title: Homo-2 sperm

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

data_processing:
Illumina Bcl2fastq 1.8.2 software was used for demultiplexing and generation of fastq files
Adapter trimming for all reads from each sample was performed using Trim Galore (Babraham Bioinformatics)
The trimmed reads were mapped against the mouse genome (mm9 build) with Bismark v0.7.12, and the methylation call for every single C was extracted by bismark methylation extractor script. All programs were performed with default setting.
Genome_build: mm9
Supplementary_files_format_and_content: summarized methylation percentage (single-base resolution)

source_name: Homo sperm

extract_protocol:
DNA was extracted in DNA lysis buffer (10 mM Tris-HCl (pH 8.5), 10 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 mg/ml proteinase K followed by phenol:chloroform extraction and ethanol precipitation.
DNA was digested with MspI (NEB), and then subjected to end repair, and ligation of methylated custom adaptors (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’, Reverse: 5’-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC-3’, where * indicates phosphorothioate bond) with a NEBNext Ultra DNA Library Prep Kit for Illumina (NEB). Size selection was conducted by purifying the adaptor-ligated DNA twice with 1.5× SPRIselect beads (Beckman Coulter). Size selected libraries were treated with sodium bisulfite using the EpiTect Fast Bisulfite Conversion Kit (QIAGEN). After clean-up, the optimal, minimum PCR cycle numbers required to generate the final libraries were determined by qPCR using KAPA 2G Robust HotStart ReadyMix (KAPA) with 0.3× SYBR I. Final libraries were generated by scaled-up PCR reactions (without SYBR I) using the cycles determined above with barcoded primers from NEBNext Multiplex Oligos kit (NEB), and purified with 1.2× SPRIselect beads.

tag: strain background

tag: genotype/variation

value: Homozygous

tag: tissue

value: sperm


title: Homo-3 sperm

status: Public on Dec 02 2013

type: SRA

city: Boston

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: Homo-4 sperm


title: Homo-1 sperm


title: Het-4 sperm

source_name: Het sperm

value: Heterozygous


title: Het-1 sperm


title: Het-2 sperm


title: Homo-1 PGC

source_name: KO_E13.5 PGC

value: Homozygous Tet1-KO

value: primordial germ cells (PGCs)


title: WT-2 PGC

source_name: WT_E13.5 PGC

value: wild type


title: 3P-seqs in mESC

city: Seoul

first: Jin-Wu

last: Nam

address: 222 Wangsimni Seongdong-gu

country: South Korea

institute: Hanyang University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.7
Reads are reverse-complemented first and mapped reads with at least one untemplated adenylate residue using Bowtie with option (bowtie -p 4 -q --phred33-quals -5 3 -l 25 -n 1 -e 240 --best --strata -m 1).
We considered as a cluster those 3P-tags ending 31 nucleotides within the most frequently implicated cleavage position, which was then regarded as a candidate poly(A) cleavage site.
To control for PCR amplification bias, we only used those clusters with at least two identifiably independent reads in our downstream analysis (e.g. tags with different ends, different number 3’-terminal adenylates, and/or from two different libraries).
Genome_build: mm9
Supplementary_files_format_and_content: bed files including 3P-seq clusters

molecule: total RNA

source_name: mouse embryonic stem cell

extract_protocol:
RNA from wild type and miR-22D (Gurha et al., 2012) mouse tissues was isolated by adding a steel bead and 1 mL TRI Reagent to tissues and then vortexing for two minutes in a TissueLyser II (Qiagen) at 30 Hz, twice. The homogenate was centrifuged for 8 min at 12,000xg and the supernatant was purified according to manufacturer’s protocol with an additional phenol/chloroform extraction after phase separation.
3P-Seq libraries were prepared from 75 μg of isolated RNA (mouse tissues, mESC, NIH3T3) as described previously (Jan et al., 2011) with modifications (see Supplemental Information).

tag: data type

value: 3P-seq fastq

value: mouse embryonic stem cell

tag: genetic background


title: Homo-2 PGC


title: WT-1 PGC


title: xHomo-10

data_processing:
Illumina Bcl2fastq 1.8.2 software was used for demultiplexing and generation of fastq files
RNA-seq data were processed with Tophat and Cufflinks using the UCSC mm9 annotation
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: xHomo_E9.5 embryo

extract_protocol:
Total RNA was purified with an RNeasy Mini Kit (QIAGEN), in which an on-column DNase treatment was included.
500 ng of purified RNA was then subjected to mRNA isolation and library preparation using a NEBNext Ultra RNA Directional Library Prep Kit for Illumina with the Poly (A) mRNA Magnetic Isolation Module (NEB) following manufacturer’s instructions.

value: xHomo

tag: developmental stage

value: embryo


title: xHomo-9


title: xHomo-7


title: xHomo-8


title: RN2_JQ1_2h

city: Cold Spring Harbor

first: Christopher

middle: R

last: Vakoc

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

data_processing:
For NSR and illumine RNA-seq, The obtained reads from illumina HiSEq 2000. were trimmed into 28 base reads corresponding to 9th to 36th position from the 5′ ends of the reads. The trimmed reads were mapped to the mouse genome (mm9) using Bowtie with no mismatch. Gene expression was analyzed by using Cufflinks software (http://cufflinks.cbcb.umd.edu/).
For JQ1 RNA-seq time course experiment, illumina sequences were split into separate files based on sample barcodes.  For each read pair one read consists of primer and a 7 base sequence identifying the sample.  Both reads are examined, the sample ID is found on one read and the other read is mapped to the mouse mm9 reference genome, from the UCSC Genome Browser ftp site, using Tophat2.  Read counts per gene are computed by counting reads that overlap the mm9 refseq gene annotations downloaded from the UCSC Genome Browser ftp site.  These counts are normalized by dividing by the total number of reads counted for all genes.  For each series of time points for each gene a best continuous piecewise linear fit is computed.  The intent is to model the response of each gene by a latency period of no response followed by a response reaching a new stable level after a period of time.  The form of this curve is three linear segments with the first and last segments slope zero and the middle segment connecting the two end segments.  The curves are defined by the pair of endpoints of the middle segment.  All pairs of points are tested to find the pair of points minimizing the sum of the squared difference to the data. Rapidly down regulated genes were identified based on two criteria: a three-fold decrease in mRNA level at 6 hours together with a good fit to two-step linear model of consistent decreases over consecutive time points.
Genome_build: mm9
Supplementary_files_format_and_content: txt

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: Murine AML cell line was cultured in RPMI1640 supplement with 10% FBS and penicillin/streptomycin

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. 1 ug of total RNA was subjected to “not-so-random” (NSR) primer-based RNA-seq library preparation according to protocols described previously (Armour et al. 2009). For the polyA+ tail RNA-seq, the library was made following the instructions of illumina Truseq RNA sample prep kit v2.
For JQ1 RNA-seq timecourse, the RNA-seq evaluation was performed using a custom method. Briefly, amplified cDNA (>2ng) was used to construct Illumina sequencing libraries following the Illumina’s Ultra Low Input mRNA-Seq Guide.  The amplified cDNA was fragmented into 200bp using Covaris acoustic shearing instrument.  The resulting fragments were end-repaired, single A base added, followed by ligation with PE adaptor and amplification by 15 cycles of PCR.  The resulting libraries are expected to show a peak at around 300bp on Bioanalyzer (Agilent).  In order to enrich the reads containing variental tag and sample barcode, we using Dynabeads® mRNA Purification Kit for mRNA Purification (Invitrogen Cat. No. 610-06).  The libraries were heat at 95C for 2min before mixing with polyT magnetic beads.  Then, we incubated the beads at 47C for overnight and run 6-8 cycles of PCR from the elution the next day.   As a result, approximately 50% of the sequencing raw reads will contain variental tags and sample barcodes.

