title: PTB/heph RNA Seq

city: Boulder

first: Joseph

middle: K

last: Heimiller

address: 347 UCB

department: MCDB

institute: Univ of Colorado Boulder

description: Sample 2

data_processing:
TopHat 2.0.9 alignment using r5.44 flybase annotation
Cufflinks 2.1.1 cuffdiff for gene differential expression and quantification
MISO v0.4.6 for isoform differential expression and quantification
DAVID v6.7 for gene ontology analysis
Genome_build: flybase r5.44
Supplementary_files_format_and_content: Cufflinks differential expression

source_name: embryos

growth_protocol: standard cornmeal 17-25 deg C

extract_protocol:
trizol poly-A purified
standard Illumina TruSeq

value: whole embryo

tag: Stage

tag: Sex

value: mixed

value: zygotic heph03429 null


title: Wild type RNA Seq

status: Public on May 10 2014

type: SRA

state: CO

country: USA

description: Sample 1

library_source: transcriptomic

molecule: total RNA

organism: Drosophila melanogaster

tag: tissue

tag: genotype

value: yw


title: E14-d6_RNA-seq

status: Public on May 12 2014

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
For hairpin-bisulfite sequencing data, each read was searched for adaptor and hairpin sequences with cross_match. Additional search on the 3’-end of sequence reads was conducted to eliminate any sub-string derived from hairpin sequence adaptor. After adaptor removal, sequence reads shorter than 40 bp were excluded from further analysis. To remove reads that are likely to be not bisulfite converted, read pairs with more than 3 methylated non-CpG in either arm were discarded.
Following steps were taken to retrieve and map the original sequences onto reference genome: 1) the two arms for each read pair were first subjected to C->T and G->A conversion, and then globally aligned using Needleman-Wunsch algorithm; 2) the sequence reads with identity less than 90% between two arms were discarded; 3) after trimming the overhangs of the aligned sequences, original sequences were recovered according to the alignment information; 4) the recovered original sequences were mapped to mouse genome using bowtie with parameters ( -n 2 –l 40 –k 1 –m 1 --best), and only uniquely mapped reads were retained.
The methylation patterns for all cytosines were extracted based on the mapping result and the raw sequences. To eliminate the influence of SNP on the data analysis, the methylation pattern calling for nucleotide bases inconsistent with reference genome were masked.
For the RNA-seq data, all the pair-end reads were mapped to the mouse reference genome using TopHat (version 2.0.3). Genome annotation files with GTF format for Known Genes were downloaded from UCSC. Reads per kilobase of transcript per million reads (RPKM) values were calculated for each gene using Cufflinks software (version 2.0.2) with default parameters and normalized using quantile method.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include methylation level and methylation fidelity for each CpG dyads; tab-delimited text files include methylation level for cytosines in CHG and CHH context. tab-delimited text files include RFKM for each transcript.

organism: Mus musculus

source_name: Embryonic stem cell

growth_protocol: Mouse ES cells (E14TG2a) were maintained on gelatin-coated dishes in ATCC-formulated Dulbecco's Modified Eagle's Medium (ATCC), supplemented with 0.1 mM of 2-mercaptoethanol, 10% fetal bovine serum (StemCell Technologies), 2mM L-glutamine, 0.1mM MEM nonessential amino acid, 100U/ml penicillin, 10µg/mlstreptomycin, and 10ng/ml LIF (StemCell Technologies). The mES cells were passaged every 2 days at a ratio of 1:5 by washing with PBS, dissociating with 0.25% trypsin (GIBCO) for 3 min at 37°C, and resuspending in mES media. Media were changed daily. The nondifferentiated state of mES cells was measured using the Alkaline Phosphatase Kit from Stemgent.

extract_protocol:
Mouse ES cell genomic DNA was isolated using DNeasy Blood and Tissue kit (Qiagen, Frederick, MD). Total RNA was extracted with the miRNeasy extraction kit (Qiagen, Frederick, MD).
Ten-microgram mouse genomic DNA was spiked with 0.01% unmethylated cl857 Sam7 Lambda DNA (Promega) and sonicated to 200bp fragments with Covaris S2 (AB). After purification (PureLink® PCR Purification Kit, Invitrogen), DNA fragments were then subjected to end repair with the end repair enzyme mix (NEB), dA tailing using Klenow 3’-5’ exo- (NEB) with purification at each step. Ligation to Biotin-modified hairpin adapter (P-CGCCGGCGGCAAG/iBiodT/GAAGCCGCCGGCGT) and Illumina TruSeq adapters were performed using T4 DNA ligase (NEB) overnight. Adapter-ligated DNA was digested with MseI and MluCI (NEB) for 1h at 37°C. After purification, DNA fragments were then pulled down using Dynabeads® MyOne™ Streptavidin C1 beads (Invitrogen). Bisulfite conversion was performed using the EpiTect Bisulphite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers (with specific index) and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. After purification, size selection of 400-600 bp fragments was conducted with LabChip XT DNA Assay (Caliper) to yield longer sequences that are more amenable for unambiguous mapping to the reference sequence. RNA-seq libraries were constructed according to Illumima protocol and sequenced with the Illumina Hiseq 2000.

treatment_protocol: To induce differentiation, the mES cells were passaged and then cultured in ES cell culturing media without LIF. Media were changed every 2 days.

tag: cell line

tag: cell subtype

value: spontaneous differentiated state

tag: age

value: 6 day of spontaneous differentiated


title: SK-HEP-1, 4U, mRNA (SOLID 3)

city: Taipei

first: mike

last: thang

state: Taipei

address: 128 Academia Road, Section 2, Nankang

department: Genome Research Center

country: Taiwan

institute: Academia Sinica

description:
mRNA; RNA-Seq
4U
Processed data file: Transcriptome.txt

data_processing:
mRNA data used Galaxy web portal for abundance measurements. Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity mapped to hg19 with 2 mismatches using tophat and cufflinks for abundance measurement.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009 (PMID 19528076). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments 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: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.

organism: Homo sapiens

source_name: Liver cell line SK-HEP-1, control, 4 hours

growth_protocol: Cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA were isolated from total RNA samples by Poly(A) Purist-MAG kit.
SOLiD™ total RNA-seq kit for whole transcriptome libraries and small RNA libraries kits were used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard SOLiD™protocols.

treatment_protocol: Treated with 0.5 mg/ml Antrodia cinnamomea fruiting body ethanol extracts or 0.5 mg/ml DMSO.

tag: treatment

value: DMSO control

tag: time

value: 4 hours


title: BNL CL.2, 4U, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
4U
Processed data file: fCL_5500.txt

data_processing:
miRNA data utilized in-house built miRNA pipeline combined with publicly available tools such as bowtie and cutadapt for pre data processing.
Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity or reads shorter than 16 bp and longer than 30 bp, then mapped to mm9 for the CL2 samples and hg19 for the human sample whole genome using bowtie v0.12.7 with perfect match for known miRNA detection. Transcripts Per Million (TPM) were calculated.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.

source_name: Liver cell line BNL CL.2, control, 4 hours

value: BNL CL.2


title: BNL CL.2, 2T, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
2T
Processed data file: fCL_5500.txt

source_name: Liver cell line BNL CL.2, Antrodia cinnamomea treated, 2 hours

value: Antrodia cinnamomea

value: 2 hours


title: SK-HEP-1, 2U, mRNA (SOLID 3)

description:
mRNA; RNA-Seq
2U
Processed data file: Transcriptome.txt

source_name: Liver cell line SK-HEP-1, control, 2 hours


title: SK-HEP-1, 2T, mRNA (SOLID 3)

description:
mRNA; RNA-Seq
2T
Processed data file: Transcriptome.txt

source_name: Liver cell line SK-HEP-1, Antrodia cinnamomea treated, 2 hours


title: MDAMB453, RNA-Seq

city: Portland

first: Laura

middle: M.

last: Heiser

state: OR

address: 3181 SW Sam Jackson Park Rd.

institute: OHSU

data_processing:
Processed with Alexa-seq software pipeline [PMID: 20835245]
Genome_build: hg18
Supplementary_files_format_and_content: Text file with fpkm-like measurement (see PMID:20835245) for each Ensembl (v53) gene

source_name: breast cancer cell line

growth_protocol: Cells in exponential growth phase

extract_protocol:
Qiagen RNAeasy
RNAseq libraries for transcriptome analysis were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system per manufacturers' instructions. Sample prep began with 1 _g of total RNA from each sample. Poly-A RNA was purified from the sample with oligo dT magnetic beads, and the poly(A) RNA was fragmented with divalent cations. Fragmented poly-A RNA was converted into cDNA through reverse transcription and were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3' A-tailing with exo-minus Klenow polymerase was followed by ligation of Illumina paired-end oligo adapters to the cDNA fragment.  Ligated DNA was PCR amplified for 15 cycles and purified using AMPure XP beads. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting libraries were analyzed using an Agilent Bioanalyzer High Sensitivity chip.

tag: cell type

value: breast cancer cell line

tag: subtype

value: Luminal


title: Maternal aging

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Base-calling software, version, parameters: SOLiD4.0 SAT pipeline, default parameters
All sequenced reads were aligned to the Mouse genome sequences (ENSEMBL56 ) using AB’s SOLiD Corona_lite_v4.2 software available at http://solidsoftwaretools.com/gf/project/corona/.  We used a recursive strategy to improve the usable sequenced reads information, that is 50mers reads were first mapped to the genome with at most 5 color-space mismatches and reads that failed to be mapped were progressively trimmed off, five bases at one time from the 3’ end and mapped to the genome again until a match was found (unless the read had been trimmed by <30 bases). All those uniquely mapped reads were used for calculating the genes RPKM values (reads per kilobase of exon per million mapped sequenced reads), which is used for define gene expression level. We identified DEGs from different samples according to an R package named DEGseq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: oocyte

growth_protocol: All mice were raised on standard diet in standard cages under controlled temperature (22 ± 2 °C) and lighting (12: 12 h light: dark cycle) and had free access to sterile water and pellet food ad libitum.

