title: H3K4me3_ChIP_Seq_rep2

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Basecalls performed using Illumina Casava1.7 software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to hg19 whole genome using tophat with default parameters.
FAIRE Peaks were called using findPeaks from HOMER (http://biowhat.ucsd.edu/homer), using a triangle-based B224distribution with a median length of 150bp with an alpha value of 0.01 (99.0% confidence interval). To identify epigenomic domains for histone modification, the MACS software on histone ChIP-seq data was applied with default settings (Zhang et al, 2008)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using makeTagDirectory and makeUCSCfile from homer with following -o auto -res 1 -fsize 5e7; FAIRE peak files were generated using following settings (-alpha 0.01 -subpeaks 0.6) and score represents number of tags found clustered together. ChIPseq peaks were processed by using MACS default settings.

growth_protocol: MDAMB231 cells were obtained from American Type Culture Collection (ATCC, Manassas, VA). MDAMB231 cells were cultured in DMEM with 5% FBS.

extract_protocol:
For FAIRE, nuclei were extracted after the crosslinking step (1% formaldehyde in PBS) of intact cells, followed by re-suspension in SDS lysis buffer before sonication. FAIRE DNA samples were purified by phenol/chloroform extraction. Input DNA was also purified by phenol/chloroform extraction after the crosslinking was reversed. ChIP assays were performed in MDAMB231 as previously described (Jia et al, 2009).
Libraries were prepared according to Illumina's instructions (refer to http://epigenome.usc.edu/services/nextgen/making_libraries.html)

tag: chip antibody


title: KW1407-YNB-Mannose 5 days

status: Public on Dec 31 2013

type: SRA

city: Vancouver

first: Ye

last: Wang

state: BC

department: Department of Wood Science

country: Canada

institute: University of British Columbia

library_source: transcriptomic

data_processing:
BWA 0.5.7
Sequenced reads were trimmed for adaptor sequence, and low-quality base pairs, then mapped to Gc reference genome using CLC genomics workbench, v5.0.1
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using CLC genomics workbench. In short, the number of reads falling in the exons of a gene were counted and normalized by the size of the total exon length for that gene, and by the size of the library (or total mapped reads)
Genome_build: Gc reference genome ACXQ00000000.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Leptographium clavigerum

source_name: fungal mycelium

growth_protocol: Inoculum incubated for a week and their spores harvested and germinated on 1% OMEA plates for 3 days before transferred to treatment plates

extract_protocol:
Mycelium was harvested and flash frozen with liquid nitrogen, grinded with mortar & pestle and RNA was extracted using the Qiagen RNA easy mini kit
Polyadenylated (PolyA+) RNA was purified using the uMACS mRNA isolation kit, with on-column DNaseI-treatment. Double-stranded cDNA was synthesized from the purified polyA+RNA using the Superscript Double-Stranded cDNA Synthesis kit. cDNA was fragmented by sonication, purified, then subjected to end-repair and phosphorylation. Picogreen quantification was performed to determine the amount of Illumina PE adapters used in the next step of adapter ligation reaction. The adapter-ligated products were purified then PCR-amplified with Phusion DNA Polymerase using Illumina’s PE primer set. PCR product of desired size range was gel purified.

treatment_protocol: Samples transferred onto MEA were supplied with either 300ul heptane or 200ul (+)-limonene added to filter paper strips (placed on the lid); samples transferred onto YNB were supplied with 200ul terpene added to filter paper strips (placed on the lid). Samples transferred to YNB and Mannose/Oleic Acid/Olive Oil, were added directly the the mixed media.

tag: strain

tag: treatment

value: YNB-Mannose

tag: time

value: 5 d


title: H3K27Ac_ChIP_Seq_rep2

city: Los Angeles

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line


title: 4sU_RNA_repeat1

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1
The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: HelaS3 cells

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer’s instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS™ Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus™ Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.
Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3’ to 5’ exo- (NEB) to add an “A” base at the 3’end of the DNA fragments, and finally ligated to adapters with a “T” overhang.  Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 × 100 bp paired-end).

tag: cell type

value: tumor cells

tag: library

value: 4sU RNA


title: Input DNA for ChIP

value: input


title: H3K27Ac_ChIP_Seq_rep1


title: H3K4me1_ChIP_Seq_rep2


title: FAIRE_Seq_rep2


title: Input DNA for FAIRE


title: H3K4me3_ChIP_Seq_rep1


title: CG-SH RNA

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

institute: University of Montreal

data_processing:
Illumina Casava1.7 software used for basecalling.
Eland2 was used (through Casava 1.7) for mapping to the human reference genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome Build: hg19
supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: acute myeloid leukemia

growth_protocol: Cells were cultured in IMDM medium with 10% FBS, penicillin (100 U/ml) and streptomycin (100 µg/ml) supplemented with cytokines (human stem cell factor (H-SCF) (100 ng/ml), interleukin 3 (IL-3) (20 ng/ml), granulocyte colony-stimulating factor (G-CSF) (20 ng/ml)

extract_protocol: Total RNA was extracted from Trizol (invitrogen) according the manufacturers guidelines. rRNA was removed through ribominus kit (Invitrogen) according to manufacturers protocol.  Remaining RNA was converted into strand specific paired-end cDNA libraries using Illumina RNA-seq kit according to manufacturers protocols.

treatment_protocol: Cells were grown in exponential phase before 1x10^7 cells were collected and placed into either DNAzol or Trizol in order to extract gDNA or RNA respectively

value: CG-SH


title: FAIRE_Seq_rep1


title: KW1407-YNB-Olive Oil 5 days

value: YNB-Olive oil


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T62t

city: Cambridge

first: Sebastian

last: Hoersch

state: MA

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

description: DNA-Seq/WGS

data_processing:
Sequencing was performed on an Illumina GAIIx Sequencer using Sequence Control software v2.6.26.
Sequences were processed with GERALD.pl (CASAVA 1.6.0 or CASAVA 1.7.0), downloaded from the Illumina Web site (http:// www.illumina.com/software/genome_analyzer_software.ilmn), with a produced read length of 34 nucleotides.
FASTQ sequence files were split into sample sets according to barcode sequences, which were then trimmed from the complete sequences using the applications fastx_barcode_splitter.pl and fastx_trimmer from the FASTX-Toolkit- 0.0.13 (http://hannonlab. cshl.edu/fastx_toolkit) package.
Illumina sequence qualities were converted to Sanger sequence qualities using the MAQ application fq_all2std.pl (http://maq.sourceforge.net/qual.shtml) (Li et al., 2008).
Sequences were then aligned to chromosomes 1-25 in the zebrafish Zv9/danRer7 assembly using bwa0.5.8c (Li and Durbin, 2009).
Unassembled "scaffold" and "NA" fragments were not included in the alignment target.
Alignments with quality scores of 10 or greater were extracted from the resulting Sequence Alignment/Map files.  At this stage, individual samples were required to have at least 100,000 aligned reads, otherwise the sample and its corresponding normal or tumor counterpart were excluded from this study.
[Processed data file #1, incl. this step] For the qualifying 294 tumor and normal samples, counts were obtained for the number of reads aligning to 13551 consecutive, adjacent 100-kb physical windows along chromosomes 1-25.
For the qualifying 294 tumor and normal samples, counts were obtained for the number of reads aligning to 13551 consecutive, adjacent 100-kb physical windows along chromosomes 1-25. The per-window counts per sample were rescaled to a total of 1 million reads.
[Processed data file #2, incl. this step] Log2 ratios were calculated for the matching tumor/normal sample pairs for all 100-kb windows or set to 0, if the read count for one or both samples was 0.
The log2 ratios were then submitted to the circular binary segmentation algorithm (Venkatraman and Olshen, 2007) as implemented in the BioConductor package DNAcopy (v1.16.0), and processed with the following key parameter settings: with smoothing, undo.SD=2.
[Processed data file #3, incl. this step] 100K bin numbers were converted to genomic coordinates fixed at window midpoint, and for each sample pair, all segment mean values obtained were mean-centered before being used for further analysis.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: FILE: Zhang2012-procData1_countsPer100K.xlsx. Data matrix with read counts (quality scores >= 10) per 100K genomic window per sample (tumor or normal separately for each T/N pair, 294 data columns)
Supplementary_files_format_and_content: FILE: Zhang2012-procData2_log2ratios.xlsx. Data matrix with log2-ratios obatined after per-column read count rescaling to 1 Mio reads.
Supplementary_files_format_and_content: FILE: Zhang2012-procData3_segmented.seg. Segment file: output of the program DNAcopy; segments per sample are mean-centered.

