title: Mouse_Liver_IP

extract_protocol: Total RNA was purified from whole mouse liver using 5PRIME PerfectPure RNA Cultured Cell kit (cat#2302340). PolyA RNA was selected by one round of Sigma GenElute mRNA Miniprep Kit (cat#MRN70-1KT). Total RNA of normal human brain was purchased from Biochain, CA, USA. RNA was fragmented chemically to ~100 nt long fragments and subjected to IP using anti-m6A antibodies. 1st strand cDNA was synthesized using Illumina random primers and Invitrogen SuperScript II Reverse Transcriptase (Cat# 18044-014) then 2strand cDNA was synthesized by Illumina's mRNA Sample preparation Kit (Part# 1004814). 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 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  ~200 bp DNA fragments (insert plus adaptor and PCR primer sequences)  were isolated from 2% agarose gel. Purified DNA fragments were PCR amplified with Illumina primers for 15 cycles and 10pM DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

tag: vendor

value: Synaptic Systems

tag: catalog#


title: Human_Brain_input

status: Public on Apr 25 2012

type: SRA

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

library_source: transcriptomic

data_processing: Supplementary_files_format_and_content: Supplementary data human brain' and 'Supplementary data mouse liver' files are provided in .txt format. They contain a dataset of all identified m6A peaks in normal human brain and nornal mouse liver, respectively. Corresponding legends are:  id – KnownCanonical identification; chr – chromosome; txStart – transcription start position on chromosome; txEnd – Transcription end position on chromosome; strand - +/- chromosome strand;  geneSymbol – official symbol of gene; desc – description;  Factor_iscoding– either coding or noncoding, depending on the annotation of the gene in the UCSC table; Meanexpquant – expression quantile of the gene based on reads in input experiment; Peaksnum – number of peaks identified in gene; Peakspos – position of peaks relative to beginning of transcript (after removing introns); Peaksexonnum – ordinal number of exons in which the peaks were identified; Peaksexlengths – lengths of the exons in which the peaks were found; Peakscores – the peakscore of the identified peaks; Annotpeakpos – segment along the gene in which the peaks.

molecule: total RNA

organism: Homo sapiens

source_name: Human brain

extract_protocol: Total RNA was purified from whole mouse liver using 5PRIME PerfectPure RNA Cultured Cell kit (cat#2302340). Total RNA of normal human brain was purchased from Biochain, CA, USA. RNA was fragmented chemically to ~100 nt long fragments and subjected to IP using anti-m6A antibodies. 1st strand cDNA was synthesized using Illumina random primers and Invitrogen SuperScript II Reverse Transcriptase (Cat# 18044-014) then 2strand cDNA was synthesized by Illumina's mRNA Sample preparation Kit (Part# 1004814). 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 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  ~200 bp DNA fragments (insert plus adaptor and PCR primer sequences)  were isolated from 2% agarose gel. Purified DNA fragments were PCR amplified with Illumina primers for 15 cycles and 10pM DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

tag: tissue

value: Normal human brain

tag: antibody


title: Input2

description: human hepatocarcinoma cell line

data_processing: Supplementary_files_format_and_content: Supplementary data HepG2 untreated' file is provided in .txt format. It contains a dataset of all identified m6A peaks in HepG2 under the various treatments described above. Corresponding legends are: id – KnownCanonical identification; chr – chromosome; txStart – transcription start position on chromosome; txEnd – Transcription end position on chromosome; strand - +/- chromosome strand;  geneSymbol – official symbol of gene; desc – description;  Factor_iscoding– either coding or noncoding, depending on the annotation of the gene in the UCSC table; Meanexpquant – expression quantile of the gene based on reads in input experiment; Peaksnum – number of peaks identified in gene; Peakspos – position of peaks relative to beginning of transcript (after removing introns); Peaksexonnum – ordinal number of exons in which the peaks were identified; Peaksexlengths – lengths of the exons in which the peaks were found; Peakscores – the peakscore of the identified peaks; Annotpeakpos – segment along the gene in which the peaks.

source_name: HepG2 cells

growth_protocol: Cells were grown in DMEM (Gibco, Invitrogen Inc.) containing 4.5 g/L glucose and L-Glutamine supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol: Total RNA was purified from the cells using 5PRIME PerfectPure RNA Cultured Cell kit (cat#2302340) and polyA+ selection was carried out using GenElute mRNA miniprep kit (Sigma Aldrich, cat#MRN70). RNA was fragmented chemically to ~100 nts long fragments and subjected to IP using anti-m6A antibodies. 1st strand cDNA was synthesized using Illumina random primers and Invitrogen SuperScript II Reverse Transcriptase (Cat# 18044-014) then 2strand cDNA was synthesized by Illumina's mRNA Sample preparation Kit (Part# 1004814). 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 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  ~200 bp DNA fragments (insert plus adaptor and PCR primer sequences)  were isolated from 2% agarose gel. Purified DNA fragments were PCR amplified with Illumina primers for 15 cycles and 10pM DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

tag: cell line


title: [E-MTAB-935] polyA+_liver_6100188, Batch_7_liver

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description: Performer: University of Lausanne, Switzerland

data_processing: processed data not provided

molecule: polyA RNA

extract_protocol:
nucleic_acid_extraction | RNA from tissues was isolated by a modified guanidium thiocynate methods followed by polyA+ RNA selection with two rounds of oligo(dT)-cellulose columns. Selected targets were then amplified by RT-PCR
sequencing | Aliquots of up to 5000 RT-PCRs reactions were pooled together and the sequencing library was prepared with no fragmentation using the TruSeq DNA protocol. DNA fragments were sequenced on a Illumina HiSeq2000 sequencer and 2 multiplexed libraries were loaded per lane. The sequencing was performed at the University of Lausanne, Lausanne, Switzerland.
bioassay_data_transformation |

tag: material type

tag: organismpart

value: liver

tag: Sex

value: male

tag: biosourcetype

tag: biosourceprovider

value: Clontech


title: Input3

description: human hepatocarcinoma cell line


title: Input1

description: human hepatocarcinoma cell line


title: IP3

description: human hepatocarcinoma cell line


title: IP4

description: human hepatocarcinoma cell line


title: Human_Brain_IP


title: IP2

description: human hepatocarcinoma cell line


title: UW_RepliSeq_BJ

status: Public on Apr 27 2012

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: genomic

molecule: genomic DNA

source_name: BJ

tag: lab

value: UW

tag: lab description

value: Stamatoyannopoulous - University of Washington

tag: datatype

value: RepliSeq

tag: datatype description

value: Assessment of DNA Replication Timing

tag: cell

value: BJ

tag: cell organism

value: human

tag: cell description

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

tag: cell karyotype

value: normal

tag: cell sex

value: M

tag: labexpid

tag: phase

tag: phase description

value: Flow sorted, G1b phase corresponds to the second half of the first DNA content window

tag: replicate


title: HepG2_HS_Input

description: human hepatocarcinoma cell line

data_processing: Supplementary_files_format_and_content: Supplementary data HepG2 treatments' file is provided in .txt format. It contains a dataset of all identified m6A peaks in  HepG2 under the various treatments described above. Corresponding legends are : id – KnownCanonical identification; chr – chromosome; txStart – transcription start position on chromosome; txEnd – Transcription end position on chromosome; strand - +/- chromosome strand;  geneSymbol – official symbol of gene; desc – description;  Factor_iscoding– either coding or noncoding, depending on the annotation of the gene in the UCSC table; Meanexpquant – expression quantile of the gene based on reads in input experiment; Peaksnum – number of peaks identified in gene; Peakspos – position of peaks relative to beginning of transcript (after removing introns); Peaksexonnum – ordinal number of exons in which the peaks were identified; Peaksexlengths – lengths of the exons in which the peaks were found; Peakscores – the peakscore of the identified peaks; Annotpeakpos – segment along the gene in which the peaks.

