title: 2249_5__58-K27me3 ChIP sample rep2

description:
2249_5__58-K27me3
sheared DNA
immunoprecipitated DNA

data_processing:
Reads were mapped with BWA against mm9. After mapping the reads were filtered for Q37 reads.
bigWig files were generated using macs
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using macs

source_name: lung tumors

extract_protocol:
Trypsin/Collegenase/Hyarulonydase/DNaseI digestion followed by SDS buffer lysis
Libraries were prepared according to Illumina's instructions. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel. The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. The purified DNA was captured on an Illumina flow cell for cluster generation. ChIP was performed by cross-linking proteins to DNA using 2mM DSG and 1% formaldehyde solution (Gargiulo et al, 2009). Immunoprecipitated DNA (ChIP-seq) and Input DNA were Libraries were sequenced on the Genome Analyzer of HiSeeq2000 following the manufacturer's protocols.

value: NSCLC orthotopic tumor

tag: genotype/variation

tag: chip antibody

value: H3K27me3 (Millipore, catalog#07-449, LOT#1154011)


title: 5_corr d-leucine rep3 total RNA

status: Public on Jan 15 2016

type: SRA

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

country: USA

institute: Stowers Institute

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA 1.8.2
Reads were clipped of adapter sequence AGATCGGAG. Reads shorter than 25 bases post-clipping and reads that didn't contain the adapter were discarded. Percent of reads retained during clipping varied from 60 to 90%.
Clipped reads were aligned to human rRNA sequences from ensembl 69 biomart using bowtie2 version 2.1.0 with parameters -k 1 -N 1 --local.
Reads that didn't align to rRNA sequences were then aligned to the human genome (hg19) using tophat 2.0.8 with -x 1 -g 1 --segment-mismatches 1 --no-coverage-search.
Downstream analysis was done in R (3.1.0)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing reads for separate strands, normalized to reads per million by taking the coverage object in R, and multiplying by 1e6, then dividing by the total alignments for each sample. Minus / C strand normalized coverage multiplied by -1 to allow visualization in positive and negative directions.

molecule: total RNA

organism: Homo sapiens

source_name: Human fibroblast

growth_protocol: human wild-type fibroblasts, ESCO2-mutant RBS fibroblasts, and ESCO2-corrected RBS fibroblasts were grown on 15-cm plates in DMEM medium supplemented with 10% Fetal Bovine Serum (FBS). At 80% confluence, the cells were washed two times with PBS, and grown for another 24 hrs in DMEM/10% FBS.

extract_protocol:
Prior to lysis, the cells were incubated for 1 minute in DMEM containing 0.1 mg/mL cycloheximide (USBiological, cat. no. C8500-10). After a rinse with ice cold PBS containing 0.1 mg/mL cycloheximide, the cells from up to three plates were collected by scraping into 800 µl chilled Mammalian Lysis Buffer (ART-Seq 1X Mammalian Polysome Buffer, 1% Triton X-100, 0.1% NP-40, 1 mM DTT, 10 U/ml DNase I, 0.1 mg/ml cycloheximide). The cell lysate was triturated 10 times through a 26G needle to insure complete lysis, incubated for 10 minutes on ice with periodic agitation, and clarified by a 10 minute centrifugation at 20,000 x g at 4°C.  The RNA concentration of the supernatant was determined using the Quant-iT RiboGreen RNA Assay Kit (Invitrogen) and a SpectraMax M2 reader (Molecular Devices) according to manufacturer’s instructions.  Aliquots were flash-frozen in liquid nitrogen and stored at -80°C.  Ribosome-protected mRNA fragments (RPFs) and fragmented total RNA depleted for ribosomal RNA were sequenced for each sample.  Footprinting was performed at room temperature for 45 min using ART-Seq Nuclease (Epicentre), then stopped with SUPERase•In™ RNase Inhibitor (Life Technologies).  For the 24 hr timepoint samples, 2.8 units of nuclease was added per µg of RNA.  For the 3 hr timepoint samples, the amount of nuclease was reduced to 0.5 units/µg.  RPFs were isolated from the nuclease/SUPERase•In™ treated lysate using Sephacryl S400 columns (GE Healthcare: MicroSpin S-400 HR, cat. no. 27-5140-01), followed by acid phenol:chloroform extraction and isopropanol precipitation. Total RNA was isolated from untreated lysate by acid phenol:chloroform extraction and isopropanol precipitation.
Ribosomal RNA was removed from 1-5 µg of RPFs and total RNA using either the Ribo-Zero™ Magnetic or the Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre). To purify the Ribo-Zero treated samples, the RNA Clean & Concentrator™-5 Kit (Zymo Research) was used as described in the ART-Seq protocol.  26-34 nt RPFs were further size selected by PAGE purification and the total RNA heat fragmented.  Libraries were constructed as described in the Mammalian ARTseq™ Ribosome Profiling Kit (Epicentre, cat. no. RPHMR12126, protocol version 2012).

treatment_protocol: The cells were supplemented with 10 mM D-Leucine or L-Leucine and incubated for either 3 hrs or 24 hrs.

tag: experiment type

value: RNA-seq

tag: genotype

value: corrected

tag: timepoint after treatment

value: 3 hours

tag: treatment

value: d-leucine


title: siPaf1_3READs_1

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
RNA-seq data analysis: Reads were mapped to the mouse genome (mm9) using bowtie2 (local mode). Uniquely mapped reads with MAPQ score>10 were used. Refseq gene model was used to calculate gene expression level. For protein-coding genes, only reads mapped to coding region were used to eliminate the effect of 3’UTR alternative polyadenylation in gene expression calculation. Reads per kilobase per million total uniquely mapped reads (RPKM) value was calculated to reflect gene expression level. Significantly regulated genes were selected based on these criteria: >1.4-fold difference of RPKM between Paf1C siRNA treated cells and siRNA control cells and P value<0.01 (Fisher’s exact test).
3’READS and data analysis.   3’READS reads were mapped to the mouse genome (mm9) using bowtie2 (local mode). Uniquely mapped reads (with MAPQ score > 10) that had at least two additional 5’ Ts not aligned to genome (presumably derived from the poly(A) tail) were named pA site supporting (PASS) reads and were used to calculate pA isoform expression. pA isoforms expressed below 5% of all isoforms of a gene were discarded.  Significantly regulated APA events were identified by the Significance Analysis of Alternative Polyadenylation (SAAP) method [Li et al., 2015].
ChIP-seq data analysis: Reads were mapped to the mouse genome (mm9) using bowtie2. Reads non-uniquely mapped (MAPQ≤10) were discarded. Multiple reads mapped to same genomic loci (defined by chromosome, strand, start and end position) were collapsed to one. To calculate enrichment score of a genomic locus in a meta-gene plot, the first nt at the 5’end of a read was counted for all genes in a group and converted to read per million total reads (RPM) value. The enrichment score was defined by log2 ratio of RPM between IP sample and input sample. The relative genomic location was binned (e.g., every 50 nt relative to TSS or every percent in gene body) before calculating enrichment score and then plotted in R.
Genome_build: mm9
Supplementary_files_format_and_content: 3READS.pA.read.counts.txt contains information of gene symbol, pA coordinates, read number of pAs in different 3'READS samples. "pAtype" is pA type based on location of a pA (I, intron; E, upstream exons; 3, pAs in 3'most exon; UA, pA in upstream antisense of a protein-coding gene.). "RNA-seq.gene.read.counts.txt" contains information of gene symbol, Refseq transcript name, read number and RPKM (read per kb per million total reads) values. Bigwig files: for visualization of ChIP-seq data, all uniquely mapped and collapsed reads were used. Reads were extended from its 5’end mapped position by 250 nts (reflecting the average fragment size in ChIP-seq DNA libraries) and converted to bigwig format files using an in-house perl script and bedGraphToBigWig program from UCSC genome browser.

organism: Mus musculus

source_name: siPaf1 for 3'READS, batch 1

growth_protocol: C2C12 myoblasts (Sigma) were grown and induced to differentiate into myotubes as described [Blais, A., et al. 2007].

extract_protocol: Preparation of solubilized chromatin fraction and immunoprecipitation: Cell pellets were resuspended in buffer A (10 mM HEPES pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1 mM dithiothreitol (DTT), and protease inhibitors (aprotinin, leupeptin, pepstatin A, and phenylmethyl sulphonyl fluoride)), supplemented with Triton X-100 (0.1%), and incubated on ice for 5 minutes.  The nuclear pellet was separated from the cytoplasmic fraction, washed once with buffer A, and collected by centrifugation.  Nuclei were lysed with buffer B (3 mM EDTA, 0.2 mM EGTA, 1 mM dithiothreitol (DTT), and protease inhibitors (aprotinin, leupeptin, pepstatin A, and phenylmethyl sulphonyl fluoride)). The solubilized chromatin fraction was separated from nucleoplasm by centrifugation at 2250 g for 4 minutes at 4°C, washed once with buffer B, and collected by centrifugation. For immunoprecipitations, the chromatin pellet was resuspended with binding buffer (20 mM Hepes pH7.9, 100 mM potassium chloride, 0.2 mM EDTA, 20% glycerol, 0.5 mM dithiothreitol (DTT), and 0.5mM AEBSF). 1 mg of protein was immunoprecipated, and antibody-protein A sepharose beads were washed three times with buffer (50 mM Hepes pH7.9, 250 mM sodium chloride, 5 mM EDTA, 0.50% NP-40, and 10% glycerol) prior to SDS–PAGE and immuno-blotting.

treatment_protocol: For transient transfection of siRNA, cells were seeded at 104 cells cm−2 for 48 h transfection. 5 μl RNAiMax in 2 ml medium and 50 nM siRNA were applied to cells by using fast-forward method.

tag: cell line

tag: cell condition

value: myoblasts

tag: library protocol


title: siCdc73_3READs_2

source_name: siCdc73 for 3'READS, batch 2


title: 9_mut d-leucine rep3 total RNA

value: esco2 mutant


title: 10_mut l-leucine rep2 RPF

value: Ribosomal profiling

value: 24 hours

value: l-leucine


title: 2249_7__60-K27me3 ChIP sample rep1

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

country: Germany

institute: Max Delbrüch Center

description:
2249_7__60-K27me3
sheared DNA
immunoprecipitated DNA

library_source: genomic

molecule: genomic DNA

growth_protocol: NSCLC were grown in F12 medium supplemented with 10% FBS, and 5% penicillin and streptomycin, hydrocortisone, recombinant hEGF, insulin-transferrin selenium and tail vein inected in Nude mice

