title: HUVEC_TCC_Notx

description:
library strategy: TCC (HiC)
tethered conformation capture

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location. RNA-Seq samples were aligned using Tophat.
GRO-Seq and RNA-Seq results were trimmed to remove A-stretches originating from the library preparation. Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
For ChIP-Seq, aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find enriched H3K4me2 regions. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
For TCC analysis, reads from paired-end sequencing were separately filtered and aligned to the genome using bowtie. Each read was trimmed from the 3’ end after GATC site and minimum read length was set to 25 bp. Paired-end reads were connected and additional filtering steps were performed using HOMER 4.3. Read pairs with exact same ends were only considered once and read pairs were removed if they were separated by less than 1.5x the estimated sequencing insert length to remove likely continuous genomic fragments or re-ligation events. Paired-end reads originating from regions of unusually high tag density were left out by removing reads from 10 kb regions that contain more than 5 times the average number of reads. Reads were filtered according to their distance from a restriction site keeping only those read pairs that had both of their reads aligning at most 1.5x fragment length estimate from a restriction site. Reads were removed if their ends form a self-ligation with adjacent restriction sites.
Genome_build: hg19
Supplementary_files_format_and_content: Annotated chromosomal interactions at 10 kB resolution are provided for TCC

source_name: human umbilical vein endothelial cells

extract_protocol: 90 million human umbilical vein endothelial were fixed with 1 % PFA/PBS in room temperature for 10 minutes and crosslinking was stopped by incubating cells 5 min in presence of 125 mM glycine. Cells were washed two times with ice-cold PBS containing 0.5 % BSA and scraped into lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 5 mM MgCl2, 0.2 % NP-40 and protease inhibitor cocktail (Roche). Samples were vortexed, incubated on ice for 10 min, centrifugated for 5 minutes in 1500 g in +4 °C and washed once again with lysis buffer. Cells were washed twice with ice-cold wash buffer containing 50 mM Tris-HCl (pH 8.0), 50 mM NaCl and 0.5M EDTA and nuclei were isolated by incubating samples 10 minutes at +65 °C in wash buffer with 0.55 % SDS and collected by sentrifugation (1000 g for 1 min). Later steps followed the protocol described (Kalhor et al., 2012), except MboI (NEB) was used to digest chromatin, T1 Streptavidin dynabeads (Invitrogen) were used in all the pulldown steps, NucleoSpin Gel & PCR Clean-up kit (Macherey-Nagel) for clean-up steps and Bioruptor NextGen sonicator for DNA shearing (High setting, 30s/30s cycles for total 35 cycles). Libraries were amplified in 15 PCR cycles, size selected for 225 – 425 bp range on 10 % TBE-gel (Invitrogen). Gel was grinded and soaked with 0.1 % Tween-20 and 150 mM NaCl and DNA was eluted through Ultrafree Centrifugal filter column (Millipore), cleaned up with ChIP DNA clean & concentrator kit (Zymo Research) and paired-end sequenced with Illumina HiSeq 2000.

tag: details

value: Pool of at least 3 individuals

tag: passage

value: human umbilical vein endothelial cells


title: TFH_TI

status: Public on Oct 27 2014

type: SRA

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

country: USA

institute: Yale University

library_source: genomic

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were mapped to the human genome (hg19 NCBI Build 37) using the BWA version 0.6.1 alignment program with default parameters.
The Model-based Alignment of ChIP-Seq (MACS) program version 1.4.0rc2 was used to identify H3K4me1 and H3K27Ac peaks using default parameters.
The MACS2 program version 2.0.10.20131216 was used to identify broad regions bound by H3K27me3
Genome_build: hg19
Supplementary_files_format_and_content: The H3K4me1 and H3K27Ac macs1.4 peaks.bed output files have a fifth field that is -10*log10(pvalue).  H3K27me3 MACS2 output is in broadPeak format.

molecule: genomic DNA

organism: Homo sapiens

source_name: TFH T cell

extract_protocol:
To obtain primary human Tfh and Teff cells, human tonsils were cut into small sections and homogenized by crushing followed by straining through a 40mM nylon filter. CD4+ T lymphocytes were enriched using a negative selection biotin-based magnetic separation kit (EasySep; StemCell Technologies) prior to cell surface staining with the antibodies to:  CD4 (clone RPA-T4), CD45RA (clone HI-100), TCRb (clone IP26), PD-1 (clone EH12.1), CXCR5 (clone RF8B2), and PSGL-1 (clone KPL-1)(all from BD Biosciences). Staining of CXCR5 was performed at room temperature (25°C) with 1 hour incubation. Stained and rinsed cells were analyzed using an LSRII Multilaser Cytometer (BD Biosciences) or specific populations sorted using a FACSAria (BD Bioscience).  ChIP assays were performed as previously described with minor variations (Steiner, L. A., Maksimova, Y., Schulz, V., Wong, C., Raha, D., Mahajan, M. C., Weissman, S. M., and Gallagher, P. G. (2009) Mol Cell Biol). 1 × 107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, followed by Dounce homogenization. Cross-linked nuclei were isolated, followed by sonication with a Covaris S2 shearing device (duty cycle 10%, intensity 5, 15 minutes), to obtain chromatin-containing DNA fragments with an average size of ~200-400bp. For each ChIP, 4 µg of antibody was used. Samples were immunoprecipitated with antibodies against monomethyl histone 3 lysine 4 (H3k4me1, Abcam ab8895), trimethyl histone 3 lysine 27 (Abcam ab6002), and acetyl histone 3 lysine 27 (H3K27Ac, Abcam ab4729).  The antigen-antibody complex was captured on protein G beads, washed four times with radioimmunoprecipitation assay buffer, and then washed with phosphate-buffered saline. The DNA-protein complex was eluted from the protein G beads with 0.1 NaHCO3/1% SDS at 65°C, and cross-linking of DNA-protein adducts was reversed by 4 hours of incubation at 65°C. After proteinase K and RNase digestion of the reverse-cross-linked sample, DNA was cleaned with the QIAquick PCR Purification Kit (Qiagen) according to manufacturer instructions.
ChIP libraries were prepared using the KAPA Library Preparation Kit (KAPA Biosystems) per the manufacturer's protocol. Briefly, ChIP DNA was end repaired, followed by addition of an adenine base at the 3' and NEXTflex ChIP-Seq Barcodes (BiooScientific) adaptor ligation. The modified DNA was then size selected on a 2% agarose and purified by using a gel extraction kit (Qiagen).  One microliter of size-selected adaptor ligated DNA was initially analyzed by SYBR Green Q-PCR to determine the number of cycles required to reach 50% of complete amplification.  Adaptor ligated DNA was PCR amplified with one initial heating step of 98°C for 45 second, followed by the pre-determined number of cycles with a melting temperature of 98°C for 15 s, an annealing temperature of 65°C for 30 s, and a product extension at 72°C for 30 s. At the end of the amplification, a final extension at 72°C for 1 min was performed. Amplified ChIP DNA was subjected to deep sequencing using standard Yale Center for Genome analysis protocols.

tag: t cell type

value: TFH

tag: tissue

value: Human tonsil

tag: cell surface markers

tag: chip antibody

value: TI


title: HUVEC-RNA-Seq-VEGFA-2h

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

library_source: transcriptomic

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location. RNA-Seq samples were aligned using Tophat.
GRO-Seq and RNA-Seq results were trimmed to remove A-stretches originating from the library preparation. Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
For ChIP-Seq, aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find enriched H3K4me2 regions. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
For TCC analysis, reads from paired-end sequencing were separately filtered and aligned to the genome using bowtie. Each read was trimmed from the 3’ end after GATC site and minimum read length was set to 25 bp. Paired-end reads were connected and additional filtering steps were performed using HOMER 4.3. Read pairs with exact same ends were only considered once and read pairs were removed if they were separated by less than 1.5x the estimated sequencing insert length to remove likely continuous genomic fragments or re-ligation events. Paired-end reads originating from regions of unusually high tag density were left out by removing reads from 10 kb regions that contain more than 5 times the average number of reads. Reads were filtered according to their distance from a restriction site keeping only those read pairs that had both of their reads aligning at most 1.5x fragment length estimate from a restriction site. Reads were removed if their ends form a self-ligation with adjacent restriction sites.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (raw tags, RPKM, log2 fold change, P-value) are provided in Series supplementary file GSE52642_Gene_Expression.txt.  UCSC Bedgraphs are also provided.

molecule: total RNA

growth_protocol: HUVECs were isolated from umbilical cords obtained from the maternity ward of the Kuopio University Hospital by the approval of the Kuopio University Hospital Ethics Committee. HUVECs were maintained in Endothelial Cell Growth medium (EGM; 0.1% human epidermal growth factor, 0.1% hydrocortisone, 0.1% Gentamicin - Amphotericin-B, 0.4% bovine brain extract, 2% FBS; Lonza) on cell culture flasks coated with 10 g/ml fibronectin (Sigma, St. Louis, MO) and 0.05 % gelatin in PBS. Human aortic endothelial cells (HAECs) were purchased from Life Technologies.

extract_protocol: RNA was purified using RNeasy Mini Kit (QIAGEN) and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit (Ambion, Austin, TX). Library cDNA was generated as above but by replacing the bead purification step with gel extraction on Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The libraries were sequenced on the Illumina HiSeq 2000 according to the manufacturer's instructions.

treatment_protocol: Cells were seeded on 10-cm dishes and allowed to adhere for 24 h after which the cells were washed with HBSS and lipoprotein deficient medium (2% LPDS) was added to the wells. After 16 h cells were treated with 50 ng/ml rhVEGF-A165 (R&D Systems, Minneapolis, MN) for 2-8h.

