: RAP-RNA using probes targeting U3 in cells crosslinked with formaldehyde

data_processing:
Align to repetitive mm9 RNA sequences from RefSeq and RepeatMasker (RNA only)
Align to mm9 genome with Bowtie2-2.1.0 (DNA) or with Tophat-2.0.8 (RNA)
Remove duplicate reads with Picard (DNA only)
Remove reads with MAPQ < 30
Connect paired-end reads to fragments (DNA only)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig: Coverage at 5bp resolution across genome

growth_protocol: Male ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).

extract_protocol:
custom strand-specific RNA-Sequencing (see Engreitz et al 2013)
RNA Antisense Purification (RAP) followed by DNA or RNA sequencing was performed as described in Engreitz et al. 2014

tag: cell line

tag: cell type

value: embryonic stem cell

tag: experiment type

value: RAP-RNA

tag: drug

tag: crosslinking

value: Formaldehyde

value: male


title: Chimera_30141


title: Xist-RAP-RNA-FADSG-140503

description: RAP-RNA using probes targeting Xist in cells crosslinked with formaldehyde-DSG

value: Formaldehyde-DSG


title: U12-RAP-RNA-FA-140503

description: RAP-RNA using probes targeting U12 in cells crosslinked with formaldehyde


title: Input-RNA-FADSG-140503

description: Input RNA from cells crosslinked with formaldehyde-DSG

value: Input RNA


title: strain160-H3K9me3-Rep2


title: Snora73a-RAP-RNA-noAMT-140425

description: RAP-RNA using probes targeting Snora73a in cells mock-crosslinked without AMT (UV only)

value: -AMT


title: Malat1-RAP-RNA-FA-140503

description: RAP-RNA using probes targeting Malat1 in cells crosslinked with formaldehyde


title: Snora73a-RAP-RNA-AMT-140425

description: RAP-RNA using probes targeting Snora73a in cells crosslinked with AMT

value: +AMT


title: Input-RNA-FA-140503

description: Input RNA from cells crosslinked with formaldehyde


title: U3-RAP-RNA-AMT-140425

description: RAP-RNA using probes targeting U3 in cells crosslinked with AMT


title: strain160-Pol2-Rep2


title: strain160-H3K9me3-Rep1


title: U3-RAP-RNA-noAMT-140425

description: RAP-RNA using probes targeting U3 in cells mock-crosslinked without AMT (UV only)


title: Input-RNA-noAMT-140425

description: Input RNA from cells mock-crosslinked without AMT (UV only)


title: Input-RNA-AMT-140425

description: Input RNA from cells crosslinked with AMT


title: Chimera_F19b1


title: LDP-microbiota recipient (ST8)

city: Buffalo

first: Jiho

last: Sohn

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

description: processed data file: CoxBlaser_NYGC_femaleSamples_count_matrix.txt

data_processing:
Alignment to the genome build mm10 with STAR (Dobin et al. 2012) v.2.3.0e (female samples) and v.2.3.1x (male samples)
Quantification of the UCSC genes with HTSeq-count v0.5.3p9 (female samples) or featureCounts v1.4.3-p1 (male samples)
Differential expression analysis performed with DESeq (Bioconductor)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited .txt files report counts

source_name: Liver

growth_protocol: C57BL6 mice were weaned at 4 weeks of age onto normal chow, then switched to a high fat diet (45% kcal from fat) at 6 weeks of age.  Or germ-free swiss webster mice were conventionalized with control or LDP-microbiota at 3 weeks of age, and fed a high fat diet (45% kcal from fat).  Livers were collected at 8 weeks of age

extract_protocol:
RNeasy Mini Kit (Qiagen, Valencia CA)
RNA-seq libraries were generated using the TruSeq v2 RNA sample prep

treatment_protocol: Control mice did not receive antibiotics, LDP mice received low-dose penicillin from birth.  Microbiota from control and LDP mice were used to then convetionalized germ-free swiss-webster mice, which did not receive further antibiotic treatment.

value: 8 weeks

value: Female

value: Germ-free Swiss Webster

tag: treatment

value: conventionalized with LDP-microbiota

tag: diet

value: D12451:45% kCAL from fat

value: liver


title: LDP-microbiota recipient (ST5)


title: LDP-microbiota recipient (ST2)


title: Chimera_30154


title: Control-microbiota recipient (CT7)


title: Snora73a-RAP-RNA-FA-140503

description: RAP-RNA using probes targeting Snora73a in cells crosslinked with formaldehyde


title: Control-microbiota recipient (CT3)


title: S_JNP_A_M

city: Seoul

first: WonCheoul

last: Park

state: Gwanak-gu

address: 599 Gwanangno

country: South Korea

institute: Seoul national university

description: Sample 6

data_processing:
Sequences reads were mapped to the Sscrofa10.2 reference genome using Tophat. Briefly, the reference genome was indexed using “Tophat index
reads were counted using HTseq (v0.5.3p3).
Genome_build: Sscrofa10.2 (http://www.ncbi.nlm.nih.gov/assembly/304498/)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Sus scrofa

source_name: Korean native_Muscle

extract_protocol:
Pig tissues were isolated, flash frozen on dry ice, and 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Korean native pig

value: muscle


title: S_JNP_A_F

description: Sample 4

source_name: Korean native_Fat

value: fat


title: S_JNP_A_L

description: Sample 5

source_name: Korean native_Liver


title: Control-microbiota recipient (CT1)

tag: strain


title: LDP-Female (ds54)

tag: gender

value: LDP


title: S_Berk_A_L

description: Sample 2

value: Berkshire


title: S_Berk_A_F

description: Sample 1


title: LDP-Female (ds39)


title: LDP-Female (ds52)


title: CTG_pH8.3

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

data_processing:
We aligned sequenced RNA fragments against release 6.1, ME49 strain of Toxoplasma gondii using TopHat-1.2. We set minimum intron size at 30 bp and maximum at 1500 bp, encompassing >98% of predicted introns. We assigned aligned reads to predicted gene models using BEDTools and generate a table describing how many reads are aligned to each gene.
Genome_build: TgME49-6.1 Available from http://www.toxodb.org/common/downloads/release-6.1/Tgondii/TgondiiME49Genomic_ToxoDB-6.1.fasta
Supplementary_files_format_and_content: Tab-delimited table of RNA fragments per gene in each sample.

organism: Toxoplasma gondii

source_name: Parasites grown in HFF cells

extract_protocol:
RNA was extracted using Invitrogen TRIzol® Reagent (cat#15596018), followed by genomic DNA removal and cleaning using Qiagen RNase-Free DNase Set kit (cat#79254) and Qiagen Mini RNeasy™ kit (cat#74104). Agilent 2100 Bioanalyzer was used to assess the integrity of the RNA samples. Only RNA samples having RNA Integrity Number between 9-10 were used.
Ambion® MicroPoly(A)Purist™ Kit (cat#AM1919) was used for enrichment of transcripts.  The SOLiD® Total RNA-Seq Kit (cat#4445374) was used to construct template cDNA for RNA-Seq following the protocol recommended by Applied Biosystems. Briefly, mRNA was fragmented using chemical hydrolysis followed by ligation with strand specific adapters and reverse transcript to generate cDNA.  The cDNA fragments, 150 to 250 bp in size, were subsequently isolated by electrophoresis in 6% Urea-TBE acrylamide gel. The isolated cDNA was amplified through 15 amplification cycles to produce the required number of templates for the SOLiD™ EZ Bead™ system, which was used to generate template bead library for the ligation base sequencing by the SOLiD™4 instrument.