tag: tissue


title: 8_corr l-leucine rep2 RPF


title: 6_corr l-leucine rep2 RPF


title: 7_corr d-leucine rep2 RPF


title: 5_corr d-leucine rep2 RPF


title: 12_mut l-leucine rep2 total RNA


title: 10_mut l-leucine rep2 total RNA


title: 9_mut d-leucine rep2 total RNA


title: 8_corr l-leucine rep2 total RNA


title: 11_mut d-leucine rep2 total RNA


title: 6_corr l-leucine rep2 total RNA


title: 7_corr d-leucine rep2 total RNA


title: 6_corr l-leucine rep1 RPF


title: 5_corr d-leucine rep2 total RNA


title: siNS_3READs_1

source_name: siRNA control for 3'READS, batch 1


title: 5_corr d-leucine rep1 RPF


title: 10_mut l-leucine rep1 total RNA


title: 2_wt l-leucine rep1 RPF

value: wt


title: 1_wt d-leucine rep1 RPF


title: 6_corr l-leucine rep1 total RNA


title: 2249_10_I59 Input sample rep1

description:
2249_10_I59
sheared DNA
non-immunoprecipitated DNA


title: HE0124D6D

city: St. Petersburg

first: Michael

last: Shamblott

state: FL

address: 601 4th St South, CRI 3005

department: Pediatrics

institute: University of South Florida Health

description: Flowthrough from positive selection was depleted using a D column

data_processing:
Sequencing datasets (fastq files) mapped to human genome with TopHat v2.0.5 against reference assembly UCSC hg19 to generate accepted_hits.bam mapping files.
Ran cufflinks v2.1.1: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -u -b /galaxy/data/hg19/sam_index/hg19.fa  Ran cufflinks v2.1.1 on each bam file: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -u -b /galaxy/data/hg19/sam_index/hg19.fa
Ran cuffmerge v1.0.0 to create a merged transcript GTF file all bam files.  Used genes.gtf as reference annotation:  cuffmerge -o cm_output  -p 4  -g /galaxy/main_pool/pool6/files/005/691/dataset_5691885.dat  -s /galaxy/data/hg19/sam_index/hg19.fa /galaxy/main_pool/pool5/tmp/job_working_directory/005/452/5452982/tmpiJv7hB
Ran CuffDiff v2.1.1 with replicate analysis using merged transcripts file: /cuffdiff --no-update-check -q --library-norm-method geometric --dispersion-method pooled -p 8 -c 10 --FDR 0.050000 -u -b genome.fa merged.gtf --labels "D6P","D6D" 1016D6P.bam,1110D6P.bam,012413D6P.bam 1016D6D.bam,1110D6D.bam,012413D6D.bam
Renamed Cuffdiff output files
Genome_build: hg19
Supplementary_files_format_and_content: *.diff files report FPKMs and differential expression data

source_name: adult pancreas exocrine

growth_protocol: Cadaveric pancreata were digested with collagenase to collect islets  on day 0 post mortem.  Remaining islet-depleted exocrine tissue was cultured in suspension for four days in Miami media 1A (day 6 post mortem).

extract_protocol:
Total RNA was extracted using an acidic phenol method, digested with RNAse free DNAse then cleaned up using a Qiagen miniprep column.
cDNA was prepared by random priming.

treatment_protocol: Day 6 post mortem exocrine tissue was trypsinized and stained with Miltenyi anti-CD133 immunomagnetic beads.  CD133+ cells were isolated with 2 passes over Miltenyi LS columns.  Positive (P) cell populations were >95% CD133+.  Cells that did not bind LS column were passed over a Miltenyi D column to remove cells weakly positive for CD133.  Depleted (D) populations were <1% CD133+.

tag: cd133 expression

value: Depleted

tag: day post mortem


title: 2_wt l-leucine rep1 total RNA


title: HE0124D6P

description: Miltenyi Biotech anti-CD133 bead,  Positive selection on LS column

value: Positive


title: HE1016D6P


title: HE1110D6D


title: EXS34 rep 1 roots

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description: roots of pho1 line expressing EXS-GFP, line EXS34, sample1

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1, Martin 2011), and filtered for low complexity with Prinseq (v. 0.20.3, Schmieder and Edwards 2011).
Reads were aligned against Arabidopsis thaliana genome TAIR10 using TopHat2 (v. 2.0.9, Kim et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3, Anders et al. 2014) using TAIR10 gene annotation.
Gene count tables were imported in R (v. 3.1.1) for normalization (package edgeR, method TMM, Robinson and Oshlack  2010) and transformation (package limma, method voom, Law et al. 2014).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: plants were grown for 25 days in Oil-Dri pellets and fertilized with Hoaglands nutrients

extract_protocol:
total RNA was extracted with Quiagen kit
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA protocol

treatment_protocol: no treatment

value: pho1-4 mutant expressing EXS domain of PHO1, line 34

tag: age

value: 25 day-old

value: roots


title: 5_corr d-leucine rep1 total RNA


title: EXS32 rep 1 roots

description: roots of pho1 line expressing EXS-GFP, line EXS32, sample 1

value: pho1-4 mutant expressing EXS domain of PHO1, line 32


title: HE1110D6P


title: EXS34 rep 2 roots


title: EXS32 rep 2 roots

description: roots of pho1 line expressing EXS-GFP, line EXS32, sample 2


title: KO rep 2 roots

description: roots of pho1-4 mutant, sample 2

value: pho1-4 knockout mutant


title: Compl rep 2 roots

description: roots of pho1 line complemented with PHO1 gene, sample 2

value: pho1-4 complemented with PHO1 gene


title: KO rep 1 roots

description: roots of pho1-4 mutant, sample 1


title: Compl rep 1 roots

description: roots of pho1 line complemented with PHO1 gene, sample 1


title: EXS32 rep 2 leaves

description: leaves of pho1 line expressing EXS-GFP, line EXS32, sample 2

source_name: leaves

value: leaves


title: Compl rep 2 leaves

description: leaves of pho1 line complemented with PHO1 gene, sample 2


title: KO rep 2 leaves

description: leaves of pho1-4 mutant, sample 2


title: 9_mut d-leucine rep1 total RNA

value: RNA-seq


title: EXS34 rep 1 leaves

description: leaves of pho1 line expressing EXS-GFP, line EXS34, sample1


title: EXS32 rep 1 leaves

description: leaves of pho1 line expressing EXS-GFP, line EXS32, sample 1


title: EXS34 rep 2 leaves


title: ros1-4_mock_rep3

city: Seoul

first: Jin Hoe

last: Huh

address: Gwanak-gu

department: Dept Plant Science

country: South Korea

institute: Seoul National University

data_processing:
Low quality trimming and artificial sequence trimming was performed with trim_galore (version 0.2.8) with parameters "--paired -t -a TACAGTCCGACGATC"
The mapping step to Arabidopsis public genome was performed with helps of Tophat software (ver. 2.0.8; Trapnell et al. 2009) with parameters "-r 240 --library-type fr-firststranded"
The resultant "accepted_hits.bam" file was processed using "samtools -h" command
The raw count data collected from the Tophat resultants using htseq-count command from HTSeq (ver. 0.6.1; Anders et al. 2014) with parameters "-m intersection-strict -i Parent --strand=yes"
Genome_build: TAIR10
Supplementary_files_format_and_content: Standard HTSeq output; a tab-delimited text file includes the read count values for each evaluated transcript model

source_name: whole parts

growth_protocol: Tweleve-d-old seedlings grown at 22 oC, 16/8 hr of light time, 70% of relative humidity

extract_protocol:
For each of three replicates, five plants were pooled to make a single RNA sample. The RNA extraction steps were performed with RNeasy plant RNA extraction kit (QIAGEN) as suggested protocol.
RNA libraries were prepared for the sequencing using standard Illumina protocols.

treatment_protocol: Collected seedlings were submerged into autoclaved water containing 50 μM of ABA (A1049, Sigma-Aldrich; ABA condition) or the solvent (mock condition) for 6 hours.

tag: developmental stage

value: whole parts

value: mock


title: Compl rep 1 leaves

description: leaves of pho1 line complemented with PHO1 gene, sample 1


title: ros1-4_mock_rep2


title: 1_wt d-leucine rep1 total RNA

value: d-leucine


title: HE1016D6D


title: ros1-4_ABA_rep3

value: ABA


title: ros1-4_ABA_rep1


title: ros1-4_ABA_rep2


title: ros1-4_mock_rep1


title: ros1-3_ABA_rep3


title: WT_mock_rep3

value: wild type


title: ros1-3_mock_rep1


title: WT_ABA_rep3


title: WT_ABA_rep1


title: ros1-3_mock_rep2


title: Ph_ML expressig S2 cells, rep.2

status: Public on Jan 14 2016

city: Montreal

first: Nicole

last: Francis

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM/University of Montreal

data_processing:
alignment to Drosophila melanogaster genome (dm3) using Tophat 2.0.12
transcript assembly and quantification using Cufflinks 2.2.1 (Cufflinks--> Cuffmerge--> Cuffquant-->Cuffdiff)
Genome_build: dm3
Supplementary_files_format_and_content: scaled bedGraph files of aligned reads for visualization; gene expresion and tss levels cuffdiff files of comparisons among all three samples

organism: Drosophila melanogaster

source_name: S2 cell line (embryonic) expressing Ph-ML

growth_protocol: Drosphila S2 cells were grown in ESF-921 media in 10 cm dishs at 27 C

extract_protocol:
Total RNA was isolated using Qiagen RNA easy kit, ribosomal RNA was depleted by using ribozero gold kit and cDNA was prepared (and fragmented) by using Trueseq kit
Sequencing libraries were generated as described previously (Bowman et al., 2013, BMC Genomics, 14: 466). Briefly, ends of the immunoprecipitated DNA were repaired, followed by A-tailing, ligating to universal adapters, and amplification for 10 cycles with indexed primers. Excess adapters were removed by purification with Agencourt AMPureXP beads (Beckman-Coulter). Fragment size was checked by Bioanalyzer using a high sensitivity DNA chip, and an average size distribution of 300-400 bp was observed.

treatment_protocol: Protein expression was induced by adding 0.5mM copper sulphate for 3 days


title: KO rep 1 leaves

description: leaves of pho1-4 mutant, sample 1


title: ros1-3_mock_rep3


title: ros1-3_ABA_rep2


title: Ph_WT expressing S2 cells, rep.1

source_name: S2 cell line (embryonic) expressing Ph-WT


title: WT_ABA_rep2


title: wild type S2 cells, rep.1

source_name: S2 cells (embryonic)


title: WT_mock_rep1


title: Ph_ML expressig S2 cells, rep.1


title: Ph_WT expressing S2 cells, rep.2


title: wild type S2 cells, rep. 2


title: 9_mut d-leucine rep2 RPF

value: Ribosomal profiling

value: esco2 mutant

value: 24 hours


title: WT_mock_rep2


title: M-DKO2 [2]

city: Bruxelles

first: Matthieu

last: Defrance

address: CP614 route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description: hmC-Seq

data_processing:
reads aligned to the mm9 & h18 genomes using BWA
peaks were called using MACS v1.4
Genome_build: mm9 & hg18
Supplementary_files_format_and_content: wig files generated using MACS

source_name: 129 mouse with combined disruption of the GPx1 and GPx2

growth_protocol: SY5Y cells (ATCC #CRL- 2266) were maintained in 1:1 Dubelcco’s modified Eagle’s medium (DMEM) and F12 medium, then supplemented with 10% fetal bovine serum and grown at 37°C under 5% CO2.

