title: EL34

city: San Francisco

first: Peter

middle: James

last: Turnbaugh

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

data_processing:
Pre-processing of raw reads: binned according to barcode, trimmed ends to min score = 20 and minimum length = 20, required both pairs, concatenated each trimmed pair
Mapped reads to E.lenta DSM2243 genome (GCA_000024265.1) using SSAHA (version 2; parameters: -best 1 -score 20 -solexa)
The number of transcripts assigned to each gene was then tallied.
Genome_build: ASM2426v1
Supplementary_files_format_and_content: Counts files were generated. Values are total reads assigned and fraction reads assigned (#reads/total reads).

organism: Eggerthella lenta DSM 2243

source_name: E.lenta DSM2243 transcriptome

growth_protocol: Exponential and stationary phase growth in rich medium containing 0.25% or 1.25% arginine

extract_protocol: Microbial cells were lysed by a bead beater (BioSpec Products), total RNA was extracted with phenol:chloroform:isoamyl alcohol (pH 4.5, 125:24:1, Ambion 9720), purified using MEGAClear columns (Ambion), and rRNA was depleted via subtractive hybridization (MICROBExpress, Ambion, in addition to custom depletion oligos). The presence of genomic DNA contamination was assessed by PCR with universal 16S rDNA primers. cDNA was synthesized using SuperScript II and random hexamers (Invitrogen), followed by second strand synthesis with RNaseH and E.coli DNA polymerase (New England Biolabs). Samples were prepared for sequencing with an Illumina GAII instrument after enzymatic fragmentation (NEBE6040L/M0348S). The size distribution of each library was quantified on an Agilent HS-DNA chip.

treatment_protocol: Digoxin was added at 10ug/ml final concentration

tag: growth phase

value: Exponential

tag: arginine

tag: drug

value: Digoxin


title: EL33

status: Public on Jun 15 2013

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain


title: Sperm bisulfite converted nucleosome associated DNA

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

library_source: genomic

data_processing:
Low-complexity reads were filtered out on the basis of dinucleotide entropy.
Read are aligned by using Bowtie.
Tab and wig files were generated in the same way as described in Stadler et al., Nature 2011, pubmed ID: 22170606
Genome_build: mm9
Supplementary_files_format_and_content: Tab file show the total and methylated alignments overlapping individual CpGs.

molecule: genomic DNA

organism: Mus musculus

source_name: Sperm

extract_protocol:
Mouse spermatozoa were collected by swim-up procedure5 from C57BL/6J mice. Round spermatids were isolated by FACS sorting using 28 day old BL6 mice. Mono-nucleosomal chromatin samples were prepared by MNase treatment. ChIP experiments for histone variants, H3.1/H3.2, H3.3, and histone modifications H3K4me3 and H3K27me3 were performed on native chromatin.
ChIP-seq and MNase-seq libraries were produced using the Illumina ChIP-seq DNA Sample Prep Kit (Cat# IP-102-1001).Before preparing RNA-seq libraries, rRNA from RNA  was depleted by using the Ribo-Zero rRNA removal kit (Epicentre Biotechnologies). Bisulfite libraries were prepared as described in Stadler et al., Nature 2011, pubmed ID: 22170606  Strand specific RNA-seq libraries were prepared by following the Illumina directional  mRNA-seq library preparation pre-release protocol.

tag: tissue

value: Sperm


title: EL32


title: EL31

value: No digoxin


title: Sperm H3K4me3 replicate2

data_processing:
Low-complexity reads were filtered out on the basis of dinucleotide entropy.
Read are aligned by using Bowtie.
Tab and wig files were generated in the same way as described in Stadler et al., Nature 2011, pubmed ID: 22170606
Genome_build: mm9
Supplementary_files_format_and_content: Wig files show the average coverage per base in 100 bp windows in the genome.

tag: antibody

value: Millipore 17-614


title: EL28


title: EL29


title: Sperm Nucleosome replicate2


title: s2

city: Guangzhou

first: Zhumei

last: He

state: Guangdong

address: 135 Xingangxi Street

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

description: read of an average length 115 bp

data_processing: After removing the artificial reads, reads adapters and reads that were shorter than 50 bp after removing the end-sequence with low quality, the remaining reads were mapped to the A. flavus genome , A. flavus EST sequencing , and rRNA sequencing  using multiple tools including TopHat(1.3.1) and Bowtie. Cufflinks(1.2.0)was used to assembles transcripts, estimates their abundances, discovery of novel transcripts, identification of alternative splicing and tests for differential expression in our two A. flavus RNA-Seq samples. The expression level of gene was normalized by calculating the number of fragments per kilobase of exon region per million mapped reads (FPKM).

organism: Aspergillus flavus

source_name: RNA from A. flavus cultured with PDB+5-AC medium

growth_protocol: Conidia of A. flavus NRRL 3357 were collected from plates using 0.05% Triton X-100. Then 3.3×107 CFU conidia medium was inoculated in 250-ml conical flasks containing 100 ml 2.4% (w/v) potato dextrose broth (PDB, purchased from Difco) and cultured in a shaker at 200 rpm and kept at 30°C.

extract_protocol: Total RNA was extracted from the fungal mycelia using a modified hot acid phenol method. A total of 2 g of the fine powder was promptly scraped into a 50-ml pre-cooled tube containing 15 ml extraction buffer (10 mM Tris-HCl, pH 8.0; 10 mM EDTA, pH 8.0; 0.5% (w/v) SDS) and 15 ml acid phenol. After incubation in the water bath at 65°C for 15 min, the tube was vortexed thoroughly and centrifuged at 11,000 rpm at 4°C for 10 min. The aqueous phase was then transferred into a pre-cooled tube with 15 ml acid phenol:chloroform:isoamylol (25:24:1, v/v/v), vortexed, and centrifuged at 10,000 rpm at 4°C for 10 min. This step was repeated several times to completely remove the impurities. Finally, only the aqueous phase was transferred to a new pre-cooled tube, and isopropanol (100%) was added to the tube at 1:1 (v/v) to precipitate RNA at -20°C overnight. The mixture was centrifuged at 10,000 rpm at 4°C for 15 min to collect the RNA. After washing with 70% ethanol twice, RNA was resuspended in DEPC-treated water. Each RNA sample was composed of three independent original samples with equal weight. The integrity of total RNA was checked using an Agilent Technologies 2100 Bioanalyzer, and all original samples and final samples had a RNA integrity number (RIN) value greater than six. The cDNA libraries were prepared using an Illumina ® TruSeq™ RNA Sample Preparation Kit according to the TruSeq™ RNA Sample Preparation guide. The first step in the workflow was purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces (380±50 bp) using divalent cations under elevated temperatures. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then went through an end repair process, an addition of a single ‘A’ base, and then ligation of the sequencing adapters using the Illumina TruSeq DNA sample preparation kit.

treatment_protocol: The 5-AC treated samples were cultured in PDB containing 1 mM 5-AC. The GA treated samples were cultured in PDB containing 1% GA (w/v).

tag: cell type

value: mycelium cells

tag: treatment

value: PDB+5-AC medium


title: EL26


title: EL24


title: EL20

value: Stationary


title: EL19


title: EL22


title: EL25


title: EL27


title: EL23


title: EL17


title: EL14


title: EL13


title: Sperm H3.1/H3.2 replicate1

value: Van Der Heijden et al. Nature Genetics, 2007, pubmed ID:17237782


title: EL15


title: EL16


title: EL18


title: T47D Methyl-MAPS

city: St. Louis

first: Nathan

last: VanderKraats

state: MO

address: 660 S. Euclid Ave

department: Center for Pharmacogenomics

institute: Washington University in St. Louis, School of Medicine

data_processing:
Library strategy: Methyl-MAPS
Tags for each sample and library (methylated and unmethylated compartment) were sequenced on two slides along with other samples.  Tags were distinguished using custom barcodes (6 bp in length) on the F3 tags.  Errors in the barcodes were recovered up to 2 bp (in colorspace).  Tags were then trimmed to 25 bp.
Tag mapping was performed using Corona Lite from the Applied Biosystems SOLiD System software analysis package.   Paired tags were mapped individually in color space, allowing up to two mismatches in each 25-bp tag to hg18.  Up to 10 hits per chromosome were recorded for each tag.
F3 and R3 tags were paired using the Corona Lite package. A mate pair was reported if a single uniquely placed pair could be made from the hits of each tag that met the contraints of order, orientation, and distance (0-15 kb).  If no mate pair could be made, then mate-pair rescue was attempted in which each hit was used as an anchor and the region where an appropriate mate should be found was scanned while allowing a total of four mismatches across both tags.  A rescued mate pair was reported if a single uniquely placed pair could be made.
Mapped reads from the same sample were pooled across slides. Fragment filtering, fragment count normalization and methylation level calculation was performed as in Edwards et al. 2010 Genome Research.
Genome_build: hg18
Supplementary_files_format_and_content: 4-column tab-delimited (chromosome, position, value, coverage)

organism: Homo sapiens

source_name: human breast cancer cell line

growth_protocol: MCF7 and T47D cell lines were maintained in RPMI 1640 medium supplemented with 5% fetal bovine serum, 10 mmol/L HEPES, 4.5 g/L glucose, 2 mmol/L L-glutamine, 1 mmol/L sodium pyruvate, and 50 µg/ml gentamicin in a humidified 37°C incubator containing 5% carbon dioxide.

extract_protocol:
Genomic DNA was isolated from 3 x 10^6 cells using the Quick-gDNA MiniPrep kit from Zymo Research (Irvine, CA) according to the manufacturers instructions. The quality of the isolated high molecular weight DNA was confirmed by agarose gel electrophoresis.
Methyl-MAPS libraries were prepared according to the protocol in Edwards et al Genome Research 2010. In brief, genomic DNA was split and unmethylated and methylated compartments were independently obtained by limit digestions of 10–15 ug of DNA with McrBC or five tetranucleotide methylation-sensitive restriction endonucleases (HpaII, HhaI, AciI, BstUI, HpyCH4IV). Digested fragments were size selected by gel-electrophoresis for fragments >800 bp. Mate-pair SOLiD sequencing libraries were then prepared using custom 6 bp barcodes. As part of the Methyl-MAPS protocol, EcoP15I CAP linkers are ligated onto the ends of the fragments.  The fragments are then circularized with biotinylated internal adapters, and digested with EcoP15I, which cleaves the DNA 25-27 bp away from its recognition site. Consequently, although we sequence 35 bp for both the F3 and R3 tags, only 25 bp are guaranteed to comprise the genomic sequence tag.

tag: cell line

value: human breast cancer


title: EL11


title: EL30


title: MCF7 Methyl-MAPS


title: 33-A59

city: Philadelphia

first: Megan

middle: Ruth

last: Elliott

state: PA

address: 3610 Hamilton Walk

department: Microbiology

institute: University of Pennsylvania

data_processing:
Casava
Sequence reads were trimmed for adaptor sequences and non-redundant sequences obtained and then mapped to the mm9 mouse genome using Bowtie v0.12.7 with parameters -f -n 2 -e 280 -l 34 -y -k100 -B 1 --suppress 5,6,7 --nomaqround -p 4
BaseMean values (reads/mapped in the library) were calculated for annotated transcripts in mm9.
DESeq v1.4.1 with R v2.13.1  was used for analysis of transcript relative abundance (infected over mock) and for obtaining Benjamini-Hochberg adjusted p-values.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text values containing baseMean counts and adjusted p-values for each transcript.

source_name: spinal cord tissue

growth_protocol: Four-week-old C57/Bl6 mice were obtained from NCI production.

extract_protocol:
Spinal cords were dissected from mice at 33 days post infection and homogenized.  Total RNA was extracted from trizol.
Polyadenylated RNA was selected using oligodT beads(Invitrogen).  RNA was fragmented with Ambion RNA Fragmentation reagent and end repaired with T4 PNK and then size selected (60-200bp).   Illumina adaptors were ligated to the 5' and 3' ends of the RNA.  The RNA library was reverse transcribed (Superscript II) and amplified by PCR (Phusion HiFi DNA polymerase).

treatment_protocol: Mice were innoculated intracranially with 2000 plaque forming units of MHV-A59

value: MHV infection

value: spinal cord

tag: age

value: 9 weeks


title: 33-mock

value: mock infection


title: abcH2- 18-hr replicate=2

status: Public on Jun 14 2013

city: Ljubljana

first: Marko

last: Toplak

address: Trzaska cesta 25

country: Slovenia

institute: University of Ljubljana

description: abcH2- at 18-hr, replicate=2

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_expr_raw.tab" contain raw expression values while files ending with "_expr_norm.tab" contain normalized expression values.

organism: Dictyostelium discoideum AX4

growth_protocol: We grew all the strains in liquid suspension in HL5 medium supplemented with streptomycin (50 mg/mL) and penicillin (50 U/mL), shaking at 220 rpm at 22°C. For collecting samples at different developmental times, we harvested the cells at log phase by centrifugation and washed them once with KK2 buffer (16.3 mM KH2PO4, 3.7 mM K2HPO4, pH 6.2). We deposited 5×107 cells onto a 5 cm nitrocellulose membrane placed on a pad saturated with 2 mL PDF buffer (9.2 mM K2HPO4, 13.2 mM KH2PO4, 20 mM KCl, 1.2 mM MgSO4, pH 6.5). We incubated the cells at 22°C in a dark humid chamber untill the specified developmental time.

