title: Wild Type Staufen associated, RNase treated mRNA

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

data_processing:
Filtering raw reads: Removal of illumina adaptors; removal of rRNA sequences by BWA aligning against representative human ribosomal RNAs (28S, 18S, 5.8S, 5S)
Filtered reads alignment: Clean reads were aligned to human genome (hg19) with BWA with default parameters
Counts per gene: After alignment, the number of reads that matched each known gene was calculated using countOverlaps function of GenomicFeatures package (www.bioconductor.org). Gene annotations and coordinates were obtained from UCSC database using the “RefGene” table.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene and per sample.

source_name: HEK293T cells transfected with pChStaufen-TAP

growth_protocol: The HEK293T (DuBridge et al, 1987) cell line was cultured as previously described (Villacé et al, 2004)

extract_protocol:
TAP-associated RNAs were obtained by treatment of Calmodulin-agarose resin with 0.2 mg/ml Proteinase K and 0.5% SDS in TNE for 1 hour at 37C. After phenol extraction, RNAs were precipitated with 2 ethanol volumes and 20 μg of glycogen (Roche) and resuspended in DEPC-treated H2O. Before cDNA synthesis, each RNA preparation was monitored using the Agilent 2100 Bioanalyzer (Agilent technologies).
RNA samples of hStau1-TAP (treated or not with RNase T1) and the untreated hStau1-Mut (100 ng each) were used to generate cDNA libraries according to Illumina mRNA-seq protocol at Fasteris SA Company (Plan-Les-Ouates, Switzerland) but the poly (A+) RNA purification step was skipped. Furthermore, mRNA fragmentation was omitted in the T1-RNase treated hStau1-associated RNA, as it already contained RNAs about 100 nt in size. cDNA libraries were subjected to ends repair reaction and Illumina adapter ligation and further purified from polyacrilamide gels. This purification step excluded the identification of putative small RNAs present in the samples.  cDNA libraries were sequenced at Fasteris SA in an Illumina HiSeq2000 sequencer. Reads length were 100nt in a single-read run cycle.

treatment_protocol: HEK293T cells were transfected with DNA plasmids using the calcium phosphate method (Wigler et al, 1979). Plasmids pChStaufen-TAP, pChMut-TAP and pC-TAP as well as rabbit and rat antibodies specific for hStau1 have been previously described  (de Lucas et al, 2010; Villacé et al, 2004).

tag: transfected with

value: pChStaufen-TAP


title: Polio RNA / RNase A / 20 min

status: Public on Feb 07 2014

type: SRA

city: Aurora

first: Daphne

middle: A.

last: Cooper

state: CO

department: Department of Microbiology

country: USA

institute: University of Colorado

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 20 min with RNase A.

library_source: transcriptomic

data_processing:
Reads were trimmed for contaminating linker sequence.
Reads were aligned using Bowtie with -m1 --best --strata options
The 8-base UMI at the 5'-end of the raw read was counted to remove PCR over-amplification bias.
Signal from No 2-5A and No RNase A timepoints was subtracted from 0, 2.5, 5, 10, and 20 minute timepoints in RNase L and RNase A data (except for PV RNase L), these processed data samples include "baseline" in the file name.
The 3'-dinucleotide from the read was obtained to characterize RNase specificity, and # of UMI reads were plotted against genome postion using R to map cleavage sites across the genome/sequence.
Genome_build: HCV: Hepatits C virus subtype 1A polyprotein gene complete cds (AF009606.1)
Genome_build: PV: Human poliovirus 1 Mahoney, complete genome (V01149.1)
Genome_build: 28S: Homo sapiens RNA, 28S ribosomal 1 (RN28S1), ribosomal RNA (NR_003287.2)
Genome_build: 18S: Homo sapiens RNA, 18S ribosomal 1 (RN18S1), ribosomal 1 (NR_003286.2),
Genome_build: 5.8S: Homo sapiens RNA, 5.8S ribosomal 1 (RN5-8S1), ribosomal RNA (NR_003285.2)
Genome_build: 5S: Homo sapiens RNA, 5S ribosomal 9 (RN5S9), ribosomal RNA (NR_023371.1)
Genome_build: U6: Homo sapiens RNA, U6 small nuclear 33 (RNU6-33), small nuclear RNA (NR_046491.1)
Supplementary_files_format_and_content: text files include tab delimited columns [genome, cleavage site, cleavage site+1, # of UMI reads, and dinucleotide]

molecule: total RNA

organism: Poliovirus 1

source_name: Poliovirus RNA

extract_protocol:
Total cellular RNA was extracted using 4M guanidine thiocyanate with acid phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation.
Illumina TruSeq RNA linker with 8-base Unique Molecular Identifier (UMI) was attached with Arabidopsis thaliana tRNA ligase (recognizes RNAs with terminal 2', 3'-cyclic phosphates). cDNA was generated using a DNA primer specific to the Illumina linker, and the IDT miRNA cloning linker 1 was attached to the 3'-end of the cDNA. cDNAs were PCR amplified, pooled, and sequenced.
2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing were used to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

tag: strain

tag: experimental condition

value: Polio RNA incubated with RNase A

tag: exptl time

value: 20 min


title: Input DNA, rep5

status: Public on Feb 06 2014

city: Kansas City

first: Samuel

middle: Richard

last: Meier

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
wce_ext49_1.bed: dm3

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Input DNA

growth_protocol: D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25 °C and 60 % humidity.

extract_protocol: DNA-protein-complexes were isolated with specific antibodies. During Illumina library preparation, the samples are run on a 2% gel at 90V for ~2 hr, and fragments corresponding to ~50 bp, ~75, and ~100 bp inserts are cut out of the gel (slices are ~25bp thick). The final libraries are run a BioAnalyzer to measure the actual average insert size.

value: Oregon R (wild type)

tag: tissue

value: whole-embryo

tag: time point

value: 2-4hr after egg laying (AEL)

tag: chip antibody


title: Input DNA, rep3

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
wce_ext72_1_1.bed: dm3


title: Polio RNA / RNase A / 0 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 0 min with RNase A.

value: 0 min


title: Input DNA, rep4

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
wce_ext72_1_2.bed: dm3


title: Wild Type Staufen associated mRNA

organism: Homo sapiens

tag: cell line


title: Input DNA, rep2

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
wce_ext107_2.bed: dm3


title: Input DNA, rep1

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
wce_ext107_1.bed: dm3

value: Anti Twist


title: Twist ChIP-Seq from 2-4 h wild type embryos, rep5

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
twist_ext49_1.bed: dm3


title: Polio-Infected / M25 HeLa cells / 2 hpa

description:
Total RNA from polio-infected M25 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Polio-Infected / M25 HeLa cells / 2 hpa

source_name: Polio-Infected / M25 HeLa cells / 2 hpa

value: M25 HeLa / dominant-negative mutant RNase L

value: Polio-Infected / M25 HeLa cells / 2 hpa

value: 2 hr post-adsorption (hpa)


title: Twist ChIP-Seq from 2-4 h wild type embryos, rep3

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
twist_ext72_1_1.bed: dm3


title: Rhodobacter sphaeroides RNase J deletion mutant

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (TRAPL)
Read mapping using segemehl version 0.1.4  (TRAPL)
Coverage calculation and normalization (TRAPL)
Genome_build: ASM1290v1 [CP000143.1, CP000144.1, CP000145.1, CP000146.1, CP000147.1, DQ232586.1, DQ232587.1]
Supplementary_files_format_and_content: [wiggle file] Normalized  (by total number of aligned reads) read coverages multiplied by 1M  in wiggle format (*_forward.wig = forward strand; *_minus.wig= forward strand)

organism: Cereibacter sphaeroides 2.4.1

growth_protocol: R. sphaeroides cultures were grown in malate minimal medium (Niel, 1944) at 32°C under micro-aerobic conditions (dissolved oxygen: 25 µM) to an OD660 0.4.

extract_protocol:
Total RNA was isolated using the hot phenol method followed by two chloroform-isoamyl alcohol treatments and precipitation with sodium acetate and ethanol. RNA was resolved in RNase free water (Roth) and concentrations were determined at a NanoDrop 1000 Spectrophotometer (Peqlab). The sample was treated with DNaseI (Invitrogen) to remove DNA
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina

tag: genotype/variation

value: RNase J deletion


title: Twist ChIP-Seq from 2-4 h wild type embryos, rep4

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
twist_ext72_1_2.bed: dm3


title: Mock-Infected / W12 HeLa cells / 8 hpa

description:
Total RNA from mock-infected W12 HeLa cells
2', 3'-cyclic phosphate cDNA library derived using RNA from Mock-Infected / W12 HeLa cells / 8 hpa

source_name: Mock-Infected / W12 HeLa cells / 8 hpa

value: W12 HeLa / wildtype RNase L

value: Mock-Infected / W12 HeLa cells / 8 hpa

value: 8 hr post-adsorption (hpa)


title: Twist ChIP-Seq from 2-4 h wild type embryos, rep2

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
twist_ext107_2.bed: dm3


title: Twist ChIP-Seq from 2-4 h wild type embryos, rep1

data_processing:
Reads were aligned uniquely to the UCSC dm3 genome, using bowtie and allowing for up to 3 mismatches.
Peakzilla, SISSRs (Jothi et al., 2008) version 1.4, Spp (Kharchenko et al., 2008) version 1.8 and GPS (Guo et al., 2010) version 0.10.1 were run with default parameters.
MACS (Zhang et al., 2008) version 1.4.1 was run with an mfold parameter 3,30 and the gsize parameter approproiate for dm3
QuEST (Valouev et al., 2008) version 2.4 was run with FDR analysis (if possible), for transcription factor binding sites, recommended (or relaxed) peak calling parameters. cisGenome (Ji et al., 2008) version 2.0 was run with default parameters and required aln files.
PeakRanger read extension length parameter was run using peakzilla’s estimated fragment length.
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED formated annotations to UCSC dm3 genome
twist_ext107_1.bed: dm3