extract_protocol: Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina)

tag: strain

tag: cell type

value: colon epithelia


title: GF4 medial prefrontal cortex

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

data_processing:
Base calling was achieved using standard Illumina CASAVA pipeline
Fastq-format reads were quality filtered and trimmed using Trimmomatic (v0.32)
Aligment to the mouse reference genome (GRCm38.p3) was achieved using the STAR aligner (v2.3.1u )
Ensembl database release 78 gene models were also used for counting mapped reads per gene using HTSeq-Count (v0.6.0)
Differential gene expression was calculated for pairwise comparisons using the DESeq2 R-package (v1.6.2) with default parameters. Genes with an FDR-adjusted p-value ≤ 0.1 were considered differentially regulated.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: .txt - tab delimited file with read counts for all samples (HTSeq)
Supplementary_files_format_and_content: .xlsx - Excel file with expression values, fold change, p-values and gene symbol (DESeq2) - three excel sheets in one excel workbook

molecule: polyA RNA

source_name: hand dissected medial prefrontal cortex from fresh brain tissue

extract_protocol:
Total RNA was extracted using the mirVanaTM miRNA isolation kit (Ambion/life technologies) and Dnase treated (Turbo DNA-free, Ambion/life technologies) according to the manufacturers recommendations. RNA concentrations and quality were determined using Nanodrop 1000 and Bioanalyzer. Equal amounts of RNA from two to three animals were then pooled to yield four samples per group
TruSeq® Stranded mRNA Sample preparation kit was performed externaly by Exiqon, Denmark

value: Swiss Webster

value: mPFC

value: 10 weeks

tag: colonization status

value: germ-free


title: M-WT2

description: hmC-Seq

source_name: 129 WT mouse


title: M-DKO2 [1]

description: hmC-Seq


title: ros1-3_ABA_rep1

tag: genotype/variation


title: exGF4 medial prefrontal cortex

value: germ-free colonized from p21 (weaning)


title: CON4 medial prefrontal cortex

value: conventional


title: CON2 medial prefrontal cortex


title: exGF3 medial prefrontal cortex


title: exGF1 medial prefrontal cortex


title: TiPS_TKA9(AIST)_methylation

city: Shinjuku-ku

first: Takuya

last: Matsumoto

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

description: protocol: CpG MethylQuest DNA Isolation Kit (Millipore:17-10035)

data_processing:
Basecalls performed using Trimmomatic-0.30
ChIP-seq reads were aligned to the hg19 genome assembly using BWA (ver.0.6.2） with the following configurations…
peaks were called using Avadis NGS 1.4.7 with the MACS.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using avadis NGS 1.4.7

source_name: iPSC

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CpG MethylQuest DNA Isolation Kit(Millipore).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: iPSC

tag: iPSc source

value: T-cell


title: CON1 medial prefrontal cortex


title: GF3 medial prefrontal cortex


title: iPS_KA23_methylation

value: fibroblast


title: exGF2 medial prefrontal cortex


title: ZR75B

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

institute: Princess Margaret Cancer Centre

data_processing:
Genomic alignment was performed with STAR  (v2.3.0) (Dobin et al., 2013), using  default parameters, except that –out SAMstrandField was set to intronMotif.
Gene expression levels were estimated with Cufflinks (v.2.2.1) (Trapnell et al., 2010), using default parameters and the Gencode V19 GTF file.
Genome_build: hg19

source_name: breast cancer cell line

extract_protocol:
extract protocol
RNA (1 ug) from each sample was reverse transcribed into cDNA by using the Illumina TruSeq Stranded mRNA kit. Libraries were sized on an Agilent Bioanalyzer, and their concentrations were validated by qPCR. Six different libraries were normalized to 10nM and pooled, 13pM of pooled libraries were loaded onto an Illumina cBot for cluster generation, and the flow cell was subjected to 50-cycles of paired-end sequencing on an Illumina HighSeq 2000.

value: breast cancer cell line


title: TiPS_TKA4(AIST)_methylation


title: M-WT1

description: hmC-Seq


title: GF1 medial prefrontal cortex


title: iPS_KA11_methylation


title: GF2 medial prefrontal cortex


title: CON3 medial prefrontal cortex


title: UACC812


title: ZR7530


title: ZR751


title: Q-RRBS_293T_rep1

city: Chong Qing

first: Xianfeng

address: Da ping

department: Department of Gastroenterology, Daping Hospital

country: China

institute: Army Medical University (Third Military Medical University)

data_processing:
library strategy: Quantitative Reduced Representation Bisulfite Sequencing (Q-RRBS)
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads. The quality of resulted clean reads was checked by FastQC
Both adaptor and UMIs of RRBS reads were trimmed, and then the clean reads were aligned to the hg19 genome assembly using bismark_v0.12.1 with 1 mismatches allowed in the seed (30 bp)
Unique mapped reads were used for DNA methylation information extraction.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Methylation level information of CpG sites: the file format is output of bismark_methylation_extractor, a bismark script.

extract_protocol:
Genomic DNA was extracted from 293T cells by using a DNeasy Blood & Tissue Kit (Qiagen, Venlo, Netherlands), and 20 mg/mL RNase (Qiagen) was used to degrade any RNA contaminants in the DNA samples. Precisely one cell (SC sample) and approximately dozens-of-cells (DC) samples were individually handpicked (using a mouth pipette) or collected using a micropipettor after trypsin digestion, washed in standard phosphate-buffered saline, serially diluted and counted. Then SC samples and DC samples were lysed using 5μL of CellsDirect solution (Invitrogen) to release naked DNA for library construction.
For each library, 500 ng of genomic DNA was digested overnight with MspI (20 units). After purification, the digested products were blunt-ended. Then dA was added, followed by methylated-adapter (Illumina, CA, USA) ligation. To obtain DNA fractions in 40-120 bp and 120-220 bp range of MspI-digested products, two ranges (160-240 bp and 240-340 bp) of adapter-ligated fractions were excised from 2% agarose gel. The size-selected DNA was bisulfite-treated for two rounds using EpiTect Bisulfite Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s standard protocol. Finally, libraries were generated by amplification with HiFi HotStart Uracil+ ReadyMix (KAPA, MA，USA) and Illumina Multiplexing PCR Primers. Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and RT-PCR were used to guarantee the quality and quantity of RRBS library. After RRBS library construction, Illumina HiSeq 2000 was used to sequence those libraries according to the manufacturer’s protocol.

value: human embryonic kidney cells


title: T47D


title: UACC3199


title: UACC893


title: SUM44


title: Q-RRBS_293T_rep2


title: SUM52


title: SUM159


title: SUM225


title: SUM185


title: SUM102


title: SKBR7


title: SUM190


title: SUM229


title: SKBR3


title: MX1


title: SUM1315


title: SUM149


title: MFM223


title: SKBR5


title: OCUBM

value: OCUBM


title: MDAMB453


title: MDAMB468


title: MDAMB361


title: MDAMB436


title: MDAMB415


title: MDAMB330


title: SW527


title: MDAMB134VI


title: MDAMB157


title: MCF7


title: MDAMB231


title: MDAMB175VII


title: MCF12A


title: MB157


title: MCF10A


title: MACLS2


title: KPL1


title: LY2


title: JIMT1


title: HS578T


title: HCC712


title: HDQP1


title: HCC70


title: HCC2185


title: HCC2218


title: HCC2688


title: HCC202


title: HCC38


title: HCC1806


title: HCC1569


title: HCC1937


title: HCC1954


title: HCC1599


title: HCC1395


title: HCC1500


title: HBL100


title: HCC1008


title: EVSAT

value: EVSAT


title: HCC1428


title: HCC1187


title: EFM192A


title: HCC1419


title: EFM19


title: HCC3153


title: DU4475


title: BT549


title: BT474


title: CAL51


title: BT483


title: CAL851


title: CAL120


title: CAMA1


title: AU565


title: 184B5


title: 184A1


title: BT20


title: HCC1143


title: O, 70 nx

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description: micro RNA

data_processing:
CLC genomic workbench 7.0
Illumina adapter sequences and sequences tags of length less than 17 and more than 27 were removed
miRNA sequences were aligned to human genome (homo sapiens GRCh 37.57) and known miRNA database (miRBase-19)
Statistical analysis: Bonferroni and FDR corrected
Filtering: Significant, above 2; Kalz test: FDR pvalue <0.05; Kalz test: FC abs value>2
Genome_build: miRBase 19
Supplementary_files_format_and_content: Excel files xlsx containing expression values  of Hx normalized against nx MSC

source_name: Bone marrow mesenchymal stem cell

growth_protocol: MSC were expended under normal oxygen condititon vs hypoxia (5%) oxygen condition

extract_protocol:
RNA from MSC cells were extracted using miRNA easy
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow mesenchymal stem cell

tag: donors age group

value: Old

tag: culture condition

value: normoxic

tag: paasage


title: O, 63 nx

description: micro RNA


title: O, 70 Hx

description: micro RNA

value: Hypoxic


title: Y, 27 nx

description: micro RNA

value: Young


title: O, 80 Hx

description: micro RNA


title: Y, 19 Hx

description: micro RNA


title: Y, 19 nx

description: micro RNA


title: R1_RNase R treated

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: RNA-seq of RNase R treated poly(A)-/ribo- RNAs from R1 cells

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map to mouse genome mm10 using Tophat(v 2.0.9)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: mES R1 cells, RNase R treated

growth_protocol: mES R1 cells were maintained on Gelatin coated plates in Knockout™ DMEM (Gibco 10829) supplemented with 10% ES Cell FBS (Gibco 30044), 1% NEAA (Gibco 11150), 1% L-Glutamin (Gibco 35050),0.1 mM β-mercaptoethanol (Sigma M-7522), 1,000 U/mL mouse leukemia inhibitory factor (LIF) (Millipore ESG1107).

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I. 20μg of total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were further depleted in nonpolyadenylated fraction by using RiboMinus kit (Invitrogen) to get the poly(A)-/ribo- RNA population. Poly(A)-/ribo- RNAs were further incubated with 5U of RNase R (Epicentre) for 3h at 37℃ and then were subjected to Trizol extraction (Invitrogen).
Library was prepared by using Illumina TruSeq RNA Library Preparation Kit v2.

tag: passages

value: Embryonic stem cells


title: CAL148

tag: cell line


title: rmr6 Drought+Salt T7 Rep2+Rep3

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
adaptor removal with CUTADAPT version 1.2rc2; parameters: -e 0.08 -O 5 -m 35
contaminant rRNA removal with ERNE_FILTER version 1.2
mapping with tophat-2.0.9; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000
RABT assembly and differential expression analysis usign Cufflinks version 2.2.0
FPKM quantification and normalization between all samples with Cuffquant and Cuffnorm
Genome_build: RefGen ZmB73 Assembly AGPv3
Supplementary_files_format_and_content: Tab-delimited matrix with normalized FPKM values for all the samples.
Supplementary_files_format_and_content: Tab-delimited text files include the raw results of differential expression analysis starting from the uploaded RNA-Seq data.