treatment_protocol: For measuring the basal transcripts level, RNA of mouse murine AML RN2 cell were isolated by using TRIzol. For detecting the rapid downregulated genes in response to JQ1, BET bromodomian inhibitor, we treated RN2 cell with 250nM JQ1, BET bromodomain inhibitor, and isolate RNA at indicated time point during 48h time course. \

tag: cell line

tag: barcode

value: ACTCTGG

tag: strain

tag: treatment

value: JQ1 treatment for 2h


title: xHomo-6


title: xHomo-5


title: xHomo-3


title: xHomo-2


title: xHomo-4


title: xHet-3

source_name: xHet_E9.5 embryo

value: xHet


title: xHet-1


title: TSS_RN2_1

data_processing:
Mapping of 4C data was performed using 4Cseqpipe, as described in (van de Werken et al. 2012). 4Cseqpipe analyzes 4C-seq experiments by including packages that allow sequence extraction, mapping, normalization, and plotting of cis-contact profiles around viewpoints. Custom restriction site tracks were built using the -build_re_db option of 4Cseqpipe for the mm8 mouse genomic version (UCSC) with HindIII and DpnII as first and second restriction cutters, respectively. A total of 3618110 PE 100x100 reads (2014321 rep1 + 1603789 rep2) were obtained for the MycTSS viewpoint experiments, and 3649354 PE 100x100 reads (2059310 rep1 + 1590044 rep2) for Enh3. Paired-end 2 reads from the first biological replicates were used for analysis in the 4Cseq pipeline as these contain the HindIII restriction site fragment. PE 2 reads were trimmed to a size of 53bp which include the 4C HindIII amplification primer in the beginning of the read (GCTTCCTTGCCTAAGACAAGCTT, 23bp) followed by 30bp of interacting sequence. These processed reads were mapped to the custom mm8 tracks with the in-built 4Cseqpipe mapper. Near-cis domainograms were generated for the whole chr15 for both viewpoints using the median stat_type and plotting the 80th quantile of the distribution of normalized contact intensities for 10Kb windows in MycTSS_4C and in Enh3_4C. These values were put into wig files for visualization using the UCSC genome browser mm8 version, where data range of the vertical axis was set to the ~7% and 8% of the maximal normalization value for MycTSS_4C and Enh3_4C, respectively, to deal with the fact that the majority of data are very close to the viewpoint.
2,958,300 PE 100x100 reads were obtained for Myc TSS shBrg1 (1465526 rep1 + 579006 rep2) and 4,860,980 (2430490 rep1 + 1400170 rep2) for Myc TSS Rluc viewpoints. For calculating the mean value of the 4C-seq data, P1+P2 (paired-end read 1 + 2) reads from replicate 1 of Brg1 and Rluc were mapped against the mm8 mouse genome using bowtie with max two mismatches and binned into 1kb windows for the whole sequence of chromosome 15. Total number of mapped reads were then normalized using rep1 TSS RN2 viewpoint read number as reference. Sliding windows of 10kb were made for chromosome 15. For each 10kb sliding window, the highest 1kb bin value in the window was substituted for the second highest value to avoid outlier bias for mean calculation.
Genome_build: mouse mm8
Supplementary_files_format_and_content: wig

extract_protocol:
Isolated nuclei were digested for 4 hrs with 200U HindIII at 37°C, followed by overnight incubation with 400U HindIII, and a final 4hr incubation with 200U HindIII. Then, samples were ligated overnight in 7ml using 50U T4 DNA ligase (at 16°C. Ligation circles were phenol-chloroform extracted and ethanol precipitated with glycogen as a carrier. These were further digested with 50U of DpnII  overnight at 37°C, followed by heat inactivation for 25 min at 65°C, and ligation in 14ml with 100U T4 DNA ligase at 16°C. These trimmed circles (4C template) were phenol-chloroform extracted and ethanol precipitated with glycogen as a carrier.
4C-seq library construction (Splinter et al. Nat Methods. 2012)

treatment_protocol: Murine AML cell lines RN2 cell line or shRNA transduced RN2 cell lines are used for 4C-seq experiments. Before crosslinking, RN2 cells transduced with indicated constructs were treated with 1ug/ml doxycycline to induce shRNA expression for 48h. TRMPV_Rluc is negative control shRNA targeting Renilla luciferase. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.


title: xHet-2


title: xHomo-1


title: Het-3 sperm


title: WT_rep3

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

description: Sample 3

data_processing:
OLB (Off-line base caller) 1.9
Raw RNA sequence data were processed through a number of sequential steps;
First, adapter sequences were removed from the raw sequences with an ad-hoc script using a non-conservative approach. Thus, even the shortest representations (one nucleotide) were eliminated. We aligned the sequences with the WS231 genome version using Tophat and results were sorted and indexed using Samtools. Coverage vectors for each sample were extracted under R statistical environment using Rsamtools library. C.elegans GTF annotation from Ensembl was applied as reference for the exon genomic ranges, parsed into R data structures. Exon expression was calculated as the median coverage for every exon genomic range as stated by annotation. Exon expression data from our 9 different samples were normalized by quantile normalization and locus expression was calculated by calculating the median of all the expression hits from distinct exons annotated to a single locus.
Library siggenes in R was applied to select the differentially expressed loci using the FDR-based SAM method. Genes presenting a d-value grater than 4 were considered altered significantly.
Genome_build: WS231 (WormBase Version WS231 at http://www.wormbase.org)
Supplementary_files_format_and_content: tab-delimited text file including quantile normalized transcripts expression for each Sample calculated as the median of all the expression hits from distinct exons annotated to a single locus.

organism: Caenorhabditis elegans

source_name: young adult worm_WT

growth_protocol: To simultaneously deplete EMR-1 and LEM-2, BN19 animals homozygous for the lem-2(tm1582) allele were subjected to emr-1 RNAi-mediated knockdown. RNAi feeding bacteria were grown in LB at 37C with agitation (180 rpm) until OD600=0.8 and then induced with 1 mM IPTG during 19 h at 20C. The feeding bacteria expressed dsRNA corresponding to either full length emr-1 cDNA or, as negative control, 185 bp of unrelated sequence from the L4440 empty plasmid. The next day, the bacteria was collected and resuspended in 1/20 initial volume of S-medium with 1 mM IPTG. Approximately 40,000 synchronized L1 worms obtained by hypochlorite treatment and hatching overnight at 20C without food were grown in 50 mL of S-medium containing 5 mL of resuspended RNAi bacteria, 100 µg/mL ampicillin and 1 mM IPTG at 20C during 53h in continuous agitation (180rpm). At this point the cultures were enriched in non-gravid young adults. Worms were recovered, frozen immediately in liquid N2 and kept at -80C until further processing.

extract_protocol:
RNA extraction was performed using 20-30 mg of worms. The worm cuticle was ruptured by 3 rounds of freezing in liquid N2 and thawing at 30C and RNA was purified using an RNeasy Mini kit (Qiagen).
Sequencing libraries were prepared using the TruSeq RNA sample preparation kit according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Briefly, polyA-containing mRNA was isolated from 1 µg of total RNA using poly-T oligo-attached magnetic beads. This mRNA was fragmented into 200 bp fragments length using divalent cations under elevated temperature. The cleaved RNA fragments were reverse transcribed into first strand cDNA using Superscript II reverse transcriptase (Invitrogen, Carsbad, CA, USA) and random primers. Next, the second strand was synthesized using DNA polymerase I and RNAse H. After end-repairing, a single ‘A’ was added to cDNA fragments at 3 ‘ end. The cDNAs were then ligated to Illumina Truseq indexed adapters, purified with Ampure XP magnetic beads (Agencourt Bioscience Corporation, Beverly, MA, USA) and then enriched by 15 cycles of PCR amplification to create the final cDNA library. Constructed libraries were validated and quantified using Biorad's Automated Electrophoresis System Experion and qPCR respectively. Pools of 3 indexed libraries were mixed (multiplexed) at equimolar ratios to yield a total oligonucleotide mix of 10 nM.