extract_protocol:
Each 18 oocytes were lysed in one tube and the total mRNAs were reversely transcripted to cDNAs.
Each 18 oocytes were lysed in one tube and the total mRNAs were reversely transcripted to cDNAs by universe primer 1 (UP1) adaptor primers containing 24 bp oligo(dT) sequence. The remaining primers were removed and poly(A) tails to the 3′ terminal of the cDNAs were added. Universe primer 2 (UP2) primers containing 24 bp oligo(dT) were used for the synthesis of the second cDNA strand. The double strand cDNA library was amplified by UP1 and UP2 for 18 cycles, and by amine-blocked UP1 and UP2 for 14 cycles. The final amplified cDNA libraries were sent to Genome institute of Beijing and sequenced by Applied Biosystem SOLiD sequencing system.

treatment_protocol: Mothers aging vs control, the oocyte transcriptome was analysed through RNA-Seq analysis.

tag: strain

value: ICR

value: oocyte at MII stage

value: 12 months


title: BNL CL.2, 2U, miRNA (SOLiD 5500xl)

description:
microRNA; small RNA-Seq
2U
Processed data file: fCL_5500.txt

source_name: Liver cell line BNL CL.2, control, 2 hours


title: Maternal control

value: 3 months


title: 8min-4

status: Public on May 09 2014

city: Rehovot

first: Gilad

last: Fuchs

address: Rehovot

country: Israel

institute: Weizmann Institute of Science

description: Nascent RNA labled with 4sU

data_processing:
All reads were aligned to the human reference genome (hg19, GRCh37) using the bowtie 2 aligner with default parameters (only setting –N 1)
For each experiment we constructed a genome-wide profile of the signal per disjoint 100 bp adjacent bins. The sum of each experiment was normalized to be 106
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file describe the transcription elongation velocity measured for all DRB-dependent genes.

source_name: Human cervical cancer

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% heat-inactivated fetal bovine serum and penicillin-streptomycin antibiotics solution

extract_protocol:
4sU labled RNA was tagged with Biotion, and enriched with Streptavidin magnetic beads.
cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer's instructions but without the polyA isolation stage

treatment_protocol: Cells were treated with DRB for 3hr and harvested after DRB removal. Cells were also labeld with 4sU for 8 min beofre harvested.

value: HeLa

value: 8 min

value: 3 h DRB 8 min 4sU


title: 4min-2

description: Nascent RNA labled with 4sU

value: 4 min

value: 3 h DRB 4 min 4sU


title: 8min-1

description: Nascent RNA labled with 4sU


title: 8min-2

description: Nascent RNA labled with 4sU


title: 4min-1

description: Nascent RNA labled with 4sU


title: 0min-2

description: Nascent RNA labled with 4sU

value: 0 min

value: 3 h DRB 0 min 4sU


title: 0min-4

description: Nascent RNA labled with 4sU


title: NT-4

description: Nascent RNA labled with 4sU

value: control

value: untreated


title: 0min-3

description: Nascent RNA labled with 4sU


title: NT-1

description: Nascent RNA labled with 4sU


title: K562 MRE-seq

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Sequencing reads were aligned to human hg19 or mouse mm9 with BWA
For MeDIP-seq, redandunt reads were discard
For MRE-seq, reads were filtered by MRE recognization site in genome.
Aligned results were further processed by methylQA (http://methylqa.sourceforge.net/) to get bigWig files
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: K562, human leukemia cell line

extract_protocol:
For MRE:  DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100–300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 µl used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 μl used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.


title: GM19239_seq

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Processed data Mapped to Hg19/Grch37

data_processing:
Cutadapt was used to trim for quality and remove adapters from reads.
Mapped using Bismark V0.6.3
Duplicates were removed using SAMtools
For each CpG methylated and unmethylated counts were obtained using Bismark V0.6.3 methylation extractor. Counts are represented as z (unmethylated CpG) and Z (methylated CpG) for each read.
Methylation levels were obtained by dividing the number of methylated reads by the total number of reads.
Genome_build: Hg19/Crch37
Supplementary_files_format_and_content: The processed data are .txt files. The files contain the methylation percentage, the number of methylated reads and the number of unmethylated reads for each CpG with an overlapping read in the sample.

extract_protocol:
Standard whole genomic DNA extraction
Bisulfite sequencing was performed using a modified version of the Illumina whole genome bisulfite sequencing protocol Specifically, extracted DNA from LCL cell lines of 10 Yoruba HapMap population individuals and spiked in unmethylated lambda phage DNA was fragmented into 100bp fragments using a Covaris ultra-sonicator. Fragmented DNA was blunt ended, repaired, and standard Illumin TruSeq adapters were ligated to the DNA fragments. DNA was then bisulfite converted using the Invitrogen MethylCode Bisulfite Conversion Kit. The bisulfite converted DNA was then PCR amplified and sequenced using the Illumina HiSeq 2000. Each individual was sequenced in at least two lanes

tag: gender

value: Male

value: Lymphoblastoid Cell Line


title: Mel MRE-seq

source_name: Mel, mouse leukemia cell line

value: Mel


title: GM12878 MRE-seq

source_name: GM12878, human lymphoblast cell line


title: Ch12 MRE-seq

source_name: Ch12, mouse lymphoblast cell line


title: GM12878 MeDIP-seq

extract_protocol:
For MeDIP, 5–15 μg DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA), than DNA was sonicated to ~100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2–5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml−1, Eurogentec. Catalog No. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml−1, Jackson Immunoresearch. Catalog No. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology. Catalog No. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml−1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).
Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.


title: K562 MeDIP-seq


title: Mel MeDIP-seq


title: 8min-3

description: Nascent RNA labled with 4sU


title: KO

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

description: Sample 2

data_processing:
Images generated by sequencers are converted by base calling into nucleotide sequences.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The clean reads were then aligned to the reference mouse genome and the corresponding annotated genes using the TopHat.
In the alignment, preliminary experiments were performed to optimize the alignment parameters to provide the most information on the alternative splicing events.
Genome_build: Mm9
Supplementary_files_format_and_content: tab-delimited text file includes the splicing loci on chrosome, gene name, ensemble ID, splicing types, and stantistially values for alternative splicing events between the two samples

source_name: KO_MEF cells

extract_protocol:
Cells were harvested and total RNA was extracted by Trizol reagent. Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected.
Libraries for paired-end sequencing were prepared using mRNA-Seq Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: genotype/variation

value: SRSF10-deficient (KO)

value: embryonic tissues

value: Embryonic fibroblast cells


title: GM18516_seq

description: Processed data Mapped to Hg19/Grch37


title: GM18522_seq

description: Processed data Mapped to Hg19/Grch37


title: GM19141_seq

description: Processed data Mapped to Hg19/Grch37


title: cytC_IP_rep1

city: Cleveland

first: Maria

last: Hatzoglou

state: OH

address: 10900 Euclid Ave

department: Pharmacology

institute: Case Western Reserve University

description: Sample 4

data_processing:
Sequences were aligned on the Mus Musculus genome, partly provided in a GeneBank flat file (ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/), and partly from the genomic tRNA database mm10 dataset (http://gtrnadb.ucsc.edu/Mmusc10/). The reads were aligned with an "in house" aligner allowing at most one mismatch and no indel with the targeted genes. Hits with the longest alignments are retained. A mountain plot of each tRNA gene was made by accumulating the reads that map to the gene: the height of the mountain for a gene position indicates the number of time that that position has been covered by reads. The enrichment plot is two mountain plots one on top of another. Here we used low frequencies Fourier transforms to smooth the plots. Red vertical bars indicate peaks of the smoothed curves, their heights proportional to the enrichment values between the two curves. The curves are normalized by the number of reads per kilobase per million mapped (rpkM) in their own set.
Genome_build: mm10
Supplementary_files_format_and_content: enriched.xlsx includes tRNA sequence and enrichment value

growth_protocol: DMEM with 10% FBS, 100 u/ml penicillin, 100 mg/ul streptomycin

extract_protocol:
MEFs were treated as above "treatment protocol", split into two parts: one part served as the control, consisting of the total RNA content of the lysates (cytC_input); the second part was Cyt c-immunoprecipitated, conisting of the RNA that is bound to Cyt c (cytC_IP).  (Cyt c antibody was from BD Biosciences, Cat: 556432, Lot: 26996)  RNA from control and Cyt c-IP were isolated using mirVana miRNA isolation kit (Life Technologies) to enrich small RNAs.  Enriched RNAs were then seperated in Urea-PAGE and gel-purified to isolate only 30-45 nt by Illumina TruSeq Small RNA Sample Preparation Kit (Cat: RS-200-0012) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Small RNA Sample Preparation Kit, RS-200-0012)

treatment_protocol: MEFs were pretreated with 0.5 mg/ml recombinant angiogenin (R&D Systems, Cat: 265-AN-250-CF, Lot: DK0413041) for 30 min and then in combination with 600 mOsm hyperosmotic medium for 2 h.

tag: strain background

value: Wild type

value: mouse embryonic fibroblast

tag: ip antibody

value: Cyt c antibody

tag: ip antibody vendor

value: BD Biosciences

tag: ip antibody cat. #

tag: ip antibody lot #

tag: molecule subtype

value: Cyt c-IP RNA


title: cytC_IP_rep2

description: Sample 5


title: 0min-1

description: Nascent RNA labled with 4sU

value: HeLa


title: NT-3

description: Nascent RNA labled with 4sU


title: NT-2

description: Nascent RNA labled with 4sU


title: GM18508_seq

description: Processed data Mapped to Hg19/Grch37

value: Female


title: SK-HEP-1, 2T, miRNA (SOLID 3)

description:
microRNA; small RNA-Seq
2T
Processed data file: miRNA_solid3.txt

data_processing:
miRNA data utilized in-house built miRNA pipeline combined with publicly available tools such as bowtie and cutadapt for pre data processing.
Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity or reads shorter than 16 bp and longer than 30 bp, then mapped to mm9 for the CL2 samples and hg19 for the human sample whole genome using bowtie v0.12.7 with perfect match for known miRNA detection. Transcripts Per Million (TPM) were calculated.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.

value: Antrodia cinnamomea

value: 2 hours


title: cytC_input_rep3

description: Sample 3

value: total RNA


title: cytC_input_rep2

description: Sample 2


title: Ch12 MeDIP-seq


title: cytC_input_rep1

description: Sample 1


title: GM18505_seq

description: Processed data Mapped to Hg19/Grch37


title: GM19204_seq

description: Processed data Mapped to Hg19/Grch37


title: GM19193_seq

description: Processed data Mapped to Hg19/Grch37


title: DGM-11111_LA-BC

status: Public on May 08 2014

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
DGM-11111
Basal cells cultured from airway epithelium samples.