treatment_protocol: HepG2 cells were incubated with either IFNg (200ng/ml) or HGF/SF (10 ng/ml) over night. Stress effects were tested in HepG2 cells by either 30 minutes incubation at 43ºC (heat shock) or UV irradiation of 0.04 J/cm2 followed by 4 hours of recovery in normal growing conditions prior to harvesting using Trypsin.

tag: cell line

tag: antibody

tag: treatment


title: HepG2_HGF_IP

description: human hepatocarcinoma cell line

tag: vendor

tag: catalog#

value: HGF/SF (10 ng/ml)


title: 12hr_Starved BC2

city: Durham

first: Colin

last: Maxwell

state: NC

address: 4314 FFSC

department: Biology

institute: Duke

description:
Reads mapping to genome and transcriptome and eads mapping to genome after 22 bp stripped from 5' end of read when the 22 bp is either SL1 or SL2
mRNA-seq: single-stranded RNA adapter ligation 5' sequencing

data_processing: We first mapped reads to the WormBase 210 version of the genome (WS210) using Bowtie (v. 0.12.7)  (Langmead et al. 2009). Reads that did not map in this step were aligned to the Wormbase 220 predicted transcriptome, whose coordinates had been mapped back to the WS210 coordinate system. We used Bowtie to map to the transcriptome as opposed to TopHat because we found that many reads mapped to transcriptome-derived splice junctions with Bowtie were not mapped with TopHat (data not shown). ~70% of genes in C. elegans are spliced to a 22 nt sequence donated by a snRNA called a ‘trans-splice leader’ (T Blumenthal 2005). The vast majority of trans-splice leaders come from two different sequences: either splice leader 1 or 2 (SL1 or SL2) (T Blumenthal 2005). We were interested in quantifying the overall levels of trans-splicing.  Therefore, reads that did not map to either the genome or the transcriptome were stripped of the first (5’) 22 nt of sequence and remapped to determine if these reads came from the 5’ end of trans-spliced mRNAs. We determined whether the stripped 22 nt sequence corresponded to SL1 or SL2 for the reads that mapped after stripping. We created alignment files of reads mapping to the genome and transcriptome along with an index linking the IDs of reads containing splice leaders to the type of splice leader contained in the read (ie, SL1 or SL2). Langmead B, Trapnell C, Pop M, and Salzberg S. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25. doi:10.1186/gb-2009-10-3-r25 Blumenthal, T. 2005. Trans-splicing and operons. In Wormbook (ed. The C. Elegans Research Community). http://www.wormbook.org.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Wild-type C. elegans strain N2 was used for RNA-seq.  The N2 stock used was from the Sternberg collection at the California Institute of Technology; this strain was obtained from the Caenorhabditis Genetics Center in 1987, expanded and frozen.  Nematodes were maintained on standard NGM plates with E. coli OP50 as food (Lewis, 1995), but liquid culture was used to prepare RNA-seq samples.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) according to the manufacturer’s protocol with minor modifications.  1 mL TRIzol was used per sample, and homogenization was supplemented with 100 mL of acid washed sand.  Poly-adenylated mRNA was isolated from total RNA using Dynal oligo-(dT) magnetic beads (Invitrogen) according to the manufacturer’s protocol.  200 ng poly-adenylated RNA was used in a Tobacco Acid Pyrophosphatase reaction (Epicentre) according to the manufacturer’s protocol in order to remove 5’ caps.  The product was purified with phenol/chloroform extraction and ethanol precipitation using GlycoBlue as a coprecipitant (Ambion).  This purified product was then used in the RNAse III fragmentation reaction at the beginning of the Solid Total RNA-Seq Kit Whole Transcriptome protocol (Applied Biosystems).  The manufacturer’s instructions were followed for the remainder of the library preparation process.  Fragmentation efficiency was analyzed with the BioAnalyzer (Agilent), and one-half of each sample (corresponding to approximately 100 ng RNA) was used for adapter ligation.  cDNA was gel purified to capture inserts of RNA fragment size 100 – 200 nt.  12 PCR cycles were used to amplify the libraries.  Libraries were processed and sequenced on the Solid 4 system according to the manufacturer’s protocols.

treatment_protocol: A starved 5 cm plate was used to inoculate 25 mL of liquid culture (S-complete plus 40 mg/mL E. coli HB101)(Lewis, 1995).  The culture was incubated at 20°C and 180 rpm for 65 hr and then bleached to produce a clean preparation of embryos.  Embryos were suspended in S-complete at 5 eggs/mL and incubated at 20°C and 180 rpm for 24 hr so that they hatch and enter L1 arrest.  After 24 hr, cultures were fed with 40 mg/mL HB101 to initiate synchronous development and they were incubated at 20°C and 180 rpm for 57 hr.  After 57 hr the cultures were bleached, and the eggs were suspended in S-complete at 10 eggs/mL.  In these conditions, the first eggs are fertilized at about 53 hr, and when bleached at 57 hr the yield is typically about 10 eggs per worm.  Animals were incubated at 20°C and 180 rpm for 24 hr so that they hatch and enter L1 arrest.  The 0 hr time point was collected 24 hr after bleaching, corresponding to approximately 12 hr L1 arrest.  The remainder of the culture was fed with 25 mg/mL HB101 and incubated at 20°C and 180 rpm with collections at 1, 3 and 6 hr after feeding .  Larvae were collected by centrifugation and washed 3 times in S-basal before being flash frozen. Lewis, J.A., and Fleming, John T. 1995. Basic Culture Methods. In Caenorhabditis elegans: Modern biological analysis of an organism (eds. H.F. Epstein, and Shakes, D. C.), pp. 4-27. Academic Press, San Diego, California.