organism: Danio rerio

source_name: Tumor from adult fish

growth_protocol: Fish were kept according to standard conditions described in: The Zebrafish Book: A Guide for the Laboratory use of Zebrafish (Danio rerio), Monte Westerfield - 1995 - Univ. of Oregon Press

extract_protocol: Tumor and normal DNA samples were individually processed for sequencing with the Illumina Genome Analyzer IIx system according to published methods (Quail MA, et al.,2008 (PMID:19034268); Bentley DR, et al.,2008 (PMID:18987734); Quail MA, et al., 2009 (PMID:19582764)). All the enzymes used in the preparation were from New England Biolabs, and the oligonucleotides were synthesized by Eurofins MWG Operon. Oligonucleotide sequences (ATTGGC; GATCTG; TCAAGT; CTGATC; AAGCTA; GTAGCC; TACAAG; CGTGAT; ACATCG; GCCTAA; TGGTCA; CACTGT) were added to the 3' end of the Illumina adaptors used for the paired-end library preparation in order to serve as barcodes so that multiple samples could be sequenced in the same reaction.

value: Zebrafish TAB strain

tag: age

value: 8-24 month

tag: tissue

value: Peripheral nerve sheath

tag: tumor type

value: MPNST, from rp gene mutation


title: Normal tail tissue, sample P53-3N-T56c

description: DNA-Seq/WGS

source_name: Tail from adult fish

value: Tail


title: Normal tail tissue, sample P53-3N-T63c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T61t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T56t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T55c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T60c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T65t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T63t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T61c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T65c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T60t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T55t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T53t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T54t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T54c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T52c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T52t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T51t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T53c

description: DNA-Seq/WGS


title: H3K4me1_ChIP_Seq_rep1


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T50t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T50c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T48c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T47t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T48t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T47c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T46t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T44t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T44c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T45t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T43t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T51c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T42c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T39t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T43c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T39c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T38t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T38c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T40t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T40c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T45c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T42t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T37t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T62c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T37c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T36c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T35c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T35t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T34c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T46c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T32c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T33c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T33t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T32t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T30t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T31t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T30c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T31c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T29c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T36t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T24t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T25t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T22t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T18t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T21t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T23c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T21c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T22c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T24c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T34t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T18c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T16t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T16c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T15t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T14t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T14c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T29t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T13t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T23t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T12c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T13c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T11t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T25c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T11c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T09c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T08t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-52c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T09t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T08c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-48t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-51t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-48c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53-3N-T15c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-50c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-47t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-46t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-47c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-46c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-45t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-50t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-45c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-44c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-44t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation, triploid), sample P53-3N-T12t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-43t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-43c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-41t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-39c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-40t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-39t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-41c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-52t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-40c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-37t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-36c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-35c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-38c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-35t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-34t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-36t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-33c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-34c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-37c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-31c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-33t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-30t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-31t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-51c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-29t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-28t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-29c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-28c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-27t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-38t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-24t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-27c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-26t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-26c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-25c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-25t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-24c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-23t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-21t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-22t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-20t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-20c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-21c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-30c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-18c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-19c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-23c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-17t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-19t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-16t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-13t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-13c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-12t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-12c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-14t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-17c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-16c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-10t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-11c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-10c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-11t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-22c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-09t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-09c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-08t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-18t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-07c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-06t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-06c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-08c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-07t

description: DNA-Seq/WGS


title: WTOPBB22

city: Blacksburg

first: Roderick

middle: V

last: Jensen

address: Washington street

department: Biological Sciences

institute: Virginia Polytechnic Institute and State University

description: total RNA depleted for rRNA and tRNA

data_processing:
The Vibrio parahaemolytius BB22OP transcriptome sequencing read files in FASTQ format were transformed into FASTA format using the SeqIO module of BioPython (5) v.1.60 (www.biopython.org) through Python 2.7.2.
The standalone BLAST+ suite (1, 4) v.2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/) was used to align the reads to the annotated Vibrio parahaemolyticus BB22OP protein coding sequences for chromosomes downloaded from the NCBI Nucleotide pages for Chromosome 1 (CP003972.1) and Chromosome 2 (CP003973.1)
A BLAST database and its index were created using the FASTA files for each of the samples using the makeblastdb and makembindex BLAST+ routines
For each sample, standalone blastn queries were performed using the nucleotide sequences for the Vibrio parahaemolyticus BB22OP protein coding genes against the BLAST databases for each sample
In blastn a word size of 16 and a maximum e-value of 1.e-10 were chosen for alignment.
The table format output (-outfmt 6) of each blastn query was subsequently processed using an awk-based shell script to count and list the total number of blastn hits for each of the protein-coding genes in the V. parahaemolyticus data set. Subsequent data processing was done using Microsoft Excel.
Genome_build: NCBI Chromosome 1 (CP003972.1) and Chromosome 2 (CP003973.1)
Supplementary_files_format_and_content: Processed data files were generated separately for Chromosome1 and Chromosome2 containing the the raw read counts as well at the normalized expression values (RPKM and RPM)  for both samples LM5312 and LM5674 in tab delimited text files.
Supplementary_files_format_and_content: The first 8 columns of the processed data file contain the data: Gene Number, Gene ID, LM5312(Reads), LM5674 (Reads), LM5312(RPKM), LM5674(RPKM), LM5312(RPM), LM5674(RMM).
Supplementary_files_format_and_content: The remaining 7 columns contain annotation information for each gene: Gene ID, Start, End, Strand, Length, Protein, and RIMD Correspondence.

organism: Vibrio parahaemolyticus

source_name: bacterium

growth_protocol: A single colony was streaked as a lawn onto an HI plate. The following day, 5 ml of HI broth was used to suspend the cells on the plate, and the cells were then diluted to an optical density at 600 nm (OD600) of 0.05. Fifty microliters of the diluted cells was spread onto an HI plate. After 6 h of growth, cells were harvested from the plate and diluted to an OD600 of 1.0 by using RNAprotect (Qiagen) that had been diluted 2-fold in 1× Dulbecco's phosphate-buffered saline (DPBS), pH 7.1 (Gibco).

extract_protocol:
RNA isolation with Qiagen miRNeasy kit with on column Dnase I digestions.  rRNA was delepted using Epicentre Gram negative rRNA depeletion kit.
RNA libraries were prepared for sequencing using standard Illumina protocols at Virginia Bioinformatics Institute

treatment_protocol: Qiagen RNAprotect diluted two fold in DPBS was added to the cell culture

tag: phenotype

value: opaque

tag: genotype

value: wild type


title: Normal tail tissue, sample P53hom-05c

description: DNA-Seq/WGS


title: dopaRTRBB22

description: total RNA depleted for rRNA and tRNA

value: translucent

value: opaR deletion


title: MPNST tumor (p53 gene mutation), sample P53hom-05t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-04c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-04t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-03c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-01c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp056c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample M71mpnst

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-02t

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-02c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp056t

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-03t

description: DNA-Seq/WGS


title: Normal tail tissue, sample M71c

description: DNA-Seq/WGS


title: Normal tail tissue, sample P53hom-14c

description: DNA-Seq/WGS


title: MPNST tumor (p53 gene mutation), sample P53hom-01t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp053c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp052t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp054t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp051c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp054c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp052c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp051t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp048t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp049t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp049c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp050c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp048c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp046t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp047t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp050t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp047c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp045t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp046c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp053t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp045c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp044c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp043t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp043c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp041t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp044t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp039c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp040t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp038t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp039t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp040c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp041c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp038c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp036t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp037t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp037c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp036c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp035t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp035c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp034t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp033t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp032c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp032t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp034c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp033c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp030c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp031c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp031t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp030t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp029t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp029c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp028t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp025t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp027c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp025c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp024c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp024t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp022t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp021t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp019c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp018t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp020c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp019t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp023c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp020t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp022c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp014t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp015c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp016t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp016c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp028c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp013t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp023t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp013c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp012t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp012c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp011t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp021c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp011c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp010c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp017t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp010t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp017c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp014c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp015t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp027t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp008t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp007c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp008c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp009c

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp003c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp007t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp005t