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using Bowtie (v0.12.8.0, http://bowtie-bio.sourceforge.net), Tophat (v2.0.4, http://tophat.cbcb.umd.edu) and Cufflinks (v2.0.2, http://cufflinks.cbcb.umd.edu).
To correct for transcript length and depth of coverage, raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM) resulting in the fpkm_tracking files.
Resultant fragments were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie.
Non-aligned reads were segmented using Tophat and re-aligned to the genome, aligning reads that span introns and determining junction splice sites. Cufflinks assembled reads into transcripts and assembled reads merged using Cuffmerge; the reads generated from a transcript are directly proportional to the transcripts relative abundance. For the analysis, Tophat (which automatically runs Bowtie) was run for each read pair in a given lane.
For each read pair, Tophat produced one file which contained all reads mapped to the human_g1k_v37 genome and RefSeq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) transcriptome.
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent Tophat results into one file. This file contains all of the aligned reads for each read pair. Finally, Cufflinks was run on the merged Tophat output to produce a file with FPKM values for each sample.
Data was analyzed using Tuxedo pipeline software.
Genome_build: GRCh37
Supplementary_files_format_and_content: fpkm_tracking files are text files that include the RefSeq gene and location, the FPKM value, high and low confidence and status.

source_name: airway basal cells, smoker

growth_protocol: Airway epithelial cells collected by brushing were cultured supplemented with growth factors according to the manufacturer's instructions. Media was changed every 2 days until time of harvest at day 7, when the cells had reached 70 to 80% confluence.

extract_protocol:
Total RNA from harvested nonsmoker and smoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA.
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIAquick PCR purification kit (Qiagen, Valencia, CA).
Samples were loaded onto an Illumina flowcell for paired-end 101 x 2 sequencing reactions using the Illumina HiSeq 2000, using a single flow cell with 4 samples multiplexed per lane of flow cell.

value: airway basal cells

tag: smoking status

value: smoker


title: DGM-10922_LA-BC

description:
DGM-10922
Basal cells cultured from airway epithelium samples.


title: DGM-10906_LA-BC

description:
DGM-10906
Basal cells cultured from airway epithelium samples.


title: DGM-11066_LA-BC

description:
DGM-11066
Basal cells cultured from airway epithelium samples.


title: DGM-10503_LA-BC

description:
DGM-10503
Basal cells cultured from airway epithelium samples.

source_name: airway basal cells, nonsmoker

value: nonsmoker


title: cytC_IP_rep3

description: Sample 6


title: DGM-10907_LA-BC

description:
DGM-10907
Basal cells cultured from airway epithelium samples.


title: DGM-11016_LA-BC

description:
DGM-11016
Basal cells cultured from airway epithelium samples.


title: DGM-10565_LA-BC

description:
DGM-10565
Basal cells cultured from airway epithelium samples.


title: DGM-10194_LA-BC

description:
DGM-10194
Basal cells cultured from airway epithelium samples.


title: GM19238_seq

description: Processed data Mapped to Hg19/Grch37

value: Lymphoblastoid Cell Line


title: DGM-10284_LA-BC

description:
DGM-10284
Basal cells cultured from airway epithelium samples.


title: GM18507_seq

description: Processed data Mapped to Hg19/Grch37

value: Male


title: DHS-seq, 3T3-L1 4h

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Using ultra deep sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J., 30(8):1459-72), we obtained 136.6 million mapped sequence tags. These were analyzed using our newly developed footprinting algorithm DNase2TF to obtain footprints of 8-30 bp (Myong-Hee Sung, Michael Guertin, Songjoon Baek, Gordon L. Hager, unpublished data). See Supplemental Experimental Methods for more details.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were created using HOMER for visualization of DHS and cutcount profiles as well as expression data in the UCSC genome browser.

source_name: 3T3-L1 pre-adipocytes (4h)

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days post confluency (day 0), the cells were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS).

extract_protocol:
DHS-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
Nuclei isolated from 3T3-L1 cells four hours after induction of differentiation were subjected to DNase I digestion and small fragments were isolated by running the digested DNA through a sucrose gradient. DNA of approximately 100-150 bp were sequenced on the Illumina platform according to the instructions of the manufacturer. All this data comes from extensive sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J, 30(8):1459-72) and these data were therefore combined with our previously published data for downstream analyses, including identification of the DHS sites and footprints found here as processed data files.

treatment_protocol: 3T3-L1 pre-adipocytes (day 0) were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Cells were harvested four hours after induction.

tag: cell line

tag: differentiation stage

value: pre-adipocytes

value: 4 hrs

value: DNase I treated


title: DGM-10568_LA-BC

description:
DGM-10568
Basal cells cultured from airway epithelium samples.


title: DHS-seq, 3T3-L1 4h (paired-end)

description: Nuclei isolated from 3T3-L1 cells four hours after induction of differentiation were subjected to DNase I digestion and small fragments were isolated by running the digested DNA through a sucrose gradient. DNA of approximately 100-150 bp were sequenced on the Illumina platform according to the instructions of the manufacturer. All this data comes from extensive sequencing of our previously published DHS-seq library (Siersbæk et al., 2011, EMBO J, 30(8):1459-72) and these data were therefore combined with our previously published data for downstream analyses, including identification of the DHS sites and footprints found here as processed data files.


title: PA-CK-2

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
gene_exp_PA.diff
sample 1

data_processing:
Bacterial RNA-seq reads were mapped to the P. auruginosa and S. aureus genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0)
P. aeruginosa PAO1 and S. aureus. Newman
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pseudomonas aeruginosa MPAO1/P1

source_name: liquid culture in LB

growth_protocol: LB medium for P. aeruginosa, and TSB for S. aureus

extract_protocol:
An RNeasy Mini Kit (Qiagen) was used for subsequent RNA purification with DNase I treatment. After removing rRNA by using MICROBExpress Kit (Ambion), mRNA was used to generate the cDNA library according to TruSeq RNA Sample Prep Kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina).
TruSeq RNA Sample Preparation Kit (Illumina)
An RNeasy Mini Kit (Qiagen) was used for subsequent RNA purification with DNase I treatment. mRNA was purified after removing rRNA by using MICROBExpress Kit (Ambion),
mRNA was used to generate the cDNA library according to TruSeq RNA Sample Prep Kit protocol (Illumina)

treatment_protocol:
Mid-log bacteria in dialysis bag
10 mM H2O2 for 10 min in dialysis bag

tag: technology

value: RNA-seq

value: control


title: PA-HP-1

description:
gene_exp_PA.diff
sample 2

treatment_protocol:
Mid-log bacteria were treated with steady dose of 10 mM H2O2 for 10 min in dialysis bag
10 mM H2O2 for 10 min in dialysis bag

tag: treatment


title: PA-CK-1

description:
gene_exp_PA.diff
sample 1


title: DGM-10638_LA-BC

description:
DGM-10638
Basal cells cultured from airway epithelium samples.


title: DGM-01774_LA-BC

description:
DGM-01774
Basal cells cultured from airway epithelium samples.


title: DGM-11374_LA-BC

description:
DGM-11374
Basal cells cultured from airway epithelium samples.


title: DGM-01620_LA-BC

description:
DGM-01620
Basal cells cultured from airway epithelium samples.


title: BMDM_UT_shPu.1_rep1

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174) with options -v 3 -m 1 -S -I 0 -X 250. All paired-end fragments with a unique match to the genome with three or fewer mismatches were retained.
Duplicated fragments were discarded and wiggle files generated with BedTools (PMID: 20110278)
mm9 (NCBI Build 37)
wiggle files
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol:
MNase digestion was performed starting from 8-12 x 10^6 cells. Cell pellets were resuspended in a 15 mM NaCl, 15 mM Tris-HCl [pH 7.6], 60 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.3 M sucrose buffer (0.5 mM PMSF, 1 mM DTT, 0.2 mM spermine, 1 mM spermidine) buffer and lysed upon addition of 0.4% NP40. Nuclei were washed with a 15 mM NaCl, 15 mM Tris-HCl [pH 7.6], 60 mM KCl, 0.3 M sucrose buffer (0.5 mM PMSF, 1 mM DTT, 0.2 mM spermine, 1 mM spermidine). Digestion was performed with 1.3 units of MNase (Roche 10107921001) in a 20 mM Tris-HCl [pH 7.6], 5 mM CaCl2 digestion buffer, for 100 minutes at 37°C. Nucleosomal DNA was isolated by diluting nucleosomes in digestion solution to a final concentration of 5 mM MgCl2, 5 mM CaCl2, 70 mM KCl and 10 mM HEPES [pH 7.9]. Digestion with 5 units of MNase was  let proceed for 100 minutes at 37°C. DNA was purified from octamer proteins with Qiagen PCR purification kit. Purified DNA was then run in a 1% agarose gel and the mononucleosomal band cut and purified first with Millipore DNA Gel Extraction Kit and then with Qiagen PCR purification kit.
Mononucleosomal DNA was prepared for HiSeq2000 sequencing using the Illumina standard protocol.

value: BMDM cells (7th day of differentiation)

tag: retroviral infection


title: BMDM_UT_shPu.1_rep2

tag: cell type


title: IV_MNase

source_name: In vitro reconstituted chromatin (genomic DNA from primary bone marrow-derived macrophages)

extract_protocol:
Naked genomic DNA was purified from bone marrow derived murine macrophages by three consecutive phenol/chloroform extractions. DNA was sonicated to obtain fragments smaller than 2 kb, and fragments ranging from 600 to 2000 kb were purified with Solid-Phase Reversible Immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter). DNA was combined with recombinant histones (EpiMark Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis (PMID: 10372352). DNA molecules were considered as multiple of 150 bp nucleosome-assembling units. Assembly reaction was performed mixing octamers and nucleosome-assembling units in a molar ratio 1:2, such that DNA was not limiting and octamer would assemble according to the sequence preference. Nucleosomal DNA was isolated by diluting nucleosomes in digestion solution to a final concentration of 5 mM MgCl2, 5 mM CaCl2, 70 mM KCl and 10 mM HEPES [pH 7.9]. Digestion with 5 units of MNase was let proceed for 100 minutes at 37°C and stopped by adding EDTA to a final concentration of 50mM. DNA was purified from octamer proteins with Qiagen PCR purification kit. Purified DNA was then run in a 1% agarose gel and the mononucleosomal band cut and purified first with Millipore DNA Gel Extraction Kit and then with Qiagen PCR purification kit.
Mononucleosomal DNA was prepared for HiSeq2000 sequencing using the Illumina standard protocol.


