title: minusDHT_SD70_hs47l8_4

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

description: GRO-seq

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to hg18 by using Bowtie2.
The bedGraph files were generated by using HOMER (http://homer.salk.edu/homer/).
The sequencing reads were counted over the genes by using HOMER (http://homer.salk.edu/homer/).
Genome_build: NCBI36
Supplementary_files_format_and_content: BedGraph files.

source_name: LNCaP cells, SD70

growth_protocol: Prostate cancer LNCaP cells were obtained from ATCC and cultured in RPMI 1640 containing 10% (vol/vol) FBS. Cells were cultured in charcoal-dextran-treated media for three days before further treatment.

extract_protocol:
Nuclei were isolated from LNCaP cells with appropriate +/- SD70 and -/+ DHT treatment. GRO-seq libraries were prepared from 10 million cells based on previously published protocols (Wang et al., 2011). Libraries were sequenced on Illumina HiSeq 2000.
After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads (Santa Cruz, sc-32323 AC). Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.

treatment_protocol: LNCaP cells were treated with SD70 (10uM) or vehicle DMSO (0.1%) for 2 hrs followed by dihydrotestosterone (DHT; 100 nM) or vehicle ethanol (0.1%) treatment for 1hr.

value: LNCaP

value: prostate cancer cell line


title: plusDHT_DMSO_hs47l8_1

status: Public on Jul 01 2014

type: SRA

state: CA

country: USA

description: GRO-seq

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP cells, DHT

tag: cell line

tag: cell type

tag: treatment

value: DHT


title: W_14_12PM_7

city: Austin

first: Thomas

middle: E

last: Juenger

state: TX

address: 2401 Speedway

institute: University of Texas, Austin

data_processing:
Trim four non-template bases from 5' end of each read
discard reads with more than 10 low quality (score<20) bases
discard reads containing homopolymers greater than 10 bp in length
discard reads matching adaptors used during library construction (cross_match, score>10)
align in color-space using SHRiMP 2.1.1b against reference transcriptome assembly
exclude short and low-quality matches
count number of reads mapping uniquely to each isogroup in the reference assembly
Genome_build: Custom transcriptome assembly (Alamo AP13) (http://datadryad.org/resource/doi:10.5061/dryad.6630k)
Supplementary_files_format_and_content: Text file listing the number of reads in each sample uiniquely mapped to each isogroup.

organism: Panicum virgatum

source_name: control_14 d_12PM

extract_protocol:
Spectrum Plant Total RNA kit, Sigma-Aldrich
3' cDNA tag libraries constructed as described in: Meyer et al (2011), Molecular Ecology, 20(17), 3599-3616.

treatment_protocol:
control: watered 1L per day
drought: no water provided during the 14-d experiment
recovery: plants from the drought treatment that were re-watered on d 14

tag: strain

value: control

tag: sampling day

tag: sampling time

tag: tissue

value: Leaf


title: plusDHT_SD70_hs47l8_3

description: GRO-seq

source_name: LNCaP cells, SD70 + DHT

value: SD70 + DHT


title: W_14_2PM_16

source_name: control_14 d_2PM


title: RW_14_2PM_6

source_name: recovery_14 d_2PM

value: recovery


title: D_14_5AM_11

source_name: drought_14 d_5AM

value: drought


title: W_14_5AM_2

source_name: control_14 d_5AM


title: W_14_5AM_4


title: plusDHT_SD70_hs35l1_4

library_source: genomic

data_processing:
Library strategy: drug-seq
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to hg18 by using Bowtie2.
The bedGraph files were generated by using HOMER (http://homer.salk.edu/homer/).
The peak finding was carried out by using HOMER (http://homer.salk.edu/homer/).
The motif enrichment analysis was carried out by using HOMER (http://homer.salk.edu/homer/).
Genome_build: NCBI36
Supplementary_files_format_and_content: BedGraph files.

molecule: genomic DNA

extract_protocol:
Approximately 10^7 treated cells were crosslinked with 1% formaldehyde at room temperature for 15 min. After sonication, the soluble chromatin was incubated with 50 ul Streptavidin Dynabeads (Life Technologies) for 2 hrs. Complexes were washed, DNA extracted and purified by QIAquick Spin columns (Qiagen).
Extracted DNA was ligated to specific adaptors followed by deep sequencing on the Illumina HiSeq 2000 system according to the manufacturer's instructions.

treatment_protocol: LNCaP cells were treated with biotinylated SD70 (10uM) or vehicle DMSO (0.1%) for 2 hrs followed by dihydrotestosterone (DHT; 100 nM) or vehicle ethanol (0.1%) treatment for 1hr.


title: minusDHT_SD70_hs35l1_3


title: 1303277 Tumor [methylation]

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
After removing the adapter sequences and filtering out the low-quality reads, the bisulfite sequencing reads were directly aligned to the human reference genome (UCSC hg19) using BSMAP 2.73 with default parameters (Xi and Li 2009), which combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping.
We extracted methylation ratios of all coveraged cytosines on the genome (*.cout.gz files) using the script included in BSMAP 2.73. Then we filtered out the CpG sites with less than 4X sequencing depth in order to guarantee accurate calculation of methylation levels. Then analysed differential promoter DNA methylation between HCCs (Tumor) and peripheral normal tissues (NTL) as following. DMRs were searched using a sliding window strategy: firstly, we selected the both covered CpG sites in two samples with sequencing depth >= 5X as candidate sites. For each of candidate site, the ChiqX or Fisher test was performed to calculate the significant test P-value. Secondly, we selected the first differentially methylated CpG (P-value < 0.05) as an initial locus of DMR, and began to merge these candidate sites into a candidate DMR with following criterion: 1, the distance between two neighbouring candidate sites <= 300bp; 2, all of candidate sites in the candidate DMR kept the same methylation status (hyper- or hypo-); and 3, a candidate DMR must harbor 5 or more candidate sites. Last, for each of the above candidate DMR, we performed a Fisher test again, and filtered out those regions whose test P-value >0.05 and difference of mean methylation levels between two sample < 0.2.
Integration of promoter methylomic and transcriptomic profiling. To further clarify the genes that are potentially regulated by promoter methylation, we further performed pair-wise comparisons on promoter methylomes to identify specific DMRs between HCCs and peripheral normal tissues. Furthermore, we evaluated differential gene expression between 8 pairs of HCC and PN samples using Illumina high-throughput RNA-seq technology.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.cout.txt.gz files include the extracted methylation ratios for all coveraged cytosines on the genome. Each of these files contain 8 columns. The format is: (1) Chromosome ID; (2) Cytosine position; (3) Watson/Crick chain; (4) Type (CG/CHH/CHG); (5) Base pattern; (6) Methylation Ratio; (7) Methylated reads num; and (8) Un-methylated reads num.

source_name: liver, HCC tumor

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen). 1µg of genomic DNA was fragmented into approximately 200-300bp using a Covarias sonication system (Covarias). After purification, the fragmented fractions were treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair blunt and phosphorylate ends. The blunt DNA fragments were subsequently 3' adenylated using Klenow Fragment (3'-5' exo-) and then ligated by T4 DNA Ligase to adapters that were synthesized with 5'-methylcytosine instead of 5'-cytosine and contain index sequences inside. After each step, the reaction products were purified using QIAquick PCR purification kit (Qiagen). The constructed libraries were quantified using a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen). The liquid hybridization capture procedure was then performed as follows. Briefly, 200 ng DNA from each of five adapter-ligated libraries were pooled together. 10 µg human Cot-1 DNA and 1nmol of adapter complementary DNA oligos were added and subsequently were dried using a SpeedVac (eppendorf) at 60°C. After that, the mixture was denatured at 95°C for 10min in a final reaction volume of 10.5µl consisting of 7.5µl 2X SC Hybridization Buffer and 3µl SC Hybridization Component A. After centrifugation, 4.5µl of designed probes were added and the mixture was hybridized in a thermal cycler at 47°C for 72 hours with the lid heated at 57°C. After hybridization, the biotinylated probes bounded with the target DNA were captured using 100µl of Dynabeads® M-280 Streptavidin (Invitrogen), which had been pre-washed two times with a total of 400µl Streptavidin Dynabead Binging and Washing Buffer. The capture program was 47°C for 45min in a thermal cycler with the lid heated at 57°C and vortexing for 3 seconds at 15min intervals. Discarded the unbounded fractions and washed the collected DNA-probe-beads complex with 100µl of 47°C pre-warmed 1X Wash Buffer I for one time and with a total of 400µl of 47°C pre-warmed 1X Stringent Wash Buffer I for two times with the incubations of 47°C for 5min. After discarding the supernatant, the collected beads complex was again washed with 200µl of 1X Wash Buffer I, 1X Wash Buffer II and 1X Wash Buffer III respectively. Finally, the captured DNA was eluted in 50µl of 10M NaOH with incubation at room temperature for 10min. The supernatant was transferred into a new tube and neutralized with 50µl of 10M HAc and then purified using MiniElute PCR purification Kit (Qiagen). For bisulfite conversion, 200ng unmethylated lambda DNA was added into each captured product as carriers and ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO) was employed to convert unmethylated cytosine into uracil according to the instructions.
After purification, PCR was carried out in a final reaction volume of 50µl consisting of 20µl converted products, 4µl 2.5mM dNTP, 5µl 10×buffer, 0.5µl JumpStart™ Taq DNA Polymerase (SIGMA), 1µl PCR primers1.0, 1µl PCR index primers (which were used to identify different captures) and 18.5µl water. The following thermal cycling program was 94°C 1 min, 15 cycles of 94 °C 10s, 58°C 30s, 72°C 30s then prolong at 72°C for 5min and hold at 12°C. The PCR products were purified using AMPure beads (Agencourt), quantified by the Bioanalyzer analysis system (Agilent) and real time PCR assay and then analyzed using Illumina Hiseq 2000. All of these samples were pooled into 7 libraries with a one-to-one correspondence 7bp barcode. The barcode information is following: s02_C-AATAACT-pooling1, s14_P-TGTAATT-pooling1, s96_P-ACTTGAT-pooling1, s00_C-AATAACT-pooling2, s13_C-TGTAATT-pooling2, s95_C-ACTTGAT-pooling2, s09_C-ATAATCT-pooling3, s15_P-TGTAATT-pooling3, s06_P-GTACATT-pooling4, s10_P-TATGCTT-pooling4, s16_C-TGTAATT-pooling4, s01_P-GTACATT-pooling5, s99_P-CGAATAT-pooling5, s95_C-CGAATAT-pooling6, s96_P-ACTTGAT-pooling6, s05_C-GTACATT-pooling7, s11_P-TATGCTT-pooling7, s12_C-TGTAATT-pooling7. The constructed libraries were quantified using a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen).