tag: cell type


title: TFH_3

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 genome using TopHat Version 2.0.4 software with default parameters
Reads in every gene were counted using htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). Genes with less than 3 samples with >1 read counts/million (cpm) were called not expressed and were not used in further analysis. The read count data was normalized using the TMM method. Differentially expressed genes were identified using the edgeR exact test.
Genome_build: hg19
Supplementary_files_format_and_content: Counts per gene and log2 RPKM

extract_protocol:
To obtain primary human Tfh and Teff cells, human tonsils were cut into small sections and homogenized by crushing followed by straining through a 40mM nylon filter. CD4+ T lymphocytes were enriched using a negative selection biotin-based magnetic separation kit (EasySep; StemCell Technologies) prior to cell surface staining with the antibodies to:  CD4 (clone RPA-T4), CD45RA (clone HI-100), TCRb (clone IP26), PD-1 (clone EH12.1), CXCR5 (clone RF8B2), and PSGL-1 (clone KPL-1)(all from BD Biosciences). Staining of CXCR5 was performed at room temperature (25°C) with 1 hour incubation. Stained and rinsed cells were analyzed using an LSRII Multilaser Cytometer (BD Biosciences) or specific populations sorted using a FACSAria (BD Bioscience). RNA was isolated from lymphocytes and prepared for RNA-seq analyses as described (Su MY, Steiner LA, Bogardus H, et al. Identification of biologically relevant enhancers in human erythroid cells. J Biol Chem. 2013;288(12):8433-8444).
Paired end RNA libraries were prepared for sequencing using standard Illumina protocols at the Yale Center for Genome Analysis.


title: HUVEC-RNA-Seq-Notx-2h


title: CUTLL1_GSI_12h_2

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

data_processing:
Illumina Casava1.7 software used for basecalling.
after QC with FastQC v0.10.1, reads were mapped to hg19 whole genome using tophat v2.0.10
A count file for each sample was generated using HTSeq-0.6.1 and Ensembl igenomes GTF file as reference.
Count files were merged into a count matrix and normalized in R using DESeq2
Differential expression analysis was done with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normailzed count values for each Sample

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol:
Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.
RNA libraries were prepared for sequencing using standard Illumina protocols with poly-A enrichment

treatment_protocol: Cells were seeded at 1*10^6 cells/ml and treated with either DMSO or 1 µM of Compound E. Cells were harvested 12 and 48h after treatment.

tag: cell line

tag: treatment

value: GSI

tag: time


title: HUVEC-GRO-Seq-Notx-2h-rep2

description: library strategy: GRO-seq

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location. RNA-Seq samples were aligned using Tophat.
GRO-Seq and RNA-Seq results were trimmed to remove A-stretches originating from the library preparation. Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
For ChIP-Seq, aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find enriched H3K4me2 regions. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
For TCC analysis, reads from paired-end sequencing were separately filtered and aligned to the genome using bowtie. Each read was trimmed from the 3’ end after GATC site and minimum read length was set to 25 bp. Paired-end reads were connected and additional filtering steps were performed using HOMER 4.3. Read pairs with exact same ends were only considered once and read pairs were removed if they were separated by less than 1.5x the estimated sequencing insert length to remove likely continuous genomic fragments or re-ligation events. Paired-end reads originating from regions of unusually high tag density were left out by removing reads from 10 kb regions that contain more than 5 times the average number of reads. Reads were filtered according to their distance from a restriction site keeping only those read pairs that had both of their reads aligning at most 1.5x fragment length estimate from a restriction site. Reads were removed if their ends form a self-ligation with adjacent restriction sites.
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (raw tags, RPKM, log2 fold change, P-value) and UCSC Bedgraphs are provided for GRO- and RNA-Seq. Positions for H3K4me2 regions are provided for ChIP-Seq. Annotated chromosomal interactions at 10 kB resolution are provided for TCC

extract_protocol:
Nuclei were extracted from 5-16 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP.
RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.


title: HAEC-GRO-Seq-VEGFA-2h

description: library strategy: GRO-Seq

source_name: human aortic endothelial cells

extract_protocol: Nuclei were extracted from 5-16 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 11-14 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina HiSeq 2000.

value: human aortic endothelial cells


title: HUVEC-GRO-Seq-VEGFA-2h-rep2

description: library strategy: GRO-seq


title: HUVEC-GRO-Seq-Notx-2h-rep1

description: library strategy: GRO-Seq


title: 12-101 positive

status: Public on Oct 29 2014

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Transcriptomic maps were created by aligning single-end reads with tophat-2.0.4 against the University of California Santa Cruz (UCSC) hg19 reference transcriptome from the Illumina iGenomes resource.
Gene counts were estimated using HTSeq-0.5.3p3.
Genome_build: hg19
Supplementary_files_format_and_content: Table containing Transcripts per million (TPM) for each sample.  TPM were calculated according to Wagner et al. (2012) http://www.ncbi.nlm.nih.gov/pubmed/22872506

source_name: Endometrial Stromal Cell

growth_protocol: Single cell suspensions of human endometrial stromal cells (HESCs) were isolated from mid-luteal biopsies. Stromal single cell suspensions were layered over Ficoll-Paque PLUS and centrifuged to remove erythrocytes. The medium / Ficoll-Paque PLUS interface, containing stromal cells, was carefully aspirated, washed with DMEM/F-12 medium, and then subjected to magnetic bead separation to isolate W5C5+ and W5C5- cells using anti-W5C5 (SUSD2) antibody. Freshly isolated W5C5+ and W5C5- cells were expanded in growth medium consisting of DMEM/F12 with 10% dextran-coated charcoal-treated fetal bovine serum , 1% L-glutamine , 1% antibiotic-antimycotic solution , insulin (2 µg / ml), estradiol (1 nM) and basic fibroblast growth factor (10 ng / ml).  Confluent cultures were harvested by lysis in RNA STAT-60.

extract_protocol:
Total RNA was purified from RNA STAT-60 lysate according to the manufacturer's protocol.  Quantity and purity were determined using the Nanodrop ND1000 spectrophotometer.  3 μg each sample was treated with Amplification Grade DNase I (Invitrogen) according to manufacturer's instructions.  Samples were cleaned up by sodium acetate/ethanol precipitation and resolubilised in nuclease-free water.  From this point onwards, all steps were performed by Source Bioscience (Nottingham, UK).  Sample quality control was performed using the Agilent 2100 Bioanalyser.  All samples had RIN ≥ 9.1
The mRNA libraries were prepared in accordance to the Illumina TruSeq RNA sample preparation v2 guide (September 2012, Rev. D) for Illumina Paired-End Multiplexed Sequencing. According to the Illumina mRNA libraries preparation protocol, poly-A mRNA in the tRNA samples were first purified using Illumina poly-T oligo-attached magnetic beads and two rounds of purification. During the second elution of the poly-A RNA, the mRNA were also fragmented and primed with random hexamers for cDNA synthesis. Cleaved mRNAs were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. The RNA template was then removed and a replacement strand synthesized to generate double-stranded cDNA. Following the standard protocol, after the first and second strands cDNA synthesis, ends were repaired, dA base added, and Illumina Indexing adapters were ligated. Finally, cDNA fragments that have adapter molecules on both ends underwent 15 cycles of PCR to amplify the amount of prepared material.

value: Endometrial Stromal Cell

tag: culture progenitor w5c5 status

value: W5C5 negative


title: Pol_II ChIPSeq TIVE

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
Illumina BCL files converted to FASTQ with Illumina BCL converter
FASTQ files converted to FASTA
sam files created by Bowtie alignment of FASTA files on genome (KSHV [hhv8] or hg19)
sam files converted to bam files with SAMtools
sorted.bam files created with SAMtools
mpileup files created with SAMtools
wig files created with custom script mpileup2wig.pl
tdf files created with the toTDF command of the igvtools package
Genome_build: hg19 or NC_009333.1 (KSHV complete genome)
Supplementary_files_format_and_content: .wig files for KSHV (hhv8) annotation tracks
Supplementary_files_format_and_content: .tdf (compressed .wig format) for hg19 annotation tracks

source_name: TIVE-LTC

growth_protocol: BCBL-1 cells were cultured in RPMI 1640 medium supplemented with 10% FCS. TIVE-LTC cells were cultured in DMEM medium supplemented with 10% FCS.

extract_protocol:
Cells were crosslinked with 1% formaldehyde at room temperature for 10 min, and glycine added to 0.125M to terminate crosslinking. Cells were washed twice in ice-cold PBS with protease inhibitors and harvested by centrifugation. Every 2x10E7 cells were lysed in 1 ml ice-cold Farnham lysis buffer (5mM PIPES [pH8.0], 85 mM KCl, 0.5% NP-40) with protease inhibitors. The nuclei were spun down and resuspended in 1 ml RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS in 1xPBS) with protease inhibitors.
ChIP-enriched DNA was blunt ended with T4 DNA polymerase and Klenow, and phosphorylated with T4 PNK. A 3’ A residue was added with Klenow exo-.  Following adapter ligation, 150 bp to 300 bp DNA fragments were gel-purified, PCR amplified for 18 cycles, quantified with QuantIT dsDNA Assay Kit, and sequenced.

value: Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells

value: Pol II (Santa Cruz Biotechnology, sc-899)

value: TIVE-LTC


title: Pol_II ChIPSeq BCBL-1

value: Primary effusion lymphoma (PEL) cell line


title: H3K4me3 ChIPSeq TIVE_SureSelect

description: The SureSelect Library Prep system (Agilent Technologies) was used to enrich KSHV DNA. Adapters were ligated to ChIP-seq DNA, and 150 bp to 300 bp fragments gel-selected and amplified with 10 PCR cycles. The PCR products were purified with Agencourt AMPure XP beads, denatured, and hybridized with custom KSHV RNA baits at 65 C for 48 h. RNA-DNA hybrids were recovered with Dynal MyOne Streptavidin T1 magnetic beads, and the DNA eluted, purified, and reamplified for 22 PCR cycles. Finally the purified PCR products were quantified and sequenced.