tag: develomental stage

value: L1 larvae


title: HepG2_UV_Input

description: human hepatocarcinoma cell line

value: UV irradiation of 0.04 J/cm2


title: Mock_control1

description: human hepatocarcinoma cell line

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to the human genome (build hg18) using TopHat 1.2.0 software
Differentially expressed genes: the number of reads mapped to each of the ensembl genes (release 54) was counted using the HTSeq python package, with the “union” overlap resolution mode, and –stranded=no. The R package DESeq v1.5.24 within the Bioconductor framework was used for differential expression analysis
Differentially expressed exons: non-overlapping exonic regions were defined using the “dexseq_prepare_annotation.py” script provided as part of the R DEXseq package. The number of reads falling in each of the defined exonic regions was counted using the DEXseq script “dexseq_count.py” with parameters -a=0 to include multi-reads mapped to different locations of the genome, and –stranded=no. Finally Differential expression analysis was done using the R package DEXSeq within the Bioconductor framework.
Differentially expressed introns: non-overlapping intronic regions which also don't overlap any exon on either strand were defined using an in-house script. The number of reads falling in each of the defined regions was counted using a modified version of the “dexseq_count.py” DEXseq script  , and differential expression analysis was done using the DESeqBioconductor package
Differentially expressed isoforms: Ensembl gtf file of all human genes (hg18 release 54) was re-processed using Cuffcompare v1.0.3 in order to add the missing tss_id and p_id attributes according to the user guide. The resulting gtf annotation file created by Cuffcompare was used as input to Cuffdiff v1.0.3 tool together with the fragment alignment files. Both Cuffcompare and Cuffdiff are part of the Cufflinks package
Genome_build: hg18
Supplementary_files_format_and_content: Tab delimited txt files, providing differential genes/isoforms/exons/introns together with their normalized intensities, fold change (FC), p values (pval), and adjusted p values(adjp)

extract_protocol: Total RNA was purified from the cells using 5PRIME PerfectPure RNA Cultured Cell kit (cat.# 2302340). RNA samples were poly(A) selected, and libraries were prepared using the Illumina TruSeq RNA sample preparation protocol (cat.# FC-122-1001).10pM DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.

treatment_protocol: Scrambled control or siRNA directed against METTL3 (Sigma-Aldrich) were transfected into HepG2 cells by using Oligofectamine reagent (Invitrogen). Cells were re-transfected after 48 and 96 hours, and harvested on day 7 to allow more efficient METTL3 silencing.

tag: sirna

value: Scrambled


title: Mock_control2

description: human hepatocarcinoma cell line


title: HepG2_UV_IP

description: human hepatocarcinoma cell line

value: Synaptic Systems


title: HepG2_IFN_IP

description: human hepatocarcinoma cell line

value: IFNg (200ng/ml)


title: HepG2_IFN_Input

description: human hepatocarcinoma cell line


title: IP1

description: human hepatocarcinoma cell line


title: HepG2_HS_IP

description: human hepatocarcinoma cell line

value: 30 minutes incubation at 43ºC (heat shock)


title: HepG2_HGF_Input

description: human hepatocarcinoma cell line


title: METTL3_KD2

description: human hepatocarcinoma cell line


title: DKI IL2 72hr RNASeq

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: treated IL-2 500U/ml

data_processing:
For ChIP-Seq, Basecalls performed using CASAVA version 1.4; For RNA-Seq, Basecalls performed using CASAVA version 1.7
ChIP-Seq reads were aligned to the mm8 genome assembly using CASAVA pipeline 1.4 and 1.7
Aligned reads are converted to BED format using CASAVA pipeline
For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database
Genome_build: mm8
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.4 and 1.7, rpkm files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

organism: Mus musculus

source_name: CD8+ T Cells

growth_protocol: For ChIP-Seq, Preactivated mouse splenic T cells were pre-activated with plate-bound anti-CD3 and soluble anti-CD28 for 3 days, washed, rested overnight. For RNA-Seq, 1.5 μg of total RNA isolated from WT and DKI CD8+ T cells

extract_protocol: For ChIP-Seq, cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication. For RNA-Seq, Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor

treatment_protocol: For ChIP-Seq, not treated or treated with 100 U/ml IL-2 for 1 hr. For RNA-Seq, not treated or treated by 500 U/ml IL-2 or 20 ng/ml IL-15 for indicated times

tag: strain

tag: source tissue

value: Spleen

tag: cell type

value: CD8+ T Cells

tag: time


title: DKI IL2 48hr RNASeq

description: treated IL-2 500U/ml


title: DKI IL2 4hr RNASeq

description: treated IL-2 500U/ml


title: METTL3_KD1

description: human hepatocarcinoma cell line


title: DKI IL2 24hr RNASeq

description: treated IL-2 500U/ml


title: DKI IL15 72hr RNASeq

description: treated IL-15 20ng/ml

value: IL-15 20ng/ml


title: DKI IL15 48hr RNASeq

description: treated IL-15 20ng/ml


title: DKI IL15 24hr RNASeq

description: treated IL-15 20ng/ml


title: DKI IL15 4hr RNASeq

description: treated IL-15 20ng/ml


title: DKI Cont RNASeq

description: non-treated

value: non-treated

value: control


title: WT IL2 72hr RNASeq

description: treated IL-2 500U/ml


title: WT IL2 48hr RNASeq

description: treated IL-2 500U/ml


title: WT IL2 24hr RNASeq

description: treated IL-2 500U/ml


title: WT IL15 72hr RNASeq

description: treated IL-15 20ng/ml


title: WT IL15 48hr RNASeq

description: treated IL-15 20ng/ml


title: WT IL15 24hr RNASeq

description: treated IL-15 20ng/ml


title: WT IL15 4hr RNASeq

description: treated IL-15 20ng/ml


title: WT IL2 4hr RNASeq

description: treated IL-2 500U/ml


title: DKI-IL2-Stat5B ChIPSeq

description: Chromatin IP against STAT5B

source_name: Total T Cells

value: total T cells

tag: chip antibody

tag: chip antibody manufacturer

value: R&D

tag: chip antibody catalog #

tag: chip antibody lot #


title: DKI-IL2-Stat5A ChIPSeq

description: Chromatin IP against STAT5A


title: DKI-control-IgG ChIPSeq

description: Chromatin IP against IgG

value: Rabbit IgG


title: DKI-control-Stat5B ChIPSeq

description: Chromatin IP against STAT5B


title: DKI-IL2-IgG ChIPSeq

description: Chromatin IP against IgG


title: Yale_RnaSeq_K562_IFNg6h_polyA

tag: lab

value: Yale

tag: lab description

value: Snyder - Yale University

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

tag: cell organism

value: human

tag: cell description

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment description

value: Interferon gamma treatment - 6 hours (Snyder)

tag: rnaextract

value: polyA

tag: rnaextract description

value: Isolated Poly(A) RNA


title: WT-IL2-Stat5B ChIPSeq

description: Chromatin IP against STAT5B

tag: strain

tag: source tissue

value: Spleen

tag: cell type

tag: chip antibody


title: Yale_RnaSeq_K562_IFNg30_polyA

tag: lab

tag: treatment

value: Interferon gamma treatment - 30 minutes (Snyder)


title: Sexual Non-irradiated [paired end]