title: BMDM_UT_rep2


title: BMDM_UT_empty_rep1

value: empty (sh-Renilla)


title: BMDM_UT_empty_rep2


title: PU.1_IV_Pu.1_depleted

description:
Chromatin IP against PU.1
Processed data file: Pu1_IV_ChIP_IgG-depleted_vs_Pu1-depleted.bed (attached to Series record)

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters except for using --nolambda and --nomodel options. Pu.1-depleted sample was used as control for the IgG-depleted sample.
mm9 (NCBI Build 37)
*_peaks.bed, list of the peaks called by MACS
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

extract_protocol:
Naked genomic DNA was purified from bone marrow derived murine macrophages by three consecutive phenol/chloroform extractions. DNA was sonicated to obtain fragments smaller than 2 kb, and fragments ranging from 600 to 2000 kb were purified with Solid-Phase Reversible Immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter). DNA was combined with recombinant histones (EpiMark Nucleosome Assembly Kit, NEB E5350) to generate nucleosomes by salt dialysis (PMID: 10372352). DNA molecules were considered as multiple of 150 bp nucleosome-assembling units. Assembly reaction was performed mixing octamers and nucleosome-assembling units in a molar ratio 1:2, such that DNA was not limiting and octamer would assemble according to the sequence preference. In vitro nucleosomes were partially digested with MNase (5U for 2 minutes in the digestion buffer described above) to obtain mainly di- and tri-nucleosomes and to eliminate any residual unwrapped DNA. They were then incubated with macrophage-derived nuclear extracts. Nuclear extracts were prepared from 2e7 cells. Cells were first lysed with hypotonic buffer (10 mM Tris-HCl, 1 mM KCl, 1.5 mM MgCl2), then nuclei were lysed with a high-salt buffer (50 mM Tris-HCl, 200 mM NaCl, 10% glycerol, 0.2% NP40) and diluted 1:2 with a dilution buffer (10 mM Tris-HCl, 2 mM EDTA). Nuclear extracts were subjected twice (2 hours and overnight) to immunodepletion with 8 μg of Pu.1 antibody or normal rabbit IgG. Incubation of nuclear extracts and in vitro nucleosomes was performed at 4°C for 2 hours, then 5 μg of anti-Pu.1 antibody were added for 1 hour and DNA-protein complexes recovered with G protein-coupled magnetic beads. Beads were washed 6 times with wash buffer (30 mM Tris-HCl, 200 mM NaCl, 10% glycerol, 0.1% NP40, 1 mM EDTA) and twice with TE. DNA was eluted in TE-2% SDS. DNA was then purified by Qiaquick PCR purification kit and quantified with PicoGreen (Invitrogen).
ChIP DNA was prepared for HiSeq2000 sequencing following standard protocols.

tag: antibody

value: Anti-PU.1 (in-house rabbit polyclonal against the N-Terminal (aa. 1-100))

value: No treatment


title: PU.1_IV_IgG_depleted

tag: strain


title: BMDM_UT_rep1


title: DGM-11852_LA-BC

description:
DGM-11852
Basal cells cultured from airway epithelium samples.


title: BMDM_UT_rep3


title: DGM-01657_LA-BC

description:
DGM-01657
Basal cells cultured from airway epithelium samples.


title: PU.1_shPU.1_rep2

description: Chromatin IP against PU.1

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters. Each IP was compared to input DNA derived from BMDM (GSM487453).
mm9 (NCBI Build 37)
*_peaks.bed, list of the peaks called by MACS
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with default parameters. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

growth_protocol: At day zero bone marrow cells were isolated from C57BL/6 mice and 4 × 10^6 cells/plate were seeded in 10 cm dishes in TET-free BM medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cells were infected twice (in two consecutive days after plating) using supernatants from transfected Phoenix-ECO packaging cells. Puromycin selection (3 μg/ml) started on day 3. At day 5, shPU.1 expression was induced for 48 hours using doxycycline (0.5 μg/ml).

extract_protocol:
ChIP lysates were generated from 5x10^8 cells. Cells were fixed in 1% formaldehyde for 10 min. Lysate was sonicated and then immunoprecipitated with 5 ug of antibody against PU.1 (or normal rabbit IgG as control). Antibodies were pre-bound overnight to 50 ul of G protein-coupled paramagnetic beads (Dynabeads) in PBS/0.5% BSA and then incubated with the lysates overnight at 4 C. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50 mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
ChIP DNA was prepared for HiSeq2000 sequencing following standard protocols.


title: PU.1_shPU.1_rep1

description: Chromatin IP against PU.1


title: PU.1_empty_rep2

description: Chromatin IP against PU.1


title: PU.1_empty_rep1

description: Chromatin IP against PU.1


title: rat2_DeepAC

city: Bunkyo-ku, Tokyo

first: Yoshifumi

last: Mori

department: Orthopaedic Surgery

country: Japan

institute: Tokyo University

data_processing:
Illumina Casava1.8 software used for basecalling.
trimmed mean of M (TMM) values were calculated using protocol described by M.D. Robinson and A. Oshlack. (Genome Biol. 11 (2010) R25)
Genome_build: RefSeq Genes and Transcripts (2012.12.15; UCSC version rn4)
Supplementary_files_format_and_content: txt with TMM values for each Sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: deeper layers of articular cartilage

extract_protocol:
Proximal tibia was removed, flash frozen in liquid nitrogen, cryosectioned and transferred to adhesive membrane. SFZ and deepAC were separately collected by LMD. Total RNA was extracted using Picopure RNA Isolation Kit. Amplified RNA (aRNA) was generated by linear amplification of mRNA using RiboAmp HS PLUS Kit. Illumina TruSeq RNA Sample Prep Kit v2 was used with 50ng of aRNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

tag: age

tag: tissue

value: deeper layers of articular cartilage (AC)


title: rat2_SFZ

source_name: SFZ

value: superficial zone (SFZ)


title: RNA-seq Scr exp3, 3T3-L1 4h

description: Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions.

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using Bowtie (Langmead et al., 2009, Genome biology, 10(3):R25). Mapped reads in exons were counted using HOMER (Heinz et al., 2010, Mol Cell, 38(4):576-89) and  differentially expressed genes (adjusted P<0.05) were identified using DESeq (Anders and Huber, 2010, Genome Biology, 11(10):R106). Bedgraph files were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were created using HOMER for visualization of DHS and cutcount profiles as well as expression data in the UCSC genome browser.

extract_protocol: Purified RNA was subjected to standard mRNA sample preparation for sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions.

tag: time

value: Scr. Lentivirus expressing shRNA against a scrambled sequence


title: RNA-seq shCEBPb exp3, 3T3-L1 D0

source_name: 3T3-L1 pre-adipocytes (D0)

value: 0 hr

value: Lentivirus expressing shRNA against C/EBPβ


title: PA-HP-2

description:
gene_exp_PA.diff
sample 2


title: RNA-seq Scr exp2, 3T3-L1 4h


title: rat1_DeepAC


title: BMDM_UT_rep4


title: RNA-seq shCEBPb exp2, 3T3-L1 D0


title: RNA-seq Scr exp2, 3T3-L1 D0


title: SA-HP-2

description:
gene_exp_SA.diff
sample 2

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: liquid culture in TSB

value: Newman


title: RNA-seq shCEBPb exp3, 3T3-L1 4h


title: SA-CK-2

description:
gene_exp_SA.diff
sample 1


title: SA-HP-1

description:
gene_exp_SA.diff
sample 2


title: rat1_SFZ


title: Al14 sRNA

status: Public on May 07 2014

city: Villeneuve d'Ascq

first: Vincent

last: Castric

address: Lille1 university

country: France

institute: CNRS

description: small RNA (15-40bp)

data_processing:
Adaptators from SOLiD small RNA sequences were trimmed using an homemade script (SOLID adaptor sequence : C33020103031311231230222031111222203122020 ).
Sequences were aligned against different S-locus haplotypes and the genome of Arabidopsis lyrata (araly1) using Bowtie (no mismatch authorized)
Reads aligned on the arabidopsis genome and on the S-locus haplotypes were removed
microRNA genes were detected on the S-locus haplotypes according to a set of criterias
Genome_build: araly1
Supplementary_files_format_and_content: abundance measurements
motif_miARN.fa: the fasta file of the 17 putative miRNA sequences.

organism: Arabidopsis lyrata

source_name: flowers stage 1-12

extract_protocol:
Total RNA were extracted by TRI reagent (Sigma) from 10-20 floral buds at various stages of development
Small RNA libraries were prepared for sequencing using standard SOLiD and PROTON protocols

tag: tissus

value: flowers

tag: slocus genotype


title: BC03

description: small RNA (15-40bp)

organism: Arabidopsis halleri


title: SA-CK-1

description:
gene_exp_SA.diff
sample 1


title: nivelle 001

description: small RNA (15-40bp)


title: nivelle 060

description: small RNA (15-40bp)


title: BC01

description: small RNA (15-40bp)


title: BC02

description: small RNA (15-40bp)


title: nivelle 045

description: small RNA (15-40bp)


title: RNA-seq Scr exp3, 3T3-L1 D0

value: pre-adipocytes


title: I9 47

description: small RNA (15-40bp)


title: I5_53

description: small RNA (15-40bp)


title: I5 77

description: small RNA (15-40bp)


title: Soybean Heart Stage Suspensor-Biological replicate 3

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

description: Compartments collected from seeds 1.7-2.5 mm in length

data_processing:
Basecalls performed using RTA version 1.12.4.2
Each lane of sequencing for each sample is attached as an individual compressed file.  The sequence data are in the fastq format.
Sequenced reads were quality-filtered, reads corresponding to rDNA sequences were removed and the resulting filtered reads were mapped to Glycine max gene models (v1.1) using bowtie v0.12.7 with parameters -v 2 -5 10 -3 4 -m 1 --best --strata
Read counts for each gene models were computed using a custom script. Normalized counts are obtained using the EdgeR package v3.0.8 (Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene    expression data. Bioinformatics 26, 139-140).
Genome_build: Glyma 1.1
Supplementary_files_format_and_content: tab-delimited text file including the normalized counts for each sample.