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 24 individual libraries separately (one from each sample) and added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II using the manufacturer's recommended pipeline (versions 1.2 and 1.3, read length = 50 bases)

treatment_protocol: We developed 5×107 cells on a 5 cm nitrocellulose membrane for the number of hours specified in the text.

tag: genotype

tag: replicate

tag: developmental stage


title: wildtype 0-hr replicate=1

description: wildtype at 0-hr, replicate=1

source_name: wildtype

value: wildtype


title: wildtype 12-hr replicate=1

description: wildtype at 12-hr, replicate=1


title: wildtype 18-hr replicate=1

description: wildtype at 18-hr, replicate=1


title: wildtype 18-hr replicate=2

description: wildtype at 18-hr, replicate=2


title: wildtype 6-hr replicate=2

description: wildtype at 6-hr, replicate=2


title: wildtype 6-hr replicate=1

description: wildtype at 6-hr, replicate=1


title: abcH2- 12-hr replicate=2

description: abcH2- at 12-hr, replicate=2


title: wildtype 12-hr replicate=2

description: wildtype at 12-hr, replicate=2


title: abcH2- 12-hr replicate=1

description: abcH2- at 12-hr, replicate=1


title: wildtype 0-hr replicate=2

description: wildtype at 0-hr, replicate=2


title: abcH2- 18-hr replicate=1

description: abcH2- at 18-hr, replicate=1


title: abcH2- 0-hr replicate=1

description: abcH2- at 0-hr, replicate=1


title: abcH2- 6-hr replicate=1

description: abcH2- at 6-hr, replicate=1


title: abcH2- 6-hr replicate=2

description: abcH2- at 6-hr, replicate=2


title: abcG7- 18-hr replicate=2

description: abcG7- at 18-hr, replicate=2


title: abcH2- 0-hr replicate=2

description: abcH2- at 0-hr, replicate=2


title: abcG7- 12-hr replicate=2

description: abcG7- at 12-hr, replicate=2


title: abcG7- 18-hr replicate=1

description: abcG7- at 18-hr, replicate=1


title: abcG7- 12-hr replicate=1

description: abcG7- at 12-hr, replicate=1


title: abcG7- 0-hr replicate=1

description: abcG7- at 0-hr, replicate=1


title: abcG7- 6-hr replicate=1

description: abcG7- at 6-hr, replicate=1


title: abcG6- 18-hr replicate=2

description: abcG6- at 18-hr, replicate=2


title: abcG7- 0-hr replicate=2

description: abcG7- at 0-hr, replicate=2


title: abcG6- 12-hr replicate=2

description: abcG6- at 12-hr, replicate=2


title: abcG6- 6-hr replicate=2

description: abcG6- at 6-hr, replicate=2


title: abcG6- 18-hr replicate=1

description: abcG6- at 18-hr, replicate=1


title: abcG6- 0-hr replicate=2

description: abcG6- at 0-hr, replicate=2


title: abcG6- 12-hr replicate=1

description: abcG6- at 12-hr, replicate=1


title: abcG5- 12-hr replicate=2

description: abcG5- at 12-hr, replicate=2


title: abcG6- 6-hr replicate=1

description: abcG6- at 6-hr, replicate=1


title: abcG5- 0-hr replicate=2

description: abcG5- at 0-hr, replicate=2


title: abcG5- 18-hr replicate=2

description: abcG5- at 18-hr, replicate=2


title: abcG6- 0-hr replicate=1

description: abcG6- at 0-hr, replicate=1


title: abcG5- 6-hr replicate=1

description: abcG5- at 6-hr, replicate=1


title: abcG5- 0-hr replicate=1

description: abcG5- at 0-hr, replicate=1


title: abcG24- 18-hr replicate=1

description: abcG24- at 18-hr, replicate=1


title: abcG24- 12-hr replicate=2

description: abcG24- at 12-hr, replicate=2


title: abcG24- 0-hr replicate=2

description: abcG24- at 0-hr, replicate=2


title: abcG24- 0-hr replicate=1

description: abcG24- at 0-hr, replicate=1


title: abcG22- 6-hr replicate=2

description: abcG22- at 6-hr, replicate=2


title: abcG5- 12-hr replicate=1

description: abcG5- at 12-hr, replicate=1


title: abcG22- 0-hr replicate=2

description: abcG22- at 0-hr, replicate=2


title: abcG22- 18-hr replicate=1

description: abcG22- at 18-hr, replicate=1


title: abcG7- 6-hr replicate=2

description: abcG7- at 6-hr, replicate=2


title: abcG22- 12-hr replicate=1

description: abcG22- at 12-hr, replicate=1


title: abcG22- 6-hr replicate=1

description: abcG22- at 6-hr, replicate=1


title: abcG22- 18-hr replicate=2

description: abcG22- at 18-hr, replicate=2


title: abcG5- 6-hr replicate=2

description: abcG5- at 6-hr, replicate=2


title: abcG24- 12-hr replicate=1

description: abcG24- at 12-hr, replicate=1


title: abcG2- 6-hr replicate=2

description: abcG2- at 6-hr, replicate=2


title: abcG22- 0-hr replicate=1

description: abcG22- at 0-hr, replicate=1


title: abcG2- 18-hr replicate=2

description: abcG2- at 18-hr, replicate=2


title: abcG2- 0-hr replicate=2

description: abcG2- at 0-hr, replicate=2


title: abcG5- 18-hr replicate=1

description: abcG5- at 18-hr, replicate=1


title: abcG2- 12-hr replicate=2

description: abcG2- at 12-hr, replicate=2


title: abcG24- 18-hr replicate=2

description: abcG24- at 18-hr, replicate=2


title: abcG24- 6-hr replicate=1

description: abcG24- at 6-hr, replicate=1


title: abcG2- 6-hr replicate=1

description: abcG2- at 6-hr, replicate=1


title: abcG2- 18-hr replicate=1

description: abcG2- at 18-hr, replicate=1


title: abcG2- 12-hr replicate=1

description: abcG2- at 12-hr, replicate=1


title: abcG19- 18-hr replicate=2

description: abcG19- at 18-hr, replicate=2


title: abcG22- 12-hr replicate=2

description: abcG22- at 12-hr, replicate=2


title: abcG19- 12-hr replicate=2

description: abcG19- at 12-hr, replicate=2


title: abcG19- 0-hr replicate=2

description: abcG19- at 0-hr, replicate=2


title: abcG19- 12-hr replicate=1

description: abcG19- at 12-hr, replicate=1


title: abcG19- 18-hr replicate=1

description: abcG19- at 18-hr, replicate=1


title: abcG18- 18-hr replicate=2

description: abcG18- at 18-hr, replicate=2


title: abcG19- 6-hr replicate=1

description: abcG19- at 6-hr, replicate=1


title: abcG19- 0-hr replicate=1

description: abcG19- at 0-hr, replicate=1


title: abcG18- 6-hr replicate=2

description: abcG18- at 6-hr, replicate=2


title: abcG18- 18-hr replicate=1

description: abcG18- at 18-hr, replicate=1


title: abcG18- 0-hr replicate=2

description: abcG18- at 0-hr, replicate=2


title: abcG18- 12-hr replicate=1

description: abcG18- at 12-hr, replicate=1


title: abcG18- 6-hr replicate=1

description: abcG18- at 6-hr, replicate=1


title: abcG18- 0-hr replicate=1

description: abcG18- at 0-hr, replicate=1


title: abcG17- 18-hr replicate=2

description: abcG17- at 18-hr, replicate=2


title: abcG18- 12-hr replicate=2

description: abcG18- at 12-hr, replicate=2


title: abcG17- 12-hr replicate=2

description: abcG17- at 12-hr, replicate=2


title: abcG17- 0-hr replicate=2

description: abcG17- at 0-hr, replicate=2


title: abcG17- 6-hr replicate=2

description: abcG17- at 6-hr, replicate=2


title: abcG17- 18-hr replicate=1

description: abcG17- at 18-hr, replicate=1


title: abcG17- 12-hr replicate=1

description: abcG17- at 12-hr, replicate=1


title: abcG2- 0-hr replicate=1

description: abcG2- at 0-hr, replicate=1


title: abcG17- 0-hr replicate=1

description: abcG17- at 0-hr, replicate=1


title: abcG16- 18-hr replicate=2

description: abcG16- at 18-hr, replicate=2


title: abcG16- 12-hr replicate=2

description: abcG16- at 12-hr, replicate=2


title: abcG19- 6-hr replicate=2

description: abcG19- at 6-hr, replicate=2


title: abcG16- 0-hr replicate=2

description: abcG16- at 0-hr, replicate=2


title: abcG16- 18-hr replicate=1

description: abcG16- at 18-hr, replicate=1


title: abcG16- 12-hr replicate=1

description: abcG16- at 12-hr, replicate=1


title: abcG16- 6-hr replicate=2

description: abcG16- at 6-hr, replicate=2


title: abcG16- 0-hr replicate=1

description: abcG16- at 0-hr, replicate=1


title: abcG16- 6-hr replicate=1

description: abcG16- at 6-hr, replicate=1


title: abcG15- 12-hr replicate=2

description: abcG15- at 12-hr, replicate=2


title: abcG15- 0-hr replicate=2

description: abcG15- at 0-hr, replicate=2


title: abcG15- 18-hr replicate=2

description: abcG15- at 18-hr, replicate=2


title: abcG15- 18-hr replicate=1

description: abcG15- at 18-hr, replicate=1


title: abcG15- 6-hr replicate=1

description: abcG15- at 6-hr, replicate=1


title: abcG15- 12-hr replicate=1

description: abcG15- at 12-hr, replicate=1


title: abcG10- 12-hr replicate=2

description: abcG10- at 12-hr, replicate=2


title: abcG15- 0-hr replicate=1

description: abcG15- at 0-hr, replicate=1


title: abcG15- 6-hr replicate=2

description: abcG15- at 6-hr, replicate=2


title: abcG10- 18-hr replicate=1

description: abcG10- at 18-hr, replicate=1


title: abcG10- 18-hr replicate=2

description: abcG10- at 18-hr, replicate=2


title: abcG10- 12-hr replicate=1

description: abcG10- at 12-hr, replicate=1


title: abcG10- 0-hr replicate=2

description: abcG10- at 0-hr, replicate=2


title: abcG10- 0-hr replicate=1

description: abcG10- at 0-hr, replicate=1


title: abcG10- 6-hr replicate=1

description: abcG10- at 6-hr, replicate=1


title: abcF4- 18-hr replicate=2

description: abcF4- at 18-hr, replicate=2


title: abcF4- 12-hr replicate=2

description: abcF4- at 12-hr, replicate=2


title: abcF4- 0-hr replicate=2

description: abcF4- at 0-hr, replicate=2


title: abcF4- 12-hr replicate=1

description: abcF4- at 12-hr, replicate=1


title: abcF4- 6-hr replicate=1

description: abcF4- at 6-hr, replicate=1


title: abcF4- 0-hr replicate=1

description: abcF4- at 0-hr, replicate=1


title: abcF4- 6-hr replicate=2

description: abcF4- at 6-hr, replicate=2


title: abcF2- 18-hr replicate=2

description: abcF2- at 18-hr, replicate=2


title: abcF2- 12-hr replicate=2

description: abcF2- at 12-hr, replicate=2


title: abcF2- 0-hr replicate=2

description: abcF2- at 0-hr, replicate=2


title: abcF2- 6-hr replicate=2

description: abcF2- at 6-hr, replicate=2


title: abcF2- 12-hr replicate=1

description: abcF2- at 12-hr, replicate=1


title: abcF2- 18-hr replicate=1

description: abcF2- at 18-hr, replicate=1


title: abcF2- 6-hr replicate=1

description: abcF2- at 6-hr, replicate=1


title: abcF2- 0-hr replicate=1

description: abcF2- at 0-hr, replicate=1


title: abcF1- 12-hr replicate=2

description: abcF1- at 12-hr, replicate=2


title: abcF1- 18-hr replicate=1

description: abcF1- at 18-hr, replicate=1