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description: Sexual strain of S. mediterranea, Non-irradiated

data_processing: The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

organism: Schmidtea mediterranea

growth_protocol: Sexual and asexual S. mediterranea animals were maintained at 22°C in ddH2O supplemented with 1.6 mM NaCl, 1.0 mM CaCl2, 1.0 mM MgSO4, 0.1 mM MgCl2, 0.1 mM KCl, 1.2 mM NaHCO3 and fed homogenized organic beef liver.  FACS purification of X1, X2 and Xins cells was carried out as follows. Briefly, planarians were cut into small pieces with a sterile scalpel on ice in cold calcium, magnesium-free medium (CMF) (15 mM HEPES, 400 mg/L NaH2PO4, 800 mg/L NaCl, 1200 mg/L KCl, 800 mg/L NaHCO3, 240 mg/L glucose at pH 7.3) and then washed twice with CMF.  The fragments were then soaked in CMF containing 0.25% (w/v) Trypsin (GIBCO) and 1% BSA (Fisher Scientific) at 4°C for 18 hours to maximize penetration of the enzyme with little trypsin activity. The fragments were then rocked for 20 minutes at 20°C and completely dissociated into single cells by gentle pipetting.  The cell mixture was then sequentially filtered through 40-µm and 20-µm nylon filters (Millipore). Cells were collected by centrifugation, resuspended in fresh CMF supplemented with 1% BSA and 0.5 mg/mL Calcein AM (Sigma), and incubated at room temperature for 20 minutes. Cells were collected and resuspended in CMF supplemented with 1% BSA, 18 mg/mL Hoechst 3342 (Sigma), and 2 mg/mL propidium iodide (Sigma). The samples were then analyzed with a LSR II flow cytometer (Becton-Dickinson).

extract_protocol: Total RNA was isolated from sexual and asexual strains of S. mediterranea before and after irradiation using Trizol. Total RNA (5ug) was used to prepare the transcriptome library using the mRNA-seq sample library preparation kit (Illumina) following the manufacturers instructions. Briefly, mRNA was purified using magnetic oligo-dT beads and fragmented. First strand synthesis of cDNA was done using SuperscriptII reverse transcriptase followed by RNase H treatment and second strand cDNA synthesis was performed using DNAPol1. Paired end adaptors (Illumina) were ligated to 5’ and 3’ ends of DNA fragments followed by PCR amplification using adaptor specific primers. PCR amplified products of 300 bp were gel purified, quantitated by Nanodrop and Bioanalyzer and sequenced on an Illumina GAIIx.

treatment_protocol: Sexual and asexual animals were gamma-irradiated with a cesium source with 90 Gy treatments.  D. tigrina animals were ordered from Carolina Biological and RNA was isolated immediately upon arrival.

value: Sexual

value: Non-irradiated


title: Sexual Non-irradiated, X1 FACS purified neoblast

description: Sexual strain of S. mediterranea, Non-irradiated, X1 FACS purified neoblast

data_processing:
FACS_X1.SAM; genome build: S. mediterranea, pseudochromosomes
FACS_X1.bedGraph; genome build: S. mediterranea, pseudochromosomes
The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

value: X1 neoblast


title: Sexual Non-irradiated, X2 FACS purified neoblast

description: Sexual strain of S. mediterranea, Non-irradiated, X2 FACS purified neoblast

data_processing:
FACS_X2.SAM; genome build: S. mediterranea, pseudochromosomes
FACS_X2.bedGraph; genome build: S. mediterranea, pseudochromosomes
The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

value: X2 neoblast


title: Sexual Non-irradiated, Xins FACS purified differentiated cells

description: Sexual strain of S. mediterranea, Non-irradiated, Xins FACS purified differentiated cells

data_processing:
FACS_Xins.SAM; genome build: S. mediterranea, pseudochromosomes
FACS_Xins.bedGraph; genome build: S. mediterranea, pseudochromosomes
The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

value: Xins differentiated cells


title: Sexual Irradiated

description: Sexual strain of S. mediterranea, Irradiated

data_processing:
SexIR_all.sam; genome build: S. mediterranea, pseudochromosomes
SexIR.bedGraph; genome build: S. mediterranea, pseudochromosomes
The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

value: Irradiated


title: DKI-control-Stat5A ChIPSeq

description: Chromatin IP against STAT5A

value: total T cells

tag: chip antibody manufacturer

value: R&D

tag: chip antibody catalog #

tag: chip antibody lot #


title: WT-IL2-Stat5A ChIPSeq

description: Chromatin IP against STAT5A


title: Yale_RnaSeq_K562_IFNa6h_polyA

value: Yale

tag: lab description

value: Snyder - Yale University

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

tag: cell organism

value: human

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: Interferon alpha treatment - 6 hours (Snyder)


title: Asexual Non-irradiated [paired end]

description: Asexual strain of S. mediterranea, Non-irradiated

value: Asexual


title: WT-control-Stat5B ChIPSeq

description: Chromatin IP against STAT5B

value: Spleen


title: Yale_RnaSeq_K562_IFNa30_polyA

tag: cell description

tag: cell karyotype

value: cancer

tag: cell lineage

value: mesoderm

tag: cell sex

value: F

tag: treatment description

value: 30 m of Interferon alpha (Snyder)

value: polyA

value: Isolated Poly(A) RNA


title: WT-control-Stat5A ChIPSeq

description: Chromatin IP against STAT5A

tag: strain

tag: source tissue

tag: cell type

value: total T cells


title: WT-control-IgG ChIPSeq

description: Chromatin IP against IgG

tag: chip antibody

value: Rabbit IgG

value: R&D


title: WT-IL2-IgG ChIPSeq

description: Chromatin IP against IgG

tag: chip antibody manufacturer


title: Asexual Non-irradiated [single end]

data_processing:
ASexNIR_all.sam; genome build: S. mediterranea, pseudochromosomes
ASexNIR.bedGraph; genome build: S. mediterranea, pseudochromosomes
The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

source_name: Asexual strain of S. mediterranea, Non-irradiated

tag: treatment

value: Non-irradiated


title: WT_Sucrose_1h_2

status: Public on Apr 24 2012

city: Berkeley

first: N

middle: Louise

last: Glass

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_1h_2.expr: N. crassa OR74A (NC10)

organism: Neurospora crassa OR74A

source_name: FGSC 2489

growth_protocol: Innoculated at 10^6 conidia/mL and grown 16 hours in sucrose media.

extract_protocol: mRNA was purified with Dynabeads® Oligo dT magnetic beads (Illumina).   Purified mRNA was fragmented with buffered zinc solution from Ambion (Cat # AM8740).  First and second strand cDNA synthesis was carried out using Superscript II Reverse Transcriptase (Invitrogen) and DNA pol I (Invitrogen) and random primers.   Illumina sequencing adapters were then ligated to the cDNA, 200bp fragments were purified by gel electrophoresis, and PCR enriched with Pfx DNA polymerase (Invitrogen).