organism: Glycine max

source_name: Soybean Heart Stage-Suspensor

growth_protocol: Soybean plants were grown at the UC Davis Greenhouses with a 16:8 day:night cycle at 22°C-30°C. Seeds were germinated in Modified UC Mix (equal parts of ground canadian sphagnum, horticultural grade sand, white pumice, redwood compost) for 10 days.  Individual seedlings were transfered to 1 gallon pots where they were grown for an additional 3 weeks before being transplanted to 3 gallon pots.  Plants were watered as needed with water containing 190 ppm Nitrogen, 40 ppm Phosphorus and 140 ppm Potassium and micronutrients.

extract_protocol:
Soybean seeds (Williams 82) were fixed in 3:1 ethanol:acetic acid for 16-20 hours at 4°C, then dehydrated with 75% ethanol, 85% ethanol, 95% ethanol, and three times with 100% ethanol, each wash in one hour intervals. Then they were infiltrated with 3:1 ethanol-xylenes, 1:1 ethanol-xylenes, 1:3 ethanol-xylenes, and three times with 100% xylenes, dilution in two hour intervals. They were then infiltrated with molten paraffin at 60 deg  C for 1-4 days, depending on the size of the tissue. Laser capture microdissection was used to isolate specific compartments of the seed after tissues were sectioned in 5-10um sections. Total RNA was isolated with Ambion RNaqueous-Micro kit (Grand Island, NY) and quantified with Quant-iT™ RiboGreen® RNA reagent (Grand Island, NY) on a Nanodrop ND-3300.
Amplification was performed using NuGen Ovation Pico WTA V1 (San Carlos, CA), starting with 15ng total RNA. Double-stranded cDNA was generated using the NuGen WT-Ovation Exon-Module (San Carlos, CA). Illumina-complatible libraries were made starting with 150 ng double-stranded cDNA using Kumar et al. (Kumar R, Ichihashi Y, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN and Sinha NR (2012) A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci. 3:202. doi: 10.3389/fpls.2012.00202) Supplemetary Methods 1 library preparation protocol, starting at Day 2.  The following modifications were done: the Illumina TruSeq DNA Sample preparation kit adapters were used (1/25 dilution) and the Agilent Pfu Turbo Cx hotstart DNA polymerase was used for the PCR enrichment step (15 cycles).  Libraries were quantified using Quant-iT PicoGreen dsDNA Reagent (Grand Island, NY) and a Nanodrop ND-3300 instrument.  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: compartment

value: Suspensor

tag: developmental stage

value: seed - heart stage


title: RNA-seq shCEBPb exp2, 3T3-L1 4h

value: 4 hrs


title: Soybean Heart Stage Suspensor-Biological replicate 1


title: Soybean Heart Stage Suspensor-Biological replicate 2


title: Soybean Heart Stage Seed Coat Outer Integument-Biological replicate 2

value: Seed Coat Outer Integument


title: Soybean Heart Stage Seed Coat Outer Integument-Biological replicate 1


title: Soybean Heart Stage Seed Coat Inner Integument-Biological replicate 3

value: Seed Coat Inner Integument


title: Soybean Heart Stage Seed Coat Inner Integument-Biological replicate 2


title: Soybean Heart Stage Seed Coat Outer Integument-Biological replicate 3


title: Soybean Heart Stage Seed Coat Hilum-Biological replicate 3

source_name: Soybean Heart Stage Seed Coat Hilum

value: Seed Coat Hilum


title: Soybean Heart Stage Seed Coat Hilum-Biological replicate 1


title: Soybean Heart Stage Seed Coat Epidermis-Biological replicate 2

source_name: Soybean Heart Stage Seed Coat Epidermis

value: Seed Coat Epidermis


title: Soybean Heart Stage Seed Coat Epidermis-Biological replicate 1


title: Soybean Heart Stage Seed Coat Epidermis-Biological replicate 3


title: I5 67

description: small RNA (15-40bp)


title: Soybean Heart Stage Seed Coat Endothelium-Biological replicate 4

value: Seed Coat Endothelium


title: Soybean Heart Stage Seed Coat Inner Integument-Biological replicate 1


title: Soybean Heart Stage Seed Coat Endothelium-Biological replicate 1


title: Soybean Heart Stage Endosperm-Biological replicate 1

source_name: Soybean Heart Stage Endosperm

value: Endosperm


title: Soybean Heart Stage Endosperm-Biological replicate 2


title: HF_70

description: small RNA (15-40bp)


title: Soybean Heart Stage Embryo Proper-Biological replicate 2

source_name: Soybean Heart Stage-Embryo Proper

value: Embryo Proper


title: Soybean Globular Stage Suspensor-Biological replicate 3

description: Compartments collected from seeds 1 mm in length

source_name: Soybean Globular Stage-Suspensor

value: seed - globular stage


title: Soybean Heart Stage Embryo Proper-Biological replicate 1


title: Soybean Globular Stage Suspensor-Biological replicate 2


title: Soybean Heart Stage Seed Coat Hilum-Biological replicate 2


title: Soybean Globular Stage Suspensor-Biological replicate 1


title: Soybean Globular Stage Seed Coat Outer Integument-Biological replicate 3


title: Soybean Globular Stage Seed Coat Outer Integument-Biological replicate 1


title: Soybean Globular Stage Seed Coat Inner Integument-Biological replicate 4


title: Soybean Globular Stage Seed Coat Inner Integument-Biological replicate 3


title: Soybean Globular Stage Seed Coat Inner Integument-Biological replicate 1


title: Soybean Globular Stage Seed Coat Outer Integument-Biological replicate 2


title: Soybean Heart Stage Endosperm-Biological replicate 3


title: Soybean Globular Stage Seed Coat Hilum-Biological replicate 5

source_name: Soybean Globular Stage Seed Coat Hilum


title: Soybean Globular Stage Seed Coat Hilum-Biological replicate 1


title: Soybean Globular Stage Seed Coat Epidermis-Biological replicate 5


title: Soybean Globular Stage Seed Coat Epidermis-Biological replicate 6


title: Soybean Globular Stage Seed Coat Epidermis-Biological replicate 4


title: Soybean Globular Stage Seed Coat Hilum-Biological replicate 2


title: ESC H3K9me3, replicate 2

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

description: ChIP-seq, antibody Abcam ab8898

data_processing:
DNA reads were aligned on the mm9 assembly version of the mouse genome with Bowtie, reporting unique hits with up to two mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: Processed ChIP-seq data are in standard BED files; Processed MNase-seq data are in tab-separated text files, which contain four columns: (1) chromosome name, (2) start site, (2) end site, (3) DNA fragment length

source_name: embryonic stem cells

growth_protocol: embryonic stem cells from 129P2/Ola mice were cultured in ESGRO complete medium (Millipore), harvested and resuspended in low salt buffer (10 mM Hepes, pH 8, 10 mM KCl, 0.5 mM DTT) at 4 °C.

extract_protocol:
For ChIP_seq, for each sample, 1 x 10^6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). Chromatin was sheared to mononucleosomal fragments. After IgG preclearance the sheared chromatin was incubated with 4 µg of either H3K9me3 (Abcam ab8898) or H3K4me3 (Abcam ab8580) antibody over night. After washes with sonication (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na–deoxycholate), high-salt-buffer (50 mM Hepes pH 7.9, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na–deoxycholate, 0.1% SDS), lithium buffer (20 mM Tris–HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na–deoxycholate) and 10 mM Tris–HCl, chromatin was eluted from the protein G magnetic beads and the crosslink was reversed over night. After RNase A and proteinase K digestion, DNA was purified and cloned in a barcoded sequencing library for the Illumina HiSeq 2000 sequencing platform (single reads of 50 bp length).
The libraries for sequencing were prepared according to the standard Illumina protocol.

value: mouse embryonic stem cells

value: blastocyst, E3.5

tag: antibody source

value: Abcam

tag: antibody catalog number


title: ESC H3K9me3, replicate 1

description: ChIP-seq, antibody Abcam ab8898


title: ESC H3K4me3, replicate 2

description: ChIP-seq, antibody Abcam ab8580


title: ESC H3K4me3, replicate 1

description: ChIP-seq, antibody Abcam ab8580


title: Soybean Globular Stage Seed Coat Endothelium-Biological replicate 1


title: Soybean Globular Stage Endosperm-Biological replicate 5

source_name: Soybean Globular Stage Endosperm


title: Soybean Globular Stage Endosperm-Biological replicate 3


title: ESC dinucleosomes, replicate 1

description: MNase-seq

extract_protocol:
After disruption of the cells with a douncer the nuclei were collected by centrifugation and washed once with the MNase Buffer (10 mM Tris–HCl, pH 7.5, 10 mM CaCl2), resuspended in the MNase Buffer and digested with 0.5 units MNase per microliter (Fermentas) and incubation for 6–11 minutes at 37 °C. The MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. After digestion with 0.1 µg µl–1 RNase A (Fermentas) and removal of protein by phenol and chloroform extraction, the DNA was ethanol precipitated and the resulting DNA pellet was dissolved in H2O. DNA fragments corresponding to mononucleosomes or dinucleosomes were separated on a 2 % agarose gel using an E-Gel electrophoresis system (Life Technologies).
The libraries for sequencing were prepared according to the standard Illumina protocol.