value: CTG

tag: developmental stage

value: in vitro bradyzoite pH 8

tag: growth time

value: three days


title: Control-Female (dc32)

tag: age

value: Control

tag: tissue


title: CTG_pH8.1


title: CTG_pH8.2


title: CTG_pH7.2

value: in vitro tachyzoite pH 7


title: Control-Male (dc6)

description: processed data file: CoxBlaser_NYGC_maleSamples_count_matrix.txt

value: Male


title: CTG_pH7.3


title: LDP-Male (ds11)

value: 8 weeks


title: Control-Female (dc29)

value: Female


title: PLK_pH8.3

value: PLK


title: Control-Male (dc7)


title: LDP-Male (ds10)


title: Control-Male (dc5)


title: S_Berk_A_M

description: Sample 3


title: PLK_pH8.1


title: PLK_pH7.2


title: CTG_pH7.1


title: LDP-Male (ds8)


title: Input-DNA-130531

description: Input DNA in cells crosslinked with formaldehyde-DSG

data_processing:
Library strategy: RAP-Seq
Align to repetitive mm9 RNA sequences from RefSeq and RepeatMasker (RNA only)
Align to mm9 genome with Bowtie2-2.1.0 (DNA) or with Tophat-2.0.8 (RNA)
Remove duplicate reads with Picard (DNA only)
Remove reads with MAPQ < 30
Connect paired-end reads to fragments (DNA only)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig: Coverage at 5bp resolution across genome

extract_protocol:
NEBNext Ultra Library Prep Kit
RNA Antisense Purification (RAP) followed by DNA or RNA sequencing was performed as described in Engreitz et al. 2014

value: embryonic stem cell

value: Input DNA

value: Formaldehyde-DSG

value: male


title: PLK_pH7.3


title: RH_pH8.2

value: RH

value: two days


title: Input-DNA-140105


title: Control-Female (dc30)

value: D12451:45% kCAL from fat

value: liver


title: PLK_pH7.1


title: Hdac2-RAP-DNA-140105

description: RAP-DNA using probes targeting Hdac2 in cells crosslinked with formaldehyde-DSG

value: RAP-DNA


title: Xist-RAP-DNA-130531

description: RAP-DNA using probes targeting Xist in cells crosslinked with formaldehyde-DSG


title: RH_pH8.1

value: in vitro bradyzoite pH 8


title: RH_pH8.3


title: PLK_pH8.2

value: PLk

value: three days


title: RH_pH7.3

value: in vitro tachyzoite pH 7


title: RH_pH7.2


title: RH_pH7.1


title: Input-DNA-DMSO-140216

description: Input DNA from cells treated with DMSO (control) for 1 hour and crosslinked with formaldehyde-DSG

value: DMSO


title: Input-DNA-Flavopiridol-140216

description: Input DNA from cells treated with flavopiridol (a transcription inhibitor) for 1 hour and crosslinked with formaldehyde-DSG

value: Flavopiridol


title: Malat1-DNA-DMSO-140120

description: RAP-DNA using probes targeting Malat in  cells treated with DMSO (control) for 1 hour and crosslinked with formaldehyde-DSG


title: 24 TOR kinase inhibition

city: Geneva 4

first: Jean-David

last: Rochaix

address: 30, quai Ernest-Ansermet

department: Department of Molecular biology and Plant Biology

institute: University of geneva

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
RNAseq reads were mapped to C.reinhardtii 169 AU10.2 release with TopHat v.1.3.1.
The table of counts with the number of reads mapping to genes features of the C.reinhardtii 169 AU10.2 release reference was prepared with HTSeq v0.5.3p9
Normalization and differential expression detrmination  was done with the R/Bionconductor package edgeR v3.0.8
Genome_build: Creinhardtii 169 AU10.2
Supplementary_files_format_and_content: tab-delimited text file containing normalized gene counts values for each sample

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii

growth_protocol: Cells from the A31 and DCH16 strain were grown in Tris-acetate medium at 25°C under light (60-40 μmol m-2 s-1) / dim light (10 μmol m-2 s-1) or in the dark.

extract_protocol:
RNA was extracted with fresh TRIzol reagent (Life Technologies) and further purified with another acid-phenol:chloroform (with indole-3-acetic acid, 125:24:1), pH 4.5, extraction (Life Technologies).
Libraries were prepared according to Illumina's instructions, Illumina TruSeq protocol up to the post ligation purification. DNA fragments enrichment was done with the AccuPrime Taq DNA Polymerase, High Fidelity from Invitrogen.

treatment_protocol: CplP1 depletion was induced through addition of vitamin B12 and thiamine to the growth medium. In other experiments rapamycin was added.

tag: time

value: rapamycin


title: U1-RAP-DNA-Flavopiridol-140216

description: RAP-DNA using probes targeting U1 in cells treated with flavopiridol (a transcription inhibitor) for 1 hour and crosslinked with formaldehyde-DSG


title: Malat1-DNA-Flavopiridol-140120

description: RAP-DNA using probes targeting Malat1 in cells treated with flavopiridol (a transcription inhibitor) for 1 hour and crosslinked with formaldehyde-DSG


title: 8 TOR kinase inhibition


title: 16bis TOR kinase inhibition


title: Input-DNA-DMSO-140120


title: 15 TOR kinase inhibition


title: Hdac2-RAP-RNA-131124

description: RAP-RNA using probes targeting Hdac2 in cells crosslinked with formaldehyde-DSG

value: RAP-RNA


title: 7bis TOR kinase inhibition


title: C7 TOR kinase inhibition


title: Input-DNA-Flavopiridol-140120

value: embryonic stem cell


title: 23 TOR kinase inhibition


title: Input-RNA-131124

description: Input RNA from cells crosslinked with formaldehyde-DSG

value: Input RNA


title: Malat1-RAP-RNA-140203

description: RAP-RNA using probes targeting Malat1 in cells crosslinked with formaldehyde-DSG

value: Formaldehyde-DSG


title: U1-RAP-RNA-NonCrosslinked-140203

description: RAP-RNA using probes targeting U1 in non-crosslinked cells

value: male


title: U1-RAP-DNA-DMSO-140216

description: RAP-DNA using probes targeting U1 in  cells treated with DMSO (control) for 1 hour and crosslinked with formaldehyde-DSG


title: Malat1-RAP-RNA-131124


title: C4 TOR kinase inhibition


title: C22 TOR kinase inhibition


title: C19 TOR kinase inhibition


title: U1-RAP-RNA-140203

description: RAP-RNA using probes targeting U1 in cells crosslinked with formaldehyde-DSG


title: Input-RNA-140203


title: Input-RNA-Flavopiridol

description: Input RNA from cells treated with flavopiridol (a transcription inhibitor) for 1 hour and crosslinked with formaldehyde-DSG

source_name: Input-RNA-Flavopiridol


title: Input-RNA-NonCrosslinked-140203

description: Input RNA from non-crosslinked cells


title: C16 TOR kinase inhibition


title: C13 TOR kinase inhibition


title: C1 TOR kinase inhibition


title: A7 TOR kinase inhibition


title: C25 TOR kinase inhibition


title: C10 TOR kinase inhibition


title: Malat1-RAP-RNA-noAMT-140203

description: RAP-RNA using probes targeting Malat1 in cells mock-crosslinked without AMT (UV only)

value: -AMT


title: Input-RNA-DMSO

description: Input RNA from cells treated with DMSO (control) for 1 hour and crosslinked with formaldehyde-DSG