treatment_protocol: Washed and transferred to fresh media with sucrose, cellulose (Avicel PH101) or no carbon source

tag: genotype/variation

value: Wild Type

tag: carbon source

value: Sucrose

tag: time after media shift

value: 1 hour


title: WT_Avicel_4h_3

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_4h_3.expr: N. crassa OR74A (NC10)

value: Avicel

value: 4 hours


title: WT_Avicel_4h_2

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_4h_2.expr: N. crassa OR74A (NC10)


title: WT_Sucrose_1h_3

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_1h_3.expr: N. crassa OR74A (NC10)


title: WT_Sucrose_4h_2

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_4h_2.expr: N. crassa OR74A (NC10)


title: WT_No_Carbon_1h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_1h.expr: N. crassa OR74A (NC10)

value: No Carbon

value: 1 hours


title: WT_No_Carbon_4h_1

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_4h_1.expr: N. crassa OR74A (NC10)


title: WT_No_Carbon_4h_2

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_4h_2.expr: N. crassa OR74A (NC10)


title: Asexual Irradiated

description: Asexual strain of S. mediterranea, Irradiated

data_processing:
ASexIR_all.sam; genome build: S. mediterranea, pseudochromosomes
ASexIR.bedGraph; genome build: S. mediterranea, pseudochromosomes
The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

value: Asexual

value: Irradiated


title: WT_No_Carbon_4h_3

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_No_Carbon_4h_3.expr: N. crassa OR74A (NC10)


title: WT_Sucrose_4h_3

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_4h_3.expr: N. crassa OR74A (NC10)


title: WT_Avicel_1h_3

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_1h_3.expr: N. crassa OR74A (NC10)


title: WT_Avicel_1h_2

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_1h_2.expr: N. crassa OR74A (NC10)


title: AP4 ChIP sequencing in DHT (5alpha-dihydrotestosterone) treated LNCaP cells

city: Singapore

first: Cheng Wei

last: Chang

address: Genome Institute of Singapore Genome #02-01 60 Biopolis Street

department: Computational and Mathematical Biology 1

country: Singapore

institute: GIS

description:
AP4 ChIP DNA
AP4 ChIP sequencing after 2 hrs DHT (5alpha-dihydrotestosterone) treatment in LNCaP cells

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer II Pipeline. In-house (Genome Institute of Singapore) BATMAN program was used for mapping the sequence tags of 36 bp to the reference genome hg18. In order to avoid potential PCR amplification bias, tags that shared the same mapping location on the same strand were removed. The uniquely-mapped reads with at most 2-mismatches were kept for further processing.
Peak calling: Binding peaks were determined using in-house Control based ChIPSeq Analysis Tools (CCAT) program with reference to a set of genomic input reads as baseline control. Peaks with a stringent cut-off of FDR 0.05 were considered.
CCAT file format: chromosome, peakcenter, regionstart, regionend, tagcount, bgcount, zscore, fdr

source_name: LNCaP prostate cancer cells

growth_protocol: Human LNCaP prostate cancer cells were maintained in RPMI Medium 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 100 units/ml penicillin, 100 ug/ml streptomycin, and 30 ug/ml gentamycin in a 37C incubator with 5% CO2. Prior to vehicle/drug stimulation, ~4 millions cells were seeded into 150 mm dish and starved with phenol red-free RPMI Medium 1640 containing 5% charcoal-dextran treated FBS (Hyclone) and the same amount of sodium pyruvate, penicillin, streptomycin and gentamycin as mentioned earlier for at least 72 hrs to ~80% confluence.

extract_protocol: All DNA samples were processed as per Illumina Solexa ChIP-seq sample processing methods. 5-15 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An A base was added to the polished DNA fragments followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification with Phusion or Pfx DNA polymerase (Invitrogen) and Illumina primers. 200-300 bp DNA size fractions were selectively excised from the 2% ultra low range agarose gel purified using the Qiagen gel extraction kit. The extracted DNA was quantified using Agilent bioanalyzer and subjected to Solexa sequencing according to the manufacturer's instruction.

treatment_protocol: Androgen-deprived cells were treated with DHT to a final concentration of 100 nM for 2 hrs prior to the ChIP procedure. Cells cross-linked with 1% formaldehyde and harvested for sonication. ChIP was performed with specific antibody against AP-4 (catalog number: sc-18593 (N-17); lot number: D2903)

value: androgen-dependent prostate cancer cells


title: cdr2_deletion_Sucrose_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr2_deletion_Sucrose_4h.expr: N. crassa OR74A (NC10)

value: NCU08042 open reading frame replaced with hygromycin resistance cassette


title: cdr2_deletion_Sucrose_1h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr2_deletion_Sucrose_1h.expr: N. crassa OR74A (NC10)


title: cdr1_deletion_Sucrose_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr1_deletion_Sucrose_4h.expr: N. crassa OR74A (NC10)

value: NCU07705 open reading frame replaced with hygromycin resistance cassette


title: cdr2_deletion_Avicel_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr2_deletion_Avicel_4h.expr: N. crassa OR74A (NC10)


title: cdr2_deletion_Avicel_1h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr2_deletion_Avicel_1h.expr: N. crassa OR74A (NC10)


title: cdr1_deletion_Avicel_4h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr1_deletion_Avicel_4h.expr: N. crassa OR74A (NC10)


title: WT_Avicel_30m

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_30m.expr: N. crassa OR74A (NC10)

value: 30 minutes


title: WT_Sucrose_1h_1

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_1h_1.expr: N. crassa OR74A (NC10)


title: WT_Avicel_2h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_2h.expr: N. crassa OR74A (NC10)

value: 2 hours


title: cdr1_deletion_Avicel_1h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr1_deletion_Avicel_1h.expr: N. crassa OR74A (NC10)


title: WT_Avicel_1h_1

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_1h_1.expr: N. crassa OR74A (NC10)


title: WT_Avicel_4h_1

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Avicel_4h_1.expr: N. crassa OR74A (NC10)


title: hnRNP L KO mouse 1

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

country: Canada

institute: University of Montreal

library_source: non-genomic

data_processing:
junction_cnt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
expression_cnt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
filtered BAM file - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters to mm9

source_name: hnRNP L KO mouse

growth_protocol: C57BL/6, LckCre transgenic, Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo and CD45.1 mice were purchased from Jackson Laboratories or were maintained at the Institut de recherches cliniques de Montreal. All animals were housed under specific pathogen-free environment at the Institut de recherches cliniques de Montreal, and all experiments were done conformed to ethical principles and guidelines approved by the institutional animal care committee.

extract_protocol: RNA was extracted from total thymocytes using Tri Reagent (Molecular Research Center) followed by a purification using Rneasy Mini kit and Rnase-free Dnase on column (Qiagen) for 15 min at room temperature both following manufacturer’s instructions. RNA integrity and quality have been confirmed using a bioanalyzer (Agilent). rRNA from each biological sample was depleted from total RNA using a RiboMinus kit (Invitrogen) and the treated RNA was then fragmented using RNase III. Ligation of the adaptor mix A and reverse transcription were performed following the manufacturer’s protocol. Libraries were size selected for fragments between 150 and 300 bp, amplified for 12 cycles of polymerase chain reaction (PCR), and purified using PureLink PCR micro kit (Invitrogen). Barcoded library concentrations were determined by quantitative PCR using a standard curve of template at known concentrations (DH10B), and approximately 0.25 ng of each library was used for each full emulsion PCR (emPCR) reaction (4 emPCR/sample). Approximately 200 millions of beads from each two samples were deposited on single full slides (2 slides for 4 samples in total) and sequenced using the Opti Fragment Library Sequencing kit-Master Mix 50.

value: thymocyte

tag: genotype

value: hnRNP L KO

tag: genetic background

value: mixed C57BL/6, LckCre transgenic, Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo and CD45.1


title: wt mouse 1

source_name: wt mouse

value: wild type


title: Sexual Non-irradiated [single end]

data_processing: The S. mediterranea draft genome assembly (version 3.1) consists of ~900 Mb distributed over 43,294 supercontigs (http://genome.wustl.edu/genomes/view/schmidtea_mediterranea/). To facilitate the analysis the supercontigs were sorted by decreasing size and concatenated into nine pseudochromosomes of ~100 Mbp each with 100 'N' residues separating each contig. These pseudochromosomes are contained in the Smed_pseudochromosomes.fasta file. Reads were aligned to the pseudochromosomes using bowtie-0.12.1 and tophat-1.1.1 using default parameters. To assemble the D. tigrina transcript contigs, a total of 23,532,916 D. tigrina reads of 40 bp were used with Velvet 0.3 using k=15.  This resulted in 14,514 contigs with an average length of 140 bp and an average coverage of 8.7X.