value: young adult

value: whole organism


title: emr-1(gk119)_rep.2

description: Sample 5

source_name: young adult worm_emr-1(gk119)


title: lem-2(tm1582)_rep.1

description: Sample 6

source_name: young adult worm_lem-2(tm1582)


title: lem-2(tm1582)_rep.2

description: Sample 7


title: emr-1(gk119)_rep.1

description: Sample 4


title: WT_rep2

description: Sample 2


title: Input sequencing in bud-stage embryo rep 3

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Input

data_processing:
Basecalls performed using CASAVA version 1.4
Alignment: sequencing reads were aligned to the zebrafish genome (version danRer6) using Bowtie version 0.12.7 with options "-q --best --strata -m 1 -p 4 --chunkmbs 1024", and only uniquely mapping reads were retained for further analysis.
Peak-calling: Binding events were detected using GPS as previously described (Guo et al. 2010). In GPS, the scaling ratio between IP and control channels was estimated using the median ratio of all 10Kbp windows along the genome. The GPS binding model was initialized to the default and iteratively updated over up to 3 training rounds, and the shape deviation threshold for final peaks was set to -0.2. In this study, we require that reported peaks contain a ChIP-seq enrichment level that is significantly greater than 1.5 times the control channel read count over the same region with p-value <0.001 as tested using a Binomial test.
Domain-calling: Histone mark domains were detected using a 200bp sliding window (offset = 100bp) along the genome, merging neighboring windows that individually contain significantly more signal reads than expected by a global Poisson background model  (p<10^-9) and significantly more signal reads than expected by local Poisson background models parameterized by the input samples (p<10^-9).
Genome_build: danRer6
Supplementary_files_format_and_content: BED: Cdx4 and Sall4 peaks.bed files are conversions of GPS output files to BED format, centered on the GPS binding event location and extended to 100bp width. Chromatin enriched domains are also output in BED format.
Supplementary_files_format_and_content: BIGWIG: WIG files were generated using custom software to summarize read counts overlapping genomic regions. All reads were artificially extended out to 200bp in length. A bin size of 20bp was used for calculating overlapping read counts. WIG files were converted to bigWig using wigToBigWig (UCSC)

organism: Danio rerio

source_name: Bud stage embryo

growth_protocol: Zebrafish were maintained and raised under standard conditions.

extract_protocol:
For each ChIP experiment, ~2000 embryos were carefully staged. 500 embryos were then collected, transferred into PBS containing 20mM Na-butyrate, protease inhibitors (Sigma). Embryos were then transferred to 5ml syringe fitted with 21G needle. After leaving ~500ul buffer above the embryos, embryos were forced through the needle by pushing the pistons to dissociate the embryos. The resulting lysed extract was collected in 2ml eppendorf tubes, and crosslinked by adding formaldehyde solution to final concentration of 1.1%. Crosslinking was conducted for 15 minutes at room temperature while samples were mixed using nutator. After crosslinking, glycine was added to 0.125M to quench the formaldehyde, and incubated on ice for 5 minutes. Tubes were then centrifuged at 470g for 10 minutes at 4C to sediment the cells. The cells were then washed twice with 500ul ice-cold PBS/Na-butyrate/protease inhibitor solution, and flash-frozen and kept at -80C until the ChIP experiment.
ChIP-seq libraries prepared using standard Illumina protocols

treatment_protocol: Wild-type (Tu) embryos were collected at the 1-cell stage, and were kept uninjected, or injected with mRNA for further experiments.

value: whole embryo

value: Tu

tag: chip antibody

value: Input


title: lem-2(tm1582)emr-1(RNAi)_rep.2

description: Sample 9

value: lem-2(tm1582) emr-1(RNAi)


title: WT_rep1

description: Sample 1


title: Input sequencing in bud-stage embryo rep 2

description: Input


title: ChIP-seq H3K27ac in bud-stage embryo

description: Chromatin IP against H3K27ac

value: Anti-Histone H3 (acetyl K27) (Abcam ab4729)


title: ChIP-seq H3K4me3 in bud-stage embryo

description: Chromatin IP against H3K4me3

value: Anti-Trimethyl-Histone H3 (Lys4) (Millipore 07-473)


title: Mock transfection to IMR90, replicate 2

description:
PolyA-selected RNAs
IMR90.exp.qn

data_processing:
Basecalls performed using CASAVA version 1.7
All RNA-seq data were mapped to the human reference genome (hg19) using Bowtie version 0.12.8 (Trapnell et al., 2009), allowing at most five genomic matches but choosing the best one (-n 1 -e 240 -m 5 --best --strata).
To measure expression level, we estimated both reads per kilobases per million reads (RPKM) values and reads per million reads (RPM) values based on RefSeq annotation (Aug-22-2011 version).
Quantile normalization was performed to reduce technical global bias of expressions between replicates and between wild type and transfected cells.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for pUC19_1, pUC19_2, miR-124_1, miR-124_2, miR-155_1, and miR-155_2

organism: Homo sapiens

source_name: IMR90 cells

extract_protocol:
After 24 hours, cells were harvested, and RNA was extracted using TRI-reagent (Life Technologies).
After RNA isolation, poly(A)+ RNA was selected using oligo(dT) beads (Invitrogen). RNA-seq libraries were prepared by either a ligation-based approach, as previously described (Guo et al., 2010), or a dUTP-based approach (Bioo Scientific), according the manufacturer’s directions.

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Invitrogen) and 100 nM miRNA duplex or pUC19, as described by the manufacturer.

tag: transfection

value: IMR90 cells

value: RNA-seq fastq


title: Mock transfection to IMR90, replicate 1

description:
PolyA-selected RNAs
IMR90.exp.qn


title: RNA_adult_female_frag

city: Vienna

first: Michaela

last: Schwaiger

address: Althanstr. 14

country: Austria

institute: University of Vienna

data_processing:
Reads were mapped to the genome using BWA with default settings and those with a quality score < 30 were discarded.
Peakfinding on each p300 and RNA Polymerase II dataset was performed using the peakzilla software, using Input reads as control. Peaks with > 2-fold enrichment over control and a score > 3 (p300) or > 5 (Pol2) were considered significant for each replicate, if they overlapped more than 2-fold enriched peaks in the other replicate. Finally, the significant peaks of the two replicates were merged.
For chromatin modifications, the bam files were converted to bed files and reads were counted in 200bp windows aross the whole Nematostella genome using bedtools.
The RNAseq reads were aligned to our gene models using tophat with default settings. FPKM values were calculated using cuffdiff v1.3.0. All RNA-seq experiments for each developmental stage were combined for calculating the stage specific FPKM values.
Genome_build: Nemvec1
Supplementary_files_format_and_content: ChIP-Seq: bed, chromatin: read counts in 200bp windows across the genome, p300 and RNA Pol2: genomic location of significant peaks

organism: Nematostella vectensis

source_name: adult female polyps

growth_protocol: Nematostella vectensis was grown in 1/3rd artificial seawater and fed with brine shrip larvae.

extract_protocol:
After removal from jelly, eggs were fixed in 2% formaldehyde for 12 minutes at room temperature. Cross-linking was stopped by adding 125mM glycine followed by rotation for 10 min at 4 degrees.  After washing with cold PBS and HEG Buffer (50mM HEPES pH7.5, 1mM EDTA, 20% Glycerol), embryos were snap-frozen and stored at -80 degrees. Embryos were homogenized in Nuclei Buffer 1 (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100, 1mM DTT) and centrifuged at 500g for 3 minutes, after which the pellet containing debris was discarded. After another centrifugation at 2000g for 10 minutes the pellet contained nuclei, which were washed with Nuclei Buffer 2 (50mM HEPES pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100) and finally resuspended in Lysis Buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 0.1% DOC, 01% Triton X-100, 0.1% SDS). After shearing the chromatin to 100-200bp using a Covaris Instrument and removing the non-soluble material, we blocked the chromatin with pre-blocked (1mg/ml tRNA, 1mg/ml BSA) protein A beads CL-4B (GE Healthcare 71-7090-00 AE). At this point we removed a small aliquot of chromatin for Input DNA and incubated the remaining chromatin with the desired antibodies, rotating at 4 degrees over night. We then added pre-blocked protein A beads to bind the antibodies and washed the beads twice with Lysis Buffer, twice with DOC Buffer (10mM Tris pH8, 0.25M LiCl, 0.5% NP-40, 0.5% DOC, 1mM EDTA), and once with TE Buffer. Chromatin was eluted from the beads with Elution Buffer (1%SDS, 0.1M NaHCO3) and de-crosslinked. RNA was isolated using Trizol.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or HiSeq machine following the manufacturer's protocols. Strand-specific RNA-seq libraries were prepared using dUTP incorporation during the 2nd strand synthesis.