title: Mutant Staufen associated mRNA

source_name: HEK293T cells transfected with pChMut-TAP

value: pChMut-TAP


title: Rhodobacter sphaeroides wild type

value: wild type


title: wild type sham2

city: Indianapolis

first: Hai

last: Lin

address: 410 W 10th St

institute: IUPUI

data_processing:
Sequence reads were aligned with BFAST (v.0.6.5) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts and RPKM was calculated with NGSUtils based on RefSeq annotation.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include row counts and RPKM values

organism: Rattus norvegicus

source_name: kidney

growth_protocol: not applicable

extract_protocol:
Trizol per manufacturer's (Invitrogen) protocol
RNA was fragmented with RNAaseIII, cDNA libraries constructed with SOLiD adaptors by reverse transcription

treatment_protocol: not applicable

value: Zucker/Spontaneously Hypertensive Heart Failure

tag: treatment

value: sham

value: kidney

tag: phenotype


title: wild type sham4


title: obese sham 1

value: obese


title: obese sham 4


title: wild type sham3


title: obese surgery 4

value: surgery


title: obese sham 3


title: Rep2 8h

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
Base calling and demultiplexing were done with RAT 1.13.48 and Casava v1.8.0.
For each read, the 3' adaptor TGGAATTCTCGGGTGCCAAGG was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least seven or ten bases, respectively. Reads with Low-complexity were filtered out based on their dinucleotide entropy (removing <1% of the reads). Only reads with a minimum length of 14nt were retained. Alignments to the miRNA database miRBase release 18 (http://www.mirbase.org/) were performed by the software bowtie (version 0.9.9.1) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
The expression of each miRNA was determined by counting the number of associated reads. To compensate for differences in the read depths of the individual libraries, each sample was divided by its total number of counts and multiplied by the average sample size. The resulting values were log2 transformed using a pseudocount of 1 (y=log2(x+1)).
Genome_build: miRBase release 18
Supplementary_files_format_and_content: 'GSMxxx_BSSE-QGF*.tab' files are tab-delimited text files containing the sequences and non-normalized, raw counts after the removal of the 3' adaptor and before the alignments.
Supplementary_files_format_and_content: 'GSE46753_normalized_miRNA_expression.ama.tab' is a tab-delimited text file that includes the normalized miRNA expression levels.

organism: Caenorhabditis elegans

source_name: L1-stage N2 worms, 8h

extract_protocol:
Worms were harvested at each sampling time point during the next 8 hours, washed three times with M9 medium, resuspended in TRIzol reagent (Life Technologies) and frozen in liquid nitrogen. The worms were broken open by five repeats of freeze and thaw using liquid nitrogen and a 42 C heating block, before RNA was extracted and purified according to the supplier's protocol with the modification that RNA was incubated with 50% 2-propanol at -80 C overnight for efficient precipitation of small RNA.
Small RNA libraries were prepared from extracted total RNA using TruSeq Small RNA Sample Prep Kit (Illumina) according to the supplier's protocol.

value: Bristol N2

tag: Stage

value: whole body

value: alpha-amanitin

tag: time after treatment


title: Rep2 6h

source_name: L1-stage N2 worms, 6h


title: obese surgery 3


title: obese surgery 2


title: obese sham 2


title: Polio RNA / RNase A / 2.5 min

description:
Polio RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from polio RNA incubated for 2.5 min with RNase A.

value: Polio RNA incubated with RNase A

value: 2.5 min


title: Rep2 2h

source_name: L1-stage N2 worms, 2h


title: Rep2 1h

source_name: L1-stage N2 worms, 1h


title: obese surgery 1


title: Rep1 8h


title: Rep1 6h


title: Rep1 4h

source_name: L1-stage N2 worms, 4h


title: Rep1 1h


title: wntless1

city: Göttingen

first: Georg

last: Oberhofer

state: Lower Saxony

address: Justus von Liebig Weg 11

department: Developmental Biology

institute: University Göttingen

description:
Reference (fastqc): FastQC A Quality Control tool for High Throughput Sequence Data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ by S. Andrews
Reference (bowtie2): Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359.
Reference (samtools): Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Subgroup, 1000 Genome Project Data Processing (2009). The Sequence Alignment/Map format and SAMtools. Bioinforma. Oxf. Engl. 25, 2078–2079.
Reference (DESeq): Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11, R106.
Reference (BLAST): Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics).
Reference transcriptome: The au2.mrna gene set was used as the mapping reference. Isoforms were removed to avoid multiple mappings. The final transcriptome contained only t1 isoforms.
Reads were mapped to the reference using bowtie2 (version 2.1.0) with the these settings: -q -D 20 -R 3 -N 1 -L 20 -i S,1,0.50
Raw count tables were obtained with samtools (version 0.1.18).
Statistical analysis was performed with DESeq (version1.12.0). Genes are considered differentially expressed if log2FoldChange >= |1| and p_adjusted<0.1
Independent filtering was applied with theta=0.25 . All other settings were default.
Gene prediction set au2:  http://bioinf.uni-greifswald.de/tcas/genes/au2/
Supplementary_files_format_and_content: Unnormalized count tables are tab-delimited text files with gene ID, length and count number, e.g. sample1.counts.txt
Supplementary_files_format_and_content: Output tables of DEseq are comma-separated text files with: gene ID, base mean of normalized counts, fold change, log2 fold change, p-values, adjusted p-values
Supplementary_files_format_and_content: Annotation of results: The au2 gene set was BLASTed against the gene set from Flybase using BLAST implemented in bioperl and a custom perl script (script written by Mario Stanke). Reciprocal best BLAST hits were reported as orthologs. Hits with an E-value < 10^-5 were considered homologs. The resulting list of au2 gene IDs with their corresponding Fbpp ID was merged to the Drosophila GO annotations from Flybase (GOC Validation Date: 01/25/2013) in R.

organism: Tribolium castaneum

source_name: whole embryo

growth_protocol: Beatles were reared at 32 °C on white flour supplemented with 5% dry yeast

extract_protocol:
RNA was extracted with Trizol (Ambion) according to the manufacturers protocol. Crude RNA extracts were DNAse digested with Turbo DNAse (Ambion) followed by Phenol/Chloroform (Ambion) extraction according to the manufacturers protocol.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 400 ng of total RNA . Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SingleRead; 1x50 bp and 1x100bp).

treatment_protocol: dsRNA was generated as described in (Posnien N. et al, Cold Spring Harb Protoc. 2009 Aug;2009(8):pdb.prot5256). 400 female pupae were injected with dsRNA and crossed with wild type males. Staged egg collections of 10-11 h old embryos were used for RNA extraction.

value: San Bernardino

value: whole embryo

tag: age

tag: type

value: parental RNAi pupal

tag: RNAi

value: dsRNA template:Tc-wntless

tag: read length

tag: read type

value: single end


title: Rep1 2h

tag: strain


title: wntless2


title: wild type sham1


title: frizzled3

value: dsRNA template:Tc-frizzled1 + Tc-frizzled2


title: frizzled1


title: arrow3

value: dsRNA template:Tc-arrow


title: Rep2 4h


title: wildtype1

description:
technical triplicate, summed up, treated as single sequencing run
Reference (fastqc): FastQC A Quality Control tool for High Throughput Sequence Data http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ by S. Andrews
Reference (bowtie2): Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359.
Reference (samtools): Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Subgroup, 1000 Genome Project Data Processing (2009). The Sequence Alignment/Map format and SAMtools. Bioinforma. Oxf. Engl. 25, 2078–2079.
Reference (DESeq): Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11, R106.
Reference (BLAST): Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

value: wild type

value: dsRNA template:-


title: arrow2


title: wildtype5


title: torso2

value: dsRNA template:Tc-torso


title: arrow1


title: torso1


title: torso3


title: orthodenticle3

value: dsRNA template:Tc-orthodenticle


title: orthodenticle2


title: orthodenticle1


title: frizzled2


title: hedgehog2

value: dsRNA template:Tc-hedgehog


title: hedgehog3


title: wntless3


title: hedgehog4


title: wildtype9


title: wildtype8


title: hedgehog1


title: wildtype7


title: Seq11

city: New York

first: Gabriel

last: Rosenfeld

state: NY

address: 1300 York Ave. Rm. LC711

department: Cell and Developmental Biology

institute: Weill Cornell

data_processing:
Basecalls, demultiplexing, and filtering of reads was  performed using Casava 1.7.0.
Read alignment was performed with the BWA alignment algorithm with native goby support using gobyweb, version: development (20110921150240) with the following parameters: Ambiguity threshold = 1, Max Number Gap Opens = 1, Max Number Gap Extensions = -1.
Differential expression was generated with the DESEQ package with native goby support using gobyweb, version: development (20110921150240) with the following parameters: q-value threshold = 1.0, weight adjustment = none, Gene counts box checked.
Data were filtered according to geneID's demonstrating a p-adjusted < 0.1, a log2 fold change > 1 for WT/G4, and Average RPKM in the comparison group > 1.
Genome_build: Zv9.61
Supplementary_files_format_and_content: Wig files were generated using gobyweb, version: development(20110921150240).  Additional supplementary .xlsx file containing RPKM, counts, and statistical values was exported from gobyweb and processed in excel.

organism: Danio rerio

source_name: sorted cardiomyocytes

growth_protocol: Embryos were grown in 1x E3 buffer for 24 hours at 28.5 degrees Celsius in petri dishes.  25 ml of E3 buffer was used per 50-60 embryos in each dish.

extract_protocol:
RNA was isolated by Trizol except that after addition of 1.5 volumes of 100% ethanol to the aqueous phase, the solution was transferred to an RNeasy minElute column (Qiagen).  On-column DNase digestion, subsequent washing, and RNA elution was performed according to the Qiagen's recommended protocol for RNeasy micro kit.
100ng of total RNA was used to prepare the libraries.  Libraries were prepared for RNA sequencing using the mRNA-Seq (seq1, seq5, and seq11) or TruSeq Kit (seq13, seq14, and seq15) according to the Illumina's recommended protocol.