organism: Zea mays

source_name: youngest wrapped leaf

growth_protocol: Maize plants were grown in greenhouse until V5-V6 leaf stage with normal watering

extract_protocol:
Total RNA was extracted from frozen tissue using the Spectrum Plant Total RNA Kit (SIGMA), and subjected to On-Column DNase Digestion (SIGMA). rRNA depletion were carried out with Ribo-Zero™ rRNA Removal Kits (Plant Leaf) from Epicenter.
TruSeq RNA Library Prep Kit for the first replicate, TruSeq Stranded RNA Library Prep Kit for the Rep2+Rep3, sequenced on Illumina HiSeq2000, multiplex level of 4

treatment_protocol: Stresses were applied for 10 days: control plants (C) were watered with 75% of disposable water at 0.1dS/m salt concentration; drought-stressed plants (D) with 25% of disposable water at 0.1dS/m salt concentration; salinity-stressed plants (S) with 75% of disposable water at 15dS/m salt concentration; drought plus salinity-stressed plants (D+S) with 25% of disposable water at 15dS/m salt concentration

tag: genotype

value: rmr6-1 mutant

tag: treatment

value: drought plus salt

tag: timepoint

value: after 7 additional days of recovery


title: 600MPE


title: rmr6 Salt T7 Rep2+Rep3

value: salt


title: rmr6 Drought+Salt T0 Rep2+Rep3

value: after 10 days of treatment


title: wt Salt T7 Rep2+Rep3

value: B73 wt


title: wt Drought+Salt T7 Rep2+Rep3


title: rmr6 Drought T0 Rep2+Rep3

value: drought


title: Y, 27 Hx

description: micro RNA


title: O, 63 Hx

description: micro RNA


title: rmr6 Salt T0 Rep2+Rep3


title: wt Control T7 Rep2+Rep3

value: control


title: wt Drought T7 Rep2+Rep3


title: wt Drought+Salt T0 Rep2+Rep3


title: wt Drought T0 Rep2+Rep3


title: Y, 21 Hx

description: micro RNA


title: Y, 21 nx

description: micro RNA


title: wt Salt T0 Rep2+Rep3


title: rmr6 Drought T7 Rep1


title: O, 80 nx

description: micro RNA


title: DMSO_no._1

city: Garching

first: Jan

last: Vomacka

address: Lichtenbergstraße 4

department: Department of Chemistry

institute: Technische Universität München

description: DMSO control, replicate 1

data_processing:
Demultiplexing
Fastq quality trimming using a cut-off value of 20 (via FastX toolkit)
Fastq to fasta conversion (via READemption)
Read mapping using segemehl (via READemption)
Coverage calculation and normalisation (via READemption)
Gene-wise quantification (via READemption)
Differential gene expression analysis (via READemption)
Genome_build: NC_007795.1
Supplementary_files_format_and_content: The pairwise expression comparision based on these gene quantifications was done with READemption's subcommand "deseq" with relies on DESeq version 1.12.1.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus whole cells

growth_protocol: 5 mL of B medium were inoculated with 50 µL ON culture (1:100). After 1-3 h the culture reached an OD600 between 0.38 and 0.59. Bacteria were then diluted in B medium in 4 steps to get a concentration of 3.4x104 bacteria per mL. Bacterial cultures were grown at 200 rpm for 20 h at 37°C.

extract_protocol:
Isolation of the RNA from 1x109 bacteria/sample was done with Precellys Bacterial/Fungal RNA Kit (12-7611-01) including a DNAse I digest. RNA was eluted with 43 µL RNAse free ddH2O.
Library construction was done according to Dugar et al. (Dugar, G., et al., High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet, 2013. 9(5): p. e1003495.)

treatment_protocol: 100 µM compound 3 dissolved in DMSO or just DMSO as a control were added before the 20 h growth period in a 1:100 volume ratio.

value: NCTC 8325


title: rmr6 Drought T7 Rep2+Rep3


title: rmr6 Control T7 Rep1


title: rmr6 Drought+Salt T7 Rep1


title: rmr6 Salt T7 Rep1


title: compound3_no._2

description: compound treated, replicate 2


title: rmr6 Control T7 Rep2+Rep3


title: rmr6 Drought T0 Rep1


title: compound3_no._1

description: compound treated, replicate 1


title: rmr6 Control T0 Rep1


title: rmr6 Control T0 Rep2+Rep3


title: wt Drought+Salt T7 Rep1


title: wt Salt T7 Rep1


title: rmr6 Drought+Salt T0 Rep1


title: wt Control T7 Rep1


title: rmr6 Salt T0 Rep1


title: wt Control T0 Rep2+Rep3


title: wt Drought T7 Rep1


title: DMSO_no._2

description: DMSO control, replicate 2


title: SY5Y-BSO

description: hmC-Seq

source_name: SY5Y treated with 500 μM BSO


title: wt Drought+Salt T0 Rep1


title: wt Drought T0 Rep1


title: wt Control T0 Rep1


title: SY5Y-NT

description: hmC-Seq

source_name: SY5Y untreated


title: Input Chimpanzee Brain ThalamicNuclei PT3

status: Public on Jan 13 2016

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
Mapping Illumina: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S --phred64-quals -q -l 40/45 -n 1
Mapping SOLiD: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S -l 50 -n 3 -C -Q -f
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g hs --nomodel --extsize 400 --llocal 100000
genome build: hg38, rheMac3, panTro4, mm10
processed data files format and content: txt files contain called peaks
processed data files format and content: narrowPeak files contain called peaks in BED format
processed data files format and content: bedGraph files contain treat pileup
processed data files format and content: bw files contain treat pileup read per million (RPM) normalized in bigWig format

organism: Pan troglodytes

source_name: Chimpanzee female thalamic nuclei tissue

extract_protocol:
Crosslink, Lyse and Immunoprecipitate
Illumina Truseq DNA library protocol

tag: tissue

value: Thalamic nuclei

tag: gender

value: Female

tag: Cause of death

value: Cardiomyopathy, endocardiosis

tag: postmortem delay

tag: experiment type

value: Input

tag: chip antibody


title: Input Chimpanzee Brain OccipitalPole PT3

source_name: Chimpanzee female occipital pole tissue

value: Occipital pole

tag: age


title: Input Chimpanzee Brain Cerebellum PT3

source_name: Chimpanzee female cerebellum tissue

value: Cerebellum


title: Input Chimpanzee Brain CaudateNucleus PT3

source_name: Chimpanzee female prefrontal cortex tissue

value: Prefrontal cortex


title: Input Chimpanzee Brain PrecentralGyrus PT3

source_name: Chimpanzee female precentral gyrus tissue

value: Precentral gyrus


title: Input Chimpanzee Brain WhiteMatter PT3

source_name: Chimpanzee female white matter tissue

value: White matter


title: Input Chimpanzee Brain PrefrontalCortex PT3


title: Input Chimpanzee Brain Putamen PT3

source_name: Chimpanzee female putamen tissue

value: Putamen


title: wt Salt T0 Rep1


title: H3K4me3 Rhesus Brain WhiteMatter RM1

organism: Macaca mulatta

source_name: Rhesus macaque female white matter tissue

value: Euthanasia

value: 0.5 hrs

value: ChIP-Seq

value: H3K4me3 (Millipore 07-473)


title: H3K4me3 Rhesus Brain Putamen RM1

source_name: Rhesus macaque female putamen tissue


title: H3K4me3 Rhesus Brain OccipitalPole RM1

source_name: Rhesus macaque female occipital pole tissue


title: H3K27ac Rhesus Brain PrefrontalCortex RM3

source_name: Rhesus macaque female prefrontal cortex tissue

value: Gyrus rectus

value: 12 hrs

value: H3K27ac (Abcam, ab4729)


title: H3K27ac Rhesus Brain Cerebellum RM3

source_name: Rhesus macaque female cerebellum tissue


title: H3K27ac Rhesus Brain Cerebellum RM1


title: H3K27ac Rhesus Brain Cerebellum RM2


title: H3K27ac Rhesus Brain PrefrontalCortex RM1


title: H3K27ac Rhesus Brain Putamen RM3


title: H3K27ac Rhesus Brain Putamen RM2


title: H3K27ac Rhesus Brain ThalamicNuclei RM3

source_name: Rhesus macaque female thalamic nuclei tissue

value: Thalamic nuclei


title: H3K27ac Rhesus Brain PrecentralGyrus RM3

source_name: Rhesus macaque female precentral gyrus tissue

value: Female


title: H3K27ac Rhesus Brain PrecentralGyrus RM1


title: H3K27ac Rhesus Brain CaudateNucleus RM3

source_name: Rhesus macaque female caudate nucleus tissue

value: Caudate nucleus


title: H3K27ac Rhesus Brain CaudateNucleus RM2


title: H3K27ac Rhesus Brain ThalamicNuclei RM2


title: H3K27ac Rhesus Brain CaudateNucleus RM1


title: H3K4me3 Rhesus Brain Cerebellum RM1


title: H3K27ac Rhesus Brain PrefrontalCortex RM2


title: H3K27ac Rhesus Brain Putamen RM1


title: H3K27ac Rhesus Brain WhiteMatter RM2


title: H3K27ac Rhesus Brain OccipitalPole RM3


title: H3K27ac Rhesus Brain OccipitalPole RM2


title: H3K27ac Rhesus Brain PrecentralGyrus RM2


title: H3K27ac Rhesus Brain OccipitalPole RM1


title: H3K27ac Chimpanzee Brain WhiteMatter PT3

value: Cardiomyopathy, endocardiosis


title: H3K27ac Rhesus Brain WhiteMatter RM1


title: H3K27ac Chimpanzee Brain ThalamicNuclei PT2

source_name: Chimpanzee male thalamic nuclei tissue

value: Male

value: Cardiomyopathy, pneumonitis

value: 6-8 hrs


title: H3K27ac Chimpanzee Brain WhiteMatter PT1

value: Cardiomyopathy, nephritis


title: H3K27ac Rhesus Brain WhiteMatter RM3

value: White matter


title: H3K27ac Chimpanzee Brain ThalamicNuclei PT3


title: H3K27ac Chimpanzee Brain Putamen PT3

value: Putamen


title: H3K27ac Chimpanzee Brain PrefrontalCortex PT1

value: Prefrontal cortex


title: H3K27ac Chimpanzee Brain PrecentralGyrus PT3

value: Precentral gyrus


title: H3K27ac Chimpanzee Brain PrefrontalCortex PT3

value: ChIP-Seq


title: H3K27ac Chimpanzee Brain Putamen PT1


title: H3K27ac Chimpanzee Brain CaudateNucleus PT1

source_name: Chimpanzee female caudate nucleus tissue


title: H3K27ac Chimpanzee Brain Cerebellum PT1

value: Cerebellum


title: H3K27ac Chimpanzee Brain Cerebellum PT2

source_name: Chimpanzee male cerebellum tissue


title: H3K27ac Chimpanzee Brain OccipitalPole PT3

source_name: Chimpanzee female occipital pole tissue

value: Occipital pole


title: H3K4me3 Chimpanzee Brain PrefrontalCortex PT3

value: H3K4me3 (Millipore 07-473)


title: H3K27ac Chimpanzee Brain CaudateNucleus PT3

value: H3K27ac (Abcam, ab4729)


title: H3K4me3 Chimpanzee Brain Cerebellum PT1

source_name: Chimpanzee female cerebellum tissue

value: 12 hrs


title: H3K4me3 Chimpanzee Brain PrefrontalCortex PT2

source_name: Chimpanzee male prefrontal cortex tissue


title: H3K4me3 Chimpanzee Brain Cerebellum PT2


title: H3K4me3 Chimpanzee Brain PrefrontalCortex PT1

source_name: Chimpanzee female prefrontal cortex tissue

value: Female


title: Input Rhesus Brain PrefrontalCortex RM1

value: Euthanasia

value: 0.5 hrs

value: Input


title: Input Rhesus Brain OccipitalPole RM1


title: Input Rhesus Brain Cerebellum RM1


title: Input Rhesus Brain WhiteMatter RM1


title: H3K27ac Human Brain PrefrontalCortex HS2

source_name: Human female prefrontal cortex tissue

value: Gyrus rectus

value: Sepsis


title: Input Rhesus Brain Putamen RM1


title: H3K27ac Chimpanzee Brain OccipitalPole PT1

value: Cardiomyopathy, nephritis


title: Input Rhesus Brain PrecentralGyrus RM1


title: Input Rhesus Brain ThalamicNuclei RM1

value: Thalamic nuclei


title: Input Rhesus Brain CaudateNucleus RM1

value: Caudate nucleus


title: H3K27ac Human Brain Cerebellum HS4

source_name: Human female cerebellum tissue

value: Unknown

value: 4.1 hrs


title: H3K27ac Chimpanzee Brain PrecentralGyrus PT1

source_name: Chimpanzee female precentral gyrus tissue

value: Precentral gyrus

value: ChIP-Seq


title: H3K27ac Human Brain Putamen HS2

source_name: Human female putamen tissue

value: Putamen


title: H3K27ac Human Brain CaudateNucleus HS2

source_name: Human female caudate nucleus tissue


title: H3K27ac Human Brain Cerebellum HS2

value: Cerebellum


title: H3K27ac Human Brain PrecentralGyrus HS2

source_name: Human female precentral gyrus tissue

value: H3K27ac (Abcam, ab4729)


title: H3K27ac Human Brain WhiteMatter HS2

source_name: Human female white matter tissue

value: White matter


title: H3K27ac Human Brain OccipitalPole HS2

source_name: Human female occipital pole tissue

value: Occipital pole

value: Female


title: WT_FP2

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
library strategy: Ribosome profiling
Reads with N bases or Phred < 20 were dropped. The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome use bowtie allowing two mismatches.
Genome_build: NC_000913ver2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