title: ESC mononucleosomes, replicate 2

description: MNase-seq


title: Soybean Globular Stage Endosperm-Biological replicate 2


title: Soybean Globular Stage Embryo Proper-Biological replicate 6

source_name: Soybean Globular Stage-Embryo Proper


title: ESC mononucleosomes, replicate 1

description: MNase-seq


title: CD49b+ NK cells 2

city: Melbourne

first: Sebastian

last: Carotta

address: 1G Royal Parade

institute: WEHI

data_processing:
In machine base-calling (Sequencing Control Software, SCS; Illumina
First 6 bases of mate 1 reads were trimmed. Mapped to mm9 genome using tophat v1.4.1 with parameters -N 2 --libraryType fr-unstranded -g 20 --segment-mismatches 1 --segment-length 15
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as follows: 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: mm9
Supplementary_files_format_and_content: tab-delimited text files with RPKM values

source_name: lymphocyte / Natural Killer Cells

extract_protocol:
Single-cell suspensions were prepared from freshly harvested liver from C57BL/6 mice. Liver mononuclear cells were separated from hepatocytes by centrifugation at 690 g in a 37% Percoll gradient at room temperature. Lysis of red blood cells of liver samples were performed before staining. TRAIL+ and CD49b+ liver derived NK cells were isolated by flow cytometric sorting. TRAIL+ NK cells were identified as  TCRb-NK1.1+NKp46+ TRAIL+CD49b-, CD49b+ NK cells as TCRb-NK1.1+NKp46+ TRAIL-CD49b+. Sorted cells were immediately lysed after sorting in RLT+ lysis buffer (Quiagen). Total RNA was isolated using RNeasy Plus Mini Kit.
standard Illumnina kits and protocols

value: Liver

value: CD49b+ liver derived NK cells


title: Soybean Heart Stage Embryo Proper-Biological replicate 3

value: Williams 82


title: Soybean Globular Stage Seed Coat Endothelium-Biological replicate 2


title: Soybean Globular Stage Seed Coat Inner Integument-Biological replicate 2


title: Soybean Globular Stage Seed Coat Endothelium-Biological replicate 4


title: Soybean Globular Stage Embryo Proper-Biological replicate 4


title: TRAIL+ NK cells 2

value: TRAIL+ liver derived NK cells


title: TRAIL+ NK cells 1


title: A3

first: Chunxiao

address: 20 Dongdajie, Fengtai District

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
The Cx. pipiens quinquefasciatus genome and gene information were downloaded from the quinquefasciatus Genome Annotation Project (https://www.vectorbase.org/organisms/culex-quinquefasciatus, GenBank accession number: AAWU00000000.1).
The remaining reads were aligned to the mosquito genome using SOAPaligner/soap2.
ERANGE software (version 4.0) (http://woldlab.caltech.edu/gitweb/) was used to calculate normalized gene locus expression levels by assigning reads to their site of origin and counting them. The expression level of a gene from RNA-Seq was normalized by the RPKM (reads per kilo bases per million reads) value.
The R package DEGseq was applied to identify DEGs with a random sampling model based on the read count for each gene in each mosquito population.
Genome_build: Mosquito Genome Annotation Project (Vectorbase) https://www.vectorbase.org/organisms/culex-quinquefasciatus
Supplementary_files_format_and_content: text files include RPKM values for each Sample

organism: Culex quinquefasciatus

source_name: Culex pipiens quinquefasciatus

extract_protocol:
Total RNA of 30 mosquito larvae of each was extracted using the TRIzol. Total RNA samples were pooled and 10 mg from each pool was used to isolate poly(A) mRNA and to prepare non-directional Illumina RNA-Seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lavae


title: A4


title: A12


title: A11

organism: Culex pipiens pallens

source_name: Culex pipiens pallens


title: D. shibae 5 h in the dark after 12 days in coculture with the dinoflagellate P. Minimum, replicate 2

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: Co-culture of D. shibae with P. minimum

extract_protocol:
RNA isolation: For RNA extraction, the sample was thawed at room temperature and then transferred to a cryotube filled with 0.3 g acid washed glass beads. The cells were homogenized using the FastPrep-24 instrument (MP Biomedicals, California, USA) at 6.0 m/s for 3 min and then incubated for 5 min at room temperature. Samples were centrifuged at 12,000 g for 10 min at 4°C and the supernatants were transferred to fresh tubes, followed by the addition of 100 µl of 1-bromo-3-chloropropane (BCP, Sigma, Germany) and incubation for 10 min at room temperature. Samples were centrifuged at 12,000 g for 10 min at 4°C, after which the aqueous phase was transferred to new tubes and mixed with 500 µl of absolute ethanol. Extracts were applied to RNeasy spin columns (RNeasy mini kit, Qiagen, Hilden, Germany) and processed according to the manufacturer’s instructions. In addition, samples were treated with DNAse I (Qiagen, Hilden, Germany). Removal of genomic DNA was verified via PCR using total RNA as template. 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 Oligotex mRNA kit (Qiagen, Hilden, Germany) was used to isolate the algal mRNA. For isolation of D. shibae mRNA, the MICROBEnrich kit (Ambion, Life Technologies, Darmstadt, Germany) was used to remove the eukaryotic rRNA and MICROBExpress kit (Ambion, Life Technologies, Darmstadt, Germany) 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: single/co-culture

value: co-culture

tag: light/dark

value: 5 h dark

tag: day of co-culture


title: D. shibae 5 h in the dark after 12 days in coculture with the dinoflagellate P. Minimum, replicate 1


title: D. shibae 5 h in the light after 12 days in coculture with the dinoflagellate P. Minimum, replicate 2

value: 5 h light


title: A10


title: A9


title: D. shibae 5 h in the light after 12 days in coculture with the dinoflagellate P. Minimum, replicate 1


title: Nucleolar small RNA preparation

city: Baltimore

first: Marikki

last: Laiho

state: MD

address: 1550 Orleans Street, CRB II, Room 444

department: Department of Radiation Oncology and Molecular Radiation Sciences

institute: The Johns Hopkins University School of Medicine

description: 10-40 nt small RNA

data_processing:
Ion Torrent base calling with instrument-provided software, standard options
tmap version 0.1.3 alignment with default options
database: hg19
classification into miRNA, snoRNA, snRNA, and other
Genome_build: hg19
Supplementary_files_format_and_content: Xls files represent small RNA read distribution, annotation, identification of snoRNA-derived small RNA reads, and miRNAs present in subcellular compartments.

source_name: Human cervical adenocarcinoma cells

growth_protocol: HeLa cervical adenocarcinoma cells (CCL-2, ATCC)  were maintained in DMEM supplemented with 10% FCS.

extract_protocol: Subcellular fractionation was carried out essentially as in Bai and Laiho (Efficient sequential recovery of nucleolar macromolecular components. Proteomics, 12, 3044-3048, 2012). Total RNA was extracted from whole cells and the isolated cellular compartments using the TRIzol. Approximately 400 µg RNA from each compartment was used to prepare cDNA libraries. Small RNAs (less than 200 nt) were isolated from the total RNA samples using mirVana Isolation Kit and separated on denaturing 15% polyacrylamide gel (15% PAA, 19:1 acrylamide/bis, 7 M urea) to purify RNAs in the approximate range of 10 - 40 nt.  The sRNA size range was confirmed and the RNA was quantified using Bioanalyzer with Agilent Small RNA kit.

tag: cell line

value: HeLa


title: ESC dinucleosomes, replicate 2

description: MNase-seq

tag: cell type


title: A1

city: Beijing


title: A7


title: Soybean Heart Stage Seed Coat Endothelium-Biological replicate 3

value: seed - heart stage


title: Cytoplasmic small RNA preparation

description: 10-40 nt small RNA

molecule: cytoplasmic RNA

extract_protocol:
Subcellular fractionation was carried out essentially as in Bai and Laiho (Efficient sequential recovery of nucleolar macromolecular components. Proteomics, 12, 3044-3048, 2012). Total RNA was extracted from whole cells and the isolated cellular compartments using the TRIzol. Approximately 400 µg RNA from each compartment was used to prepare cDNA libraries. Small RNAs (less than 200 nt) were isolated from the total RNA samples using mirVana Isolation Kit and separated on denaturing 15% polyacrylamide gel (15% PAA, 19:1 acrylamide/bis, 7 M urea) to purify RNAs in the approximate range of 10 - 40 nt.  The sRNA size range was confirmed and the RNA was quantified using Bioanalyzer with Agilent Small RNA kit.
cDNA libraries were constructed using the Ion Torrent RNA-seq kit v1 for small RNA libraries, and their purity and concentration was confirmed using Bioanalyzer with the Agilent DNA kit. sRNA library sequencing was performed on a 314 chip on a Ion Torrent sequencing platform.


title: A6


title: Nuclear small RNA preparation

description: 10-40 nt small RNA

molecule: nuclear RNA


title: CD49b+ NK cells 1


title: Soybean Globular Stage Embryo Proper-Biological replicate 5


title: Total cell small RNA preparation

description: 10-40 nt small RNA


title: A5


title: a55-0-R

status: Public on May 06 2014

city: jinan

first: juren

last: zhang

address: shanda nanlv 27

institute: shandong university

data_processing:
Sequencing-received raw image data is transformed by base calling into sequence data, which is called raw data or raw reads, is stored in FASTQ format. This type of files is that the client gets, in which stores reads sequences and quality.
Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences are transformed into Clean Tags after certain steps of data-processing.Tags after filtering dirty tags from raw data.
Sequence quality assessment; Saturation analysis of sequencing; Experimental repeatability analysis; Distribution of clean tag copy number; Alignment statistics of the Clean tags
Gene expression annotation A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences (if there are no reference gene sequences for the species, sequences from closely related species can be used for reference). All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). ('t Hoen, Ariyurek, et al . 2008; Morrissy, Morin, et al . 2009).
Statistics of Clean Tags; Screening of differentially expressed genes; All downstream analyses are performed by BGI. Co., Ltd (Shenzhen, China).
Supplementary_files_format_and_content: TPM

organism: Zea mays

source_name: root of V3 stage

growth_protocol: Maize (Zea mays L.) inbred line DH4866 and its ZmPIN1a sense and antisense transgenic lines were used in this study. Seeds of the maize inbred line were surface sterilized and held at 28°C in darkness. Seedlings (4 days old) were transferred to a nutrient solution (Ca(NO3)2.4H2O 2 mM, NH4NO3 1.25 mM, 1,000 μM KH2PO4, KCl 0.1 mM, K2SO4 0.65 mM, MgSO4 0.65 mM, H3BO3 10.0 mM, (NH4)6Mo7O24 0.5 mM, MnSO4 1.0 mM, CuSO4.5H2O 0.1 mM, ZnSO4.7H2O 1.0 mM, Fe-EDTA 0.1 mM), allowed to grow for V3 stage. The plants were grown under a 32°C/25°C (day/night) temperature regime at a photon flux density (PFD) of 700 μmol m-2 s-1 with a 14 h/10 h light/dark cycle in a greenhouse with approximately 65% relative humidity.

extract_protocol:
Total RNA was extracted from the frozen samples using the method of McCarty (1986).
Then, 6 µg total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA. The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 95bp fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp.

treatment_protocol: The root and leaf of different maize lines were harvested respectively for digital gene expression profiling. The samples were frozen in liquid nitrogen immediately and stored at -80℃ for further analysis. Each sample contended 10 plants.