tag: disease status

value: hepatocellular carcinoma (HCC)

value: liver tumor

tag: gender

value: F

tag: age (y)

tag: patient


title: 1303277 NTL [methylation]

source_name: liver, NTL

value: non-tumor liver


title: 1306706 Tumor [methylation]

value: M


title: minusDHT_DMSO_hs47l8_2

description: GRO-seq

source_name: LNCaP cells, vehicle only

value: vehicle only


title: Dshibae, second run, day 2, 4 h dark

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
Sequencing was done on the Genome Analyzer IIx (Illumina, San Diego, CA, USA) following a standard protocol. The fluorescent images were processed to sequences and transformed to FastQ format using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina, San Diego, CA, USA).
The sequencing output (50 bp single end short reads) of the Genome Analyzer IIx was controlled for general quality features using the fastq-mcf tool of ea-utils (http://code.google.com/p/ea-utils) and was mapped against the genome sequence of D.shibae (NC_009952.1, NC_009955.1, NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1) using BWA v 0.5.9-r16.
Genome_build: NC_009952.1, NC_009955.1, NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1
Supplementary_files_format_and_content: tab-delimited text files include unique and total mapped reads and RPKM values for each gene of one sample

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: D. shibae cultivated in a chemostat under light/dark cycles

extract_protocol:
For isolation and purification the RNeasy-kit (Qiagen) was used according to the manufacturer’s manual. Modifications are listed below. Cells lysis was performed enzymatically using 15 mg/mL lysozyme in Tris-EDTA-buffer (ph 8.0) and mechanically by vortexing for 3 min with acid washed glass beads. A first digestion of genomic DNA was performed on the column, using RNase-free DNase I (Qiagen) according to the manufacturer’s protocol. Total RNA was eluted in 88 µL RNase-free H2O and a second DNase I-digestion of genomic DNA was performed in solution, followed by a second RNeasy purification step. In this second purification an additional washing step with 80 % ethanol was performed prior to elution with 30µl RNase-free water. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA). Ribosomal RNA depletion:  The Ribo-Zero (gram-negative) kit (Madison, Wisconsin, USA) to remove the prokaryotic rRNA, according to the manufacturer’s instructions.
Libraries of 300 bp for RNA sequencing were prepared using the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA) according the manufacturer’s instructions. Quality control of the prepared libraries was validated using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, USA). Cluster generation was performed using the Illumina cluster station.

tag: chemostat run

tag: light/dark-cycle

tag: time in light or darkness

tag: light(l)/dark(d)

value: d


title: 1306706 NTL [methylation]


title: 1304203 Tumor [methylation]


title: Dshibae, second run, day 2, 8 h light

value: l


title: Dshibae, second run, day 3, 12 h dark


title: Dshibae, second run, day 2, 12 h light


title: Dshibae, second run, day 3, 4 h light


title: 1304203 NTL [methylation]


title: 1308388 NTL [methylation]


title: 1308388 Tumor [methylation]


title: D_14_12PM_17

source_name: drought_14 d_12PM


title: 1308849 NTL [methylation]


title: Dshibae, second run, day 2, 4 h light


title: Dshibae, second run, day 2, 1 h light


title: Dshibae, second run, day 3, 12 h light


title: Dshibae, second run, day 2, 12 h dark


title: Dshibae, first run, day 2, 4 h light


title: Dshibae, first run, day 3, 12 h light


title: Dshibae, first run, day 3, 8 h light


title: 1159804 Tumor [methylation]


title: 1159804 NTL [methylation]


title: Dshibae, first run, day 3, 12 h dark-2


title: 1308849 Tumor [methylation]


title: 1305780 NTL [methylation]


title: 1306734 Tumor [methylation]


title: 1306734 NTL [methylation]


title: T11P ChIP-Seq, R1881-treated LNCaP cells

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

data_processing:
Alignment:  Sequence reads were obtained and mapped to the human hg18 genome using Bowtie 0.12.9 with default alignment parameters.
Peaks:  Peak detection was performed using the HOMER software package http://homer.salk.edu/homer/ngs/index.html.  Peaks were annotated to the nearest gene.
Tag directories were generated in HOMER using the -tbp 1 command to remove  clonal reads.  Default peak calling stringency settings were used (FDR 0.10%) for all ChIPseq samples and T11P and WDR5 peaks were called using Input DNA from EtOH-treated or R1881-treated cells as controls.
Colocalization:  A 500 base pair window was used to assess for colocalization between H3 T11P marks and WDR5 binding to determine their overlap.
Visualization: bedGraph files were generated using HOMER which were viewed on the UCSC genome browser.
Genome_build: hg18

source_name: prostate adenocarcinoma

extract_protocol:
LNCaP cells were cultured for 3 h in the presence of 10 nM R1881 or vehicle control as indicated and cross-linked by the addition of 1/10 volume of freshly-prepared formaldehyde cross-linking buffer (11% formaldehyde, 10 mM HEPES-KOH [pH 7.6], 100mM NaCl, 1 mM EDTA, 0.5 mM EGTA) to cell culture dishes and incubated for 10 min at room temperature.Glycine was added to a final concentration of 125 mM and cells were incubated for 5 min at room temperature. The samples were sonicated and the sonicated lysates were subjected to immunoprecipitation using the indicated antibodies and protein G Dynabeads.  Precipitates were washed and DNA was extracted.
KAPA Library Prep Kit

value: LNCaP cells

tag: antibody

value: H3 phospho T11, AbCam (ab5168)


title: 1305780 Tumor [methylation]


title: WDR5 ChIP-Seq, R1881-treated LNCaP cells

value: WDR5, Bethyl Labs (A302-429A)


title: WDR5 ChIP-Seq, EtOH-treated LNCaP cells

value: EtOH


title: Dshibae, first run, day 3, 4 h light


title: Dshibae, first run, day 3, 12 h dark


title: Dshibae, first run, day 3, 4 h dark


title: Dshibae, first run, day 2, 12 h light


title: Input Control DNA, R1881-treated LNCaP cells


title: T11P ChIP-Seq, EtOH-treated LNCaP cells


title: Kd_3 (HE016) alternative name, KD3

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

description: neuronal differentiation induced after recovery and selection in puromycin

data_processing:
We obtained 101-bp mate-paired reads from DNA fragments of with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8). We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18). The category of transcripts is described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html. Transcript abundances were measured in Transcripts Per Million (TPM), which is calculated by multiplying the estimated fraction of transcripts made up by a given gene by 106.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: NPCs derived from iPSCs_ZNF804A KD

extract_protocol:
total cellular RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, total RNA were extracted to produce cDNA using DT-T7 primers. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Neural progenitor cells (NPCs) developed from iPSCs

tag: transduced with

value: ZNF804A KD vector


title: Kd_4 (ZNF) alternative name, KD4

description: neuronal differentiation continued for 4 more days in puromycin selection

value: day 10 neurons


title: Kd_1 (ZNF2) alternative name, KD1


title: Treated AZA BS-seq Rep1

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: Bisulphite sequencing of AZA treated cells

data_processing:
Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to hg18 whole genome using bismark v0.5.1 (bowtie v0.12.7) with directional setting and chunkmbs set to 256.  Remaining default settings.
Multiple reads where both ends of the fragment align to the same genomic positions on the same strand were reduced to a single instance.  Reads with more than 3 methylated cytosines in non-CpG contexts are discarded.
Reads are summarised on a per-CpG basis.
Genome_build: hg18
Supplementary_files_format_and_content: Summary files represent the number of reads supporting methylated/unmethylated bases at each CpG sequenced in that sample (Format is: chr <tab>  position  <tab>  methylated reads  <tab>   unmethylated reads).  bigWig files represent the percentage methylation at a given CpG (filtered to exclude CpGs with low coverage on a per replicate basis – >=10 reads in at least one sample & >=3 read in the other) and generated using UCSC wigToBigWig.

growth_protocol: OCI-AML3 cells were cultured in suspension in RPMI media supplemented with FBS 20%, Penicllin 5% and L-Glutamine 5%, incubated at 37°C in humidified conditions and 5% CO2. To passage, cells were counted by haemocytometer and either centrifuged to a pellet and resuspended in fresh media or resuspended in 50% fresh media at a concentration of 0.5 x 106/ml every 2-3 days.

extract_protocol:
DNA was extracted with phenol-chloroform method.
Libraries were prepared by BGI, Shenzhen.  Briefly, DNA is fragmented and methylated adapters are ligated to DNA fragments.  DNA is bisulphite treated and sequenced on Illumina platforms as per manufacturers instructions.

treatment_protocol: AzaC was dissolved from lyophilised powder into culture-sterile DMSO to produce a 20 mM stock solution and stored as 15μl aliquots at -80°C. For each new experiment a fresh aliquot of AzaC was diluted in RPMI/20% FBS to produce a 2 mM working stock which was diluted directly onto cells in culture.