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

source_name: WT_ribosome footprints

growth_protocol: 400 mL cultures in complete synthetic MOPS media were grown until an OD600 of 0.25, filtered, and flash frozen in liquid nitrogen

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. Cell lysates were clarified, digested with MNase, and monosomes were purified over a sucrose gradient.
Ribosome footprints 15 - 45 in length and total RNA fragments 20 - 40 nt in length (for RNAseq) were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

tag: genotype/variation

value: wild type

tag: sample type

value: cell cultures


title: WT_RNAseq2

data_processing:
Reads with N bases or Phred < 20 were dropped. The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome use bowtie allowing two mismatches.
Genome_build: NC_000913ver2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.


title: siFoxA1 CREB1 ChIP-seq_rep2

city: Columbus

first: Qianben

last: Wang

state: Ohio

address: 460 W 12th Avenue

department: Molecular and Cellular Biochemistry and the Comprehensive Cancer Center

institute: Ohio State University

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq reads were aligned to the hg19 genome assembly using tophat-2.0.8 (Bowtie2-2.1.0) with default parameters and UCSC refGene annotation file. Mapped reads with multiple accepted alignments were removed using a Perl program.
HTSeq-0.5.3p9 was used to count the uniquely mapped reads in union mode.
Genes with differential expressions were detected using edgeR_3.0.6 with FDR threshold 0.05.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0 with parameters '-k 2 -v 2' to report up to two valid alignments. Mapped reads with two valid alignments were removed using a Perl program. Uniquely mapped reads from replicates of the same sample were pooled.
Peaks were called using MACS v1.4.2 with parameters '-m 3,30 -g hs -p 1e-8'.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: LNCaP-abl siFoxA1

growth_protocol: LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium when treatment are performed.LNCaP abl cells were cultured in 10% charcoal stripped FBS in RPMI 1640 medium, 1:2 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium when treatment are performed.

extract_protocol:
For RNA, follow protocol in Rneasy Mini Kit. For Chip-seq, lysates were clarified from sonicated nuclei and CREB1-DNA  complexes were isolated with corresponing antibody.
For ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.For RNA-seq, follow instruction for TruSeq RNA Sample Preparation Kit v2 from Illumina(cat  RS-122-2001).

treatment_protocol: LNCaP or LNCaP-abl cellswere treated with 40nM siControl or siFoxA1,SiCREB1 from Dharmacon company for 3 days.

tag: cell type

value: prostate cancer cells

value: LNCaP-abl

value: CREB1 (Abcam ab31387)


title: WT_FP3


title: WT_RNAseq1


title: WT_FP1


title: siFoxA1 CREB1 ChIP-seq_rep1


title: siControl CREB1 ChIP-seq_rep2

source_name: LNCaP-abl siControl


title: highly downregulated Satb1, replicate 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
reduced level of Satb1
high.Satb1.2

data_processing:
RNA-Seq data analyzing was done with rsem(ver. 1.2.12) and mm9 genome with UCSC known gene set.
DESeq2 was used for differentail expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and raw count values for all UCSC genes across 6 samples

source_name: Satb1_tumor-associated DC

growth_protocol: mice (C57BL/6) bearing ID8-Defb29/Vegf-a grown for 32-38 days

extract_protocol:
Total RNA was isolated for RNA-Seq using Trizol reagent.
RNA-Seq library was prepared using the TruSeq Stranded Total RNA Library Preparation kit (Illumina).

treatment_protocol: mice (C57BL/6) were treated for 32-38 days with 100 μg of Non-Targeting (NT) or Satb1 siRNA-Rhodamine conjugated polyethylenimine nanocomplexes (Satb1)

tag: strain background

value: bearing ID8-Defb29/Vegf-a

tag: treated with

tag: satb1 status

value: knockdown

value: Cancer-Associated Dendritic Cells (DCs)

tag: replicate


title: siCREB1 FoxA1 ChIP-seq_rep1

source_name: LNCaP-abl siCREB1

tag: passages

tag: cell line

value: FoxA1 (Abcam ab23738)


title: siControl CREB1 ChIP-seq_rep1


title: highly downregulated Satb1, replicate 1

description:
reduced level of Satb1
high.Satb1.1

value: Satb1 siRNA-Rhodamine conjugated polyethylenimine nanocomplexes (Satb1)


title: siControl FoxA1 ChIP-seq_rep1


title: siControl FoxA1 ChIP-seq_rep2


title: control for experiment with highly downregulated Satb1, replicate 1

description:
endogenous level of Satb1
high.NT.1

source_name: WT_tumor-associated DC

value: Non-Targeting (NT) siRNA

value: wildtype


title: control for experiment with highly downregulated Satb1, replicate 2

description:
endogenous level of Satb1
high.NT.2


title: LNCaP-siControl RNA-seq

description: Prostate cancer derived cell lines

data_processing:
Basecalls were performed using CASAVA version 1.8.
RNA-seq reads were aligned to the hg19 genome assembly using tophat-2.0.8 (Bowtie2-2.1.0) with default parameters and UCSC refGene annotation file. Mapped reads with multiple accepted alignments were removed using a Perl program.
HTSeq-0.5.3p9 was used to count the uniquely mapped reads in union mode.
Genes with differential expressions were detected using edgeR_3.0.6 with FDR threshold 0.05.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0 with parameters '-k 2 -v 2' to report up to two valid alignments. Mapped reads with two valid alignments were removed using a Perl program. Uniquely mapped reads from replicates of the same sample were pooled.
Peaks were called using MACS v1.4.2 with parameters '-m 3,30 -g hs -p 1e-8'.
Genome_build: hg19
Supplementary_files_format_and_content: wig, txt

source_name: LNCaP-siControl RNA-seq

value: LNCaP

tag: passage number

tag: group

value: androgen dependent

tag: transfection

value: siControl


title: LNCaP-siCREB1 RNA-seq

description: Prostate cancer derived cell lines

source_name: LNCaP-siCREB1 RNA-seq


title: abl-siFoxA1 RNA-seq

description: Prostate cancer derived cell lines

source_name: abl-siFoxA1 RNA-seq

value: androgen independent


title: abl-siControl RNA-seq

description: Prostate cancer derived cell lines

source_name: abl-siControl RNA-seq


title: H3K27ac Mouse Brain Cerebellum MM1

source_name: Mouse female cerebellum tissue

tag: tissue

value: Cerebellum

tag: gender

value: Female

value: ChIP-Seq

value: H3K27ac (Abcam, ab4729)


title: Input Human Brain CaudateNucleus HS1

value: Caudate nucleus

tag: Cause of death

value: Myocardial decompensation with sepsis

tag: postmortem delay

value: 4.2 hrs

tag: experiment type

value: Input


title: abl_FOXA1 ChIP-seq

description: Prostate cancer derived cell lines

source_name: abl_FOXA1 ChIP-seq

value: LNCaP-abl

tag: antibody


title: abl_CREB1 ChIP-seq

description: Prostate cancer derived cell lines

source_name: abl_CREB1 ChIP-seq


title: abl-siCREB1 RNA-seq

description: Prostate cancer derived cell lines

source_name: abl-siCREB1 RNA-seq


title: Input Human Brain PrecentralGyrus HS1

source_name: Human female precentral gyrus tissue

value: Precentral gyrus

tag: age

tag: chip antibody


title: LNCaP_CREB1 ChIP-seq

description: Prostate cancer derived cell lines

source_name: LNCaP_CREB1 ChIP-seq


title: siCREB1 FoxA1 ChIP-seq_rep2

tag: cell type

value: prostate cancer cells

value: FoxA1 (Abcam ab23738)


title: NRD1243 input 2

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description:
Total RNA
1243-input-2_1
1243-input-2_2

data_processing:
Sequencing reads were aligned to the E. coli K-12 MG1655 genome by Axeq Technoloigies, Inc using Bowtie with the following comman line settings: > bowtie -S -I 30 –X 530 -p 24 --fr -m 1 --max sampleA_maxRead --un sampleA_unmappedRead -- chunkmbs 500 reference -1 sampleA_1.fastq -2 sampleA_2.fastq > sampleA.sam
RPKM calculations were performed by Axeq using a proprietary in-house script
Supplementary_files_format_and_content: Processed data files provided as an excel document.

source_name: Total RNA for biological replicate 2 in the absence of tungstate

growth_protocol: Strains were grown in Luria broth at 37oC to an OD600 of ~1.0

extract_protocol:
RNA was isolated from total cell extracts or immunoprecipitated samples by the hot phenol lysis method.  RNA was subsequently precipitated with isopropanol at -80oC overnight and suspended in DEPC treated water.
The library was generated by removing DNA by DNase treatment, depleting rRNA with the Illumina Ribo-Zero rRNA removal kit for bacteria, and then performing sequencing with the Illumina TruSeq Stranded Total RNA Library Kit.

treatment_protocol: Cells were lysed by with 0.1 mm glass beads, cell debris was removed by centrifugation, and immunoprecipitations were performed using anti-FLAG M2 resin (Sigma-Aldrich).

tag: strain


title: NRD1243 input 1

description:
Total RNA
1243-input-1_1
1243-input-1_2

source_name: Total RNA for biological replicate 1 in the absence of tungstate


title: NRD1243 + WO4 output 1

description:
RNA co-immunoprecipitated with PNPase-3xFLAG from NRD1243 + WO4 input 1
WO4-output-1_1
WO4-output-1_2

source_name: Immunoprecipitated RNA for biological replicate 1 in the presence of tungstate (2 mM).


title: NRD1243 + WO4 input 2

description:
Total RNA
WO4-input-2_1
WO4-input-2_2

source_name: Total RNA for biological replicate 2 in the presence of tungstate (2 mM)


title: NRD1243 + WO4 input 1

description:
Total RNA
WO4-input-1_1
WO4-input-1_2

source_name: Total RNA for biological replicate 1 in the presence of tungstate (2 mM)


title: NRD1243 ouptut 2

description:
RNA co-immunoprecipitated with PNPase-3xFLAG from NRD1243 input 2
1243-output-2_1
1243-output-2_2

source_name: Immunoprecipitated RNA for biological replicate 2 in the absence of tungstate.


title: LS

city: Nanchang

first: Yi

last: Zhou

state: Jiangxi

address: No. 99, Ziyang Rd

institute: Jiangxi Normal University

data_processing:
Basecalls performed using CASAVA version 1.8
The raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 50% Q<10 bases. Then  the low-quality bases (Q<10) at the 5’ and 3’ ends of the remaining reads were discarded. Passed filter reads were mapped onto the Nipponbare reference genome (IRGSP build 5.0)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated to detect gene expression levels.
Genome_build: Nipponbare reference genome (IRGSP build 5.0)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza rufipogon

source_name: Leaf_salt stressed

growth_protocol: Seeds of Dongxiang wild rice (Oryza rufipogon Griff.) were immersed in distilled water in the dark, and the uniformly germinated seeds were sown in 96-well plates supported by a plastic container. Seeds were grown in a growth chamber and the growth culture solution was renewed every 3 days.