value: H3K4me3 (Abcam, ab8580)


title: LANA ChIPSeq BCBL-1 BR2

value: rat LANA (ABI Inc., LN53)


title: H3K4me3 ChIPSeq TIVE BR1


title: LANA ChIPSeq TIVE BR1


title: H3K27me3 ChIPSeq TIVE_SureSelect


title: LANA ChIPSeq TIVE_SureSelect


title: H3K27me3 ChIPSeq TIVE


title: LANA ChIPSeq TIVE BR2


title: H3K4me3 ChIPSeq TIVE BR2


title: H3K4me3 ChIPSeq BCBL-1 BR2


title: H3K27me3 ChIPSeq BCBL-1


title: Rabbit IgG ChIPSeq BCBL-1

value: control rabbit IgG (Santa Cruz Biotechnology, sc-2027)


title: HUVEC-GRO-Seq-VEGFA-2h-rep1

description: library strategy: GRO-Seq


title: Pol_II ChIPSeq TIVE_SureSelect


title: DSM 2360 exponential

status: Public on Oct 26 2014

city: Winnipeg

first: Richard

last: Sparling

state: MB

address: 418 Buller Building

department: Microbiology

country: Canada

institute: University of Manitoba

data_processing:
Basecalls performed using CASAVA version 1.8
Trimming step – Adaper clipping and quality filtering: Raw illumina reads were trimmed and filtered by Trimmomatic-0.22 with parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 and all the occurred adapters in the first 8k paired end raw reads from "Illumina Adapter Sequences Letter" for clipping accompanying parameters <seed mismatches>:<palindrome clip threshold>:<simple clip threshold> - 2:40:15.
FPKM (fragments per kilobase of exon per million fragments mapped) files were generated with Bowtie2-2.0.2, Tophat-2.0.6, Cufflinks-2.0.2 with commands 1. tophat2 -p 24 -r 300 --mate-std-dev 50 -o $Tophat_PairedOUTPUT -G $GTF $BINDEX $R1,$R2; 2. bed_to_juncs < $Tophat_PairedOUTPUT/junctions.bed > $Tophat_PairedOUTPUT/unpaired_list.juncs; 3. tophat2 -j $Tophat_PairedOUTPUT/unpaired_list.juncs -p 24 -r 300 --mate-std-dev 50 -o $Tophat_UnpairedOUTPUT -G $GTF $BINDEX $Unpaired; 4. samtools sort $bam_file1 $merge_bam/paired.sort; 5. samtools sort $bam_file2 $merge_bam/unpaired.sort; 6. samtools merge -f $merge_bam/total.bam $merge_bam/paired.sort.bam $merge_bam/unpaired.sort.bam; 7. cufflinks --max-bundle-frags 4000000 -b $TRANSINDEX -u -o $Cufflinks_OUTPUT -G $GTF -p 12 -v $merge_bam/total.bam
Supplementary_files_format_and_content: Paired and unpaired fastq files from trimming step – each sample has two files of paired reads R1 and R2 and a file of unpaired reads
Supplementary_files_format_and_content: tab-delimited text files include FPKM values from Cufflinks for each Sample

organism: Acetivibrio thermocellus

source_name: DSM 2360_Exponential

growth_protocol: The type strains of Clostridium thermocellum, DSM 1237, 2360, and 4150, obtained from the German Type Culture collection, were employed for all growth experiments. Fresh cultures were maintained by routinely transferring 10% (v/v) mid-exponential phase inoculum into complex 1191 medium containing 2.2 g L-1 (11.8 mM) cellobiose. Cultures were grown at 60C and stored anaerobically at 4C. Cells for RNAseq sampling were grown in anaerobic Balch tubes (26 mL; Bellco Glass Inc., Vineland, NJ) in 10 mL of 1191 medium (pH 7.2) on 2.2 g L-1 cellobiose. 1191 media preparation and inoculation protocols were followed as described by Islam, Cisek, Sparling &Levin (2006). Samples were taken in exponential and stationary phase (OD600 ~ 0.37 and ~0.80, respectively).

extract_protocol:
Cells for RNAseq sampling were grown in anaerobic Balch tubes (26 mL; Bellco Glass Inc., Vineland, NJ) in 10 mL of 1191 medium (pH 7.2) on 2.2 g L-1 cellobiose.  1191 media preparation and inoculation protocols were followed as described by Islam et al.  Samples were taken in exponential and stationary phase (OD600 ~ 0.37 and ~0.80, respectively).  Cell pellets were stored at -80 °C in 1 ml RNAlater until ready for processing. Total RNA was extracted from 10 ml mid-exponential and late exponential  (OD600 ~ 0.37 and ~0.80, respectively) Clostridium thermocellum cultures using the RNeasy Mini kit (QIAGEN, Valencia, CA, USA) protocol as described for gram-positive bacteria, but with the following modifications.  Cell pellets were collected by centrifugation and re-suspended in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) containing 20 mg/ml lysozyme and incubated at 37 °C for 30 minutes.  To ensure efficient lysis, a mechanical shearing step was included that involved passing the cell pellets 10 times through a 22G syringe prior to the addition of ethanol.  Total RNA was eluted in 30 μl RNase-free water.  Following the first elution, the entire volume was re-applied to the mini column, incubated for 3 minutes and finally centrifuged at 8000 x g for 1 minute.
Illumina Truseq mRNA

tag: strain

tag: growth phase

value: Exponential


title: DSM 4150 exponential

source_name: DSM 4150_Exponential


title: DSM 1237 stationary replicate 1

source_name: DSM 1237_Stationary

value: Stationary


title: DSM 1237 exponential replicate 1

source_name: DSM 1237_Exponential


title: DSM 1237 exponential replicate 2


title: GFP-expressing retina sample 3

city: Los Angeles

first: Philip

middle: James

last: Uren

state: CA

address: 1050 Childs Way, RRI201

institute: University of Southern California

data_processing:
Reads were mapped to mm9 using RMAP
Non-mapping reads were then mapped to a junction databse constructed from RefSeq transcripts (aquired from UCSC table browser)
Reads were counted to genes using in-house python scripts. Paired-end reads were treated as independed reads and pooled.
Genome_build: mm9
Supplementary_files_format_and_content: BED format counts of reads mapped to genes defined from RefSeq transcripts collapsed to single-super transcript. Transcript/gene definitions from UCSC table browser.

molecule: polyA RNA

organism: Mus musculus

source_name: whole retina, mouse

growth_protocol: Retinae were dissected from six to nine-week mice, and slight variation may stem from the different ages when samples were collected: rd10 mice at P61, wild-type at P48, Gg13 at P42.

extract_protocol:
Following whole retina isolation, sample tissue was placed in 100 μl Trizol reagent within a 1.5 ml Eppendorf (Qiagen, Valencia, CA). Each sample contained 2 whole retinae. With a pestle rotor and RNA-free mortar, we dissociated the retina with brief pulsations for 60 seconds until homogenous, followed by a gentle trituration.
Poly (A)-containing mRNA molecules were purified from total RNA using poly (T) oligo-attached magnetic beads, then mRNA were fragmented into small pieces using fragmentation reagent; First-strand cDNA was generated using random hexamer-primed reverse transcription. This was followed by a second-strand cDNA synthesis and a cDNA purify using purification Kit; The second-strand cDNA synthesis was performed after the first-strand synthesis finished. This was followed by a cDNA purification using purification kits; The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments; The products of the ligation reaction were purified on TAE-agarose gel. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; The Library was validating on the Agilent Technologies 2100 Bio-analyzer and the ABI StepOnePlus Real-Time PCR System.

tag: retina condition

value: Normal

tag: genotype

value: GFP-expressing

value: retina


title: GFP-expressing retina sample 2


title: GFP-expressing retina sample 1


title: rd10 retina sample rep 3

value: Degenerated


title: 21B

status: Public on Oct 25 2014

city: East Lansing

first: Nicholas

middle: Louis

last: Panchy

state: MI

address: 1066 Bouge St., Room 2275

department: Genetics

institute: Michigan State University

data_processing:
Reads of each of samples were mapped using Tophat with default parameters except for intron length (min 13, max 8712) and max-multi-hits (1). Gene models on non-chromosomal fragments were not considered.
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) per gene was calculated using Cufflinks (Trapnell et al. 2010) with parameter –I 8712.
Upper quartile normalization was applied to all samples to correct for technical variation as recommend by (Bullard et al. 2010).
Genome_build: C. reinhardtii genome version 4.3 from Phytozome

organism: Chlamydomonas reinhardtii

source_name: Whole cells

growth_protocol: C. reinhardtii dw15.1 was grown in 200 mL TAP culture in flasks without aeration to density of 25 million cells mL-1 in constant light (50 mmol s-1 m-2), at 100 rpm, and 22 °C. Using this culture we set up 50 mL cultures of 0.5 million cells mL-1 that were transferred to 12 h light (50 mmol s-1 m-2) and 12 h dark conditions for 48 hours prior to sampling.

extract_protocol:
2 mL of the culture was placed in a 2 mL tube and centrifuged at max speed in at 4°C for 10 min. The supernatant was removed in the dark and the pellets were snap frozen in liquid nitrogen. The frozen samples were ground using the Qiagen tissue lyser.  RNA was extracted using the Omega eZNA Plant RNA kit. The RNA was eluted in 50 mL DEPC-H2O and the concentration was measured using a Nanodrop (Thermo-Fisher).
Library preperation was dond using the Illumina Tru-Seq Stranded kit

treatment_protocol: Two biological replicates were collected every 3 hours between ZT (Zeitgeber Time, hours since last dawn) 0 and ZT 21. Each sample originated from an independent 50 mL culture. Samples collected during the light to dark or dark to light transition were taken just prior to change of conditions

tag: zt (zeitgeber time)


title: Wild-type retina sample rep 1

value: wild type


title: Wild-type retina sample rep 3


title: rd10 retina sample rep 1


title: LANA ChIPSeq BCBL-1 BR1


title: Wild-type retina sample rep 2


title: 18B


title: 18A


title: rd10 retina sample rep 2


title: H3K4me3 ChIPSeq BCBL-1 BR1


title: DSM 1237 stationary replicate 2


title: 12A


title: 21A


title: 15B


title: 12B


title: 9B


title: HAEC-GRO-Seq-Notx-2h

description: library strategy: GRO-Seq

value: Pool of at least 3 individuals

value: human aortic endothelial cells


title: 9A


title: Rat IgG ChIPSeq BCBL-1

value: control rat IgG ((Santa Cruz Biotechnology, sc-2026)


title: 3A


title: 0B


title: 6A


title: 3B


title: 0A


title: 26-4

city: Portland

first: David

last: Ellison

state: OR

address: 3181 SW Sam Jackson Park Rd CR145

institute: Oregon Health and Science University

data_processing:
We removed reads with adapter contamination using cutadapt 1.2.1
For all samples, we trimmed 3 bp from the 5 prime end and 1 bp from the 3 prime end.
All samples were aligned to the unmasked mouse genome (mm10) using subread 1.3.6-p1.
Transcript and exon data (gtf file) was obtained from UCSC.  We mapped isoforms to gene using the UCSC Table Browser.  Gene counts was obtained by summing the counts of all isoforms
The biomaRT package from Bioconductor was used to annotate UCSC Gene ID to Ensembl ID.
Differential Expression Analysis was conducted using the edgeR package from Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited edgeR Output with common and tagwise dispersion analysis results.