treatment_protocol: Embryos were injected with morpholino before the 4-cell stage of development.  2nl of a 0.7mM concentration of Gata4 morpholino (5'-TCCACAGGTGAGCGATTATTGCTTC-3') were injected per individual embryo.  At 24 hours post fertilization (hpf), batches of approximately 200 embryos were pooled into 1.5 ml tube.  Embryos were dissociated by manual agitation with a pellet pestle (Fisher) and trypsinized with pre-heated TrypLE (Life Technologies) at 32C for 15 min on a rotator. Trypsinized samples were pipetted through a 35um cell strainer into a 5ml tube, trypsin inhibited by addition of 4ml FACS buffer (L-15 medium supplemented with 1% heat inactivated FCS, 0.8mM CaCl2, 50U/ml penicillin, and 0.05 mg/ml streptomycin) followed by addition of FCS to 7.5% final concentration. Cells were pelleted at 300 RCF for 5 min and then washed with FACS buffer. Dissociated embryonic cells were resuspended at 7.5x106 cells/ml in FACS buffer. FACS was performed on a Vantage cell sorter (BD) into Trizol LS (Life Technologies), and stored at -80C until RNA isolation.

tag: developmental stage

tag: transgenic line

tag: experimental group

value: Gata4 morphant


title: Seq5

value: Wildtype


title: Seq1


title: J1_U

city: Yangling

first: Xiaoyan

last: Shi

address: Taicheng Road

country: China

institute: Northwest A&F University

data_processing:
Raw 50nt sequence tags from Solexa Hiseq sequencing (DMSO: 20,265,047; AICAR: 21,853,897)
Filter low quality reads and obtain high quality reads with no N, no more than 4 bases whose quality score is lower than 10 and no more than 6 bases whose quality score is lower than 13 (DMSO: 20,205,623, 100%; AICAR: 21,790,447, 100%)
Getting rid of reads with 5’ primer contaminants and without  3’ primer, with poly A and without the insert tag, and those shorter than 18nt, obtain clean reads (DMSO: 18,870,345, 93.39%; AICAR: 21,091,226, 96.79%)
Summarize the common and specific tags of two samples (Total: 39,961,571, 100%; DMSO & AICAR: 37,895,956, 94.83%; DMSO: 845,351, 2.12%; AICAR: 1,220,264, 3.05%)
Mapping the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome (DMSO: 12,147,800, 64.38%; AICAR: 11,978,538, 56.79%; )
Summarize the length distribution of the clean reads.
Small RNA annotation (DMSO: miRNA: 2,177,256, 11.54%; rRNA: 11,821,995, 62.65%; unann: 2,315,893, 12.27%; AICAR: miRNA: 3,316,207, 15.72%; rRNA: 10,672,087, 50.60%; unann: 3,819,289, 18.11%)
Compare the known miRNA expression between DMSO and AICAR treated samples to find out the differentially expressed miRNA.
Predict novel miRNAs using prediction software Mireap by exploring the secondary structure, Dicer cleavage site and free energy
Genome_build: mm9

organism: Mus musculus

growth_protocol: The J1 mESC was gelatin adapted and plated on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF at condition of 37℃ and 5% CO2.

extract_protocol:
Total cellular RNA was isolated from J1 mESC using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The J1 mESCs were treated with a final concentration of 1mM AICAR or equal volumn of DMSO

value: DMSO

tag: cell type

value: mESC


title: NP460 (miRNA)

status: Public on Feb 05 2014

city: Hong Kong

first: Chi Ho

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Raw RNASeq reads were filtered for adapters and ribosomal RNA, followed by alignment to the human genome (hg19) and mouse genome (mm9) using the Tophat (Langmead et al., 2009; Trapnell et al., 2009) v2.0.3.1.
Reads mapped to multiple locations were discarded using the –G option of Tophat. UCSC gene models were used for analysis with both software and downloaded from the Tophat website (http://tophat.cbcb.umd.edu/igenomes.html).
CLC genomics workbench v5.5 (CLC bio, Denmark) was used for small RNA analysis. Adapters were trimmed under default parameter setting to retain only reads with lengths ≥ 15 bp. These reads were then mapped and annotated against the miRBase (Griffiths-Jones, 2004; Griffiths-Jones et al., 2006; Griffiths-Jones et al., 2008; Kozomara and Griffiths-Jones, 2011) (release 19).
Read counts of the annotated miRNA were exported from CLC genomics workbench and RPM (Reads per million base pairs) were calculated using customs scripts. Non-annotated reads were further mapped to Ribosomal RNA (rRNA), Transfer RNA (tRNA), Small nucleolar RNA (snoRNA), Messenger RNA (mRNA), Small nuclear RNA (snRNA), and genomic repeats.
Isomirs werewas analyzed based on CLC results using custom scripts based on mature reference sequences from miRBase and novel EBV-miRNA from Chen et. al, 2010(Chen et al., 2010).
Genome_build: Human genome (hg19)

source_name: nasopharyngeal epithelium

growth_protocol: Early passages of NPC cell lines, HK1, C666, and NP460, and the X666 xenograft were utilized for this study.All of the cell lines were re-grown in standard conditions (Cheung et al., 1999; Huang et al., 1980; Li et al., 2006). Cells were collected from three subsequent culture passages upon reaching ~80% confluence, as described.

extract_protocol:
Total RNA was extracted with TRIZOL reagent (Invitrogen, NY, USA) according to standard procedures.
The sequencing library was prepared with the standard Illumina protocol. Briefly, total RNA was poly-A-selected to deplete the ribosomal RNA fraction. The cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and PCR amplification, followed by PAGE purification before sequencing. Stranded small RNA libraries were prepared by ligating different 3’ and 5’ adaptors sequentially to the total RNA followed by reverse transcription and PCR amplification. Small RNAs with insert sizes of 20-70 bp were PAGE-purified for sequencing. Both mRNA and small RNA libraries were sequenced on the Illumina Solexa GAIIx sequencer with 58 bp single-end reads, according to the standard manufacturer’s protocol.
Integrity of RNA was checked by Agilent 2100 bioanalyzer using the RNA 6000 Nano total RNA assay, with RIN value >8.9. RNA from the earliest passage of each cell line was selected for Solexa sequencing.

tag: sample type

value: immortalized nasopharyngeal epithelial cell line


title: 108hpf_wt

city: Parkville

first: Joan

middle: Kathleen

last: Heath

state: Victoria

address: 1G Royal Parade

department: Development and Cancer

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
50bp single-end reads were mapped  using the X-MATE recursive mapping pipeline (42), allowing for 5 color space mismatches per 50bp read (CS-50-5)
The uniquely mappable regions (uniqueome) of the ZV9 assembly were calculated using the same mapping parameters (CS-50-5)
For intron retention analysis, RPKM were calculated for annotated Refseq introns + manually annotated U12-type introns using Galaxy
For gene expression analysis, RPKM were calculated for annotated Refseq coding regions using Galaxy
Genome_build: Zebrafish Zv9

molecule: polyA RNA

growth_protocol: Embryos for all experiments were produced by natural spawning, transferred into petri dishes with pre-warmed egg water (60mg of sea salt/1L ddH20) and placed in a 28.5°C incubator on a 12h light/dark cycle.

extract_protocol:
Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate-phenol-chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first, and aqueous phases of all homozygous wildtype and mutant larvae, respectively, were pooled prior to RNA precipiation with isopropanol. For RNA sequencing, RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPoly(A)Purist Kit (Ambion).
Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F, 08/2009. 8μl of poly(A) RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease-free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of ~5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer (Agilent) using an RNA Nano 6000 chip (Agilent) to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. After o/n ligation, samples were reverse-transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100-200bp fragments were size selected by excision from a 6% polyacrylamide, 8M urea-TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns (Invitrogen). The majority of cDNAs in the library was between 150 and 250bp in size and less than 2-8% of cDNAs fell in the 25-150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.

treatment_protocol: Starting at 24 hpf, embryos were transferred into egg water containing 0.003% 1-Phenyl-2-thiourea (PTU) to prevent pigmentation

value: wildtype

value: 108 hours post-fertilization (hpf)

tag: tissue

value: whole larvae


title: 108hpf_clbn

tag: genotype/variation


title: X666 (miRNA)

tag: cell line

value: undifferentiated Epstein-Barr virus (EBV)-positive NPC xenograft


title: Plasmablast CTCF

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome with Bowtie using the following options to ensure each read mapped to a unique location -m 1 -n 1
HOMER software (Heinz et al. Mol Cell, 38:576-589) using the default parameters was used to identify significantly enriched CTCF peaks over input control for B cells and Plasmablasts
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using HOMER and represent reads per million.  Bed files contain the genomic locations of significantly enriched peaks, a unique peak ID, and the peak score as determined by the HOMER analysis

source_name: splenic Plasmablasts

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717).  Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-400 bp.  30 μg chromatin was immunoprecipitated with anti-CTCF (Millipore) antibody or control IgG serum over night at 4 degrees.  Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified.  Input fraction was isolated from the IgG supernatant prior to washing.
Sequencing libraries were prepared using the ChIP-seq Library Preparation Kit (Illumina) according to the manufacturers instructions using 10 ng of ChIP or input control DNA.  B cell samples were sequenced on a single lane of an Illumina Genome Analyzer II instrument.  Plasmablast samples were sequenced on a single lane of an Illumina HiSeq 2000 instrument.

tag: chip antibody

value: CTCF

tag: chip antibody manufacturer

value: Millipore

value: splenic Plasmablasts

tag: cell surface markers

tag: cell isolation

value: Plasmablasts were induced by injecting 6-week old mice with 50 ug LPS retro-orbitally.  3 days post-injection spleens were harvested and plasmablasts purified by flow cytometry based on surface expression of CD138.