tag: cell line

value: Aza


title: Untreated AZA BS-seq Rep1

description: Bisulphite sequencing of untreated cells

value: untreated


title: Treated AZA BS-seq Rep2


title: Kd_2 (ZNF5) alternative name, KD2

tag: cell type


title: Untreated AZA BS-seq Rep2

tag: treatment


title: Scr_4 (Scr) alternative name, control 4

source_name: NPCs derived from iPSCs_control

value: Scrambled vector (control)


title: Scr_3 (Contr01) alternative name, Control 3


title: Scr_2 (control_L1) alternative name, Control 2


title: Scr_1 (control160) alternative name, Control 1


title: Caco-2 +TNFa 2

city: Copenhagen N

first: Berit

last: Lilje

address: Ole Maaløes Vej 5

department: Department of Biology, Section for Computational and RNA Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Assigned reads were trimmed to remove linker sequences and subsequently filtered for a minimum sequencing quality of 30 in 50% of the bases using the FASTX-Toolkit
Mapping to the human genome (hg19) was performed using Bowtie version 0.12.7 parameters: --best --strata -v 2 -k 10 -y -p 6 --phred33-quals --chunkmbs 512 -e 120, allowing for multiple good alignments and subsequently filtering for uniquely mapping reads
Reads that mapped to unplaced chromosome patches or chrM were discarded
Tags are represtented by 5' ends, tags with a distance <20bp are merged into clusters
Cluters with a width of 1bp are discareded, and cluster boundaries are defined as covering 90% of tags
TPM normalize
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files of clustered tags, score column shows TPM normalized score for the given TC

source_name: Colon cancer cell line

extract_protocol:
Purelink mini kit (Ambion, Austin, TX, USA)
Libraries were prepared as described in the CAGE protocol

value: 10mM TNFa


title: Input Control DNA, EtOH-treated LNCaP cells


title: Caco-2 -TNFa 3


title: Caco-2 +TNFa 3


title: Caco-2 +TNFa 1


title: Caco-2 -TNFa 2


title: Caco-2 -TNFa 1


title: AGS-H3K27me3-ChIP-BS-repeat2

description:
stomach  epithelial cells
AGS-H3K27me3-ChIP-BS-repeat2

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of ChIP-seq reads were mapped to hg18 SOAP libraries using default parameters. For ChIP-BS library,We change C->T and G->A of reference respectively and build SOAP library using them, then, translate the C of sequences fq1 to T, G of fq2 to A, and mapped them with above libraries. (Lister R et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.)
Using unique mapped reads, and after duplication reads (the pair end mapped reads share same postion only use the best mapped pair reads to eliminate the affect of PCR). then extract the methylation of CpG and the read densi  ty of each sample. we further analysis the enrichment of each sample using RSEG software(0.4.4) the parameter using default with bin size 500bp and posterior cutoff 0.95.
Genome_build: hg18
Supplementary_files_format_and_content: bed files:ChIP information it contained chromsome,reads strart site,reads end sites; and for CpG Methylation of ChIP-BS it contained chromsome,CpG site,enriched reads number,and methylation of CpG; wig files include each samples ChIP signal on enriched sites.

source_name: gastric adenocarcinoma cells

growth_protocol: A lymphoblastoid cell line was generated from a male Han Chinese individual (YH), whose genome sequence was reported previously [28]. Two human gastric cancer cell lines (BGC-823 and AGS) were provided by Beijing Tumor Hospital; the HeLa cell line was purchased from the American Type Culture Collection (ATCC). Cells were cultured with RPMI1640 (Gibco C22400500BT) supplemented with 10% fetal bovine serum (Gibco 12657-029) in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: ChIP-seq, approximately 5×106 cells were used. Proteins were cross-linked to DNA with 1% formaldehyde in 10 ml PBS at 37°C for 10 min, thenand then the cells were washed with pre-cooled PBS with 0.5% bovine serum and by PBS supplemented with protease inhibitor compound (PIC). The cells were collected by centrifugation at 850g for 3 min after each wash. The cells were resuspended in 200 μl ice-cold lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, plus PIC) and then thawed on ice for 10 min to allow lysis. The cell lysate was then sonicated for 180 s using a BioruptorTM 200 at the highest power (pulses: 30 s on/30 s off) to generate chromatin fragments between 100 and 700 bp. As input, one-tenth of the sonicated chromatin sample was removed. The remaining chromatin was immunoprecipitated in ChIP dilution buffer (1% Triton, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl) with 4 µg antibody against H3K4me3 (Millipore; 17-614) or H3K27me3 (Millipore; 17-622) that had been pre-incubated with protein A/G magnetic beads (Invitrogen; 10003D). After immunoprecipitation overnight, the beads were washed twice with each of the following buffers at 4°C: RIPA buffer (10 mM Tris, 1 mM EDTA, 0.1% SDS, 0.1% Na-deoxycholate, 0.1% Triton X-100); RIPA buffer plus 0.3 M NaCl; LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and TE buffer. The beads were collected on a magnet for recovery. The bound DNA was then eluted from the beads with elution buffer（1% SDS, 0.1 M NaHCO3）at 65°C for 2-3 h.then sequenced on Illumina Hiseq2000 using a standard pair-end 50bp (PE50) sequencing protocol.  ChIP-BS-seq:Ends of the immunoprecipitated DNA (60ng) from ChIP procedure were repaired in a 100μl reaction containing 1XT4 PNK buffer, 3 units T4 DNA polymerase (ENZYMATICS; P708), 0.5 unit klenow enzyme (ENZYMATICS; P7060), 10 units T4-PNK (ENZYMATICS; Y9040) and dNTP (0.125mM for each) for 30min at 20℃. Followed by treatment with 15 unit Klenow fragment (3’-5’exo, ENZYMATICS; P7010-LC) in a 50μl reaction containing 1Xblue buffer (ENZYMATICS; B011) and 0.2mM dATP at 37℃ for 30min to generate a protruding 3’A base. Then methylated pair-end adapters were ligated to the DNA fragment using 2400 unit of rapid T4 DNA ligase (ENZYMATICS; L6030-HC) at 37℃ for 15 min. After purification, 200ng exogenous λ-DNA fragments were added to the samples, and the sodium bisulfite conversion assay (ZYMO D5006) was performed, followed by 16 cycles of PCR amplification that was consisted of denaturation (94℃ for 15s), annealing (60℃ for 30s), extension (72℃ for 30s). Then, the PCR products were size-selected on 2% agarose gels, retaining 250-350 bp DNA fragments. The purified DNA (ChIP-BS libraries) was used for cluster generation and standard PE50 sequencing using Illumina Hiseq 2000.

value: gastric adenocarcinoma cells

tag: chip antibody

value: AGS

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot #


title: BGC-823-RNA-seq

description:
stomach  epithelial cells
BGC-823-RNA-seq

data_processing:
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of  RNA sequencing reads were aligned to the reference genome (UCSC hg18) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample

extract_protocol: Total RNA was isolated from BGC-823, AGS cells and YH cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Total RNA was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The cDNA was then used for Illumina sequencing library preparation. DNA fragments were end-repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls, and adapters were ligated for paired-end sequencing on an Illumina HiSeq 2000.


title: HeLa-H3K27me3-ChIP-repeat

description:
cervix epithelial cells
HeLa-H3K27me3-ChIP-repeat

source_name: cervix adenocarcinoma clells

value: cervix adenocarcinoma clells

value: HeLa


title: HeLa-H3K27me3-ChIP

description:
cervix epithelial cells
HeLa-H3K27me3-ChIP


title: HeLa-H3K27me3-ChIP-BS

description:
cervix epithelial cells
HeLa-H3K27me3-ChIP-BS


title: YH-H3K4me3-ChIP_BS

description:
lymphoblastoid cells
YH-H3K4me3-ChIP_BS

source_name: lymphoblastoid cells

value: lymphoblastoid cells

value: YH


title: YH-H3K27me3-ChIP-BS

description:
lymphoblastoid cells
YH-H3K27me3-ChIP-BS


title: HeLa-H3K27me3-ChIP-BS-repeat

description:
cervix epithelial cells
HeLa-H3K27me3-ChIP-BS-repeat


title: AGS-RNA-seq

description:
stomach  epithelial cells
AGS-RNA-seq


title: BGC-823-H3K27me3-ChIP-BS

description:
stomach  epithelial cells
BGC-823-H3K27me3-ChIP-BS


title: AGS-H3K4me3-ChIP-BS

description:
stomach  epithelial cells
AGS-H3K4me3-ChIP-BS


title: BGC-823-H3K4me3-ChIP-BS

description:
stomach  epithelial cells
BGC-823-H3K4me3-ChIP-BS


title: AGS-H3K27me3-ChIP-BS-repeat1

description:
stomach  epithelial cells
AGS-H3K27me3-ChIP-BS-repeat1


title: YH-RNA-seq

description:
lymphoblastoid cells
YH-RNA-seq


title: Tumor RNA BT73

city: Bar Harbor

first: Edison

last: Liu

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Sequenced reads were aligned to the human genome hg18 assembly using BioScope v1.3.1
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cufflinks, version 1.0.3 (Trapnell et al., Nature Biotechnology, 2010) and the hg18 RefSeq Genes track downloaded from the UCSC genome browser as the gene annotation file. Gene-based values were generated as the sum of the FPKM of all of the transcripts correspoding to the same gene.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include trasncript- and gene-based FPKM values for each sample

source_name: Primary breast cancer

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini kit (Qiagen) and enriched for poly(A) mRNA using a μMACS™ poly(T) kit (Life Technologies). 500 ng of purified poly(A) RNA was used for library preparation.
RNA libraries were prepared for sequencing using a SOLiD™ Total RNA-Seq Kit (Applied Biosystems), according to the manufacturer's instructions.

tag: tissue

value: breast cancer tumor

tag: breast cancer subtype

value: Luminal B

tag: library id


title: CD8_DC_LPS

city: Camperdown

first: David

middle: Graeme

last: Hancock

state: NSW

address: Building 93, RPAH, Missenden Road

country: Australia

institute: Centenary Institute

data_processing:
Basecalls performed using Illumina RTA 1.9.35
Raw basecall data was converted to FASTQ sequence files using Off-Line Basecaller (Ilumina) and a custom Perl script.
Reads were aligned to the mm9 mouse genome and ensembl transcripts with TopHat version 2.05 and Bowtie1 version 0.12.7 with the search for novel junctions disabled.
Genomic coordinates were then transformed into counts of chimeric protein-coding Ensembl genes with the htseq-count script in the intersection-nonempty mode
Genome_build: mm9
Supplementary_files_format_and_content: tab delimeted text files containing raw count data for each sample

organism: Mus musculus

source_name: Spleen

extract_protocol:
Spleens from LPS-stimulated and unstimulated mice were digested with Collagenase from Clostridium histolyticum (Sigma-Aldrich) and a single-cell suspension was prepared by teasing through a mesh sieve. Splenocytes were stained with CD3, Ter119, Gr1, B220, and CD19 hybridomas, and negatively selected with anti-rat IgG MicroBeads (Miltenyi Biotec).CD11c+ cells were then enriched for using CD11c MicroBeads (Miltenyi Biotec). CD8 and CD11b DC subsets were further purifed by cell sorting on a FACS Aria II. Total RNA was extracted using a RNAeasy Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols. Unique Illumina barcode indexes were attached to each sample.