source_name: 15 (+/- 0.5) day fetal liver

growth_protocol: For HFD studies, C57BL/6 CD45.2 female mice (Jackson Labs) were fed a 60% kcal% fat diet (D12492, Research Diets, New Brunswick, NJ) or a 13.5% kcal% fat diet (Laboratory Rodent Diet 5001, Lab Diet, St. Louis, MO) ad libitum.

extract_protocol:
Whole livers from 6 control and 6 HFD male fetuses were frozen in RNALater and total RNA was extracted using RNeasy (Qiagen).
An mRNA library was prepared by the OHSU Massively Parallel Sequencing Shared Resource, using the Illumina TruSeq RNA Sample Prep Kit v2. Starting with total RNA, mRNA was purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Next, the second strand was generated to create double-stranded cDNA. Blunt-end DNA fragments were then generated using fill-in reactions and exonuclease activity. An ‘A’- base was added to the blunt ends of each strand, preparing them for ligation to the coded sequencing adapters. Once the adapters were ligated, the constructs were then subject to 10 rounds of PCR. The amplified libraries were purified and underwent quantitative PCR with an ABI StepOne real-time PCR system. Libraries are diluted to an empirically determined concentration appropriate for the flow cell in use and applied using an Illumina cBot. Flow cells were sequenced on an Illumina HiSeq 2000.

treatment_protocol: A cohort of dams were fed HFD or control diet for 12-14 weeks, and their offspring were harvested at 15 +/- 0.5 dpc.

tag: diet

value: High-fat

value: liver


title: 21-9


title: 23-2


title: 26-7


title: 23-1


title: 26-3


title: 15-7

value: Control


title: 15A


title: 15-6


title: 15-3


title: 15-1


title: co-exo_1

status: Public on Oct 24 2014

city: Philadelphia

first: Andy

last: Minn

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description: exosome RNA

data_processing:
Basecalls performed using Illumina CASAVA software.
Sequenced reads were trimmed for adaptor sequence, then mapped to consensus rRNA sequences using bowtie2 v2.1.0 to remove rRNA reads (parameter --local), then mapped to human hg19 genome with tophat2 v2.0.10 (parameter  -g 1 --library-type fr-firststrand)
Mapped RNA reads were catergorized (transcripts, repeat elements, ingtergenic region etc.) with a customized R script (use countOverlaps function in GenomicRanges package).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including percentage of different RNA catergories in each sample.

source_name: co-culture of 1833 and MRC5

growth_protocol: Cells were cultured at 37º C in DMEM. Media was supplemented with 10% FBS, 100 U/mlpenicillin and 100 μg/ml streptomycin, 2 mM L-glutamine, and 10 mM HEPES. For co-cultures, breast cancer cells were mixed 1:1 with stroma, and cultured in DMEM with 10% FBS.

extract_protocol:
Exosomes were isolated from conditioned media by ultra-centrifugation.  RNA were extracted with Trizol reagent.
rRNAs were removed from cellular RNA by RiboZero Gold kit.  RNA-seq library were constructed with NEBNext Ultra Directional RNA Library Prep Kit.  Size selection steps were modified to keep smaller RNA fragments.

tag: culture type

value: co-culture

tag: sequence index

value: CAGATC


title: co-cel_1

description: total cellular RNA

value: TGACCA


title: DNA2.2

city: San Francisco

first: Peter

last: Turnbaugh

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

data_processing:
Pre-processing of raw reads: binned according to barcode, trimmed ends to min score = 20 and minimum length = 20
Mapped reads to 539 human-associated microbial genomes using SSAHA (version 2; parameters: -best 1 -score 20 -solexa)
The number of transcripts assigned to each gene was then tallied.
Genome_build: http://www.hmpdacc.org/
Supplementary_files_format_and_content: Counts files were generated. Values are total reads assigned and fraction reads assigned (#reads/total reads).

organism: mouse gut metagenome

source_name: Fecal microbial community

growth_protocol: Fecal samples were collected and stored at -80C.

extract_protocol: DNA and RNA was isolated using the guanidinium thiocyanate/cesium chloride gradient method. RNA was subjected to DNase treatment (Ambion), purification using MEGAClear columns (Ambion), and rRNA depletion via subtractive hybridization (MICROBExpress, Ambion, in addition to custom depletion oligos). The presence of genomic DNA contamination was assessed by PCR with universal 16S rDNA primers. cDNA was synthesized using SuperScript II and random hexamers (Invitrogen), followed by second strand synthesis with RNaseH and E.coli DNA polymerase (New England Biolabs). Samples were prepared for sequencing with an Illumina HiSeq instrument after enzymatic fragmentation (NEBE6040L/M0348S). Libraries were quantified by quantitative PCR (qPCR) according to the Illumina protocol. qPCR assays were run using ABsoluteTM QPCR SYBR Green ROX Mix (Thermo Scientific) on an Mx3000P QPCR System instrument (Stratagene, La Jolla, CA). The size distribution of each library was quantified on an Agilent HS- DNA chip.

treatment_protocol: Mice were sampled before and after exposure to LPS.

tag: mouse

tag: timepoint

value: Post-LPS

tag: cage

value: KO


title: 19-8

tag: tissue


title: co-exo_2

description: exosome RNA

value: TAGCTT


title: co-exo_3

description: exosome RNA

value: CTTGTA


title: DNA1.1

value: Pre-LPS


title: DNA1.2


title: DNA2.1


title: DNA6.2


title: 6B


title: DNA6.1


title: DNA4.2

value: Het


title: DNA4.1


title: DNA3.1


title: 19-6


title: Pol α BrdU IP repeat

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

description: Sample name: y39

data_processing:
Reads were aligned to the yeast genome (sacCer3) using the Bowtie2 software. Only the consist pair reads were used for the further analysis.
The genome-wide reads coverage of Watson and Crick strand was calculated by BEDTools and  in-house Perl  programs.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: For G1 cell synchronization, alpha factor was added at cell density OD600=0.4-0.5 to finial concentration at 5ug/ml for wild type Bar1 and 50ng/ml for bar1 mutants.  After 3hr arrest at 30°C, the cell was released to fresh YPD medium with or without 200mM hydroxyurea.

extract_protocol:
the collected samples were incubated with 1% fresh-made formaldehyde at 25°C for 20mins, and quenched with 0.125M Glysine for 5mins.  The harvested cells were lysed with glass beads, and the chromatin pellet were washed and sonicated. The average DNA fragment size is about 200-400bp.  Sheared chromatin was immunoprecipitated with an protein-specific antibody. The chromatin was reverse-cross-linked and immunoprecipitated.  DNA was exacted with the Chelex-100 method
ssDNA library preparation method was modified from previous one (Meyer et al., 2012). To preserve the strand information, we use a specific RNA ligase, which also can ligated the ssDNAs in a sequence-independent way. The ssDNA library strand information was kept by sequential 3’ end and  5’ end ligation.

tag: media

value: YPD+HU

tag: cell cycle stage

value: S

tag: chip antibody

value: Anti-BrdU (BD BioScience, 347580)


title: DNA5.2


title: RUNX1_2

city: La Jolla

first: Kentson

last: Lam

address: 3855 Health Sciences Drive

institute: University of California, San Diego

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly.
MACS was used for peak calling.
Genome_build: mm9
Supplementary_files_format_and_content: peak chromosomal coordinates and values

source_name: EML cells

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: EML

value: Rabbit polyclonal  anti-RUNX1 (non-commercial antibody)


title: RNA2.2


title: DNA3.2


title: IgG2

value: Rabbit Serum IgG (Sigma I5006)


title: IgG1


title: RNA2.1


title: RNA1.2


title: RNA6.1


title: RUNX1_1


title: RNA4.2


title: RNA5.2


title: RNA3.1


title: RNA5.1


title: 1 uM S-equol rep2 4529

city: Columbia

first: Charles

middle: Michael

last: Greenlief

state: MO

address: 601 S. College Ave.

department: Department of Chemistry

institute: University of Missouri

description: The MCF-7 were infected with either control adenovirus expressing B-galactosidase (Ad) or adenovirus expressing ERB (AdERbeta) for 72 h.  For knockdown of the endogenous ERa in MCF-7 cells, cells were treated with siRNA for 24h (AdERbeta+SiERalpha).  Then cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 uM BEs for 24h.

data_processing:
Illumina Casava 1.8.2 software used for basescalling
The read data from the HiSeq 2000 were processed and analyzed through a series of steps. First, FASTX-Toolkit [35] was used to trim RNA-Seq reads to remove adaptors and filter out reads with low quality (quality score <20). TopHat [36] and Bowtie [37] were employed to map RNA-Seq reads to versions hg18 and hg19 of the Homo sapiens reference genomes in the UCSC genome browser [38], in conjunction with the RefSeq genome reference annotation [39]. The threshold of the maximum number of mismatches was set to 2. MULTICOM-MAP [40-42] was used to remove reads mapped to multiple locations on a reference genome from the mapped data in the BAM/SAM format [43]. Only reads that mapped to a unique location on the genome were retained to calculate the read counts of the genes. Gene expression values (raw read counts) were calculated using our in-house tool MULTICOM-MAP [40-42] and a public tool HTseq [44] according to the genome mapping output and the RefSeq genome reference annotation [39]. Differentially expressed genes were then determined. The control samples were compared to each of the treatment samples.