value: adult polyps

tag: gender

value: female

tag: mrna isolation

value: polyA selection (Illumina)

tag: fragmentation

value: RNA fragmentation (Illumina protocol)

tag: library method

value: Illumina RNAseq

tag: read length


title: RNA_adult_female_ss

value: ribosomal RNA depletion (Invitrogen ribo-minus)

value: sonication

value: Illumina RNAseq, strand specific


title: RNA_adult_female


title: RNA_gastrula_ss

source_name: gastrulae (24h)

value: gastrulae (24h)


title: RNA_gastrula


title: miR-124 transfection to IMR90, replicate 2

description:
PolyA-selected RNAs
IMR90.exp.qn


title: RNA_planula

source_name: planulae (4 days)

value: planulae (4 days)


title: lem-2(tm1582)emr-1(RNAi)_rep.1

description: Sample 8

tag: strain background

value: young adult

value: whole organism


title: Pol2_planula

value: unphosphorylated CTD of RNA Polymerase II

value: ChIP-Seq


title: Pol2_gastrula

tag: chip antibody source

value: mouse monoclonal antibody against the unphosphorylated C-terminal repeat of RNA Polymerase II (8WG16, gift from C. Wirbelauer)


title: p300_gastrula

value: Nematostella p300/CBP

value: We used a 146 aa peptide of the C-terminus of Nematostella p300 protein, including a N-terminal 10x His tag for immunization of two rabbits each. The p300 peptide sequence was HPNSQAQQPPGQHYQAKQMQPRLMSPQAPPPMSPQQGGLPSQSPRPVMSPQPHANTLSPRQQTMSPAHPQQSLTSPRPAQSPHQSHMDPSNLGDKPNLFTQPLSARMTLTPLAAPSESDMSLGQEDSETVPPLTPQDQLTKFVENL. P300 antisera and purified p300 antibodies were generated by Primm (www.primmbiotech.com).


title: miR-124 transfection to IMR90, replicate 1

description:
PolyA-selected RNAs
IMR90.exp.qn

value: IMR90 cells

value: RNA-seq fastq


title: p300_planula


title: Mock transfection to Huh7, replicate 3

description:
PolyA-selected RNAs
Huh7.exp.qn

source_name: Huh7 cells

value: Huh7 cells


title: Mock transfection to Huh7, replicate 4

description:
PolyA-selected RNAs
Huh7.exp.qn


title: Input_planula


title: miR-124 transfection to Huh7, replicate 1

description:
PolyA-selected RNAs
Huh7.exp.qn


title: Mock transfection to Huh7, replicate 1

description:
PolyA-selected RNAs
Huh7.exp.qn


title: miR-155 transfection to Huh7, replicate 2

description:
PolyA-selected RNAs
Huh7.exp.qn


title: miR-155 transfection to Huh7, replicate 1

description:
PolyA-selected RNAs
Huh7.exp.qn


title: Mock transfection to Huh7, replicate 2

description:
PolyA-selected RNAs
Huh7.exp.qn


title: miR-124 transfection to Huh7, replicate 2

description:
PolyA-selected RNAs
Huh7.exp.qn


title: Hippocampus_8mon 2

status: Public on Dec 01 2013

city: Ansan

first: Hyemyung

last: Seo

address: Hanyang University

description: Gene expression data from hippocampus of littermate control at 8 months of age

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
smallRNA-seq reads were aligned to mirbase using bowtie version2 with one mismatch
readcount were calculated using a in house perl script
Supplementary_files_format_and_content: tab-delimited text files include readcount for each miRNA

source_name: Hippocampus, littermate

growth_protocol: Tg6799 transgenic mice were purchased from The Jackson Laboratory (USA) and were housed under a 12h light-dark cycle with free access to food and water

extract_protocol:
RNA samples were isolated fromhippocampus of mouse brain region in TRI-Reagent (Sigma-Aldrich, St. Louis, MO) and total RNA was isolated using a phenol/chloroform protocol (Sigma-Aldrich).
For the construction of micro RNA libraries using the IonTotal RNA-Seq Kit v2 and Ion Xpress™ RNA-Seq Barcode kit(Lifetechnologies, USA).The  Ion Total RNA-Seq Kit v2 (Lifetechnologies, USA) was used for the preparation of micro RNA libraries according to the manufacturer's instructions starting with 100ng total RNA. Template is prepared from the libraries using the Ion OneTouch™ System (Lifetechnologies, USA) and sequenced on the Ion PGM™ Sequencer (Lifetechnologies, USA).

tag: tissue

value: Brain Hippocampus

tag: genotype

value: littermate

tag: age

value: 8 months

value: female


title: Hippocampus_8mon 3

description: Gene expression data from hippocampus of AD mutant mouse at 8 months of age

source_name: Hippocampus, mutant

value: AD mutant


title: Hippocampus_8mon 4


title: Hippocampus_4mon 4

description: Gene expression data from hippocampus of AD mutant mouse at 4 months of age

value: 4 months


title: Hippocampus_4mon 2

description: Gene expression data from hippocampus of littermate control at  4 months of age


title: Hippocampus_4mon 1

description: Gene expression data from hippocampus of littermate control at 4 months of age


title: Hippocampus_4mon 3


title: Hippocampus_8mon 1


title: Small-tailed Han sheep RNA-Seq

city: Tai'an

first: Dong

last: fei

state: Shandong

address: No.61 Daizong street

country: China

institute: Shandong Agricultural University

description:
SH_L1_1.fq
SH_L1_2.fq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ovis aries whole genome using SOAP2 software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
fqlfiles generated using LIF (Large Text File) Viewer 5.2u
Genome_build: CSIRO oar2.0 (http://www.livestockgenomics.csiro.au/sheep/oar2.0.php)

organism: Ovis aries

source_name: muscle

extract_protocol:
Muscles 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

tag: breed

value: Small-tailed Han sheep

value: biceps brachii


title: Dorper sheep RNA-Seq

description:
DP_L1_1.fq
DP_L1_2.fq

value: Dorper sheep


title: CCsNphT7BCn_r2

city: Tsurumi, Yokohama

first: Minami

last: Matsui

state: Kanagawa

address: 1-7-22 Suehiro-cho,

department: Biomass Engineering Program

country: Japan

institute: Riken Yokohama Institute

description: rRNA-depleted total RNA

data_processing:
The RNA-seq data analysis was performed using CLC Genomics Workbench 6 software (CLC bio, Denmark).
Sequence reads were pre-processed to trim low-quality reads and filter reads shorter than 20 bp.
The qualified sequence reads were mapped to the Synechocystis sp. PCC 6803 genome, allowing a maximum of two mismatches.
The transcript levels were expressed as reads per kilobase of exon model per million mapped reads (RPKM)
Genome_build: NC_000911
Supplementary_files_format_and_content: The tab-delimited .txt files include RPKM abundance measurements for each sample

organism: Synechocystis sp. PCC 6803

source_name: recombinant Synechocystis sp. cells

growth_protocol: cells cultivated for 7 days in N-deficient BG-11 under photoautotrophic condition.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Invitrogen, USA) in combination with PureLink RNA Mini Kit (Invitrogen, USA) according to manufacturer’s protocol.
The cDNA libraries were constructed from total RNA depleted of rRNA using Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina, USA) according to the manufacturer’s specifications.