treatment_protocol: Mice were injected intraperitoneally with 25 μg LPS

tag: strain

tag: timepoint

tag: group

value: LPS stimulated

value: spleen

value: CD8 Dendritic Cells


title: CD11b_DC_Ctrl

value: Control

value: CD11b Dendritic Cells


title: CD8_DC_Ctrl


title: CD11b_DC_LPS


title: RSP_3341_3xMyc_ChIP_Seq

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

data_processing:
100 bp reads were trimmed to 70bp to remove unreliable base calls. 50bp reads were not trimmed
Mapping was done to the R. sphaeroides reference genome using SOAP version 2.21 allowing for 3 mismatches for 70bp reads and 2 mismatches for 50bp reads
Peaks were identified using MOSAiCS at a false discovery rate of 0.05 using a two-sample analysis with Input DNA or mock chip used as control.
Genome_build: ASM1290v2, ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Rhodobacter_sphaeroides_2_4_1_uid57653/
Supplementary_files_format_and_content: Processed data files are provided as wig files with scores representing the normalized ratio of reads between a sample ChIP and INPUT DNA

organism: Cereibacter sphaeroides 2.4.1

source_name: Bacteria culture (SIS - Photo)

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) or aerobically (bubbling with 69% N2, 30% O2, 1% CO2) on Sistrom's minimal media and harvested at exponential phase. Where necessary 1 to 5μL of IPTG was added at the start of the culture to induce protein expression.

extract_protocol:
At midexponential phase (~2×108 colony-forming units/ml), formaldehyde and sodium phosphate were added to a final concentration of 1% and 10 mM, respectively. This mixture was incubated at 30 °C for 4 min before glycine was added to 100 mM, and the solution was placed on ice for 30 min with gentle agitation to quench excess formaldehyde. Cells were centrifuged at 3000g, washed twice with chilled phosphate buffered saline, centrifuged, and flash-frozen at −80 °C. About 2×1010 cells were suspended in 0.5 ml of 100 mM Tris (pH 8.0), 300 mM NaCl, 2% Triton X-100, RNase A (0.5 μg) and 1 mM phenylmethylsulfonyl fluoride, and sonicated in a Misonix water bath for 8 mins with 10s pulses and intervals. Cell debris was removed by centrifugation for 10 min at 12,000g, and an aliquot was removed to analyze DNA fragmentation by agarose gel eletrophoresis (desired size of ~200–1000 bp with enrichment for ~500-bp molecules). The resulting supernatant was incubated with gentle mixing with 20 μl of Staphylococcus aureus protein A Sepharose beads (Sigma-Aldrich, St. Louis, MO) for 3 h at 4 °C as pretreatment to remove potential nonspecific binding to the beads. After the beads had been removed by centrifugation (5 min at 3000g), one-tenth of the sample was removed and used as non-antibody-treated control. Five microlitre of Myc epitope antibody (ab9132, Abcam plc) was added and the mixture was incubated overnight at 4 °C with gentle mixing before being incubated with protein A Sepharose beads (30 μl) for 3 h at 4 °C. The beads were recovered by centrifugation; washed once (4 °C) with 250 mM LiCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 600 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 300 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; and washed twice with TE buffer (10 mM Tris pH 8.0 and 1 mM EDTA). Protein–DNA complexes were eluted from the beads by incubating at 65 °C for 30 min in 50 mM Tris (pH 8.0), 10 nM EDTA, and 1% sodium dodecyl sulfate. The beads were removed by centrifugation, and protein–DNA cross-linking was reversed by incubating the samples for 12 h at 65 °C. DNA was purified using the QIAquick PCR Purification Kit. Samples were sent to UW-Madison Biotech center for further processing and sequencing.
Libraries were prepared according to Illumina's instructions by UW-Madison biotech center

tag: genotype/variation

value: ΔRSP_3341 complemented with 3xMyc tagged RSP_3341 from an IPTG inducible plasmid

tag: chip-antibody


title: RSP_0489_3xMyc_ChIP_Seq

value: ΔRSP_0489 complemented with 3xMyc tagged RSP_0489 from an IPTG inducible plasmid

value: Myc epitope antibody (ab9132, Abcam plc)


title: AGS-H3K27me3-ChIP-BS

description:
stomach  epithelial cells
AGS-H3K27me3-ChIP-BS

value: gastric adenocarcinoma cells


title: IPO323_Bd

status: Public on Jun 30 2014

city: Marburg

first: Ronny

last: Kellner

address: Karl-von-Frischstrasse 10

country: Germany

institute: MPI for Terrestrial Microbiology

data_processing:
Quality evaluation using FastQC
Trimming: 12 bp from left and 5 bp from right for: 234_A, 234_B, 234_C, 234_D, 234_E, 234_F
Quality filtering and Masking: Reads with an overall quality score below 20 as well as reads having less than 25% of nucleotides with a quality score above 20 were discarded. For the remaining reads nucleotides with quality scores below 20 were masked with Ns.
Filtering for plant reads: In order to account for incorrect mapping of plant reads with high similarity to fungal sequences, reads from infected plant tissue were mapped to both the plant genomes and the genome of Z. tritici IPO323. All plant reads were removed for further downstream analyses. To this end reads with 100% identity to the plant genomes and a maximum of 25% N positions were filtered out in fastq_screen v0.4.1 (www.bioinformatics.babraham.ac.uk/projects/fastq_screen) applying a sensitive local Bowtie2 alignment
Read Mapping: Mapping of single end RNAseq reads to the genome of the Z. tritici isolate IPO323 (Goodwin et al. 2011) was carried out with tophat v2.0.9 (Kim et al. 2013). Mapping was disabled for novel splice discovery and used the JGI transcript annotation of IPO323 as reference (Goodwin et al. 2011; http://genome.jgi.doe.gov/Mycgr3/Mycgr3.home.html). The maximum number of read mismatches and read gap length were set to 2. Reads that mapped to more than 10 locations were eliminated from the analysis. Relative abundances for predicted transcripts of IPO323 were estimated in cufflinks v2.1.1 (Trapnell et al. 2012). Total read counts per transcript were estimated in htseq-count  (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) applying the intersection-strict mode.
Supplementary_files_format_and_content: csv files with FPKM values and total counts for each transcript of IPO323 (Z. tritici)

organism: Zymoseptoria tritici

source_name: infected B. distachyon leaf

growth_protocol: Cultures were inoculated onto solid YMS agar (4 g yeast extract, 4 g malt extract, 4 g sucrose, 20 g bacto agar, 1 l H2O) at 18°C. For transcriptional profiling of axenic culture, yeast-like cells were isolated from these plates after 72 h. For transcriptional profiling of plant infections, 15 day old wheat seedlings of the cultivar Obelisk and the Brachypodium distachyon accession Bd21 were inoculated as follows. A distinct area of the second leaf (10 - 15 cm) was marked and a spore solution of 1 x 107 yeast cells/ml containing 0.1% Tween 20 was brushed onto these areas. After an initial incubation for 48 h at 100% humidity and 22°C, inoculated plants were incubated with a 16 h light period at 75% humidity and 22°C for four days.

extract_protocol:
To extract total RNA from fungal axenic culture or freeze-dried leaf tissue infected with Z. tritici, 100 mg of sample was crushed in liquid nitrogen and total RNA was extracted using the TRIZOL reagent (Invitrogen) following the manufacturer’s protocol. RNA samples were purified twice with Dynal oligo(dT) magnetic beads (Invitrogen), following the manufacturer's instructions.
RNA-seq libraries for plant infection replicates were prepared from an input of 4 µg total purified polyA RNA according to recommendations of the supplier (TruSeq RNA sample preparation v2 guide, Illumina).

value: leaf

tag: age

value: 4 days post inoculation

tag: genotype

value: wild type


title: Campylobacter jejuni fur perR mutant RNA-seq

city: Norfolk

first: Arnoud

last: van Vliet

address: Colney Lane

department: Gut Health and Food Safety Programme

institute: Institute of Food Research

description: cDNA libraries constructed, using standard Illumina protocols. Libraries are not strand-specific

data_processing:
Sequences were obtained from FASTQ files, processed by the software provided by the HiSeq2000 sequencing service at The Genome Analysis Centre, Norwich, UK
Transcript levels of individual genes were expressed as Reads Per Kilobase per Million mapped reads (RPKM) values, calculated after mapping of reads using CLC Genomics Workbench v5 (CLC Bio).
The reads were also aligned against the C. jejuni genome NCTC 11168 genome sequence using Segemehl version 0.0.9.3 (Hoffmann et al., 2009), and converted into number of reads per nucleotide position, for the plus and minus strand of the genome (*.gr files)
Graphs representing the number of mapped reads per nucleotide were loaded in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009).
Genome_build: Campylobacter jejuni  NCTC11168: NC_002163.1
Supplementary_files_format_and_content: Histogram files for use in the Integrated Genome Browser software from Affymetrix (Nicol et al., 2009). Scores represent the number of reads per nucleotide position
Supplementary_files_format_and_content: CSV files containing gene designation, RPKM value and coordinates used for Chromosome region start and Chromosome region end

organism: Campylobacter jejuni

source_name: Bacteria

growth_protocol: The wildtype and fur perR mutant of Campylobacter jejuni strain NCTC 11168 were grown to late log phase

extract_protocol:
Total RNA was purified omitting size selection, to avoid the loss of small RNA molecules. The exclusion of rRNA and tRNA was also omitted, to avoid the potential loss of other RNA species. RNA was isolated using hot phenol (Mattatall & Sanderson, 1996), to ensure that small RNAs would not be removed by the extraction procedure. The RNA was treated with DNase I to remove residual genomic DNA.
The RNA samples were used to generate strand-inspecific RNA-seq libraries for Illumina sequencing, using instructions from the manufacturer (Illumina), and further analysed using an Illumina HiSeq2000 sequencer.