title: NP460 (mRNA)

data_processing:
Raw RNASeq reads were filtered for adapters and ribosomal RNA, followed by alignment to the human genome (hg19) and mouse genome (mm9) using the Tophat (Langmead et al., 2009; Trapnell et al., 2009) v2.0.3.1.
Reads mapped to multiple locations were discarded using the –G option of Tophat. UCSC gene models were used for analysis with both software and downloaded from the Tophat website (http://tophat.cbcb.umd.edu/igenomes.html).
CLC genomics workbench v5.5 (CLC bio, Denmark) was used for small RNA analysis. Adapters were trimmed under default parameter setting to retain only reads with lengths ≥ 15 bp. These reads were then mapped and annotated against the miRBase (Griffiths-Jones, 2004; Griffiths-Jones et al., 2006; Griffiths-Jones et al., 2008; Kozomara and Griffiths-Jones, 2011) (release 19).
Genome_build: Human genome (hg19)


title: C666 (miRNA)

value: undifferentiated Epstein-Barr virus (EBV)-positive NPC cell line


title: X666 (mRNA)


title: wildtype2

value: San Bernardino

value: whole embryo

tag: age

tag: type

value: wild type

value: dsRNA template:-

value: single end


title: C666 (mRNA)


title: AICAR

tag: treatment

value: AICAR


title: E. coli stationary 1

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
The amplified cDNA libraries from two biological replicates for each E. coli were sequenced on an Illumina Genome Analyzer. Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained. Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs. Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs.
Sequence reads for cDNA libraries were aligned onto E. coli K12 MG1655 genome, using Mosaik with following arguments: hash size=10, mismatch=0. Only reads that aligned to the unique genomic location were retained.
Two biological replicates were processed seperatedly, and only sequence reads presented in both biological replciates were considered for further process. The genomic coordinates of the 5'-end of these uniquely aligned reads were defined as potential TSSs.
Among potential TSSs, only TSSs with the strongest signal within 10 bp window were kept to remove possible noise signals, and TSSs with greater than or equal to 40% of the strongest signal upstream of an annotated gene were considered as multiple TSSs.
Genome_build: NC_000913/ASM584v1
Supplementary_files_format_and_content: counts

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Cells at stationary phase (OD600nm 1.5) in M9 glucose media

growth_protocol: E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min.

extract_protocol: Total mRNA isolated from each cell culture was treated with Terminator 5' Phosphate Dependent Exonuclease (Epicentre) to enrich 5' tri-phosphorylated mRNAs. Intact tri-phosphorylated RNAs were then treated with RNA 5'-Polyphosphatase (Epicentre) to generate 5'-end monophosphorylated RNA for ligation to RNA adaptors. cDNAs were synthesized using the adaptor-ligated mRNAs as template using a modified small RNA RT primer from Illumina and Superscript II Reverse Transcriptase (Invitrogen). The cDNA samples were amplified, and size fractionated from 100 to 300 bp.

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: stationary phase


title: E. coli heatshock 1

source_name: Cells at mid-log phase (OD600nm 0.5) in M9 glucose (0.2%) media, with 42oC heatshock for 10 min.

value: heat shock


title: E. coli stationary 2


title: E. coli glutamine 2

source_name: Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine

value: glutamine


title: Plasmablast Input


title: NB1 shDHX9 KIF1Bbeta biol repl C

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

description: NB1 cells expressing shDHX9 and KIF1Bbeta(600-1400) construct, replicate C

data_processing:
Alignment by bowtie version 0.12.7 (option --best) to genome (excluding small contigs in _random files) and exon-exon junctions (http://sandberg.cmb.ki.se/media/data/rnaseq/hg19_junctions_100.fa.gz)
Conversion of junction coordinates to genome coordinates for reads overlapping a junction
Gene expression values from rpkmforgenes (http://sandberg.cmb.ki.se/rnaseq/) version 3 May 2011
Genome_build: hg19
Supplementary_files_format_and_content: BED (aligned reads) and tab-delimited text (gene expression values)

source_name: NB1 cell line

extract_protocol:
RNeasy Mini Kit (Qiagen)
Illumina TruSeq

tag: shRNA

tag: plasmid


title: NB1 shDHX9 KIF1Bbeta biol repl A

description: NB1 cells expressing shDHX9 and KIF1Bbeta(600-1400) construct, replicate A


title: NB1 shDHX9 controlplasmid biol repl C

description: NB1 cells expressing shDHX9 and containing control plasmid, replicate C

value: empty pcDNA3.1 vector


title: NB1 shDHX9 controlplasmid biol repl B

description: NB1 cells expressing shDHX9 and containing control plasmid, replicate B


title: NB1 shSCR KIF1Bbeta biol repl C

description: NB1 cells expressing shSCR and KIF1Bbeta(600-1400) construct, replicate C

value: scrambled control


title: NB1 shDHX9 controlplasmid biol repl A

description: NB1 cells expressing shDHX9 and containing control plasmid, replicate A


title: NB1 shSCR KIF1Bbeta biol repl B

description: NB1 cells expressing shSCR and KIF1Bbeta(600-1400) construct, replicate B


title: NB1 shSCR KIF1Bbeta biol repl A

description: NB1 cells expressing shSCR and KIF1Bbeta(600-1400) construct, replicate A


title: HK1 (miRNA)

value: well-differentiated NPC cell line


title: NB1 shSCR controlplasmid biol repl C

description: NB1 cells expressing shSCR and containing control plasmid, replicate C


title: E. coli glutamine 1

tag: strain


title: E. coli heatshock 2


title: NB1 shSCR controlplasmid biol repl A

description: NB1 cells expressing shSCR and containing control plasmid, replicate A


title: BF-T12-A

city: Portland

first: Willscott

middle: Edward

last: Naugler

state: OR

address: 3181 SW Sam Jackson Park Blvd

department: Med/GI&Hepatology

institute: Oregon Health & Science University

description:
Biliary fistula, bile acid infusion, partial hepatectomy 24 h after surgery, collect liver 12 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

data_processing:
Sample libraries are diluted and applied to an Illumina paired end flow cell at a concentration appropriate to generate about 180 million reads per lane. All libraries are prepared with indexing barcodes to permit multiplex runs. 100 cycle single read sequencing will be used to generate base call files. Illumina’s CASAVA package will be used to assemble the reads into standard fastq formatted data.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Each RPKM data column (ex: "Cont-T0-A") was made from (1) raw data from one rat sample, and (2) raw data from combined RNA from 3 rats.  Thus, two RNA sequencing runs per condition per timepoint were done; this data included 4 biological samples (1 in the first sample, and 3 in the second sample).  Two RPKM file were made for each condition 4 biological samples (1 in the first sample, and 3 in the second sample).  Two RPKM file were made for each condition and timepoint, then these were combined to make one RPKM file.
Genome_build: rn4
Supplementary_files_format_and_content: Text file include RPKM values

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

tag: Sex

value: Male


title: BF-T24-A

description:
Biliary fistula, bile acid infusion, partial hepatectomy 24 h after surgery, collect liver 24 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4


title: NB1 shSCR controlplasmid biol repl B

description: NB1 cells expressing shSCR and containing control plasmid, replicate B


title: B cell CTCF

source_name: splenic B cells

value: CTCF

value: Millipore

value: splenic B cells

value: B cells were purified from the spleens of 6-week old mice using a magnetic bead based CD43- B cell Isolation Kit (Miltenyi).


title: BF-T0-A

description:
Biliary fistula, bile acid infusion, partial hepatectomy 24 h after surgery, collect liver 0 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4


title: BA-T24-A

description:
Biliary fistula, partial hepatectomy 24 h after surgery, collect liver 24 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_biliary_fistula_no_bile_24h


title: Cont-T12-A

description:
Sham biliary fistula, partial hepatectomy 24 h after sham, collect liver 12 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_sham_biliary_fistula_12h


title: BA-T4-A

description:
Biliary fistula, partial hepatectomy 24 h after surgery, collect liver 4 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_biliary_fistula_no_bile_4h


title: BA-T0-A

description:
Biliary fistula, partial hepatectomy 24 h after surgery, collect liver 0 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_biliary_fistula_no_bile_0h


title: Cont-T24-A

description:
Sham biliary fistula, partial hepatectomy 24 h after sham, collect liver 24 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_sham_biliary_fistula_24h


title: HK1 (mRNA)


title: Rat retina, Time series, ZT23 (1 hr before lights on)

city: Bethesda

first: Steven

last: Coon

state: MD

address: 49 Convent Drive Room 6A83

department: NICHD/PDEGEN

institute: NIH

data_processing:
Image analysis and base calling were done using RTA1.12.4.2 and CASAVA1.8.0.
RNA-Seq reads were aligned to the rn4 genome assembly using Tophat-1.3.1.Linux_x86_64
FPKM values were calculated using Cufflinks-1.2.0.Linux_x86_64
Genome_build: rn4
Supplementary_files_format_and_content: FPKM abundance measurements

source_name: Rat retina, ZT23 (1 hr before lights on)

extract_protocol:
Total RNA was extracted with Trizol, followed by clean-up using RNeasy Micro kit with on-column DNase treatment. Quantitation and quality assuance were performed using a NanoDrop and Bioanalyzer, respectively.
A SPRI-TE kit (Beckman-Coulter) was used wherein 10 µg of total RNA was polyA-RNA-enriched using streptavidin-coated magnetic beads, followed by Covaris RNA fragmentation. Fragmented RNA was used to generate cDNA using reverse transcriptase (SuperScript II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase), was ligated to Illumina paired end (PE) adaptors containing a 6-basepair bar-code. Size selection was performed using a Pippin Prep 1.5% cartridge. Libraries were enriched using 16 cycles of PCR and purified using Ampure XP Beads (Agencourt). Each library was run as one of six bar-coded samples per lane on an Illumina HiSeq machine yielding paired-end,  101-base sequencing reads. Image analysis and base calling were done using RTA1.12.4.2 and CASAVA1.8.0.

