title: S-MEFs_WGBS

description:
WGBS
S-MEFs

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
The trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For methyl-seq libraries, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
genome build: mm10
Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA
For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina).


title: 2i_ESC_15_XX_RNA-seq

status: Public on Jul 27 2017

type: SRA

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

description:
RNA-seq
2i-ESC #15 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

library_source: transcriptomic

data_processing:
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina)
For RNA-seq analysis, the sequenced reads were mapped to the mouse reference genome (mm10) using tophat-2.1.0 11 with the GENCODE version M9 annotation gtf file and the aligner Bowtie2-2.2.5 6 after trimming adaptor sequences and low-quality bases by cutadapt-1.9.1 12. For allelic expression analysis of RNA-seq, the trimmed reads were also mapped to MSM genomes described as above, and the reads mapped to the same chromosome and positions of both B6 and MSM/Ms genomes with high mapping quality (MAPQ>=20) were used for further analyses. The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
genome build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes RPKMs for each sample.

molecule: total RNA

organism: Mus musculus

source_name: ES cells

extract_protocol:
RNAeasy plus Mini Kit (QIAGEN) for RNA.
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

tag: passage

tag: strain

value: F1 (129X1/SvJ and MSM/Ms)

tag: cell type

value: ES cells

tag: gender

value: female


title: S-ESCs_9_XX_p3_WGBS

description:
WGBS
S-ESC #9 XX

library_source: genomic

molecule: genomic DNA


title: H3K9me3_clr4Δ_SPY815

city: Boston

first: Gloria

last: Jih

state: MA

address: 240 Longwood Ave, LHRRB 517

department: Cell Biology

country: USA

institute: Harvard Medical School

description: barcode sequence: GTCTACAT

data_processing:
Raw reads were separated by barcode. Barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using Bowtie's default parameters. Mapped reads were normalized to reads per million, tiled with igvtools, and visualized in Integrated Genome Viewer (IGV).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million, tiled with igvtools for visualization in Integrated Genome Viewer (IGV).

organism: Schizosaccharomyces pombe

extract_protocol:
ChIP was performed as previously described (Yu et al., 2014). Conditions for fixation and immunoprecipitation (IP) are briefly described here. 50 ml cultures of cells were grown overnight (or 24 hours when 2.5 ug/ml tetracycline was added) in YES to an optical density (OD) of 2 and fixed as follows. For H3K9me2, H3K9me3, and Chp1 ChIP, cell were fixed with 1% formaldehyde for 15 min. For Swi6 and Flag-protein ChIP, we used a modified dual-crosslinking protocol in which cells were first incubated at 18 °C for two hours, resuspended in 5 ml of room temperature PBS, and fixed with 1.5 mM ethylene glycol bis-succinimidyl succinate (EGS, Thermo Scientific #21565) for 30 min, followed by addition of formaldehyde to 1% final concentration for another 30 min (Zeng et al., 2006). For Swi6 ChIP in Figure S4, the 2 hr incubation at 18 °C was omitted. For each IP, ~ 2 ug of antibody was pre-incubated with 30 ul of Invitrogen Dynabeads Protein A or Protein G: anti-H3K9me2 (Abcam 1220) with Protein A, anti-H3K4me3 (Millipore 04-745) with protein G, anti-H3K36me3 (Abcam 9050) with protein A, anti-H4K16ac (Active Motif 39167) with protein A, anti-Chp1 (Ab18191) with protein A, anti-Flag (Sigma F1804) with protein G, anti-Swi6 (rabbit polyclonal) with protein A, anti-RNA pol II 8WG16 (BioLegend MMS-126R-500) with protein A. For IP with H3K9me3 antibody, Dynabeads M-280 Streptavidin beads were first incubated with 1 ug of anti-H3K9me3 (Diagenode C15500003), followed by blocking with 5 uM biotin. Sheared chromatin lysate was added to the antibody-bead mixture and incubated for 2 hr at 4 °C on a rotating device.
Immunoprecipitated DNA was cleaned up using the Qiagen PCR Purification Kit after reversing cross-links, RNaseA, and proteinase K treatment. Immunoprecipitated DNA was eluted from column with the provided elution buffer (50 ul x 2), subjected to additional shearing in a Qsonica water bath sonicator at 20% amplitude for 15 minutes of total shearing time (each cycle is 15” on + 15” off), followed by vacuum centrifugation to reduce the volume to 30 ul. DNA concentration was measured using Qubit dsDNA HS Kit.1 to 10 ng of immunoprecipitated DNA was used for standard Illumina library construction using barcoded adapters and protocol described previously (Wong et al., 2013). Libraries were pooled and sequenced on the Illumina HiSeq2000 or 2500.

tag: genotype

tag: media

value: YES

tag: antibody

value: H3K9me3 (Diagenode C15500003)


title: 2i_MEF_15_XX_RNA-seq

description:
RNA-seq
2i-MEF #15 XX
Processed data file: ProcessedDataMatrixRPKMfin.txt.gz

source_name: MEFs

value: MEFs


title: H3K9me2_swi6Δ_SPY1098

description: barcode sequence: GGCTAC


title: H3K9me2_chp2Δ_SPY1368

description: barcode sequence: TAGCTT


title: H3K9me3_clr4F449Y_SPY4642

description: barcode sequence: TCGCGTAC


title: H3K9me2_chp1Δ_SPY2421

description: barcode sequence: GATCAG


title: H3K9me2_clr4F449Y_SPY4642

description: barcode sequence: GCCAAT


title: H3K9me2_clr4I418P_SPY6537

description: barcode sequence: ATATAGGA


title: H3K9me2_clr4Δ_SPY815

description: barcode sequence: TTAGGC


title: a2i_ESC_4_XX_p15_WGBS

description:
WGBS
a2i-ESC #a4 XX p15

value: F1 (129X1/SvJ and C57BL6)


title: c2i_ESC_4_XX_p15_WGBS

description:
WGBS
2i-ESC #c4 XX p15


title: a2i_ESC_1_XY_p15_WGBS

description:
WGBS
a2i-ESC #a1 XY p15

value: male


title: serum_ESC_17_XX_WGBS

description:
WGBS
serum-ESC #17 XX


title: a2i_ESC_18_XX_p15_WGBS

description:
WGBS
a2i-ESC #a18 XX p15


title: H3K9me2_WT_SPY137

description: barcode sequence: CGATGT

value: WT


title: a2i_ESC_3_XY_p15_WGBS

description:
WGBS
a2i-ESC #a3 XY p15


title: serum_46_XX_p3_WGBS

description:
WGBS
serum-ESC #46 XX


title: S_ESC_8_XX_p15_WGBS

description:
WGBS
S-ESC #8 XX p15


title: c2i_ESC_3_XX_p15_WGBS

description:
WGBS
2i-ESC #c3 XX p15


title: c2i_ESC_6_XY_p15_WGBS

description:
WGBS
2i-ESC #c6 XY p15


title: a2i_ESC_1_XY_WGBS

description:
WGBS
a2i-ESC #a1 XY


title: serum ESC #16, XY_WGBS

description:
WGBS
serum-ESC #16 XY


title: a2i_ESC_3_XY_WGBS

description:
WGBS
a2i-ESC #a3 XY


title: S_ESC_9_XX_p15_WGBS

description:
WGBS
S-ESC #9 XX p15


title: c2i_ESC_2_XY_WGBS

description:
WGBS
2i-ESC #c2 XY


title: c2i_ESC_6_XY_WGBS

description:
WGBS
2i-ESC #c6 XY


title: 02_2i_ESC_2_XY_WGBS

description:
WGBS
t2i-ESC #t2 XY


title: H3K9me2_clr4W31G_SPY5562

description: barcode sequence: GCAGCCTC


title: 4n_2i_MEFs_WGBS

description:
WGBS
4n-2i-MEF


title: 2n_2i_MEFs_WGBS

description:
WGBS
2n-2i-MEF


title: c2i_ESC_2_XY_p15_WGBS

description:
WGBS
2i-ESC #c2 XY p15


title: S_ESC_12_XY_WGBS

description:
WGBS
S-ESC #12 XY


title: S_ESC_31_XY_WGBS

description:
WGBS
S-ESC #31 XY


title: serum_ESC_10_XY_WGBS

description:
WGBS
serum-ESC #10 XY


title: 02_2i_ESC_6_XY_WGBS

description:
WGBS
t2i-ESC #t6 XY


title: 2i_ESC_20_XY_WGBS

description:
WGBS
2i-ESC #20 XY


title: 02_2i_ESC_3_XX_WGBS

description:
WGBS
t2i-ESC #t3 XX


title: 2i_ESC_2_XX_WGBS

description:
WGBS
2i-ESC #2 XX


title: 02_2i_ESC_1_XX_WGBS

description:
WGBS
t2i-ESC #t1 XX


title: a2i_ESC_18_XX_WGBS

description:
WGBS
a2i-ESC #a18 XX


title: S_ESC_8_XX_WGBS

description:
WGBS
S-ESC #8 XX


title: Drosha-deficient ES cells, derived from  AB1 ES cells

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Data were mapped to the Mus musculus GRCm38 reference genome
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: tab delimited text file

growth_protocol: ES cells were cultured in ES cell media which consists of Dulbecco modified Eagle medium (DMEM) supplemented with 15% fetal bovine serum, 100 IU/mL penicillin, 100mg/mL streptomycin, 2 mmol/L L-glutamine, MEM non-essential amino acids, 0.12 mmol/L β-mercaptoethanol, and leukemia inhibitory factor (LIF)

extract_protocol: Genomic DNA was prepared from fresh cell pellets using GeneJET Genomic DNA Purification Kit (ThermoScientific) according to the manufacturers protocol.

tag: strain background

tag: genotype/variation

value: Drosha-deficient

value: embryonic stem cells (ES cells)


title: RNA_seq_Torin

status: Public on Jul 26 2017

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

country: China

institute: Zhejiang University

description: total RNA following rRNA removal

data_processing:
For replicate 1, the 3' adaptor AAAAAAAAAA and low quality bases were trimmed by Cutadapt. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted.
For replicate 2, the 3' adaptor CTGTAGGCACCATCAAT were trimmed by Cutadapt. The first 6 nucleotide and the last 4 nucleotides were also clipped after adaptor removal. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted. The PCR duplicates were removed from the mapped reads using the methods in Lecanda et al., 2016 (PMID: 27450428)
Genome_build: GRCm38.83
Supplementary_files_format_and_content: RPKM files were generated. Each line represents one mRNAs. RPKM values were separated by Tabs.

source_name: mammalian cells

growth_protocol: MEF wild-type and knock-down cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
MEF cells were washed using ice-cold PBS containing 100 µg ml-1 cycloheximide and then lysed in polysome lysis buffer ((10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 100 µg ml-1 cycloheximide and 2% Triton X-100). Cell debris were removed by centrifugation at14,000 rpm for 10 min at 4°C.
Fragmented RNA were dephosphorylated for 1 hr at 37°C in 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 40-60 nt (for RNA-seq ) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 μl gel elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U/ml SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.Purified RNA fragments were tailed followed by reverse transcription. Reverse transcription products were purified on a 10% polyacrylamide TBE-urea gel and circularized. Circular single-strand DNA was re-linearized and the expected 100-nt product bands were excised for purification followed by PCR amplification. PCR products were recovered and sent for deep sequencing.