tag: phenotype

value: high PHA-producing potential


title: mESC_K9me2_helicos

city: Shanghai

first: Zhen

last: Shao

address: 320 Yueyang Road

institute: Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

description: wild type mouse ES cells

data_processing:
Basecalls performed using Solexa pipeline for data generated by HiSeq 2000 or Helicos pipeline for data generated by Helicos Heliscope.
Sequencing reads were aligned to mouse genome assembly mm9 using Illumina software pipeline (data generated by HiSeq 2000) or Helisphere (data generated by Helicos).
Only ChIP-seq reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read bed file (reporting the coordinates of aligned reads) which were converted from BAM files by using BAMtools; wig file which contain the read densities normalized by sequencing depth; and peak bed file which were outputed by MACs (reporting the coordinates of peaks called by MACS).

source_name: Mouse ES cells

growth_protocol: mESCs were grown in standard mouse ES cells media with LIF

extract_protocol:
[Illumina] Purified ChIP DNA was measured in Qubit (Invitrogen). 2-10ng of purified ChIP DNA was used to prepare sequencing libraries, using NEB next generation ChIP sequencing Kit and Illumina ChIP seq kit according to the manufacturer's instructions.
[Helicos] ChIP DNA was processed for 3' polyA tailing, followed by 3'ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing.

treatment_protocol: mESCs were crosslinked with 1% formaldehyde, reaction was quenched by 0.125M glycine, trypsinized, sonicated in SDS Chip buffer, followed by incubation with 5µg of antibodies overnight. Protein A or G beads were added to ChIP reactions to immunoprecipitate chromatin. Beads were washed several times, de-crosslinked at 65ºC overnight, followed by RNase and Proteinase K treatment to collect ChIP-ed DNA, which was ready for library preparation. For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol.

value: agouti

value: male

tag: cell type

value: ESC

tag: genotype/variation

value: wild type

value: H3K9me2 (ab1220), Abcam


title: CCsABCn_r2

description: rRNA-depleted total RNA

tag: strain

value: CCsABCn

value: medium PHA-producing potential


title: pTKP2031V_r2

description: rRNA-depleted total RNA

value: low PHA-producing potential


title: CCsABCn_r1

description: rRNA-depleted total RNA


title: pTKP2031V_r1

description: rRNA-depleted total RNA


title: CCsNphT7BCn_r1

description: rRNA-depleted total RNA


title: mESC_K36me2_helicos

description: wild type mouse ES cells

tag: chip antibody

value: H3K36me2 (07-274), Millipore


title: HBrateC75

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
The adapter sequences were trimmed from raw sequence reads.
Remaining small RNA sequences were chopped to a maximum length of 50 nucleotides.
Reads shorter than 18 nucleotides were discarded.
Reads were aligned to Clostridium genome using Tophat v2.0.5, allowing 0 mismatches
Genome_build: Clostridium acetobutylicum (http://www.ncbi.nlm.nih.gov/genome/1022?project_id=57677)
Supplementary_files_format_and_content: tag count file

organism: Clostridium acetobutylicum

source_name: High butyric acid stress_75 min

growth_protocol: Cultures of C. acetobutylicum were grown in batch mode in 4-L bioreactors up to the mid-exponential phase of growth (O.D ~ 1.0), at which point the cultures were stressed with three different concentrations of butanol and butyric acid, respectively, in 3 biological-replicate experiments each. For butanol stress experiments, the cultures were stressed with 30 mM (low), 60 mM (medium) and 90 mM (high), while for butyric-acid stress, 30 mM (low), 40 mM (medium) and 50 mM (high) butyrate concentrations were used. Cultures were sampled at 15, 30, 60 and 75 min post stress for RNA isolation and sequencing.

extract_protocol:
Samples for RNA isolation were collected by centrifugation at 5000 rpm at 4°C for 10 min and the pellets were stored at -80°C.  RNA isolation was carried out using the Qiagen’s miRNeasy Mini kit (Jones et al, 2008). After RNA extraction, mRNA and sRNA were enriched by using Microbe Express kit from Ambion ® kit as per the manufacturer’s protocol.
The Ovation Prokaryotic RNA-Seq System (NuGEN® Technologies, Inc, San Carlos, CA) was used to synthesize cDNA from 500 ng of enriched RNA. 50 μL of cDNA was used to construct libraries using the TruSeq DNA Sample preparation kit .

tag: stressed with

value: 50mM butyric acid

tag: time point

value: 75 min post stress


title: HBrateD75


title: HBrateB60

source_name: High butyric acid stress_60 min

value: 60 min post stress


title: HBrateB75


title: HBrateC30

source_name: High butyric acid stress_30 min

value: 30 min post stress


title: HBrateD15

source_name: High butyric acid stress_15 min

value: 15 min post stress


title: HBrateD60


title: HBrateB15


title: HBrateD30


title: MBrateD60

source_name: Medium butyric acid stress_60 min

value: 40mM butyric acid


title: MBrateB60


title: HBrateC15


title: MBrateC75

source_name: Medium butyric acid stress_75 min


title: MBrateB75


title: MBrateC30

source_name: Medium butyric acid stress_30 min


title: MBrateD30


title: MBrateD75


title: MBrateB30


title: MBrateB15

source_name: Medium butyric acid stress_15 min


title: MBrateC15


title: MBrateD15


title: MBrateC60


title: HBrateC60


title: LBrateB75

source_name: Low butyric acid stress_75 min

value: 30mM butyric acid


title: LBrateA75


title: LBrateA60

source_name: Low butyric acid stress_60 min


title: LBrateC75


title: LBrateB60


title: HBrateB30


title: LBrateA30

source_name: Low butyric acid stress_30 min


title: LBrateC30


title: LBrateB30


title: LBrateB15

source_name: Low butyric acid stress_15 min


title: LBrateC15


title: HBnolB75

source_name: High butanol stress_75 min

value: 90mM butanol


title: HBnolC75


title: LBrateA15


title: HBnolC60

source_name: High butanol stress_60 min


title: HBnolB60


title: HBnolA60


title: HBnolC30

source_name: High butanol stress_30 min


title: HBnolB15

source_name: High butanol stress_15 min


title: HBnolA30


title: HBnolC15


title: LBrateC60


title: MBnolC75

source_name: Medium butanol stress_75 min

value: 60mM butanol


title: HBnolA15


title: MBnolC60

source_name: Medium butanol stress_60 min


title: MBnolA75


title: MBnolB60


title: MBnolB75


title: MBnolC30

source_name: Medium butanol stress_30 min


title: MBnolB30


title: MBnolA60


title: MBnolB15

source_name: Medium butanol stress_15 min


title: MBnolC15


title: MBnolA15


title: HBnolA75


title: MBnolA30


title: LBnolC75

source_name: Low butanol stress_75 min

value: 30mM butanol


title: LBnolC60

source_name: Low butanol stress_60 min


title: LBnolA75


title: LBnolA60


title: LBnolC30

source_name: Low butanol stress_30 min


title: HBnolB30


title: Lu028

city: Stanford

first: Zhipeng

last: Lu

state: CA

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu028.final.rpkm: dm3
Lu028.newregions.txt: dm3
Lu028.wig: dm3

organism: Drosophila melanogaster

growth_protocol: Oregon Red or transgenic newly-eclosed fruitflies were grown on corn syrup solids with yeast for 2~4 days before ovary dissection. HeLa cells are cultured in DMEM +10%FBS + penicilin/streptomycin

extract_protocol: Lysates were clarified from dissected Drosophila ovaries or HeLa cells and RNA-Sm protein complexes were isolated with antibody. RNA was purified from the immunoprecipitate, reverse transcribed and made into doublestranded DNA.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was fragmented, ligated to adapters and PCR amplified with Illumina primers for 15 cycles. The resultant DNA was purified from an agarose gel and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: nosGal4 VFP-LSm11

value: ovary

tag: rip antibody

value: GFP


title: LBnolB30


title: Lu027

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu027.final.rpkm: dm3
Lu027.newregions.txt: dm3
Lu027.wig: dm3


title: LBnolC15

source_name: Low butanol stress_15 min


title: Lu020

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu020.final.rpkm: dm3
Lu020.newregions.txt: dm3
Lu020.wig: dm3

value: Tralpt


title: LBnolB15


title: NS_D75

source_name: Non-stress control_75 min

value: none (no-stress control)

value: 75 min


title: LBnolA15


title: Lu019

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu019.final.rpkm: dm3
Lu019.newregions.txt: dm3
Lu019.wig: dm3


title: NS_B75


title: LBnolB60


title: NS_A75


title: NS_D60

source_name: Non-stress control_60 min

value: 60 min


title: LBnolB75


title: Lu024

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu024.final.rpkm: dm3
Lu024.newregions.txt: dm3
Lu024.wig: dm3

growth_protocol: Oregon Red or transgenic newly-eclosed fruitflies were grown on corn syrup solids with yeast for 2~4 days before ovary dissection.