value: fur::kan perR:cm

tag: phase

value: late log growth


title: AGS-H3K4me3-ChIP-BS-repeat

description:
stomach  epithelial cells
AGS-H3K4me3-ChIP-BS-repeat

tag: cell type

tag: cell line

value: AGS

value: Millipore


title: Campylobacter jejuni wildtype RNA-seq

value: wildtype


title: IPO323_YMS

source_name: yeast cells

value: yeast

value: freshly grown liquid culture (YMS medium)


title: IPO323_Ta

source_name: infected wheat leaf


title: ago3 piRNA

city: Beijing

first: Haidong

last: Huang

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: piRNA

data_processing:
basecalling and adapter clipping were performed in PGM instrument.
After adapter removal, reads in fastq files were mapped to genome through bowtie 0.12.7 without mismatch.
Genome_build: dmel_release 5.0

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: flies were grown at 25 degrees on standard medium

extract_protocol:
total RNAs were extracted with Trizol followed by depletion of 2s rRNA, and then 15-35nt small RNAs were isolated through urea-PAGE and gel cut.
small-RNAs were cloned according to the instruction of Ion Total RNA-Seq Kit

tag: Stage

value: from 3-5 days old flies

value: ovary


title: CONsiRNA

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

data_processing:
Alignment - bowtie2 (v2.1.0) options --very-sensitive -X 400
Sort & Index - Picard Tools (v1.99) SortSam.jar (VALIDATION_STRINGENCY=LENIENT MAX_RECORDS_IN_RAM=20000000 CREATE_INDEX=true SORT_ORDER=queryname)
Filter unmapped reads - Picard Tools (v1.99) FilterSamReads.jar (FILTER=includeAligned)
Identify differentially methylated regions - MEDIPS (Bioconductor)
Find differentially methylated regions in/near GENCODE (release 16) genes - BedTools (v 2.17.0) - intersectBed
Genome_build: hg19
Supplementary_files_format_and_content: text table, 100bp windows with bam counts, RPKM, genome-wide

source_name: HUVEC cells

growth_protocol: HuVECs (passage 3) were seeded into 75-cm2 flasks at a density of approximately 1 x106 cells per flask and maintained at 37_¡C in a humidified atmosphere of 5% CO2 in air in EGMª endothelial growth medium supplemented with & EGMª-2 BulletKitª. All tissue culture reagents were supplied by Lonza. The medium was replaced twice weekly. Experiments were carried out at passage 5-6 in EGMª endothelial growth medium supplemented with 2% (v/v) fetal calf serum (Sigma) and 60 _g/ml gentamycin (Sigma).

extract_protocol:
DNA was extracted from HuVECs using the QIAamp¨ DNA Mini Kit (Qiagen) and quantified by Quant-iTª PicoGreen¨ dsDNA Assay Kit (Invitrogen). Quality of the DNA was assessed using the Nanordrop 1000 (Thermoscientific), OD 260/280 was between 1.8 and 2.0. Enrichment of HuVEC DNA for the methylated fraction was carried out by NXT-DX, The Netherlands. DNA was fragmented to an average length of 200 bp by sonication and analysed using the Agilent 2100 Bioanalyser (Agilent Technologies). Methylated DNA was captured using the MethylCap kit (Diagenode), based on binding to methylated DNA of a recombinant H6-GST-MBD protein then capture on magnetic beads coated with GSH. For each condition (SIRT1 overexpressed by transfection with pCMV6-ENTRY-SIRT1, corresponding vector control, each of the siRNAs that target SIRT1 and control siRNA) six biological replicates were pooled for analysis.
Library preparation is a modification of the ‘multiplexed paired end ChIP protocol’ (Illumina, San Diego, California, USA). The DNA Sample Prep Master Mix Set 1 (NEB E6040) was used in combination with the Multiplexing Sample Preparation Oligo Kit (96 samples, Illumina PE-400-1001). 250ng of fragmented DNA was used for library preparation on Apollo 324 with PrepX-DNA Library Kit (24 samples per kit, 400007) or PrepX-32-DNA Library Kit (96 samples per kit, 400021) according to the kit’s protocol. Library amplification proceeded according to multiplexed paired end ChIP protocol including the indexes from Multiplexing Sample Preparation Oligo Kit. A fragment of 300 bp +/- 50bp was excised from an agarose gel and eluted on a Qiagen Gel Extraction Kit column (Qiagen 28704), then eluted it in 23 μl EB. All samples were adjusted to 10nM and indexed samples were pooled per lane. The paired end (PE) flow cell was prepared according to the Cluster Station User Guide.

treatment_protocol: Overexpression of SIRT1 in HuVECs was by transient transfection with the plasmid pCMV6-ENTRY-SIRT1 (Origene) and knockdown of SIRT1 was achieved using two different siRNAs, and compared with a control siRNA, as described previously for Caco-2 cells (Ions et al. 2012).  Cells were treated with 0.1 ng/ml tumour necrosis factor alpha (Roche) in 1 % BSA in PBS for 48 hours. Control cells were treated with 1% BSA in PBS.

value: HUVEC

tag: mdb capture

value: Methylated DNA was captured using the MethylCap kit (Diagenode AF-100-0048, Belgium)

tag: tnf treatment

value: 1 % BSA in PBS for 48 hours

tag: construct

value: Control siRNA


title: CONsiRNATNF

value: cells treated with 0.1 ng/ml tumour necrosis factor alpha (Roche) in 1 % BSA in PBS for 48 hours


title: 510_control

city: Boston

first: Stefano

last: Sioletic

state: Ma

address: 450 Brookline Ave, Boston,

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat read mapper with the default parameters to annotated transcripts only.
Transcript/gene expression FPKM values were quantified with Cufflinks software.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with FPKM values for each sample in this study.

source_name: Control 510 cell line

growth_protocol: Cell lines were maintained in DMEM/F-12 supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA extraction and RT-PCR.  Total RNA was extracted using Trizol reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions. 1000 ng of total RNA was used for cDNA synthesis with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems).
According to the manufacturer’s instruction for the mRNA purification of the polyA containing mRNA molecules, poly-T oligo attached magnetic beads has been used for two rounds. During the second elution of the polyA RNA, the RNA is also fragmented and primed for cDNA synthesis. The first strand reverse transcribes the cleaved RNA fragments that were primed with random hexamers into first strand cDNA using reverse transcriptase and random primers.  The addition of Actinomycin D to the First Stand Synthesis Act D mix (FSA) prevents spurious DNA-dependent synthesis, while allowing RNA-dependent synthesis, improving strand synthesis.   The second strand synthesis removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. The incorporation of dUTP quenches the second strand during amplification, because the polymerase does not incorporate past this nucleotide. AMPure XP beads are used to separate the ds cDNA from the second strand reaction mix. At the end of this process, you have blunt-ended cDNA. A single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. A corresponding single ‘T’ nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragment. Multiple indexing adapters ligates to the ends of the ds cDNA, preparing them for hybridization onto a flow cell. PCR is performed with a PCR Primer Cocktail that anneals to the ends of the adapters. The library is validated by the bioanalyzer.

treatment_protocol: Lentivirus was produced by transient cotransfection of 293T cells using FUGENE, Δ8.9 packaging plasmid and VSVg expression plasmid.  Media containing lentivirus was harvested 24 and 48 hours after transfection. Precision LentiORF Human JUN (Clone ID: PLOHS_100010892), ENPP2 PLOHS_100009279 or RFP Control [Thermo Scientific] was produced in 293T cells to overexpress these genes. Infected cells were selected with blasticidin (10ng/ml) for 5 days and sorted with BD FACSAria II SORP UV to obtain an infection rate close to 100%.

value: dedifferentiated liposarcoma (DDLPS)


title: LPS12_control

source_name: Control LPS12 cell line


title: NFATc1-ChIP-Seq-shSTAT3

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: NKC tumor cells were stably transfected with STAT3-specific shRNA

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse mm9 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
PeakRanger1.15 was used to call peaks at default settings (p-value < 10E-04, FDR < 5E-02) where the Input sample was used as control.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were produced using Macs 1.4 at 10bp resolution
Supplementary_files_format_and_content: Aligned reads were converted to BED format using BedTools.

growth_protocol: Tumor cells were isolated from the pancreas of transgenic mice bearing constitutive nuclear NFATc1 and mutated KrasG12D in the pancreas (referred to as "NKC" cells) and were maintained in 10% FCS and non-essential amino acids

extract_protocol: Briefly, 10^6 NKC tumor cells stably expressing scramble or shSTAT3 vectors were cross-linked with formaldehyde and sonicated. Sonicated chromatin was pre-cleared and incubated with 4 µg of NFATc1 antibody (Abcam) overnight at 4°C. After reversing the crosslinks, DNA was treated with Proteinase K and RNAse A and purified using the Qiagen PCR purification kit (Qiagen). ChIP DNA was end repaired and A tailed. Illumina adaptors were ligated to the ChIP DNA fragments. 175 - 225 bp size fractions were cut out from a gel, eluted by by Qiagen gel extraction kit and enriched by 20 cycles of PCR amplification. The library-size was controlled with the Experion-system (BioRad) and subsequently quantified by picogreen assay and subjected to Illumna GAIIx sequencing according to the manufacturer’s instruction. Only high quality reads passing the internal Illumina-Raw data-filter (PF-cluster) were considered.

tag: strain background

value: mixed (129S6 and C57BL/6)

value: NKC pancreatic cancer cells

tag: stably transfected with

value: STAT3-specific shRNA

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: siRNA2

value: SIRT1 siRNA 2


title: NEO

value: Vector Control


title: siRNA2TNF


title: 141_control

source_name: Control 141 cell line


title: Input DNA

description: NKC-scramble tumor cells

source_name: Input DNA


title: SIRT1OE


title: NFATc1-ChIP-Seq-scramble

description: NKC tumor cells were stably transfected with scramble vector

value: scramble vector


title: Hepatocellular carcinoma (HCC),parent

city: Shanghai

first: Wei zhong

last: Wu

address: Fenglin Rd 180, Xuhui district

department: Zhongshan Hospital

institute: Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags
Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01
Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM).       Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000
Calculate fold-change and P-value from the normalized expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Human Hepatocellular Carcinomar cell line

growth_protocol: The three HCC cell strains were cultured in DMEM medium.

extract_protocol: Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Hepatocellular Carcinomar

tag: organ-tropism

value: low metastasis


title: 141_Jun

source_name: Jun overexpressed 141 cell line


title: siRNA1

value: SIRT1 siRNA 1


title: WT piRNA

description: piRNA

value: from 3-5 days old flies

tag: tissue

value: ovary


title: 510_Jun

source_name: Jun overexpressed 510 cell line


title: Hepatocellular carcinoma (HCC),subclone2

value: dual metastasis ability to lung and celiac lymph node


title: Hepatocellular carcinoma (HCC),subclone1

value: higher metastasis ability specific to lung


title: DD piRNA

description: piRNA


title: LPS12_Jun

source_name: Jun overexpressed LPS12 cell line


title: DH1097

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

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: ASM18296v1
Supplementary_files_format_and_content: text files containing RPKM values for each Sample

organism: Candida albicans

source_name: candida albicans - white

growth_protocol: white, gray and opaque cells of strain BJ1097 were inoculated into Lee's Glucose medium and cultured at 25 oC for 24h.