title: abcG10- 6-hr replicate=2

description: abcG10- at 6-hr, replicate=2


title: abcF1- 0-hr replicate=2

description: abcF1- at 0-hr, replicate=2


title: abcF1- 12-hr replicate=1

description: abcF1- at 12-hr, replicate=1


title: abcF1- 18-hr replicate=2

description: abcF1- at 18-hr, replicate=2


title: abcF1- 6-hr replicate=1

description: abcF1- at 6-hr, replicate=1


title: abcF4- 18-hr replicate=1

description: abcF4- at 18-hr, replicate=1


title: abcD2- 18-hr replicate=2

description: abcD2- at 18-hr, replicate=2


title: abcD2- 0-hr replicate=2

description: abcD2- at 0-hr, replicate=2


title: abcF1- 0-hr replicate=1

description: abcF1- at 0-hr, replicate=1


title: abcD2- 12-hr replicate=1

description: abcD2- at 12-hr, replicate=1


title: abcD2- 6-hr replicate=1

description: abcD2- at 6-hr, replicate=1


title: abcC8- 18-hr replicate=2

description: abcC8- at 18-hr, replicate=2


title: abcD2- 6-hr replicate=2

description: abcD2- at 6-hr, replicate=2


title: abcC8- 6-hr replicate=2

description: abcC8- at 6-hr, replicate=2


title: abcC8- 18-hr replicate=1

description: abcC8- at 18-hr, replicate=1


title: abcC8- 0-hr replicate=2

description: abcC8- at 0-hr, replicate=2


title: abcC8- 6-hr replicate=1

description: abcC8- at 6-hr, replicate=1


title: abcC8- 12-hr replicate=2

description: abcC8- at 12-hr, replicate=2


title: abcC8- 12-hr replicate=1

description: abcC8- at 12-hr, replicate=1


title: abcC6- 6-hr replicate=2

description: abcC6- at 6-hr, replicate=2


title: abcC6- 18-hr replicate=2

description: abcC6- at 18-hr, replicate=2


title: abcF1- 6-hr replicate=2

description: abcF1- at 6-hr, replicate=2


title: abcC6- 12-hr replicate=2

description: abcC6- at 12-hr, replicate=2


title: abcC6- 0-hr replicate=2

description: abcC6- at 0-hr, replicate=2


title: abcC6- 12-hr replicate=1

description: abcC6- at 12-hr, replicate=1


title: abcD2- 12-hr replicate=2

description: abcD2- at 12-hr, replicate=2


title: abcC6- 0-hr replicate=1

description: abcC6- at 0-hr, replicate=1


title: abcD2- 18-hr replicate=1

description: abcD2- at 18-hr, replicate=1


title: abcC3- 18-hr replicate=2

description: abcC3- at 18-hr, replicate=2


title: abcC3- 0-hr replicate=2

description: abcC3- at 0-hr, replicate=2


title: abcC3- 12-hr replicate=1

description: abcC3- at 12-hr, replicate=1


title: abcC3- 18-hr replicate=1

description: abcC3- at 18-hr, replicate=1


title: abcC3- 6-hr replicate=1

description: abcC3- at 6-hr, replicate=1


title: abcC2- 0-hr replicate=2

description: abcC2- at 0-hr, replicate=2


title: abcC2- 12-hr replicate=2

description: abcC2- at 12-hr, replicate=2


title: abcC8- 0-hr replicate=1

description: abcC8- at 0-hr, replicate=1


title: abcC2- 18-hr replicate=2

description: abcC2- at 18-hr, replicate=2


title: abcC2- 12-hr replicate=1

description: abcC2- at 12-hr, replicate=1


title: abcC2- 6-hr replicate=1

description: abcC2- at 6-hr, replicate=1


title: abcC2- 6-hr replicate=2

description: abcC2- at 6-hr, replicate=2


title: abcC2- 18-hr replicate=1

description: abcC2- at 18-hr, replicate=1


title: abcC14- 6-hr replicate=2

description: abcC14- at 6-hr, replicate=2


title: abcC2- 0-hr replicate=1

description: abcC2- at 0-hr, replicate=1


title: abcC14- 18-hr replicate=2

description: abcC14- at 18-hr, replicate=2


title: abcC14- 12-hr replicate=2

description: abcC14- at 12-hr, replicate=2


title: abcC14- 0-hr replicate=2

description: abcC14- at 0-hr, replicate=2


title: abcC6- 18-hr replicate=1

description: abcC6- at 18-hr, replicate=1


title: abcC6- 6-hr replicate=1

description: abcC6- at 6-hr, replicate=1


title: abcC14- 6-hr replicate=1

description: abcC14- at 6-hr, replicate=1


title: abcC13- 18-hr replicate=2

description: abcC13- at 18-hr, replicate=2


title: abcC3- 12-hr replicate=2

description: abcC3- at 12-hr, replicate=2


title: abcC3- 6-hr replicate=2

description: abcC3- at 6-hr, replicate=2


title: abcC14- 12-hr replicate=1

description: abcC14- at 12-hr, replicate=1


title: abcC13- 18-hr replicate=1

description: abcC13- at 18-hr, replicate=1


title: abcC13- 6-hr replicate=2

description: abcC13- at 6-hr, replicate=2


title: abcC13- 12-hr replicate=2

description: abcC13- at 12-hr, replicate=2


title: abcC13- 0-hr replicate=2

description: abcC13- at 0-hr, replicate=2


title: abcC13- 6-hr replicate=1

description: abcC13- at 6-hr, replicate=1


title: abcC12- 18-hr replicate=2

description: abcC12- at 18-hr, replicate=2


title: abcC12- 12-hr replicate=2

description: abcC12- at 12-hr, replicate=2


title: abcC12- 6-hr replicate=2

description: abcC12- at 6-hr, replicate=2


title: abcC12- 12-hr replicate=1

description: abcC12- at 12-hr, replicate=1


title: abcC12- 0-hr replicate=1

description: abcC12- at 0-hr, replicate=1


title: abcC12- 6-hr replicate=1

description: abcC12- at 6-hr, replicate=1


title: abcB5- 18-hr replicate=2

description: abcB5- at 18-hr, replicate=2


title: abcB5- 18-hr replicate=1

description: abcB5- at 18-hr, replicate=1


title: abcB5- 12-hr replicate=2

description: abcB5- at 12-hr, replicate=2


title: abcB5- 6-hr replicate=1

description: abcB5- at 6-hr, replicate=1


title: abcB4- 18-hr replicate=2

description: abcB4- at 18-hr, replicate=2


title: abcB5- 0-hr replicate=2

description: abcB5- at 0-hr, replicate=2


title: abcC13- 12-hr replicate=1

description: abcC13- at 12-hr, replicate=1


title: abcC12- 18-hr replicate=1

description: abcC12- at 18-hr, replicate=1


title: abcB4- 12-hr replicate=2

description: abcB4- at 12-hr, replicate=2


title: abcB4- 6-hr replicate=2

description: abcB4- at 6-hr, replicate=2


title: abcC12- 0-hr replicate=2

description: abcC12- at 0-hr, replicate=2


title: abcB5- 0-hr replicate=1

description: abcB5- at 0-hr, replicate=1


title: abcB4- 0-hr replicate=2

description: abcB4- at 0-hr, replicate=2


title: abcB4- 12-hr replicate=1

description: abcB4- at 12-hr, replicate=1


title: abcB4- 18-hr replicate=1

description: abcB4- at 18-hr, replicate=1


title: abcB4- 6-hr replicate=1

description: abcB4- at 6-hr, replicate=1


title: abcB4- 0-hr replicate=1

description: abcB4- at 0-hr, replicate=1


title: abcB5- 12-hr replicate=1

description: abcB5- at 12-hr, replicate=1


title: abcB1- 6-hr replicate=2

description: abcB1- at 6-hr, replicate=2


title: abcB1- 12-hr replicate=2

description: abcB1- at 12-hr, replicate=2


title: abcC13- 0-hr replicate=1

description: abcC13- at 0-hr, replicate=1


title: abcB1- 18-hr replicate=2

description: abcB1- at 18-hr, replicate=2


title: abcB1- 0-hr replicate=2

description: abcB1- at 0-hr, replicate=2


title: abcB1- 6-hr replicate=1

description: abcB1- at 6-hr, replicate=1


title: abcB1- 18-hr replicate=1

description: abcB1- at 18-hr, replicate=1


title: abcB5- 6-hr replicate=2

description: abcB5- at 6-hr, replicate=2


title: abcA9- 18-hr replicate=2

description: abcA9- at 18-hr, replicate=2


title: abcA9- 6-hr replicate=2

description: abcA9- at 6-hr, replicate=2


title: abcA9- 12-hr replicate=2

description: abcA9- at 12-hr, replicate=2


title: abcA9- 0-hr replicate=2

description: abcA9- at 0-hr, replicate=2


title: abcB1- 12-hr replicate=1

description: abcB1- at 12-hr, replicate=1


title: abcA9- 18-hr replicate=1

description: abcA9- at 18-hr, replicate=1


title: abcA9- 12-hr replicate=1

description: abcA9- at 12-hr, replicate=1


title: abcA7- 12-hr replicate=2

description: abcA7- at 12-hr, replicate=2


title: abcA9- 6-hr replicate=1

description: abcA9- at 6-hr, replicate=1


title: abcA7- 18-hr replicate=2

description: abcA7- at 18-hr, replicate=2


title: abcA7- 12-hr replicate=1

description: abcA7- at 12-hr, replicate=1


title: abcA7- 6-hr replicate=1

description: abcA7- at 6-hr, replicate=1


title: abcA7- 18-hr replicate=1

description: abcA7- at 18-hr, replicate=1


title: abcA7- 6-hr replicate=2

description: abcA7- at 6-hr, replicate=2


title: abcA7- 0-hr replicate=1

description: abcA7- at 0-hr, replicate=1


title: abcA6- 12-hr replicate=2

description: abcA6- at 12-hr, replicate=2


title: abcA6- 6-hr replicate=2

description: abcA6- at 6-hr, replicate=2


title: abcA6- 18-hr replicate=2

description: abcA6- at 18-hr, replicate=2


title: abcA9- 0-hr replicate=1

description: abcA9- at 0-hr, replicate=1


title: abcB1- 0-hr replicate=1

description: abcB1- at 0-hr, replicate=1


title: abcA6- 0-hr replicate=2

description: abcA6- at 0-hr, replicate=2


title: abcA7- 0-hr replicate=2

description: abcA7- at 0-hr, replicate=2


title: abcA6- 18-hr replicate=1

description: abcA6- at 18-hr, replicate=1


title: abcA6- 12-hr replicate=1

description: abcA6- at 12-hr, replicate=1


title: abcA6- 0-hr replicate=1

description: abcA6- at 0-hr, replicate=1


title: abcA6- 6-hr replicate=1

description: abcA6- at 6-hr, replicate=1


title: abcA5- 12-hr replicate=2

description: abcA5- at 12-hr, replicate=2


title: abcA5- 6-hr replicate=2

description: abcA5- at 6-hr, replicate=2


title: abcA5- 0-hr replicate=2

description: abcA5- at 0-hr, replicate=2


title: abcA5- 18-hr replicate=1

description: abcA5- at 18-hr, replicate=1


title: abcA5- 12-hr replicate=1

description: abcA5- at 12-hr, replicate=1


title: abcA5- 0-hr replicate=1

description: abcA5- at 0-hr, replicate=1


title: abcA4- 6-hr replicate=2

description: abcA4- at 6-hr, replicate=2


title: abcA4- 0-hr replicate=2

description: abcA4- at 0-hr, replicate=2


title: abcA4- 18-hr replicate=2

description: abcA4- at 18-hr, replicate=2


title: abcA5- 6-hr replicate=1

description: abcA5- at 6-hr, replicate=1


title: abcA4- 6-hr replicate=1

description: abcA4- at 6-hr, replicate=1


title: abcA4- 12-hr replicate=1

description: abcA4- at 12-hr, replicate=1


title: abcA4- 18-hr replicate=1

description: abcA4- at 18-hr, replicate=1


title: abcA3- 18-hr replicate=2

description: abcA3- at 18-hr, replicate=2


title: abcA3- 6-hr replicate=2

description: abcA3- at 6-hr, replicate=2


title: abcA3- 12-hr replicate=2

description: abcA3- at 12-hr, replicate=2


title: abcA4- 0-hr replicate=1

description: abcA4- at 0-hr, replicate=1