treatment_protocol: MEF cells  were grown to 80% confluence on 10-cm petri dish and treated with DMSO or 250 nM Torin1 for 2 h.

value: mouse embryonic fibroblast


title: c2i_ESC_3_XX_WGBS

description:
WGBS
2i-ESC #c3 XX


title: Dnmt1-deficient ES cells derived from J1 ES cells


title: a2i_ESC_4_XX_WGBS

description:
WGBS
a2i-ESC #a4 XX


title: c2i_ESC_4_XX_WGBS

description:
WGBS
2i-ESC #c4 XX


title: RNA_seq_shABCF1_rep2

description: total RNA following rRNA removal


title: 2i_ESC_15_F_Nextseq_WGBS

description:
WGBS
2i-ESC #15 XX


title: 2i_ESC_23_M_Nextseq_WGBS

description:
WGBS
2i-ESC #23 XY


title: S_ESC_36_F_Nextseq_WGBS

description:
WGBS
S-ESC #36 XX


title: Os_root.tip.ATAC_rep2

city: Atlanta

first: Roger

middle: B

last: Deal

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

data_processing:
Raw reads were aligned to the appropriate genome using Bowtie2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks (transposase hypersensitive sites; THSs) were identified using the Findpeaks function of the Homer package, with the parameters "-region" and "-minDist 150". Bed files of the THS regions are included for each dataset.
Genome_build: Arabidopsis thaliana TAIR10, Medicago truncatula Mt4.0, Solanum lycopersicum SL2.4, and Oryza sativa IRGSP 1.0.30
Supplementary_files_format_and_content: .bed files containing ATAC-seq transposase hypersensitive site locations as defined using the findPeaks function of the Homer software package.

organism: Oryza sativa

source_name: Root tip

growth_protocol: All plants were grown under 16hr light/8 hr dark cycles on vertically-oriented nutrient agar plates.

extract_protocol:
Tn5 Transposase treatment (using the Illumina Nextera kit) was performed on 50,000 nuclei from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit.
Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.

treatment_protocol: One centimeter root tips or fully differentiated root zone (above first fully expanded root hairs but below any lateral roots) were harvested using a razor blade. Total root tip nuclei were purified using INTACT affinity purification or by tissue lysis followed by sucrose sedimentation. Arabidopsis root hair and non-hair cell nuclei were purified by INTACT from the fully differentiated root zones.

tag: strain/background

value: Nipponbare

tag: tissue or cell type

value: 1 cm root tip

tag: nuclei purification method

value: INTACT streptavidin affinity purification


title: RNA_seq_shABCF1_rep1

description: total RNA following rRNA removal


title: RNA_seq_shMETTL3_rep1

description: total RNA following rRNA removal


title: RNA_seq_Scram_rep2

description: total RNA following rRNA removal


title: RNA_seq_Scram_rep1

description: total RNA following rRNA removal


title: RNA_seq_shMETTL3_rep2

description: total RNA following rRNA removal


title: Ribo_seq_shABCF1_rep2

description: total RNA following rRNA removal

data_processing:
Library strategy: RIBO-seq
For replicate 1, the 3' adaptor AAAAAAAAAA and low quality bases were trimmed by Cutadapt. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted.
For replicate 2, the 3' adaptor CTGTAGGCACCATCAAT were trimmed by Cutadapt. The first 6 nucleotide and the last 4 nucleotides were also clipped after adaptor removal. The trimmed reads were mapped to Mouse transcriptom (GRCm38.83) by Bowtie, using parameters: -a --best -m1 --strata. Two mismatches were permitted. The PCR duplicates were removed from the mapped reads using the methods in Lecanda et al., 2016 (PMID: 27450428)
Genome_build: GRCm38.83
Supplementary_files_format_and_content: RPKM files were generated. Each line represents one mRNAs. RPKM values were separated by Tabs.


title: Ribo_seq_Torin

description: total RNA following rRNA removal


title: Ribo_seq_shMETTL3_rep2

description: total RNA following rRNA removal


title: Ribo_seq_shABCF1_rep1

description: total RNA following rRNA removal


title: Ribo_seq_Scram_rep2

description: total RNA following rRNA removal


title: WT, AB1 (129Sv/Ev) ES cells

value: wild type


title: Ribo_seq_Scram_rep1

description: total RNA following rRNA removal


title: IJ1_24

city: London

first: Michalis

last: Barkoulas

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: 24 hrs post L4

data_processing:
Reads aligned to a custom transcriptome dataset having built this as a genome using bowtie2 in paired end mode
The alignments were converted to count files using bedtools coverageBed module using the options -s and -counts.
Genome_build: WS190
Supplementary_files_format_and_content: tab-delimited text file with raw counts
Supplementary_files_format_and_content: tab-delimited text file with DESeq2 normalized counts

organism: Caenorhabditis elegans

source_name: whole adult animal

growth_protocol: The strains used in this study were cultured and handled according to standard protocols (Brenner, 1974). Animals for infection assays were synchronized to L4 by bleaching gravid hermaphrodites.

extract_protocol:
RNA was extracted from a total of 50 infected and control animals after 12 hrs and 24 hrs post-exposure to pathogen using TRIzol ® reagent and the Direct-zolTM RNA extraction kit (Zymo Research), according to the manufacturer’s instructions. The quality and quantity of RNA was determined using the Agilent® RNA ScreenType System on an Agilent ® 2100 Bioanalyzer.
The library preparation was done using the Illumina TruSeq RNA stranded mRNA library prep kit.

treatment_protocol: All infection assays were carried out at 25 °C on nematode growth medium seeded with 50 ul of OP50 E. coli culture. Infection assays were carried out in triplicates and consisted of 50 animals being transferred onto plates containing 3 infected animals, or onto control plates devoid of pathogen.

tag: tissue

value: whole adult animal

tag: Stage

value: Control animals

tag: mutation

value: wt


title: IJ3_24

description: 24 hrs post L4


title: IJ2_24

description: 24 hrs post L4


title: CJ1_24

description: 24 hrs post L4

value: Infected animals


title: IJ1_12

description: 12 hrs post L4


title: CJ2_24

description: 24 hrs post L4


title: CJ3_24

description: 24 hrs post L4


title: IJ2_12

description: 12 hrs post L4


title: CJ3_12

description: 12 hrs post L4


title: CJ2_12

description: 12 hrs post L4


title: IJ3_12

description: 12 hrs post L4


title: RNA-seq_ZT10_shProx1_rep3

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description: processed data file: DEseq2_HDAC3_KO_PROX1_KD.xlsx

data_processing:
Alignment was performed using bowtie v0.12.7
Genome_build: mm9
Supplementary_files_format_and_content: UCSC bigwig files and peak files were generated using HOMER

source_name: liver

extract_protocol:
Livers were isolated, flash frozen on liquid nitrogen, and later processed for RNA extraction with Trizol, or fixed with 1% formaldehyde for ChIP.
Libraries were prepared using standard Illumnia protocols

value: liver

tag: age

value: 11 weeks old


title: RNA-seq_ZT10_shLuciferase_rep3


title: RNA-seq_ZT10_shProx1_rep1


title: IN1_24

description: 24 hrs post L4


title: SU-DIPGXIII-FL

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

data_processing:
Mapping: tophat2, default parameters were used against hg19 reference genome
Gene expression: quantified using featureCounts against an RefSeq hg19 GTF
Normalization: FPKM values were calculated using length of exons and total number of assigned reads
Genome_build: hg19

molecule: polyA RNA

organism: Homo sapiens

source_name: patient-derived cell culture

growth_protocol: Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin. See Grasso et al 2015.

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated.
After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. Libraries were end-repaired using T4 DNA Polymerase, E. coli Klenow fragment, and T4 polynucleotide kinase. DNA was then A-tailed using exo(-) Klenow fragment and ligated to adaptors from NEBNext MultiPlex Oligos using New England BioLabs Quick Ligase.
Libraries were sequenced at 1x75 on an Illumina NextSeq 500

treatment_protocol: Untreated cells were collected in biological duplicate.

value: Diffuse Intrinsic Pontine Glioma cell culture


title: Ribo_seq_shMETTL3_rep1

description: total RNA following rRNA removal


title: IN2_24

description: 24 hrs post L4


title: IN3_24

description: 24 hrs post L4


title: RNA-seq_ZT10_shLuciferase_rep1


title: SU-DIPGXIII-P


title: CN2_24

description: 24 hrs post L4


title: CN3_12

description: 12 hrs post L4


title: CN1_24

description: 24 hrs post L4


title: CN2_12

description: 12 hrs post L4


title: CN3_24

description: 24 hrs post L4


title: CN1_12

description: 12 hrs post L4


title: RNA-seq_ZT10_shLuciferase_rep2


title: RNA-seq_ZT10_shProx1_rep2


title: CJ1_12

description: 12 hrs post L4


title: IN3_12

description: 12 hrs post L4


title: IN1_12

description: 12 hrs post L4


title: IN2_12

description: 12 hrs post L4


title: WT_AA_H3K4me3_Rep1

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description: H3K4me3 ChIP-seq for worms with antimycin A (AA) treatment.