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp004t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp006c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample RP002t

description: DNA-Seq/WGS


title: Normal tail tissue, sample RP002c

description: DNA-Seq/WGS


title: MPNST tumor (rp gene mutation), sample Rp001t

description: DNA-Seq/WGS


title: Normal tail tissue, sample Rp001c

description: DNA-Seq/WGS


title: D. pseudoobscura imaginal discs / CNS

city: Ann Arbor

first: Yang

last: Lyu

state: Michigan

address: 109 Zina Pitcher Place

institute: University of Michigan

description: small RNAs

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome (droSim1 or dp4) using bowtie v0.12.7 with parameters -n 0 -v 0 -f -k 50 -a -p
Reads Per Million (RPM) was calculated using in-house perl scripts. The number of reads for each miRNA were counted and normalized by the total reads mapped to all miRNAs.
Genome_build: D. simulans http://www.ncbi.nlm.nih.gov/assembly/GCF_000259055.1/
Genome_build: D. pseudoobscura http://www.ncbi.nlm.nih.gov/assembly/GCF_000001765.2/
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each miRNAs

organism: Drosophila pseudoobscura

source_name: Drosophila pseudoobscura imaginal discs / CNS

growth_protocol: Fruit flies were cultured under 25℃

extract_protocol:
Tissues were dissected on dry ice, and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions

value: 3rd larvae

value: imaginal discs / CNS


title: D. pseudoobscura ovaries

description: small RNAs

source_name: Drosophila pseudoobscura ovaries

value: 3-5d adult

value: ovaries


title: short-hairpin Drosha (shDr) day 7 myeloid (D7 GMM) rep2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
The csfasta files were processed by cutadapt v0.9.3 to remove the 3'-adapter, Then the trimmed reads were aligned to hg19 genome with Bowtie v0.12.7 with default options.
The miRNA expression levels were counted using customized R script using miRBase v16
All counts were scaled to the total number of aligned reads across all samples
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format containing the log2 transformed scaled counts

source_name: CD34+ HSPCs

extract_protocol:
Cells were sorted (D0), collected, washed and gently centrifuged. Cell pellets were lysed in Ambion's miRVana RNA extraction lysis buffer and applied to kit columns. Total RNA was eluted and concentrations were assessed using a nanodrop spectrophotometer. Bioanalysis of total RNA to assess quality and subsequent size fractionation by gel electrophoresis was done at Medomics, Inc. (Azusa, CA).
The guidelines provided in the user guide by Applied Biosystems were followed. Total RNA samples were used to generate cDNA libraries. Each cDNA had adapters on both ends giving a total of approximately 42 extra baseparis. The fragments were size selected on gels by excising fragments in the of 55 to 90 bp (target size 60-80 bp). These size-selected cDNAs were then sequenced on the SOLiD 4.0 platform.

tag: source tissue

value: umbilical cord blood

value: transduced with the lentivector encoding a short-hairpin RNA targeting Drosha

tag: cell culture

value: GMM liquid culture (myeloid) containg G-CSF and GM-CSF

tag: time-points collected

value: day 7


title: empty vector (EV) day 7 myeloid (D7 GMM) rep2

value: transduced with the empty lentivector


title: short-hairpin Drosha (shDr) day 0 (D0) rep2

description: short-hairpin Drosha (shDr) day 0 (D0)

value: serum-free MEM containing SCF, TPO, FLT-3L, IL-3 and IL-6

value: day 0 (immediately after sorting)


title: D. pseudoobscura testes

description: small RNAs

source_name: Drosophila pseudoobscura testes

value: testes


title: empty vector (EV) day 7 myeloid (D7 GMM) rep1


title: MPNST tumor (rp gene mutation), sample Rp006t

description: DNA-Seq/WGS

value: Zebrafish TAB strain

value: 8-24 month

value: Peripheral nerve sheath

value: MPNST, from rp gene mutation


title: empty vector (EV) day 0 (D0) rep2

description: empty vector (EV) day 0 (D0)


title: Normal tail tissue, sample Rp005c

description: DNA-Seq/WGS

value: Tail


title: Normal tail tissue, sample Rp004c

description: DNA-Seq/WGS


title: short-hairpin Drosha (shDr) day 0 (D0) rep1

description: short-hairpin Drosha (shDr) day 0 (D0)


title: empty vector (EV) day 0 (D0) rep1

description: empty vector (EV) day 0 (D0)


title: MPNST tumor (rp gene mutation), sample Rp003t

description: DNA-Seq/WGS


title: ChIP-seq_Wholetissue_E2KOp13_H3K27me3

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

description: DNA from pooled tissues of three individual mice.

data_processing:
Basecalls performed using the CASAVA software.
Sequenced reads were aligned to the mm9 genome assembly using BWA (Li and Durbin, Bioinformatics, 2009) or Bowtie1 (Langmead et al., Genome biology, 2009) or TopHat (Trapnell et al., Bioinformatics, 2009).
ChIP-seq: The HiSeq 2000 sequence reads (single-end) were aligned to the mouse reference genome (mm9) using Bowtie1 (Langmead et al., 2009). The GAII sequence reads (single-end) were aligned to the mouse reference genome (mm9) using BWA (Li and Durbin, 2009). Total mapped reads per sample were normalized to 10 million using the HOMER program (Heinz et al., 2010).
mRNA-seq: After assessing the quality of sequenced single-end reads by FastQC (http://www.bioinformatics.babraham.ac.uk/project/fastqc), contaminating adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore). The trimmed reads from biological triplicates per each sample were aligned to the mouse reference genome (mm9 assembly) using the TopHat program (Trapnell et al., 2012). Transcript abundance was estimated by means of fragment per kilobase of exon per million fragments mapped (FPKM) using Cufflinks (Trapnell et al., 2012). Rarely expressed genes (below 5 FPKM in samples for comparison) were discarded and FPKM values were converted to z-score. We initially identified differentially expressed genes (DEGs) between samples with an FDR-adjusted P value cutoff (< 0.05) using Cuffdiff (Trapnell et al., 2012). Among non-DEGs, we further defined genes showing 0.1 z-score difference and more than 3-fold changes between samples as DEGs.
Genome_build: MGSCv37
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text file contains FPKM values (normalized expression levels) of genes in each sample.

organism: Mus musculus

source_name: mammary tissues, E2KO, p13, no treatment, H3K27me3 ChIP

growth_protocol: We mated Ezh2f/f mice (Ezhkova et al., 2011; Wang et al., 2010) with the control transgenic mouse line A (Wagner et al., 1997) in order to generate mice with mammary-specific deletion of Ezh2. Ezh1 knockout mice were obtained from Rockefeller University (Ezhkova et al., 2011). Genotyping was confirmed by PCR using DNAs from ear clips or mammary epithelial cells (MECs). All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Diseses Animal Care and Use Committee.

extract_protocol:
ChIP-seq: Frozen-stored mammary tissues from p13 were broken into powder with mortar and pestle. With MECs, cells were cross-linked with 1% formaldehyde for 10 min at RT. Nuclei were extracted in Farnham lysis buffer (5mM PIPES PH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Antibodies against STAT5 (Santa Cruz Biotechnology, cat# sc-1081; L-20, lot# L2012, 10ug) and H3K4me3 (Millipore, cat# 17-164, lot# JBC1793805, 5ug) were used for ChIP. Active Motif performed ChIP with in-house H3K27me3 antibody using pooled tissues from three individual mice of p13.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ten- to twelve-week-old mature virgin female mice were checked for stage of estrous cycle by vaginal cytology and anesthetized at estrus with an intraperitoneal injection of avertin and the left 4th mammary fat pad was collected after removal of the lymph node. Two hours after recovery from anesthesia, PRL (prolactin, 5 μg/g body weight) was injected intraperitoneally. The right 4th mammary fat pads were collected two hours later.

tag: strain/background

value: outbred

tag: genotype/variation

value: mammary

tag: developmental stage

value: day 13 of pregnancy


title: PARP-14 -/- (KO) + PJ34

city: Indianapolis

first: Purvi

last: Mehrotra

state: IN

address: 1044 West Walnut Street, R4-279

department: Pediatric Pulmomology

institute: Indiana School of medicine

data_processing:
36-nt sequence reads ID'd using Illumina's Genome Analyzer 2, mapped to genome using ELAND.
Peak-calling performed using SICER.
Tag Normalization by truncating tag number of all samples to number of tags present in smallest sample
False peak filtering performed by comparing intervals present in Input of IgG control samples to Intervals in ChIP samples.
Genome_build: mm9

source_name: Naïve CD4+ T cells

growth_protocol: Naive CD4+CD62L+ T cells were purified from spleens by magnetic selection (Miltenyi Biotec). Naive CD4+ T cells were activated with plate-bound anti-CD3 (2 mg/ml;BD Pharmingen) and soluble anti-CD28 (1 mg/ml; BD Pharmingen) and cultured under Th2 conditions (IL-4 [10 ng/ ml; PeproTech] and anti–IFN-g [10 ng/ ml; XMG;BD BIosciences]). After 3 d, cultures were expanded with fresh complete RPMI 1640 medium containing IL-2 (50U/mL: PeproTech)and IL-4 (10 ng/mL) for 4 days.

extract_protocol: Cells were fixed and sonicated according to active motif protocol

treatment_protocol: Th2 differentiated cells were treated with 10uM PJ34 (Sigma).