title: abcA3- 12-hr replicate=1

description: abcA3- at 12-hr, replicate=1


title: abcA3- 18-hr replicate=1

description: abcA3- at 18-hr, replicate=1


title: abcA5- 18-hr replicate=2

description: abcA5- at 18-hr, replicate=2


title: abcA11- 12-hr replicate=2

description: abcA11- at 12-hr, replicate=2


title: abcA3- 6-hr replicate=1

description: abcA3- at 6-hr, replicate=1


title: abcA11- 18-hr replicate=2

description: abcA11- at 18-hr, replicate=2


title: abcA11- 6-hr replicate=2

description: abcA11- at 6-hr, replicate=2


title: abcA3- 0-hr replicate=1

description: abcA3- at 0-hr, replicate=1


title: abcA3- 0-hr replicate=2

description: abcA3- at 0-hr, replicate=2


title: abcA11- 6-hr replicate=1

description: abcA11- at 6-hr, replicate=1


title: abcA11- 12-hr replicate=1

description: abcA11- at 12-hr, replicate=1


title: abcA11- 0-hr replicate=1

description: abcA11- at 0-hr, replicate=1


title: abcA4- 12-hr replicate=2

description: abcA4- at 12-hr, replicate=2


title: abcA10- 12-hr replicate=2

description: abcA10- at 12-hr, replicate=2


title: abcA10- 18-hr replicate=2

description: abcA10- at 18-hr, replicate=2


title: abcA10- 6-hr replicate=2

description: abcA10- at 6-hr, replicate=2


title: abcA10- 18-hr replicate=1

description: abcA10- at 18-hr, replicate=1


title: abcA10- 0-hr replicate=2

description: abcA10- at 0-hr, replicate=2


title: abcA10- 6-hr replicate=1

description: abcA10- at 6-hr, replicate=1


title: abcA11- 18-hr replicate=1

description: abcA11- at 18-hr, replicate=1


title: abcA11- 0-hr replicate=2

description: abcA11- at 0-hr, replicate=2


title: miR-seq WT

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

country: South Korea

institute: Dankook University

description: miR-seq

data_processing:
Basecalls performed using the CASAVA software
Sequenced reads were aligned to the mm9 genome assembly using the TopHat program (Trapnell et al., Bioinformatics, 2009) for mRNA-seq and BWA (Li et al., Bioinformatics, 2009) for miR-seq.
For mRNA-seq, Fragments Per Kilobase of transcript per million mapped reads (FPKM) were calculated using a protocol (Trapnell et al., Nat. Prot., 2012). Differentially expressed genes (DEGs) were identified by using Cuffdiff2, edgeR and DESeq with an adjusted p-value cutoff (< 0.05). For miR-seq, we used the miRDeep2 program to detect miRs (Friedlander et al, Nucleic Acids Res. 2011). Differentially expressed miRs were assesed by using DESeq (Anders et al, Geome biol. 2010) with an adjusted P-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: miR-seq_DESeq_RPM.txt: Tab-delimited text file (Null over WT)
Supplementary_files_format_and_content: RNA-seq_FPKM.txt: Tab-delimited text file (Null and WT)

source_name: Brown Fat

growth_protocol: Animals were handled and housed in accordance with the guidelines of NIH and all experiments were approved by the Animal Care and Use Committee of NIDDK. Female MMTV-Cre miR-193bf/+ mice were mated with miR-193bf/+ males to produce heterozygous offspring and to segregate out the MMTV-Cre transgene.

extract_protocol:
mRNA-seq: Poly(A) RNA was purified twice from 1 mg total RNA and cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA), and sequenced using HiSeq 2000 (Illumina).
miR-seq: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), Small RNA libraries were prepared with a small RNA version 1.5 sample preparation kit (Illumina, San Diego, CA).

tag: sample tag

value: brown adipose tissue

value: 2m old mice


title: mmu-mir-193b BAT 2m WT rep2

description: mRNA-seq

molecule: polyA RNA


title: mmu-mir-193b BAT 2m WT rep3

description: mRNA-seq


title: mmu-mir-193b BAT 2m NULL rep1

description: mRNA-seq


title: mmu-mir-193b BAT 2m NULL rep3

description: mRNA-seq


title: mmu-mir-193b BAT 2m NULL rep2

description: mRNA-seq


title: mmu-mir-193b BAT 2m WT rep1

description: mRNA-seq


title: LNCaP Input

status: Public on Jun 13 2013

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: Input DNA used for peak calling

data_processing:
All reads (36-bp) from ChIP-Seq were aligned to the human genome (build 36, or hg18) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one
Peaks were called using MACS 1.4 comparing with input DNA of LNCaP cells
Genome_build: hg18
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks

source_name: LNCaP cells

growth_protocol: LNCaP cells were grown in 10% FBS. For baseline ChIP-Seq (ETV1 and H3K4me1 ChIP), 100 million and 20 million cells were harvested respectively. For ETV1 and scrambled knockdown experiments, 25 million cells were infected with lentiviral shRNA at MOI~5 and cells were harvested 72 hours later.

extract_protocol:
Cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with 5 ug of the indicated antibody, washed, eluted, reverse cross-linked, and purified.
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. DNA was purified using Ampure beads and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: prostate cancer

tag: chip antibody


title: LNCaP-ETV1sh2-AR ChIP

description: LNCaP Cells infected with ETV1 shRNA (25 million), AR ChIP-Seq

value: Rabbit Anti-AR (Epitomics Clone ER179)

value: ETV1sh2 infection


title: kitpos_D_FPKM

first: Betty

last: Chang

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

description:
mRNA-seq
GFP+CD45+kitpos

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite.
Alignment to mm9 using Tophat release 1.4.1 and Bowtie release 0.12.7.
Differential expression performed with Cufflinks release 1.3.0 and Mus musculus mm9 reference annotation.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Cufflinks cuffdiff differential expression genes. fpkm_tracking output tab-delimited file. See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.

source_name: mouse embryonic fibroblast transduced with Gata2+cFos+Gfi1b+Etv6, kitpos, day 35

extract_protocol:
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with up to 1 ug of total RNA for the construction of sequencing libraries according to Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.

tag: strain/background

value: embryonic fibroblasts

tag: transduction

tag: time

value: day 35


title: LNCaP-shScr-AR ChIP

description: LNCaP Cells infected with scrambled shRNA (25 million), AR ChIP-Seq

value: Scrambled shRNA infection x3 days


title: MmES_Input_chromatin

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
basecalls using CASAVA
fastq to fasta conversion
reads were aligned to mm9 mouse genome using BOWTIE, allowing up to 2 missmatches
coordinates of reads that map only once to the mouse genome were converted to BED format
Genome_build: mm9
Supplementary_files_format_and_content: bed format, contents: chromosome, start, end, read_name, n times mapped to genome, strand

source_name: embryonic stem cells

growth_protocol: Wild type embryonic stem cells derived from mixed 129-C57Bl/6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol. Differentiation was performed as previously described (Bibel et al).

extract_protocol: For cross-linking and chromatin extraction, cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in presence of 1.2M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS and 150 mM NaCl for 2 hours on ice. Crosslinked chromatin was subjected to sonication in a Bioruptor instrument (Diagenode). ProteinA-dynabeads pre-cleared 150-250 µg chromatin were incubated with 40 µl blocked (1%CFSG, 100ng tRNA) Streptavidin-M280 magnetic beads over night at 4°C. Beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation.

value: embryonic stem cells

value: wild type

tag: background strain

value: mixed 129-C57Bl/6


title: kitneg_3_FPKM

description:
mRNA-seq
GFP+CD45+kitneg

source_name: mouse embryonic fibroblast transduced with Gata2+cFos+Gfi1b+Etv6, kitneg, day 35


title: day20_B_FPKM

description:
mRNA-seq
GFP+Sca1+Prom1+

source_name: mouse embryonic fibroblast transduced with Gata2+cFos+Gfi1b+Etv6, day 20

value: day 20


title: day20_2_FPKM

description:
mRNA-seq
GFP+Sca1+Prom1+


title: mefs_1_FPKM

description:
mRNA-seq
CD45neg

source_name: mouse embryonic fibroblast


title: mefs_A_FPKM

description:
mRNA-seq
CD45neg


title: abcA10- 0-hr replicate=1

description: abcA10- at 0-hr, replicate=1


title: abcA10- 12-hr replicate=1

description: abcA10- at 12-hr, replicate=1


title: Mouse_PTEN_input_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline.
The generated BAM file is used as input control for MACS 1.4.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks

source_name: Mouse Prostate

growth_protocol: Mouse of each genotype was fed adlib. Prostate was isolated at 6 months of age

extract_protocol:
Prostates were dissected and then minced in 1.5ml tube with fine scissors. They were crosslinked for 15-minutes in 1% parformaldehyde. After quenching with glycine, the cross-linked chromatin was dounced and then sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with 5 ug of the indicated antibody, washed, eluted, reverse cross-linked, and purified.
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. DNA was purified using Ampure beads and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Pten-f/f

value: 6 months


title: miR-seq NULL

description: miR-seq


title: Mouse_PTEN-ERG_input_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline.
The BAM file is used as input control for peak calling by MACS 1.4.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks


title: Mouse_PTEN-ERG_H3K4me3_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one Peaks were called using MACS 1.4 comparing with input DNA of Pten-f/f;R26-ERG/ERG prostates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks

value: Rabbit anti-Histone H3 trimethyl K4 (activemotif 35159, lot #:01609004)


title: Mouse_PTEN-ERG_H3K4me1_IP

value: Rabbit Anti-Histone monomethyl-H3 (Abcam ab8895, Lot GR61280-1)


title: Mouse_PTEN-ERG_ERG_IP

value: Rabbit Anti-ERG (Epitomics Clone EPR3864)


title: kitpos_4_FPKM

description:
mRNA-seq
GFP+CD45+kitpos


title: Mouse_PTEN-ERG_AR_IP


title: LNCaP-H3K4me1 ChIP

description: LNCaP Cells (25 million), H3K4me1 ChIP-Seq.