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the UCSC ce10 genome assembly using bwa 0.7.13 with default settings
Only the reads with no more than  4%  mismatches and uniquely mapped to reference genome were kept by using Bash Shell.
Peaks were called using MACS2 (version 2.1.0).
Genome_build: ce10
Supplementary_files_format_and_content: bigwig files were generated using deepTools

growth_protocol: Worms were grown on NGM agar, and maintained at 22℃.

extract_protocol:
Worms were collected when became L3-L4 mix and handled with standard ChIP protocol.
Purified DNA was used for DNA library construction using NEBNext Ultra DNA Library Prep Kit for Illumina.

treatment_protocol: Worms were treated with or without antimycin A.

tag: developmental stage

value: L3-L4 mix

tag: treated with

value: antimycin A (AA)

value: whole body

tag: chip antibody

value: H3K4me3 (Abcam, #ab8580)


title: WT_NT_H3K4me3_Rep2

description: H3K4me3 ChIP-seq for no treatment (NT) worms .

value: none; no treatment (NT)


title: WT_AA_H3K4me3_Rep2


title: WT_AA_Input_Rep1

description: ChIP-seq input for  worms with antimycin A (AA) treatment.


title: WT_NT_Input_Rep1

description: ChIP-seq input for no treatment (NT) worms .


title: mouse_HL_W6_rep2

city: La Jolla

first: Marcelo

last: Rivas

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: University of California San Diego

data_processing:
Sequenced reads werepreprocessed to remove Illumina adaptors, and bases with qualities below 20 at the read's 3 prime end were trimmed. Reads from mouse, opossum, and pig were aligned using STAR (--outFilterMultimapNmax 10, --outFilterMismatchNmax 3, --outFilterScoreMin 0, --clip3pNbases 0, --clip5pNbases 0). Reads from bat were aligned using RSEM (--fragment-length-mean 425.0 --fragment-length-sd 150.0).
Gene expression (fragments per kilobase of transcript per million mapped reads, FPKM) were computed using cufflinks (for mouse, opossum, and pig) and RSEM (bat).
Genome_build: For mouse, opossum, and pig, we used their corresponding Ensembl reference genomes and annotation assemblies: GRCm38 (mouse), BROADO5 (opossum), and Sscrofa10.2 (pig). For bat reads, we used as a reference a de novo assembly. In short, we merged all libraries (from all stages) and called a de novo transcriptome using Trinity, then from the resulting de novo transcriptome we filtered out any sequence not matching the SwissProt database (blastx, e-value<1e-20).
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include RSEM gene expression (FPKM).
Supplementary_files_format_and_content: *_genes.fpkm_tracking: Tab-delimited text files include CUFFLINKS gene expression (FPKM).

growth_protocol:
Embryonic mice (ICR strain, Taconic) and opossums were obtained from timed matings [1, 2] in breeding colonies housed in the Sears Lab at the University of Illinois. Pig embryos were obtained through timed inseminations following ovulations at the University of Illinois pig farm [3]. Bat embryos were obtained from field collections in Trinidad and staged according to Cretekos et al. 2005 [4].
1. Keyte AL, Smith KK. Basic maintenance and breeding of the opossum monodelphis domestica. CSH Protoc. 2008;2008:pdb prot5073.
2. Suckow MA, Danneman P, Brayton C. The laboratory mouse. Boca Raton: CRC Press; 2001.
3. Artificial Insemination (AI) [http://livestocktrail.illinois.edu/swinerepronet/paperDisplay.cfm?ContentID=6267]. Accessed May-June 2016.
4. Cretekos CJ, Weatherbee SD, Chen CH, Badwaik NK, Niswander L, Behringer RR, Rasweiler JJ. Embryonic staging system for the short-tailed fruit bat, Carollia perspicillata, a model organism for the mammalian order Chiroptera, based upon timed pregnancies in captive-bred animals. Dev Dyn. 2005;233(3):721–38.

extract_protocol:
Limbs were removed from embryos and stored in RNALater in -20° C until further processing. RNA was extracted from tissues using E.Z.N.A. Total RNA Kit I (OMEGA bio-tek #R6834), and converted into RNASeq libraries with the Illumina TruSeq RNA Sample Preparation Kit (Illumina RS-122-2001).
Libraries were sequenced on an Illumina HiSeq 2500 housed in the Roy G. Carver Biotechnology Center at the University of Illinois.

value: hind-limb


title: L_M_negative_rep2

city: Vilnius

first: Elena

last: Serviene

address: Akademijos 2

country: Lithuania

institute: Nature Research Centre

data_processing:
Sequenced reads were trimmed for adaptor sequence, and for low-complexity or low-quality sequence, then mapped to S288C reference genome using CLC Genomics workbench v8.5 with the following alignment parameters: maximum number of mismatches 2; minimum length fraction 0.9; minimum identity within the mapped sequence 0.95; maximum number of best-scoring hits for a read 30.
The expression values for each transcript were calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using CLC Genomic workbench v8.5
Genome_build: sacCer3
Supplementary_files_format_and_content: .txt files report abundance measurements

organism: Saccharomyces cerevisiae

source_name: L_M_negative yeast cells

extract_protocol:
The total RNA was isolated using GeneJET RNA Purification Kit (Thermo Fisher), according to the Yeast Total RNA Purification Protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: infection

tag: cell type

value: yeast cells


title: mouse_HL_W6_rep4


title: mouse_HL_W3_4_rep3


title: L_M_negative_rep3


title: mouse_HL_W3_4_rep1


title: L_M_negative_rep1


title: L_positive_M_negative_rep2

source_name: L_positive_M_negative yeast cells


title: mouse_HL_W3_4_rep2


title: L_positive_M_negative_rep1


title: L_positive_M_negative_rep3


title: mouse_HL_W2_rep1


title: mouse_HL_W2_rep2


title: L_M_positive_rep3

source_name: L_M_positive yeast cells

value: M437 (wt HM/HM [kil-K2])


title: mouse_FL_W2_rep3

value: fore-limb


title: L_M_positive_rep2


title: L_M_positive_rep1


title: mouse_HL_W6_rep3


title: mouse_HL_W6_rep1


title: mouse_FL_W2_rep1


title: mouse_FL_W2_rep2


title: PSF-1

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description:
PSF CLIP-seq 1
PSF_fwd.bigWig
PSF_rev.bigWig

data_processing:
For each CLIP-seq read, the first 4nt index sequence was extracted and the 3'-adaptor sequence CTCGTATGCCGTCTTCTGCTTG was removed with program cutadapt (version 1.8.3). The reads with at least 18nt were mapped to the human genome (hg19) by Bowtie (version 1.1.1) with parameters '-l25 -n2 -k1 -m10 -e 200 --best --strata'.
For each small RNA-seq read, the firsst 5nt NNNTC was extracted and 3' adaptor sequence 'NNCTCGTATGCCGTCTTCTGCTTG' was removed with program cutadapt (version 1.8.3). The target insert sequences were required to be at least 16 nt. The filtered reads were mapped to the genome genome (hg19) by Bowtie (version 1.1.1) with parameters '-n 0 -e 80 -l 18 -a -m 5 --best --strata'.
The mapped reads were used to generate the genomic coverage profiles in bigWig format with programs genomeCoverageBed (bedtools version 2.24) and samtools (version 0.1.19).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig for coverage in both strands

source_name: cervical adenocarcinoma

growth_protocol: HeLa cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS) plus 100 U penicillin/streptomycin (Gibico) at 37oC in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted by TRIZOL reagent.  For CLIP-seq, HeLa cells were UV irradiated at 400 mj and collected by scraping the cells from 15 cm plates. Cell lysis was treated by RQI DNAse to digest genomic DNA and the supernatant was collected for subsequent immunoprecipitation. For each immunoprecipitation, 2µg NONO or PSF antibody was incubated with 200µl Dynabeads (Invitrogen) for 2hrs at 4℃. Then, cell lysis was added to the washed beads and rotated with the beads for another 2-4hrs at 4℃. 3' linker was ligated to RNA on the Immunoprecipitated protein-RNA complex. After western blotting onto nitrocellulose, recovery of protein-RNA complex, and removal of proteins by proteinse K digestion, a 5'linker was ligated to RNA.
Isolated total RNA (5-8 μg) was mixed with 10 μM pre-adenylated 3’ linker in 1x RNA ligase buffer containing 50% (w/v) PEG 8000, 1 μl RNase inhibitor, and 1 μl T4 RNA ligase 2 (NEB), and incubated at room temperature for 1 hrs, then at 16℃ for 3 hrs.  After 3’ linker ligation, the reaction was size fractionated on 15% polyacrylamide gel and RNAs between 42 to 54 nt were recovered by incubating the corresponding gel slice at 4oC in 600 μl of 0.3 M NaCl with constant agitation.  5’ linker ligation was next performed in 1x RNA ligase buffer containing 50% (w/v) PEG 8000, 1 mM ATP, 10 μM 5’ linker, 1 μl RNase inhibitor and 1 μl T4 RNA ligase 1 (NEB) at 37℃ for 4 hrs.  Linker-ligated RNAs were reverse transcribed with Superscript III (Life Technology) and PCR-amplified with Phusion polymerase (ThermoFisher).  The product was fractionated on 4% agarose gel and recovered DNA was quantified for deep sequencing.  And for CLIP-seq, immunoprecipitated RNA was extracted using Trizol, and after DNase I (Promega) treatment, RNA was reverse transcribed into cDNA using superscript III with random primer. The resulting cDNA was quantified for deep sequencing.
small RNA-seq and CLIP-seq

treatment_protocol: siRNA were transfected into cells with  RNAi Max. Cells were harvested 72 hrs post-transfection for subsequent analysis.  There is no treatment to wild type cell for CLIP-seq.

value: HeLa cell

value: PSF


title: RhoJ KO rep 4

city: Irvine

first: Anand

last: Ganesan

address: 836 Health Science Rd

department: Dermatology

institute: University of California, Irvine

data_processing:
Paired-end sequencing reads were analyzed for quality using the Fastqc program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and aligned to the mouse reference genome version mm10 using the Tophat alignment software (version 2.0.12). Tophat2 parameters include -T –G mm10.gtf -o [SampleName]_thout
The Deseq2 library of the R statistical environment was used for differential gene expression analysis of mapped read counts.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values files include base mean, log2 fold change, log fold change standard error (lfcSE), stat (Wald statistic), pvalue, padj (Benjamini-Hochberg).

source_name: mouse primary tumor

extract_protocol:
Skin samples were homogenized using the Precellys24 high-throughput tissue homogenizer in hard tissue homogenizing reinforced tubes that contain 2.8 mm ceramic beads. RNA was extracted using the Rneasy Firous Tissue Mini Kit according to the manufacturer's instructions.
Library construction was performed according to the Illumina TruSeq RNA v2 protocol. Briefly, the input quantity for total RNA was 1g and mRNA was enriched using oligo dT magnetic beads. The enriched mRNA was chemically fragmented for four minutes. First strand synthesis used random primers and reverse transcriptase to make cDNA. After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated. Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.

treatment_protocol: Mice were treated with 4-hydroxytamoxifen at P2, P3, and P4 to indcue tumor growth

tag: genotype

value: Braf CA/+; PTEN fl/+; Cre; RhoJ -/-


title: PSF-2

description:
PSF CLIP-seq 2
PSF_fwd.bigWig
PSF_rev.bigWig

tag: antibody


title: RhoJ KO rep 5


title: WT_NT_H3K4me3_Rep1


title: NONO-1

description:
NONO CLIP-seq 1
NONO_fwd.bigWig
NONO_rev.bigWig

value: NONO


title: RhoJ KO rep 2


title: RhoJ WT rep 5

value: Braf CA/+; PTEN fl/+; Cre; RhoJ +/+


title: siNONO-2

description:
small RNA-seq under NONO knockdown 2
siNONO_fwd.bigWig
siNONO_rev.bigWig

tag: sirna

value: siNONO


title: siPSF-1

description:
small RNA-seq under PSF knockdown 1
siPSF_fwd.bigWig
siPSF_rev.bigWig

value: siPSF


title: siPSF-2

description:
small RNA-seq under PSF knockdown 2
siPSF_fwd.bigWig
siPSF_rev.bigWig


title: RhoJ KO rep 1


title: RhoJ WT rep 2


title: siPSPC1-1

description:
small RNA-seq under PSPC1 knockdown 1
siPSPC1_fwd.bigWig
siPSPC1_rev.bigWig


title: siNONO-1

description:
small RNA-seq under NONO knockdown 1
siNONO_fwd.bigWig
siNONO_rev.bigWig


title: RhoJ WT rep 4


title: RhoJ WT rep 3


title: siNEAT1_V2-2

description:
small RNA-seq under NEAT1_V2 knockdown 2
siNEAT1_V2_fwd.bigWig
siNEAT1_V2_rev.bigWig


title: RNA_P5_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the UCSC mm10 genome assembly using STAR (v2.5.2a) with default settings.
Only the reads with no more than  2 bp mismatches and uniquely mapped to reference genome were kept by using Bash Shell.
Differentially expressed genes are analyzed using featureCounts (v1.5.0-p2) and DESeq2 (v1.12.3).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Peking University and Boston Children’s Hospital.