source_name: Sexual strain of S. mediterranea, Non-irradiated

value: Sexual

value: Non-irradiated


title: WT Cont RNASeq

description: non-treated

data_processing:
For ChIP-Seq, Basecalls performed using CASAVA version 1.4; For RNA-Seq, Basecalls performed using CASAVA version 1.7
ChIP-Seq reads were aligned to the mm8 genome assembly using CASAVA pipeline 1.4 and 1.7
Aligned reads are converted to BED format using CASAVA pipeline
For ChIP-Seq, peaks are called using MACS 1.3.7.1; For RNA-Seq, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using mm8 refseq database
Genome_build: mm8
Supplementary_files_format_and_content: BED files are generated using CASAVA pipeline 1.4 and 1.7, rpkm files are generated using definition in [Mortazavi et al., 2008] and unpublished python scripts

value: Spleen

value: CD8+ T Cells

value: non-treated

tag: time

value: control


title: hnRNP L KO mouse 2


title: wt mouse 2


title: Stanford_Nucleosome_GM12878

status: Public on Apr 20 2012

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhNsome
instrument name: AB SOLiD 3 Plus System

tag: lab

value: Stanford

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: Nucleosome

tag: datatype description

value: Nucleosome Position

tag: cell

tag: cell organism

value: human

tag: cell description

value: lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal

value: mesoderm

value: F

tag: replicate


title: Stanford_Nucleosome_K562

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

tag: cell karyotype

value: cancer

tag: cell lineage

tag: cell sex


title: iCLIP_EZH2 RIPSeq

status: Public on Apr 23 2012

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

data_processing:
Counts: for RIP-seq data, after passing Solexa CHASTITY quality filter, the clean reads were aligned to human genome (UCSC hg19), human mRNA data base (Ensembl 64) and human LncRNA database (Arraystar) using novoalign software (v2.07.11) The tag counts were calculated within each transcript, and then all tag counts were normalized (i.e., tag count*10M/total uniquely aligned tag counts in each sample).
Genome Build:
iCLIP_EZH2_Homo_sapiens_HG19_novoalign_alignment_lncrna_raw.txt: hg19
iCLIP_EZH2_Homo_sapiens_HG19_novoalign_alignment_mRNA_raw.txt: hg19
Enriched_LncRNAs.csv: hg19
Enriched_mRNAs.csv: hg19

source_name: colorectal cells

extract_protocol: After stringent washing, RNAs were ligated at their 3′ends to an RNA adapter and radioactively labelled to allow visualization. Denaturing gel electrophoresis and transfer to a nitrocellulose membrane removed RNAs that were not covalently linked to the protein. RNA fractions were recovered from the membrane by proteinase K digestion. The oligonucleotides for reverse transcription contained two inversely oriented adapter regions separated by a BamHI restriction site as well as a three nucleotide random barcode to mark individual cDNA molecules. cDNA molecules were size-purified using denaturing gel electrophoresis, circularized by single-stranded DNA ligase, annealed to an oligonucleotide complementary to the restriction site and cut between the two adapter regions by BamHI. Linearized cDNAs were then PCR-amplified using primers complementary to the adapter regions.

treatment_protocol: HCT116 cells were irradiated with UV-C light to covalently cross-link proteins to nucleic acids in vivo. Upon cell lysis, RNA was partially fragmented using low concentrations of RNase I. For control sample, RNAse I, and non-specific protein-RNA complexes were immuno-purified with a rabbit IgG control antibody immobilized on immunoglobulin G-coated magnetic beads, and for EZH2 sample, EZH2 RNA complexes were immuno-purified with the antibody immobilized on immunoglobulin G-coated magnetic beads.

tag: cell line

tag: passages

value: below 30

tag: antibody


title: WT_Sucrose_4h_1

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
WT_Sucrose_4h_1.expr: N. crassa OR74A (NC10)

tag: genotype/variation

value: Wild Type

tag: carbon source

value: Sucrose

tag: time after media shift

value: 4 hours


title: Control

data_processing:
Counts: for RIP-seq data, after passing Solexa CHASTITY quality filter, the clean reads were aligned to human genome (UCSC hg19), human mRNA data base (Ensembl 64) and human LncRNA database (Arraystar) using novoalign software (v2.07.11) The tag counts were calculated within each transcript, and then all tag counts were normalized (i.e., tag count*10M/total uniquely aligned tag counts in each sample).
Genome Build:
Control_Homo_sapiens_HG19_novoalign_alignment_mRNA_raw.txt: hg19
Control_Homo_sapiens_HG19_novoalign_alignment_lncrna_raw.txt: hg19

tag: cell type


title: mat72_11

status: Public on Apr 19 2012

city: Santa Cruz

first: Alan

middle: M

last: Zahler

address: Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

description: Illumina smallRNA TruSeq

data_processing:
100base paired-end reads obtained.All 11 libraries in a single lane of a Illumina HiSeq2000
Indexing and trimming of linker sequences
Reads of at least 16nt that are 100% identical in both directions were further processed (77% of total)
Bowtie was used to align libraries to non-coding RNAs from Oxytricha trifallax as a filter
Bowtie was used to align reads that survive the filter to the Oxytricha macronuclear genome partial assembly WGS2.1.1.
Genome_build: Oxytricha trifallax macronuclear genome WGS2.1.1 partial assembly
Supplementary_files_format_and_content: Tab-delimited files. For all 7 libraries from mating cells, the txt files list all distinct 26-28nt long RNAs from the library that survived the non-coding RNA filter. Table shows #_of_occurrences, sequence, sequence_length

organism: Oxytricha trifallax

source_name: mating 72hr post-mixing

extract_protocol:
Total RNA was purified using the mirVana miRNA Isolation kit using the total RNA purification protocol. 1µg of total RNA was used to prepare smallRNA libraries using the TruSeq small RNA Sample Prep Kit (Illumina) following standard protocol.
small RNA sequencing runs were size selected for inserts of 15-45 bases in length prior to the run. Reads were set to 100 base paired-end reads and ended up with complete overlap of the sequence in both directions. For the processed data, we only chose to look at the 77% of raw reads that were identical in both directions.