title: LNCaP-ETV1ChIP

description: LNCaP cells (100 million), ETV1 ChIP-Seq.

value: Rabbit Anti-ETV1 (Abcam 81086, Lot 787879)


title: Mouse_ERG_H3K4me3_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one Peaks were called using MACS 1.4 comparing with input DNA of R26-ERG/ERG prostates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks


title: Mouse_ERG_input_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline. The generated BAM file is used as input control for peak calling by MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks


title: Mouse_ERG_H3K4me1_IP


title: kitneg_C_FPKM

description:
mRNA-seq
GFP+CD45+kitneg


title: Mouse_WT_input_IP

value: WT


title: Mouse_WT_H3K4me3_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one Peaks were called using MACS 1.4 comparing with input DNA of WT prostates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks


title: Mouse_WT_H3K4me1_IP


title: FS

city: Bogota

first: Patricia

last: Del Portillo

address: Carrera 5 No. 66A-34

country: Colombia

institute: corpogen

data_processing:
Quality assessment of the reads was done using the FASTX toolkit v. 0.0.13
The reads were mapped against the M. tuberculosis H37Rv reference genome (accession number NC_000962.2) using Bowtie v. 0.12.7; Reads that mapped to more than one site where excluded
Calculate RPKMs with a script own; For the analysis, only those reads for which 50% of the sequence length fell within the annotated open reading frame (ORF) were considered as being part of the ORF
Genome_build: ASM19595v1

organism: Mycobacterium tuberculosis H37Rv

source_name: Culture in Long Fatty Acids: Stationary phase

extract_protocol:
Total RNA was isolated from cultures in exponential and stationary phases. Basically, cultures were harvested by centrifugation and pellets were resuspended in Guanidinium Chloride buffer (6M guanidinium chloride, 0.1% Tween 80, 1mM, 2-ß-mercaptoethanol, 10mM EDTA) in a proportion of 1ml of buffer per 100 ml of culture. Cells were lysed mechanically in a FastPrepTM (Thermo Scientific) using 150-200 µm glass beads (Sigma Aldrich) by doing 4 lysis cycles at high speed (6.5 m/s) during 15 s each. Nucleic acids were purified with phenol-chloroform-isoamyl alcohol (25:24:1) and RNA was differentially precipitated with 0.4 vol of absolute ethanol (added drop by drop). Finally, RNA was washed 3 times with TrizolTM reagent (Invitrogen). RNA integrity was analyzed using a bioanalyzer (Agilent technologies) and quantified by spectrophotometer using the nanodrop ND-1000 (Thermo Scientific).
Directional RNA-seq, Waldbauer J.R et al (2012)

tag: phase growth

value: Stationary

tag: medium

value: Long Fatty Acid


title: FE

source_name: Culture in Long Fatty Acids: exponential phase

value: Exponential

tag: strain


title: DE

source_name: Culture in Dubos: exponential phase

value: Dubos


title: DS

source_name: Culture in Dubos: Stationary phase


title: Mouse_WT_ERG_IP


title: AKTA HiTrapQ small RNAs

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS

description: Anion-exchange chromatography (HiTrapQ column) purification with AKTA apparatus

data_processing:
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.)
Sequenced reads were stripped of the adapter (CTGTAGGCACCATCAA) in the 3’-end and the retrieved small RNA reads were mapped to the genome sequence of Drosophila melanogaster (release 5) according to sequencing quality using Novoalign (www.novocraft.com). Only reads perfectly matching the fly genome were analyzed (one mismatch was nevertheless allowed on low-sequencing quality nucleotides, -e 20 option).
Libraries were then annotated according to reference databases containing ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), micro RNAs (miRNAs), transcripts, small nuclear RNAs (snRNAs) and transposable element sequences. rRNAs, tRNAs and snRNAs were retrieved from modEncode (http://www.modencode.org/ (Celniker et al. 2009)), miRNAs from miRBase (http://www.mirbase.org/ (Kozomara and Griffiths-Jones 2011)), transcripts from Flybase (http://flybase.org/) and transposable elements from Repbase (http://www.girinst.org/repbase/index.html (Jurka et al. 2005)).
After subtracting reads matching abundant cellular species such as rRNAs, tRNAs and snRNAs, the remainders, called bona fide reads, were split into siRNAs (21nt), miRNAs (22nt) and piRNAs (23-29nt). For the piRNA identification, we selected bona fide reads strictly exceeding 22 nt in length and not annotated as miRNAs.
Genome_build: dm5
Supplementary_files_format_and_content: Read counts (second column) for each bona fide sequence (first column)

organism: Drosophila melanogaster

source_name: 3 day-old ovaries

growth_protocol: Flies were grown at 21 degrees C

extract_protocol: Extracted small RNAs were cloned by Fasteris SA (Switzerland) after being selected on acrylamide gel between 18 and 30 nucleotides

treatment_protocol:
MG_Size isolation: Small RNAs (18-30nt) were isolated using Trizol and size-isolation procedure
MG_HQ: Small RNAs (18-30nt) were isolated by anion exchange chromatography using AKTA FPLC purifier system
MG_manualHQ: Small RNAs (18-30nt) were isolated by manual anion exchange chromatography procedure

value: MG derived

tag: tissue

value: Ovaries

value: 3 day-old

tag: gender

value: female

tag: purification procedure


title: Size-isolated small RNAs

description: Size-fractionation purification

value: Size-fractionation purification


title: N40_Stroma_SAGEseq

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing: 21 base pair (bp) of each read is used in this study. The first 4 bp is always CATG, as this is the recognition site of NlaIII. Our analysis was based around the alignment of the rest of the 17bp tags to human genome  composed of segments between nearest NlaIII sites flanking BssHII recognition sites where as 17 bp SAGE tags were aligned to transcripts.

source_name: human breast stromal cells

growth_protocol: Primary cells purified from normal human breast tissue

extract_protocol:
For SAGE-seq: mRNA isolated from atleast 50-100K cells were captured on oligo(dT) beads followed by cDNA synthesis. cDNA was then cleaved with anchoring enzyme NlAIII following ligation of adapter 1. cDNA was subsequently released by tagging enzyme MmeI and ligated to adapter 2. The resulting 85 bp DNA fragments were amplified by Primer 1 and Primer 2 and purified in 12% PAGE. Purified libraries were sequenced on the Illumina Solexa 1G platform. All the adapters and primers were from Illumina.
For MSDK-seq: 1-2ug of DNA was digested with methylation sensitive restriction enzyme BssHII (NEB) and ligated to biotinylated linker. DNA was then fragmented with another restriction enzyme NlaIII (NEB) and the resulting fragmented DNA with biotinylated linker was captured on streptavidin beads. Fragmented DNA was then ligated to Adapter 1 followed by release of DNA from beads by tagging enzyme MmeI (NEB) with subsequent ligation to Adapter 2. The resulting 85 bp DNA fragments were amplified by Primer 1 and Primer 2 and purified in 12% PAGE. Purified libraries were sequenced on the Illumina Solexa 1G platform. All the adapters and primers were supplied by  Illumina.

value: breast

tag: cell type

value: bead purified stromal cells

tag: parity

value: parous


title: Mouse_PTEN_ERG_IP

tag: genotype

value: Pten-f/f

tag: age

value: 6 months


title: Mouse_PTEN_AR_IP

data_processing:
All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one Peaks were called using MACS 1.4 comparing with input DNA of Pten-f/f prostates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks

value: Rabbit Anti-AR (Epitomics Clone ER179)


title: Mouse_WT_AR_IP


title: Mouse_PTEN_H3K4me3_IP

value: Rabbit anti-Histone H3 trimethyl K4 (activemotif 35159, lot #:01609004)


title: Manual HiTrapQ small RNAs

description: Manual anion-exchange chromatography (HiTrapQ column) purification

tag: developmental stage


title: Mouse_ERG_ERG_IP

value: Rabbit Anti-ERG (Epitomics Clone EPR3864)


title: N_161_BRCA2_44_SAGEseq

description: SAGE library prepared using Illumina adapters and primers using NLAIII fragmenting enzyme

source_name: expression library from cd44+ cells from BRCA1 and BRCA2 mutation carriers

growth_protocol: not applicable

extract_protocol: For SAGE-seq: mRNA isolated from atleast 50-100K cells were captured on oligo(dT) beads followed by cDNA synthesis. cDNA was then cleaved with anchoring enzyme NlAIII following ligation of adapter 1. cDNA was subsequently released by tagging enzyme MmeI and ligated to adapter 2. The resulting 85 bp DNA fragments were amplified by Primer 1 and Primer 2 and purified in 12% PAGE. Purified libraries were sequenced on the Illumina Solexa 1G platform. All the adapters and primers were from Illumina.

treatment_protocol: cells isolated tissue after digesting and sequential filtration and bead purification or FACS purification

value: mammary gland

value: cd44+ cells from BRCA2 mutation carrier


title: Mouse_ERG_AR_IP


title: N37_Stroma_SAGEseq


title: Polyribosome DMSO 2

city: Santa Cruz

first: Jeremy

last: Sanford

address: 1156 High Street

department: MCD Biology

institute: UC Santa Cruz

data_processing:
Library strategy: Frac-Seq
Illumina Casava1.8.2 software used for basecalling.
All paired end reads were trimmed at the 3' end to a final length of 75x58bp
Reads were mapped with bowtie2 to the set of human repeatMasker elements and these reads were eliminated from further processing.
The trimmed, repeatMasker filtered, sequenced reads (75bp read1, 58bp read2) were mapped to hg19 with tophat (2.0.4) using bowtie2 (2.0.0-beta7), with an estimated mean distance between the read pairs of 5bp (100bp std dev). A gtf file of the hg19 UCSC Known Genes browser track was supplied to TopHat.
In the case of multiply mapped reads, the single best hit as scored by bowtie2 was kept. Single-end mappings were discarded.
Potential PCR duplicates at each mapping position were removed using Samtools rmdup.
Genome_build: hg19
Transcript levels in HEK293 cytosolic and polyribosomal fractions was determined using HiSeq2000. We used the Mixture of Isoforms (MISO) Bayesian Inference model v1.0 for quantification of alternative RNA processing events (Katz et al. 2010). The MISO algorithm counts the numbers of reads that are common to both events and the reads that are exclusive to one isoform or the other, in order to estimate the %-spliced-in (Y) in a given sample. We employed an “event-centric” approach, considering annotated alternative mRNA processing events with at least 20 exclusive reads and a maximum confidence interval width of 0.45 for the MISO estimated posterior distribution of percent-spliced-in (“Psi”, Y, Supplemental Table 5 lists all of the MISO outputs). The MISO output is described in the linked supplementary files (*MISO.txt). Additionally the tables include annotations of cis-regulatory elements that overlap either the Y or 1-Y isoform.