extract_protocol:
mRNA was isolated from total RNA using Dynabeads Oligo(dT), followed by first and second strands synthesis. RNA-seq libraries were prepared from fragmented double-stranded cDNA using ScriptSeq v2 (Epicenter)
RNA-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit.
2 independent RNA-seq samples were used for one single RNA-seq library preparation

treatment_protocol: mice were injected with AAV9 by intraperitoneal or intravascular injection where indicated as described previously (Lin, et al. Circ Res. 2015)

value: Heart

value: WT P5 heart apex

tag: genotype/variation

value: WT

tag: injected with

value: No


title: RhoJ WT rep 1


title: RNA_P5_rep1


title: siNEAT1_V2-1

description:
small RNA-seq under NEAT1_V2 knockdown 1
siNEAT1_V2_fwd.bigWig
siNEAT1_V2_rev.bigWig


title: siNEAT1-2

description:
small RNA-seq under NEAT1 knockdown 2
siNEAT1_fwd.bigWig
siNEAT1_rev.bigWig


title: RNA_P13_AAVGFP_P10MI_rep2

value: GFP overexpression P13 heart apex suffered MI at P10

value: AAV-GFP


title: NONO-2

description:
NONO CLIP-seq 2
NONO_fwd.bigWig
NONO_rev.bigWig


title: RNA_P13_AAVGFP_P10MI_rep1


title: RhoJ KO rep 3


title: siNEAT1-1

description:
small RNA-seq under NEAT1 knockdown 1
siNEAT1_fwd.bigWig
siNEAT1_rev.bigWig


title: siGFP-2

description:
small RNA-seq WT 2
siGFP_fwd.bigWig,
siGFP_rev.bigWig

value: siGFP(control)


title: siGFP-1

description:
small RNA-seq WT 1
siGFP_fwd.bigWig,
siGFP_rev.bigWig

value: siGFP(control )


title: siPSPC1-2

description:
small RNA-seq under PSPC1 knockdown 2
siPSPC1_fwd.bigWig
siPSPC1_rev.bigWig


title: bat_HL_15_rep2

organism: Carollia perspicillata

value: hind-limb


title: RNA_P13_AAVEZH1_P10MI_rep2

value: EZH1 overexpression P13 heart apex suffered MI at P10


title: RNA_P13_AAVEZH1_P10MI_rep1


title: RNA_P12_rep2

value: sham-WT P12  heart apex


title: bat_HL_15_rep1


title: bat_HL_14_rep3


title: RNA_E12.5_WT_rep1

value: WT E12.5 heart ventricular


title: RNA_E12.5_WT_rep2


title: RNA_E12.5_E2KO_rep2

value: EZH2 knock out E12.5 heart ventricular

value: EZH2 Knockout


title: bat_HL_13_rep3


title: bat_HL_13_rep2


title: bat_HL_14_rep2


title: RNA_E12.5_E1KO_rep2

value: EZH1 knock out E12.5 heart ventricular

value: EZH1 Knockout


title: bat_HL_14_rep1


title: RNA_E12.5_E1KO_rep1


title: bat_FL_14_rep3

value: fore-limb


title: bat_HL_13_rep1


title: bat_FL_13_rep3


title: bat_FL_13_rep1


title: RNA_E12.5_DKO_rep2

value: Heart

value: DKO E12.5 heart ventricular

value: EZH1-EZH2 Double Knockout


title: RNA_E12.5_DKO_rep1

value: No


title: input_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the UCSC mm10 genome assembly using bwa 0.7.12 with default settings.
Only the reads with no more than  2bp  mismatches and uniquely mapped to reference genome were kept by using Bash Shell.
Peaks were called using MACS2 (version 2.1.0) with the following setting:  –keep-dup=1, --broad .
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit.
2 independent ChIP samples were used for one single ChIP-seq library preparation

value: the heart apex below the ligation site

value: WT

value: Mix

value: input


title: input_rep1


title: H3K27me3_P13_AAVGFP_P10MI_rep2

value: AAV-GFP

value: H3K27me3 (millipore 07-449)


title: bat_FL_13_rep2


title: H3K27me3_P13_AAVGFP_P10MI_rep1


title: RNA_E12.5_E2KO_rep1


title: RNA_P12_rep1

value: sham-WT P12  heart apex


title: H3K27ac_P13_AAVEZH1_P10MI_rep2

value: H3K27ac (active motif cat#:39133)


title: H3K27ac_P13_AAVGFP_P10MI_rep1


title: H3K27me3_P13_AAVEZH1_P10MI_rep2


title: EZH1_P13_AAVGFP_P10MI_rep2

value: EZH1 (a gitf from Jian Xu)


title: EZH1_P13_AAVEZH1_P10MI_rep2


title: EZH1_P13_AAVEZH1_P10MI_rep1


title: EZH1_P13_AAVGFP_P10MI_rep1


title: H3K27me3_P13_AAVEZH1_P10MI_rep1


title: H3K27ac_P13_AAVEZH1_P10MI_rep1


title: 8467_S12_RNAseq

city: Beijing

first: Weilong

last: Guo

address: Intergrated Science Building

institute: Peking University

description:
Processed data file: mouse_RNAseq_summary.txt
8467_S12

data_processing:
The mice RNA-seq data were 100bp paired-end and mapped to mm9 using tophat (v2.0.13) utilizing bowtie with defaullt parameters. The 22Rv1 human cell line RNA-seq data were 100bp paired-end and mapped to Hg19 using TOPHAT2.
The FPKMs were calculated and normalized by cufflinks (v2.2.1).
The differentially transcribed gene analysis was carried out by cuffdiff.
For the 22Rv1 isogenic cell clones RNA-seq raw data were aligned to the human genome GRCh37.61 using TopHat (v2.0.7) with default parameters and transcripts were assembled based on Homo_sapiens.
GRCh37.61.gtf file. Relative expression level, represented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM), were estimated by cufflinks v2.2.1 and normalized against total mapped reads per sample.
Genome_build: mm9 for mice, hg19 for humans
Supplementary_files_format_and_content: [.txt] tab-delimited text files include FPKM values for each Sample.

source_name: murine right anterior lobes

extract_protocol:
RNA extraction was performed by the UCLA Clinical Microarray Core (http://pathology.ucla.edu/cmc). For 22Rv1 cells RNA was extracted using the Quick RNA kit (Zymo Research).
RNA quality control, library preparation, and sequencing were performed by the UCLA Clinical Microarray Core (http://pathology.ucla.edu/cmc) and Tumor profiling Unit at the ICR (http://www.icr.ac.uk/our-research/our-research-centres/tumour-profiling-unit).

tag: group

value: prostate, right anterior lobe


title: 6322_S6_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
6322_S6


title: 6320_S4_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
6320_S4


title: 8470_S14_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
8470_S14


title: M3748_S17_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
M3748_S17


title: M3765_S18_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
M3765_S18


title: 8468_S13_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
8468_S13


title: 6317_S1_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
6317_S1


title: 6323_S7_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
6323_S7


title: 6321_S5_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
6321_S5


title: Xh_03_Right

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

institute: MIT Lincoln Laboratory

description: control

data_processing:
RNA data in BAM format was aligned to the reference mouse genome (mm9) using the TopHat aligner
The aligned reads were then analyzed with the Cufflinks 21 software suite (v2.1.1)
Cuffmerge was applied to the assembled transcripts to create a single merged transcriptome annotation for each condition (injured or control)
Cuffdiff was used to find differentially expressed genes and isoforms across time points and conditions, as well as detect differential splicing and alternative promoter usage
CummeRBund R package was used to compute statistics on differentially expressed genes and isoforms
Genome_build: mouse genome (mm9)
Supplementary_files_format_and_content: Excel format - one worksheet for genes and one worksheet for isoforms

source_name: tibialis anterior muscle

extract_protocol:
Total RNA was isolated from the homogenized tissue in Trizol using the miRNeasy Mini Kit (Qiagen) as per the manufacturer’s instructions
At least 1 μg of isolated total RNA was used to produce strand-specific cDNA libraries using the Truseq protocol, as per the manufacturer’s instructions and previously described [Levin et al. 2010]

treatment_protocol: Freeze injury was induced by applying a 6 mm diameter steel probe (cooled to the temperature of dry ice, −70C) to the belly of the TA muscle (directly below incision site) for 10 seconds