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

tag: strain

tag: phenotype

value: white


title: Total RNA from Candida albicans wild-type strain (SC5314) yeast cells Replicate 3

city: Aberdeen

first: Sophie

last: Shaw

state: Aberdeen City

address: 23 St. Machar Drive

department: Centre for Genome Enabled Biology and Medicine

institute: University of Aberdeen

data_processing:
CLCBio software was used to align each set of replicate sequences to the 14217 Assembly 19 diploid reference ORFs detailed by Jones et al  (2004).  Standard parameters were set to allow up to 2 mismatches per read. For diploid alignments, non-unique matches to the ORFs were discarded. This ensured that only reads which were able to distinguish between alternative alleles were considered.  For haploid alignments, all matches were counted.
Genome Build:
ypd3.txt: C. albicans SC5314 Assembly 19
Ca19-orfs-haploid_3_RNA-Seq.txt: C. albicans SC5314 Assembly 19

source_name: Yeast cells, wild-type

growth_protocol: Cells grown in rich broth medium (YPD) until OD (600 nm) = 1

extract_protocol: 5 x 107 cells  were disrupted with glass beads using a FASTPREP-24 bead beater (3 x 20 s at 6 m/s).  Total RNA was then extracted from each sample using a Qiagen RNeasy mini  kit following the manufacturers instructions. RNA was quantified (nanodrop) and purity assessed using an Agilent Bioanalyser. Double stranded cDNA was generated using reverse transcription with random hexamers. Double-stranded cDNA was then fragmented using a Bioruptor sonication device and libraries prepared for Illumina GA2 sequencing using the standard Illumina protocol.

treatment_protocol: Overnight YPD broth culture of Candida albicans SC5314 diluted to OD600 nm =  0.25 in 10 ml fresh YPD broth and incubated at 30 °C with shaking (200 rpm) until OD600 nm = 1.0

value: Yeast

tag: growth stage


title: Total RNA from Candida albicans wild-type strain (SC5314) yeast cells Replicate 1

data_processing:
CLCBio software was used to align each set of replicate sequences to the 14217 Assembly 19 diploid reference ORFs detailed by Jones et al  (2004).  Standard parameters were set to allow up to 2 mismatches per read. For diploid alignments, non-unique matches to the ORFs were discarded. This ensured that only reads which were able to distinguish between alternative alleles were considered.  For haploid alignments, all matches were counted.
Genome Build:
ypd1.txt: C. albicans SC5314 Assembly 19
Ca19-orfs-haploid_1_RNA-Seq.txt: C. albicans SC5314 Assembly 19

tag: cell type


title: Liver_Veh_repl1

first: Gavin

middle: R.

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

data_processing:
step 1: Reads were trimmed to remove the first 8 bases, which tend to be of lower quality, using fastx_toolkit-0.0.6 fastx_trimmer, or using the -5 8 command line option in Bowtie
step 2: Bowtie version 0.12.5 was used to map approximately 150-200 million reads per condition to unique locations on the mm9 UCSC build of the mouse genome using the setting -n 2 (allowing at most 2 mismatches in the first 28 bp of the trimmed read) and –m 1 (keeps only those reads that map to a single, unique location in the genome).
step 3: We prepared a .gtf file containing only the exons of refseq annotated transcripts (downloaded from the UCSC genome browser for the mouse mm9 build). Because it has been shown that the read density in 3' untranslated regions correlates poorly with mRNA expression levels (Ramskold D, Wang ET, Burge CB, Sandberg R 2009 An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5:e1000598), we modified the .gtf file to exclude the 3' UTR sequences.
step 4: We used the function HTSeq.scripts.count in HTSeq version 0.4.5p7 (using the --stranded=no option, but otherwise with default settings) to count reads per gene for each condition and replicate.
step 5: Differential expression calls were made using EdgeR version 3.4.2. To account for different methods of library preparation we included a batch effect in the design matrix (all 8 NuGen libraries were Batch 1 and all 8 PolyA+ libaries were batch 2). The contrasts made were Ao.E-Ao.V, Li.E-Li.V, and (Ao.E-Ao.V)-(Li.E-Li.V). Genes were counted as regulated if the fold change was greater than 1.5 and the raw p. value was less than 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Table with counts per transcript values for all 16 samples using HTSeq unstranded with other settings at default
Supplementary_files_format_and_content: Microsoft Excel file with E2vVeh expression calls for Aorta & Liver & differential AoE-V - LiE-V, using EdgeR, includes workflow and table of fitted reads-per-million-reads normalized count data

source_name: liver, ethanol vehicle

growth_protocol: Wild-type female C57BL/6 mice were ovariectomized at 6-7 weeks of age.  Aortas and livers were harvested from these animals one week post surgery.  All animals were handled according to National Institutes of Health standards and protocols approved by the Tufts Medical Center Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted from both tissues using the fibrous tissue mini kit (Qiagen)
For samples 1 through 8: 50 ng RNA from each sample was converted to cDNA using the Ovation RNA-seq System kit (Nugen), which uses limited amplification with specialized primers to reduce rRNA signal. The cDNAs were then prepared essentially as per the Illumina protocol (starting from the end repair step), except that we used the End-It kit (Epicentre Biotech.) for end repair, Taq polymerase for A addition, Tufts core facility oligos (OLJ131 5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and OLJ137 5’ p-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) for adapter ligation, and Easy A thermostable polymerase (Agilent Technologies) with Tufts core oligos (OLJ 139 5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA and OLJ 140 5’ CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAAC) was used  for the final limited amplification. Ligated or final amplified products of ~300 bp size were isolated by E-gel or 1.6% agarose gel electrophoresis followed by Qiagen Gel Extraction kit purification. For all other steps, products were purified by addition of 30 mg glycogen (invitrogen #1286677) and EtOH precipitation, followed by a 70% EtOH wash. The library was quantified using the Quant-IT dsDNA HS kit (Invitrogen) and approximately 10 ng submitted for sequencing on an Illumina Genome Analyzer machine (first biological replicate) or an Illumina HiSeq 2000 machine (2nd replicate). For samples 9 through 16: Poly-A+ selected libraries were prepared using 600ng of RNA extracted from a single aorta or liver fragment. Library preparation was done using the TrueSeq RNA v2 sample prep kit and supplied adapter oligos (RS-122-2001, Illumina Inc., San Dieco, CA) on a Sciclone NGS Workstation (P/N SG3-31020-0300, PerkinElmer, Waltham, MA) using vendor instrument protocols and 14 cycles of amplification.

treatment_protocol: Aortas and livers (tip of the major lobe) were treated ex vivo with either 10-8M 17b-estradiol (E2, the active endogenous form of estrogen) or ethanol vehicle for 4 hours at 37oC in DMEM (Invitrogen).

value: liver

tag: 4hr ex vivo treatment

value: ethanol vehicle


title: Mid log_wildtype_glc minimal media + L-tryptophan_aerobic

city: La Jolla

first: Bernhard

middle: O

last: Palsson

address: 9500 Gilman Dr

department: Bioengineering

institute: UC San Diego

data_processing:
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type
Genome_build: NC_000913
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons

organism: Escherichia coli K-12

source_name: WT + L-trp

growth_protocol: E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where.

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen).
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming.

treatment_protocol: Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use.

tag: genotype/variation

value: wild type; MG1655

value: mid exponetial phase

tag: basal media

value: M9 + 4 g/L glc (glucose minimal media)

tag: oxygen condition

value: aerobic

tag: supplementation

value: L-tryptophan (20 mg/L)


title: Mid log_cra KO_glc minimal media + L-tryptophan_aerobic

source_name: cra KO + L-trp

value: cra KO; BW25113 Dcra


title: Mid log_mntR KO_glc minimal media_anaerobic

source_name: mntR KO -O2

value: mntR KO; BW25113 DmntR

value: anaerobic


title: Mid log_wildtype_glc minimal media + adenine_aerobic

source_name: WT + ade

value: adenine (10 mM)


title: Mid log_wildtype_glc minimal media_aerobic rep3

source_name: WT


title: Mid log_nac KO_glc minimal media + adenine_aerobic

source_name: nac KO + ade

value: nac KO; BW25113 Dnac


title: Mid log_nac KO_glc minimal media_aerobic

source_name: nac KO


title: Mid log_mntR KO_glc minimal media_aerobic

source_name: mntR KO


title: Mid log_wildtype_glc minimal media_anaerobic rep2

source_name: WT -O2


title: Liver_E2_repl1

source_name: liver, 10 nM beta-estradiol (E2)

value: 10 nM beta-estradiol (E2)


title: Hepatocellular carcinoma (HCC), subclone2

data_processing:
Illumina Casava1.7 software used for basecalling.
Remove reads with adaptors, remove reads in which unknown bases are more than 10%, Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Human Hepatocellular Carcinoma cell line

extract_protocol: Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Hepatocellular Carcinoma

tag: cell line

value: dual metastasis ability to lung and celiac lymph node


title: Hepatocellular carcinoma (HCC), subclone1

value: higher metastasis ability specific to lung


title: Hepatocellular carcinoma (HCC), parent

value: low metastasis ability


title: Mid log_cra KO_glc minimal media_aerobic

source_name: cra KO


title: Mid log_wildtype_glc minimal media_anaerobic rep1


title: HZAU_M_huakuii_Bacteroid_BT7653R3

city: Wuhan

first: Youguo

last: Li

state: Hebei

address: No.1,Shizishan Street · Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

description: This sample is of M. huakuii 7653R during bacteroid at 32 days postinoculation.