extract_protocol: Lysates were clarified from dissected Drosophila ovaries and RNA-Sm protein complexes were isolated with antibody. RNA was purified from the immunoprecipitate, reverse transcribed and made into doublestranded DNA.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was fragmented, ligated to adapters and PCR amplified with Illumina primers for 15 cycles. The resultant DNA was purified from an agarose gel and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Oregon R


title: Lu014

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu014.final.rpkm: dm3
Lu014.newregions.txt: dm3
Lu014.wig: dm3

value: nos Gal4 VFP-SmB


title: Lu025

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu025.final.rpkm: dm3
Lu025.newregions.txt: dm3
Lu025.wig: dm3


title: Lu013

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu013.final.rpkm: dm3
Lu013.newregions.txt: dm3
Lu013.wig: dm3


title: NS_D30

source_name: Non-stress control_30 min

value: 30 min


title: NS_B60


title: Lu023

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu023.final.rpkm: dm3
Lu023.newregions.txt: dm3
Lu023.wig: dm3


title: Lu016

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu016.final.rpkm: dm3
Lu016.newregions.txt: dm3
Lu016.wig: dm3


title: Lu026

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu026.final.rpkm: dm3
Lu026.newregions.txt: dm3
Lu026.wig: dm3


title: Lu012

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu012.final.rpkm: dm3
Lu012.newregions.txt: dm3
Lu012.wig: dm3

value: nos Gal4 VFP-SmE


title: Lu015

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu015.final.rpkm: dm3
Lu015.newregions.txt: dm3
Lu015.wig: dm3


title: Lu011

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu011.final.rpkm: dm3
Lu011.newregions.txt: dm3
Lu011.wig: dm3


title: NS_B30


title: LBnolA30

value: 30 min post stress


title: NS_D15

source_name: Non-stress control_15 min

value: 15 min


title: NS_A30


title: NS_B15


title: Lu010

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu010.final.rpkm: dm3
Lu010.newregions.txt: dm3
Lu010.wig: dm3


title: Lu008

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu008.final.rpkm: dm3
Lu008.newregions.txt: dm3
Lu008.wig: dm3

value: nos Gal4 VFP-SmD3


title: Lu009

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu009.final.rpkm: dm3
Lu009.newregions.txt: dm3
Lu009.wig: dm3


title: NS_A15

data_processing:
The adapter sequences were trimmed from raw sequence reads.
Remaining small RNA sequences were chopped to a maximum length of 50 nucleotides.
Reads shorter than 18 nucleotides were discarded.
Reads were aligned to Clostridium genome using Tophat v2.0.5, allowing 0 mismatches
Genome_build: Clostridium acetobutylicum (http://www.ncbi.nlm.nih.gov/genome/1022?project_id=57677)
Supplementary_files_format_and_content: tag count file


title: Lu006

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu006.final.rpkm: dm3
Lu006.newregions.txt: dm3
Lu006.wig: dm3


title: Lu005

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu005.final.rpkm: dm3
Lu005.newregions.txt: dm3
Lu005.wig: dm3


title: NS_A60


title: Lu007

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu007.final.rpkm: dm3
Lu007.newregions.txt: dm3
Lu007.wig: dm3


title: Lu004

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu004.final.rpkm: dm3
Lu004.newregions.txt: dm3
Lu004.wig: dm3


title: Lu003

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu003.final.rpkm: dm3
Lu003.newregions.txt: dm3
Lu003.wig: dm3


title: Lu002

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu002.final.rpkm: dm3
Lu002.newregions.txt: dm3
Lu002.wig: dm3


title: Twin-DS-iPSC Rep3

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalling performed with CASAVA version 1.8
Mapping performed with BWA version 0.5.9-r16, default parameters
Genome_build: hg19
Supplementary_files_format_and_content: text file: chromosome, start, end, gene name, strand, RPKM value for each sample

source_name: Twin_Trisomy 21_iPSC

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy MiniKit according to the manufacturer’s protocol (Invitrogen).
Illumina TruSeq™ RNA Sample Preparation kit

tag: disease

value: Trisomy 21

value: induced pluripotent stem cells


title: Twin-DS-iPSC Rep2


title: Twin-DS-iPSC Rep1


title: Twin-N-iPSC Rep1

value: Control (euploid)


title: A2780-p181a_2

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

data_processing:
Transcriptome raw reads from Illumina HiSeq 2000 were mapped to the human reference genome
The coverage over the length of the gene is variable due to various biases inherent to the sequencing and sample preparation process. To avoid problems arising from this, we generated a density profile using windows of 50 bp sliding over the length of each gene, and the median of this density profile was picked as the representative coverage for the gene using an in-house mRNA-seq expression profile pipeline. The coverage is corrected using log-transformation and quantile normalization. Putative miRNA targets were predicted using TargetScan (http://www.targetscan.org) and miRConnect (http://mirconnect.org).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Ovarian cancer cell line

growth_protocol: A2780 cellswere cultivated  in DMEM media supplemented with 10% FBS and 1% Penicillin-Streptomycin (recommended media). Cells were cultured in a humidified atmosphere (5% CO2) at 37°C. Trypsin (0.25%)/EDTA solution was used to detach the cells from the culture flask for passaging.

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen)  from two polyclonal pools of A2780 cells expressing exogenous miR-181a (p181a #1 and p181a #2) and pBABE contro.l
The Illumina RNASeq kit was used to prepare sequencing libraries. The method is as follows: 1 μg of high quality total RNA was incubated with oligo(dT) magnetic beads (SeraMag) in order to enrich for mRNA with poly-A tails. Eluted RNA was randomly cleaved by incubation at 94°C with a magnesium buffer. The RNA is ethanol-precipitated and then reverse transcribed (Invitrogen SuperScript II). DNA polymerase is added to generate a second strand. dsDNA after second strand synthesis contains ends with 5´ and 3´ overhangs, and these are filled in using T4 polymerase and T4 polynucleotide kinase resulting in a blunt-ended DNA molecule. Then a deoxyadenosine (dA) 5´ tail is added to DNA strands using the Klenow fragment (exo-). dsDNA adapters with 3´ thymidine overhangs are ligated to the dA-tailed library using T4 ligase. The library was then size selected on a 2% agarose gel, and amplified with 15 cycles of PCR (NEB Phusion polymerase). This procedure adds the sequences needed for binding to the Illumina flow cell and sequencing primer-binding sites. RNA-Seq libraries were sequenced using the Illumina HiSeq 2000 for a 100nt read length. Transcriptome raw reads from Illumina HiSeq 2000 were mapped to the human reference genome (hg19). The coverage over the length of the gene is variable due to various biases inherent to the sequencing and sample preparation process. To avoid problems arising from this, we generated a density profile using windows of 50 bp sliding over the length of each gene, and the median of this density profile was picked as the representative coverage for the gene using an in-house mRNA-seq expression profile pipeline. The coverage is corrected using log-transformation and quantile normalization.