value: tibialis anterior muscle

tag: timepoint

value: unknown

tag: treatment

value: control


title: 72h_05_Right

description: 72 hours control

tag: tissue

value: 72 hours


title: Os_root.tip.ATAC_rep1

tag: strain/background

value: Nipponbare

tag: tissue or cell type

value: 1 cm root tip

tag: nuclei purification method

value: INTACT streptavidin affinity purification


title: 72h_05_Left

description: 72 hours injured

value: freeze injury


title: 72h_04_Right

description: 72 hours control


title: H3K27ac_P13_AAVGFP_P10MI_rep2

value: Heart

value: the heart apex below the ligation site

tag: developmental stage

value: WT


title: 72h_03_Right

description: 72 hours control


title: 72h_02_Right

description: 72 hours control


title: 72h_04_Left

description: 72 hours injured


title: 72h_03_Left

description: 72 hours injured


title: 6319_S3_RNAseq

description:
Processed data file: mouse_RNAseq_summary.txt
6319_S3


title: 72h_01_Left

description: 72 hours injured


title: 72h_01_Right

description: 72 hours control


title: 48h_05_Right

description: 48 hours control

value: 48 hours


title: 72h_02_Left

description: 72 hours injured


title: 48h_01_Right

description: 48 hours control


title: 48h_05_Left

description: 48 hours injured


title: 28d_05_Right

description: 28 days control

value: 28 days


title: 48h_02_Right

description: 48 hours control


title: 48h_04_Left

description: 48 hours injured


title: 48h_04_Right

description: 48 hours control


title: 28d_05_Left

description: 28 days injured


title: 28d_04_Right

description: 28 days control


title: 48h_01_Left

description: 48 hours injured


title: 28d_03_Left

description: 28 days injured


title: 28d_02_Right

description: 28 days control


title: 28d_01_Right

description: 28 days control


title: 28d_04_Left

description: 28 days injured


title: 24h_05_Left

description: 24 hours injured

value: 24 hours


title: 24h_05_Right

description: 24 hours control


title: 28d_02_Left

description: 28 days injured


title: 28d_03_Right

description: 28 days control


title: 24h_03_Right_B

description: 24 hours control


title: 24h_04_Left

description: 24 hours injured


title: 24h_04_Right

description: 24 hours control


title: 24h_03_Right_A

description: 24 hours control


title: 28d_01_Left

description: 28 days injured


title: 24h_03_Left_B

description: 24 hours injured


title: 24h_02_Left

description: 24 hours injured


title: 24h_03_Left_A

description: 24 hours injured


title: 24h_02_Right

description: 24 hours control


title: 24h_01_Right

description: 24 hours control


title: 21d_05_Right

description: 21 days control

value: 21 days


title: 21d_04_Right

description: 21 days control


title: 21d_01_Right

description: 21 days control


title: 21d_04_Left

description: 21 days injured


title: 21d_01_Left

description: 21 days injured


title: 14d_05_Right

description: 14 days control

value: 14 days


title: 14d_05_Left

description: 14 days injured


title: 14d_04_Right

description: 14 days control


title: 14d_04_Left

description: 14 days injured


title: 14d_03_Right

description: 14 days control


title: 14d_03_Left

description: 14 days injured


title: 14d_02_Left

description: 14 days injured


title: 14d_02_Right

description: 14 days control


title: 14d_01_Left

description: 14 days injured


title: 10h_16_Left

description: 10 hours injured

value: 10 hours


title: 10h_15_Left

description: 10 hours injured

value: tibialis anterior muscle


title: 10h_16_Right

description: 10 hours control


title: RNA-seq_ZT10_HDAC3_KO_rep3

description: processed data file: DEseq2_HDAC3_KO_PROX1_KD.xlsx

value: liver

tag: age

value: 10 weeks old

tag: gender

value: male


title: 14d_01_Right

description: 14 days control

value: control


title: 10h_05_Right

description: 10 hours control


title: 10h_15_Right

description: 10 hours control


title: 10h_04_Right

description: 10 hours control


title: RNA-seq_ZT10_HDAC3_KO_rep2

tag: strain


title: 24h_01_Left

description: 24 hours injured


title: 10h_05_Left

description: 10 hours injured


title: 21d_05_Left

description: 21 days injured


title: RNA-seq_ZT10_HDAC3_KO_rep1


title: 10h_04_Left

description: 10 hours injured


title: 10h_03_Right

description: 10 hours control


title: RNA-seq_ZT10_WT_rep1


title: 21d_03_Left

description: 21 days injured


title: 10h_02_Right

description: 10 hours control


title: 10h_03_Left

description: 10 hours injured


title: 10h_02_Left

description: 10 hours injured


title: H3K27Ac_ChIP-seq_ZT10_shProx1

value: 14 weeks old


title: H3K27Ac_ChIP-seq_ZT10_HDAC3_KO


title: H3K27Ac_ChIP-seq_ZT10_WT


title: 10h_01_Left

description: 10 hours injured


title: 07d_11_Right

description: 7 days control

value: 7 days


title: 07d_11_Left

description: 7 days injured

value: freeze injury


title: IgG_ChIP-seq_ZT10_WT

value: IgG


title: HNF4A_ChIP-seq_ZT10_HNF4A_floxed_liver_KO_rep1


title: HNF4A_ChIP-seq_ZT10_HNF4A_floxed_liver_KO_rep2


title: 07d_10_Right

description: 7 days control


title: PROX1_ChIP-seq_ZT10_HNF4A_floxed_liver_KO_rep1


title: 07d_10_Left

description: 7 days injured


title: HDAC3_ChIP-seq_ZT10_HNF4A_floxed_liver_KO_rep2


title: 07d_05_Right

description: 7 days control


title: HDAC3_ChIP-seq_ZT10_HNF4A_floxed_liver_KO_rep1


title: 07d_05_Left

description: 7 days injured


title: HNF4A_ChIP-seq_ZT10_HNF4A_floxed_rep2


title: RNA-seq_ZT10_WT_rep2


title: 07d_04_Right

description: 7 days control


title: 07d_04_Left

description: 7 days injured


title: H3K27Ac_ChIP-seq_ZT10_shLuciferase


title: HNF4A_ChIP-seq_ZT10_HNF4A_floxed_rep1


title: PROX1_ChIP-seq_ZT10_HNF4A_floxed_liver_KO_rep2


title: 10h_01_Right

description: 10 hours control


title: 07d_03_Left

description: 7 days injured


title: PROX1_ChIP-seq_ZT10_HNF4A_floxed_rep2


title: PROX1_ChIP-seq_ZT10_HNF4A_floxed_rep1


title: 07d_02_Right

description: 7 days control


title: HDAC3_ChIP-seq_ZT10_HNF4A_floxed_rep1


title: HDAC3_ChIP-seq_ZT10_HNF4A_floxed_rep2


title: 03h_15_Right

description: 3 hours control

value: 3 hours


title: PROX1_ChIP-seq_ZT10_Control_rep3


title: 03h_14_Left

description: 3 hours injured


title: 03h_14_Right

description: 3 hours control


title: PROX1_ChIP-seq_ZT10_Control_rep1


title: 03h_12_Right

description: 3 hours control


title: HDAC3_ChIP-seq_ZT10_Control_rep2


title: 03h_12_Left

description: 3 hours injured


title: HDAC3_ChIP-seq_ZT10_Control_rep1


title: 03h_11_Right

description: 3 hours control


title: 07d_03_Right

description: 7 days control


title: 03h_11_Left

description: 3 hours injured


title: 03h_10_Right

description: 3 hours control


title: 07d_02_Left

description: 7 days injured


title: 2011-024 (FECD with expansion)

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling Illumina CASAVA v1.8.2
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The sequencing reads were processed by MAP-RSeq v.1.2 workflow [1], the Mayo Bioinformatics Core pipeline. The alignment in MAPRseq was performed with TopHat 2.0.6 and the gene counts was obtained using HTSeq-count v0.5.3p9
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file includes raw gene counts

source_name: FECD with expansion

extract_protocol:
RNA was extracted using QIAzol and QIAcube. As part of the QIAcube process, RNA was treated with DNase and then eluted in 30  l of RNase-free 1  Tris/EDTA buffer. 2 ng of totalRNAwas used to preparecDNA using an iScript cDNA synthesis kit (Bio-Rad). RT-PCR was performed using a Platinum PCR SuperMix High Fidelity kit (Invitrogen) and primer sets described previously (19, 20). Products were analyzed by electrophoresis on 2% agarose gels and stained with ethidium bromide.
RNA libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA). Briefly, poly(A) mRNA was purified from total RNA using oligo(dT) magnetic beads, fragmented at 95 °C for 8 min, eluted from the beads, and primed for first-strand cDNA synthesis using SuperScript III reverse transcriptase and random primers (Invitrogen). Second- strand cDNA synthesis was performed using DNA polymerase I and RNase H, and double-stranded cDNA was purified using a single AMPure XP bead cleanup step (Agencourt, Danvers, MA). The cDNA ends were repaired and phosphorylated using Klenow fragment, T4 polymerase, and T4 polynucleotide kinase, followed by a single AMPure XP bead cleanup step. The blunt-ended cDNAs were modified to include a single 3 -adenylate residue using Klenow exo  (3  to 5  exo ), and paired-end DNA adaptors (Illumina) with a single T base overhang at the 3 -end were ligated to the A-tailed cDNA population. Unique indexes, included in the standard TruSeq kits (12- Set A and 12-Set B), were incorporated at the adaptor ligation step for multiplex sample loading on the flow cells. The resulting constructs were purified by two consecutive AMPure XP bead cleanup steps and enriched by 12 cycles of PCR using primers included in TruSeq RNA Sample Prep Kit v2. Libraries were loaded onto paired-end flow cells at concentrations of 8?10 pM to generate cluster densities of 700,000/mm2 using cBot and cBot Paired-end Cluster Kit v3 (Illumina) following the manufacturer?s standard protocol. The flow cells were sequenced as 51   2 paired-end reads on an Illumina HiSeq 2000 system using TruSeq SBS Sequencing Kit v3 and SCS v1.4.8 data collection software.

tag: subject status

value: Fuchs endothelial corneal dystrophy

value: corneal endothelium


title: 2011-041 (FECD with expansion)


title: 6004


title: Control 2

source_name: Normal


title: 2011-038 (FECD with expansion)


title: Control 1


title: 2011-020 (FECD with expansion)


title: 03h_15_Left

description: 3 hours injured


title: MM1.S/Vector 2nd sample

first: Xuewei

last: Wang

address: 200 1st street

description:
s_MM1_S_pCDH_d3_ist
Processed data file: FAM46C_RPKM.txt

data_processing:
Base calling by CASAVA.
Alignment by Tophat2.
Gene count by featureCount.
Normalization by edgeR.
All above steps are wrapped in an interal workflow (MAPRSeq).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FAM46C_RPKM.txt: Tab-delimited text file includes gene RPKM values.

source_name: patient-derived multiple myeloma cell line

growth_protocol: Cells were maintained in RPMI-1640 media, supplemented with 5% of sterile fetal calf serum and antibiotics.

extract_protocol:
Total RNA was prepared using RNeasy plus kit under the protocols of the manufacturer (Qiagen, Valencia, CA).
Libraries were constructed.

tag: cell line

tag: cell type

value: multiple myeloma cell line

tag: lentivrius

value: vector


title: MM1.S/Vector 1st sample

description:
s_Vec_MM1_S_d3
Processed data file: FAM46C_RPKM.txt


title: PROX1_ChIP-seq_ZT10_Control_rep2

tag: antibody


title: evglu 1

city: New York

first: Ivan

last: Gusarov

state: NY

address: 450E 29th street

department: Biochemistry

institute: NYU School of Medicine

data_processing:
basecalls performed by basespace (Illumina)
reads alignment, transcripts assembly and quantification and differential expression analysis were performed using tuxedo software suite (v2.1.1). Read were aligned to known transcriptome of WS220 C.elegans genome assembly (Ensembl) using tophat with the following paramters: --b2-sensitive, --no-novel junctions.
Transcripts assembly and quantification was performed by cufflinks with default parameters.
Differential expression analysis was performed by cuffdiff with default parameters.
Genome_build: Ensembl WS220
Supplementary_files_format_and_content: gene_exp.diff, genes.fpkm_tracking

source_name: whole body

growth_protocol: worms were grown on NGM seeded with E.coli OP50 at 20oC

extract_protocol:
Worms were picked, washed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Glucose was mixed in the NGM media

value: one day old adults

tag: media

value: NGM+ 2%Glucose


title: KMS11/Vector 2nd sample

description:
s_KMS11_pCDH_d3_2nd
Processed data file: FAM46C_RPKM.txt


title: HDAC3_ChIP-seq_ZT10_Control_rep3


title: KMS11/FAM46C 2nd sample

description:
s_KMS11_FAM46C_d3_2nd
Processed data file: FAM46C_RPKM.txt


title: At_genomic.DNA.ATAC

description: gDNA

data_processing:
Raw reads were aligned to the appropriate genome using Bowtie2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks (transposase hypersensitive sites; THSs) were identified using the Findpeaks function of the Homer package, with the parameters "-region" and "-minDist 150". Bed files of the THS regions are included for each dataset.
Genome_build: Arabidopsis thaliana TAIR10, Medicago truncatula Mt4.0, Solanum lycopersicum SL2.4, and Oryza sativa IRGSP 1.0.30
Supplementary_files_format_and_content: .bed files containing ATAC-seq transposase hypersensitive site locations as defined using the findPeaks function of the Homer software package.