treatment_protocol: Rats were housed in 14:10 lighting cycle

value: Sprague-Dawley

value: Retina

tag: animals in pool

tag: time of day

value: ZT23 (1 hr before lights on)

value: 6-8 weeks


title: Rat non-pineal mixed tissue, ZT19 (mid-night)

description: For the mixed tissues sample, the following tissues from three Sprague-Dawley rats sacrificed at ZT19 were used: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland. Total RNA was extracted from each tissue, and then equal amounts of each of the 15 tissues were combined for the final pooled sample.

value: Non-pineal mixed tissue

value: ZT19 (mid-night)


title: BA-T12-A

description:
Biliary fistula, partial hepatectomy 24 h after surgery, collect liver 12 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_biliary_fistula_no_bile_12h


title: Rat retina, Time series, ZT13 (1 hr before lights off)

source_name: Rat retina, ZT13 (1 hr before lights off)

value: ZT13 (1 hr before lights off)


title: Cont-T0-A

description:
Sham biliary fistula, partial hepatectomy 24 h after sham, collect liver 0 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_sham_biliary_fistula_0h


title: Rat retina, Time series, ZT1 (1 hr after lights on)

source_name: Rat retina, ZT1 (1 hr after lights on)

value: ZT1 (1 hr after lights on)


title: NB1 shDHX9 KIF1Bbeta biol repl B

description: NB1 cells expressing shDHX9 and KIF1Bbeta(600-1400) construct, replicate B


title: Rat retina, Time series, ZT15 (1 hr after lights off)

source_name: Rat retina, ZT15 (1 hr after lights off)

value: ZT15 (1 hr after lights off)


title: BF-T4-A

description:
Biliary fistula, bile acid infusion, partial hepatectomy 24 h after surgery, collect liver 4 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4


title: B cell Input

tag: cell type


title: Rat retina, Time series, ZT7 (mid-day)

source_name: Rat retina, ZT7 (mid-day)

tag: tissue

value: ZT7 (mid-day)


title: Rat pineal gland, Time series, ZT23 (1 hr before lights on)

source_name: Rat pineal gland, ZT23 (1 hr before lights on)

value: Pineal gland


title: Rat pineal gland, Time series, ZT15 (1 hr after lights off)

source_name: Rat pineal gland, ZT15 (1 hr after lights off)


title: Rat pineal gland, Time series, ZT19 (mid-night)

source_name: Rat pineal gland, ZT19 (mid-night)


title: Rat pineal gland, Time series, ZT1 (1 hr after lights on)

source_name: Rat pineal gland, ZT1 (1 hr after lights on)


title: Rat pineal gland, Time series, ZT7 (mid-day)

source_name: Rat pineal gland, ZT7 (mid-day)


title: Rat pineal gland, Time series, ZT13 (1 hr before lights off)

source_name: Rat pineal gland, ZT13 (1 hr before lights off)


title: wt_MNaseSeq

status: Public on Feb 04 2014

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

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

organism: Saccharomyces cerevisiae

source_name: Wild type yeast cells

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

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

tag: strains


title: Cont-T4-A

description:
Sham biliary fistula, partial hepatectomy 24 h after sham, collect liver 4 h after partial hepatectomy
sequencing run 1 was performed on biological replicate 1
sequencing run 2 was performed on pooled biological replicates 2-4

source_name: Whole liver_sham_biliary_fistula_4h

value: Sprague Dawley


title: Rat non-pineal mixed tissue, ZT7 (mid-day)

description: For the mixed tissues sample, the following tissues from three Sprague-Dawley rats sacrificed at ZT7 were used: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland. Total RNA was extracted from each tissue, and then equal amounts of each of the 15 tissues were combined for the final pooled sample.


title: Rat retina, Time series, ZT19 (mid-night)

source_name: Rat retina, ZT19 (mid-night)


title: SMORE-seq_WT_TAP-_rep2

description: Sample 4

data_processing:
The 100 bp read sequences were trimmed to 50 bp before alignment.
Alignment of sequencing reads was performed with bwa (version 0.6.2) using default options
Three TAP+ and TAP- replicates were merged, respectively, using samtools (version 0.1.18)
Reads that mapped to snRNA and rRNA were removed.
Gaussian kernel density estimation was utilized for peak calling, and a bandwidth of 5 and a read threshold of 2 were applied.
When TAP+ peaks were present within ±50bp of TAP- peaks, the peaks were corrected.
The base position with the highest read stack within the highest corrected peak was called as the TSS and PAS.
Genome_build: sacCer3
Supplementary_files_format_and_content: 1-based TSS and PAS coordinates

growth_protocol: Cells were grown in yeast extract-peptone-dextrose (YPD) at 30°C to an A600 OD of 0.8. We harvested the cells by centrifugation at 3000 rcf for 5 min, and the cell pellets were frozen in liquid nitrogen after discarding supernatant

extract_protocol:
Hot phenol total RNA extraction
Poly(A)+ RNA was purified and mixed with 5 units (1 μl) Tobacco Acid Pyrophosphatase (TAP). A parallel reaction without TAP enzyme was also performed. The RNA was combined with 5’ SR Adaptor (NEBNext Small RNA Library Prep Set for Illumina). This RNA was fragmented for 4 minutes at 94C using NEB fragmentation reagent. The RNA was then ligated to a 3’ sequencing adapter followed by reverse transcription and 10 cycles of PCR. PCR products of ~250 bp were selected and subjected to another 8 cycles of PCR

tag: genotype/variation

value: wild type

tag: replicate


title: SMORE-seq_WT_TAP+_rep3

description: Sample 5


title: SMORE-seq_WT_TAP+_rep2

description: Sample 3


title: SMORE-seq_WT_TAP+_rep1

description: Sample 1


title: MIA2-GM

city: Sendai

first: Toru

last: Furukawa

address: 2-1 Seiryomachi, Aobaku

department: Department of Investigative Pathology

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
library strategy: SAGE-seq
XSQ files generated from 5500xl SOLiD sequencer were converted into CSFASTA and QUAL files using XSQ Tools.
Sequenced reads were aligned to the NCBI RefSeq reference sequence and SAGE tags were counted using SOLiD SAGE Analysis Software v1.10.
SAGE tag counts were normalized to reads per million (RPM) using R.
Values of RPM were expressed as binary logarithm values (log2 RPM).
Genome_build: NCBI RefSeq
Supplementary_files_format_and_content: log2 RPM

source_name: MIA PaCa-2_pcDNA3.1-GNAS/R201H-V5/His

growth_protocol: PCI35 and PK8 were cultured with RPMI1640 medium supplemented with 10% fetal bovine serum. MIA PaCa-2 was cultures with Dulbecco's modified Eagles medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNAs were isolated using the RNeasy Mini kit (Qiagen, Hilden, Germany).
Serial analysis of gene expression (SAGE) library was constructed using a SOLiD SAGE Kit (Life Technologies) according to the manufacture’s instruction.

treatment_protocol: Cells of pancreatic cancer cell lines, PK-8, PCI-35,and MIA PaCa-2, were seeded at 4 × 105 cells/well in 6-well plates and incubated for 24 hours at 37°C in 5% CO2 with humid atmosphere. Then the cells were transfected with either pcDNA 3.1/V5-His vector or pcDNA3.1-GNAS(R201H)-V5-His vector using Lipofectamine 2000 reagent (Life Technologies) according to the manufacturer’s recommendations. The cells were incubated for 24 hours and collected by dissociation using trypsin.

tag: cell line

value: MIA PaCa-2

value: human pancreatic cancer cell line

tag: transfected with


title: PK8-GM


title: PK8-V

source_name: PK8_pcDNA3.1-V5/His vector

value: pcDNA3.1-V5/His vector


title: PCI35-GM


title: PCI35-V

source_name: PCI35_pcDNA3.1-V5/His vector


title: 180h nitrogen starved cell rep1

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

institute: University of Washington

data_processing:
Xpression was used for filtering reads
Xpression called BWA to align reads against the R. palustris strain CGA009 genome (BX571963.1)
Xpresssion was used for quantifying, normalizing, and visualizing read counts
DESeq was used for identifying differentially expressed genes
Genome_build: ASM19577v1, GI:39748133
Supplementary_files_format_and_content: Processed data contains raw read count and reads per kilobase per million uniquely mapped (RPKM) number

organism: Rhodopseudomonas palustris CGA009

source_name: 180h nitrogen starved cell rep1

growth_protocol: R. palustris CGA009 was grown anaerobically in the light in mineral medium with nitrogen gas as the sole nitrogen source and 20mM acetate as the sole carbon source

extract_protocol:
RNA was purified by using the QIAGEN miRNeasy Mini kit followed by Ambion's Turbo DNase treatment
RNA-seq library was constructed by using R. palustris-specific selective primers and NuGENs Ovation Ultralow DR Multiplex System

treatment_protocol: When cells reached the mid-logarithmic phase of growth, the headspace was flushed with argon gas for 10 min (t0), cells were starved for nitrogen for 12, 30, 50, 90 140, and 180h, and harvested for RNA purification

tag: time point


title: 140h nitrogen starved cell rep1

source_name: 140h nitrogen starved cell rep1


title: 140h nitrogen starved cell rep2

source_name: 140h nitrogen starved cell rep2


title: 50h nitrogen starved cell rep1

source_name: 50h nitrogen starved cell rep1


title: 90h nitrogen starved cell rep1

source_name: 90h nitrogen starved cell rep1


title: 50h nitrogen starved cell rep2

source_name: 50h nitrogen starved cell rep2


title: 12h nitrogen starved cell rep2

source_name: 12h nitrogen starved cell rep2


title: 30h nitrogen starved cell rep1

source_name: 30h nitrogen starved cell rep1


title: SMORE-seq_WT_TAP-_rep3

description: Sample 6


title: 30h nitrogen starved cell rep2

source_name: 30h nitrogen starved cell rep2


title: 0h nitrogen starved cell rep2

source_name: 0h nitrogen starved cell rep2


title: 0h nitrogen starved cell rep1

source_name: 0h nitrogen starved cell rep1


title: 12h nitrogen starved cell rep1

source_name: 12h nitrogen starved cell rep1


title: SMORE-seq_WT_TAP-_rep1

description: Sample 2


title: MIA2-V

source_name: MIA PaCa-2_pcDNA3.1-V5/His vector


title: 180h nitrogen starved cell rep2

source_name: 180h nitrogen starved cell rep2


title: TOF-21_RV_mRNA

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

description: mRNA-Seq.