source_name: Input-RNA-DMSO


title: Input-RNA-noAMT-140203

description: Input RNA from cells mock-crosslinked without AMT (UV only)


title: A4 TOR kinase inhibition


title: Input-RNA-AMT-140203

description: Input RNA from cells crosslinked with AMT

value: +AMT


title: A25 TOR kinase inhibition


title: Malat1-RAP-RNA-AMT-140203

description: RAP-RNA using probes targeting Malat1 in cells crosslinked with AMT


title: Input-RNA-noAMT-131108


title: A22 TOR kinase inhibition


title: A16 TOR kinase inhibition


title: A13 TOR kinase inhibition


title: U1-RAP-RNA-noAMT-131108

description: RAP-RNA using probes targeting U1 in cells mock-crosslinked without AMT (UV only)


title: A10 TOR kinase inhibition


title: Input-RNA-AMT-131108


title: Input-DNA-130928

description: Input DNA in cells crosslinked with formaldehyde-DSG

value: Input DNA


title: U1-RAP-RNA-AMT-131108

description: RAP-RNA using probes targeting U1 in cells crosslinked with AMT


title: C7 ClpP1 depletion

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
RNAseq reads were mapped to C.reinhardtii 169 AU10.2 release with TopHat v.1.3.1.
The table of counts with the number of reads mapping to genes features of the C.reinhardtii 169 AU10.2 release reference was prepared with HTSeq v0.5.3p9
Normalization and differential expression detrmination  was done with the R/Bionconductor package edgeR v3.0.8
Genome_build: Creinhardtii 169 AU10.2
Supplementary_files_format_and_content: tab-delimited text file containing normalized gene counts values for each sample (see ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Creinhardtii/annotation/)

treatment_protocol: CplP1 depletion was induced through addition of vitamin B12 and thiamine to the growth medium.

value: vitamin B12 and thiamine


title: C25 ClpP1 depletion


title: C22 ClpP1 depletion


title: A1 TOR kinase inhibition


title: nTreg_rep2

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

country: United Kingdom

institute: University of Warwick

description: Biological replicate 2 of 2

data_processing: Data is mapped to mm9 genome assembly using Tophat with parameters: -r 328 -butterfly-search-solexal1.3-quals

source_name: Mouse nTreg cells

growth_protocol: Spleens of C57BL/6 mice aged from 7 weeks to 4 months were removed and softly homogenized through a nylon mesh. The medium used throughout the cell cultures was IMDM supplemented with 10 % FCS, 2 mM L-glutamine, penicillin, streptomycin and 50 mM b-mercaptoethanol. Cells were washed twice and purified using Ficoll density gradient centrifugation. CD4+CD62L+ cells were isolated by a two-step MACS purification using the CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into 24 well plates that had been coated with a mix of anti-CD3 (1 mg/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 mg/ml, clone 37.51, eBioscience) antibodies overnight, at a density of 250,000 cells/ml and a total volume of 2 ml. The following cytokines and antibodies, respectively, were added to the cultures: Th1, recombinant murine IL-12 (5 ng/ml, R&D Systems), Th2, recombinant murine IL-4 (10 ng/ml, R&D Systems) and neutralizing IFN-g (5 mg/ml, Sigma), Th17, recombinant human IL-6 (30 ng/ml, Immunotools), recombinant human TGF-beta (5 ng/ml, Sigma) and recombinant murine mIL-1beta (Immunotools). Cells were cultured for 4 to 5 days at 37C in 5 % CO2. After this, cells were taken away from the activation stimulus, diluted 1:2 in fresh medium containing the same cytokine concentration as before. RNA was prepared after 3 days resting time. Cell preparation for Treg cells was the same as for Th cells, with the following differences. The medium used throughout was RPMI supplemented with 10 % FCS, gentamycin and 10 mM b-mercaptoethanol.  CD4+CD25- cells were isolated by negative depletion of lymphocytes stained with FITC-conjugated anti-CD8, anti-CD11b, anti-CD11c, anti-CD19, anti-Ly6G and anti-CD25 by MACS. For the generation of iTregs, cells were seeded out in anti-CD3e (0.6 ug/ml) coated plates at 200.000 cells per well of a 96-well plate and cultured in medium containing 20 ng/mL recombinant IL-2, anti-CD28 (4ug/ml) and rhTGF-beta (50ng/mL) for four days after which the RNA was prepared (no resting phase). For nTregs, the depletion step for CD4+ enrichment was followed by positive selection for CD25.

extract_protocol: Illumina ChIP-seq sample prep

value: 7 weeks to 4 months

value: spleen

value: Natural T regulatory cell (nTreg)

tag: average fragment length

value: 400bp (standard deviation:20bp)


title: nTreg_rep1

description: Biological replicate 1 of 2


title: Th17

description: Biological replicate 1 of 1

data_processing: Data is mapped to mm9 genome assembly using Tophat with parameters:  -butterfly-search-solexal1.3-quals

source_name: Mouse Th17 cells

value: T helper cell type 17 (Th17)


title: iTreg_rep2

description: Biological replicate 2 of 2

source_name: Mouse iTreg cells

value: Induced T regulatory cell (iTreg)


title: iTreg_rep1

description: Biological replicate 1 of 2


title: C16 ClpP1 depletion


title: C13 ClpP1 depletion


title: A19 TOR kinase inhibition


title: Th1_rep2

description: Biological replicate 2 of 2

source_name: Mouse Th1 cells

value: T helper cell type 1 (Th1)


title: Th1_rep1

description: Biological replicate 1 of 2


title: C1 ClpP1 depletion


title: Naive_rep2

description: Biological replicate 2 of 2

source_name: Mouse Naive CD4+ T cells

value: Naive CD4+ T cell


title: C10 ClpP1 depletion


title: Naive_rep1

description: Biological replicate 1 of 2


title: A7 ClpP1 depletion


title: YCCEL-1

city: Goyaongsi

first: Charny

state: Gyeonggi-do

address: 323 Ilsan-ro,

institute: National Cancer Center

data_processing:
Mapped to hg19 using Tophat2.0.12 with option --no-coverage-search --mate-inner-dist 200 --mate-std-dev 100 --no-mixed -p 20 --b2-fast
FPKM quantified by Cufflinks 2.2.12 with option --upper-quartile-norm -u --trim-3-avgcov-thresh 7
Genome_build: hg19
Supplementary_files_format_and_content: FPKM txt file for each samples

source_name: human gastric carcinoma_naturally infected with EBV

growth_protocol: Cells were cultured in RPMI 1640 media supplemented with 10% fetal calf serum.  Where necessary, EBV-negativ GC cells were in vitro infected with AKATA EBV strain which was tagged with enhanced green fluorescence protein (EGFP). Infected cells were sorted by flow cytometry and plated in the same culture media. Cells in log phase growth were subjected to RNA isolation

extract_protocol:
Standard protocol of RNAeasy kit (Qiagen) was used
The Illumina (IL) library libraries were prepared using mRNA-Seq 8 sample prep kit (Illumina Inc. San Diego, USA) according to the manufacturer’s protocol. For HTR library preparations, mRNA isolation with both Dynabeads (Invitrogen) and Sera-Mag oligo dT magnetic beads (Thermo Scientific, Cat. # 3815-2103-010150) were performed based on the Dynabeads mRNA direct kit (Invitrogen) protocol with minor adjustments.
All samples were purified and multiplexed using eight of the three-nucleotide barcoded adapters, randomly assigned to three different pools with eight samples per pool.