organism: Arabidopsis thaliana

source_name: Purified genomic DNA


title: KMS11/FAM46C 1st sample

description:
s_KMS11_FAM46C_d3_1st
Processed data file: FAM46C_RPKM.txt


title: WT3_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
WT3

tag: group

tag: genotype/variation

value: WT

value: prostate carcinoma epithelial cell line 22Rv1


title: WT2_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
WT2


title: At_root.hair.cell.ATAC_rep2

source_name: Root hair cell

value: Fully differentiated root epidermal hair cell

value: INTACT streptavidin affinity purification


title: At_root.non.hair.cell.ATAC_rep2

source_name: Root non-hair cell

value: Fully differentiated root epidermal non-hair cell


title: 3G113_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
3G11c


title: MM1.S/FAM46C 2nd sample

description:
s_MM1_S_FAM46C_1st
Processed data file: FAM46C_RPKM.txt


title: At_root.tip.ATAC_Crude_rep2

source_name: Root tip

value: 1 cm root tip

value: Sucrose sedimentation


title: MM1.S/FAM46C 1st sample

description:
s_FAM46C_MM1_S_d3
Processed data file: FAM46C_RPKM.txt


title: 3G112_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
3G11b


title: 1E63_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
1E63


title: 1E62_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
1E62


title: At_root.non.hair.cell.ATAC_rep1


title: KMS11/Vector 1st sample

description:
s_KMS11_pCDH_d3_1st
Processed data file: FAM46C_RPKM.txt


title: At_root.tip.ATAC_rep1


title: At_root.tip.ATAC_Crude_rep1


title: pig_HL_26_rep2

organism: Sus scrofa

value: hind-limb


title: pig_HL_26_rep4


title: pig_HL_26_rep3


title: At_root.tip.ATAC_rep2


title: 3G111_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
3G11a


title: 1E61_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
1E61


title: opossum_HL_32_2

organism: Monodelphis domestica


title: opossum_HL_32_1


title: WT1_RNAseq

description:
Processed data file: human_RNAseq_summary.txt
WT1


title: At_root.hair.cell.ATAC_rep1


title: pig_HL_26_rep1


title: opossum_HL_32_3


title: opossum_HL_31_5


title: opossum_HL_31_4


title: pig_HL_22_rep3


title: opossum_HL_31_2


title: pig_HL_22_rep2


title: opossum_HL_31_1


title: pig_HL_22_rep1


title: opossum_HL_30_3


title: pig_HL_20_rep2


title: opossum_HL_30_2


title: opossum_HL_30_1


title: opossum_FL_27_3

value: fore-limb


title: pig_FL_26_rep2


title: pig_FL_22_rep3


title: pig_FL_26_rep4


title: Mt_root.tip.ATAC_rep2

organism: Medicago truncatula


title: Strain showing downregulation of celA rep1

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

description: Strain showing deletion of celA rep1

data_processing:
Raw FASTA files were imported in CLC Genomics Workbench 9.0.1. Sequences were filtered and trimmed according to the following criteria: sequence length>35bp, sequence quality score <0.01, no ambiguity in the sequence, trimming using Illumina adaptors, hard trim of 8 base pairs (bp) at the 5’ end and 2 bp at the 3’ end, resulting in a longest length of 64 bp.
For each library, the mapping was performed with the following settings: a maximum hit per reads of 3, similarity fraction=0.9, a length fraction=0.9, a mismatch, insertion and deletion cost of 3 (stringent mapping). The expression values were then calculated using the RPKM method (Mortazavi et al., 2008).
In order to highlight the differentially expressed genes, a t-test with 2 groups (control and celA-) each composed of three biological replicates was performed. Only genes with a p-value below 0.05 were selected. A cut-off threshold was also applied to the fold change (log2 FC absolute value>1).
Genome_build: The A. nidulans FGSC A4 reference transcriptome was downloaded at the Aspergillus Genome Database site http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/current/
Supplementary_files_format_and_content: The tab-delimited text file includes: Transcript IDr, p-value, Gene symbol,  Gene annotation,  Unique gene reads, RPKM values for each sample, average of the three biological replicates, Gene size.

organism: Aspergillus nidulans

source_name: Strain showing downregulation of celA

growth_protocol:
The strain used in this study is SAA.111 (genotype veA1; biA1; ΔargB :: trpC; riboB2; pyroA4; wA3) and it was grown according to Bernreiter et al. (2007).
Minimal medium was prepared with 0.4% w/v glucose as C source and ammonium tartrate at final concentration of 10 mM as N source. Trace metal solution  0.02% v/v was supplemented to the medium.

extract_protocol:
Total RNA from mycelia was extracted from 100 mg of finely ground tissue, by using the RNeasy Plant Mini Kit (Qiagen), coupled with the on-column DNaseI digestion. RNA Integrity was measured using the Agilent bioanalyzer and RNA integrity numbers (RINs) were >7 for all the samples. RNA concentrations were measured using a ND-1000 spectrophotometer (NanoDrop). One microgram of extracted RNA was retro-transcribed using the ProtoScript II Reverse Transcriptase (NEB) following the manufacturer’s instructions.
Libraries were prepared from 3µg of total RNA extracted from the mycelium after 3 days of growth at 37°C with the SMARTer Stranded RNA-Seq kit (Clontech). The isolation of mRNAs was performed using the Illumina beads and the TruSeq protocol (Illumina), as described in Behr et al. (2016). The synthesis of cDNA and shearing were performed with ten ng mRNA, according to the manufacturer’s instruction. The enrichment step was carried out using 14 cycles of PCR. The libraries were then checked using a 2100 Bioanalyzer (DNA High sensitivity Kit) to estimate the average fragment size. Library quantification was performed using the KAPA library quantification kit (KAPA Biosystems) and a ViiA7 Real-Time PCR System (Life technologies). The pooled libraries (at a concentration of 20 pM) were sequenced on an Illumina MiSeq (MiSeq reagent kit V3, 150 cycles) generating 76 base pairs paired-end reads.

treatment_protocol: Gene replacement of ANIA_08444 was performed with the double joint-PCR (DJ-PCR), as described in Yu et al. (2004): the cassette containing the selectable marker argB (ANIA_04409) was inserted to replace the entire locus ANIA_08444.

value: downregulated celA-

tag: biological replicate

tag: growth conditions

value: Mycelium grown in liquid minimal  medium at 37°C for 3 days

value: Mycelium


title: opossum_HL_31_3

tag: tissue


title: opossum_FL_27_1


title: Sl_root.tip.ATAC_rep1

organism: Solanum lycopersicum

extract_protocol:
Tn5 Transposase treatment (using the Illumina Nextera kit) was performed on 50,000 nuclei from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit.
Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.

tag: strain/background

tag: tissue or cell type


title: Mt_root.tip.ATAC_rep1

tag: nuclei purification method


title: Strain showing downregulation of celA rep3

description: Strain showing deletion of celA rep3


title: pig_FL_22_rep2

tag: developmental stage


title: Strain showing downregulation of celA rep2

description: Strain showing deletion of celA rep2


title: pig_HL_20_rep1


title: Sl_root.tip.ATAC_rep2


title: opossum_FL_27_2


title: pig_FL_26_rep3


title: BirA cells_ChIP

status: Public on Jul 25 2017

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using tophat or macs2.
RPKM were calculated using 'cufflinks' and peaks were called using 'callpeak'.
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq, *.fpkm_tracking files from Cufflinks containing FPKM values are provided. For ChIP-seq, peaks.bed files containing peak locations and summits are provided. For ATAC-seq, peaks.txt files containing peak locations are provided.

source_name: BirA cells_mock  control

growth_protocol: The cells were grown in 0/1% gelatin coated dishes. The cells were maintained in either ES+ medium or TS+ meidum.

extract_protocol:
For RNA-seq, total RNAs were extracted using Rneasy plus mini kit (Qiagen).
RNA- and ChIP-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions. ATAC-seq samples were performed as previously described (Buenrostro et al., 2015)

value: BirA cells

tag: chip antibody

value: Dynabeads MyOne Streptavidin T1

tag: chip antibody vendor

value: Invitrogen by Life Technologies

tag: chip antibody cat #

tag: chip antibody lot/batch #


title: TS cells_ChIP

source_name: TS cells

tag: cell type

value: trophoblast stem-like (TS) cells

value: 1:1 mixed with home-made (Webb et al., 2011) and from Santa Cruz Biotechnology


title: OEGata3_TS+_ChIP

value: CAG factor-mediated reprogramming cells

value: Gata3 overexpression

tag: cultured in

value: TS+ media


title: OEArid3a_TS+_ChIP

value: Arid3a overexpression


title: OEGata3_ES+_ChIP

value: ES+ media


title: OECdx2_TS+_ChIP

value: Cdx2 overexpression


title: Control strain SAA.111 rep3

source_name: Control strain SAA.111

value: control


title: Control strain SAA.111 rep2


title: OEArid3a_ES+_ChIP


title: OECdx2_ES+_ChIP


title: ES cells_ChIP

source_name: ES cells

value: J1 embryonic stem cells


title: TS cells_ATAC


title: OEGata3_TS+_ATAC


title: Control strain SAA.111 rep1


title: pig_FL_20_rep1

value: fore-limb


title: OEArid3a_TS+_ATAC


title: OECdx2_ES+_ATAC


title: OEGata3_ES+_ATAC


title: ES cells_ATAC


title: OEArid3a_TS+_RNA


title: OECdx2_TS+_RNA


title: OEArid3a_ES+_ATAC


title: OEArid3a_ES+_RNA


title: OEGata3_TS+_RNA


title: OECdx2_ES+_RNA


title: Ablated_2

city: URBANA

first: Sumbul

last: Khan

address: 601 S. Goodwin Ave, CLSL C615

department: Cell and Development Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
FASTQ Quality Trimmer (v.1.0.0)
Clip (v.1.0.1)
Tophat2 (v.0.6)
Cufflinks (v.0.0.7)
Cuffdiff
Genome_build: Drosophila melanogaster genome (NCBI, build 5.41)

organism: Drosophila melanogaster

source_name: Wing imaginal disc

growth_protocol: Animals were grown at 18 degree C. Tissue ablation was carried out by genetic methods by shifting the temperature to 30 degree C for 24 hours. Wing discs were dissected after 24 hours of recovery when a regenerating blastema is formed. Control animals were treated in the same way, except they did not carry the reaper transgene to induce the ablation.