value: V3 stage maize

value: root of V3 stage

tag: genotype


title: A17-0-R


title: A2


title: a55-0-L

source_name: leaf of V3 stage (the tip and  basal were removed)


title: A17-0-L

value: leaf of V3 stage (the tip and  basal were removed)


title: WT-0-L

value: wild type


title: A8


title: 0.4

city: Yangling

first: Xiaodong

last: Liu

state: Shaanxi

address: NO. 22 Xinong Road

department: College of Life Sciences

institute: Northwest Agriculture & Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to M. alhagi CCNWXJ12-2 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Mesorhizobium alhagi CCNWXJ12-2

source_name: Mesorhizobium alhagi CCNWXJ12-2

growth_protocol: Mesorhizobium alhagi CCNWXJ12-2 was pre-cultured in TY medium at 28℃ to OD600≈0.8.

extract_protocol:
The total RNA was extracted as decrisbed by Rivas R etc. in 2001.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One milliliter of the CCNWXJ12-2 suspension was then inoculated  into 100 ml TY broth medium supplemented with 0.4 M NaCl also at the same time a blank experiment was conducted. At the end of the exponential phase, cells were harvested in order to isolate RNA.

value: WT

tag: treatment

value: 0.4 M NaCl


title: CK

value: control


title: KOT-RNAseq

first: wang

last: xiaona

address: Bei Chen Xi Lu #1

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology,Chinese Academy of Sciences

description: Digital Gene Expression Tag Profiling

data_processing:
Illumina Casava1.7 used for basecalling
Filtered the adaptor sequence and PCR-duplication reads
Aligment to UCSC Mouse Genome mm9 by BWA 0.6.2-r126 with maximum 5 mismatch
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited .txt files report statistics of gene annotation and expression for each sample.

source_name: Primary Sertoli cell_Wt1-deficient

growth_protocol: Sertoli cells were growth in DMEM  containing  10%  fetal  calf  serum  and  incubated  at  37°C  and  5%  CO2

extract_protocol:
Total RNA was extracted from Sertoli cells (Control and Wt1-KOT) using TRIzolH
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wt1 was deleted after 4OH-tamoxifen treatment in Sertoli cells from Wt1-/flox;Cre-ERTM mice

tag: strain

value: testis

value: Primary Sertoli cell

tag: genotype/variation

value: Wt1-/flox;Cre-ERTM (Wt1-deficient)


title: rpoS_rep2

status: Public on May 05 2014

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

description:
Processed data file: GSE46380_S_Norel_statistics_WT-rpoSdb.xls
Processed data file: GSE46380_S_Norel_statistics_rpoSdb-deltarpoS.xls

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and for low-quality sequence using in-house program. Only sequence with a minimum length of 30 were considered, then mapped to 14028S whole genome sequence and plasmid (CP001363.1 and CP001362.1) using bowtie v0.12.7 with parameters --chunkmbs 200 -m 50 -e 59 -a --best --solexa1.3-quals
HTseq-count was used for counting genes with parameters -m -intersection-nonempty -s yes -t gene
Statistical analyses were performed using R version 2.15.1 and Bioconductor packages. Genes with nul raw counts in the nine samples were excluded from the data table. Normalisation and differential analysis were performed using DESeq version 1.8.3.
The whole dataset was first normalized using the normalization function of DESeq and dispersion was estimated with default parameters.
The statistical test was then applied on pairs of strains. Resulting p-values were adjusted for multiple comparisons according to the BH method. Two significance thresholds (0.05 and 0.001) were applied on adjusted p-values in order to declare genes as differentially expressed.
Genome_build: GenBank CP001363.1 and CP001362.1 (14028S).
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name, Salmonella typhimurium LT2 orthologs), Raw Counts (WT, Delta-rpoS, rpoSdb), Normalized Counts (WT, Delta-rpoS, rpoSdb), Statistics (rpoSdb/WT, Delta-rpoS/WT, Delta-rpoS/rpoSdb).

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Mutant rpoS double mutation 14028S

growth_protocol: Strains were grown aerobically to late stationary phase in rich medium (LB, 37°C, 200 rpm, 18h).

extract_protocol:
Total RNA was isolated from Salmonella cells using TRIzol, digested with DNase I and the RNA quality was analyzed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: rpoS double mutation


title: rpoS_rep1


title: Delta_rep2

description:
Processed data file: GSE46380_S_Norel_statistics_WT-deltarpoS.xls
Processed data file: GSE46380_S_Norel_statistics_rpoSdb-deltarpoS.xls

source_name: Mutant rpoS 14028S

value: delta-rpoS


title: WT-0-R

tag: tissue


title: Delta_rep1


title: rpoS_rep0


title: Delta_rep0


title: KO-RNAseq

description: Digital Gene Expression Tag Profiling

source_name: Primary Sertoli cell_control

value: Wt1flox/flox (control)


title: WT_rep1

description:
Processed data file: GSE46380_S_Norel_statistics_WT-rpoSdb.xls
Processed data file: GSE46380_S_Norel_statistics_WT-deltarpoS.xls

source_name: Wild-type strain 14028S


title: PhyA-GFP_1 [ChIP-seq]

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing:
Bowtie for alignment, v1, default parameter
MACS for peak-calling, v1.4.4, default paremeter
Genome_build: TAIR10
Supplementary_files_format_and_content: BED, peaks called by MACS, column headers: chr start end length summit tags -10*LOG10(pvalue) fold_enrichment FDR(%)

organism: Arabidopsis thaliana

growth_protocol: Four day-old etiolated seedlings of phyAGFP/phyA201 were treated by FR for 3h.

extract_protocol:
5 g of seedlings were first cross-linked with 1% formaldehyde under vacuum, and then the samples were ground to powder in liquid nitrogen. The chromatin complexes were isolated and sonicated and then incubated with  antibodies. The precipitated DNA was recovered and used to generate Illumina sequencing libraries according to the manufacturer’s instructions.
standard Illumina ChIP-seq protocol

tag: gentotype/variation

value: phyA-GFP phyA201 transgenic

value: 4-day old seedling

tag: chip antibody

value: anti-GFP

tag: chip antibody vendor

value: Clontech

tag: chip antibody cat. #


title: PhyA-input  [ChIP-seq]


title: WT_rep0


title: PhyA-GFP_3 [ChIP-seq]


title: PhyA-GFP_2 [ChIP-seq]


title: WSB_PR8_D4_64

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2
Reads were mapped against specific CC founder strain transcriptome with SOAPaligner/soap2 and following command : soap -m 20 -x 500 -r 2 -v 2
To determine fragment count on gene level from SOAP output, we used a custom script in Java reproducing HTSeq paired and strand-specific union mode
Technical replicates were summed
Three samples were excluded based on their low raw gene counts distribution ("PWK_MA15_D2_116", "NOD_MA15_D2_17", "CAST_MA15_D2_99").
Data normalization was performed by scaling as implemented in the DESeq bioconductor package
Genome_build: CC founder pseudogenomes
Supplementary_files_format_and_content: tab-delimited text files include scaled/normalized gene counts for each sample

source_name: lung

growth_protocol: Whole Animal

extract_protocol:
Qiagen miRNeasy Isolation Kit from Trizol homogenates
Illumina TruSeq Total RNA