tag: strain

value: Spleen


title: PARP-14 +/+ (WT)


title: ChIP-seq_Wholetissue_InputforK27

source_name: mammary tissues, p13, no treatment, input

tag: treatment

tag: chip antibody


title: ChIP-seq_Wholetissue_Controlp13_H3K27me3

source_name: mammary tissues, control, p13, no treatment, H3K27me3 ChIP

value: MMTV-Cre


title: short-hairpin Drosha (shDr) day 7 myeloid (D7 GMM) rep1

value: umbilical cord blood

value: transduced with the lentivector encoding a short-hairpin RNA targeting Drosha


title: 29CHIP_mock

city: New Delhi

first: Sanjay

last: Kapoor

address: Benito Huarez MArg

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi, South Campus

description: mock immunoprecipitated chromatin

data_processing:
Reads were aligned to MSU RGAP Release 6.1 - Unified Rice Pseudomolecules version, using CLCBIO (defalt paprameters) and the resultant bam files were imported in Avadis NGS for analysis
Aligned reads were filtered using Quality threshold >= 30 Alignment score threshold >= 90
Peaks detected using MACS Algorithm. Treatment Sample: 29CHIP_IPsample mapping  Control Sample: 29CHIP_Input mapping;  Algorithm: Model-based Analysis for ChIP-Seq   Parameters:    Read Length (bp) = 36;   Average Fragment Length (bp) = 350; Effective Genome Size (bp) = 3.33712896E8; p-value Cutoff = 9.999999747378752E-6;    Enrichment Factor = 10
Peaks were also detected using MACS Algorithm. Treatment Sample: 29CHIP_IPsample mapping  Control Sample: 29CHIP_mock mapping;  Algorithm: Model-based Analysis for ChIP-Seq   Parameters:    Read Length (bp) = 36;   Average Fragment Length (bp) = 350; Effective Genome Size (bp) = 3.33712896E8; p-value Cutoff = 9.999999747378752E-6;    Enrichment Factor = 2
The peak regions satisfying both the above criteria were shortlisted and annotated with Genic parts, e.g. Upstream (2kb), 5"UTR, Exonic, Intronic, 3'UTR, Downstream (2 kb)
Genome_build: genome build: MSU RGAP Release 6.1 - Unified Rice Pseudomolecules version
Supplementary_files_format_and_content: Unique peaks (378) were idenfied by mapping the summit to a specific genic part

organism: Oryza sativa

source_name: Seed

extract_protocol:
Extraction of chromatin was done as per proctocol mentioned in Haring et al's paper- Chromatin immunoprecipitation: optimization, quantitative  analysis and data normalization, Plant Methods 2007, 3:11.
Library construction was done according to Illumina's protocol

tag: seed development stage

value: 9 Days after pollination seed


title: 29CHIP_Input

description: total fragmented chromatin


title: 29CHIP_IPsample

description: immunoprecipitated chromatin


title: Compound 26 (10uM)

city: San Diego

first: Zhou

last: Zhu

address: 10646 Science Center Drive (CB4)

institute: Pfizer Worldwide Research & Development

data_processing:
Alignment: Sequence reads were mapped to the human genome (hg19) with ELAND (Illumina CASAVA 1.5 pipeline) software. Those that pass quality filtering, with an alignment score of at least 10 and perfect genomic match were used for peak detection.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (1.4.0rc 2), followed by filtering for high-confidence ones with higher statistical significance than any of the "negative" peaks from swappping the ChIP-Seq and control channels.

source_name: Hormone refractory prostate cancer cells

growth_protocol: VCaP human prostate cell lines were obtained from ATCC and grown in DMEM (GIBCO Cat# 11995) 10% FBS (SIGMA Cat# 12103C-500ml). Medium was supplemented with standard antibiotics (Penicillin-Streptomycin, GIBCO #15070-063).

extract_protocol: ChIP reactions were performed using precleared chromatin and antibody AR (Santa Cruz Biotechnology, Cat# sc-13062, Lot# D0610). The resulting ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit protocol. DNAs were purified by phenol-chloroform extraction and ethanol precipitated.

treatment_protocol: Cells were allowed to attach overnight and then were treated with various doses of the AR antagonists or vehicle alone (0.1% DMSO) in the absence or presence of 1nM R1881. Cells were incubated for 30min at 37oC, 5%CO2 and then processed.

tag: cells

value: VCaP

value: AR


title: Compound 26 (1uM)

value: R1881 (1nM), Compound 26 (1uM)


title: Input

value: Pooled


title: R1881(-)

value: Vehicle (0.1% DMSO)


title: Compound 26 (0.1uM)


title: Compound 30 (0.1uM)


title: Compound 30 (10uM)


title: R1881(+)


title: Axenic Amastigotes from CL causing Ldo isolate

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

description: SL RNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.3
Quality of the reads in fastq files were determined using fastqc and internal tools
SL RNA-Seq reads were aligned against Leishmania donovani genome from Nepal downloaded from www.genedb.org
Samtools v0.1.19 was used to convert alignment files from one format to another
Internal tools were used to estimate splice leader counts against each gene
Genome_build: LdoBPK282/0cl4
Supplementary_files_format_and_content: Gene level splice leader read count data generated using custom scripts. The read counts are normalzied using edgeR package

organism: Leishmania donovani

source_name: laboratory culture, whole cell lysate

growth_protocol: L. donovani parasites were isolated from two Sri Lankan patients with completely different pathology.  The CL isolate was derived from a skin lesion on the nose from a 28 year old male and the VL isolate was obtained from the bone marrow of a 53 year old male with chronic fever, hepatosplenomegaly, lymphadenopathy, low haemoglobin and seropositive for rK39 Leishmania antigen. The biopsy samples were directly inoculated into Leishmania promastigote culture medium: M199 medium (pH 7.4) supplemented with 10% heat-inactivated fetal bovine serum, 40 mM Hepes (pH 7.4), 0.1 mM Adenine, 5 mg /L Haemin, 1 mg /L Biotin, 1 mg /L Biopterin, 50 U/ml Penicillin and 50 µg/ ml Streptomycin at room temperature and 27°C after arriving in the laboratory. For  axenic amastigote culture, Leishmania promastigotes were  shifted to 37°C, pH 5.5 culture media to mimic the macrophage phagolysosome environment associated with the amastigote stage.

extract_protocol:
Promastigotes total RNA were extracted from late log phase promastigotes culture; 2. Axenic amastigotes total RNA were extracted from axenic amastigotes culture twenty two hours after inoculating promastigotes in axenic amastigotes culture; 3. Infected B10R macrophages. B10R macrophages were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum, 40 mM Hepes (pH 7.4),  50 U/ml Penicillin and 50 µg/ ml Streptomycin in a 37°C, 5% CO2 incubator. CL and VL axenic amastigotes from overnight axenic amastigotes culture were used to infect B10R cells at an amastigote / macrophage ratio of 10/1 in suspension  in DMEM medium overnight. The Leishmania infection levels were examined before extracting total RNA from these infected B10R cells. The percentage of infected macrophages is 72% for CL and 95% for VL; the average amastigotes number in an infected B10R cell is 3.6 for CL and 3.3 for VL. The infected B10R macrophage cells were harvested at 1200 RPM for 5 minutes to remove the uninfected Leishmania cells and the cell pellets were directly suspended in Trizol reagent for total RNA extraction.
SL RNA-seq libraries were prepared using a protocol adapted from Armour et al. 2009. First strand cDNA was synthesized from 1 μg of DNase-treated total RNA using Superscript III (Invitrogen) and primer 1 (5'-TCCGATCTCTNNNNNNN-3'). The reaction was performed by incubating for 90 min at 40°C followed by 15 min at 70°C.The samples were then treated with 2U RNase H (Invitro- gen; 37°C for 20 min) to remove the RNA component of the RNA/DNA heteroduplex, and the resulting first strand DNA was purified on a QIAquick PCR purification column (QIAGEN). Second strand synthesis reaction was performed using the first strand DNA as template in a reaction mix containing a primer (5'-TCAGTTTCTGTA-3') that matches the Leishmania SL sequence and 3'-5' exo- Klenow Fragment (New England Biolabs, Inc.) according to the manufacturer’s protocol (incubation at 37°C for 30 min). The resulting double-stranded DNA was purified using the QIAquick PCR purification kit. Enrichment of DNA fragments with adapters was performed by PCR amplification of the purified double stranded DNA samples using the Expand Plus High Fidelity PCR System (Roche) and primers (5'-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTCT-3' and 5'-AATGATACGGCGACCACCGACACTCTTTCCCTACATCAGTTTCTGTACTTTA-3').A 2-min denaturation step at 94°C followed by two cycles (94°C for 10 s, 40°C for 2 min, 72°C for 1 min) and an additional 13–16 cycles (94°C for 10 s, 60°C for 30 s, and 72°C for 1 min) with a final 5-min, 72°C elongation step were performed. The resulting enriched fragments were purified on a QIAquick PCR purification column and represented the SL RNA library.