data_processing:
Sequencing reads were extracted from the image files using the open source Firecrest and Bustard applications (Illumina Genome Analyzer pipeline 1.3.2, 1.4.0 and 1.5.0). mRNA reads were mapped to the human reference genome (NCBI v36.1; hg18) using RazerS allowing at most 10 equally-best hits and two mismatches (no InDels) per read. Multimatched reads were proportionately assigned to each of their mapping locations using MuMRescueLite software with a window size of 200 bp. Reads were assigned to genes and transcripts if their mapped location is inside of exon boundaries as defined by ENSEMBL (v54)5. To further assign unmapped reads, a gene-wise splice junction sequence library was produced from pairwise connection of exon sequences corresponding to all known 5' to 3' splice junctions (supported by the analysis of aligned EST and cDNA sequences). For transcripts, the read counts were adjusted using the proportion estimation (POEM) method in the Solas package. Read count normalization for mRNAs (genes and transcripts) was performed using the RNA composition adjustment by trimmed mean of M-values (TMM) and quantile-to-quantile count adjustment implemented in the edgeR package.

Processed data files are linked to the Series record as supplementary files.

source_name: right ventricle from TOF human heart

extract_protocol: Total RNA was isolated from human heart samples using TRIzol reagent. Messenger RNAs were isolated from total RNA and prepared for sequencing using Illumina Kit RS-100-0801 according to the manufacturer's protocol (Preparing Samples for Sequencing of mRNA Sept 2008). The sequencing libraries were generated using a non-strand-specific library construction method.

value: heart, right ventricle

tag: disease state

value: Tetralogy of Fallot (TOF)


title: TOF-19_RV_mRNA

description: mRNA-Seq.


title: TOF-16_RV_mRNA

description: mRNA-Seq.


title: TOF-17_RV_mRNA

description: mRNA-Seq.


title: TOF-20_RV_mRNA

description: mRNA-Seq.


title: TOF-22_RV_mRNA

description: mRNA-Seq.


title: TOF-15_RV_mRNA

description: mRNA-Seq.


title: TOF-13_RV_mRNA

description: mRNA-Seq.


title: TOF-12_RV_mRNA

description: mRNA-Seq.


title: TOF-14_RV_mRNA

description: mRNA-Seq.


title: TOF-10_RV_mRNA

description: mRNA-Seq.


title: TOF-08_RV_mRNA

description: mRNA-Seq.


title: TOF-09_RV_mRNA

description: mRNA-Seq.


title: TOF-11_RV_mRNA

description: mRNA-Seq.


title: TOF-07_RV_mRNA

description: mRNA-Seq.


title: 90h nitrogen starved cell rep2

source_name: 90h nitrogen starved cell rep2


title: TOF-06_RV_mRNA

description: mRNA-Seq.


title: TOF-02_RV_mRNA

description: mRNA-Seq.


title: TOF-05_RV_mRNA

description: mRNA-Seq.


title: TOF-04_RV_mRNA

description: mRNA-Seq.


title: TOF-03_RV_mRNA

description: mRNA-Seq.


title: TOF-01_RV_mRNA

description: mRNA-Seq.


title: NH-08_RV_mRNA

description: mRNA-Seq.

source_name: right ventricle from normal human heart

value: healthy


title: NH-07_LV_mRNA

description: mRNA-Seq.

source_name: left ventricle from normal human heart

value: heart, left ventricle


title: NH-06_RV_mRNA

description: mRNA-Seq.


title: TOF-18_RV_mRNA

description: mRNA-Seq.


title: NH-05_LV_mRNA

description: mRNA-Seq.


title: NH-03_LV_mRNA

description: mRNA-Seq.


title: NH-01_LV_mRNA

description: mRNA-Seq.


title: NH-04_RV_mRNA

description: mRNA-Seq.


title: Grimmond_hs_thymus

city: Boston

first: David

middle: A

last: Harmin

state: MA

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

description: Total RNA was depleted of rRNA by hybridization (using RiboMinus) and heat fragmented. Strand-specific RNA-Seq libraries were prepared using the Small RNA Expression (cat#4399434b) method on SOLiD (for human tissues and mouse neurons).

data_processing:
Base calling was performed using standard approaches.
Illumina raw reads in .fastq files were aligned using bwa 0.6.2.  Target sequences included (1) 24 hg19 autosomal and sex chromosomes plus (2) a read-length-dependent splice library (~3M sequences, each 50-98bp).  The latter comprised all possible minimal intragenic sequences of two or more exons (based on the RefSeq annotation) for which one or more exon-exon junctions could be crossed by reads of the required length.  After bwa-indexing the targets with the bwtsw algorithm, reads were aligned with zero trimming, zero gaps, and allowing up to 5 mismatches.  Reads for each end of the two samples with paired-end reads were aligned as single reads only to test their consistency; thereafter only the "1" ends were used.  The sam/bam files output by bwa were indexed and sorted and served as input for further processing.
SOLiD raw reads were aligned using Corona with 0-3 cs mismatches for 35-bp reads.  Uniquely mapped reads output to SOLiD-format "unique.csfasta.ma" files served as input for further processing.    SOLiD quality scores are in the .qual files.
Aligned reads were minimally filtered for QC, removing any reads with uncalled bases or with unmapped or nonuniquely mapped sequences.
Employing "MAPtoFeatures" perl scripts, the loci of uniquely mapped reads were compared to the loci of all genic features (exons, introns, UTRs, CDSs, etc., and all junctions between them) of (1) all genes based on the RefSeq annotation and (2) all rRNA genes based on RepeatMasker, for the alignment target genome.  Every overlap of an individual read with genic features, including exon-exon splice junctions, was counted towards the features' "nrds" while the number of bases overlapped was added to their "rdbp".  For every genic feature the average Density (read coverage per bp) was calculated, equal to rdbp per feature length.  Each sample's Densities were renormalized from total reads not in noncoding genes and not in rRNA to a standard total of 10M reads, and to a standard read length of 35bp.  With these conventions, units of Density always equal RPKM times 0.35.  Normalized Densities were treated as expression levels comparable among all samples.
Genome_build: For the 3 mouse samples (Total1):  mm9 (NCBI ref_C57BL-6J assembly 37, build 1, July 2007).    For the other 26 samples (IsoG-CPT, LCL, Grimmond), all human:  hg19 (NCBI GRCh37 assembly 37, build 1, Feb. 2009).
Supplementary_files_format_and_content: The "Genes-FEATURES-READS" .tsv files are spreadsheets output by MAPtoFeatures.  Each row has data for one gene (with NCBI Entrez Gene IDs) or, in some case, one rRNA locus (with artifical IDs).  A 1-line header labels 14-16 columns containing genomic information, followed by blocks of columns labeled "num" (number of each feature type per gene), "bp" (total length of each feature type per gene), and in some cases "rdbp_avail" (total length of all reads that could uniformly cover all features of each type per gene), followed by data columns.  Data in the remaining blocks are distinguished by reads that mapped S[ense] or A[ntisense] to each gene:  "nrds" (number of overlapping reads wholly contained within each feature type per gene), "rdbp" (total number of bases of reads that overlap each feature type at all, including reads crossing feature junctions), "Density" (expression levels, equal to normalized coverage as described above).  Some columns labeled "-ALL" give concatenated values for all individual features, listed 5' to 3', within each gene.  Exon-exon junctions, labeled "SPL", are notated as <count>(<exons>) with "^" between adjoining exons; e.g., "2(5^6)" indicates 2 reads crossing the junctions between exons 5 and 6, and "1(3^5^6)" for 1 read crossing from exon 3 to 5, through all of 5, and crossing to exon 6.  Exon-intron junctions, labeled "JXN", are notated as, e.g., "1(8>8<)" for 1 read crossing from exon 8 into intron 8 or "3(8<9>)" for 3 reads crossing intron 8 and exon 9.
Supplementary_files_format_and_content: The "cross_reads_and_features__LOG" .txt files document each MAPtoFeatures analysis, including total reads used for normalization, totals per feature across the genome, and other statistics.
Supplementary_files_format_and_content: The "BINS-READS-Densities" .tsv files contain tiled Densities per every individual intron in the annotated genome of interest.  Each intron is divided into 100 bins of equal size (fractional bp); the contributions of reads that only partially overlap a bin are pro rated to it (a single read's average Density in a bin equals the fraction of the bin it covers).  Average Densities per bin are renormalized as in MAPtoFeatures, but only Sense reads are included.  About 20 columns of genic and locus information for the ~200k introns are followed by 100 columns listing each intron's 100 normalized Densities ordered from its 5'-most to its 3'-most bin.  These Densities are used to quantify the slopes of the differential abundance of nascent transcripts across introns.
Supplementary_files_format_and_content: The bigWig .bw files are in standard format for compressed variable-step wiggle tracks.  Most samples listed here have two bigWig files, intended for separate tracks for POS and NEG strands.  (There are only POS tracks for the 6 strand-nonspecific LCL samples, except additionally both strands are shown for each end for the 2 samples with paired ends.  See "Exceptions" below.)
Supplementary_files_format_and_content: A single .txt file contains example track lines for all the .bw files in this set.
Supplementary_files_format_and_content: Exceptions:    LCL__BM1_4SU__1 & LCL__BM1_4SU__2 refer to companion sets of paired end reads for a single sample.  Similarly for LCL__BM2_4SU__1 & LCL__BM2_4SU__2.  There are bigWig files for both ends for both these samples.  Although these are strand-nonspecific samples, reads mapped to each strand are shown.  There are no MAPtoFeatures spreadsheets for these individual data sets.    The other 4 LCL samples (BM3_4SU and 3 riboMinus) have neither strand-specific nor paired-end reads, and so were analyzed with all reads assigned to the POS strand and flagged as mapping S[ense] to all gene features.  The "1" end of BM1_4SU and BM2_4SU were also analyzed disregarding strand and sense, yielding 6 sets of similarly generated bigWig tracks and MAPtoFeatures spreadsheets for the 6 LCL samples.  The slopes of these data sets were not analyzed so binned Density tables for them are not included here.    Raw sequence data for the Total1 samples have been published elsewhere (Kim et al., Nature 2010) so .csfasta files for them are not included here.