extract_protocol:
RNA was isolated from the GFP labeled control and regenerating cells.
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles  on a HiSeq2000 using a TruSeq SBS sequencing kit version 3. Fastq files were generated with with Casava 1.8.2

treatment_protocol: Control and regenerating wing discs that carry a GFP transgene expressed in the pouch domain were treated with TrypLE for dissociation into single cells. The GFP labeled cells were isolated through FACS

tag: tissue type

value: Wing imaginal disc

value: GFP labeled regenerating blastema cells


title: ES cells_RNA


title: TS cells_RNA


title: Control_2

value: GFP labeled wing disc pouch cells


title: Ablated_1


title: Control_1


title: MPAT-Seq PDE12-/- + mtPAP

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

institute: University of Cambridge

description:
Sample 12
Pooled DNA Amplicons
targeted resequencing after circularization

data_processing:
qualitiy and adapter trimming performed using Trim_Galore! keeping only reads longer than 20nt
For MPAT-Seq aditional primer trimming using cutadapt
alignment was performed using Bowtie2
For RNAseq reads mapped to 12S or 16S mt-rRNA were removed using Samtools. Rsubread was used to generate count tables and DESeq2 was used for statistical analysis of differential gene expression
Genome_build: GRCh38 (for MPAT, 30 N's were added on the 3' end of the mitochondrial rRNA and tRNA sequences
Supplementary_files_format_and_content: csv

source_name: PDE12-/- + mtPAP

growth_protocol: cells were grown in DMEM + FCS. Overexpression was induced by doxycyline

extract_protocol:
RNA extraction after mitochondrial enrichment. For RNAseq Ribo Zero Gold treatment was performed according to Illumina's protocol to remove rRNA
libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded Total RNA library prep kit
Samples 1-6: RNA-Seq ; samples 7-12 targeted resequencing after circularization

tag: cell line

value: Human embryonic kidney cells 293 (HEK293T)

tag: passages

value: PDE12-/- + mtPAP


title: Ablated_3


title: MPAT-Seq PDE12+/+ + mtPAP

description:
Sample 11
Pooled DNA Amplicons
targeted resequencing after circularization

source_name: PDE12+/+ + mtPAP

tag: genotype/variation

value: PDE12+/+ + mtPAP


title: MPAT-Seq PDE12-/- + WT

description:
Sample 9
Pooled DNA Amplicons
targeted resequencing after circularization


title: MPAT-Seq PDE12-/- + E351A

description:
Sample 10
Pooled DNA Amplicons
targeted resequencing after circularization


title: MPAT-Seq PDE12-/-

description:
Sample 8
Pooled DNA Amplicons
targeted resequencing after circularization


title: RNAseq PDE12-/- repeat 3

description:
Sample 6
mitochondrial-enriched RNA


title: OEGata3_ES+_RNA


title: OECdx2_TS+_ATAC


title: MPAT-Seq PDE12+/+

description:
Sample 7
Pooled DNA Amplicons
targeted resequencing after circularization


title: RNAseq PDE12-/- repeat  1

description:
Sample 4
mitochondrial-enriched RNA


title: RNAseq PDE12+/+repeat  3

description:
Sample 3
mitochondrial-enriched RNA


title: RNAseq PDE12+/+repeat  2

description:
Sample 2
mitochondrial-enriched RNA


title: RNAseq PDE12+/+ repeat 1

description:
Sample 1
mitochondrial-enriched RNA


title: aCM1

city: Catanzaro

first: Daniele

last: Torella

address: Viale Europa

department: Medical and Surgical Sciences

country: Italy

institute: Magna Graecia University

data_processing:
All libraries were sequenced on the Illumina HiSeq 1000 generating 100 bp paired end reads.
RNA-seq has been performed by using StrandNGS with its default parameters
Raw data sequences  have been pre-processed and then been aligned to rattus norvegicus genome (rno5). Parameters have been set as follows: (i) minimum percentage identity = 90 %; (ii) maximum percentage gaps = 5 %; (iii) maximum number of novel splices = 1; (iv) minimum match length = 25.
Reads with less than 5 valid matches have been filtered out, finally obtaining expression values for reads (quantification phase). To detect novel genes and exons we set the parameters, in term of percentile, as follows: minimum exon length equals to 10.0; minimum intron length equals to 10.0; maximum intron length equals to 90.0; minimum gene length equals to 10.0; minimum exon RPKM equals to 50.0, where RPKM, stands for Reads Per Kilo base Per Million reads, used to represent read counts over a region of interest.
Differential expressions were performed using DESeq algorithm, available in StrandNGS. We performed fold change (FC) analysis on filtered expression values using normalized signal values that are in log-scale. We considered a fold change cut off equals to 1.5 to identify up and down regulated genes.
Gene Ontology, DAVID and Ingenuity Pathways Analysis (IPA) have been used to functional enrich the data
Genome_build: rno5
Supplementary_files_format_and_content: The .xls file includes read counts and normalized values for the nCMs, CSCs, iCMs and aCMs samples. It also contains the read counts for cCSCs samples.

organism: Rattus norvegicus

source_name: Adult Cardiomyocytes

extract_protocol:
RNA was extracted from cardiomyocytes and CSCs using TRIzol Reagent (Ambion). The extracted RNA integrity was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and a sample with an RNA Integrity Number greater than or equal to 8 was considered acceptable.
The libraries were generated using depleted RNA obtained from 1μg total RNA by TruSeq Sample Preparation RNA Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer’s without further modifications. The first step involves the removal of ribosomal RNA rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads that depletes samples of both cytoplasmic and mitochondrial rRNA. Following purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter  (Multiple indexing adapters were ligate to the ends of the ds cDNA). The products are purified and enriched with PCR to create the final cDNA library.

tag: strain

value: Wistar

tag: age

value: 12 week-old

value: Adult Cardiomyocytes


title: cCSC1

source_name: clone Cardiac Stem Cells

value: clone Cardiac Stem Cells


title: Control_3


title: cCSC2


title: cCSC3


title: aCM2


title: aCM3


title: Kre33-data-II

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

description:
UV cross-linked RNA
CRAC library

data_processing:
Library strategy: CRAC-seq
CRAC data processing steps: All processing steps were performed using the pyCRAC package version 1.2.2.6. Demultiplexing was performed using pyBarcodeFilter.py (version 2.3.4). 3' adapter removal and 3' end quality trimming (min Phred = 30) was performed using FlexBar (version 2.5). Reads were collapsed using random nucleotides present in 5' barcodes using pyFastqDuplicateRemover.py (version 0.0.2). Reads were mapped to the S. cerevisiae geneome (EF.64; source ENSEMBL) using novoalign (version 2.0.4) and feature counts were generated using pyReadCounters (version 0.5.3). Mapped files were further analyzed using the pyCRAC package.
Genome_build: EF64
Supplementary_files_format_and_content: text files with mapped reads (gtf) and hit-tables generated using pyReadCounters.py from the pyCRAC package

growth_protocol: For each experiment 1000 ml of cells were grown in synthetic medium with glucose (SD-TRP) to exponential phase (OD600 ~0.5) at 30ºC and were UV cross-linked  with 254nm (Granneman et al. PNAS 2009) and then harvested by rapidly passing the cells through a 0.8 µm filter (Millipore) using a home-made vacuum filtration device. This yielded ~0.7g of cells for each prep.

extract_protocol:
Cells were lysed in 1V/w of TN150 (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% NP-40, 5 mM b-mercaptoethanol) and 3V of Zirkonia beads (0.5 mm; Thistle Scientific) as previously described (Granneman et al. PNAS 2009). Three milliliter of lysis buffer was added and extracts were clarified by centrifugation (20 min at 4,500 g and 20 min at 20,000 g at 4 °C). Extracts were incubated with 250 µl of equilibrated IgG Sepharose beads (GE Healthcare) for 2h at 4 °C.
linker ligations were performed as previously described (Granneman et al., PNAS 2009) using adapters provided in the Experimental Procedures of the manuscript. Cross-linked protein-RNA complexes were resolved on 1mm thick 4-12% NuPAGE gels (Thermo Fisher Scientific), transferred to nitrocellulose membranes and visualized by autoradiography. Bands corresponding to the size of the protein of interest, including a region 0.5 cm above the band, were cut from the nitrocellulose membrane. Radiolabeled RNA was extracted by incubating the membrane slices with 200 µg of proteinase K in 800 µl of wash buffer II containing 1% SDS and 5 mM EDTA. The solution was transferred to a new tube and the RNA was subsequently phenol-chloroform-extracted and ethanol-precipitated. Reverse transcription with SuperScript III was performed as per manufacturer's procedures (Thermo Fisher Scientific) using the reverse transcription primer listed in the Experimental Procedures. The cDNAs were purified using the Zymo DNA Clean & Concentrator 5 kit and eluted into a final volume of 10 µl. Five µl of cDNA was PCR amplified using Pfu polymerase (Promega) for 24 cycles (95ºC 30s, 52ºC 30s and 72ºC 1min) using PCR oligonucleotides listed in the Experimental Procedures. PCR products were resolved on 2% Metaphor agarose gels (Lonza) and 180-300 bp fragments were gel purified using the miniElute kit (Qiagen) according to manufacturer’s procedures. Paired-end sequencing (50 bp) was performed by Edinburgh Genomics using the Illumina HiSeq 2500 platform. Data-set II is ~ 5 more complex than Data-set I and used for generating figures.

value: BY4741:MATa; his3delta1; leu2delta0; met15delta0; ura3delta0; KRE33::HTP::klURA3


title: iCM2

source_name: Induced-Cardiomyocytes

value: Induced-Cardiomyocytes


title: CSC2

source_name: Cardiac Stem Cells

value: Cardiac Stem Cells


title: CSC3


title: nCM3

source_name: Neonatal cardiomyocytes

value: 1-2 post-natal day

value: Neonatal cardiomyocytes


title: CSC1 and cCSC4

description: The datasets of CSC1,2 and 3 are from a biological triplicate of the same cardiac stem cell clone. In particular, the dataset of the sample entitled CSC1 has also been used in a different experiment with the title of cCSC4. This dataset was compared with three datasets respectively from three different cardiac stem cell clones (cCSC1, 2, and 3) for clonal identity analysis.


title: nCM2


title: nCM1


title: BMP4_11h

city: Montreal

first: Maxime

last: Bouchard

state: Québec

address: 1160 Pine Avenue West, Rm 408

country: Canada

institute: McGill University

data_processing:
The sequencing reads were trimmed using CutAdapt (Martin, 2011).
Reads were then mapped to the mouse reference genome (mm10) using STAR aligner (version 2.4.0e) (Dobin et al., 2013), with default parameters.
Reads were annotated using the Gencode M2 (version M2, 2013) annotation (Mudge and Harrow, 2015)
Htseq-counts (part of the 'HTSeq' (Anders et al., 2015) framework, version 0.5.4p5.) was used for expression quantification, and DESeq (Anders and Huber, 2010) for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-deliminated text files contain HTSeq counts for each sample

source_name: Mesoderm progenitor cells

growth_protocol: Mesoderm progenitor cells were cultured in media containing DMEM with 10% FBS and 1% penicillin-streptomycin in presence of mitomycin C treated (Sigma- 10ug/ml) mouse embryonic fibroblasts (MEFs) feeder layers, which were obtained from wild type C57Bl/6 mice.