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences, which are called raw data or raw reads and are stored in FASTQ format. FASTQ files are text files that store both reads sequences and their corresponding quality scores.The line 1 and 3 are sequence name generated by the sequencer; line 2 is sequence; line 4 is sequencing quality scores, in which every letter corresponds to a base in line 2; the base's sequencing quality is the ASCII value that the letter in line 4 refers to minus 64 (Specification). Using llumina GA Pipeline v1.6, Solexa quality value of sequencing bases ranged from 2 to 35. Denote E as sequencing error rate and sQ as sequencing quality value, then we have:sQ = -10log10E
Filter dirty raw reads: removing reads containing sequencing adapters,unknown nucleotides larger than 10% and reads of low quality (reads containing Ns >5)
Clean reads were mapped to M.huakuii 7653R genome and genes sequences respectively using SOAP2 (Li, 2009), allowing up to 5 base mismatches.
The calculation of Unigene expression uses RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Genome_build: M.huakuii 7653R genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mesorhizobium huakuii 7653R

source_name: M.huakuii 7653R during bacteroid at 32 days postinoculation

growth_protocol:
M. huakuii 7653R was grown to mid-log phase (O.D.600nm 1-2)at 28°C in TY medium(Beringer, J.E.J Gen Microbiol, 1974. 84(1): p. 188-98)
A. sinicus seeds were sterilized, germinated, planted, and inoculated with M. huakuii 7653R strains(Chen, D.S.et al.Plant Cell Rep, 2007. 26(8): p. 1421-30.)At 32 days postinoculation, the nodules of plants were harvested.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) and purified by column NucleoSpin® RNA clean-up kit（Macherey-Nagel,Germany）RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.
To isolate bacteroids RNA, total nodules RNA passed though MICROBEnrich™ kit (Ambion) according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: bacteroids


title: Mid log_wildtype_glc minimal media_anaerobic rep3


title: HZAU_M_huakuii_Free-living_MH7653R

description: This sample is of free-living M. huakuii 7653R.

source_name: M.huakuii 7653R free-living cells

value: plate cultures


title: DH1099-2

source_name: candida albicans - opaque

value: opaque


title: Total RNA from Candida albicans wild-type strain (SC5314) yeast cells Replicate 2

data_processing:
CLCBio software was used to align each set of replicate sequences to the 14217 Assembly 19 diploid reference ORFs detailed by Jones et al  (2004).  Standard parameters were set to allow up to 2 mismatches per read. For diploid alignments, non-unique matches to the ORFs were discarded. This ensured that only reads which were able to distinguish between alternative alleles were considered.  For haploid alignments, all matches were counted.
Genome Build:
ypd2.txt: C. albicans SC5314 Assembly 19
Ca19-orfs-haploid_2_RNA-Seq.txt: C. albicans SC5314 Assembly 19

source_name: Yeast cells, wild-type

value: Yeast


title: Aorta_E2_repl1

source_name: aorta, 10 nM beta-estradiol (E2)

value: aorta


title: Aorta_Veh_repl1

source_name: aorta, ethanol vehicle

value: ethanol vehicle


title: DH1099-1

source_name: candida albicans - gray

value: gray


title: control MCF7L-shPTEN cells (no DOX, no reduced PTEN)

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

data_processing:
Illumina Casava-1.8.2 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to hg19 whole genome using Tophat-1.3.0 with parameters -p 8 -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks-1.3.0.  UCSC known transcripts were supplied in GTF format file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: MCF7L breast cancer cells

growth_protocol: Human breast cancer cell line MCF7L (from Dr. Marc Lippman) were all authenticated and maintained in RPMI/1640 medium supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin/glutamine, and incubated at 37°C in 5% CO2.

extract_protocol:
Invitrogen Trizol
Illumina TruSeq RNA, according to standard protocol

treatment_protocol: pINDUCER Lentiviral System to reduced PTEN was carried out as previously described (PMID:21307310).

value: control


title: MCF7L-shPTEN cells with DOX, and reduced PTEN

value: reduced PTEN


title: Aorta_Veh_repl3


title: Liver_ERa_INPUT_E2_repl2

description:
LiE_INPUT_eqnum_OnN_nwst_28bp_dedup.bed.gz
LiE_man2_n_newest3_eqnum_dup1_nomod148_p1e-4_control_afterfiting_all.bdg.gz

data_processing:
Reads were mapped to the mouse mm9 genome build using Bowtie version 0.12.5, with the following parameters --best --strata -n 1 (keeping alignments with at most 1 mismatch) -m 1 (keeping only reads that align to one location in the genome), and also trimmed to remove the first 8 bp (bowtie parameter -5 8) and trimmed on the 3' end to give a mapped read length of 28 bp (e.g. for 51 bp reads, -5 8 and -3 15 resulted in 28 bp read lengths). All mapped reads for each sample were concatenated together, sorted and deduplicated (keeping only one of any set of reads starting at the exact same base). Finally, an equal number of deduplicated reads from replicate 1 and replicate 2 were combined, to ensure equal weighting of each replicate (accomplished by randomly subsampling the longer file and concatenating it with the smaller file). The final counts of reads were 33.4 million, 70.1 million, 44.5 million and 73.9 million for the combined aorta ChIP, aorta input, liver ChIP and liver input samples, respectively.
ERa binding peaks that were significantly different from the input control were called using MACs version 1.4, a Poisson-based algorithm which evaluates the likelihood of ERa binding at a specific site over random chance, with the following parameters: --format=BED --keep-dup=1 --nomodel --bw=200 --shiftsize=100 --pvalue=1e-4 -B -S -c INPUT.bed -t ERaIP.bed --name output_prefix. We found that we got the best ratio of positive to negative(false) peaks when we did not use MACS to estimate fragment size, but instead used experimentally determined fragment sizes (using the MACS parameter --nomodel and supplying fragment size and 1/2 fragment size values as --bw and --shiftsize). Fragment sizes were 200 for the Aorta IP and 148 for the Liver IP.
Peaks were called as high probability ERalpha binding sites if they showed >=3-fold enrichment over background, p<=10-5 and empirical FDR of <=10%. With these thresholds we found 1754 high quality ERBSes in aorta, and 33273 in liver.
Genome_build: mm9
Supplementary_files_format_and_content: Two types of processed files are included: 1) .bed files containing an equal number of mapped, deduplicated reads from replicate 1 & 2 of each sample type (input data to MACS, whose inclusion is important because of the random subsampling we used to give equal read numbers for each replicate) and 2) .wig files of shifted read densities for input and IP data (output from MACS).
Supplementary_files_format_and_content: peak file containing peak calls (p. <1e-5, FDR<10%, Fold-enrichment > 3)

source_name: liver

extract_protocol:
Samples were cross-linked with 1% formaldehyde at 37°C for 15 minutes and quenched with 0.125M glycine.  Tissues were then rinsed with 1X PBS, minced with scissors, and homogenized.  Samples were pelleted by brief centrifugation and resuspended in 0.5 ml lysis buffer (1% SDS, 10mM EDTA pH 8.0, 50mM Tris pH 8.0, 1x Complete Protease Inhibitors (Roche 1187358001)).  DNA was fragmented by seven rounds of sonication with a Sonifier 250 tip sonicator (Branson Ultransonics) at output setting 5 for 5 seconds followed by 1 minute on ice.  Samples were centrifuged at 13500 rpm for 15 minutes at 4°C and the supernatant collected.  14.5 l of Protein A Dynabeads and 14.5 l of protein G Dynabeads (invitrogen) were washed by magnetic pull down 3x at 4oC with PBS+5mg/ml BSA. 15 l of anti-ER HC-20 antibody (Santa Cruz) and 10 l of anti-ER Ab-10 (Neomarkers) were incubated with the beads for 6 to 8 hours. Beads were washed 2x w/ PBS+BSA to remove unbound antibody, and resuspended in 0.5ml PBS+BSA. 280l of fixed chromatin (in sonication buffer) was mixed with 1.12 ml of Dilution Buffer (1% Triton X-100, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl pH 8.1) and added to the beads, followed by overnight incubation with rocking at 4oC. Beads were collected by magnetic pull down and washed 6X with RIPA buffer (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 0.7% Sodium Deoxycholate, 1% NP40, 0.5M LiCl) using 20 minute and 5 minute alternating wash times, and twice with TE for 5 minutes. DNA was released and cross-links reversed by resuspending in Elution Buffer (100mM NaHCO3, 1% SDS) and incubating at 65oC overnight (vortexing every 5 minutes for the first 30 minutes). Samples of input chromatin were also resuspended in elution buffer and incubated at 65oC to reverse crosslinks. DNA was purified using the Qiaquick PCR kit (Qiagen) and quantified using the Quant-IT dsDNA HS kit (Invitrogen).
4ng of input and ChIP samples from two biological replicates were prepared for sequencing essentially using the standard Illumina protocol, with the following modifications: we used the End-It kit (Epicentre Biotech.) for end repair, Taq polymerase for A addition, and Easy A thermostable polymerase (Agilent Technologies) for the final limited amplification. Ligated or final amplified products of between ~220 and ~320 bp size were isolated by E-gel or 1.6% agarose gel electrophoresis followed by Qiagen Gel Extraction kit purification. For all other steps, products were purified by addition of 30 mg glycogen (invitrogen #1286677) and EtOH precipitation, followed by a 70% EtOH wash. The library was quantified using the Quant-IT dsDNA HS kit (Invitrogen) and approximately 10 ng submitted for sequencing. First replicate samples were not multiplexed. 2nd replicate samples were multiplexed using Illumina multiplex adapters and run together on one HiSeq lane (Aorta_IP=Barcode 2, Aorta INPUT=barcode 6, Liver IP=Barcode 4, Liver input= barcode 8). Raw data files were de-multiplexed by the sequencing facility.

treatment_protocol: Aortas and livers (tip of the major lobe) were treated ex vivo with either 10-8M 17b-estradiol (E2, the active endogenous form of estrogen) or ethanol vehicle for 45 minutes at 37oC in DMEM (Invitrogen).