tag: isolate

value: Causing Cutaneous Leishmaniasis

value: amastigotes

value: wildtype

tag: growth phase

value: 24h post inoculation in axenic amastigotes medium


title: Compound 30 (1uM)

value: R1881 (1nM), Compound 30 (1uM)


title: PARP-14 WT/KO Input

tag: tissue

value: 50:50 Mixture of PARP-14 +/+ and PARP-14 -/-


title: PARP-14 -/- (KO)


title: Macrophage derived Amastigotes from CL causing Ldo isolate

description: SL RNA-Seq


title: Cutured promastigotes from VL causing Ldo isolate

description: SL RNA-Seq

value: Causing Viceral Leishmaniasis

value: promastigotes

value: late log phase


title: Cutured promastigotes from CL causing Ldo isolate

description: SL RNA-Seq


title: Axenic Amastigotes from VL causing Ldo isolate

description: SL RNA-Seq


title: PARP-14 +/+ (WT) + Pj34

value: Spleen


title: Late-term cervix tissue rep4

city: west Haven

first: Mauris

middle: Chukwudebelu

last: Nnamani

state: CT

address: 300 heffernan drive B31-ABC/rm269

department: Systems Biology institute, EEB

institute: Yale University

description:
GpLT004
replicate 4

data_processing:
Basecalls performed using CASAVA 1.8.2 according to the manufacturer’s protocols
Sequence reads were aligned to the Cavia porcellus reference genome (cavPor3.69) using the splice junction mapper for RNA-seq reads TopHat2
After alignment, read counts were determined with HTSeq-count v0.5.4p1 as described by the authors
Relative RNA abundance was measured as Transcripts Per Million Transcripts (TPM) as recommended in (Li, Ruotti et al. 2010; Wagner, Kin et al. 2012) rather than RPKM or FPKM. The reason is that units of RPKM are not consistent between samples and are thus problematic when comparing RNA abundance between samples of different transcript composition
Genome_build: Cavpor3.0
Supplementary_files_format_and_content: Matrix (linked as supplementary file on Series record) of TPM and HTSeq counts for each sample.  Columns labled by sample name.

organism: Cavia porcellus

source_name: Late-term cervix tissue

extract_protocol:
Total RNA was extracted using the RNeasy extraction kit (Qiagen, cat# 75142) following manufactures instructions that included an in-column DNAse digestion.  Poly A RNA sselection.  Quality of the RNA was then confirmed using Agilent 2100 Bioanalyzer.
RNA library preparation and high-throughput sequencing were performed on an Illumina HiSeq 2000 sequencing system following the protocol recommended by Illumina for sequencing total RNA samples.   Strand-specific library prep.  Sequencing was done for each biological replicates at 1 x 75bp strand specific by the Yale Center for Genome Analysis

value: Hartley

tag: gestation stage

value: late-term (65.2 ± 1.2 days)

value: cervical tissue


title: Late-term cervix tissue rep3

description:
GpLT003
replicate 3


title: Late-term cervix tissue rep1

description:
GpLT001
replicate 1


title: MPNST tumor (rp gene mutation), sample Rp009t

description: DNA-Seq/WGS

value: Zebrafish TAB strain

tag: age

value: 8-24 month

value: Peripheral nerve sheath

tag: tumor type

value: MPNST, from rp gene mutation


title: Macrophage derived Amastigotes from VL causing Ldo isolate

description: SL RNA-Seq

tag: genotype


title: Mid-term cervix tissue rep1

description:
GpMT586
replicate 1

source_name: Mid-term cervix tissue

value: mid-term (43.6 ± 0.5 days)


title: Mid-term cervix tissue rep2

description:
GpMT587
replicate 2


title: Non-pregnant cervix tissue rep2

description:
GpNP406
replicate 2

source_name: Non-pregnant cervix tissue

value: non-pregnant


title: Non-pregnant cervix tissue rep1

description:
GpNP405
replicate 1


title: Non-pregnant cervix tissue rep3

description:
GpNP538
replicate 3


title: wounded stems of three-year-old Aquilria sinensis

city: Beijing

first: Xu

last: Yanhong

address: No. 151,Malianwa North Road, Hai Dian District

institute: The Institute of Medicinal Plant Development

description: all of the stems from the wounded plants were mixed in equal proportion to generate material for the wounded library

data_processing:
Reads were sequenced by 454 GS FLX, and Basecalls performed using sff_extract version 0.2.6
A Perl script was used to remove vector sequences and Poly(A)/(T) tails from the original sequences. Reads shorter than 100 bp were deemed low quality reads and removed before assembly.
The remaining high-quality reads were assembled using MIRA (Chevreux et al. 2004) to construct unique consensus unigenes.
The processed data file contains four columns: #ID = assembled sequence, #Length = length of assembled sequence, #Counts = number of reads in this assembled sequence, and #TPM = number of reads in this assembled sequence per million

organism: Aquilaria sinensis

growth_protocol: Three-year-old A. sinensis trees were planted in Hainan Province of China.

extract_protocol:
Total RNA was isolated from the wounded and healthy materials in the libraries using a TRIzol kit (Invitrogen, USA) and purified to enrich messenger (mRNA) and exclude transfer and ribosomal RNA using an mRNA purification kit (Promega, USA) according to manufacturer instructions.
The mRNA was reverse-transcribed with PowerScript™ II (Takara, Japan) using SMART IV™ oligonucleotide PCR primers (5′-AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGC CGGG-3′) and a CDS III/3′ PCR primer (5′-ATTCTAGAGGCCGAGCGGCCGACATG-d[T]30N-1N-3′). Long-distance PCR for double-stranded cDNA amplification was performed with LA Taq enzyme (Takara, Japan) for 25 cycles (95°C for 30 s, 68°C for 8 min) according to the SMART™ cDNA Library Construction Kit user manual. Finally, the double-stranded cDNA was purified using a DNA purification kit (Qiagen, Germany) to generate high-quality cDNA. Approximately 10 μg cDNA was sheared and used for 454 sequencing. The cDNA sample was end-repaired and ligated to adapters. Streptavidin bead enrichment, DNA denaturation, and emulsion PCR were performed according to a procedure described by Margulies et al. (2005). Each portion of the preparations from the healthy and wounded libraries were loaded on a full plate and sequenced in one run.

treatment_protocol: The stems were pruned with a knife, and samples were taken from 6 cm below the pruned site at various times after pruning: 2 h, 4 h, 6 h, 8 h, 12 h, 24 h, 3 d, and 5 d. All of the stems from the wounded plants were mixed in equal proportion to generate material for the wounded library

value: wounded stems

tag: development stage

value: three-year-old Aquilria sinensis


title: cDNA from pooled RNAs of healthy stems of three-year-old Aquilria sinensis

description: total RNA from stems were pooled and then reverse transcribed using the Super SMARTTM PCR cDNA Synthesis kit (Clontech, CA, USA) combined with a modified poly (T) primer

value: healthy stems


title: p65 control KB

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
Macs 1.4 was used to call peaks at default settings
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were produced using Macs 1.4 at 10bp resolution
Supplementary_files_format_and_content: BED files describing peak intervals were produced using Macs 1.4.

source_name: ChIP-Seq Analysis of NF-kB p65 in KB Cells

growth_protocol: cells were cultured in DMEM, 10% FCS, to subconfluency

extract_protocol:
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by IP and purification of DNA
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions

treatment_protocol: IL-1 alpha was added directly to the cell culture medium

tag: antibody

value: anti-p65 (Santa Cruz, sc-372)


title: H3K9Ac IL1 KB

description: ChIP-seq

source_name: ChIP-Seq Analysis of H3K9Ac in KB Cells

value: 10ng/ml IL-1alpha for 1 h

value: anti-H3K9ac (Millipore, 07-352)


title: p65 IL1 KB

description: ChIP-seq


title: H3K9Ac control KB

description: ChIP-seq


title: H3K9me3 control KB

description: ChIP-seq

source_name: ChIP-Seq Analysis of H3K9me3 in KB Cells

value: anti-H3K9me3 (Abcam, ab8898)


title: Pol II control KB

description: ChIP-seq

source_name: ChIP-Seq Analysis of RNA Pol II in KB Cells

value: anti-Pol II (Millipore, 17-620)


title: Pol II IL1 KB

description: ChIP-seq


title: H3K9me3 IL1 KB

description: ChIP-seq


title: CDK6 control KB

description: ChIP-seq

source_name: ChIP-Seq Analysis of CDK6 in KB Cells

value: anti-CDK6 (Santa Cruz, sc-177)


title: Mid-term cervix tissue rep3

description:
GpMT588
replicate 3

value: Hartley


title: Late-term cervix tissue rep2

description:
GpLT002
replicate 2

value: late-term (65.2 ± 1.2 days)

value: cervical tissue


title: KW1407-mutant-MEA-Terpene 12 hours

source_name: fungal mycelium

value: MMEA-Terpene

tag: time


title: rdr2, seedling, control for submergene and salt

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

description:
Small RNA
r2SC3

data_processing:
The raw sequencing data was converted to SCARF format, trimmed of adapters, and matched to the Arabidopsis genome (TAIR9) by custom Perl scripts.
Genome_build: TAIR9
Supplementary_files_format_and_content: Text file containing distinct small RNAs with their raw abundance after removing the adapter sequences.

organism: Arabidopsis thaliana

source_name: Seedling, rdr2 mutant, untreated

growth_protocol: For flowers, seeds were sown directly onto soil and grown at 21°C in a growth chamber with 16 hours of light for six weeks.  For seedlings, surface-sterilized seeds were plated onto Murashige and Skooge (MS) media and grown in a chamber at 21°C with 16 hours of light for two weeks.