tag: strain

tag: Stage

value: mating 72hr post-mixing

tag: rna subset

value: small RNA


title: mat48_08

description: Illumina smallRNA TruSeq

source_name: mating 48hr post-mixing

value: mating 48hr post-mixing


title: veg09_04

description: Illumina smallRNA TruSeq

source_name: vegetative strain ALXC9

value: vegetative


title: mat55_10

description: Illumina smallRNA TruSeq

source_name: mating 55hr post-mixing

value: mating 55hr post-mixing


title: mat24_06

description: Illumina smallRNA TruSeq

source_name: mating 24hr post-mixing

value: mating 24hr post-mixing


title: mat30_07

description: Illumina smallRNA TruSeq

source_name: mating 30hr post-mixing

value: mating 30hr post-mixing


title: mat24_05

description: Illumina smallRNA TruSeq


title: veg09_03

description: Illumina smallRNA TruSeq


title: mat48_09

description: Illumina smallRNA TruSeq


title: LICR_ChipSeq_Spleen_Input_adult-8wks

source_name: Spleen

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: tissue

value: mouse

value: Spleen

tag: Sex

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: softwareversion

value: ELAND

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: cdr1_deletion_Sucrose_1h

data_processing:
Sequenced libraries were mapped against predicted transcripts from the N. crassa OR74A genome (version 10) with Tophat.  Transcript abundance (FPKM) was estimated with Cufflinks v0.9.3 using upper quartile normalization and mapping against reference isoforms. Raw counts for reads mapping to unique exons were tallied with HTSeq and used as inputs for both the EdgeR and DESeq software packages.  Genes with a multiple-hypothesis-adjusted p-value below 0.05 from both models were taken as differentially expressed between conditions.  Hierarchical clusters of differentially expressed genes were grenerated with the Cluster 3.0 software suite using the average linkage method with uncentered correlation as the similarity metric. Prior to clustering, FPKMs were log transformed, normalized across strains/conditions and centered on the geometric mean across strains/conditions on a per-gene basis.
Genome Build:
cdr1_deletion_Sucrose_1h.expr: N. crassa OR74A (NC10)

tag: genotype/variation

value: NCU07705 open reading frame replaced with hygromycin resistance cassette

tag: carbon source

value: Sucrose

tag: time after media shift

value: 1 hour


title: wild-type_rosetteleaf_5week

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

institute: Pennsylvania State University

data_processing: The raw colorspace reads containing inserts derived from 20-25nt RNAs were identified by searching for 3' matches (allowing up to two mismatches) to the sequencing adapter sequence (in colorspace); the inferred adapter sequences were then trimmed, leaving 20-25nt colorspace reads.  These data were then translated into DNA space while simultaneously discarding any reads with ambiguous (e.g., one or more "." characters) data.  The data in the Sample data tables are simple counts of each of these 20-25nt total RNAs.

organism: Arabidopsis thaliana

source_name: rosette leaves, wild-type

growth_protocol: 12hr light / 12hr dark, 21C.

extract_protocol: Life Tech Total RNA-seq kit, total RNA modification, per manufacturer's instructions.

tag: ecotype

tag: genotype

value: wild-type

tag: tissue

value: rosette leaves


title: veg01_01

description: Illumina smallRNA TruSeq

source_name: vegetative strain ALXC2

tag: strain

tag: Stage

value: vegetative

tag: rna subset

value: small RNA


title: veg02_02

description: Illumina smallRNA TruSeq


title: LICR_ChipSeq_BoneMarrow_Pol2_adult-8wks

source_name: BoneMarrow

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: BoneMarrow

tag: cell organism

value: mouse

tag: cell description

value: Bone Marrow

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

tag: antibody targetdescription

value: RNA Polymerase II

tag: antibody vendorname

value: Covance

tag: antibody vendorid

tag: age

tag: replicate


title: LICR_ChipSeq_Cerebellum_CTCF_adult-8wks

source_name: Cerebellum

value: Cerebellum

value: M

value: CTCF

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: softwareversion

value: ELAND

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_BoneMarrow_CTCF_adult-8wks

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: BoneMarrow

tag: cell organism

tag: cell description


title: LICR_ChipSeq_Heart_Input_adult-8wks

source_name: Heart

value: tissue

value: mouse

value: heart

tag: Sex

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age


title: LICR_ChipSeq_Heart_CTCF_adult-8wks

value: Heart

tag: cell sex

value: M

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

tag: antibody vendorid

tag: age description

tag: control

tag: control description

tag: replicate


title: LICR_ChipSeq_MEF_Pol2_adult-8wks

source_name: MEF

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: MEF

value: Mouse Embryonic Fibroblast

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

value: Adult 8 weeks

value: std

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: softwareversion

value: ELAND

tag: strain

tag: strain description


title: LICR_ChipSeq_ES-Bruce4_Input_E0

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: line

tag: cell organism

value: mouse

value: mouse embryonic stem cells

tag: cell sex

tag: antibody

tag: antibody description

tag: age

value: Embryonic day 0 (stem cell)

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Kidney_Pol2_adult-8wks

source_name: Kidney

tag: cell

value: Kidney

tag: cell description

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: age description

tag: control

tag: control description


title: LICR_ChipSeq_Liver_Input_E14.5

source_name: Liver

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Liver

value: U

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Embryonic day 14.5

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion

value: Bowtie

tag: strain


title: LICR_ChipSeq_WholeBrain_Input_E14.5

source_name: WholeBrain

value: tissue

tag: cell organism

value: Whole Brain

tag: Sex

value: not determined

tag: antibody

tag: antibody description

tag: age

value: std

value: Standard input signal for most experiments.

tag: strain description


title: LICR_ChipSeq_ES-Bruce4_p300_E0

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: mouse

tag: cell description

tag: cell sex

tag: antibody antibodydescription

value: Rabbit Polyclonal. Antibody Target:P300

tag: antibody targetdescription

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: age description

tag: control

value: 12/23/09 SOLEXA2 Lane 3

value: ELAND


title: LICR_ChipSeq_Heart_p300_adult-8wks

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Heart

value: M

value: Adult 8 weeks

tag: control description

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_ES-Bruce4_Pol2_E0

tag: cell

tag: cell organism

tag: cell description

value: mouse embryonic stem cells

tag: antibody

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: age

value: Embryonic day 0 (stem cell)

value: 12/23/09 SOLEXA1 Lane 1

value: Bowtie

tag: strain

tag: strain description


title: LICR_ChipSeq_MEF_CTCF_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

value: MEF

value: Mouse Embryonic Fibroblast

tag: cell sex

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: age description

tag: control

value: std

value: Standard input signal for most experiments.


title: LICR_ChipSeq_Lung_Input_adult-8wks

source_name: Lung

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Lung

value: mouse

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Adult 8 weeks

tag: control description

tag: controlid

tag: labversion

value: ELAND

value: C57 black 6, the most common inbred strain of laboratory mouse


title: wild-type_flower_8week

source_name: flowers and flower buds, wild-type

tag: ecotype

tag: genotype

value: wild-type

tag: tissue

value: flowers and flower buds


title: LICR_ChipSeq_Liver_Pol2_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: Liver

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: age

tag: replicate

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_Spleen_Pol2_adult-8wks

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Spleen

value: mouse

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: age description

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: LICR_ChipSeq_MEF_Input_adult-8wks

tag: cell

value: MEF

tag: cell organism

tag: cell description

value: Mouse Embryonic Fibroblast

tag: cell sex

value: M

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: Adult 8 weeks

tag: controlid

tag: labversion


title: LICR_ChipSeq_WholeBrain_CTCF_E14.5

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

value: WholeBrain

value: Whole Brain

value: U

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore

tag: age

value: Embryonic day 14.5

tag: replicate

tag: softwareversion

value: Bowtie

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Cortex_Input_adult-8wks

source_name: Cortex

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: Cortex

value: mouse

tag: age description

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

value: ELAND


title: hyl1-2-dcl1-21_rosetteleaf_5week

source_name: rosette leaves, hyl1-2/dcl1-21

tag: ecotype

tag: genotype

tag: tissue

value: rosette leaves


title: LICR_ChipSeq_Kidney_CTCF_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

tag: cell

value: Kidney

tag: cell organism

tag: cell description

tag: cell sex

value: M

tag: antibody

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: Adult 8 weeks

tag: controlid

tag: labversion


title: LICR_ChipSeq_Cortex_Pol2_adult-8wks

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: antibody antibodydescription