source_name: HEK293 Polyribosome DMSO 2

extract_protocol:
Cytosolic extracts (detergent lysis) were prepared from control and rapa treated cells. 10% of cytosolic extract was used to prepare RNA with TrireagentLS. The remainder was fractionated across 15-45% sucrose gradients centriguged at 100,000xg in Beckman SW41 rotor. Polyribosome peaks were purified using a Gradient Station by Biocomp Instruments.
TruSeq mRNA (Illumina)

treatment_protocol: HEK cells starved for glutamine for 12h. 30 minutes proior to feeding with complete media, 100nM rapamycin was added to the starvation media. After 30 minutes, complete media -/+ rapamycin was added and cells were cultured for 7h.

tag: cell line

value: human embryonic kidney


title: Cytoplasm DMSO 2

source_name: HEK293 Cytoplasm DMSO 2


title: Polyribosome DMSO 1

source_name: HEK293 Polyribosome DMSO 1


title: hiPS_B36

status: Public on Jun 12 2013

city: Cambridge

first: Rahul

last: Karnik

address: 419 Broadway

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using MAQ bisulfite alignment mode.
Aligned bam files were processed using custom software (PMID:20852634).
Genome_build: hg19
Supplementary_files_format_and_content: RRBS.bed: chrom, chromstart, chromend,'number methylated cytosines/number total cytosines',score,strand

source_name: hiPS B36

extract_protocol:
Please see Gu et al., 2011 and Smith et al., 2012
RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)

tag: individual

value: Individual B

value: PgiPSC


title: hiPS_B41

source_name: hiPS B41


title: N43_CD44+_SAGEseq

source_name: human CD44+ breast progenitor cells

value: bead purified CD44+ progenitor cells

value: nulliparous


title: N39_Stroma_SAGEseq


title: Cytoplasm DMSO 1

source_name: HEK293 Cytoplasm DMSO 1


title: hiPS_B34

source_name: hiPS B34


title: N_172_BRCA2_44_SAGEseq


title: hiPS_A26

source_name: hiPS A26

value: Individual A


title: hiPS_A20

source_name: hiPS A20


title: hFib_fibA

source_name: fibroblast A

value: fibroblast


title: Mouse_PTEN_H3K4me1_IP

source_name: Mouse Prostate

tag: chip antibody

value: Rabbit Anti-Histone monomethyl-H3 (Abcam ab8895, Lot GR61280-1)


title: IgG.I_CLIPSeq

first: Jessica

last: Hurt

address: 77 Massachusetts Avenue

department: Biology

institute: Massachusetts Institute of Technology

description: small RNA fragments bound to IgG

data_processing:
Library strategy: CLIP-Seq
Paired-end mRNA-Seq and ribosome footprinting libraries were mapped to the mouse genome (mm9) with a splice junction database using Tophat v.1.4.0 (Trapnell et al. 2009) allowing 2 mismatches but disallowing splice site mismatches and novel intron discovery (--solexa1.3-quals --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --no-novel-juncs).  Isoform and gene expression values were then estimated using Cufflinks v.1.3.0 (Trapnell et al. 2010) and a combined Ensembl and UCSC annotation database of predicted coding genes (with duplicate isoforms removed) (--compatible-hits-norm).  To maximize detection of lowly expressed isoforms, mapped files from like shRNA hairpins were merged before gene expression quantitation.  For mRNA-Seq libraries, mapping to the entire mature mRNA sequence was used to estimate isoform and gene expression values.  For ribosome footprinting libraries, mapping to only the coding sequence was used to estimate gene expression values.
CLIP-Seq libraries were filtered for unique sequences, trimmed for remaining adapters and 2 nucleotide randomized barcode, and mapped uniquely to the mouse genome (mm9) and a database of splice junction sequences using Bowtie v.0.12.6 (Langmead et al. 2009) allowing 2 nucleotide mismatches  (-m 1 --best –strata).  Reads from each IgG library were amplified by 10x and then subtracted from their experimentally matched Upf1 library by iteratively cancelling out reads that overlapped.  Barcodes which were likely (p >= 0.05) misreads of other highly amplified barcoded reads at the same position were then predicted based on a Poisson model and removed.
Genome_build: mm9
Supplementary_files_format_and_content: For mRNA-Seq and ribosome footprinting libraries, isoform and gene expression values (output of Cufflinks software) are provided.
Supplementary_files_format_and_content: For CLIP-Seq libraries, a bed file describing read positions is provided for each Upf1 sample.  This file has been filtered for overlapping IgG reads and "one-off" barcodes that were predicted to be due to PCR amplification.  Note that for determiniation of gene binding, Upf1 positions were further collapsed for unique barcode/position combinations.

source_name: IgG control CLIP-Seq

growth_protocol: mESCs were cultured on MEFs in standard mESC medium with LIF at 37deg, 5% CO2.  For shRNA-expressing clones, 1.5ug/ml puromycin was added to media.  Prior to any RNA isolation technique, mESCs were pre-plated for 30minutes on gelatinized culture dishes to remove MEFs.  Only mESCs remianing in suspension were collected for analysis.  For shRNA-expressing clones, puromycin was removed from media 48hours prior to analysis.  For CLIP-Seq libraries, mESCs were pre-plated to remove MEFs and plated off of MEFs 24 hours in gelatinized culture dishes prior to UV irradiation.

extract_protocol:
For CLIP-Seq libraries, mESCs were UV irradiated (254 nm, 400mJ/cm2) in 4ml PBS on ice and then trypsinized, washed with PBS, and snap frozen in liquid nitrogen.  Frozen cell pellets were lysed directly in lysis buffer (see Methods).
CLIP-Seq libraries were prepared essentially as described in Wang et al. 2012 that added 3' and 5' adapters by RNA ligation. 5' adapter added 2 randomized nucleotides to enable filtering of reads based on PCR amplificaiton.

treatment_protocol: For CHX treatment, 100ug/ml cycloheximide was added to culture media for 2hours at 37deg prior to harvest.

tag: antibody

value: rabbit IgG (Upstate Antibodies Cat No. 12-370)

value: Embryonic stem cells


title: Upf1.A1_CLIPSeq

description: small RNA fragments bound to Upf1

source_name: CLIP-Seq analysis of Upf1

value: rabbit anti-Upf1 (Bethyl Labs Cat. No. A301-902A)


title: Upf1.I_CLIPSeq

description: small RNA fragments bound to Upf1


title: hiPS_A11

source_name: hiPS A11


title: v6.5_RiboSeq

description: small RNA fragments protected by ribosomes

data_processing:
Paired-end mRNA-Seq and ribosome footprinting libraries were mapped to the mouse genome (mm9) with a splice junction database using Tophat v.1.4.0 (Trapnell et al. 2009) allowing 2 mismatches but disallowing splice site mismatches and novel intron discovery (--solexa1.3-quals --splice-mismatches 0 --min-intron-length 10 --max-intron-length 1000000 --min-isoform-fraction 0.0 --no-novel-juncs).  Isoform and gene expression values were then estimated using Cufflinks v.1.3.0 (Trapnell et al. 2010) and a combined Ensembl and UCSC annotation database of predicted coding genes (with duplicate isoforms removed) (--compatible-hits-norm).  To maximize detection of lowly expressed isoforms, mapped files from like shRNA hairpins were merged before gene expression quantitation.  For mRNA-Seq libraries, mapping to the entire mature mRNA sequence was used to estimate isoform and gene expression values.  For ribosome footprinting libraries, mapping to only the coding sequence was used to estimate gene expression values.
CLIP-Seq libraries were filtered for unique sequences, trimmed for remaining adapters and 2 nucleotide randomized barcode, and mapped uniquely to the mouse genome (mm9) and a database of splice junction sequences using Bowtie v.0.12.6 (Langmead et al. 2009) allowing 2 nucleotide mismatches  (-m 1 --best –strata).  Reads from each IgG library were amplified by 10x and then subtracted from their experimentally matched Upf1 library by iteratively cancelling out reads that overlapped.  Barcodes which were likely (p >= 0.05) misreads of other highly amplified barcoded reads at the same position were then predicted based on a Poisson model and removed.
Genome_build: mm9
Supplementary_files_format_and_content: For mRNA-Seq and ribosome footprinting libraries, isoform and gene expression values (output of Cufflinks software) are provided.
Supplementary_files_format_and_content: For CLIP-Seq libraries, a bed file describing read positions is provided for each Upf1 sample.  This file has been filtered for overlapping IgG reads and "one-off" barcodes that were predicted to be due to PCR amplification.  Note that for determiniation of gene binding, Upf1 positions were further collapsed for unique barcode/position combinations.

source_name: Ribosome footprint profiling of wildtype

extract_protocol:
For ribosome footprinting libraries, mESCs were washed 1xPBS and snap frozen in liquid nitrogen.  Frozen cell pellets were lysed directly in lysis buffer (see Methods).
Ribosome footprinting libraries were prepared essentially as described in Wang et al. 2012 using ultra-centrifugation to isolate ribosome protected RNA fragments.  Polyadenylation and circularization was used to add adapters as developed by Ingolia et al. 2009.


title: GFP_2.6_RiboSeq

source_name: Ribosome footprint profiling of control-depleted


title: IgG.CHX.A2_CLIPSeq

description: small RNA fragments bound to IgG


title: IgG.CHX.A1_CLIPSeq

description: small RNA fragments bound to IgG


title: N58_Stroma_SAGEseq

source_name: human breast stromal cells

value: breast

value: bead purified stromal cells


title: IgG.A1_CLIPSeq

description: small RNA fragments bound to IgG


title: IgG.A2_CLIPSeq

description: small RNA fragments bound to IgG


title: N33_Stroma_SAGEseq


title: N_152_BRCA2_44_SAGEseq

source_name: expression library from cd44+ cells from BRCA1 and BRCA2 mutation carriers


title: hFib_fibB

source_name: fibroblast B


title: Upf1.CHX.A2_CLIPSeq

description: small RNA fragments bound to Upf1


title: Upf1-1_4.7_RiboSeq

source_name: Ribosome footprint profiling of Upf1-depleted


title: Upf1.A2_CLIPSeq

description: small RNA fragments bound to Upf1


title: Upf1.CHX.A1_CLIPSeq

description: small RNA fragments bound to Upf1


title: v6.5_CHX_p24_mRNASeq

description:
v6.5_CHX_merge_genes.fpkm_tracking
v6.5_CHX_merge_isoforms.fpkm_tracking

source_name: mRNA-Seq analysis of translationally inhibited (by cycloheximide treatment)

extract_protocol:
For mRNA-Seq libraries, total RNA was isolated using TRIZOL reagent followed by chloroform extraction and precipitation by isopropanol.  RNA was further purified over RNAeasy columns (Qiagen) and treated with DNAse (on-column).
Paired-end mRNA-Seq libraries were prepared from poly(A)-selected RNA using a strand-specific, dUTP-incorporation, protocol (Parkhomchuk et al. 2009) and employing the SPRIworks Fragment library system (Beckman Coulter).  cDNA amplification was performed using 14 cycles of PCR and final libraries were sized selected by agarose gel analysis.


title: v6.5_CHX_p22_mRNASeq


title: v6.5_p24_mRNASeq

description:
v6.5_NoCHX_merge_genes.fpkm_tracking
v6.5_NoCHX_merge_isoforms.fpkm_tracking

source_name: mRNA-Seq analysis of wildtype


title: N35_Stroma_SAGEseq


title: Upf1-2_5.7_mRNASeq

description:
Upf1.2_merge_genes.fpkm_tracking
Upf1.2_merge_isoforms.fpkm_tracking

source_name: mRNA-Seq analysis of Upf1-depleted


title: N43_CD24+_SAGEseq

source_name: human CD24+ breast epithelial cells

value: bead purified CD24+ epithelial cells


title: Upf1-2_5.2_mRNASeq


title: Upf1-1_4.4_mRNASeq

description:
Upf1.1_merge_genes.fpkm_tracking
Upf1.1_merge_isoforms.fpkm_tracking


title: Upf1-1_4.7_mRNASeq


title: GFP_2.4_mRNASeq

description:
GFP_merge_genes.fpkm_tracking
GFP_merge_isoforms.fpkm_tracking

source_name: mRNA-Seq analysis of control-depleted


title: GFP_2.6_mRNASeq


title: v6.5_p22_mRNASeq


title: SPARE col-0

city: Rosario

first: Uciel

middle: Pablo

last: Chorostecki

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

description: Total RNA depleted of rRNA.