extract_protocol:
RNA was extracted using Trizol reagent.
Small RNA libraries were constructed as previously described (Lu et al. 2007 (PMID 17889797)) and sequenced on an llumina Genome Analyzer II. Sequencing was performed at Illumina or the Delaware Biotechnology Institute.

treatment_protocol: For flowers, submergence stress was applied by submerging plants under sterile water for four hours prior to harvesting. For salt stress, 0.1 M NaCl or 0.3 M NaCl solutions were added to plants for 24 hours before harvesting. Cold stress was carried out by transferring plants to a 4°C cold room with continuous light for 24 hours. For seedlings, salt and submergence stresses were carried out by pouring 40 mL of sterile water with 0.3 M NaCl (salt) or without (submergence) eight hours before harvesting. Phosphate starvation stress was carried out by plating onto MS containing one tenth the normal amount of phosphate. For roots, 40 plants each of four-day-old Col-0 plants germinated on MS (with 3% sucrose) media were transferred to magenta boxes containing a mesh for separating roots and shoots with 100 mL each of MS liquid medium (with 1% sucrose). Further, the boxes were incubated on a rotary shaker set at 90 RPM illuminated with cool white fluorescent light at 25 ± 2 °C. The treatment flasks received 50 µM NiNO3 and control plants did not receive any NiNO3. Both the treatment and control flasks were incubated for 15 days, and the roots were harvested on the 15th day and the RNA was isolated for preparing the library.

tag: background

value: rdr2 mutant

value: seedling


title: rdr2, seedling, submergence and salt

description:
Small RNA
r2SNaSb

source_name: Seedling, rdr2 mutant, salt and submergence

value: salt and submergence


title: Col-0, flower, control for submergence

description:
Small RNA
C0FCSb

source_name: Flower, wild type, untreated

value: wild type

value: flower


title: rdr2, seedling, submergence

description:
Small RNA
r2SSb

source_name: Seedling, rdr2 mutant, submergence

value: submergence


title: CDK6 IL1 KB

description: ChIP-seq


title: rdr2, flower, drought

description:
Small RNA
r2FD

source_name: Flower, rdr2 mutant, drought

value: drought


title: rdr2, seedling, salt #2

description:
Small RNA
r2SNa2

source_name: Seedling, rdr2 mutant, salt

value: salt


title: Col-0, flower, submergence

description:
Small RNA
C0FSb

source_name: Flower, wild type, submergence


title: KW1407-MEA-Terpene 12 hours

city: Vancouver

value: MEA-Terpene


title: KW1407-mutant-MEA-Control 12 hours

value: MMEA-Control


title: D. simulans ovaries

description: small RNAs

organism: Drosophila simulans

source_name: Drosophila simulans ovaries

value: 3-5d adult

value: ovaries


title: D. simulans testes

description: small RNAs

source_name: Drosophila simulans testes

value: testes


title: KW1407-MEA-Control 12 hours

value: MEA-Control


title: rdr2, flower, cold

description:
Small RNA
r2FL

source_name: Flower, rdr2 mutant, cold

value: cold


title: rdr2, flower, salt #2

description:
Small RNA
r2FNa2

source_name: Flower, rdr2 mutant, salt


title: rdr2, flower, submergence

description:
Small RNA
r2FSb

source_name: Flower, rdr2 mutant, submergence


title: rdr2, flower, untreated #1

description:
Small RNA
r2F1

source_name: Flower, rdr2 mutant, untreated


title: rdr2, flower, salt and submergence

description:
Small RNA
r2FNaSb

source_name: Flower, rdr2 mutant, salt and submergence


title: dcl1-7, flower, untreated #2

description:
Small RNA
d1F2

source_name: Flower, dcl1-7 mutant, untreated

value: dcl1-7 mutant


title: dcl234, flower, untreated #2

description:
Small RNA
d234F2

source_name: Flower, dcl234 mutant, untreated

value: dcl234 mutant


title: KW1407-YNB-Mannose 3 days

source_name: fungal mycelium

value: YNB-Mannose

value: 3 d


title: dcl1-7, flower, untreated #1

description:
Small RNA
d1F1


title: Col-0, flower, untreated #2

description:
Small RNA
C0F2


title: Col-0, flower, untreated #1

description:
Small RNA
C0F1


title: Tau, Input round #1

city: Boston

first: Bess

last: Frost

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
ChIP-seq reads were aligned to the Drosophila reference genome using Bowtie
PCR duplicates were removed
Reads were extended to 350 base pairs
Total read count was normalized to 10,000,000 reads
Input sequences were subtracted from ChIPped sequences
Genome_build: Dmel Release 5
Supplementary_files_format_and_content: Processed bw files are suitable for upload into genome browsers

organism: Drosophila melanogaster

source_name: Tau, Input

growth_protocol: Drosophila melanogaster crosses and aging were performed at 25°C. The pan-neuronal elav-GAL4 driver was used to drive tauR406W  transgene expression.

extract_protocol:
2 grams of fly heads were ground in liquid nitrogen and DNA was crosslinked to protein with formaldehyde. Chromatin was sheared to 500 bp prior to ChIP
Libraries were prepared using the NEBNext ChIP-seq Library Prep Reagent Set for Illumina according to the manufacturer's recommendations

value: 10 days old

tag: genotype/variation

tag: Sex

value: male

value: whole heads

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: molecule subtype

value: input genomice DNA


title: Control, Input round #2

source_name: Control, Input

tag: chip antibody


title: Tau, Input round #2


title: Control, Input round #1


title: Control, ChIP-seq round #2

source_name: Control, ChIP-seq

value: H3K9me2 ChIPed DNA


title: Tau, ChIP-seq round #2

source_name: Tau, ChIP-seq


title: KW1407-YNB-Terpene 7 days

first: Ye

last: Wang

institute: University of British Columbia

data_processing:
BWA 0.5.7
Sequenced reads were trimmed for adaptor sequence, and low-quality base pairs, then mapped to Gc reference genome using CLC genomics workbench, v5.0.1
Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using CLC genomics workbench. In short, the number of reads falling in the exons of a gene were counted and normalized by the size of the total exon length for that gene, and by the size of the library (or total mapped reads)
Genome_build: Gc reference genome ACXQ00000000.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Mycelium was harvested and flash frozen with liquid nitrogen, grinded with mortar & pestle and RNA was extracted using the Qiagen RNA easy mini kit
Polyadenylated (PolyA+) RNA was purified using the uMACS mRNA isolation kit, with on-column DNaseI-treatment. Double-stranded cDNA was synthesized from the purified polyA+RNA using the Superscript Double-Stranded cDNA Synthesis kit. cDNA was fragmented by sonication, purified, then subjected to end-repair and phosphorylation. Picogreen quantification was performed to determine the amount of Illumina PE adapters used in the next step of adapter ligation reaction. The adapter-ligated products were purified then PCR-amplified with Phusion DNA Polymerase using Illumina’s PE primer set. PCR product of desired size range was gel purified.

tag: strain

tag: treatment

value: YNB-Terpene

value: 7 d


title: Fetal liver sample for RNA-seq 3

data_processing:
_junc.txt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
Fetal_liver_XXXXX_wt/ko.txt - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters
BAM file - Generated by Bioscope transcriptome analysis (ver 1.3) using default parameters

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 fetal liver cells 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: hnRNP L -/-


title: Fetal liver sample for RNA-seq 4


title: Fetal liver sample for RNA-seq 2

source_name: wt mouse

value: wild type


title: Tau, ChIP-seq round #1

tag: tissue


title: rdr2, flower, salt #1

description:
Small RNA
r2FNa1

value: rdr2 mutant

value: flower

value: salt


title: RNA-seq_Wholetissue_Controlp18-rep3

description:
mRNA
Processed data file: virgin_p13_p18_FPKM.txt

source_name: mammary tissues, control, p18, no treatment

extract_protocol:
RNA-seq: Poly(A) RNA were purified twice with Trizol and RNeasy® Plus Mini Kit (Qiagen). cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina).
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: outbred

value: MMTV-Cre

value: mammary

tag: developmental stage

value: day 18 of pregnancy


title: Sporocyst

city: Urbana

first: James

last: Collins

address: 601 S. Goodwin

institute: University of Illinois at Urbana Champaign

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads Per Kilobase of transcript per Million mapped reads were determined using the RNAseq module in CLC Genomics Workbench (version 4) using default settings.
Samples were mapped to the annotated Schistosoma mansoni genome version 5. The GFF file used for annotation was downloaded from the Wellcome Trust Sanger Institute Schistosoma mansoni ftp site: ftp://ftp.sanger.ac.uk/pub/pathogens/Schistosoma/mansoni/genome/GFF/
Genome_build: Schistosoma mansoni Version 5
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values and other important metrics (e.g., total gene reads) for each sample.