tag: cell line

tag: expression

value: p181a#2( clone 2 expressing miR-181a)

tag: tumor histology

value: ovarian cancer cell line derived from an undifferentiated ovarian tumor


title: Twin-N-iPSC Rep3


title: Lu001

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
Lu001.final.rpkm: dm3
Lu001.newregions.txt: dm3
Lu001.wig: dm3

value: ovary


title: Twin-N-iPSC Rep2


title: A2780-pBABE

value: pBABE vector


title: TUTase KD

first: Peng

last: Du

state: MA

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

data_processing:
18-30nt small RNA sequences were used for analysis, after removing the adaptor sequences.
Bowtie program (http://bowtie-bio.sourceforge.net/index.shtml) was used for aligning small RNAs to annotated human miRNA sequences in miRBase database (http://www.mirbase.org), and two mismatches were permitted.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include small RNA sequences and reads number

source_name: TUTase KD

extract_protocol:
50ug of Trizol-purified total RNA (Invitrogen) was fractionated using miRvana columns (Invitrogen) and 300ng of <200nt RNA was used in the cloning reactions.Resulting libraries were gel purified from a NativePage 4-16% Bis-tris acrylamide gel (Life Technologies #BN1002BOX) and subjected to Illumina sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa

value: TUTase knock-down by shRNA


title: Twin-N-iPSC Rep4


title: cell.alpha

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
adapter trimming: 3' Solexa or Illumina adapter sequence was trimmed from reads allowing up to 1 mismatch per 4 bases.
alignment: Trimmed reads were aligned to mature miRNAs, RefSeqs, and human genome using ELAND and allowing up to 2 mismatches
family grouping: mature miRNAs that shared reads with lengths between 19 and 25bp were put into ad hoc groups for reporting read counts
read taillying: reads were tallied for groups of miRNAs then normalized to reads per million
differential expression: reads per million where quantile normalized then evaluated for statistical significance using SAMR (T2D v Control only)
Genome_build: mirBase 20

growth_protocol: Human islets and relevant donor information including age, gender, diabetes status, hemoglobin A1c and BMI were obtained from the Islet Cell Resource Center of the University of Pennsylvania, the NIDDK-supported Integrated Islet Distribution Program (iidp.coh.org) and the National Disease Research Interchange. The donorÕs diabetes status was defined by the patientÕs medical record, and, when available, the hemoglobin A1c.

extract_protocol:
Small RNA was isolated from the islets by using the mirVana miRNA Isolation Kit (Ambion Cat# AM1560).
The glucose experiment and sorted alpha/beta cells were processed with the Illumina truSeq small RNA kit, whereas the whole islet T2D v CTL experiments were processed with the older v1 pre-truSeq kit from Illumina using the long multi-day protocol. Briefly Illumina's 3' adapter then 5' adapter were ligated to small RNA, then amplified using RT-PCR. RT was done with Illumina's RT primer, then PCR with the Primer 1 and Primer 2. Finally libraries were size selected using a gel and aiming for products which correspond to inserts of 22 to 30nt. Consequently, prior to alignment either the truSeq adapter sequence that begins TGGAATTCTCGGGTGCCAAGG or the v1 adapter sequence that begins with TCGTATGCCGTCTTCTGCTTGT need to be trimmed from the reads.

treatment_protocol:
FACS sorting on dispersed human islets was performed as described in Bramswig, N. C. et al. Epigenomic plasticity enables human pancreatic alpha to beta cell reprogramming. The Journal of clinical investigation 123, 1275-1284,  doi:10.1172/JCI66514 (2013).
15,000 IEQ of human islets obtained from three donors were incubated in 5.56mM glucose for 6 hours. Islets were washed twice in 1x PBS and then divided and re-plated in media containing 1mM, 5.56mM or 16.7mM glucose for 16 hours

tag: condition

value: control

value: alpha cell


title: cell.beta

tag: tissue

value: beta cell


title: CebpaKO H3K27Me3 ChIP-seq 2

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaloes vej 5

department: BRIC/Finsen Laboratory

country: Denmark

institute: University of Copenhagen/Rigshospitalet

data_processing:
Alignment to Mus genome Using bowtie v. 0.12.8 with standard parameters
Processing for coverage calculation: Bedtools version 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files containing read coverage

source_name: Hematopoietic Stem Cells

growth_protocol: In vivo

extract_protocol:
FACS sorting on hematopoietic stem cell markers (Lin- Sca-1+ Kit+)
Kit: NEBNEXT ChIP-seq prep set1 (E6200S)

value: Hematopoietic Stem Cells

tag: compartment

value: LSK (Lin- Sca-1+ Kit+)

tag: antibody

value: H3K27Me3,Cell Signaling, C36B11

value: C57BL/6 cebpa flox/flox;Mx1Cre

value: knock out


title: WT, reps 1-3

city: Gainesville

first: Maurice

last: Swanson

state: Fl

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description:
Total RNA-Protein Complex
BED files from all the 3 bioreps of WT were merged to produce one final processed file.

data_processing:
Library strategy: HITS-CLIP
Raw reads filtered to remove low quality reads by requiring a minimum score of 20 in 4nt barcode positions and an average score of 20 in the following 25 nucleotides.
The filtered reads were then aligned to the mouse reference genome (UCSC mm9) by BWA.
Potential PCR duplicates, as judged from the starting position of genomic mapping and the barcode sequences, were removed to identify unique CLIP tags.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED

source_name: Quadriceps, WT

extract_protocol:
Quadriceps muscle was dissected from WT and Mbnl1-/- mice (15-16 weeks of age), snap frozen and powdered in liquid N2 and crosslinked with UV-light using a Stratalinker 1800 (Stratagene). Cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation.
Immunoprecipitation was performed using Mbnl2-specific antibody ((Santa Cruz Biotechnology); Catalog number: sc 136167), mAb 3B4 and RNA tags were generated using RNase A concentrations of 38.6 U/ml and 0.0386 U/ml for high and low RNase, respectively. RNA tags bound to Mbnl2 were separated on a SDS gel, isolated, purified, precipitated and converted to cDNA libraries. These libraries were tagged with linkers and Illumina-specific sequencing adapters during the preparation and submitted for sequencing on the Illumina Genome Analyzer IIx.

tag: strain/background

value: WT

tag: age

value: 15-16 weeks

value: quadriceps muscle


title: Mbnl1-/-, reps 1-3

description:
Total RNA-Protein Complex
BED files from all the 3 bioreps of Mbnl1-/- were merged to produce one final processed file.

source_name: Quadriceps, Mbnl1-/-


title: CebpaWT H3K27Me3 ChIP-seq 1

tag: cell type

value: wild type


title: CebpaKO H3K4Me3 ChIP-seq 2

value: H3K4Me3, Cell Signaling, C42D

tag: genotype/variation


title: CebpaKO H3K4Me3 ChIP-seq 1

tag: strain


title: CebpaWT H3K4Me3 ChIP-seq 1


title: CebpaWT H3K4Me3 ChIP-seq 2


title: LU047

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
LU047norm.bg.gz: hg19

value: ovary


title: Control

city: Boston

source_name: Control

tag: genotype


title: LU046

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
LU046norm.bg.gz: hg19


title: A2780-p181a_1

value: p181a#1( clone 1 expressing miR-181a)

value: ovarian cancer cell line derived from an undifferentiated ovarian tumor


title: HEK 293 SINV 6hpi

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

description: 15 to 35nt RNA

data_processing:
adapters were identified using the first 8nt of the Illumina v1.5 adapter (Stocks et al, 2012)
reads longer than 17nt were matched to the Human and Sindbis genomes using PaTmaN (Prueffer et al, 2008)
the quality check of the data was conducted as described in (Mohorianu et al, 2011)
the miRNAs were identified using miRcat and miRprof (Moxon et al, 2008)
Genome_build: Human: hg19, GRCh37
Genome_build: Sindbis virus: NC_001547.1 (http://www.ncbi.nlm.nih.gov/nuccore/9790313)
Supplementary_files_format_and_content: tab-delimited tables with miRNAs identified using miRcat and miRprof

source_name: HEK 293 SINV 6hpi

growth_protocol: HEK 293 cells were grown in DMEM Glutamax and 10% FCS

extract_protocol:
The mirVana (Ambion) kit was used according to the manufacturer’s instructions to isolate total RNA for Illumina Solexa sequencing of small RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols
High-throughput sequencing was carried out using v1.5 of the Illumina adapters The total RNA was isolated, reverse transcribed with v1.5 adapters and amplified (18 cycles). The 90-110nt (75nt adapter-adapter) band was excised, corresponding to 15 to 35nt RNA  sequences