data_processing:
Adapter sequences and low quality tags where removed with in house perl script.
Reads were mapped to Arabidopsis miRNA precursor sequences using Bowtie, allowing only perfect matches to the plus strand.
Removal of sequences shorter or equal than 25 nucleotides.
MiRNA precursors were defined as 200 nt surrounding the miRNA/miRNA*.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files, which hold the miRNA identifier, the sequence reads (tags) and their corresponding number of copies (abundance) generated by the Illumina deep-sequencing.

organism: Arabidopsis thaliana

source_name: Mix of seedlings, leaves and inflorescences, wild type

growth_protocol: Inflorescences tissues and leaves were harvested from plants grown at 23°C in soil in a growth chamber with 16 h of light for 5 weeks. Seedlings were grown at 23°C under the same 16 h, long-day conditions and were harvested after 2 weeks.

extract_protocol:
Total RNA was isolated using Trizol reagents (Invitrogen).
Total RNAs (1 μg) depleted of ribosomal RNA from 5-week-old inflorescence and leaf tissues and 2-week-old seedlings isolated using RiboMinus Plant Kit for RNA-Seq (Invitrogen) and an RNA oligonucleotide adaptor (5'-GUUCAGAGUUCUACAGUCCG AC-3'; Dharmacon Research) was ligated using T4 RNA ligase (Fermentas). The ligated products were purified and used as a template in ten multiplex reverse transcription reaction using ~18 different precursor-specific oligos in each multiplex reaction and Superscript III reverse transcriptase (Invitrogen). Each precursor-specific oligo also contain a 5' generic adaptor tale with the sequence 5'-AGCAGAAGACGGCATACGA-3'. Then using mix of the ten multiplex reaction is amplified by PCR using the generic P5 primer 5'-AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA-3' (Integrated DNA Technologies) and P7 primer 5'-CAAGCAGAAGACGGCATACGA-3' (Integrated DNA Technologies). The conditions for PCR were 18 cycles of 94 °C for 20 s, 60 °C for 20 s and 72°C for 20 s. PCR products were gel purified and subjected to SBS sequencing.

tag: ecotype

value: wild type

value: seedlings, leaves and inflorescences


title: Input_Tcf1_WT

city: Bethesda

first: Marei

last: Dose

state: MD

address: 9000 Rockville Pk

institute: National Institutes of Health

data_processing:
base-calling: Illumina
alignment: bowtie-0.12.8/bowtie -S -m 1 -p 20 -a --best --strata -n 2
filtering (uniquely aligned reads): samtools-0.1.18/samtools view -S -b -F4
normalized tag density: custom script, maximum 2 reads with the same start position allowed
Genome_build: mm9
Supplementary_files_format_and_content: .wig files contain tag counts in 100 nt windows divided by windowsize and library size in millions to obtain normalized read counts (rpkm)

source_name: thymus

extract_protocol:
1e08 WT thymocytes were fixed in 3ml of RPMI containing 1% formaldehyde for 10 min at room temperature. The fixative was quenched with glycine, samples were washed twice with ice cold PBS and cells were lysed in RIPA buffer for 10 min on ice. Samples were then sonicated using Diagnode's Bioruptor water bath sonicator (desired fragment size=200bp, conditions vary). Lysates were cleared by centrifugation and incubated overnight with Tcf-1 antibodies [a kind gift of Hiroshi Kawamoto (Riken Yokohama Institute, Yokohama, Japan)] coupled to Protein G Dynabeads (Life Technologies). Immunoprecipitation and input samples were de-cross-linked overnight at 65 °C in elution buffer [50 mM Tris·HCl (pH 8)/10 mM EDTA/1% SDS/ 0.3 M NaCl]. DNA was extracted with phenol/chloroform, quantified, and quality-checked for enrichment of known target regions of Tcf-1 by real-time PCR. ChIP-Seq libraries were prepared from 10 ng of immunoprecipitated material according to an Illumina ChIP DNA library preparation kit.
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 15 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 II following the manufacturer's protocols.

value: WT

value: 4-6 weeks

value: none, input


title: SPARE fiery

description: Total RNA depleted of rRNA.

source_name: Mix of seedlings, leaves and inflorescences, fiery

value: fiery


title: EGF replicate 3

status: Public on Jun 11 2013

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium supplemented with EGF for 6 additional hours. Biological replicate 3 of 3

data_processing:
After annealing of the sequencing primer, libraries were sequenced using a GAII instrument (Illumina). Images taken during sequencing were processed by Illumina’s software (v.192) Firecast/Burstard/Gerald.
Raw data were processed using the Illumina pipeline version 0.3.0.
Data were further processed to specifically analyze miRNA sequences using the MIRO software (http://seq.crg.es/download/software/Miro/)  (Koffler et al, unpublished)
3’ adapters were recognized and trimmed using a perl script that penalizes mismatches to a lesser extent at read ends, following the distribution of sequencing errors along Solexa reads (Dohm et al. 2008). Where no adaptor could be recognized, sequence was cut down to 22 nt.
The compiled collection of reads with removed adapters was aligned against the reduced-complexity set of miRbase version 12.0 entries (including miRbase primary miRNA, mature miRNA and star miRNAs). The mapping was performed by applying Eland iteratively in order to include all possible product sizes.
Reads mapping unambiguously were counted for each unique miRbase entry within the reduced-complexity miRbase reference set
The per-miRNA count data from Illumina sequencing was normalized according to estimated effective library sizes (Robinson and Oshlack 2010).
Genome_build: mirBase 12.0
Supplementary_files_format_and_content: (.txt) MIRO pipeline output of run_Mapping.pl script (http://seq.crg.es/download/software/Miro/) containing the mapping to reference sequence and count information  / column1: just some id for the read and the number how often the given read has been counted / column2: sequence of the read /column3: reference sequence id / column4: ambiguity (1=unambiguous) / column5: number of mismatches (0, 1, or 2) / column6: strand (F..forward,R..reverse) / column7: position in miRbase reference sequence

source_name: Cervical cancer cell line (HeLa)

growth_protocol: Cells were cultured at 37ºC in a 95/5 Air/CO2 water saturated  atmosphere in Dulbecco’s  modified  Eagle’s medium (DMEM) containing 10% heat inactivated foetal bovine serum (FBS), 2 mM  L-glutamine and 100U/ml Penicilin/streptomycine (complete growth medium).

extract_protocol:
Total RNA from HeLa cells was extracted using the miRvana Isolation kit (Ambion) following manufacturer's instructions. RNA quantification was performed with a Nanodrop spectrophotometer, and the RNA integrity was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE). For each of the six samples, 1 ug of small-RNA-enriched total RNA was separated by acrylamide gel purification of RNA bands corresponding to the size range 18–30 nucleotides
We performed successive ligation of of 5' and 3' adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification. Ligated RNA was reverse transcribed into short cDNA and size selected by acrylamide gel purification. Finally, purified size selected short cDNA was amplified by PCR to generate template library for cluster generation on a flow cell.

treatment_protocol: For treatments, the cells were transferred to 60 mm dishes and cultured for 48h in complete growth medium, after which they were starved for 24h in DMEM containing 2% FBS after which they were grown in complete growth medium or the same supplemented with EGF (150 ng/ml) during 6 hours

value: HeLa

tag: agent

value: EGF

tag: biological replicate


title: Tc1f_WT

tag: antibody provider

value: antiserum provided by Dr. Kawamoto


title: EGF replicate 2

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium supplemented with EGF for 6 additional hours. Biological replicate 2 of 3


title: Control replicate 3

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium for 6 additional hours. Biological replicate 3 of 3

value: Control


title: Control replicate 1

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium for 6 additional hours. Biological replicate 1 of 3


title: Control replicate 2

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium for 6 additional hours. Biological replicate 2 of 3


title: 2i unsorted rep 2

city: Copenhagen

first: Joshua

last: Brickman

address: Blegdamsvej 3B

department: The Danish Stem Cell Centre (DanStem)

country: Denmark

institute: University of Copenhagen

data_processing:
Bowtie was used to align sequence reads to GenBank mRNA sequences(max 2 mismatches; max 10 alignments).
Total number of aligned tags is counted for each transcript, and then converted to RPKM (reads per 1K mRNA length and 1M reads) and RPM (reads per 1M reads).
Data on sorted cells was adjusted so that the average of log-transformed read counts for each mRNA in venus-positive (HV+) and venus-negative (HV-) cells matched between replication #1 and replication #2. Data n1+, n1-, n2+, and n2- (where index 1, 2 correspond to replication, and +, - correspond to HV+ and HV-) was log-transformed into x1+, x1-, x2+, and x2-. Then, averages were estimated for each replication: m1 = [( x1+) + (x1-)]/2 and m2 = [( x2+) + (x2-)]/2. Then adjusted log-transformed values were estimated: (x1+)' = (x1+) - (m1 - m2)/2; (x1-)' = (x1-) - (m1 - m2)/2; (x2+)' = (x2+) + (m1 - m2)/2; (x2-)' = (x2-) + (m1 - m2)/2
Finally, adjusted log-transformed data were converted back using exponent function.
Genome_build: RefSeq release 54
Supplementary_files_format_and_content: RPKM

source_name: Embryonic stem cells

growth_protocol: Mouse ES cells were cultured standardly in either serum/LIF conditions or in 2i or 2i/LIF conditions (serum-free conditions containing 1µM PD032 MEK inhibitor and CHIR99021 3µM GSK3 inhibitor). Cells were passaged every 2 days. For sorting by flow cytometry, Hex-venus low (HV-) or Hex-venus high (HV+) cells were sorted from the lower and upper 25% of Hex expressing cells contained within the DAPI negative (viable cells), Pecam positive (undifferentiated ES cell) population.

extract_protocol:
Total RNA was extracted from ES cells using Qiagen RNAeasy kit. Approx. 10 µg of total RNA underwent 2 rounds of mRNA enrichment with Dynalbeads Oligo(dT)25 (61005, Life tech).
Solid whole transcriptome libraries were made according to the Solid Total RNA-seq protocol with the exception of RNA fragmentation (4445374, Life tech). RNA was fragmented by chemical hydrolysis; heating to 95°C, 10 min in 1x RNAse III buffer (AM2290, Life tech) and snap cooled on ice. ATP (0.83mM, 11140965001, Roche) and 10 U of T4 PNK (M0201L, NEB) were added and incubated at 37°C, 30 min. RNA was purified using Purelink RNA Micro Kit (12183-016, Life tech). Equimolar pools of RNA-seq libraries were made following qPCR quantification using Kapa Library Quantification kit (KK4823, Kapa Biosystems). ePCR and templated bead enrichment was carried out with Solid EZ bead system according to manufacturer’s guidelines. Enriched beads were sequenced on an ABi SOLiD 4 analyser according to the manufacturer’s instructions to generate 50 bp reads in colour space.