source_name: Breast

extract_protocol:
After treatment RNA was extracted from the cells using the Illumina truseq RNA seq v2 kit. A total of 2.5 ug of total RNA was used for the library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment

value: 1 uM S-equol

tag: cell line

tag: cell

value: AdERbeta

value: Epithelial

tag: cell subtype

value: Adenocarcinoma

tag: age

tag: Sex

value: Female

tag: culture collection

value: ATCC

tag: biomaterial provider


title: 1 uM Liq rep2 4541

value: 1 uM liquiritigenin


title: RNA4.1

tag: genotype


title: DNA5.1

tag: mouse


title: 1 uM Liq rep2 4493

value: AdERbeta+SiERalpha


title: 1 uM Liq rep1 4492


title: 1 uM S-equol rep1 4528


title: 1 uM S-equol rep1 4486


title: 1 uM S-equol rep2 4487


title: 1 uM Liq rep1 4540


title: RNA1.1

tag: timepoint

value: KO


title: RNA6.2

value: Post-LPS

tag: cage


title: V rep2 4474

value: control


title: V rep1 4473


title: 10 nM E2 rep2 4477

value: 10 nM E2


title: 10 nM E2 rep2 4432


title: RNA3.2

value: Het


title: V rep2 4428


title: 1 uM Liq rep1 4399

value: Ad


title: Rat pineal gland, post-natal day 40 (P40), mid-night (ZT19)

city: Bethesda

first: Steven

last: Coon

state: MD

address: 49 Convent Drive Room 6A83

department: NICHD/PDEGEN

institute: NIH

data_processing:
Image analysis and base calling were done using RTA1.10.36 and CASAVA1.7.0.
RNA-Seq reads were aligned to the rn4 genome assembly using Tophat-1.3.1.Linux_x86_64
FPKM values were calculated using Cufflinks-1.2.0.Linux_x86_64
Genome_build: rn4

organism: Rattus norvegicus

source_name: Pineal gland

extract_protocol:
Total RNA was extracted with Trizol, followed by clean-up using RNeasy Micro kit with on-column DNase treatment. Quantitation and quality assurance were performed using a NanoDrop and Bioanalyzer, respectively.
An NEB Master Mix kit was used wherein 10 µg of total RNA was polyA-RNA-enriched using streptavidin-coated magnetic beads, followed by Covaris RNA fragmentation. Fragmented RNA was used to generate cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was ligated to Illumina paired end (PE) adaptors containing a 6-basepair bar-code. Size selection was performed using a Pippin Prep 1.5% cartridge. Libraries were enriched using 16 cycles of PCR and purified using the Ampure XP Beads (Agencourt). Each library was run as one of four bar-coded samples per lane on an Illumina HiSeq machine yielding paired-end,  101-base sequencing reads. Image analysis and base calling were done using RTA1.10.36 and CASAVA1.7.0.

treatment_protocol: Rats were housed in 14:10 lighting cycle

tag: strain

value: Sprague-Dawley

tag: tissue

value: Pineal gland

tag: animals in pool

tag: time of day

value: mid-night (ZT19)

value: post-natal day 40 (P40)


title: Rat pineal gland, post-natal day 40 (P40), mid-day (ZT7)

value: mid-day (ZT7)


title: Rat pineal gland, post-natal day 20 (P20), mid-night (ZT19)

value: post-natal day 20 (P20)


title: Rat pineal gland, post-natal day 20 (P20), mid-day (ZT7)


title: 1 uM S-equol rep1 4393

value: 1 uM S-equol

tag: cell type

value: Epithelial

value: Adenocarcinoma


title: 1 uM Gen rep2 4481

tag: treatment

value: 1 uM genistein

value: Female

value: ATCC


title: 1 uM Gen rep1 4480

tag: cell line

value: AdERbeta+SiERalpha


title: Rat pineal gland, post-natal day 5 (P5), mid-night (ZT19)

value: post-natal day 5 (P5)


title: Rat pineal gland, post-natal day 5 (P5), mid-day (ZT7)


title: 1 uM Gen rep1 4387

tag: cell


title: 10 nM E2 rep2 4382

value: 10 nM E2

tag: cell subtype


title: Rat pineal gland, embryonic day 21 (E21), mid-day (ZT7)

tag: age

value: embryonic day 21 (E21)


title: 10 nM E2 rep1 4431

value: AdERbeta

tag: Sex


title: V rep2 4379

value: control

value: Ad

tag: culture collection


title: 10 nM E2 rep1 4381

tag: biomaterial provider


title: 1 uM S-equol rep2 4395


title: 1 uM Liq rep2 4401

value: 1 uM liquiritigenin


title: V rep1 4378


title: PD-2_2

first: Aiqun

last: Li

address: 3960 Broadway

department: Research Institute

institute: The New York Stem Cell Foundation

data_processing:
The reads were mapped to a reference genome (Human: NCBI/build37.2) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). The relative abundance (aka expression level) of genes and splice isoforms were evaluated using cufflinks (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq. The differential expression signature and differential pathways enrichment were identified with a statistical significance (P < 0.01). To specifically discover the profile of genes involved in DA synthesis, storage, release, re-uptake, metabolism, and PD pathogenesis in both twins, the average FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) value from four biological replicates of each twin and their ratio of FPKM (affected twin vs. unaffected twin) were calculated. Positive/negative fold change mean an up-regulation and a down-regulation, respectively. 2-fold change was used as an arbitrary cut- off point in this analysis.
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: csv files include FPKM values for each Sample

source_name: iPS cell-derived neuronal samples

extract_protocol:
RNA was extracted using RNeasy Micro Kit (QIAGEN). Quality control of the RNA was carried out with the Agilent Bio-analyzer, Qubit 2.0 at the MPSR of Columbia University. 100 ng of RNA with RIN ≥ 9 were used for generating mRNA-focused libraries.
RNA libraries were prepared using TruSeq RNA Sample Preparation Kit v2

value: iPS cell-derived neuronal samples

tag: diferentiation day

value: ~ day 33

tag: disease

value: Parkinson's Disease

tag: genotype

value: GBA +/N370S


title: 1 uM Gen rep1 4434

value: Epithelial


title: 1 uM Gen rep2 4389

value: Adenocarcinoma


title: Non-PD-2_2

value: Healthy


title: PD-1_1


title: Non-PD-2_1


title: Non-PD-1_2


title: Non-PD-1_1


title: C2_2

value: Wild Type GBA


title: Sporadic PD-1_1


title: C1_2


title: 10 nM E2 rep1 4476

value: Female

value: ATCC


title: C2_1


title: PD-2_1


title: C1_1


title: Rat pineal gland, embryonic day 21 (E21), mid-night (ZT19)

value: Sprague-Dawley

value: Pineal gland

value: mid-night (ZT19)


title: 3 months rep2

status: Public on Oct 23 2014

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

data_processing:
Reads were aligned using BWA (Li and Durbin, 2009) to mm9. Duplicate reads (replicate 1) and fragments (replicate 2) were removed from the analysis. Reads (replicate 1) and fragments (replicate 2) (phred score > 30) that aligned uniquely were used for subsequent analysis.
Reads for each sample were down sampled to the same number (150 million). Nucleosome calls (~8.5 million nucleosome peaks) and changes in nucleosome occupancy were calculated by the DANPOS software (p-value < 1X10-7 in Poisson test, parameters: w=150, d=150, extend=148 for single-end, 74 for paired-end).
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet peaks file produced by DANPOS with nucleosome occupancy values. Columns include (Chr:  chromosome, Start: peak start position, End: peak end position, Smt_pos: peak summit position, Smt_value: peak summit value,   Smt_Pval: P-value of the summit value, Fuzziness_score: peak fuzziness score, Fuzziness_pval: P-value of the peak fuzziness score). Further DANPOS documentation can be found at https://code.google.com/p/danpos/)

source_name: Liver

extract_protocol:
Digestion was performed on snap-frozen liver. 100 mg of tissue was pulverized (Covaris cryoPrep impactor), and nuclei were purified using a sucrose gradient. The nuclei were digested with MNase (Roche catalog number 10107921001) at 37ºC for 12 minutes. Several titrations of MNase enzyme were tested. Samples that were well-digested, with most of the input as a mononucleosome (150 bp) and a slight band of a dinucleosome (300 bp) visible on a BioAnalyzer trace, to prevent over-digestion, were used for subsequent library preparation.
Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Broad custom adapters were then ligated to the ends of the modified DNA.  After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp mononucleosome insert plus ~130-bp adaptor and PCR primer sequences) were  isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Hiseq 2000 following the manufacturer's protocols.

value: Liver

value: 3 months


title: 21 months rep2

value: 21 months


title: 3 months rep1


title: V rep1 4427

value: control

value: AdERbeta


title: Sporadic PD-1_2

value: iPS cell-derived neuronal samples

value: ~ day 33


title: 21 months rep1


title: 18 somites stage, straightened, sectioned tail to head

city: Utrecht

first: Jan Philipp

last: Junker

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: only trunk and tail of embryo

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The mouse transcriptome contained all RefSeq gene models based on the mouse genome release mm10. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the manuscript (Table S1). The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)
Genome_build: mm10 and zv9 (with improved 3' annotation)
Supplementary_files_format_and_content: text files: read count matrices in which rows correspond to genes and columns to sections

organism: Danio rerio

source_name: deyolked embryo, head removed

extract_protocol:
RNA was isolated by TRIzol extraction
mRNA was barcoded and amplified using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012)

treatment_protocol: Unfixed samples (zebrafish embryos or mouse forelimbs) were embedded in tissue freezing medium. Blocks were cryosectioned, and individual slices were transferred to Eppendorf tubes on dry ice.

tag: Stage

value: 18 somites

tag: sectioning direction

value: tail to head

tag: section thickness

value: 24 µm

tag: embedding strategy

value: deyolked and straightened embryo


title: 15 somites stage, straightened, sectioned tail to head

source_name: deyolked embryo

value: 15 somites

value: 18 µm


title: 15 somites stage, straightened, sectioned head to tail

value: head to tail


title: 15 somite stage, sectioned from left to right

source_name: whole embryo

value: left-right

value: intact embryo


title: 15 somite stage, sectioned from dorsal to ventral end

value: dorsal-ventral


title: 15 somite stage, sectioned from ventral to dorsal end

value: ventral-dorsal


title: 15 somites stage, straightened, sectioned tail to head, replicate


title: 15 somite stage, sectioned from anterior to posterior end

value: anterior-posterior


title: 15 somite stage, sectioned from posterior to anterior end

value: posterior-anterior


title: 10 somite stage, sectioned from right to left

value: 10 somites

value: right-left


title: 10 somite stage, sectioned from left to right


title: sections 97-108 for samples dr_15ss_TH and dr_15ss_HT

description: dr_15ss_TH sections 97-108 have barcodes 1-12; dr_15ss_HT sections 97-108 have barcodes 13-24 [only 96 different barcodes were used in this study, but these embryos were sectioned into 108 slices]

value: head to tail and tail to head


title: 1 uM Gen rep2 4435

value: 1 uM genistein

value: AdERbeta

value: Epithelial

value: Adenocarcinoma

value: Female

value: ATCC


title: shield stage, sectioned from dorsal to ventral end, replicate

value: shield stage

value: 18 µm


title: 10 somite stage, sectioned from anterior to posterior end, replicate


title: 10 somite stage, sectioned from anterior to posterior end


title: H82 H3K27ac

city: Cambridge

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads in 50 bp bins with each read extended 200 in the direction of alignment as calculated by MACS and normalized to million mapped reads
Supplementary_files_format_and_content: Corrected WIG files represent counts of aligned reads in 50 bp bins with each read extended 200bp in the direction of alignment as calculated by MACS.  Background correction was used by subtracting values from the Input RPM-normalized WIG from the H3K27ac RPM-normalized WIG

source_name: Small Cell Lung Carcinoma

growth_protocol: NCI-H82 cells were obtained from ATCC and grown in RPMI with 10% FBS and 1% penn/strep.  NCI-H82 cells were grown and passaged at 0.5x10^6 cells /ml.