source_name: Ambion

extract_protocol:
Illumina library construction and sequencing.  RNA-seq libraries were constructed using the strand-specific dUTP method, with minor modifications.  Briefly, 3ug of DNAse treated RNA was depleted of rRNA using Ribozero (Epicentre).  Two batches of rRNA-depleted samples were combined, cleaned by RiboMinus concentration module (Invitrogen) and fragmented at 90°C for 3 min (NEB fragmentation buffer).  First strand synthesis was followed by cleanup with RNAClean XP SPRI beads (Agencourt).  Second strand synthesis incorporated dUTP, followed by sample clean up with MinElute PCR purification Kit (Qiagen).  Fragment ends were repaired, adenylated, then ligated to True-Seq barcoded adaptors and cleaned up with AMPure XP SPRI beads (Agencourt).  The libraries were then amplified by PCR for 12 cycles and cleaned up with AMPure XP SPRI beads.  Illumina sequencing (1 x 50-bp read length) was performed on a HiSeq 2000.  4SU libraries were prepared non-strand-specifically using standard Illumina RNA-Seq.
SOLiD RNA-Seq library construction and sequencing.  Total RNA was depleted of ribosomal RNA by hybridization using RiboMinus (Invitrogen) and was heat-fragmented.  rRNA-depleted, fragmented RNA was processed into SOLiD sequencing libraries using the Small RNA Expression Kit.  Sequencing was performed on SOLiD with 35-bp read lengths (human tissues, mouse neurons).

value: Ambion

value: human thymus


title: Grimmond_hs_placenta

value: human placenta


title: Grimmond_hs_lung

value: human lung


title: Grimmond_hs_liver

value: human liver


title: Grimmond_hs_testis

value: human testis


title: Grimmond_hs_heart

value: human heart


title: Grimmond_hs_spleen

value: human spleen


title: LCL__BM3_4SU

description: Isolation of nascent transcripts. Nascent and transcripts were isolated using modified methods previously described (Cleary, 2008; Cleary et al., 2005a; Dölken et al., 2008)(Kenzelmann et al., 2007b). Briefly, lymphoblastoid cells were pulse-labeled with 200 μM of 4-thiouridine (4SU) for 5 minutes.  Cells labeled in DMSO (without 4SU) served as negative controls. Following incubation in 4SU, cells were harvested by centrifugation and RNA extracted using Trizol (Invitrogen).  Extracted RNA was further purified using RNeasy columns (Qiagen) and eluted to a concentration >0.4 ng/μl.  Purified RNA was denatured, and the 4SU-incorporated sites were biotinylated using 1 mg/ml EZ-link biotin-HPDP (Cleary, 2008) by incubating at 65°C for 1.5 hours and then 25°C for an additional 1.5 hours. Unincorporated biotin-HPDP was removed twice using chloroform-isoamyl alcohol (24:1) and centrifuging the mixture in phase-lock-gel tubes (Eppendorf) as described (Dolken et al., 2008).  Biotinylated RNA was captured and purified using MyOne streptavidin C1 beads (Invitrogen) and eluted in 5% β-mercaptoethanol as described (Cleary, 2008).  RNA-seq libraries were constructed using TruSeq library preparations (Illumina).

source_name: Lymphocyte cell lines

value: Lymphocyte cell lines

value: 4-thiouridine 5' lableing


title: Grimmond_hs_ovary

value: human ovary


title: Grimmond_hs_kidney

value: human kidney


title: LCL__BM1_4SU__2


title: OsDCL3aIR-3 RNA-seq

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

description: Sample 3

data_processing:
RNA-seq Data Analysis: The RNA-seq reads with strand direction were aligned to the release 7 of the Rice Genome using tophat-1.3.0 (Trapnell et al., 2009). Only uniquely mapped reads were remained for subsequent analysis. The expression levels for gene models from Release 7 of the MSU Rice Genome Annotation Project were measured and normalized as reads per kilobase of exon model per million mapped reads (RPKM)[PMID 18516045]. Then P-values for each gene were calculated by DEGseq basing on MA-plot-based method with random sampling model (MARS) [PMID 19855105].. Genes with more than 1.5-fold change and P < 0.01 in both dcl3-1 and dcl3-3 library were regarded as the differentially expressed genes. The Rice Oligonucleotide Array Database (http://www.ricearray.org/) was used for GO enrichment analysis, which identified significantly enriched biological processes for the up-regulated genes (P < 0.05).

Small RNA-seq Data Analysis: Bowtie-0.12.7 [PMID 19261174] was used for mapping small RNAs with perfect match to release 7 of the Rice Genome (http://rice.plantbiology.msu.edu/). Small RNAs were normalized to small RNA library size to calculate the value of reads per twenty five million (RP25M) which was futher normalized for multiple mapped reads by dividing RP25M by the number of genomic locations following previous method [PMID 22647529]. Then the abundance of 24-nt small RNAs with fixed-size bins (500 nt) was calculated and clusters with more than three-fold change were identified. Based on TIGR_Oryza_Repeats.v3.3, small RNA clusters were annotated according to the overlapping relation between the genomic coordinates of repeats and small RNA clusters.
Genome_build: Rice Genome (http://rice.plantbiology.msu.edu/) release 7
Supplementary_files_format_and_content: wig files were generated using MACS program

organism: Oryza sativa

source_name: 3a-3_lamina joints of flag leaf

growth_protocol: These transgenic plants and wild-type (Nipponbare) were grown in the field for phenotypic observation. RNA were extracted from the lamina joints of the flag leaf used for RNA-seq and small RNA-seq analysis.

extract_protocol:
Total RNAs were extracted from the lamina joints of the rice flag leaf with TRIzol Reagent (15596–026; Invitrogen).
Strand-specific RNA-Seq libraries generated from Wild, dcl3-1 and dcl3-3 were constructed according to the Illumina Directional mRNA-Seq library prep v1.5 protocol and sequenced on Illumina GAII.

treatment_protocol: No treatment

value: OsDCL3aIR-3 (mutant)

value: lamina joints of the rice flag leaf


title: OsDCL3aIR-1 RNA-seq

description: Sample 2

source_name: 3a-1_lamina joints of flag leaf

value: OsDCL3aIR-1 (mutant)


title: WT RNA-seq

description: Sample 1

source_name: WT_lamina joints of flag leaf

value: wild type


title: Grimmond_hs_brain

value: human brain


title: LCL__BM3_riboMinus

description: Total RNA was depleted of rRNA by hybridization (using RiboZero) and heat fragmented. RNA-Seq libraries were prepared using the TrueSeq method on Illumina.

value: control


title: LCL__BM2_riboMinus


title: LCL__BM1_4SU__1


title: LCL__BM1_riboMinus


title: HiSeq_IsoG-CPT__D8-01_IsG

description: Total RNA was depleted of rRNA by hybridization (using RiboZero) and heat fragmented. Strand-specific RNA-Seq libraries were prepared using the dUTP method on Illumina (for CPT, IsoG, and lymphocyte total RNA libraries).

source_name: HeLa cells

value: HeLa cells

value: Isoginkgetin


title: HiSeq_IsoG-CPT__D9-19_IsG


title: HiSeq_IsoG-CPT__D9-19_c60

value: vehicle


title: HiSeq_IsoG-CPT__D8-01_c60


title: HiSeq_IsoG-CPT__D7-10_CPT

value: camptothecin


title: HiSeq_IsoG-CPT__D6-26_IsG


title: HiSeq_IsoG-CPT__D7-10_c10


title: HiSeq_IsoG-CPT__D6-26_c60


title: HiSeq_IsoG-CPT__D6-26_CPT


title: LCL__BM2_4SU__1


title: LCL__BM2_4SU__2


title: INPUT_r2

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

description: INPUT DNA from T47D-MTVL cells

data_processing:
Base calling；HCS1.4.8+RTA1.12
Data were filtered using the following steps:1.removed adpter,2removed the low quality tags which were with N-rate more than 10%,or bases with Q <=20 account for more than 50% of the total.
ChIP-seq reads were aligned to the hg18 genome assembly by SOAP 2.21 with the following configurations.Parameters： -p 4 -l 23 -v 2 -s 35
peaks were called using MACS version 1.4.0 with the following parameters： --tsize 49 --bw 177 --gsize 2.7e9 --pvalue 1e-5 --wig --wigextend 300 --space 50 --diag Ture --mfold 10,30
enriched islands were called using the tool SICER (version 1.1). FDR cut off used were 0.01. and Fold change cut off were at least 2.
Genome_build: hg18
Supplementary_files_format_and_content: Input subtracted normalized WIG files were produced from duplicate removed aligned reads using the program javaGenomicsToolKit

growth_protocol: RPMI 1640 medium + 10%FBS, 1%glutamine, 1%penicillin/streptomycin

extract_protocol:
T47D-MTVL cells were fixed using 1% formaldehyde, harvested and sonicated using a Diagenode Bioruptor to generate chromatin fragments between 200 and 500 bp. To perform the chromatin immunoprecipitation, 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Santa Cruz Biothechnology) was used as a control for nonspecific interaction of DNA. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: gender