tag: genetic background

tag: treatment

value: 2i unsorted


title: 2i/LIF unsorted rep 2

value: 2i/LIF unsorted


title: 2i unsorted rep 1

value: Embryonic stem cells


title: N39_CD10+_SAGEseq

source_name: human CD10+ breast myoepithelial cells

tag: tissue

value: bead purified CD10+ myoepithelial cells

value: parous


title: N48_CD10+_SAGEseq

value: breast

value: nulliparous


title: 2i/LIF HV+ rep 1

value: 2i/LIF HV+


title: serum/LIF HV+ rep 2

value: serum/LIF HV+


title: serum/LIF HV+ rep 1


title: serum/LIF HV- rep 1

value: serum/LIF HV-


title: serum/LIF HV- rep 2


title: 2i/LIF unsorted rep 1


title: 2i/LIF HV- rep 1

value: 2i/LIF HV-


title: 2i/LIF HV+ rep 2


title: sperm PS RNA-Seq rep2

status: Public on Jun 10 2013

city: Detroit

first: Stephen

last: Krawetz

state: MI

address: 275 E. Hancock

department: Center for Molecular Medicine and Genetics

institute: Wayne State University School of Medicine

data_processing:
Short reads were mapped to NCBI build 37.2 of the human reference genome using TopHat [7] (version 1.3.2) at paired-end base with default parameters. Alignment results were confirmed independently using Novoalign (Novocraft Technologies v.2.07). The relative abundance of each transcript as FPKM (fragments per kilobase exon per million fragments mapped) was calculated using Cufflinks [8] (version 1.1.0).
Genome Build:
S2_PS.bed: hg19

source_name: Fertile Human Sperm

extract_protocol: The standard RNA-Seq libraries were prepared using the Illumina TruSeq Sample Prep Kit (Part #RS-930-2001) according to the manufacturer’s protocol. Briefly, 500 ng of total RNA was subject to two rounds of isolation and purification with oligo-dT beads (Illumina). Purified mRNA was then fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and reverse transcriptase. Second strand cDNA synthesis was performed using RNAseH and DNA PolI. Following cDNA synthesis, double stranded products were end repaired, a single base ‘A’ was added, and Illumina PE adaptors were ligated onto the cDNA products followed by 15 rounds of PCR enrichment. All samples were subject to paired-end sequencing using the Illumina Genome Analyzer (GAIIx) for 34 cycles. Image analysis, base calling, FASTQ generation and demultiplexing were performed using the genome analyzer pipeline software CASAVA (version 1.8.1).

treatment_protocol: Semen was collected then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).

value: Mature sperm

tag: sample source

value: Semen from a normally fertile donor


title: sperm PS RNA-Seq rep1

data_processing:
Short reads were mapped to NCBI build 37.2 of the human reference genome using TopHat [7] (version 1.3.2) at paired-end base with default parameters. Alignment results were confirmed independently using Novoalign (Novocraft Technologies v.2.07). The relative abundance of each transcript as FPKM (fragments per kilobase exon per million fragments mapped) was calculated using Cufflinks [8] (version 1.1.0).
Genome Build:
S1_PS.bed: hg19

tag: cell type


title: 2i/LIF HV- rep 2


title: testis RNA-Seq rep1

data_processing:
Short reads were mapped to NCBI build 37.2 of the human reference genome using TopHat [7] (version 1.3.2) at paired-end base with default parameters. Alignment results were confirmed independently using Novoalign (Novocraft Technologies v.2.07). The relative abundance of each transcript as FPKM (fragments per kilobase exon per million fragments mapped) was calculated using Cufflinks [8] (version 1.1.0).
Genome Build:
T1.bed: hg19

source_name: Testes

value: testes

value: From commercial libraries


title: N48_CD44+_MSDKseq

source_name: human CD44+ breast progenitor cells

value: bead purified CD44+ progenitor cells

tag: parity


title: sRNA.6009.6h.Linezo

city: Heidelberg

first: Ben

last: Howden

state: VIC

address: Austin Health

department: Infectious Diseases Department

country: Australia

institute: Austin Health

data_processing:
Read clipping using nesoni clip tool. Nesoni url: http://vicbioinformatics.com/software.nesoni.shtml
Read alignment using SHRiMP 2.2.2. SHRiMP url: http://compbio.cs.toronto.edu/shrimp/
Alignment selection using nesoni filter tool. Only top scoring alignments were kept. Where there were multiple equal best alignments, one was chosen at random.
Counting of alignments to annotated CDS sequences and sRNA sequences, using nesoni count tool. Alignments were required to be on the correct strand.
Normalization factors to render expression levels comparable between samples were calculated using BioConductor package edgeR's implementation of the TMM normalization method.
Genome_build: CP002120.1
Supplementary_files_format_and_content: The *-count.csv files contain counts of the numbers of reads aligning to each feature. The accompanying *-counts-norm.txt files give normalization factors for each sample.

organism: Staphylococcus aureus

growth_protocol: S. aureus were grown in Mueller Hinton broth for 2 or 6 hours.

extract_protocol: Total RNA was extracted using the Rneasy Kit (Qiagen). RNAs were then treated with the MICROBExpress kit (AMBION) to limit the contamination by rRNAs, following manufacturer’s recommendations. At each step, RNA quality was controlled by Bioanalyzer (Agilent) using the RNA Nano Chips, and quantity was assessed using the ND-8000 (NanoDrop Technologies. Extracted RNA was prepared to enrich for mRNA or sRNA as follows. For mRNA preparations, initial fragmentation using Zinc was followed by treatment with first Antartic Phosphatase and then with PNK enzyme. Single-stranded ligation of the 3’ Illumina v1.5 adapter was followed by single-stranded ligation of 5’ bar-coded adapter. Reverse transcription and PCR amplification was performed to generate a cDNA colonies template library, and gel purification with selection of fragments of 20-300 nts was performed. Quality control of the DNA colony template library was performed by cloning an aliquot into a TOPO plasmid and sequencing 8 clones. The same process was used for sRNA preparation, without the Zinc fragmentation, and using a size selection of 20-200 nt.

treatment_protocol: Antibiotics exposure was for 10 minutes at 0.5 x MIC.

tag: antibiotic

value: Linezolid

tag: growth time

value: 6 hours

tag: rna preparation

value: sRNA


title: sRNA.6009.6h.Vanco

value: Vancomycin


title: N35_CD10+_SAGEseq

value: bead purified CD10+ myoepithelial cells


title: sRNA.6009.6h.Cefto

value: Ceftobiprole


title: sRNA.6009.6h.TEM


title: sRNA.6009.2h.Vanco

value: 2 hours


title: sRNA.6009.2h.Tige

value: Tigecycline


title: sRNA.6009.2h.Linezo


title: sRNA.6009.2h.Cefto


title: sRNA.6009.6h.Tige


title: sRNA.6009.2h.TEM


title: EGF replicate 1

description: HeLa cells, serum deprived for 24 hours, followed by culture in complete medium supplemented with EGF for 6 additional hours. Biological replicate 1 of 3

tag: cell line

value: HeLa

value: EGF


title: sRNA.6008.6h.Vanco


title: sRNA.6008.6h.Linezo


title: sRNA.6008.6h.Tige


title: N123_CD10+_SAGEseq

value: breast

value: parous


title: sRNA.6008.6h.Cefto


title: sRNA.6008.2h.Vanco


title: sRNA.6008.6h.TEM


title: sRNA.6008.2h.Linezo


title: sRNA.6008.2h.Cefto


title: sRNA.6008.2h.Tige


title: sRNA.6008.2h.TEM


title: mRNA.6009.6h.Tige

value: mRNA


title: mRNA.6009.6h.Linezo


title: mRNA.6009.6h.Cefto


title: N40_CD10+_SAGEseq


title: mRNA.6009.6h.Vanco


title: mRNA.6009.6h.TEM


title: mRNA.6009.2h.Tige


title: mRNA.6009.2h.Vanco


title: mRNA.6008.6h.Vanco


title: mRNA.6009.2h.Cefto


title: mRNA.6009.2h.Linezo


title: mRNA.6009.2h.TEM


title: mRNA.6008.6h.Tige


title: P_CD44_BRCA1_N174_SAGEseq

source_name: expression library from cd44+ cells from BRCA1 and BRCA2 mutation carriers

value: mammary gland

value: cd44+ cells from BRCA1 mutation carrier


title: N43_CD10+_SAGEseq

value: nulliparous


title: N48_CD24+_MSDKseq

value: bead purified CD24+ epithelial cells


title: mRNA.6008.6h.Cefto


title: mRNA.6008.6h.Linezo

value: Linezolid


title: P_CD44_BRCA1_N105_SAGEseq


title: shGata6Hopx.1

city: New Haven

first: Don

last: Nguyen

state: CT

address: 310 Cedar St

institute: Yale Shcool of Medicine

description: KD

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf
Reads per gene was calculated using HtSeq-count in union mode
Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample.

extract_protocol: Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturer’s instructions with single-end 50 base pair reads.

treatment_protocol: Doxycycline (1ug/ml) for 5 days

value: human lung Adenocarcinoma

tag: transfected with

value: lentivirus harboring shRNA of both GATA6 and HOPX


title: shCtrl.3

description: Ctrl

source_name: shCtrl

value: lentivirus harboring shRNA of control (Arab1)


title: shCtrl.2

description: Ctrl


title: shGata6Hopx.2

description: KD


title: mRNA.6008.2h.Vanco

value: Vancomycin


title: mRNA.6008.2h.Tige


title: shGata6Hopx.3

description: KD


title: P_CD44_BRCA1_N171_SAGEseq


title: Input DNA for H3K36me3 ChIP

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

description: input for H3K36me3 (noWGA)

data_processing:
Input-FB-CMM023_023_unique_hits.tags.txt; genome build: mm8
The tags were extended by 200 bp to make wiggle track for sequenced libraries binning whole genome in 200bp bins. For finding peaks in H3K4me3 ChIPseq Dfilter was used. The peaks are provided in supplementary material. The ChIPseq data was also used by EFilter to predict expression of gene in mouse forebrain. For Efilter GC correction was done for both ChIP libraries using corresponding input libararies.

source_name: Input DNA for H3K36me3 ChIP

extract_protocol: Mouse embryonic forebrain tissues were micro-dissected and pooled from 11.5 dpc embryos. Dissected tissues were mechanically dissociated by passing cell strainer and fixed in 1% formaldehyde (diluted from 37% stock solution, Sigma, F8775) simultaneously following pre-treatment with 0.125% tripsin/versene solution. 36 forebrain pieces were used for each ChIP-seq library preparation. Cells were resuspended in SDS buffer and sonicated 12 times for 30 seconds with 30 seconds interval with Bioruptor water bath sonicator (Diagenode). Following sonication, samples were diluted with IP dilution buffer and incubated with 50 micro-litter affinity resin coupled with 10 micro-litter anti-H3K4me3 antibodies (Upstate, Cat# 07-473, Lot# 32497). Following washing steps, chromatin was reverse-crosslinked for purification of DNA. H3K4me3 ChIPed DNA and 0.5 % input DNA samples were amplified for 8 cycles with GenomePlex Single Cell Whole Genome Amplification Kit (WGA4, Sigma) using universal primer linked to BpmI restriction site. Amplified DNA samples were digested with BpmI to remove universal primer. After quantification of DNA with Quant-iT PicoGreen sdDNA Assay Kit (Invitrogen, P7589), 12 ng of the DNA sample was directly used for Illumina sequencing adaptor preparation. Illumina sequencing was performed using GAII platform in GIS. H3K36me3 data was obtained similarly using 15 micro-litter of anti-H3K36me3 antibody (Abcam, Cat# Ab9050, Lot# 707981). As DNA yield of H3K36me3 antibody ChIP was much higher, WGA amplification step was not performed and ChIP DNA was directly used for Illumina sample preparation.

tag: strain

tag: develepmental stage

value: forebrain

tag: chip antibody


title: mRNA.6008.2h.Linezo

value: 2 hours


title: shCtrl.1

description: Ctrl


title: mRNA.6008.2h.Cefto

value: Ceftobiprole