treatment_protocol: Intranasally infected or mock infected

value: WSB

tag: virus

tag: day-post-infection


title: WSB_PR8_D2_60


title: WSB_PR8_D2_59


title: WSB_PR8_D4_61


title: WSB_PR8_D2_58


title: WSB_MOCK_D4_63

value: MOCK


title: WSB_MOCK_D4_56


title: WSB_MOCK_D2_57


title: WSB_MA15_D4_54


title: WSB_MOCK_D2_49


title: WSB_MA15_D2_50


title: WSB_MA15_D2_51


title: WSB_MA15_D2_52


title: WSB_PR8_D4_62


title: PWK_PR8_D4_128

value: PWK


title: PWK_PR8_D4_127


title: PWK_PR8_D2_124


title: PWK_PR8_D2_121


title: PWK_PR8_D4_125


title: PWK_MOCK_D4_120


title: PWK_MOCK_D4_126


title: PWK_MOCK_D2_122


title: WT_rep2

value: wild type


title: PWK_MOCK_D2_115


title: PWK_MA15_D4_117


title: PWK_MA15_D4_118


title: PWK_MA15_D2_116


title: PWK_MA15_D2_113


title: NZO_PR8_D4_43

value: NZO


title: PWK_MA15_D2_114


title: PWK_MA15_D4_119


title: NZO_PR8_D2_42


title: WSB_MA15_D4_55


title: NZO_PR8_D4_45


title: NZO_PR8_D4_44


title: WSB_MA15_D4_53


title: NZO_PR8_D2_40


title: NZO_MOCK_D4_38


title: NZO_PR8_D2_39


title: NZO_MOCK_D2_41


title: NZO_MOCK_D4_46


title: NZO_MA15_D4_36


title: NZO_MOCK_D2_35


title: NZO_MA15_D4_37


title: NZO_MA15_D2_33


title: NZO_MA15_D2_34


title: NOD_PR8_D4_32

value: NOD


title: NOD_PR8_D4_30


title: NOD_PR8_D4_31


title: NOD_PR8_D2_28


title: NOD_PR8_D2_27


title: NOD_PR8_D2_25


title: NOD_MOCK_D4_29


title: NOD_MOCK_D2_26


title: NOD_MA15_D4_21


title: NOD_MOCK_D2_20


title: NOD_MA15_D2_19


title: CAST_PR8_D4_110

value: CAST


title: NOD_MA15_D4_23


title: NOD_MA15_D4_22


title: NOD_MA15_D2_17


title: CAST_PR8_D4_109


title: CAST_MOCK_D4_111


title: CAST_MOCK_D4_104


title: CAST_PR8_D2_108


title: CAST_PR8_D2_105


title: CAST_PR8_D2_106


title: CAST_MOCK_D2_107


title: CAST_MA15_D4_101


title: CAST_MOCK_D2_100


title: CAST_MA15_D2_98


title: CAST_MA15_D4_103


title: CAST_MA15_D2_99


title: CAST_MA15_D4_102


title: CAST_MA15_D2_97


title: C57BL6J_PR8_D4_94


title: C57BL6J_PR8_D2_91


title: C57BL6J_PR8_D4_93


title: C57BL6J_PR8_D2_90


title: C57BL6J_PR8_D4_95


title: NOD_MA15_D2_18


title: NOD_MOCK_D4_24


title: C57BL6J_MOCK_D4_85


title: C57BL6J_PR8_D2_89


title: C57BL6J_MOCK_D4_96


title: C57BL6J_MA15_D4_86


title: C57BL6J_MA15_D2_82


title: C57BL6J_MA15_D2_83


title: AJ_PR8_D4_80

value: AJ


title: AJ_PR8_D4_78


title: AJ_PR8_D2_76


title: C57BL6J_MOCK_D2_92


title: C57BL6J_MA15_D2_81


title: C57BL6J_MA15_D4_88


title: AJ_PR8_D2_74


title: AJ_PR8_D2_73


title: AJ_MOCK_D4_79


title: AJ_MOCK_D2_68


title: AJ_MOCK_D2_75


title: AJ_PR8_D4_77


title: AJ_MA15_D4_72


title: AJ_MA15_D4_70


title: AJ_MA15_D4_69


title: AJ_MA15_D2_67


title: 129S1_PR8_D4_15


title: C57BL6J_MOCK_D2_84


title: 129S1_PR8_D4_14


title: 129S1_PR8_D2_9


title: C57BL6J_MA15_D4_87


title: 129S1_PR8_D2_12


title: 129S1_PR8_D2_10


title: 129S1_MOCK_D4_13


title: 129S1_PR8_D4_16


title: 129S1_MOCK_D4_8


title: 129S1_MOCK_D2_11


title: 129S1_MOCK_D2_4


title: Bsubtilis_WT_NETseq

city: San Francisco

first: Matthew

middle: H

last: Larson

address: 499 Illinois St

institute: Grail, Inc.

description: library strategy: NET-seq

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were aligned using Bowtie v0.12.7 against the reference genome using parameters -a -v 3 -m 1
Bowtie alignments against the reference genome were converted to wiggle files. The position of each alignment was mapped to the 3' end of the nascent transcript.
After alignment and mapping of the reads, pause detection was performed using custom scripts written in Python 2.7. Positions with counts greater than four standard deviations above the mean were scored as pauses.
Genome_build: B. subtilis: NC000964
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).
Supplementary_files_format_and_content: The fas.txt contains two lines for each pause; the first line denotes the gene, strand, pause index, and relative peak height. The second line denotes the sequence 15 nt upstream and downstream of the pause position.

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: For each sample, 500 mL liquid cultures were grown in 2.8 L flasks with shaking (180 rpm) at 37 °C from an OD (600 nm) 0.05 to OD 0.45 ± 0.05. Cells were grown in LB.

extract_protocol:
Cell culture was rapidly filtered in 250 mL increments at 37 °C over 0.22 μm nitrocellulose ﬁlters (GE) and frozen in liquid nitrogen to simultaneously halt all transcriptional progress. Frozen cells (100 μg) were pulverized on a Qiagen TissueLyser II mixer mill 6 times at 15 Hz for 3 min in the presence of 500 μL frozen lysis buffer (20 mM Tris pH 8, 0.4% Triton X-100, 0.1% NP-40, 100 mM NH4Cl, 50 U/mL SUPERase•In (Ambion)) and 1X protease inhibitor cocktail (Complete, EDTA-free, Roche), supplemented with 10 mM MnCl2. The lysate was resuspended on ice by pipetting. RQ1 DNase I (110 U total, Promega) was added and incubated for 20 min on ice. The reaction was quenched with EDTA (25 mM final), which releases polysomes from the transcript and reduces contamination from ribosomal RNA and ribosome-associated tRNAs. The lysate was clarified at 4 °C by centrifugation at 20,000 g for 10 min. The lysate was loaded onto a PD MiniTrap G-25 column (GE Healthcare) and eluted with lysis buffer supplemented with 1 mM EDTA. For nascent RNA purification, the clarified lysate was added to 0.5 mL anti-FLAG M2 affinity gel (Sigma Aldrich). The affinity gel was washed twice with lysis buffer supplemented with 1 mM EDTA before incubation with the clarified lysate at 4 °C for 2.5 h with nutation. The immunoprecipitation was washed 4 × 10 mL with lysis buffer supplemented with 300 mM KCl, and bound RNAP was eluted twice with lysis buffer supplemented with 1 mM EDTA and 2 mg/mL 3XFLAG peptide (Sigma Aldrich). Nascent RNA was purified from the eluate using the miRNeasy kit (Qiagen).
The full library construction protocol was described in detail previously (Churchman et al., Nature 2011). Purified nascent RNA was ligated to a 5' adenylated DNA oligo and fragmented to generate RNA ranging from 30-100 nt. The RNA was reverse transcribed, and the single-stranded DNA circularized and PCR amplified.

tag: strain background

tag: molecule subtype

value: Nascent RNA

tag: media

value: LB


title: 129S1_MA15_D4_7


title: 129S1_MA15_D4_6


title: 129S1_MA15_D2_3


title: 129S1_MA15_D2_2


title: AJ_MOCK_D4_71


title: AJ_MA15_D2_66


title: EMSA-Seq of p50p50 round 2 of SELEX

city: Nanjing

first: Jinke

last: Wang

state: Jiangsu

address: Sipailou 2

department: Biomedicine

institute: Southeast Uiniversity

description: EMSA-Seq selection of ligands that bind a transcription factor

data_processing:
Basecalls performed using CASAVA version 1.4
Raw data in the form of reads (FASTQ format) obtained after deep sequencing has been subsequently processed using both UNIX and perl scripts. The main processes included (i)trimming the adaptor sequence from each reads; (ii) matching the sequences of the paired reads to remove the reads with unmatcghed sequences; (iii) checking the definite base calling (A, C,G and T) to remove reads with N; (iv) checking the valid barcode and constant regions to remove reads with invallid barcode and constant regions including incorrect bases and length; (v)checking the unique random sequence at the length of 16 bp to remove reads with incorrect length; (vi)sorting reads according to barcodes: the reads belonging to Round 4 to 0 were ended with AAAA and TTTT, GAAG and GTTT, AGAG and GTCT, AAAG and GTGT, and CAAG and GTGC, respectively; (vii) removing flanking constant regions and barcode sequences from reads and obtained the 16-mer target sequences.
Genome_build: No genome build was perfomed. This item is inapplicable to this study.
Supplementary_files_format_and_content: Fasta files for the final 16-mer sequences obtained for Round 0 to 4.

extract_protocol:
For each round of SELEX selection, two protein binding reactions (all 10 μl) were performed simultaneously. Reaction 1 contained 200 ng 64-bp positive dsDNA, 115 ng (Reaction 2) p50 protein (Promega) in 10 mM Tris-HCl, pH7.5, 50 mM NaCl, 0.5 mM EDTA, 3 mM MgCl2, 1 % glycerol, 0.5 mg/ml BSA, 0.05% NP-40, 0.01 mM DTT. Reaction 2 contained 200 ng 64-bp random dsDNA, 115 ng p50 protein in 10 mM Tris-HCl, pH7.5, 50 mM NaCl, 0.5 mM EDTA, 3 mM MgCl2, 1 % glycerol, 0.5 mg/ml BSA, 0.05% NP-40, 0.01 mM DTT and 0.1 μg polydI-dC (Amersham). The protein binding reactions were incubated at room temperature for 60 min and loaded on 6% native polyacrylamide gel and migrated in 0.5 × TBE buffer for 1.5 hs. After electrophoresis, the gel was directly visualized on UV transilluminator and the gel slice containing the shifted dsDNA (Reaction 2) was excised according to the position of the shifted band of Reaction 1. The gel slice was socked in 100 μl diffusion buffer [0.5 M NH4Ac, 10 mM Mg(Ac)2, 1 mM EDTA, pH8.0, 0.1% SDS] overnight at 37°C. The diffusion buffer was purified with Microcon YM-30 and DNA was eluted in 25 μl ddH2O. For experiments in which several rounds of SELEX were carried out the following procedure was adopted. DNA obtained after the first round of TF-DNA binding followed by EMSA, elution and purification was amplified using a high-fidelity PCR procedure. Briefly, multiple 10 μl reactions each comprised of 1 mM dNTPs, 4μM of Primers 1 and 2 (using nested primers: R-F1 and R-R1 for Round 1, R-F2 and R-R2 for Round 2; R-F3 and R-R3 for Round 3; R-F4 and R-R4 for Round 4), together with 1 units of PrimerStar® HS Taq polymerase (TaKaRa) buffered in accompanying 1X PCR Buffer were incubated for 3min at 94°C, then subjected to 20 PCR cycles (1min 94°C, 1min 60°C, 2 min 70°C). DNA was pooled, purified with Microcon YM-30 (Millipore). This was subsequently used as starting material for TF-DNA binding in the second round of SELEX.
The dsDNAs selected in Round 0 to 4 were pooled in equal molar to form a multiplexed sample for sequencing.

tag: selex round

tag: nf-kb dimer


title: EMSA-Seq of p50p50 round 3 of SELEX


title: EMSA-Seq of p50p50 round 1 of SELEX


title: EMSA-Seq of p50p50 round 0 of SELEX


title: Ecoli_olacZ_bicyclomycin_NETseq

description: library strategy: NET-seq

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were aligned using Bowtie v0.12.7 against the reference genome using parameters -a -v 3 -m 1
Bowtie alignments against the reference genome were converted to wiggle files. The position of each alignment was mapped to the 3' end of the nascent transcript.
Genome_build: E. coli: NC_000913
Supplementary_files_format_and_content: wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Escherichia coli

growth_protocol: For each sample, 500 mL liquid cultures were grown in 2.8 L flasks with shaking (180 rpm) at 37 °C from an OD (600 nm) 0.05 to OD 0.45 ± 0.05. Cells were grown in MOPS EZ rich defined medium with 0.2% glucose (Teknova).

treatment_protocol: For analysis of lacZ transcription, IPTG was added to a final concentration of 1 mM. For bicyclomycin (BCM) treated samples, cells were grown from an initial OD of 0.01 in the absence of BCM. BCM was added to a final concentration of 20 ug/mL when the cells reached OD 0.05.

tag: treated with

value: bicyclomycin (BCM)

value: MOPS EZ Rich Defined Media