value: human gastric cancer cell line with natural EBV infection

tag: ebv infection status

value: EBV(+); naturally infected with EBV


title: Malat1-RAP-DNA-130928

description: RAP-DNA using probes targeting Malat1 in cells crosslinked with formaldehyde-DSG

tag: cell line

value: embryonic stem cell

value: RAP-DNA


title: A4 ClpP1 depletion


title: SNU-719

tag: cell type


title: SNU-638-EBV

source_name: human gastric carcinoma_experimentally infected with EBV

value: SNU-638 in vitro infected with EBV

value: EBV(+); experimentally infected with EBV


title: A22 ClpP1 depletion


title: SNU-638

source_name: human gastric carcinoma

value: human gastric cancer cell line

value: EBV(-)


title: C19 ClpP1 depletion

value: vitamin B12 and thiamine


title: A19 ClpP1 depletion


title: SNU-484


title: C4 ClpP1 depletion


title: A13 ClpP1 depletion


title: NUGC3-EBV

value: NUGC3 in vitro infected with EBV


title: A16 ClpP1 depletion


title: NCC-24


title: A10 ClpP1 depletion


title: A1 ClpP1 depletion


title: NUGC3


title: Normal_huLiver

source_name: Normal human liver biopsy

value: Liver tissue

tag: injury


title: TKO_Input_ChIPseq_2

city: Chicago

first: Relja

last: Popovic

address: 303 East Superior Street

institute: Northwestern University

data_processing:
Basecalls were performed using Casava version 1.7
All samples were aligned to human genome (hg19) using bowtie 1
Several reads mapping to the same exact location were considered amplification artifacts and were excluded from the analysis.
The read density tracks were made using the HOMER tool (using default parameters), where each sample was normalized into 10 million reads.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: Multiple myeloma

growth_protocol: Cells were grown in RPMI1640 supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed according to the manufacture's protocol (ChIP kit, Millipore) with the following modifications: 107 cells were used per sample. After cell lysis, extracts were subjected to sonication with a 60 Sonic Dismembrator (Fisher Scientific) at 4°C for 20 cycles, cycling ON for 20 seconds and OFF for 1 minute at 4.5 power leading to a DNA average size of 200 bp. Immunoprecipitations were performed overnight at 4°C using 5 μg of antibody. Imunoprecipitated chromatin was extracted using QIAquick PCR Purification Kit (QIAGEN).
10 ng of input and ChIP material was processed using the Illumina kit (IP-102-1001)

value: Multiple myeloma

tag: phenotype

value: Low levels of MMSET

tag: passage

tag: chip antibody

tag: antibody lot #


title: TKO_H3K36me2_ChIPseq_2

value: Millipore 07-369


title: TKO_H3K36me3_ChIPseq_2

value: Abcam ab9050


title: NTKO_H3K36me3_ChIPseq_2

value: High levels of MMSET


title: NTKO_H3K27me3_ChIPseq_2

value: Millipore 07-449


title: TKO_H3K27me3_ChIPseq_2


title: TKO_H3K36me3_ChIPseq_1


title: NTKO_H3K36me2_ChIPseq_2


title: A25 ClpP1 depletion

tag: treatment


title: TKO_H3K36me2_ChIPseq_1


title: TKO_Input_ChIPseq_1


title: NTKO_Input_ChIPseq_2


title: NTKO_H3K36me3_ChIPseq_1


title: NTKO_H3K36me2_ChIPseq_1


title: NTKO_Input_ChIPseq_1


title: F1_CastxB6_R3

city: St. Louis

first: Joseph

middle: C

last: Corbo

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description: Index: ATGACAG

data_processing:
Reads were filtered and trimmed with Trim Galore! v0.2.6.
Reads were aligned with Bowtie v0.12.9 to a strain-specific reference transcriptome (for F0 data) or a hybrid reference transcriptome (for F1 data). Transcriptomes were constructed using the mouse_strain_transcriptomes.sh script within the MMSEQ package. The reference transcriptomes were based on the Ensembl Release 67 cDNA files and the Wellcome Trust Mouse Genomes Project Release 2 VCF files (which use mm9/NCBI37 as the reference genome) based on November 2012 HiSeq 2x100 bp sequencing with 39x coverage of the Cast/EiJ genome.
MMSEQ v1.0.0 beta was used to estimate gene expression levels for the F0 samples and allele-specific gene expression levels for the F1 samples.
MMDIFF was used to determine parent-of-origin effects.
MMDIFF was used to determine cis and trans effects.
Genome_build: mm9
Supplementary_files_format_and_content: Results of MMSEQ and MMDIFF as tab-delimited text files

source_name: Retina

extract_protocol:
Retinas were dissected in cold sterile HBSS with calcium and magnesium (Gibco) and stored at -80 ⁰C until use. Total RNA was extracted using TRIzol (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen) with on-column DNaseI digestion (Qiagen).
Polyadenylated mRNA was captured from total RNA using Dynabeads (Invitrogen). The mRNA was fragmented and reverse-transcribed to double-stranded cDNA using random hexamers. The cDNA was blunt-ended and 3’-adenylated before ligation to sequencing adapters. Ligated fragments were amplified for 12 cycles with primers to incorporate unique sample barcodes. Libraries were subjected to paired-end 2x101 bp sequencing on the Illumina HiSeq 2000. One lane of sequencing was conducted for all F0 and F1 samples, and a second lane of sequencing was conducted for the F1 samples only.

value: retina

tag: strain

value: F1 hybrid of Cast/EiJ (male) x C57BL/6J (female)

value: 8 weeks

value: Male


title: NTKO_H3K27me3_ChIPseq_1


title: TKO_Input_ChIPseq_1

description: Sample 7

data_processing:
Basecalls were performed using Casava version 1.8
All samples were aligned to human genome (hg18) using BWA
Several reads mapping to the same exact location were considered amplification artifacts and were excluded from the analysis. Each ChIP-seq data set was normalized to its corresponding input lane.
ChIP-seq peak calling, genomic annotation of peaks, target genes and comparison of EZH2 peaks in TKO and NTKO cells were performed using ChIPseeqer. The default parameters were used for peak detection (i.e., 2-fold difference between ChIP and INPUT signal, and 10-15 statistical significance of the detected peaks).
Genome_build: hg18
Supplementary_files_format_and_content: Processed files (i.e., peak files) contain the following columns- Chromosome name, the first (genomic) coordinate of the peak, the second (genomic) coordinate of the peak, average log p-value of the nucleotides in the normalized peak region, score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available), the position of the maximum height of the peak, the maximum peak height (in reads), the relative position of the maximum height of the peak, the size of the peak (in bp), the middle position of the peak, the distance of the maximum height from the middle of the peak

extract_protocol:
For chromatin immunoprecipitation crosslinked cells were resuspended in nuclei lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 0.2% NP-40, protease inhibitors) for ten minutes, centrifuged, washed and resuspended in SZAK RIPA buffer (150 mM NaCl, 1%v/v Nonidet P-40, 0.5% w/v deoxycholate, 0.1% w/v SDS, 50 mM Tris pH8, 5 mM EDTA, 0.5 mM PMSF, protease inhibitors) for sonication. Immunoprecipitations were performed overnight at 4°C using and imunoprecipitated chromatin was extracted using QIAquick PCR Purification Kit (Qiagen).
10 ng of input and ChIP material was processed using the Illumina kit (IP-102-1001)