extract_protocol:
Total RNA was extracted for the three biological replicates from the sampled leaf or root tissues collected from the three seedlings for each biological replicate using the TRIzol kit following the manufacturer’s instructions (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the seedlings had been grown for 14 days, they were transferred on their 96-well plates into containers filled with 200 mM NaCl solution, or with control solution for 3 days.

tag: genotype/variation

value: Dongxiang wild rice

tag: developemental stage

value: seedling stage

value: leaf

tag: exposed to

value: 200 mM NaCl solution for 3 days


title: LCK

value: control solution for 3 days


title: RS

source_name: Root_salt stressed

value: root


title: RCK


title: R95-1705

city: St. Louis

first: Yong-qiang (Charles)

last: An

address: 975 North Warson Road

department: Plant Genetics Research

institute: United States Department of Agriculture, Agricultural Research Service at Donald Danforth Plant Science Center

description: high protein line

data_processing:
CASAVA 1.8.2 was used to produce purity filtered reads, which were de-multiplexed and had the adaptors removed using ea-utils-1.1.2 by Expression Analysis
FASTQ/A Trimmer from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) was used to remove the last 10 bases of each read leaving 90 bp pair-end reads for the nine genotypes
Bowtie version 0.12.8 and TopHat version 1.4.0 was used to align each sample to the Glycine max cv. Williams 82 reference genome from Phytozome version 9.1 keeping only uniquely aligned read with no more than two mismatches
Cufflinks version 2.1.1 was run on each sample BAM file to assemble the transcripts. Subsequently Cuffmerge version 2.1.1 was used to produce the merged transcriptome file and Cuffdiff version 2.1.1 to quantify the normalized expression values across the nine soybean lines
Z-scores of log2-transformed FPKM values for each individual gene in all nine lines were used to determine significant expression variation.
Genome_build: Glycine max cv. Williams 82 reference genome from Phytozome version 9.1
Supplementary_files_format_and_content: tab delimited text file containing the Z-Scores for each of the nine lines at each expressed loci

organism: Glycine max

source_name: mid stage whole seed

growth_protocol: All soybean (Glycine max (L.) Merrill) lines were grown in growth chambers with temperature set at 25°C day/ 23°C night, the humidity at 50% and 16 hour days at up to 1,000 µmol of supplemental lighting. The plants were watered, fertilized and managed for pests and disease as needed. Seeds at the S6 stage of seed maturation were carefully selected based on seed weight and color, and were harvested for RNA preparation.

extract_protocol:
Samples were ground in liquid nitrogen. Then rna was separated out with phenol chloroform and then purified and precipitated out using a Qiagen RNeasy Kit
RNA-seq libraries were constructed and sequenced at Expression Analysis, Inc., Durham NC (www.ExpressionAnalysis.com). RNA-seq libraries were prepared with the TruSeqTM RNA Sample Preparation Kit v2 from Illumina, Inc., San Diego, CA, and 100 bp paired-end reads were generated on the Illumina HiSeq 2000 platform.

value: seed

tag: developmental stage

tag: cultivar


title: R08-1450

description: high oil line


title: R05-591

description: high oil line


title: NRD1243 ouput 1

description:
RNA co-immunoprecipitated with PNPase-3xFLAG from NRD1243 input 1
1243-output-1_1
1243-output-1_2

source_name: Immunoprecipitated RNA for biological replicate 1 in the absence of tungstate.


title: R05-4256

description: high oil line


title: RNAPII_ChIPSeq

city: Basel

first: Quan

last: Xu

address: Grenzacherstrasse 124

institute: Institute of Human Biology (IHB)

data_processing:
Illumina Casava software used for base calling.
Sequenced reads were trimmed for adaptor sequence using python, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie1.
Peak calling using the MACS tool.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

source_name: Neuroblastoma

extract_protocol: Lysates were clarified from sonicated nuclei and CTCF,Rad21,RNAPII, histone-DNA complexes were isolated with antibody.

tag: cell line

value: neuroblastoma cell line SK-N-SH

value: RNAPII (Millipore, catalog# 05-623B)


title: LNCaP-siFoxA1 RNA-seq

description: Prostate cancer derived cell lines

source_name: LNCaP-siFoxA1 RNA-seq

value: LNCaP

tag: passage number

tag: group

value: androgen dependent

tag: transfection


title: low downregulation of Satb1, replicate 1

description:
reduced level of Satb1
low.Satb1.1

source_name: Satb1_tumor-associated DC

tag: strain background

value: bearing ID8-Defb29/Vegf-a

tag: treated with

value: Satb1 siRNA-Rhodamine conjugated polyethylenimine nanocomplexes (Satb1)

tag: satb1 status

value: knockdown

value: Cancer-Associated Dendritic Cells (DCs)

tag: replicate


title: Jack

description: oil composition and content similar to commodity oil

tag: tissue

value: Jack


title: control for experiment with low downregulation of Satb1, replicate 1

description:
endogenous level of Satb1
low.NT.1

source_name: WT_tumor-associated DC

value: Non-Targeting (NT) siRNA

value: wildtype


title: HIF-1alpha-H1299

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

data_processing:
Raw sequencing reads were mapped to the human genome
(assembly hg19) using Bowtie v0.12.7 algorithm with m1 and v3 parameters. The
binding regions for HAUSP and HIF1 were identified by MACS v1.4.2 algorithm with
default parameter and then annotated by the Bioconductor package, ChIPpeakAnno.
Genome_build: hg19
Supplementary_files_format_and_content: bed file for the peak information

source_name: HIF-1alpha, H1299

growth_protocol: H1299 and MDA-MB-231 cells were cultured in DMEM/10% fetal bovine serum

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
genomic DNA libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody


title: H3K27me3_ChIPSeq

value: H3K27me3 (Millipore, catalog# 17-622)


title: Input-H1299

source_name: Input, H1299


title: N0304-303-3

description: low palmitic acid, mid oleic acid, low linolenic acid line


title: HAUSP-H1299

source_name: HAUSP, H1299

value: HAUSP


title: NRD1243 + WO4 output 2

description:
RNA co-immunoprecipitated with PNPase-3xFLAG from NRD1243 + WO4 input 2
WO4-output-2_1
WO4-output-2_2

source_name: Immunoprecipitated RNA for biological replicate 2 in the presence of tungstate (2 mM).

tag: antibody


title: H3K4me3 Human Brain Putamen HS1

source_name: Human female putamen tissue

value: Putamen

tag: gender

value: Female

tag: age

tag: Cause of death

value: Myocardial decompensation with sepsis

tag: postmortem delay

value: 4.2 hrs

tag: experiment type

value: ChIP-Seq

value: H3K4me3 (Millipore 07-473)


title: 45hrs APF rep2

city: Los Angeles

first: Lawrence

middle: S.

last: Zipursky

address: Howard Hughes Medical Institu675 Charles E. Young Drive South 5-784 MacDonald Research Laboratories

institute: University of California, Los Angeles

description: Sample 8

data_processing:
Illumina Casava1.7 software used for basecalling.
After filtering out reads with low quality and reads containing sequencing adapters, we mapped raw reads to the D. melanogaster reference genome (release FB2013_01) with the gapped aligner Tophat, allowing up to two mismatches. The Drosophila melanogaster gene model annotation (i.e. Drosophila_melanogaster.BDGP5.73.gtf) was downloaded from the Ensembl database and supplied to Tophat. Only reads uniquely aligned were collected.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using customized scripts written in Perl.
Genome_build: flybase5.13 (FB2013_01)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Photoreceptor neurons

extract_protocol:
Brain dissections were performed in dissection buffer.  The central brain was discarded and optic lobes and retina were frozen on dry ice and maintained at -80 in Lysis buffer until enough optic lobes were accumulated.  For each replicate with the Chp-GAL4 driver, 40 optic lobes were used. RNA is then isolated using the RNA-min elute kit from Qiagen.  RNA was then amplified in a linear fashion using Arcuturus RiboAmp HS kit (Life Technologies).  cDNA was then generated for quality assessment and then sequencing libraries were prepared.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Photoreceptor neurons

value: retina

value: 45 hrs APF

tag: genotype/variation

value: wild type


title: M23

description: mid oleic acid line

value: seed

tag: developmental stage

tag: cultivar


title: H3K4me3_ChIPSeq

tag: cell line

value: neuroblastoma cell line SK-N-SH

value: H3K4me3 (Millipore, catalog# 17-614)


title: 53hrs APF rep2

description: Sample 10

value: 53 hrs APF


title: 45hrs APF rep1

description: Sample 7


title: Rad21_ChIPSeq

value: Rad21 (Abcam, catalog# ab992)


title: 65hrs APF rep1

description: Sample 11

value: 65 hrs APF


title: H3K4me3 Human Brain Cerebellum HS1

source_name: Human female cerebellum tissue

value: Cerebellum


title: H3K27ac Human Brain Cerebellum HS1

value: H3K27ac (Abcam, ab4729)


title: FAM94

description: high stearic acid


title: CTCF_ChIPSeq

value: CTCF (Millipore, catalog# 07-729)


title: 35hrs APF rep2

description: Sample 4

value: 35 hrs APF


title: 53hrs APF rep1

description: Sample 9


title: 24hrs APF rep2

description: Sample 2

value: 24 hrs APF


title: 40hrs APF rep2

description: Sample 6

value: 40 hrs APF


title: 96hrs APF rep2

description: Sample 14

value: 96 hrs APF


title: H3K27ac Human Brain PrecentralGyrus HS3

source_name: Human female precentral gyrus tissue

value: Precentral gyrus

value: Female

value: Uremic coma, brain tumor

value: 7.0 hrs

value: ChIP-Seq


title: 96hrs APF rep1

description: Sample 13

value: Photoreceptor neurons

value: retina

value: wild type


title: 24hrs APF rep1

description: Sample 1


title: H3K27ac Human Brain PrecentralGyrus HS1

value: Myocardial decompensation with sepsis

value: 4.2 hrs


title: H3K27ac Human Brain Putamen HS1

value: Putamen


title: 65hrs APF rep2

description: Sample 12

value: 65 hrs APF


title: H3K4me3 Human Brain WhiteMatter HS1 Rep2

source_name: Human female white matter tissue

value: White matter

value: H3K4me3 (Millipore 07-473)


title: HAUSP-MDA-MB-231

source_name: HAUSP, MDA-MB-231

value: HAUSP


title: H3K4me3 Human Brain WhiteMatter HS1 Rep1


title: 35hrs APF rep1

description: Sample 3

value: 35 hrs APF


title: R02-6268F

description: high oil line

value: seed


title: H3K4me3 Human Brain PrecentralGyrus HS1

value: Precentral gyrus


title: H3K4me3 Human Brain OccipitalPole HS1

source_name: Human female occipital pole tissue

value: Occipital pole

value: Female


title: 40hrs APF rep1

description: Sample 5

value: 40 hrs APF


title: H3K27ac Human Brain CaudateNucleus HS1

source_name: Human female caudate nucleus tissue

value: Caudate nucleus

value: ChIP-Seq

value: H3K27ac (Abcam, ab4729)


title: H3K27ac Human Brain PrefrontalCortex HS1

source_name: Human female prefrontal cortex tissue

value: Gyrus rectus


title: 45 EPZ004777

status: Public on Jan 12 2016

city: Aurora

first: Tobias

last: Neff

state: CO

department: Pediatric Oncology

institute: University of Colorado Denver AMC

description: sorted on day 7 after Cre induction, directly processed to  RNA.