extract_protocol:
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin.

treatment_protocol: Cells were grown at 0.5x10^6 cells in RPMI medium and treated with DMSO for 6 hours and then cross linked with formaldehyde.

tag: chip antibody

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: system

value: Lung

tag: cell number

value: 20 million

tag: drug

value: DMSO

tag: concentration

tag: time point

value: 6 hrs


title: H69 input

growth_protocol: NCI-H69 cells were obtained from ATCC and were grown in RPMI with 10% FBS and 1% penn/strep.  NCI-H69 cells were grown and passaged at 0.5x10^6 cells /ml.

tag: cell type


title: GLC16 H3K27ac

growth_protocol: GLC16 was grown in RPMI with 10% FBS and 1% penn/strep.  GLC16 cells were grown and passaged at 0.5x10^6 cells /ml.

treatment_protocol: Cells were grown at 0.5x10^6 cells in RPMI medium and treated with 0.1% DMSO for 6 hours and then cross linked with formaldehyde.


title: 15 somite stage, sectioned from right to left

value: 15 somites

value: intact embryo


title: shield stage, sectioned from ventral to dorsal end

value: ventral-dorsal


title: shield stage, sectioned from left to right

value: left-right


title: shield stage, sectioned from right to left

value: right-left


title: shield stage, sectioned from dorsal to ventral end

value: dorsal-ventral


title: H69 H3K27ac


title: H82 input


title: shield stage, sectioned from vegetal to animal pole

value: vegetal-animal


title: GLC16 input


title: shield stage, sectioned from vegetal to animal pole, replicate


title: shield stage, sectioned from animal to vegetal pole

value: animal-vegetal


title: old whole gut rep2

city: Baltimore

first: Yixian

last: Zheng

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

data_processing:
Bases are called using Illumina pipeline Casava 1.8.
Reads are mapped to the drosophila genome using Tophat2. Refseq annotations of known exon junctions are provided with -G option.
Number of reads on each gene were counted using custom script, and differentially expressed genes were called using edgeR.
Genome_build: Dm3
Supplementary_files_format_and_content: tab-delimited text file listing the number of reads on each gene

organism: Drosophila melanogaster

source_name: whole gut

extract_protocol:
Dissected adult fat bodies, midguts, or whole guts were used to prepare RNA using Arcturus PicoPure RNA  isolation kit (Life Technologies # KIT0204).
Poly-A selected mRNA was purified and sequencing libraries were built using Illumina TruSeq RNA sample prep kit V2 (Illumina  # RS-122-2001).

treatment_protocol: Natural aging or RNAi

tag: age(days)

tag: treatment

value: no


title: 10 somite stage, sectioned from posterior to anterior end

value: 10 somites

value: anterior-posterior


title: old whole gut rep1


title: chd1ChIP_set2del_rep1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the sacCer3 genome assembly using BWA (Version: 0.5.9-r16) with default options
Genome_build: sacCer3
Supplementary_files_format_and_content: Wig format

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Growth conditions were 30°C in YPD media with shaking at 250 rpm. Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8), and fixed with formaldehyde.

extract_protocol:
Cross-linked chromatins were sheared using a sonicator, and immunoprecipitated using the following beads or anti-body:anti-Myc conjugated agarose bead (Sigma Aldrich, cat.# E6654) to pull-down Chd1 in the Chd1-13XMyc strains, and RNAPII Ser5P/Ser2P antibody (Abcam, cat.# ab5131 and ab5095) to pull-down elongating RNAPII.
The NEB ChIP-seq library preparation for Illumina (New England BioLabs) was used to sequence the samples using Illumina HiSeq 2000.

tag: genotype/variation

value: SET2 deletion

tag: ChIP


title: pol2ser2ChIP_chd1del

value: CHD1 deletion

value: RNAPII Ser2P antibody (Abcam, ab5095)


title: chd1ChIP_wt_rep2

value: wildtype


title: 306wor1

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

description: Sample 1

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text files containing RPKM values for each Sample

organism: Candida albicans

source_name: candida albicans

growth_protocol: Cells were grown in Lee’s glucose liquid medium at 25°C for 24 hours and inoculated into fresh Lee’s glucose medium (1 x 107 cells/ml). a-Pheromone peptide was added to the cultures every 8 hours over a 24 hours period.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: white cell

value: control


title: chd1ChIP_set2del_rep2


title: Lam-RNAi midgut rep2

source_name: midgut

value: Lamin-RNAi


title: 306wor1+ factor

description: Sample 2

value: a-Pheromone peptide


title: 10 somite stage, sectioned from ventral to dorsal end

tag: Stage

value: ventral-dorsal

value: 18 µm

value: intact embryo


title: young  whole gut rep2


title: Lam-RNAi midgut rep1


title: PD-1_2

value: iPS cell-derived neuronal samples

tag: diferentiation day

value: ~ day 33

tag: disease

value: Parkinson's Disease

tag: genotype

value: GBA +/N370S


title: young  whole gut rep1

value: no


title: pol2ser2ChIP_wt


title: chd1ChIP_wt_rep1


title: old midgut rep2


title: pol2ser5ChIP_wt

value: RNAPII Ser5P antibody (Abcam, cat.# ab5131)


title: Lam-RNAi fatbody rep2

source_name: fatbody


title: young  midgut rep1


title: old midgut rep1


title: Lam-RNAi fatbody rep1


title: old fatbody rep2


title: young  midgut rep2


title: pol2ser5ChIP_chd1del


title: old fatbody rep3


title: young  fatbody rep2


title: old fatbody rep1


title: young  fatbody rep1


title: G1183 mRNA-seq

city: Durham

first: Perry

last: Blackshear

address: 101 Alexander Dr.

institute: NIEHS

data_processing:
raw reads were mapped to cDNA sequences from flybase(ver r5.49) using the default paired-end read mapping protocol
the reads that were not mapped in-pair were filtered out
total read count of each transcript were reported and normalized by EpiCenter
FPKM were caculated using R script
Genome_build: flybase version r5.49
Supplementary_files_format_and_content: FPKM data in text file format

source_name: Male G1183

growth_protocol: Living flies; normal growth conditions

extract_protocol:
RNA was isolated from flies using the GE Healthcare RNA isolation kit. The RNA was quantitated using a Qubit fluorometer (Invitrogen)
Libraries were prepared according to Illumina's Instructions

tag: developmental stage

value: 1-5 day old

tag: gender

value: male


title: WT2 mRNA-seq

source_name: Male y w67c23 Wild Type


title: CPB_NT

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

data_processing:
Sequenced reads were trimmed for adaptor sequence, low quality reads (below Q20) were removed, overlapping pairs were merged and reads were mapped to StNIB potato transcriptome in CLC Genomics Workbench 6 using following parameters: minimum length fraction "0.8", minimum similarity fraction"0.8", unspecific match limit "10", Use strand specific assembly "No", Count paired reads as two "No" and Organism type "PROKARYOTE".
Reads Per Kilobase per Million mapped reads (RPKM) were calculated by summarizing read counts for transcripts belonging to same StNIB putative paralogue group and taking in account hte representative StNIB transcript length.
Genome_build: StNIB potato transcriptome available at http://gomapman.org/export/input/stNIB-v1_data/stNIB-v1_2013-02-18_3_seq_cds_nonredundant-CDS_fasta.rar
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for putative paralogue groups for all analysed samples.

organism: Solanum tuberosum

source_name: infested plant

growth_protocol: Plants were grown in a growth chamber and kept at 21 C in the light and 18 C in the dark, at a relative humidity of 75%, with 70–90 mmol/m2/s2 radiation and a 16-h photoperiod. Plants infested with CPB larvae were placed in  glass containers CPB feeding assays and non-infested (control) plants were grown outside glass containers in the same growth chamber.

extract_protocol:
Potato leaf samples (approx. 150 mg) were homogenised using TissueLyzer (Qiagen, Germany) and total RNA was extracted using RNeasy Plant Mini kit (Qiagen, Germany) as described in Baebler et al. (2009). RNA samples from potato leaves collected 24 h post CPB infestation were pooled to obtain four samples for each cultivar. Pooled samples were treated with DNase I and enriched for mRNA using oligo(dT) beads.
RNA libraries were prepared for sequencing using standard Illumina protocols at BGI Tech.

treatment_protocol: For the feeding assays, first instar CPB larvae were placed on upper developed leaves of four potato plants in each glass container. Leaves from infested and control plants were sampled 24 hours post infestation.

tag: cultivar

value: Desiree

tag: tissue

value: leaf

value: CPB infestation (24 hpi)

value: Desiree NT


title: Hdac3 21 old rep2

description: processed data file: Hdac3_old.bed

data_processing:
The reads were aligned to mouse genome (mm9; NCBI Build 37) using BWA (Li and Durbin, 2009). Duplicate reads were removed from the analysis. Reads (phred score > 20) that aligned uniquely were used for subsequent analysis.
Reads from two biological replicates were merged for each condition (Foxa2 young, Foxa2 old, Hdac3 young, Hdac3 old). PeakSeq algorithm (Rozowsky et al., 2009) was used to identify bound peaks against input controls (Foxa2: FDR 10%, q-value =0.12; Hdac3: FDR 5%, q-value=0.2).
Genome_build: mm9
Supplementary_files_format_and_content: bed files with peak calls from PeakSeq with the following columns: chromosome, begin coordinate, end coordinate, enrichment, q-value

source_name: C57BL/6_liver_old_Hdac3 ChIP-seq

extract_protocol:
Snap-frozen mouse liver (100 mg) from wild type mice was used to prepare chromatin. Foxa2-specific rabbit antiserum (Seven Hills Bioreagents, WRAB-1200) and rabbit antibody to Hdac3 (Abcam, ab7030) were used for immunoprecipitation.
Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Broad custom adapters were then ligated to the ends of the modified DNA.  After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~230 bp (~100-bp mononucleosome insert plus ~130-bp adaptor and PCR primer sequences) were  isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Hiseq 2500 following the manufacturer's protocols.