value: TKO

tag: cell phenotype

value: low levels of MMSET


title: F1_CastxB6_R2

description: Index: GCTTAGA

tag: gender


title: NTKO_Input_ChIPseq_1

description: Sample 5

value: NTKO

value: high levels of MMSET


title: NTKO_Input_ChIPseq_2

description: Sample 6


title: TKO_EZH2_ChIPseq_1

description: Sample 3

value: anti-Ezh2 (Cell Signaling, catalog# 5246s, lot# 5)


title: SNU-484-EBV

value: SNU-484 in vitro infected with EBV

value: EBV(+); experimentally infected with EBV


title: TKO_EZH2_ChIPseq_2

description: Sample 4

value: Multiple myeloma


title: F1_B6xCast_R2

description: Index: TACTCTA

value: F1 hybrid of C57BL6J (male) x Cast/EiJ (female)


title: F1_CastxB6_R1

description: Index: TGAGGTT


title: F0_Cast_R3

description: Index: ATCGAGC

value: Cast/EiJ


title: TKO_H3K27me3_ChIPseq_1

value: Low levels of MMSET


title: NTKO_EZH2_ChIPseq_2

description: Sample 2


title: NTKO_EZH2_ChIPseq_1

description: Sample 1


title: F0_Cast_R1

description: Index: GGCAGCG


title: F0_B6_R3

description: Index: CCGATTA


title: KMS11_GSK669_2

data_processing:
Basecalls were performed using Casava version 1.8.2
RNA-seq samples were aligned to hg19 using the STAR aligner (v2.3.0)
For the calculation of FPKM values, cuffdiff was used (v2.1.2) and the UCSC hg19 annotation from igenomes
FPKM 0.1 was used as a cutoff point
Genome_build: hg19
Supplementary_files_format_and_content: Contains FPKM RNA abundace measurements for the samples. Q1 corresponds to KMS11_GSK343, q2 is KMS11_GSK669, q3 is TKO_GSK343 and q4 is TKO_GSK669.

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 2uM of GSK343 (active compund) or GSK669 (inactive control compound) fro seven days.

value: High levels of MMSET


title: KMS11_GSK669_1


title: F0_B6_R1

description: Index: TAACAAG


title: TKO_GSK669_2


title: TKO_Input_ChIPseq_2

description: Sample 8


title: TKO_GSK343_1


title: KMS11_GSK343_2


title: KMS11_GSK343_1


title: NA12891_RNASeq

first: Xin

last: Li

address: 300 Pasteur Dr

department: Pathology

data_processing:
RNA-Seq reads were aligned to the hg19 genome assembly using Tophat 2.0.0, -G option, with Gencode.v12 annotation
Gene and transcript expression levels are quantified using cufflinks 2.0.0
eQTL on gene and transcript levels are tested using linear regression (expression levels ~ genotypes)
Genome_build: hg19
Supplementary_files_format_and_content: CEU.family1463.gene.transcript.FPKM.txt include FPKM values for each transcript and individual, gene level FPKM values are obtained by summing up transcripts.
Supplementary_files_format_and_content: CEU.family1463.haplotype.txt include phased haplotypes for all individuals.
Supplementary_files_format_and_content: CEU.family1463.inheritance.txt include haplotype blocks for all individuals.
Supplementary_files_format_and_content: CEU.family1463.gene.cis-eQTL.txt include cis-eQTL pvalues and effect sizes for all tested genes.
Supplementary_files_format_and_content: CEU.family1463.transcript.cis-sQTL.txt include cis-sQTL (splicing QTLs) pvalues and effect sizes for all tested transcripts.

source_name: lymphoblastoid cell lines (LCL)

growth_protocol: CEPH/UTAH family EBV transformed peripheral blood B lymphocytes (Cat# XC01463) were purchased from the Coriell Institute and grown in RPMI 1640 supplemented with 10% FCS and penicillin/streptomycin in humidified 5% CO2 at a concentration of ~1x106 cells/ml.

extract_protocol:
Total RNA was isolated using Trizol.
RNA quality was assessed with the Agilent Bioanalyzer 2100 and RIN scores above 9 were used for cDNA production. One microgram of polyA purified mRNA was used for cDNA library construction using the Illumina TruSeq RNA Preparation Kit. Strand specificity was performed using dUTP during second strand synthesis. All samples were indexed with Illumina adapters and sequenced using an Illumina HiScan. Each cDNA library was subsequently sequenced on an Illumina HiSeq to obtain 30 million 75bp paired-end reads per individual.

tag: individual


title: TKO_GSK343_2


title: NA12890_RNASeq

value: EBV transformed peripheral blood B lymphocytes


title: NA12886_RNASeq


title: F1_B6xCast_R1

description: Index: CCATCAT

value: retina

tag: age


title: NA12882_RNASeq


title: NA12884_RNASeq


title: NA12883_RNASeq


title: NA12885_RNASeq


title: F0_Cast_R2

description: Index: CACCTCC

tag: tissue


title: NA12893_RNASeq


title: NA12888_RNASeq


title: F0_B6_R2

description: Index: CTTGGAA


title: TKO_GSK669_1


title: NA12887_RNASeq


title: NA12880_RNASeq


title: NA12881_RNASeq


title: NA12879_RNASeq


title: NA12878_RNASeq


title: T311_BGT

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

description: BGT libraray (indicating unmodified or methylated cytosines) of the sample

data_processing:
Library strategy: HSMT-Seq
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean HMST-seq reads were mapped to hg19 virtual library with no more than one mismatch using open-source programming language Perl.
The data for three libraries were normalized according to a previous method (Global Rank-invariant Set Normalization, GRSN) (Pelz et al. 2008) based on the normalized tag counts, and the modification abundance of a specific CCGG site was determined as the ratio between the tag counts of two libraries. For instance, the hydroxymethylation level can be defined as the ratio between “C+mC+hmC” and “C+mC” tags. Furthermore, CCGG sites with significantly different tag counts (sequencing depth >10X, FDR <0.001) based on Poisson distribution with a ratio of tags between two libraries larger than 1 were determined to be significantly modified sites.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include tags abundance, p-value of Poisson test and FDR for each sample.

source_name: Hepatocellular carcinoma tissue

extract_protocol:
All HCC tissue  were obtained from patients who underwent surgical resection for their tumors and provided informed consent prior to liver surgery. The primary tumor specimens were immediately frozen at -80°C until DNA/RNA extraction. Genomic DNA was extracted from all patients and cells using the QIAamp DNA Blood Mini Kit (Qiagen).
HSMT-Seq library construction was performed following our previously reported protocol (Gao et al. 2013). The libraries were sequenced using single-end 50 bp sequencing strategy with an Illumina HiSeq2000 sequencing system.

value: Hepatocellular carcinoma


title: Human_Duct_HH1930

data_processing:
Base calling performed by CASAVA
Alignment was performed with Bowtie version 0.12.7 set to allow no mismatches.  I trimmed the first 4 bases from each read and aligned to the next 44 bases.  Only tags with unique alignments were counted.
Tags counts were compiled into a matrix using custom R-scripts
Genome_build: A custom transcriptome of 42 NCBI Refseq genes was used
Supplementary_files_format_and_content: tab-delimited text files include unique mapped reads for each sample and gene

source_name: FACS sorted human intrahepatic ducts

value: Duct cells


title: T311_MspI

description: HpaII libraray (indicating unmodified, methylated or hydroxymethylated cytosines) of the sample


title: T273_HpaII

description: HpaII library (indicating unmodified cytosines) of the sample


title: T273_BGT


title: Rituximad resistant DOHH2 xenograft

city: Waltham

first: Zhongwu

last: Lai

state: Massachusetts

address: 35 Gatehouse Dr.