organism: Schistosoma mansoni

source_name: Sporocyst

growth_protocol: Free-swimming miracidia were hatched in artificial pond water under bright light for 3 h. Unhatched eggs and empty egg shells were removed by centrifugation. Miracidia were transformed in vitro to mother sporocysts by exchanging pond water with sporocyst culture medium. The sporocyst suspensions were co-cultured with Bge cells at 37°C/5% CO2/5% O2 for 48 hours.

extract_protocol:
Total RNA from 10,000 parasites using Trizol (invitrogen) and DNase treatment (DNA-free RNA Kit, Zymo Research, Irvine, CA).
Libraries were constucted using the TruSeq RNAseq Sample Prep kit. The libraries were quantitated by qPCR, pooled and sequenced on one lane for 100 cycles on an Illumina HiSeq 2000 using a TruSeq SBS sequencing kit version 3.

value: NMRI

value: 48 h post-transformation sporocyst

value: whole body


title: Miracidia

source_name: Miracidia

value: miracidia


title: RNA-seq_Wholetissue_Controlp18-rep1


title: RNA-seq_Wholetissue_Controlp18-rep2


title: RNA-seq_Wholetissue_E1+-E2KOp18-rep1

source_name: mammary tissues, E1+/-E2KO, p18, no treatment


title: RNA-seq_Wholetissue_E1KOp18-rep2

source_name: mammary tissues, E1KO, p18, no treatment


title: RNA-seq_Wholetissue_E2KOp18-rep2

source_name: mammary tissues, E2KO, p18, no treatment


title: RNA-seq_Wholetissue_E1KOp18-rep1


title: RNA-seq_Wholetissue_E1+-E2KOp18-rep3


title: RNA-seq_Wholetissue_E2KOp18-rep1


title: dcl234, flower, untreated #1

description:
Small RNA
d234F1

value: dcl234 mutant


title: RNA-seq_Wholetissue_E2KOp18-rep3


title: RNA-seq_Wholetissue_Controlp13-rep3

source_name: mammary tissues, control, p13, no treatment

value: day 13 of pregnancy


title: Fetal liver sample for RNA-seq 1

city: Montreal

first: Brian

last: Wilhelm

institute: University of Montreal


title: Control, ChIP-seq round #1

tag: age

value: 10 days old

value: male

value: whole heads

value: Abcam

value: H3K9me2 ChIPed DNA


title: RNA-seq_Wholetissue_E1+-E2KOp13-rep3

source_name: mammary tissues, E1+/-E2KO, p13, no treatment


title: RNA-seq_Wholetissue_Controlp13-rep1


title: RNA-seq_Wholetissue_E1+-E2KOp13-rep2


title: RNA-seq_Wholetissue_E1KOp13-rep2

source_name: mammary tissues, E1KO, p13, no treatment


title: RNA-seq_Wholetissue_E2KOp13-rep3

source_name: mammary tissues, E2KO, p13, no treatment


title: RNA-seq_Wholetissue_E1KOp13-rep3


title: RNA-seq_Wholetissue_E2KOp13-rep2


title: RNA-seq_Wholetissue_E2KOp13-rep1


title: RNA-seq_Wholetissue_ControlVirgin-rep2_PRL

source_name: mammary tissues, control, 12-week-old mature virgin, prolactin

value: twelve-week-old mature virgin

value: prolactin


title: RNA-seq_Wholetissue_E1KOp13-rep1

value: outbred


title: RNA-seq_Wholetissue_ControlVirgin-rep1_PRL

value: MMTV-Cre


title: RNA-seq_Wholetissue_ControlVirgin-rep1_noPRL

source_name: mammary tissues, control, 12-week-old mature virgin, no treatment

value: mammary


title: Normal tail tissue, sample Rp018c

city: Cambridge

first: Sebastian

last: Hoersch

institute: Massachusetts Institute of Technology

description: DNA-Seq/WGS

data_processing:
Sequencing was performed on an Illumina GAIIx Sequencer using Sequence Control software v2.6.26.
Sequences were processed with GERALD.pl (CASAVA 1.6.0 or CASAVA 1.7.0), downloaded from the Illumina Web site (http:// www.illumina.com/software/genome_analyzer_software.ilmn), with a produced read length of 34 nucleotides.
FASTQ sequence files were split into sample sets according to barcode sequences, which were then trimmed from the complete sequences using the applications fastx_barcode_splitter.pl and fastx_trimmer from the FASTX-Toolkit- 0.0.13 (http://hannonlab. cshl.edu/fastx_toolkit) package.
Illumina sequence qualities were converted to Sanger sequence qualities using the MAQ application fq_all2std.pl (http://maq.sourceforge.net/qual.shtml) (Li et al., 2008).
Sequences were then aligned to chromosomes 1-25 in the zebrafish Zv9/danRer7 assembly using bwa0.5.8c (Li and Durbin, 2009).
Unassembled "scaffold" and "NA" fragments were not included in the alignment target.
Alignments with quality scores of 10 or greater were extracted from the resulting Sequence Alignment/Map files.  At this stage, individual samples were required to have at least 100,000 aligned reads, otherwise the sample and its corresponding normal or tumor counterpart were excluded from this study.
[Processed data file #1, incl. this step] For the qualifying 294 tumor and normal samples, counts were obtained for the number of reads aligning to 13551 consecutive, adjacent 100-kb physical windows along chromosomes 1-25.
For the qualifying 294 tumor and normal samples, counts were obtained for the number of reads aligning to 13551 consecutive, adjacent 100-kb physical windows along chromosomes 1-25. The per-window counts per sample were rescaled to a total of 1 million reads.
[Processed data file #2, incl. this step] Log2 ratios were calculated for the matching tumor/normal sample pairs for all 100-kb windows or set to 0, if the read count for one or both samples was 0.
The log2 ratios were then submitted to the circular binary segmentation algorithm (Venkatraman and Olshen, 2007) as implemented in the BioConductor package DNAcopy (v1.16.0), and processed with the following key parameter settings: with smoothing, undo.SD=2.
[Processed data file #3, incl. this step] 100K bin numbers were converted to genomic coordinates fixed at window midpoint, and for each sample pair, all segment mean values obtained were mean-centered before being used for further analysis.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: FILE: Zhang2012-procData1_countsPer100K.xlsx. Data matrix with read counts (quality scores >= 10) per 100K genomic window per sample (tumor or normal separately for each T/N pair, 294 data columns)
Supplementary_files_format_and_content: FILE: Zhang2012-procData2_log2ratios.xlsx. Data matrix with log2-ratios obatined after per-column read count rescaling to 1 Mio reads.
Supplementary_files_format_and_content: FILE: Zhang2012-procData3_segmented.seg. Segment file: output of the program DNAcopy; segments per sample are mean-centered.

source_name: Tail from adult fish

extract_protocol: Tumor and normal DNA samples were individually processed for sequencing with the Illumina Genome Analyzer IIx system according to published methods (Quail MA, et al.,2008 (PMID:19034268); Bentley DR, et al.,2008 (PMID:18987734); Quail MA, et al., 2009 (PMID:19582764)). All the enzymes used in the preparation were from New England Biolabs, and the oligonucleotides were synthesized by Eurofins MWG Operon. Oligonucleotide sequences (ATTGGC; GATCTG; TCAAGT; CTGATC; AAGCTA; GTAGCC; TACAAG; CGTGAT; ACATCG; GCCTAA; TGGTCA; CACTGT) were added to the 3' end of the Illumina adaptors used for the paired-end library preparation in order to serve as barcodes so that multiple samples could be sequenced in the same reaction.

value: Zebrafish TAB strain

value: 8-24 month

value: Tail

tag: tumor type


title: RNA-seq_Wholetissue_E1+-E2KOp18-rep2

value: day 18 of pregnancy


title: RNA-seq_Wholetissue_E2KOVirgin-rep1_PRL

source_name: mammary tissues, E2KO, 12-week-old mature virgin, prolactin


title: RNA-seq_Wholetissue_E2KOVirgin-rep2_PRL


title: RNA-seq_Wholetissue_E2KOVirgin-rep2_noPRL

source_name: mammary tissues, E2KO, 12-week-old mature virgin, no treatment


title: RNA-seq_Wholetissue_E2KOVirgin-rep1_noPRL


title: ChIP-seq_Wholetissue_InputforStat5

source_name: mammary tissues, p13, no treatment, input


title: ChIP-seq_MECs_E2KOp13_H3K4me3

source_name: MECs, E2KO, p13, no treatment, H3K4me3 ChIP

tag: cell type

value: mammary epithelial cells (MECs)


title: ChIP-seq_Wholetissue_Controlp13_Stat5

source_name: mammary tissues, control, p13, no treatment, Stat5 ChIP


title: ChIP-seq_Wholetissue_E2KOp13_Stat5

source_name: mammary tissues, E2KO, p13, no treatment, Stat5 ChIP


title: ChIP-seq_MECs_Controlp13_H3K4me3

source_name: MECs, control, p13, no treatment, H3K4me3 ChIP


title: Liver_input

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

description: Liver input control

data_processing:
Estrogen receptor alpha binding sites (peaks) were identified using MACS v1.3.7.1 by comparing ChIP experiment with an input control from the same tissue.  The following parameters were used: --pvalue=1e-10 --mfold=15 --tsize=50
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are txt files created by MACS v1.3.7.1

source_name: Mouse liver

growth_protocol: Flash-frozen liver and uterus dissected from 8-week old female C57BL/6J mice were obtained from The Jackson Laboratories.