tag: strain

tag: age

value: 21 months

value: liver

tag: chip antibody

value: rabbit antibody to Hdac3

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Hdac3 young rep2

description: processed data file: Hdac3_young.bed

source_name: C57BL/6_liver_young_Hdac3 ChIP-seq

value: 3 months


title: CONT_NT

source_name: control non-infested plant

value: control


title: CONT_PVY

value: Igor

value: Igor NT


title: CPB_PVY


title: CONT_H


title: CPB_H


title: Hdac3 21 old rep1

description: processed data file: Hdac3_old.bed


title: Hdac3 young rep1

description: processed data file: Hdac3_young.bed


title: Foxa2 21 old rep2

description: processed data file: Foxa2_old.bed

value: Foxa2-specific rabbit antiserum

value: Seven Hills Bioreagents


title: Foxa2 young rep1

description: processed data file: Foxa2_young.bed


title: Foxa2 21 old rep1

description: processed data file: Foxa2_old.bed


title: Foxa2 young rep2

description: processed data file: Foxa2_young.bed


title: chd1del_his3mx_mnase

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the sacCer3 genome assembly using BWA (Version: 0.5.9-r16) with default options
Genome_build: sacCer3
Supplementary_files_format_and_content: Wig format

source_name: yeast cells

growth_protocol: Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8) at 30°C in YPD media with shaking at 250 rpm, and fixed with formaldehyde.

extract_protocol:
Cells were resuspended 20 ml of zymolyase buffer, and spheroplasts were made with 250 μg of zymolyase. The spheroplasts were spun down and resuspended in 2 ml NP buffer. Then, micrococcal nuclease (MNase) was added at a concentration from 40 U-100 U for 10 min at 37 °C. Digested chromatin was reverse-crosslinked with Proteinase K in 1% SDS and 10 mM EDTA solution at 65 °C overnight. After RNase A treatment, DNA was purified by phenol chloroform extraction followed by ethanol precipitation. Finally, DNA fragments of ~147 bp were size-selected with an E-gel system
The NEB ChIP-seq library preparation for Illumina (New England BioLabs) were used

treatment_protocol: For heat shock, mid-log phase yeast cells were collected and re-suspended in pre-warmed 39°C YPD media, then incubated for 15 min at 39°C.

tag: background genotype

tag: gene deletion

value: CHD1 by His3MX6

tag: temperature


title: set2del_kanmx_mnase

value: SET2 by KanMX6


title: wt_39_rep1_mnase


title: chd1del_kanmx_mnase

value: CHD1 by KanMX6


title: wt_30_rep2_mnase


title: forelimb, Gli3-/-, low resolution, sample 1

source_name: forelimb

tag: sectioning direction

value: posterior-anterior

tag: section thickness

value: 48 µm

tag: embedding strategy

value: forelimb


title: forelimb, wildtype, low resolution, sample 3

tag: Stage


title: forelimb, Gli3-/-, low resolution, sample 2


title: forelimb, Gli3-/-, low resolution, sample 3


title: CPB_coi1

value: Desiree

value: leaf

tag: treatment

value: CPB infestation (24 hpi)

tag: genotype

value: Desiree coi1


title: forelimb, Gli3-/- high resolution

value: 24 µm


title: CONT_coi1


title: forelimb, wildtype, low resolution, sample 2


title: forelimb, wildtype, low resolution, sample 1


title: 3 months rep3

data_processing:
RNA-Seq reads were aligned using TopHat (Trapnell et al., 2009) to mouse genome build mm9
Expression levels were calculated using RSEM algorithm (Li and Dewey, 2011).
Differential expression analysis of RNA-seq (p-value <0.05) was performed in R using EdgeR package (Robinson et al., 2010), with a Benjamini-Hochberg FDR of 5%.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files with abundance counts calculated by RSEM algorithm, including expected_count, TPM (transcript per million, and FPKM  values (full details on format @ http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html#output)

source_name: Liver

extract_protocol:
Isolation of total cellular RNA from  liver was performed using Trizol and RNeasy Kit (Qiagen). RNA was quantified using the RNA 6000 Nano Assay program of the Agilent 2100 Bioanalyzer (Agilent Technologies)
Total RNA (2 µg) was enriched for mRNA (Dynabeads mRNA direct kit, Life Technologies) used for strand-specific library preparation. mRNA was fragmented (Ambion fragmentation buffer, 70°C for 3 min), dephosphorylated, and concentrated (RNA Clean & Concentrator columns, Zymo Research). Ligation with RNA adapters was followed by first strand cDNA synthesis (AffinityScript reverse transcriptase enzyme). RNA was degraded (EDTA & NaOH) while adapters containing barcodes were ligated to cDNA, which subsequently was amplified for 10 cycles of PCR (KAPA HiFi DNA Polymerase, Kapa Biosystems).

value: Liver

value: 3 months


title: Jun-D knockdown in PC3 cells using shRNa replicate 2

city: Bloomington

last: Hollenhorst

state: Indiana

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using TopHat2 (v2.0.7) running BowTie2 (v2.0.6) and Samtools (v.0.1.18) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The parameters used were -G -p 8
Differential expression of aligned reads was produced using Cufflinks (v2.1.1) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The three replicates for each shRNA PC3 cell line were combined for the differential expression analysis. The parameters used were -b -p 8 -u -L
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include for each combination of replicates: RPKM values, locus, status, log2(fold_change), test_stat, p-value, q-value, and significance

source_name: Jun-D knockdown in PC3 cells using shRNA

growth_protocol: PC3 cells were maintained in F12K media (Mediatech-Cellgro) with 10% FBS, 100 U/ml Penicillin/Streptomycin, and 2 microgram/ml puromycin

extract_protocol:
Total RNA was isolated from PC3 cells transduced with lentiviral shRNA knockdown vectors using the Rneasy mini kit (Qiagen) according to manufacturer's instruction
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol.Total RNA was DNAase treated with TURBO DNase (Invitrogen) The DNase treated RNA was polyA selected with oligo(dT) beads (Invitrogen). A Superscript III Reverse Transcriptase First-Strand Synthesis (Invitrogen) system was used to generate cDNA from the polyA selected RNA with random hexamer primers (Invitrogen). After first strand synthesis a second strand was generated using E. coli DNA ligase (New England BioLabs) and E. coli DNA polymerase I (New England BioLabs). The double stranded cDNAs were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

tag: cell line

tag: source tissue

value: bone metastasis of grade IV prostate cancer

tag: cell type

value: prostate cancer cells

tag: genotype/variation

value: Jun-D knockdown


title: 21 months rep1

tag: strain

tag: tissue

tag: age

value: 21 months


title: 3 months rep4


title: 21 months rep3


title: Jun-D knockdown in PC3 cells using shRNa replicate 3


title: Jun-D knockdown in PC3 cells using shRNa replicate 1


title: 3 months rep2


title: wt_30_rep1_mnase


title: 21 months rep2


title: 3 months rep1


title: c-Jun knockdown in PC3 cells using shRNa replicate 2

source_name: c-Jun knockdown in PC3 cells using shRNA

value: c-Jun knockdown


title: c-Jun knockdown in PC3 cells using shRNa replicate 1


title: c-Jun knockdown in PC3 cells using shRNa replicate 3


title: Luciferase knockdown in PC3 cells using shRNa replicate 1

source_name: Luciferase knockdown in PC3 cells using shRNA

value: WT (Luciferase knockdown control)


title: Luciferase knockdown in PC3 cells using shRNa replicate 2


title: Luciferase knockdown in PC3 cells using shRNa replicate 3


title: 14L RNA-seq

city: Duarte

first: Marc

last: Jung

address: 1500 East Duarte Street

department: Biology

institute: City Of Hope

data_processing:
Illumina Casava1.8 software used for basecalling.
Transcripts assembly was done for individual sample by using tophat v2.0.6 (default parameters; PMID 23618408) and cufflinks v2.1.1 (default paramters; PMID: 23222703) against hg19 genome sequence and using GENCODE version 16 as GTF guidance reference file. Transcripts from all non-strand-specific-RNA-Seq samples were then merged by using cuffmerge v1.0.0 (default paramters).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample as defined by cufflinks

source_name: primary skin fibroblast, late timepoint (L)

growth_protocol: Primary Skin Fibroblast cells were grown with culture medium (DMEM supplemented with 6% fetal bovine serum) for 2 -3 passages.