department: Cancer Informatics

institute: AstraZeneca

description: total RNA was extracted from xenograft and contained mouse sequences

data_processing:
Raw sequences were first quality assessed and low quality reads were removed.
The clean reads were then aligned to both human (hg19) and mouse (mm10) using TopHat (v2.0.4)
In house customized analysis pipeline was used to separate human and mouse sequences based on alignment qualities.  Mouse sequences were then filtered from human alignment before quantification analysis.
Expression was quantified into RPKM using HTSeq (v0.5.3p9) and RSeQC (v2.3.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Rituximad resistant DOHH2 xenograft

growth_protocol: The DOHH2 cell line (source: ATCC) was maintained in RPMI 1640 (Life Techologies), 10% fetal bovine serum or FBS (Gibco), penicillin and streptomycin. All cells were cultured at 370C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from cells using standard protocol. Messenger RNA was enriched by using the oligo (dT) magnetic beads. Size selected mRNA (~200 bp) was used to  synthesize cDNA. Purified cDNA were ligated to sequencing adaptors, the ligated fragments were purified, enriched and used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The DOHH2 model is a fast growing model with a doubling time of 4 to 5 days. It has a greater than 95% take rate in SCID mice. The animals were randomized when tumor size reached 200-250 mm3. The treatment started at day 10-12 with rituximab dosed 25 mg/kg, IP three times a week over 21 days.

value: diffuse large B-cell lymphoma (DLBCL)

tag: xenograft host

value: SCID mice

tag: tumor subtype

value: germinal center B-cell like

tag: tissue type

value: Rituximad resistant DOHH2 xenograft


title: Mouse_Hep_225

source_name: FACS sorted mouse ducts

value: ddc


title: Parental DOHH2 xenograft

source_name: Parental DOHH2 xenograft

tag: cell line

value: Parental DOHH2 xenograft


title: NA12877_RNASeq

tag: cell type


title: T273_MspI


title: NA12889_RNASeq


title: F1_B6xCast_R3

description: Index: AGACTGA

value: 8 weeks

value: Male


title: T083062_MspI


title: T311_HpaII


title: Mouse_1C3_225

source_name: FACS sorted mouse hepatocytes

value: Hepatocyte cells

tag: injury


title: Hepatocyte (DDC) 118

description: Hepatocytes

data_processing:
Base calling performed by CASAVA
Aligned to mm9 using Bowtie version 0.12.7, I trimmed the first 4 bases from each read and aligned to the next 44 bases, allowing up to 3 mismatches, but requiring unique best matches
R scripts to count tags that aligned to the exons of UCSC RefSeq gene model
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
Cells were lysed in trizol.  The aqueous layer was alcohol precipitated and cleaned up on Qiagen Rneasy Micro columns with on column DNAse digestion
75ng-200ng total RNA was prepared with the Illumina Truseq RNA sample prep kit v2

treatment_protocol: Mice were treated with 0.1% DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine) for 5-8 weeks.  Cells were dissocated for liver by collagenase digestion.

value: liver

value: hepatocyte


title: T083062_BGT


title: T083062_HpaII


title: Hepatocyte (DDC) 248

description: Hepatocytes


title: Hepatocyte (DDC) 611

description: Hepatocytes


title: T080949_HpaII


title: NA12892_RNASeq


title: Hepatocyte (DDC) 225

description: Hepatocytes


title: T080949_MspI


title: Host-derived ducts neg4 611

description: Host cholangiocyte-derived ductal cells (MIC1-1C3+ CD11b/26/31/45- SSC-low mTomato-neg)

value: cholangiocyte


title: T068206_BGT


title: T080949_BGT


title: Host-derived ducts neg3 225


title: T068206_HpaII


title: Donor-derived ducts mT5 611

description: Donor hepatocyte-derived ductal cells (MIC1-1C3+ CD11b/26/31/45- SSC-low mTomato+ )

value: oval cell


title: N321_HpaII

source_name: Normal liver tissue

value: Normal liver


title: Host-derived ducts neg1 118


title: N321_BGT


title: N321_MspI


title: N283_MspI


title: T068206_MspI


title: Donor-derived ducts mT3 225


title: Host-derived ducts neg2 120


title: Donor-derived ducts mT2 219


title: Donor-derived ducts mT4 248


title: N283_BGT


title: N084999_MspI


title: Donor-derived ducts mT1 120


title: N080949_MspI


title: N084999_BGT


title: Adult Input

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

description: input control sample

data_processing:
Base-calls were made using RTA  version 1.12.4.2
Reads were aligned to mouse genome mm9 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using macs14, with input aligned sequences as the control file (E16.5 for embryonic ChIPs, and Day2 Depilation for adult ChIPs)
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: mouse mm9
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations

source_name: adult mouse epidermis

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. 28 ug of sonicated chromatin was used for the Grhl3 IPs.
Sequencing libraries were generated for the Grhl3 and Input samples using Illumina Tru-Seq ChIP-Seq kit, multiplexed to be sequenced in a single lane, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [Schmidt D, Methods, 2009]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.

treatment_protocol: adult epidermis (depilation and imiquimod samples) was isolated by digestion in 50% media/dispase II with for two hours at 37°C, then chopped into small pieces prior to fixation for ChIP.

value: adult


title: E16.5 Grhl3 rep1

description: grhl3 chip sample

source_name: whole embryonic mouse skin

value: Grhl3 (custom made)


title: E16.5 Input

description: input control sample


title: Day 4 Depilation Grhl3

description: grhl3 chip sample


title: Imiquimod  Grhl3

description: grhl3 chip sample


title: N045268_MspI


title: N080949_HpaII


title: N084999_HpaII


title: N045268_BGT


title: N045268_HpaII


title: Host-derived ducts neg5 219


title: E16.5 Grhl3 rep2

description: grhl3 chip sample


title: LM6_MspI

source_name: Hepatocellular carcinoma cell line

value: Hepatocellular carcinoma cell line


title: N080949_BGT


title: LM6_BGT


title: 97L_BGT


title: LM6_HpaII


title: 97L_MspI


title: 97L_HpaII


title: N283_HpaII


title: Sequencing of input DNA from human monocytes P4 Input

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the  hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup ( version 0.1.18) function.
Samtools was used to convert aligned reads to BAM format.
Genome_build: hg19
Supplementary_files_format_and_content: Smoothed and normalized coverage vectors were produced in 25 bp steps using custom software. Data was subsequently converted into indexed binary wiggle (bigwig) files using wigToBigWig utility downloaded from UCSC genome browser homepage.