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: age

tag: replicate

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_Lung_Pol2_adult-8wks

tag: cell

value: Lung

tag: cell organism

tag: cell description

tag: cell sex

tag: age description

tag: control

tag: control description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Cerebellum_Pol2_adult-8wks

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

value: Cerebellum

tag: antibody

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: controlid

tag: labversion


title: hyl1-2-dcl1-21_flower_8week

source_name: flowers and flower buds, hyl1-2/dcl1-21

tag: ecotype

tag: genotype

tag: tissue

value: flowers and flower buds


title: LICR_ChipSeq_BoneMarrow_Input_adult-8wks

tag: lab description

tag: datatype

tag: datatype description

tag: cell

value: BoneMarrow

value: mouse

value: Bone Marrow

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age

value: std

value: Standard input signal for most experiments.

tag: replicate

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_Cortex_CTCF_adult-8wks

tag: lab

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: Cortex

tag: cell organism

tag: cell description

tag: cell sex

value: M

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: age description

value: Adult 8 weeks

tag: control

tag: control description

value: ELAND


title: LICR_ChipSeq_Lung_CTCF_adult-8wks

tag: lab description

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: Lung

tag: antibody vendorid

tag: controlid

tag: labversion

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Heart_Pol2_adult-8wks

tag: lab

value: Heart

tag: cell organism

value: mouse

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: age

tag: replicate

tag: softwareversion

tag: strain

tag: strain description


title: LICR_ChipSeq_Kidney_Input_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: Kidney

tag: cell description

tag: cell sex

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age description

value: std

value: Standard input signal for most experiments.


title: LICR_ChipSeq_SmIntestine_Input_adult-8wks

source_name: SmIntestine

tag: lab description

tag: datatype

tag: datatype description

value: SmIntestine

value: Small Intestine

value: M

value: Adult 8 weeks

tag: control

tag: control description

value: Bowtie


title: hyl1-2_rosetteleaf_5week

source_name: rosette leaves, hyl1-2

tag: ecotype

tag: genotype

tag: tissue

value: rosette leaves


title: LICR_ChipSeq_Limb_Input_E14.5

source_name: Limb

tag: lab

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: Limb

tag: cell organism

value: mouse

value: U

tag: age

value: Embryonic day 14.5

tag: controlid

tag: labversion

tag: replicate

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_Liver_CTCF_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: Liver

tag: cell description

tag: cell sex

tag: antibody

value: CTCF

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:CTCF

tag: antibody targetdescription

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: softwareversion

value: ELAND

tag: strain

tag: strain description


title: LICR_ChipSeq_Cerebellum_Input_adult-8wks

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: Cerebellum

value: M

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.


title: LICR_ChipSeq_Testis_CTCF_adult-8wks

source_name: Testis

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

value: Testis

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: age

tag: controlid

tag: labversion

tag: replicate

value: Bowtie


title: LICR_ChipSeq_SmIntestine_CTCF_adult-8wks

value: LICR-m

value: Ren - Ludwig Institue for Cancer Research

value: SmIntestine

value: Small Intestine

tag: antibody

value: CTCF

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: softwareversion

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


title: LICR_ChipSeq_WholeBrain_Pol2_E14.5

tag: lab

tag: lab description

tag: datatype

tag: datatype description

value: WholeBrain

value: Whole Brain

value: U

value: mouse monoclonal, clone 8WG16. Antibody Target:POL2

value: RNA Polymerase II

value: Covance

tag: age description

value: Embryonic day 14.5

tag: control

tag: control description


title: Caltech_ChipSeq_C2C12_H3ac_(06-599)_Control_32bp_EqS_2.0pct_24hr

value: Caltech-m

value: Wold - Califonia Institute of Technology

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

tag: cell description

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

tag: cell sex

value: F

value: rabbit polyclonal antibody raised against a KLH-conjugated peptide corresponding to amino acids 1-20 of Tetrahymena histone H3 (ARTKQTAR[K*]STGG[K*]APRKQLC) where K* is acetylated. Antibody Target:H3ac

value: missing

value: Millipore

value: This data represents a control being compared to experiments using read length of 32 bp

tag: treatment

tag: treatment description

value: 24 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

value: immortalized

value: Immortal cells

tag: controlid

tag: labexpid

tag: labversion

value: Myocyte

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_H3ac_(06-599)_Control_32bp

tag: lab

tag: lab description

value: mouse

tag: antibody

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

value: No special treatment or protocol applies

value: Myoblast

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_Input_Control_32bp

value: Caltech-m

value: Wold - Califonia Institute of Technology

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

tag: control description

tag: treatment

tag: age description


title: Caltech_ChipSeq_C2C12_Input_Control_32bp_EqS_2.0pct_60hr

tag: lab

tag: lab description

value: ChipSeq

value: Chromatin IP Sequencing

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: F

tag: antibody

tag: treatment description

value: 60 h with 2.0% Equine Serum and Insulin (Wold)

tag: age

tag: controlid

tag: labexpid

tag: labversion

tag: labversion description


title: Caltech_ChipSeq_C2C12_Input_Control_50bp

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

value: This data represents a control being compared to experiments using read length of 50 bp

tag: replicate

tag: strain

tag: strain description


title: Caltech_ChipSeq_C2C12_H3K79me3_(ab2621)_Control_50bp

tag: cell description

tag: cell sex

tag: antibody antibodydescription

value: Rabbit polyclonal. Antibody Target:H3K79me3

tag: antibody targetdescription

value: Associated with the gene body of actively transcribed genes

tag: antibody vendorname

value: Abcam

tag: antibody vendorid

tag: control

tag: control description

tag: treatment

value: immortalized

tag: age description


title: Caltech_ChipSeq_C2C12_H3K4me2_(ab32356)_Control_50bp_EqS_2.0pct_60hr

tag: lab

tag: lab description

tag: datatype

value: mouse

tag: antibody

value: Rabbit polyclonal. Antibody Target:H3K4me2

value: Histone H3 (di methyl K4). Marks promoters and enhancers.

tag: treatment description

tag: age

value: Immortal cells

tag: controlid

tag: labexpid

tag: labversion

value: Myocyte

tag: labversion description

value: Strain C3H, Very related to C57BL/6


title: Caltech_ChipSeq_C2C12_Input_Control_32bp_EqS_2.0pct_24hr

value: Caltech-m

value: Wold - Califonia Institute of Technology

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

value: This data represents a control being compared to experiments using read length of 32 bp

value: 24 h with 2.0% Equine Serum and Insulin (Wold)

tag: replicate

tag: strain

tag: strain description