extract_protocol: ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009

treatment_protocol: 100 mg tissue was pulverized on dry ice and cross-linked at room temperature in phosphate buffered saline with 1% formaldehyde for 15 minutes.  Crosslinking was stopped by adding glycine to a final concentration of 125 mM and incubating at room temperature for five minutes.  Tissue material was then washed in PBS three times before proceeding with the standard ChIP protocol.

value: Liver

value: 8 week old

value: input


title: Uterus_input

description: Uterus input control

source_name: Mouse uterus

value: Uterus


title: Uterus_ER

description: Uterus ESR1 ChIP-seq


title: Liver_ER

description: Liver ESR1 ChIP-seq


title: RNA-seq_Wholetissue_E1+-E2KOp13-rep1

value: day 13 of pregnancy


title: RNA-seq_Wholetissue_ControlVirgin-rep2_noPRL


title: MBD-Th1

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

institute: Helmholtz-Centre for Infection Research

data_processing:
Illumina Casava1.8.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, subjected to FASTQC quality control tool 0.10.0.
Sequenced reads were then mapped to NCBI37/mm9 whole genome using bowtie v0.12.7 with 0 mismatches in the seed.
Only unique paired reads were retained and both fragments must be located within 400bp of each other on the reference genome.
Fragments that were identical but mapped into the same region were translated into an activity value. The activity value was used to classify the grade of methylation.
Genome_build: mm9
Supplementary_files_format_and_content: File 'Methylation_T_cell_subsets.xls' contains region ID, gene ID, chromosomal location, CpG content, activity and classification into methylated and non-methylated in Tnaive, Th1 or Th17 cells.
Supplementary_files_format_and_content: File 'TH17_vs_T_cell_subsets.txt' contains region ID, gene ID, gene label, chromosomal location, loci classification and activity in Tnaive, Th1 cells, Th17 cells and Tregs. The list of 10000 regions was filtered for no activity in Th17 cells but in all other T cell subsets. Integration of Treg MBD-seq to effector T cells required a normalization, so that every value is normalized on the total amount of mapped reads.

source_name: T helper 1 cells

extract_protocol:
Genomic DNA from FACS-sorted T cell subsets (see markers above) was isolated by using the NucleoSpin Tissue XS kit (Macherey-Nagel).
Fragmentation of genomic DNA was performed on a Covaris S2. The size of the fragments was controlled with an Agilent 2100 system (Agilent Technologies). Methylated DNA was enriched by using a MethylCap kit (Diagenode AF-100-0048, Belgium). The procedure was done according to the manufacturer's protocol. We used a modified multiplexed paired end ChIP protocol (Illumina) to generate a library for next generation sequencing from 250ng precipitated DNA. Briefly, we used the DNA Sample Prep Master Mix Set 1 (New England Biolabs, E6040) in combination with the Multiplexing Sample Preparation Oligo Kit (Illumina, PE-400-1001). The preparation was performed on an Apollo 324 (IntegenX) with PrepX DNA or PrepX-32-DNA Library Kit (400007; 400021) according to the manufacturer's protocol. Small DNA fragments were removed from the samples by separation on a 2% agarose gel. Fragments between 250 and 350bp were excised and purified by using a Gel Extraction Kit (Qiagen, No. 28704).

treatment_protocol: Ex vivo-isolated spleen and lymph node cells were magnetically enriched for CD4+ cells by using the Miltenyi Biotech autoMACS system. The cells were stimulated for 3 hours by PMA (10ng/ml)/Ionomycin (500ng/ml) and then labelled by using a cytokine secretion assay for IL-17A and Interferon g (Miltenyi Biotech). All procedures were performed according to the manufacturers protocols. For purification of regulatory T cells we first sorted CD3+CD4+CD25++ cells by FACS and stimulated them finally in the presence of PMA/Ionomycin for 3 hours.

value: T helper 1 cells

tag: surface marker

tag: cytokine expression

value: Balb/c

value: female


title: MBD-Treg

source_name: regulatory T cells

value: regulatory T cells


title: MBD-Tnaive

source_name: naive T cells

value: naive T cells


title: MBD-Th17

source_name: T helper 17 cells

value: T helper 17 cells


title: 60g, smRNA

city: Kiel

first: Till

last: Bayer

address: Düsternbrookerweg 20

department: Marine Ecology

institute: GEOMAR Helmholtz Centre for Ocean Research

description:
60g
Small RNA

data_processing:
Illumina Casava 1.7.0 software was used for basecalling.
Trimming of low 3' ends of small RNA reads and filtering of high-quality reads.
Adapter trimming with cutadapt v1.0 with -a ATCTCGTATGCCGTCTTCTGCTTG -g CGACAGGTTCAGAGTTCTACAGTCCGACGATC -O 4.
Small RNA reads were assembled with Velvet (kmer =25) and searched with blastn (-max_target_seqs 5 -outfmt 5) against NCBI nt (11/2012) and the Symbiodinium transcriptome, contigs/reads matching known ncRNA were removed.
Remaining small RNA reads were used for miRNA prediction with miRDeep2 with default parameters.
Supplementary_files_format_and_content: A tab-delimited text file containing short reads and their number of occurences in the dataset.

organism: Symbiodinium sp. A1

source_name: Hypersalinity culture

growth_protocol: Cultured at 23°C in f/2 medium (Guillard and Ryther 1962) on a 12h/12h day/night regime (daytime: 6 am to 6 pm; night-time: 6 pm to 6 am, light intensity 80 μmolm-2s-1). Salt content in the medium was set to 40 g/l.

extract_protocol:
Cells were frozen in liquid nitrogen, ground with silica beads, and the mirVana miRNA Isolation Kit (Ambion, Austin, TX) was used for extraction of miRNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cold shock (4°C for 4 hours), cold stress (16°C for 4 hours), heat stress (34°C for 12 hours), heat shock (36°C for 4 hours), hyposalinity (20 g/L NaCl salt content for 4 hours), hypersalinity (60 g/L NaCl salt content for 4 hours), dark stress (24 hour dark period), dark cycle (12h/12h night/night, sampled at midnight), or control (12h/12h night/night, sampled at noon).

value: 60 g/L NaCl salt content for 4 hours


title: Noon, smRNA

description:
Noon
Small RNA

source_name: Control culture

value: 12h/12h night/night, sampled at noon


title: 36°C, smRNA

description:
36C
Small RNA

source_name: Heat shock culture

value: 36°C for 4 hours


title: DS, smRNA

description:
DS
Small RNA

source_name: Dark stress culture

value: 24 hour dark period


title: 20g, smRNA

description:
20g
Small RNA

source_name: Hyposalinity culture

value: 20 g/L NaCl salt content for 4 hours


title: WT Rep3

city: Duarte

first: Haiqing

last: Li

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

description: Sample 11

data_processing:
Basecalls and barcode analysis were performed using CASAVA version 1.7
Sequenced reads were mapped to mm9 whole genome using rnaseq alignment tool tophat 1.3.1 (bowtie ver 0.12.7) with parameters --max-insertion-length 10 --max-deletion-length 10 --segment-length 20. Other configuarions were kept default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genome Suite ver 6.12.0713. An expectation/maximization algorithm was used to determine relative isoform abundance levels, and the isoform abundance counts were summarized to the gene level for normalized gene expression abundance counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (normalized gene expression abundance counts)

source_name: WT_myeloid cells

growth_protocol: Freshly isolated primary myeloid cells without in vitro culture.

extract_protocol:
CD11b-positive tumor-infiltrating myeloid cells were enriched using specific antibodies and magnetic bead isolation (StemCell Technologies). The total RNA was isolated by using miRVana™ kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Subcutaneously implanted tumors were locally irradiated at 15 Gy and harvested four days later.

tag: strain background

value: Wild Type (WT)


title: DC, smRNA

description:
DC
Small RNA

source_name: Dark cycle culture

value: 12h/12h night/night, sampled at midnight


title: 16°C, smRNA

description:
16C
Small RNA

source_name: Cold stress culture

value: 16°C for 4 hours


title: 34°C, smRNA

description:
34C
Small RNA

source_name: Heat stress culture

value: 34°C for 12 hours


title: WT Rep2

description: Sample 10

tag: genotype/variation

value: CD11b-positive tumor-infiltrating myeloid cells