source_name: CD14++ CD16- monocytes from blood donor 4

extract_protocol:
A blood sample of 30 ml was taken and peripheral blood mononuclear cells were isolated using ficoll-based density gradient centrifugation. Further isolation of CD14++ CD16- monocytes was conducted using magnetic cell sorting to deplete CD16++ monocytes and separate CD14++ monocytes. Purity of isolation was checked by flow cytometric analysis of the CD14+ cell fraction. Cells were cross-linked for 10 min using formaldehyde (final concentration 1%). Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris/HCl, pH8.1, 1x concentrated protease inhibitors) and sonciated using a Branson-250 Sonicator (http.www.bransonultrasonics.com) using the microtip setting. Fragment size of the obtained chromatin was checked to be between 100 bp and 300 bp. Sheared chromatin was diluted 1/10 with dilution buffer (SDS 0.01%, Triton X-100 1%, EDTA 1.2 mM, Tris/HCl, pH 8.1 16.7 mM, NaCl 167 mM). Chromatin was precleared using a protein A/G-sepharose mixture for 1 hr at 4°C and incubated with apprpriate antibodies over night. Immune complexes were precipitated with protein A/G-sepharose and washed with low salt (SDS 0.1%, Triton X-100 1%, EDTA 2 mM, Tris/HCl, pH8.1 20 mM, NaCl 150 mM), high salt (SDS 0.1%, Triton X-100 1%, EDTA 2 mM, Tris/HCl, pH8.1 20 mM, NaCl 500 mM), LiCl buffer (LiCl 0.25 M, NP40 1%, Deoxycholat 1%, EDTA 1 mM, Tris/HCl, pH8.1 10 mM) and twice with TE. After crosslink reversal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare).
ChIP-seq library preparation using MicroPlex kit from Diagenode

value: CD14++ CD16- monocytes

tag: donor id

tag: disease state

value: control participant


title: ChIP-seq analysis of H3K9Ac  in human monocytes P4 H3K9Ac

description: ChIP-seq

tag: chip antibody

value: H3K9Ac Abcam ab4441


title: ChIP-seq analysis of H3K27me3 in human monocytes P4 H3K27me3

description: ChIP-seq

value: H3K27me3 Abcam ab6002


title: ChIP-seq analysis of H3K27me3 in human monocytes P2 H3K27me3

description: ChIP-seq

source_name: CD14++ CD16- monocytes from blood donor 2


title: BS69-2 rep1

city: Los Angeles

first: Yi

last: Xing

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

description: BS69 knock down, siRNA-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 65) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cufflinks v2.0.2 with uniquely and properly mapped pairs.
Genome_build: hg19
Supplementary_files_format_and_content: a text file includes FPKM values for each Sample

source_name: HeLa cells

extract_protocol:
HeLa cells were infected with lentiviruses carrying control and BS69 shRNA, after the selection by puromycine for 7 days; RNAs were extracted by TRIZOL and subjected to 100bp x 2 paired-end RNA-seq, the equipment is HiSeq 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa

value: Cervical Cancer

tag: transfection

value: lentivirus carrying BS69-2 shRNA


title: CTRL rep1

description: Control Sample

value: lentivirus carrying control shRNA


title: ChIP-seq analysis of H3K4me3  in human monocytes P4 H3K4me3

description: ChIP-seq

value: H3K4me3 Abcam ab8580


title: BS69-2 rep3

description: BS69 knock down, siRNA-2


title: BS69-1 rep1

description: BS69 knock down, siRNA-1

value: lentivirus carrying BS69-1 shRNA


title: Sequencing of input DNA from human monocytes P3 Input

description: ChIP-seq

source_name: CD14++ CD16- monocytes from blood donor 3


title: BS69-1 rep3

description: BS69 knock down, siRNA-1


title: CTRL rep3

description: Control Sample


title: ChIP-seq analysis of H3K9Ac  in human monocytes P3 H3K9Ac

description: ChIP-seq


title: ChIP-seq analysis of H3K27me3 in human monocytes P3 H3K27me3

description: ChIP-seq


title: BS69-1 rep2

description: BS69 knock down, siRNA-1


title: ChIP-seq analysis of H3K4me3  in human monocytes P3_H3K4me3

description: ChIP-seq


title: BS69-2 rep2

description: BS69 knock down, siRNA-2


title: Sequencing of input DNA from human monocytes P2 Input

description: ChIP-seq


title: ChIP-seq analysis of H3K9Ac  in human monocytes P1 H3K9ac

description: ChIP-seq

source_name: CD14++ CD16- monocytes from blood donor 1

value: H3K9ac Abcam ab4441


title: ChIP-seq analysis of H3K9Ac  in human monocytes P2 H3K9Ac

description: ChIP-seq


title: standard control_infected_rep3

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

data_processing:
Image analysis and base calling was done by the Illumina HCS version 1.15.1; One sequencing run for sample 1 and 23 was performed while the raw data from 2 sequencing runs (sample 25) and 3 sequencing runs (samples 2, 11-16, 24 and 26) were combined to generate one fastq file and one tsv file each. The generated fastq files were used to calculate average insert sizes and standard deviations for paired end experiments.
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Zv9_67) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Danio_rerio.Zv9.67.dna.toplevel / Danio_rerio.Zv9.67.cdna.all.fa (http://www.ensembl.org/info/data/ftp/index.html)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: zebrafish embryo injected with control morpholino, M. marinum infected, 4 dpi

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts) containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich)

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides.

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. At 5 days post fertilization (4 days post infection) pools of 30 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using QIAZOL reagent.

tag: morpholino injection at 1-cell stage

value: control morpholino 0.2 mM

tag: blood island injection at 28 hpf

value: M. marinum, Mma20 strain 200 cfu

tag: developmental stage rna isolation

value: 4 dpi


title: ptpn6 morphant_uninfected_rep4

source_name: zebrafish embryo injected with ptpn6 morpholino, not-infected

value: ptpn6 morpholino 0.06 mM


title: ChIP-seq analysis of H3K4me3  in human monocytes P2 H3K4me3

description: ChIP-seq


title: ptpn6 morphant_infected_rep4

source_name: zebrafish embryo injected with ptpn6 morpholino, M. marinum infected, 4 dpi


title: ChIP-seq analysis of H3K4me3  in human monocytes P1 H3K4me3

description: ChIP-seq


title: standard control_infected_rep4

value: control morpholino 0.06 mM


title: CTRL rep2

description: Control Sample


title: standard control_uninfected_rep3

source_name: zebrafish embryo injected with control morpholino, not-infected


title: Sequencing of input DNA from human monocytes P1 Input

description: ChIP-seq


title: standard control_uninfected_rep2


title: mpeg1 morphant_uninfected_rep2

source_name: zebrafish embryo injected with mpeg1 morpholino1, not-infected

value: mpeg1 mo1 0.2 mM


title: standard control_infected_rep2


title: mpeg1 morphant_infected_rep2

source_name: zebrafish embryo injected with mpeg1 morpholino1, M. marinum infected, 4 dpi


title: standard control_infected_rep1


title: Long day

city: Leicester

first: Eran

last: Tauber

address: University Road

institute: University of Leicester

data_processing:
Demultiplexing and trim using custom Perl scripts
3' adaptor trimming (Trim-galore v.0.2.5)
Quality filtering (FAST-X toolkit v. 0.0.13)
Alignment fo Nvit-2.0 reference genome (Bismark v.0.7.7)
Coverage filtering using MethylKit version 0.5.6
Genome_build: Nvit_2.0
Supplementary_files_format_and_content: Tab delimited files listing methylation values for each reference cytosine

organism: Nasonia vitripennis

source_name: whole body

growth_protocol: Nasonia adult females were maintained at 18C for 10 days. Fed with blowfly pupae every 3-4 days.

extract_protocol:
genomic DNA was extracted using QIAGEN Dneasy kit.
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as in Gu et al (2011). Genomic DNA was  digested by MspI generating CpG dinucleotides ends. After end-repair, A-tailing and ligation to methylated Illumina adapters, DNA was size selected (~40-220bp) and subjected to bisulfite conversion.  The converted DNA was enriched by PCR, generating the RRBS libraries.

treatment_protocol: wasps were maintened in long (18 hr) or short (6 hr) photoperiod.