treatment_protocol: Cells were infected at an moi 8 of Sindbis virus AR339

value: HEK 293

value: human epithelial kidney

tag: virus

value: Sindbis virus AR339

tag: hours postinfection (hpi)


title: HEK 293 SINV 0hpi

description: 15 to 35nt RNA

source_name: HEK 293 SINV 0hpi

value: uninfected


title: HEK 293 SINV 4hpi

description: 15 to 35nt RNA

source_name: HEK 293 SINV 4hpi


title: HEMn_H3

city: Houston

first: HAI

last: LONG

state: TX

address: 1515 Holcombe Blvd., Unit 425

department: Leukemia

institute: University of Texas MD Anderson Cancer Center

description: Chromatin IP against H3, as a control

data_processing:
HEMn_H3.bed; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

source_name: Human Epidermal Melanocytes, neonatal, lightly pigmented donor (HEMn-LP)

growth_protocol: Melanoma cell lines SK-MEL-28 and LOXIMVI were cultured in Dulbecco’s modiﬁed Eagle's minimal essential medium (DMEM) and RPMI 1640 medium, respectively, supplemented with 2 mM L-glutamine and 10% fetal bovine serum. Two types of normal melanocytes, HEMn-LP and HEMa-LP, were purchased from Invitrogen (Carlsbad, CA) and grown in Medium 254 supplemented with HMGS-2 (Human Melanocyte Growth Supplement-2, PMA-Free) for 3-6 passages before we harvested them. All cells were grown at 37°C in an atmosphere containing 5% CO2. For ChIP-seq experiments, the cultured cells were crosslinked with 1% formaldehyde for 10 minutes when they reached 70%-80% confluency.

extract_protocol: For each chromatin immunoprecipitation (ChIP) reaction, 0.5 million cells were used. ChIP was performed using Dynabeads Protein G (Invitrogen, Carlsbad, CA) as per manufacturer’s protocol. ChIP libraries for sequencing were prepared as per Illumina’s standard protocol (Illumina, San Diego, CA) with minor modifications. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow enzyme (DNA Polymerase I Large Fragment) and T4 polynucleotide kinase (NEB, Ipswich, MA). The blunt phosphorylated DNA fragments were treated with Klenow fragment (3’ to 5’ exo minus) (NEB) and dATP to add an ‘A’ base to the 3’ end. Sequencing adapters were ligated to the ends of the DNA fragments using Quick T4 DNA Ligase (Enzymatics, Beverly, MA) and Genomic Adapter Oligo Mix (Illumina, part # 1000521). The ligation products were size selected by electrophoresis in a 2% agarose gel. A slice corresponding to 300 (± 25) bp size window based on DNA ladder was cut out and DNA is extracted from agarose. Eluted DNA was amplified by 14 cycles of PCR using Phusion High-Fidelity DNA Polymerase (NEB) and Illumina’s PCR primer 1.1 and PCR primer 2.1. Resulting sequencing library was cleaned with AMPure magnetic beads (Agencourt, Beverly, MA) and ready for single-read sequencing on Illumina Genome Analyzer II.

tag: gender

value: Male

value: neonatal

value: normal skin

value: HEMn melanocytes

tag: chip antibody

tag: antibody cat. #

value: Abcam ab1791

tag: antibody lot. #


title: HEMn_H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
HEMn_H3K27me3.bed; genome build: hg18
HEMn_H3K27me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

value: Millipore 07-449


title: CebpaWT H3K27Me3 ChIP-seq 2

value: Hematopoietic Stem Cells

value: LSK (Lin- Sca-1+ Kit+)

value: H3K27Me3,Cell Signaling, C36B11

value: C57BL/6 cebpa flox/flox;Mx1Cre


title: HEMa_H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
HEMa_H3K27me3.bed; genome build: hg18
HEMa_H3K27me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

source_name: Human Epidermal Melanocytes, adult, lightly pigmented donor (HEMa-LP)

value: adult

value: HEMa melanocytes


title: LU045

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
LU045norm.bg.gz: hg19

tag: cell line

value: HeLa

value: ovary

tag: rip antibody


title: LOXIMVI_H3

description: Chromatin IP against H3, as a control

data_processing:
LOXIMVI_H3.bed; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

source_name: melanoma cell line LOXIMVI

value: 58 years adult

tag: tissue

value: malignant melanoma, lymph node metastasis

value: melanoma cell line LOXIMVI


title: HEMa_H3K4me3

description: Chromatin IP against H3K4me3

data_processing:
HEMa_H3K4me3.bed; genome build: hg18
HEMa_H3K4me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

value: Male

value: Millipore 17-614


title: HEMn_H3K4me3

description: Chromatin IP against H3K4me3

data_processing:
HEMn_H3K4me3.bed; genome build: hg18
HEMn_H3K4me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

value: neonatal

value: normal skin


title: HEMa_H3

description: Chromatin IP against H3, as a control

data_processing:
HEMa_H3.bed; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

value: Abcam ab1791


title: SK-MEL-28_H3K4me3

description: Chromatin IP against H3K4me3

data_processing:
SK-MEL-28_H3K4me3.bed; genome build: hg18
SK-MEL-28_H3K4me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

source_name: melanoma cell line SK-MEL-28

value: 51 years adult

value: malignant melanoma, noncutaneous metastasis

value: melanoma cell line SK-MEL-28


title: SK-MEL-28_H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
SK-MEL-28_H3K27me3.bed; genome build: hg18
SK-MEL-28_H3K27me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.

value: Millipore 07-449


title: SK-MEL-28_H3

description: Chromatin IP against H3, as a control

data_processing:
SK-MEL-28_H3.bed; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.


title: LOXIMVI_H3K27me3

description: Chromatin IP against H3K27me3

data_processing:
LOXIMVI_H3K27me3.bed; genome build: hg18
LOXIMVI_H3K27me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.


title: LOXIMVI_H3K4me3

description: Chromatin IP against H3K4me3

data_processing:
LOXIMVI_H3K4me3.bed; genome build: hg18
LOXIMVI_H3K4me3_peaks.txt; genome build: hg18
alignment: Sequenced DNA tags were mapped to human genome hg18 using the Illumina Genome Analyzer Pipeline and uniquely mapped tags were kept. To avoid PCR bias, for the multiple tags that were mapped to the same genomic location, only one copy was kept.
peak: SICER (version 1.03, http://home.gwu.edu/~wpeng/Software.htm) was used to detect peaks using total H3 as control. The window size was set as 200 bp as default. The gap size was determined as recommended by the software, or at most 2 kb. E-value was set at FDR≤5%, which was estimated as E-value divided by the number of identified candidate domains. The FDR cutoff to further filter out the candidate domains by comparing to control was set as 5%.


title: Adult Human Islet T2D ICR08

data_processing:
adapter trimming: 3' Solexa or Illumina adapter sequence was trimmed from reads allowing up to 1 mismatch per 4 bases.
alignment: Trimmed reads were aligned to mature miRNAs, RefSeqs, and human genome using ELAND and allowing up to 2 mismatches
family grouping: mature miRNAs that shared reads with lengths between 19 and 25bp were put into ad hoc groups for reporting read counts
read taillying: reads were tallied for groups of miRNAs then normalized to reads per million
differential expression: reads per million where quantile normalized then evaluated for statistical significance using SAMR (T2D v Control only)
Genome_build: mirBase 20

tag: condition

value: whole islet


title: Adult Human Islet T2D ICRH011


title: Adult Human Islet T2D


title: Adult Human Islet Control CITH037

value: Control


title: Adult Human Islet Control CITH028


title: Adult Human Islet Control CITH026


title: LU048

description: RIP-seq

data_processing:
A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
For HeLa RIP-seq, reads were processed using the Tophat/Cufflinks pipeline
To create the Drosophila wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
To create the human bedgraph files, sequence files were mapped to human genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build:
LU048norm.bg.gz: hg19


title: Islet glucose-1

value: low glucose


title: Islet glucose-5

value: medium glucose


title: Islet glucose-16.7

value: high glucose