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d hg19_total -v snp135_strict --use-splicing=hg19_total.ucscRefGeneSpliceSites --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Differential gene expression was detemined using Cuffdiff. Genes with low levels (<0.5 in both samples, or 0 in one and <5 in the other sample) were excluded. Genes with 'Fail' and 'Notest' Cuffdiff status were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM (Cuffdiff)

growth_protocol: OP9 co-culture in IMDM with 20%  FBS, IL3, IL6 and SCF

extract_protocol:
RNA was isolated using Qiagen RNAeasy kit
Illumina Stranded mRNA kit

treatment_protocol: 5 uM EPZ004777 or DMSO control for 7  days.

value: primary AML patient sample

tag: genotype

tag: growth conditions


title: 51 DMSO

value: OP9 co-culture in IMDM with 20%  FBS, IL3, IL6 and SCF


title: H3K27ac Human Brain ThalamicNuclei HS3

source_name: Human female thalamic nuclei tissue

value: Thalamic nuclei

value: Uremic coma, brain tumor

value: 7.0 hrs


title: H3K27ac Human Brain ThalamicNuclei HS2

value: Sepsis


title: H3K27ac Human Brain PrefrontalCortex HS3


title: 51 EPZ004777


title: H3K27ac Human Brain WhiteMatter HS3

value: White matter


title: H3K27ac Human Brain CaudateNucleus HS3


title: H3K27ac Human Brain ThalamicNuclei HS1

value: Myocardial decompensation with sepsis

value: 4.2 hrs


title: Molm14 - EPZ00477

description: ChIP-Seq for H3K79me2 after 6 days in culture in the presence of 3uM EPZ004777 or DMSO control

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d hg19_total -v snp135_strict --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Sorted Bam-files were used to generate bedgraph files using 'genomeCoverageBed' (bedtools v2.25.0), and bedGraph files were converted to BigWig using 'bedGraphToBigWig' (UCSC).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

growth_protocol: Molm14 and Loucy: RPM1 with 10% FBS and Pen/Strep, Mutz: alphaMEM with  20% FBS, 2 mM L-glutamine, Pen/Strep and 40 ng/ul GM-CSF

extract_protocol:
DNA was isolated using standard ChIP protocol
Nugen Ovation Ultra low system V2

treatment_protocol: 3uM EPZ004777 or DMSO control x 6 days (media change on day 3)

value: human MLL-rearranged myeloid leukemia cell line

value: MLL-rearrangement

tag: chip-antibody

value: Abcam anti-H3K79me2 (ab3594)


title: 45 DMSO


title: Molm14 - DMSO control


title: Loucy - DMSO control

value: Loucy

value: human early T-cell precursor lymphoid leukemia cell line

value: non-MLL-rearranged


title: H3K27ac Rhesus Brain ThalamicNuclei RM1

source_name: Rhesus macaque female thalamic nuclei tissue

value: Female

value: Euthanasia

value: 0.5 hrs

value: ChIP-Seq

value: H3K27ac (Abcam, ab4729)


title: H3K27Ac_Control_1_USC646_ChIPseq

city: LA

first: Peggy

last: Farnham

state: CA

address: 1450 Biggy St.

department: GMCB

institute: University of Southern California

data_processing:
Illumina Casava (version: BCL2FASTQ Conversion Software 1.8.4)  was used for basecalling.
RNA-seq reads were aligned to hg19 genome assembly using Tophat2 after trimming some raw reads using the quality score in Partek Flow version 3. HTSeq 0.6.1 was used to count aligend sequencing reads (bam file) using htseq-count script ( options: -format=bam -m=intersectio-strict -stranded=no). Also gencodev19 gff file was used for running htseq-count script.
ChIP-seq reads were aligned to hg19 genome assembly using bwa (0.6.2)and bam file was converted to bed file using bedtools. Bed files were converted to sgr files for visualization using a script from Sole-Search program.
4C-seq: Processed files of sequenced 4C-seq reads is from 4Cseqpipe program (http://compgenomics.weizmann.ac.il/tanay/?page_id=367)
hg19
processed data files format and content: RNA-seq: Tab-delimited text files that include counts for each gene
processed data files format and content: ChIP-seq: SGR files which are tab-delimited graph format showing base coordinates and scores.
processed data files format and content: 4C-seq: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins.  Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns:  column 1 – the starting coordinate of the 1kb bin  column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin  column 3 – the 80th percentile of values in the window  column 4 – the 20th percentile of values in the window  column 5-145 – as columns 2-4, but with linearly increasing window size, going up to 50kb

source_name: Human colorectal cancer cell-line HCT116

growth_protocol: HCT116 cells and HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin until 80% confluent.

extract_protocol:
For RNA-seq, RNA was prepared using Trizol (Life Technologies, Carlsbad, CA)
For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
For 4C-seq, cells were cross linked using 1% formalehyde for 10 minutes and nuclei were isolated, followed by chromatin is digested with a first restriction enzyme (DpnII) and ligated. After reverse cross-linking, DNA is treated with secondary restriction enzyme (Csp6I) followed by second ligation.
RNA-seq:Single-end libraries were prepared using the Illumina TruSeqV2 Sample Prep Kit (Catalog #15596-026), starting with 1 ug total RNA. Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an NextSeq500.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes), pooled, and sequenced using an Illumina HiSeq2000 or NextSeq500
4C-seq: Libraries were made through inverse PCR using primers that anneal to the bait fragment-end, customized barcode and adaptor seqeunces. Libraries were sequenced using an Illumina HiSeq2500

tag: clone

value: Control Clone 1


title: H3K27Ac_Control_2_USC659_ChIPseq


title: H3K27ac Human Brain OccipitalPole HS1

tag: tissue

value: Occipital pole


title: Mutz3 - DMSO control

value: human myeloid leukemia cell line with high MN1 expression


title: Loucy - EPZ00477


title: H3K27ac Human Brain OccipitalPole HS3

value: Uremic coma, brain tumor

value: 7.0 hrs

tag: chip antibody


title: Mutz3 - EPZ00477


title: H3K27Ac_E7Del_1_USC652_ChIPseq

tag: antibody

value: E7 Deletion Clone


title: H3K27Ac_E7Del_2_USC660_ChIPseq


title: Input_rep1_Control_HCT116_ChIPseq

value: none, input


title: Ag Sp Treg 1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Raw sequencing reads were processed using custom scripts. Read 1 contains the transcript sequence, Read 2 the UMIs. Raw reads were first trimmed using the FASTX-Tollkit v0.0.13 (fastx_trimmer –Q 33). Read 2 was trimmed in order to extract the UMI (5-12bp), and Read 1 was trimmed to 30bp in order to eliminate a potential oligo-dT sequence.
Reads were filtered for quality (more than 80% of the sequences having a Sanger Phred+33 quality score > 33) using fastq_quality_filter -v -Q 33 -q 20 - p 80.
Mapping was performed with Tophat2 to the mm10 mouse transcriptome (Kim et al., 2013) keeping the strand information with the following options: tophat -p 2 --library- type fr-firststrand --read- mismatches 5 --read-gap-length 5 --read-edit-dist 5 --no- coverage-search --segment- length 15 --transcriptome-index.
Duplicated mapping reads were filtered out using the UMIs as follows. First, duplicated mapped reads were marked using picard-tools- 1.79/MarkDuplicates.jar. Then the genomic positions of the duplicated reads were extracted and for each of these positions, only reads having different UMIs were kept. Reads that mapped to multiple positions were filtered out using samtools 0.1.19 flag 256 (Li et al., 2009). Finally, reads were assigned to genes using a modified version of htseq-count with the mm10 gene annotation from UCSC Transcript database.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Splenic Treg

extract_protocol:
RNA was extracted from Trizol using chloroform.
RNA was reverse transcribed using ArrayScript (Ambion), second-strand synthesized using mRNA second strand synthesis module (NEBNext) and amplified via in vitro transcription using MEGAshortscript (Invitrogen) for 9 hours. Transcripts were then fragmented using Mg RNA fragmentation module (NEB), reversed transcribed using Superscript II (Invitrogen) and amplified by PCR for 15 cycles using HiFi hotstart PCR kit (KAPA). cDNA cleanup and size selection were performed on AMPure XP beads.

treatment_protocol: Tibialis anterior, quadricep and gastrocnemius muscles were injured with 0.9ug cardiotoxin/muscle. Muscles and spleen were harvested 4 days post-injury. 1500 Tregs were double sorted directly into Trizol.

value: >6 month old

tag: Sex

value: Male

tag: genetic background


title: Yg Muscle Treg 2

source_name: Muscle Treg

tag: age

value: 2 month old


title: Ag Sp Treg 2


title: Ag Muscle Treg 1


title: Ag Muscle Treg 2


title: Yg Muscle Treg 1


title: Yg Sp Treg 1


title: Yg Sp Treg 2


title: SR-cellBFC1

city: Barcelona

first: Gregoire

last: Stik

state: select a state

address: 88 Dr Aiguader

country: Spain

institute: CRG

description: processed data txt files: SR-fisher_BFC_EXOvsCELL; SR-fisher_CELL_AFTvsBFC; SR_Normalized_allsamples

data_processing:
Illumina Casava1.7 software used for basecalling.
Galaxy server was used to perform the bio informatic analysis
For polyA-RNA libraries, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat allowing 2 mismatch. Cufflinks tool was used to define RPKM and feature counts and fisher's test tools were used to identify differentially expressed transcripts. For small-RNA libraries, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to mm10 genome build and then to different non coding RNA databases (Ensembl and miRbase) using bowtie tool. After miRNA parsing, fisher's tests were used to identify differentially expressed miRNAs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized transcript read numbers, RPKM and fisher's test value for each polyA sample. tab-delimited text files include normalized miRNA read numbers, and fisher's test values for each small RNA sample.

source_name: BFC012_Cell_Small RNA

extract_protocol:
RNAs from exosomes and cells were harvested using Trizol reagent.
RNA libraries were prepared by Fasteris Life Science (Geneva, Switzerland). Briefly, total RNA was submitted to a poly-A mRNA purification using oligo dT magnetic beads. Supernatants were kept for small RNA libraries preparation (TruSeq Small RNA Library Prep Kit, Illumina). polyA-RNAs libraries were prepared after elution of the beads according to the manufacturer’s protocols (TrueSeq RNA Sample PrepKit V2, Illumina).

tag: strain background

tag: tissue source

value: Fetal liver

value: fetal liver-derived stromal lines

tag: hspc supporting capacity

value: non-supportive

tag: sample type

value: Cell

tag: molecule subtype

value: Small RNA


title: SR-cellAFT1

description: processed data txt files: SR-fisher_AFT_EXOvsCELL; SR-fisher_CELL_AFTvsBFC; SR_Normalized_allsamples

source_name: AFT024_Cell_Small RNA

tag: cell type

value: supportive


title: SR-cellAFT2

tag: cell line


title: SR-cellBFC2


title: SR-exoBFC1

description: processed data txt files: SR-fisher_BFC_EXOvsCELL; SR-fisher_EXO_AFTvsBFC; SR_Normalized_allsamples

source_name: BFC012_Exosome_Small RNA

value: Exosome


title: SR-exoBFC2


title: Muscle.Treg.PBS

data_processing:
Data was separated by barcode and aligned using Tophat version 2.0.10 (Kim et al. 2013) with default settings.
Transcripts were quantified by the BTL computational pipeline using the Cufflinks suite version 2.2.1 (Trapnell et al. 2012).
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

extract_protocol:
RNA was extracted from Trizol using chloroform.
RNA was purified using RNA-SPRI beads. Poly(A)-mRNA was converted to cDNA and then amplified. cDNA was subject to transposon-based fragmentation  that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Sequencing was carried out as paired end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: Tibialis anterior, quadricep and gastrocnemius muscles were injured with cardiotoxin and rIL-33 (0.3ug) or PBS intramuscularly. Muscles were harvested 4 days post-injury. 5000 Tregs were double sorted directly into Trizol.