value: female

value: breast cancer ductal carcinoma

tag: antibody


title: H1.4-HA_r3

description: H1.4-HA histone protein immunoprecipitated DNA

source_name: T47D-MTVLstably overexpressing H1.4-HA


title: H1.2endo_r2

description: endogenous H1.2 histone protein immunoprecipitated DNA

value: anti-H1.2 (Abcam 4086)


title: H3_r3

description: endogenous H3 histone protein immunoprecipitated DNA

value: anti-H3 (Abcam 1791)


title: INPUT_r3

description: INPUT DNA from T47D-MTVL cells


title: H1.2endo_r3


title: HiSeq_IsoG-CPT__D6-26_c10

tag: treatment


title: H1.2-HA_r2

description: H1.2-HA histone protein immunoprecipitated DNA

source_name: T47D-MTVLstably overexpressing H1.2-HA


title: H1.0-HA_r2

description: H1.0-HA histone protein immunoprecipitated DNA

source_name: T47D-MTVLstably overexpressing H1.0-HA

value: anti-HA (Abcam 9110)


title: OsDCL3aIR-1 Small RNA-Seq

description: Sample 5


title: OsDCL3aIR-3 Small RNA-Seq

description: Sample 6


title: H1Xendo_r3

description: endogenous H1X histone protein immunoprecipitated DNA

value: anti-H1X (Abcam 31972)


title: PSB-D mock TChAP output, replicate 2

city: Gent

first: Ken

last: Heyndrickx

address: Technologiepark 927

department: Department of Plant Biotechnology and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
Basecalls performed using GA pipeline 1.4.0
Read mapping was done with BWA 0.5.9 using default settings
Reads that did not map uniquely to one of the five chromosomes were discarded from further analysis
Peak calling was performed using MACS v1.3.7 with default setting, except for MFOLD = 6, and g = 90 Mb
Subsamples were made from each of the experiments and to define majority genes, the peak annotations from the different sub-samples were combined.
Only those genes, together with their maximum peak score, recovered in 50% or more of the samples were retained
Genome_build: TAIR9
Supplementary_files_format_and_content: BED files were generated by MACS

organism: Arabidopsis thaliana

source_name: Plant cell suspension cells

growth_protocol: Wild-type and transgenic PSB-D cell suspension cultures are maintained by weekly subculturing in MSMO medium (4.43 g/liter MSMO (Sigma-Aldrich), 30 g/liter sucrose, 0.5 mg/liter α-naphthaleneacetic acid, 0.05 mg/liter kinetin, pH  5.7)  at 25 °C in the dark by gentle agitation (130 rpm).

extract_protocol:
Cells were grinded in N2(l) and solubilized in NLB buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 µg/ml pepstatin A, 1 µg/ml aprotinin, 1 µg/ml leupeptin, 1 mM PMSF). After chromatin fragmentation by sonication, the extract was clarified by centrifugation and used for chromatin isolation.  E2Fa_HBH-DNA complexes were isolated through ChIP using an E2Fa antibody, ChAP using Streptavidin-sepharose, and TChAP using  Ni2+-NTA and Streptavidin-sepharose beads.
Standard Illumina Protocol

treatment_protocol: Cells were treated with 0.75% formaldehyde for 10 minutes. After crosslinking, formaldehyde was quenched with 250mM glycine and cells were washed with PBS

value: PSB-D dark growing cell suspension cells

tag: ecotype

value: Landsberg erecta

tag: genotype

tag: age

value: cells were crosslinked and harvested 2 days after subculturing


title: E2Fa-HBH TChAP output, replicate 2

value: Ni2+-NTA and Streptavidin-sepharose


title: PSB-D mock ChAP output

value: wild type


title: WT Small RNA-Seq

description: Sample 4

value: lamina joints of the rice flag leaf


title: E2Fa-HBH ChIP output


title: PSB-D mock TChAP output, replicate 1


title: E2Fa-HBH mock ChIP output


title: TKO 47

status: Public on Feb 03 2014

city: New Haven

first: Haifan

last: Lin

state: CT

address: 10 Amistad Street

institute: Yale University

description: Sample 7

data_processing:
BWA aligner 0.7.5a w/ default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: mapped reads counts

source_name: iPS cells

growth_protocol: cells were grown in mouse ESC medium containing D-MEM with 15% fetal bovine serum (Gemini Bio-Products), 0.1 mM MEM Non-Essential Amino Acids (Life Technologies), 6 mM L-glutamine (Life Technologies) 0.1 mM 2-mercaptoethanol (Sigma), 1% Pen-Strep (Life Technologies) and 103Uml-1 of LIF (Millipore-ESGRO).

extract_protocol:
Total RNA from individual iPS clones were isolated using the High Pure RNA Isolation Kit (Roche Diagnostics, Indianapolis, IN). For all samples, genomic DNA was digested with RNase-free DNase I.
Library preparation were performed using the Illumina TruSeq RNA Sample Preparation kit. Samples were sequenced on an Illumina HiSeq 2000.

value: MEF-derived iPS cells

tag: passages

tag: strain

value: mixed background

value: Piwi triple knockout


title: TKO 48

description: Sample 8

tag: cell type


title: E2Fa-HBH TChAP output, replicate 1


title: Ctrl 43

description: Sample 4

value: control


title: TKO 37

description: Sample 6


title: TKO 35

description: Sample 5


title: Ctrl 41

description: Sample 3


title: Ctrl 34

description: Sample 2


title: Ctrl 33

description: Sample 1


title: shTUNA_Day6_rep1

city: San Diego

first: xiayu

last: huang

state: CA

address: 3010 Science Park Road

institute: Sanford|Burnham Medical Research Institute

data_processing:
Reads which did not pass the internal Illumina QC were removed.
The rest reads were mapped to mm9 genome using BWA and result bam files were quantified and normalized with the method DESeq in Avadis NGS.
The raw counts after applying the normalization on them are called the `normalized counts'.
The normalized counts are log-transformed to result in what are called `normalized signal values'.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited txt file with log transformed data

source_name: CCE mouse embryonic stem cells

growth_protocol: mES media consisting of DMEM supplemented with 15% FBS, 1% L-glutamine, 1% MEM NEAA, 0.00086% 1-Thioglycerol and 0.01% LIF

extract_protocol:
Total RNA from transduced cells were extracted by Trizol reagent on days 2, 4 and 6 post-transduction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CCE mES cells were transduced with pLKO.1-puro lentivirus expression shRNA. After 24hr, the media was removed and replaced with media containing 1µg/ml puromycin. The media was changed every other day with fresh media with 1µg/ml puromycin.

value: Mouse embryonic stem cells

value: CCE

value: Lentiviral shTUNA transduction

tag: time

value: 6 days


title: shTUNA_Day6_rep2


title: shTUNA_Day4_rep3

value: 4 days


title: shTUNA_Day4_rep2


title: E2Fa-HBH ChAP output

value: Streptavidin-sepharose


title: shTUNA_Day6_rep3


title: shTUNA_Day2_rep1

value: 2 days


title: shTUNA_Day2_rep3


title: shTUNA_Day4_rep1


title: shControl_rep1

value: Lentiviral control shRNA transduction


title: shTUNA_Day2_rep2


title: h9ESC short 1

city: Taipei

first: Chan-Shuo

last: Wu

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: RiboMinus Transcriptome isolation, Strand specific

data_processing: We aligned the h9ESC SOLiD reads and the h1ESC Illumina reads (downloaded from GSE20301) against the non-co-linear junction regions of the 9,093 candidates using BFAST. For each non-co-linear junction region, both of the non-overlapping regions of mapping parts are restricted to being longer than 10 bp in length and showing greater than or equal to 95% alignment to the mapping short reads. Only one mismatch and no insertion/deletion are allowed in a mapping between a non-co-linear junction region and a short read. A matched short read is discarded if it can also map to the human genome or well-annotated transcripts (including UCSC- and Ensemble-annotated transcripts). After the filter of short reads, TSscan nominates 47 non-co-linear RNA candidates. The mapping results of short reads against the non-co-linear junction regions are also provided (i.e., mapping.rar).

source_name: Embryonic stem cells

growth_protocol: The hESC H9 was grown on MEF feeders (2 Ã 104 cells/cm2) in DMEM/F12 medium plus 20% Knockout Serum Replacement (Invitrogen, Carlsbad, CA) and bFGF (4 ng/ml, Sigma-Aldrich, St. Louis, MO).

extract_protocol: 10ug total RNA was harvested from hESC H9 by Tri-reagent (Ambion) for cDNA library preparation. The enrichment of mRNA by depleting ribosomal RNA was performed by RiboMinusTM Transcriptome isolation Kit (Invirogen) according to manufacturerâs instruction. One ug RiboMinus RNA was fragmented by treating RNase III 10 minutes and cleaned up by RiboMinus Concentration Module (Invitrogen). The fragmented RiboMinus RNA was ligased with SOLiD adaptor A and reverse transcribed by ArrayScript Reverse Transcriptase. The product of reverse transcription was purified by MinElute PCR Purification Kit (Qiagen) and size-selected on 6% TBE âUrea Gel for a size range from 100nt to 200nt. The cDNA library with proper size was amplified by SOLiD PCR Kit. To prepare the sequencing template, size selected cDNA library was coupled with SOLiD P1 DNA beads and mixed with emulsion PCR mixture by ULTRA-TURRAX Tube Drive from IKA. The emulsion PCR was performed by GeneAmp PCR system 9700 according to manufacturerâs program. The templates on SOLiD P1 DNA beads amplified by emulsion PCR were washed, denatured and enriched by SOLiD P2 bead incubation. The enriched templates were then modified at the 3â end with bead linker by terminal transferase reaction. The 3â end modified templates were washed and deposited to SOLiD slide. Sequencing of templates were performed by SOLiD 3 instrument according to the operation guide. Data was processed with SOLiD Analysis Tool Pipeline.

tag: developmental stage

value: Embryonic stem cells