tag: treatment

tag: chip antibody

value: Input chromatin

value: liver


title: Fra1_ChIPSeq

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations.
Data were filtered using the Partek Genomics Suite 6.6.
Peaks were called using Partek Genomics Suite's Detect Peaks option with the following setting: Maximum average fragment size=200, window size=100, Peak cut-off FDR=0.001.
Galaxy web-based platform was used to generate common peaks between 2 lists.
Genome_build: GRCh37
Supplementary_files_format_and_content: Bed and .txt files containg peaks were generated.

source_name: BT549 breast cancer cells, Fra1 ChIP

growth_protocol: The human breast cancer cell line BT549 was maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol:
Standard Illumina DNA library construction.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.

value: triple negative breast cancer cells

value: Fra-1 (R-20, Santa Cruz)


title: IgG_ChIPSeq

source_name: BT549 breast cancer cells, IgG ChIP

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


title: Aorta_E2_repl4

value: 10 nM beta-estradiol (E2)


title: Liver_ERa_ChIP_E2_repl2

description:
LiE_IP_eqnum_OnN_nwst_28bp_dedup.bed.gz
LiE_man2_n_newest3_eqnum_dup1_nomod148_p1e-4_treat_afterfiting_all.bdg.gz

value: anti mouse ER-alpha


title: Aorta_ERa_INPUT_E2_repl1

description:
AoE_INPUT_eqnum_OnN_nwst_28bp_dedup.bed.gz
AoE_NnO_n_newest3_eqnum_dup1_nomod200_p1e-4_control_afterfiting_all.bdg.gz

source_name: aorta


title: Liver_E2_repl2


title: Input DNA

source_name: BT549 breast cancer cells, input


title: Aorta_E2_repl3


title: Aorta_ERa_ChIP_E2_repl1

description:
AoE_IP_eqnum_OnN_nwst_28bp_dedup.bed.gz
AoE_NnO_n_newest3_eqnum_dup1_nomod200_p1e-4_treat_afterfiting_all.bdg.gz


title: Aorta_ERa_ChIP_E2_repl2


title: Liver_ERa_INPUT_E2_repl1


title: Liver_Veh_repl4

source_name: liver, ethanol vehicle


title: Liver_Veh_repl2


title: Aorta_ERa_INPUT_E2_repl2


title: cJun_ChIPSeq

source_name: BT549 breast cancer cells, cJun ChIP

value: c-Jun (H-79, Santa Cruz)


title: Liver_E2_repl4

source_name: liver, 10 nM beta-estradiol (E2)


title: Liver_E2_repl3


title: Aorta_E2_repl2


title: Aorta_Veh_repl2


title: Liver_ERa_ChIP_E2_repl1


title: Aorta_Veh_repl4


title: HNF4A ChIPSeq DSS

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Illumina CASAVA 1.8.2 for basecalling
ELAND mapping
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using MACS1.0, HNF4A ChIP-seq bed files generated using MACS2, H3K27ac Bed files were generated using NPS and BINOCh. The top 1000 scoring regions (indicating most dynamic chromatin between conditions) for each condition used for data analysis were retained in the bed file.

source_name: colonic epithelial cells

growth_protocol: Adult mice, 2-4 months old

extract_protocol:
Colonic epithelial scraping
Tru-seq Illumina Kit according to manufacturer's instructions

treatment_protocol: 3% DSS for 6 days or water only controls

tag: antibody

value: 3% DSS


title: Liver_Veh_repl3


title: HNF4A_ChIPSeq control

value: water only


title: Input DNA

first: Hui-Ju

last: Lee

state: Texas

address: One Baylor Plaza

department: Molecular & Cellular Biology

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied. Illumina chastity-filtered reads with phred+33 quality scores.
Sequences (50 nt reads, single end) were aligned to the mouse genome (mm9) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 150 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in BAR files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7 (default settings).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: bigWig. Files with extension *.bw. Binary files that can be opened in the Integrated Genome Browser (IGB) and show the fragment density for 32-nt bins along the genome (“signal map”). An indexed binary format that can be uploaded to the UCSC browser.

source_name: SRC-2OE/+ prostate

extract_protocol:
Prostates were removed from the mice, snap frozen in liquid N2 and stored at -80°C until shipment on dry ice to ActiveMotif. For fixation, prostates were cut into small pieces in PBS + 1% formaldehyde and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycin (final) and tissue pieces were treated with a TissueTearer. Chromatin was isolated by disrupting the cells with a Dounce homogenizer. Lysates were sonicated using a Misonix Sonicator 3000 equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and stored at -80 C. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNaseA, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified on a NanoDrop spectrophotometer. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and antibodies and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. Immune complexes were eluted from the beads with SDS buffer, and subjected to RNase treatment and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3'-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

value: Prostate

tag: genotype

value: Probasin-cre; PTEN flox/+; SRC-2 OE/+


title: SRC-2_ChIP-seq

value: SRC-2 (A300-346A, Bethyl Lab., Inc.)


title: H3K27ac_ChIPSeq DSS


title: Id2_3_dKO_Treg

status: Public on Jun 29 2014

first: Kazuko

last: Miyazaki

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: University of California, San Diego

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were trimmed for adaptor sequence.
The sequencing reads were mapped using TopHat (v.1.4.0).
RPKM was caliculated using Cuffdiff (v.0.0.6).
Genome_build: mm9
Supplementary_files_format_and_content: GSE57682_Id2_3_Treg_G42_Cuffdiff.txt: Tab-delimited text file includes RPKM values of control and sample.

source_name: sorted regulatory T cells, Id2 Id3 dKO

extract_protocol:
CD4+TCRb+CD25hi Foxp3+ cells were sorted and total RNA was isolated from them using the RNeasy-Mini Kit (Qiagen). mRNA was purified using Dynabeads mRNA purification kit (Invitrogen). The mRNA was then subjected to first-strand cDNA synthesis using a combination of random hexamers and oligo-dT. Second-strand synthesis was performed using dUTP instead of dTTP. The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).
Sonicated cDNA was next ligated to adaptors and size selected. The size-selected cDNA was treated with Uracil-N-Glycosylase and then multiplex amplified by PCR. cDNA libraries were sequenced with a HiSeq 2000 sequencer (Illumina).

tag: strain/background

tag: age

value: 3 weeks

value: lymph node

value: CD4+TCRb+CD25hi Foxp3+ cells


title: Control_Treg

source_name: sorted regulatory T cells, control

tag: tissue


title: Control_Treg_rep1

description: mRNA

data_processing:
Illumina Casava1.8 software was used for basecalling.
Alignment and trimming of reads was performed using the OSA algorithm against the mm10 mouse genome reference in Array Studio.
RNA transcripts were quantified using RSEM methods as implemented in Array Studio.
Principal Component Analysis (PCA) was then performed to check for possible batch effects.
Abundance values (counts) were normalized and compared between control vs. double KO mice using DESeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: GSE57682_DEseq_table.txt: Tab-delimited text file includes the abundance values (raw counts) of the control group (2 samples: reps1-2) and dKO group (3 samples: reps1-3) with P-value.

extract_protocol:
CD4+TCRb+CD25hi Foxp3+ cells were sorted and total RNA was isolated from them using the RNeasy-Mini Kit (Qiagen). mRNA was purified using Dynabeads mRNA purification kit (Invitrogen). The mRNA was then subjected to first-strand cDNA synthesis using a combination of random hexamers and oligo-dT. Second-strand synthesis was performed using dUTP instead of dTTP. The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).
Sonicated cDNA was next ligated to adaptors and size selected. The size-selected cDNA was treated with Uracil-N-Glycosylase and then multiplex amplified by PCR. cDNA libraries were sequenced with a HiSeq 2500 sequencer (Illumina).


title: Id2_3_dKO_Treg_rep1

description: mRNA


title: Id2_3_dKO_Treg_rep2

description: mRNA


title: Id2_3_dKO_Treg_rep3

description: mRNA


title: H3K27me3_ChipSeq

status: Public on Jun 27 2014

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H3K27me3

data_processing:
Image analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: For all samples, aligned sequences were extended automatically by MACS and allocated into 50bp bins. Read counts in 50bp are shown.

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 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.

value: V6.5 embryonic stem cells

tag: strain

tag: antibody catalog number

value: Abcam AB6002


title: Stimulated OB, mouse 3 (30 min)

first: Yarden

last: Katz

department: Dept. of Biology and Whitehead Institute

institute: MIT

description:
processed data file: rpkm.table.txt
Stim30_4

data_processing:
Alignment to mouse genome (mm9) using Bowtie to genome and set of 35-bp splice junctions, followed by calculation of RPKM using constitutive exons of protein-coding (CDS-containing) genes.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for samples. Contains the gene ID (Ensembl), the read counts in the set of constitutive exons, the length of the region being considered (sum of lengths of constitutive exons), and the RPKM value.

molecule: polyA RNA

source_name: stimulated_30m_olfactory bulb

extract_protocol:
RNA was extracted using Trizol. RNA was Dnase I-treated and cleaned up on a column using Rneasy kit.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.

treatment_protocol: Odorant stimulation (30 min)

value: adult (6-8 weeks or older)

tag: exposed to

value: cocktail of odorants for 30 min

tag: time point

value: 30 min

value: olfactory bulb


title: Control_Treg_rep2

description: mRNA

tag: genotype/variation

tag: cell type


title: Control OB, mouse 1 (clean air)

description:
processed data file: rpkm.table.txt
Control_C1

source_name: control_olfactory bulb

treatment_protocol: Clean air

value: clean air

value: control


title: Stimulated OB, mouse 1 (30 min)

description:
processed data file: rpkm.table.txt
Stim30_1


title: Stimulated OB, mouse 2 (30 min)

description:
processed data file: rpkm.table.txt
Stim30_3


title: Stimulated OB, mouse 2 (120 min)

description:
processed data file: rpkm.table.txt
Stim120_3

source_name: stimulated_120m_olfactory bulb

treatment_protocol: Odorant stimulation (30 min stimulation, 90 min clean air)

value: cocktail of odorants for 30 min followed by clean air for 90min

value: 120 min