extract_protocol:
Total RNA from human skin fibroblasts was prepared using PureLink RNA Mini kit (Ambion, Cat#12183018A). The cells were lysed by addition of lysis buffer, the lysate was then homogenized using QIAshredder (QIAGEN, cat# 79654) by centrifugation at 14,000g for 2 min, and then processed following the manufacturer's instructions. The isolated total RNA was aliquoted, and the quality of the prepared RNA was evaluated using Bioanalyzer. The RNA samples were used for RNA-seq with a range of RIN values between 8.50 and 10. A cDNA library for deep sequencing was prepared using oligo d(T) primer. The Illumina protocol (kit) was followed for later steps.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age (yr)

value: primary skin fibroblast

tag: time point

value: late timepoint (L)


title: 13L RNA-seq


title: 16L RNA-seq


title: 6L RNA-seq


title: forelimb, wildtype, high resolution

value: posterior-anterior


title: 16E RNA-seq

source_name: primary skin fibroblast, early timepoint (E)

value: early timepoint (E)


title: 9L RNA-seq


title: 5L RNA-seq


title: 1L RNA-seq


title: 2L RNA-seq


title: 11E RNA-seq


title: 9E RNA-seq


title: 13E RNA-seq


title: 7E RNA-seq


title: 6E RNA-seq


title: ybeY_37_1

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

institute: University of Helsinki

data_processing:
Clean and merge reads using the adapter sequences and discarding the shortest ones; TOOL=SeqPrep; VERSION=v0.4-5-gb62f433; PARAMETERS=-f reads_1.fq -r reads_2.fq -1 reads_adapterClean_1.fq.gz -2 reads_adapterClean_2.fq.gz -s reads_adapterClean_pairedSingle.fq.gz -L 35 -y I -A CTGTCTCTTATAC -B CTGTCTCTTATAC
Filter out reads with homopolymers (>70% read length) and trim the bases at the end of the read with lower quality values (<20); TOOL=At-home perl script; PARAMETERS=--quality_threshold 20 --homopolymer_threshold 70
Filter reads aligning to rRNA or tRNA; TOOL=bowtie2; VERSION=2.1.0; PARAMETERS=-D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -k 20 --local  --score-min L,-0.6,-0.6
Alignment of the reads to reference genome; TOOL=Tophat2; VERSION=v2.0.8b; PARAMETERS= --bowtie1  --mate-inner-dist NNN --mate-std-dev NN -G organism.gtf --library-type fr-secondstrand --no-discordant
Estimation of gene FPKM values; TOOL=Cufflinks; VERSION=v2.0.2; PARAMETERS=--library-type fr-secondstrand --frag-bias-correct genome.fa -b genome.fa --GTF organism.gtf
Genome_build: ASM25317v1; FR729477
Supplementary_files_format_and_content: Tab-delimited text files containing FPKM values for each sample separately

organism: Yersinia enterocolitica subsp. palearctica Y11

growth_protocol: Overnight cultures were diluted in fresh sterile LB broth and incubated at either 22°C or 37°C with vigorous shaking till the OD = 0.6 was reached.

extract_protocol:
The total RNA was isolated using the SV Total RNA Isolation System (Promega). The qualities of the isolated RNA, as well as the rRNA profiles were determined using Bioanalyzer (Agilent).
The ribosomal RNA was removed using Ribo-ZeroTM rRNA Removal Kit for Gram-negative Bacteria (Epicentre); RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: logarythmic phase

value: ybeY-

tag: growth temperature


title: 5E RNA-seq


title: 1E RNA-seq


title: 2E RNA-seq


title: KO mRNA-seq

source_name: Male IE35/BSC5 Knockout

tag: developmental stage

value: 1-5 day old

tag: gender

value: male


title: ybeY_22_2


title: ybeY_22_1


title: 7L RNA-seq


title: WT_37_2

value: wild type


title: WT_37_1


title: 11L RNA-seq


title: Human Female low BMD_methylation_5

status: Public on Oct 22 2014

city: Chang sha

first: shishi

last: min

state: Hunan

address: Lu shan  road

department: College of life sciences

institute: Hunan Normal University

data_processing:
The completed libraries were quantified and checked for quantity with Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System.
Subsequently sequenced on Illumina HiSeq 2000 (with single-end, 49bp reads)
Sequencing reads that passed through the HiSeq 2000 quality filter were aligned to the human genome reference sequence (GRCh37/hg19) using SOAP (Version 2.20).
DNA methylation profiles were inferred from the uniquely aligned reads by using the MEDIPS analysis package
the corresponding genomic locations were obtained from the UCSC Genome Brower.
Genome_build: hg19
Supplementary_files_format_and_content: pvalues for methylation status

source_name: Healthy female_low_BMD

growth_protocol: One hundred and fifty milliliters of peripheral blood were drawn for each selected subject.

extract_protocol:
Genomic DNA was extracted from the freshly isolated PBMs. The concentration of DNA was assessed by using Qubit 2.0 Fluorometer (Invitrogen,).
1.5μg of sonicated DNA was end-repaired, 3’A added, and ligated to single-end adapters following the standard Illumina genomic DNA protocol.

treatment_protocol: Monocyte isolation,A monocyte negative isolation kit (Order No. 130-091-153, Miltenyi Biotec Inc., Auburn, CA, USA) was used to isolate circulating monocytes from 150mL whole blood following the procedures

value: Peripheral blood monocytes

value: blood

tag: Sex

value: female


title: WT_22_1


title: WT_22_2


title: Human Female low BMD_methylation_2


title: Human Female low BMD_methylation_1


title: Human Female low BMD_methylation_3


title: Human Female high BMD_methylation_5

source_name: Healthy female_high_BMD


title: Human Female low BMD_methylation_4


title: WT-1 mRNA-seq

source_name: Male W1118/BSC5 Wild Type


title: Human Female high BMD_methylation_4


title: ybeY_37_2


title: Human Female high BMD_methylation_3


title: Human Female high BMD_methylation_2


title: Human Female high BMD_methylation_1


title: Honeysuckle

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
Sequence reads were obtained by Illumina pipeline. Reads of low quality were removed and adaptor sequence were trimed by our Perl scripts.
Clean Reads were then aligned to known miRNA seqeunces obtained from miRBase 14.0 with no more than one mismatches.
Profiles of two RNA samples were generated from the alignment results.
Supplementary_files_format_and_content: tab-delimited text files including miRNA ID，Read No., Sequence, Other Names(same sequence).

organism: Lonicera japonica

source_name: Honeysuckle

extract_protocol: Total RNA was isolated from 1g HS or 5ml HS decoction using the Universal Plant MicorRNA Kit (Bioteke, Beijing, China) according to the manufacturer's instructions.

treatment_protocol: HS decoction was prepared by boiling 10g HS in 100 ml water for 30 mins.

value: Dried HS


title: 14E RNA-seq


title: Degradome_B73_ear_II

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agricultural University

data_processing:
Small RNA reads and degradome reads were both generated from an Illumina Genome Analyzer II. The raw data were preprocessed by the Fastx-toolkit pipeline to remove low quality reads and clip adapter sequences. As for the small RNA library, small RNAs ranging from 18-25 nt were collected and mapped to the maize genome (B73 RefGen_v2 (release 5b. 60 in February 2011)) reference sequences by SOAP2. Sequences with perfect match were retained for further analysis. To further analyze the RNA secondary structures comprising matched Solexa reads, a 250-nt genomic sequence flanking each side of these sequences were extracted, and secondary structure modeling of the DNA fragment was performed mFold 3.5 [62] and analyzed by MIREAP (https://sourceforge.net/projects/mireap/) under default settings. Segments that could potentially form the canonical stem-loop signature of a precursor miRNA were marked as candidate miRNAs. This candidate list was further trimmed based on the following criteria [51]: (1) mature miRNAs are present in one arm of the hairpin precursors, which lack large internal loops or bulges, (2) secondary structures of the hairpins are steady, with the free energy of hybridization lower than -20 kcal/mol, (3) hairpins are located in intergenic regions or introns, (4) overlapping loci were reduced to non-redundant representations, (5) loci that overlapped transposable and other repetitive elements were removed, (6) loci in which the matched mature miRNA was in the wrong orientation were removed, (7) each predicted secondary structure was curated manually and those with spurious stem-loop structures were removed, and (8) miRNA families that had no evidence of expression in the small RNA libraries. The final refined list of predicted miRNAs consisted of 132 individual miRNAs from 43 miRNA families. Based on the hairpin structure of the pre-miRNA, the mature miRNA and corresponding miRNA* sequence were identified for each.
As for the degradome library, only 20-21 nt sequences with high quality were collected for subsequent analysis. The raw sequences were first normalized to “reads per 10 million” (RP10M). The distinct reads that perfectly matched maize cDNA sequences remained. The 15 nt of sequence upstream and downstream of the 5’ end of matched reads were extracted to constitute 30-nt sequence tags for searching corresponding miRNA. The CleaveLand pipeline [49] was used to align the 30 nt sequence to maize known miRNAs from miRBase and our newly identified miRNAs. All alignments with scores up to 7 and no mismatches at the cleavage site (between the 10th and 11th nucleotides) were considered candidate targets.
Genome_build: n/a
Supplementary_files_format_and_content: abundance

organism: Zea mays

source_name: Zea mays L.B73

extract_protocol:
All the samples were harvested and immediately frozen in liquid nitrogen and stored at -80°C. The total RNA from each sample was then isolated using Trizol (Invitrogen) according to the manufacturer’s instructions.
Small RNA library preparation and sequencing: the total RNAs from four developmental stages were pooled for Solexa sequencing. After small RNA cloning, the sequencing procedures were conducted as described previously. In brief, the sequencing was performed as follows: approximately 100 ug of total RNA was purified by polyacrylamide gel electrophoresis (PAGE), to enrich for molecules in the range of 18–30 nt, and ligated with proprietary adapters to the 5’ and 3’ termini of the RNA. The small RNA molecules samples were used as templates for cDNA synthesis. The cDNA was amplified with 18 PCR cycles and fragments of around 90 nt (small RNA + adaptors) were isolated from agarose gels. The purified DNA was used directly for cluster generation and Solexa sequencing analysis performed by the Illumina platform. The image files generated by the sequencer were then processed to produce digital-quality data. After masking of adaptor sequences and removal of contaminated reads, clean reads were processed for computational analysis. Degradome library construction: Small cDNA libraries using the sliced ends of polyadenylated transcripts from maize ears of four developmental stages were constructed according to previous report. In brief, poly(A) RNA was extracted from 200 μg of total RNA using the Oligotex kit (Qiagen), and it’s possessing 5’ monophosphates were ligated to an RNA adapter consisting of a MmeI recognition site in its 3’ end. After ligation, first-strand cDNA was generated using oligo d(T) and the PCR product was amplified using five PCR cycles. The PCR product was purified and digested with MmeI. The digested PCR product was then ligated to a double-stranded DNA oligo with degenerate nucleotides at the 5’ or 3’ end. The ligation product was further gel purified and amplified using 10 PCR cycles. The final PCR product was purified and sequenced using SBS sequencing technology.

value: ears (female inflorescences)

value: ears at spikelet differentiation phase

tag: cultivar


title: SmallRNA_B73_ear_I

value: mixed ears at the growth point elongation, spikelet differentiation, floret primordium differentiation and floret organ differentiation phase, respectively


title: Degradome_B73_ear_III

value: ears at the floret primordium differentiation phase


title: Degradome_B73_ear_IV

value: ears at floret organ differentiation phase