value: 8 weeks old

tag: treatment

value: Cardiotoxin/PBS


title: Muscle.Treg.IL33


title: polyA-exoBFC2

description: processed data txt files: PolyA-fisher_BFC_EXOvsCELL; PolyA-fisher_EXO_AFTvsBFC; polyA-RNA_allsamples_RPKM

source_name: BFC012_Exosome_polyA RNA

value: polyA RNA


title: polyA-cellAFT1

description: processed data txt files: PolyA-fisher_AFT_EXOvsCELL; PolyA-fisher_CELL_AFTvsBFC; polyA-RNA_allsamples_RPKM

source_name: AFT024_Cell_polyA RNA


title: SR-exoAFT2

description: processed data txt files: SR-fisher_AFT_EXOvsCELL; SR-fisher_EXO_AFTvsBFC; SR_Normalized_allsamples

source_name: AFT024_Exosome_Small RNA


title: polyA-cellBFC1

description: processed data txt files: PolyA-fisher_BFC_EXOvsCELL; PolyA-fisher_CELL_AFTvsBFC; polyA-RNA_allsamples_RPKM

source_name: BFC012_Cell_polyA RNA


title: polyA-cellBFC2


title: polyA-exoAFT1

description: processed data txt files: PolyA-fisher_AFT_EXOvsCELL; PolyA-fisher_EXO_AFTvsBFC; polyA-RNA_allsamples_RPKM

source_name: AFT024_Exosome_polyA RNA


title: polyA-exoAFT2


title: polyA-exoBFC1


title: polyA-cellAFT2


title: SR-exoAFT1


title: Early SKM rep3

city: Minneapolis

first: Sunny

middle: Sun-Kin

last: Chan

state: MN

department: Pediatrics

institute: University of Minnesota

description:
Mm_minus_SC409_minus_D6_minus_control
Sample.040015

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
PCA, hierarchical clustering and ANOVA of TPM values from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing normalized "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: CPM-derived D6 (early)_SKM

growth_protocol: Mesp1-inducible mouse embryonic stem cells were growth as embryoid bodies in serum-free EB differentiation for 5 days.  Cells were dissociated on day 5 and subsequently cultured as a monolayer until day 12.  Doxycycline (500 ng/ml) was added from day 5 to day 12 to induce Mesp1.

extract_protocol:
RNA was extracted using Qiagen RNeasy mini kit.  RNA was treated with DNase I at a later date using Qiagen RNase-free DNase set and Qiagen RNeasy mini kit column
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

treatment_protocol: BMP4 (20 ng/ml) was added from day 5 to day 12 for cardiac differentiation.  The default (control) is skeletal myogenic differentiation.

tag: strain

tag: day of differentiation

value: Day 6

tag: treated with

value: Cardiopharyngeal mesoderm (CPM) derivatives

tag: cell subtype

value: skeletal myogenic (SKM) progenitors


title: Early CM rep3

description:
Mm_minus_SC409_minus_D6_minus_bmp
Sample.040016

source_name: CPM-derived D6 (early) CM

value: BMP4, 20 ng/ml

value: cardiac progenitors


title: Late SKM rep3

description:
Mm_minus_SC409_minus_D12_minus_control
Sample.040017

source_name: CPM-derived D12 (late)_SKM

value: Day 12


title: Late CM rep2

description:
Mm_minus_SC354_minus_D12_minus_bmp
Sample.040014

source_name: CPM-derived D12 (late)_CM


title: Early CM rep2

description:
Mm_minus_SC354_minus_D6_minus_bmp
Sample.040012


title: Late CM rep3

description:
Mm_minus_SC409_minus_D12_minus_bmp
Sample.040018


title: Early SKM rep2

description:
Mm_minus_SC354_minus_D6_minus_control
Sample.040011


title: Late SKM rep2

description:
Mm_minus_SC354_minus_D12_minus_control
Sample.040013


title: H3K27ac Human Brain WhiteMatter HS1

data_processing:
Mapping Illumina: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S --phred64-quals -q -l 40/45 -n 1
Mapping SOLiD: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S -l 50 -n 3 -C -Q -f
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g hs --nomodel --extsize 400 --llocal 100000
genome build: hg38, rheMac3, panTro4, mm10
processed data files format and content: txt files contain called peaks
processed data files format and content: narrowPeak files contain called peaks in BED format
processed data files format and content: bedGraph files contain treat pileup
processed data files format and content: bw files contain treat pileup read per million (RPM) normalized in bigWig format

source_name: Human female white matter tissue

extract_protocol:
Crosslink, Lyse and Immunoprecipitate
Illumina Truseq DNA library protocol

tag: tissue

value: White matter

tag: gender

value: Female

tag: Cause of death

value: Myocardial decompensation with sepsis

tag: postmortem delay

value: 4.2 hrs

tag: experiment type

value: ChIP-Seq

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: Late SKM rep1

description:
Mm_minus_HH40_minus_D12_minus_control
Sample.040009


title: Early SKM rep1

description:
Mm_minus_HH40_minus_D6_minus_control
Sample.040007


title: Early CM rep1

description:
Mm_minus_HH40_minus_D6_minus_bmp
Sample.040008

source_name: CPM-derived D6 (early)_CM


title: MLL1-Control-2

description: sorted on day 7 after Cre induction, directly processed to  RNA.

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --use-splicing=ucscRefGeneSpliceSites_mm9 --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Differential gene expression was detemined using Cuffdiff. Genes with low levels (<0.5 in both samples, or 0 in one and <5 in the other sample) were excluded. Genes with 'Fail' and 'Notest' Cuffdiff status were exluded.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM (Cuffdiff). Comparison was conducted between Dot1l ff/ko and between MLL1  ff/ko

source_name: common myeloid progenitors (CMP) transformed using MSCV-MN1-IRES-GFP

tag: genotype

value: MLL1 flox/flox day 7 after transduction with control

tag: growth conditions

value: M3234 supplemented with FBS, IL3, IL6 and SCF


title: Late CM rep1

description:
Mm_minus_HH40_minus_D12_minus_bmp
Sample.040010


title: Dot1l-Cre-3

value: common myeloid progenitors (CMP) transformed using MSCV-MN1-IRES-GFP

value: Dot1l -/- day 7 after transduction with cre


title: MLL1-Control-1


title: MLL1-Cre-1

value: MLL1 -/- day 7 after transduction with cre


title: MLL1-Cre-2


title: MLL1-Control-3


title: Dot1l-Control-3

value: Dot1l flox/flox day 7 after transduction with control


title: Dot1l-Control-1


title: CMP-MN1-L input_1

description: Leukemic cells harvested from a moribund mouse were  briefly cultured in M3234 with FBS, Il3, Il6 and SCF to ensure adequate numbers and good viability.

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Sorted Bam-files were used to generate bedgraph files using 'genomeCoverageBed' (bedtools v2.25.0), and bedGraph files were converted to BigWig using 'bedGraphToBigWig' (UCSC).
Bam files for H3K79me2 were catenated and  Peaks were identified using MACS2 with the parameters  --broad -g mm --broad-cutoff 0.1, using input as control.  Peaks were intersected with Refseq mm9 coordinates (UCSC table browser) using intersectBed.
Genome_build: mm9
Supplementary_files_format_and_content: .bw files are  Chip-seq tracks for visualization as BigWig-file; excel file with H3K79me2 peaks (as determined by MACS2) in bed file format for all three leukemias combined, using all three input files combined as background.

source_name: myeloid leukemia

value: Bone marrow leukemic blasts sorted from moribund mice that had been transplanted with CMP-cells transformed with MN1

value: Genotype:Dot1l f/f (conditional allele, NOT inactivated)

tag: chip-antibody

value: N/A (input)


title: Dot1l-Cre-2


title: CMP-MN1-L input_2

growth_protocol: Leukemic cells harvested from a moribund mouse were  briefly cultured in M3234 with FBS, Il3, Il6 and SCF to ensure adequate numbers and good viability.


title: CMP-MN1-L input_3


title: CMP-MN1-L H3K79me2_3

value: Abcam anti-H3K79me2 (ab3594)


title: Dot1l-Cre-1


title: Dot1l-Control-2


title: CMP-MN1-L H3K79me2_2


title: Senes_Treated_Replicate_3

city: Glasgow

first: Peter

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

data_processing:
Reads were trimmed using Trim Galore (v0.3.0).
Paired-end reads are aligned to the human genome (hg19) using tophat2. Reference splice junctions were provided by a reference transcriptome (Ensembl build 73).
FPKMs were determined using cufflinks under default settings.
Differentially expressed genes were called using cuffdiff under default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of FPKMs for all samples, as called by cufflinks. Differential gene expression for uninduced vs induced samples, as called by cuffdiff.

growth_protocol: MRC5 human fibroblasts were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, Sigma, Dorset, UK) supplemented with 10% heat inactivated foetal calf serum (FCS), 100 units/ml penicillin, 100 μgml-1 streptomycin, 2mM glutamine and 50 μgml-1 uridine at 37oC in a humidified atmosphere incubator with 5% CO2

extract_protocol:
Total RNA was extracted using Qiagen RNeasy mini kit according to the manufacturer instructions with on the column DNASE I digestion.
Quality of RNA was assessed on Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit (Agilen Technologis), before creating oligo-dT based cDNA library using Illumina TruSeq RNA Sample Prep Kit,v2.0. kit.
The library was sequenced on a NextSeq500, using a NextSeq500 Mid Output kit 150 cycles flowcell.

treatment_protocol: Parkin-expressing MRC5 fibroblasts were irradiated with 20Gy X-ray and 2 days after were treated with 12.5uM CCCP for 48h (refreshed every 24 hours). At day 4 after irradiation, CCCP was removed and cells were kept in culture with normal serum supplemented medium. Cells were harvested at day 10 after irradiation (6 days after CCCP treatment) for RNA-seq analysis.

value: Parkin-expressing MRC5 fibroblasts

tag: cell state

value: Mitochondrial deficient senescent

value: CCCP


title: Organoid Mock n3

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: polyA+ RNA

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm9 using STAR.
The GENCODE mV1 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample.

source_name: Mammary tumor

growth_protocol: Organoids from MMTV-PyMT tumors were prepared as described previously (Ewald AJ et al, Dev. Cell 2008) and cultured in matrigel in the presence of FGF2.

extract_protocol:
Total RNA was extracted using TRIzol reagent from both organoids and homogenized tumor tissue.
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

treatment_protocol: Tumors: 125 mg/kg/week of ASOs targeting Malat1 or ScASO were injected subcutaneously into MMTV-PyMT mice for several weeks. Organoids: 500 nM of Malat1 ASO1, ASO2 or ScASO were added to the medium and replenished after 3 days. Total treatment time: 6 days.

value: MMTV-PyMT

value: Mammary tumor

value: Mock


title: Organoid Mock n2

description: polyA+ RNA