tag: strain

value: AsymC

tag: developmental stage

value: Adult

tag: Sex

value: female

tag: photoperiod

value: long day


title: Short day

value: short day


title: standard control_uninfected_rep1


title: ChIP-seq analysis of H3K27me3 in human monocytes P1 H3K27me3

description: ChIP-seq

value: CD14++ CD16- monocytes

value: H3K27me3 Abcam ab6002

value: control participant


title: Red v. Green E6 + 15DIV, Green

city: Saint Louis

first: Jennifer

last: Enright

address: 660 S. Euclid, Box 8118

description:
Sample 8
amplified cDNA (NuGen Ovation kit)
processed data file: redgrn_late_cuffdiff_out.diff.txt
processed data file: redgrn_late_edgeR_out.csv

data_processing:
Basecalls performed using Casava v1.7 (samples 1 and 2) or Casava v1.8 (samples 3-10)
Reads were aligned to galGal4 using Bowtie v0.12.7 and splice junctions called with TopHat v1.4.0
Differential expression was determined using cufflinks v1.3.0.
Differential expression was also determined by generating a counts table from the bowtie output, and then using R v.3.0.2 to implement edgeR.
Red, blue, and violet opsin are not fully represented in galGal4. To assess expression of these genes, reads were separately aligned to a set of 24 transcripts known to be expressed in photoreceptors, including all of the opsins, using Bowtie v.0.12.7 [The 24 transcripts are: Green Opsin (M92038.1), Red Opsin (NM_205440.1), Blue Opsin (NM_205517.1), Violet Opsin (NM_205438.1), RHO (NM_001030606.1), CRX (NM_204499.1), L-MAF (AF034570.1), NR2E3 (NM_204594.1), THRB (Z50188.1), RXRG (NM_205294.1), IRBP (AY994153.1), VSNL1 (NM_205255.1), GNAT2 (NM_204690.1), GNAT1 (NM_204691.1), PDE6C (NM_204986.1), PDE6H (NM_204408.1), CNGA1 (NM_205220.1), CNGA3 (NM_205221.1), ARR3 (NM_001097533.1), PDE6G (NM_204445.1), PDE6B (XM_424876.3), PDE6D (XM_422739.3), CRY1 (NM_204245.1), CNTFRA (U29245.1)]. Read counts for red, blue, and violet opsin were included in the edgeR analysis described above.
Genome_build: galGal4
Supplementary_files_format_and_content: cuffdiff output file containing tab-delimited differential gene expression data, and edgeR output as a comma separated values (csv) file

organism: Gallus gallus

source_name: Retinal explant culture

growth_protocol: Eggs were maintained at 38°C in a rocking, humidified chamber for 6 days. Retinas were then harvested and electroporated with reporter constructs, and grown in culture as explants for either 9 or 15 days.

extract_protocol:
Total RNA was isolated using the Rneasy kit, with on-column DNase treatment. cDNA was generated and amplified using the NuGen Ovation RNAseq kit.
Libraries were generated with Illumina adapters, and barcoded to allow all 6 samples for a single experiment (3 biological replicates for each of two cell populations) to be run on a single lane.

treatment_protocol: Retinal explants were disociated using trypsin and trituration. For each experiment, two populations (DsRed+ and GFP+) were isolated from the same set of explants using FACS.

tag: tissue harvest

value: embryonic day 6 (H&H Stage 26-28)

tag: electroporated with

value: Red::DsRed and Green::GFP

tag: days in vitro

value: 15 DIV

value: Retinal explant culture


title: Red v. Rho E6 + 15DIV, Red

description:
Sample 5
amplified cDNA (NuGen Ovation kit)
processed data file: redrho_late_cuffdiff_out.diff.txt
processed data file: redrho_late_edgeR_out.csv

value: Red::DsRed and Rho::GFP


title: Red v. Green E6 + 15DIV, Red

description:
Sample 7
amplified cDNA (NuGen Ovation kit)
processed data file: redgrn_late_cuffdiff_out.diff.txt
processed data file: redgrn_late_edgeR_out.csv


title: Rho v. Green E6 + 9DIV, Rho

description:
Sample 1
amplified cDNA (NuGen Ovation kit)
processed data file: rhogrn_early_cuffdiff_out.diff.txt
processed data file: rhogrn_early_edgeR_out.csv

value: Rho::DsRed and Green::GFP

value: 9 DIV


title: Red v. Green E6 + 9DIV, Green

description:
Sample 4
amplified cDNA (NuGen Ovation kit)
processed data file: redgrn_early_cuffdiff_out.diff.txt
processed data file: redgrn_early_edgeR_out.csv


title: Red v. Violet E6 + 15DIV, Red

description:
Sample 9
amplified cDNA (NuGen Ovation kit)
processed data file: redvio_late_cuffdiff_out.diff.txt
processed data file: redvio_late_edgeR_out.csv

value: Red::DsRed and Violet::GFP


title: standard control_uninfected_rep4

value: control morpholino 0.06 mM

value: 4 dpi


title: Red v. Green E6 +9DIV, Red

description:
Sample 3
amplified cDNA (NuGen Ovation kit)
processed data file: redgrn_early_cuffdiff_out.diff.txt
processed data file: redgrn_early_edgeR_out.csv


title: P014

city: Tartu

first: Tauno

last: Metsalu

address: Liivi 2

country: Estonia

institute: University of Tartu

data_processing:
DESeq package in the R statistical language and environment (version 3.0.2) was used to calculate the reads per kilobase per million reads (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts and RPKM values for each sample

source_name: placenta

extract_protocol:
mirVana™ miRNA  Isolation Kit (Ambion®, Life Technologies™) according to manufacturer’s instructions
Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) + SOLiD 5500 System; DNA fragment library kit (Life Technologies, Carlsbad, CA, USA), both according to manufacturer's instructions.
45 ng total RNA was used to consruct WT RNA seq library (cDNA synthesis, cDNA amplification, SOLiDi 5500 adaptor ligation and library amplification), barcoded adaptors were applied for multiplex sequencing

tag: person

value: child

tag: trio


title: P012


title: P007


title: P008


title: P009


title: Red v. Rho E6 + 15DIV, Rho

description:
Sample 6
amplified cDNA (NuGen Ovation kit)
processed data file: redrho_late_cuffdiff_out.diff.txt
processed data file: redrho_late_edgeR_out.csv

tag: cell type


title: Red v. Violet E6 + 15DIV, Violet

description:
Sample 10
amplified cDNA (NuGen Ovation kit)
processed data file: redvio_late_cuffdiff_out.diff.txt
processed data file: redvio_late_edgeR_out.csv


title: P006


title: P005


title: Rho v. Green E6 + 9DIV, Green

description:
Sample 2
amplified cDNA (NuGen Ovation kit)
processed data file: rhogrn_early_cuffdiff_out.diff.txt
processed data file: rhogrn_early_edgeR_out.csv


title: P002


title: sRNA from strawberry flower

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

data_processing:
FASTA toolkits (http://hannonlab.cshl.edu/fastx_toolkit/) was used for data processing, including format conversion, adaptor trimming and read collapsing.
Genome_build: n/a

organism: Fragaria vesca

source_name: flower

extract_protocol: Total RNAs were isolated from 1 day-opening flowers of  the inbred line Yellow Wonder 5AF7  grown in growth chambers (Hollender et al., 2012) using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Small RNAs were enriched by precipitating the supernatant passing through Qiashedder spin column. The recovered small RNA samples were used for library construction and deep sequencing in Genomics Resources Core Facility at Weill Cornell Medical College (New York, NY).

tag: line

value: inbred line ‘Yellow Wonder 5AF7’

tag: tissue

value: flowers

value: 1 day-opening


title: P001