extract_protocol:
Total-RNA was obtained following manufacturers protocol using RNAeasy micro kit (Qiagen)
Sequencing libraries were prepared by Genome Quebec Innovation Centre (Montreal, Canada), using the TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: Co-cultures were incubated at 37oC in 5% CO2 for 96 hours before treatment with recombinant proteins/growth factors.

value: Mesoderm progenitor cells

tag: time in culture

tag: growth factor


title: RNAseq PDE12-/-  repeat 2

description:
Sample 5
mitochondrial-enriched RNA


title: BMP4_FGF4_11h

value: rhBMP4 and rhFGF4


title: BMP4_FGF8_5h

value: rhBMP4 and rhFGF8


title: BMP4_5h


title: 0h_untreated


title: iCM3


title: Kre33-data-I

description:
UV cross-linked RNA
CRAC library


title: 96h_untreated


title: GQE3

city: Kyoto

first: Koichi

last: Murata

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

institute: Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSChg Hg19 using TopHat v0.9.0 using Garaxy (Goecks et al. 2010)
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) was calculated using Cuffdiff program (V2.2.1) using Garaxy
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Macrophage with Control LNA and RANKL for 24h_rep#2

extract_protocol:
RNA was harvested using RNeasy. Illumina TruSeq RNA Sample Prep Kit was use for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Macrophage


title: iCM1


title: KME4

source_name: Macrophage with antisense E2F1 24h


title: GQE2

source_name: Macrophage with antisense E2F1 24h_rep#2


title: KME5

source_name: Macrophage with antisense E2F1 and RANKL for 24h


title: GQE1

source_name: Macrophage with Control LNA 24h_rep#2


title: KMC20

source_name: Macrophage with COMMD1 siRNA and RANKL for 48h_rep#2


title: KME1

source_name: Macrophage with Control LNA 24h


title: HOXB13 siERG ChIP-seq, rep3

city: Toronto

first: Ken

last: Kron

state: ON

address: 101 College Street, TMDT, 11th floor, room 11-601B

institute: University Health Network

description: VCaP_siERG_HOXB13 3

data_processing:
Raw reads were generated using Casava v1.8.2.
Bowtie 2 was used to align reads to the reference hg19 genome.
MACS2 was used to call peaks using default parameters.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed files correspond to the called peaks files from MACS2 after aligning to hg19 using Bowtie 2.

source_name: VCaP prostate cancer cells, siERG, HOXB13 ChIP

growth_protocol: 22Rv1 and LNCaP cells were cultured in RPMI supplemented with 10% FBS and 1% Pen/Strep. VCaP cells were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
Genomic DNA was extracted following sonication, clearing of lysates, and immunoprecipitation of protein/DNA complexes.
Libraries were constructed using Rubicon Thruplex FD kit using manufacturer's recommended protocol.

treatment_protocol: VCaP cells were reverse transfected with 600 pmol of siRNA in 45 uL lipofectamine RNAiMAX (Thermo-Fisher Scientific) in 10 cm plates. Cells were incubated for 72 hours prior to harvesting for chromatin. The following Silencer Select siRNAs (Thermo-Fisher Scientific) were used for knockdown experiments: negative control - 4390844; ERG - s4813.

value: VCaP

value: prostate cancer cell line

tag: sirna

value: siERG

tag: passage

value: HOXB13 (Santa Cruz Biotechnology cat. sc-66923)


title: KMC19

source_name: Macrophage with COMMD1 siRNA 48h_rep#2


title: HOXB13 siERG ChIP-seq, rep2

description: VCaP_siERG_HOXB13 2


title: KMC17

source_name: Macrophage with Control siRNA 48h_rep#2


title: KMC18

source_name: Macrophage with Control siRNA and RANKL for 48h_rep#2


title: HOXB13 siERG ChIP-seq, rep1

description: VCaP_siERG_HOXB13 1


title: KMC12

source_name: Macrophage with COMMD1 siRNA and RANKL for 24h_rep#2


title: KMC11

source_name: Macrophage with COMMD1 siRNA 24h_rep#2


title: KMC9

source_name: Macrophage with Control siRNA 24h_rep#2


title: KMC10

source_name: Macrophage with Control siRNA and RANKL for 24h_rep#2


title: KMC8

source_name: Macrophage with COMMD1 siRNA and RANKL for 48h


title: HOXB13 siCtl ChIP-seq, rep2

description: VCaP_siCtl_HOXB13 2

source_name: VCaP prostate cancer cells, siCtl, HOXB13 ChIP

value: siCtl


title: FOXA1 siERG ChIP-seq, rep3

description: VCaP_siERG_FOXA1 3

source_name: VCaP prostate cancer cells, siERG, FOXA1 ChIP

value: FOXA1 (EMD Millipore cat. 17-10267)


title: HOXB13 siCtl ChIP-seq, rep1

description: VCaP_siCtl_HOXB13 1


title: FOXA1 siERG ChIP-seq, rep2

description: VCaP_siERG_FOXA1 2


title: KMC7

source_name: Macrophage with COMMD1 siRNA 48h


title: FOXA1 siERG ChIP-seq, rep1

description: VCaP_siERG_FOXA1 1


title: KME2

source_name: Macrophage with Control LNA and RANKL for 24h


title: KMC6

source_name: Macrophage with Control siRNA and RANKL for 48h


title: FOXA1 siCtl ChIP-seq, rep3

description: VCaP_siCtl_FOXA1 3

source_name: VCaP prostate cancer cells, siCtl, FOXA1 ChIP


title: FOXA1 siCtl ChIP-seq, rep2

description: VCaP_siCtl_FOXA1 2


title: KMC5

source_name: Macrophage with Control siRNA 48h


title: KMC4

source_name: Macrophage with COMMD1 siRNA and RANKL for 24h


title: KMC3

source_name: Macrophage with COMMD1 siRNA 24h


title: HOXB13 siCtl ChIP-seq, rep3

description: VCaP_siCtl_HOXB13 3


title: KM16

source_name: Macrophage in Hypoxia with RANKL for 48h_rep#2


title: KMC1

source_name: Macrophage with Control siRNA 24h


title: KMC2

source_name: Macrophage with Control siRNA and RANKL for 24h


title: H3K27ac siCtl ChIP-seq, rep3

description: VCaP_siCtl_H3K27ac 3

source_name: VCaP prostate cancer cells, siCtl, H3K27ac ChIP

value: H3K27ac (Abcam cat. ab4729)


title: FOXA1 siCtl ChIP-seq, rep1

description: VCaP_siCtl_FOXA1 1


title: H3K27ac siERG ChIP-seq, rep2

description: VCaP_siERG_H3K27ac 2

source_name: VCaP prostate cancer cells, siERG, H3K27ac ChIP


title: H3K27ac siERG ChIP-seq, rep3

description: VCaP_siERG_H3K27ac 3


title: H3K27ac siCtl ChIP-seq, rep1

description: VCaP_siCtl_H3K27ac 1


title: KM15

source_name: Macrophage in Hypoxia for 48h_rep#2


title: HOXB13 ChIP-seq

description:
LNCaP HOXB13
Processed data file: LNCaP_HOXB13_calledpeaks.bed

source_name: LNCaP prostate cancer cells, HOXB13 ChIP

value: LNCaP


title: KM13

source_name: Macrophage in Normoxia 48h_rep#2


title: KM11

source_name: Macrophage in Hypoxia 24h_rep#2


title: KM10

source_name: Macrophage in Normoxia with RANKL for 24h_rep#2


title: KM9

source_name: Macrophage in Normoxia 24h_rep#2


title: FOXA1 ChIP-seq, rep1

description:
22Rv1_FOXA1 1
Processed data file: 22Rv1_FOXA1_calledpeaks.bed

source_name: 22Rv1 prostate cancer cells, FOXA1 ChIP


title: HOXB13 ChIP-seq, rep2

description:
22Rv1_HOXB13 2
Processed data file: 22Rv1_HOXB13_calledpeaks.bed

source_name: 22Rv1 prostate cancer cells, HOXB13 ChIP


title: KM8

source_name: Macrophage in Hypoxia with RANKL for 48h


title: HOXB13 ChIP-seq, rep1

description:
22Rv1_HOXB13 1
Processed data file: 22Rv1_HOXB13_calledpeaks.bed


title: KM7

source_name: Macrophage in Hypoxia for 48h


title: AR ChIP-seq, rep2

description:
22Rv1_AR 2
Processed data file: 22Rv1_AR_calledpeaks.bed

source_name: 22Rv1 prostate cancer cells, AR ChIP

value: AR (Santa Cruz Biotechnology cat. sc-816)


title: H3K27ac siCtl ChIP-seq, rep2

description: VCaP_siCtl_H3K27ac 2


title: KM14

source_name: Macrophage in Normoxia with RANKL for 48h_rep#2


title: AR ChIP-seq, rep1

description:
22Rv1_AR 1
Processed data file: 22Rv1_AR_calledpeaks.bed


title: GQE4

source_name: Macrophage with antisense E2F1 and RANKL for 24h_rep#2


title: KM3

source_name: Macrophage in Hypoxia 24h


title: KM5

source_name: Macrophage in Normoxia 48h


title: EPCs_MeDIP Seq

city: Daejeon

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

country: South Korea

institute: Korea Institute of Science and Technology Information

data_processing:
Quality trimming using FastQC and Fastx-toolkit
Alignment using BWA v0.7.5a to hg19
Methylation scores were calculated with MEDIPS v1.8.0 package
Genome_build: hg19
Supplementary_files_format_and_content: Wig file were generated using MEDIPS package

source_name: endothelial progenitor cells

growth_protocol: Cord blood derived EPCs were isolated by Ficoll-Paque density gradient centrifugation. and cultured in EBM™-2 (Clonetics Cell Systems, St Katharinen, Germany) supplemented with 20% heat-inactivated fetal bovine serum (FBS) and EGM™-2 SingleQuots® (Clonetics Cell Systems). After 3 days, nonadherent cells were removed, and fresh culture medium was added. Cultures were maintained for 7 days.

extract_protocol:
Genomic DNA was isolated using NucleoSpin-Tissue Kit (Macherey-Nagel)
Libraries were prepared according to the manufacturer’s instructions (Illumina Chip DNA Prep Kit).

value: cord blood derived endothelial progenitor cells


title: KM6

source_name: Macrophage in Normoxia with RANKL for 48h


title: EPCs_RNA Seq

data_processing:
Quality trimming using FastQC and Fastx-toolkit
Alignment using Tophat v2.0.9 to hg19
Expression quantification using Cufflinks v2.1.1
Differential expression analysis using edgeR, DESeq, DEGSeq and NOISeq
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM value for each sample

extract_protocol:
Total RNA was isolated using an RNeasy Kit (Qiagen)
Libraries of mRNA sequences were prepared using the Illumina Truseq RNA Prep Kit, and mRNA was purified (two rounds) and fragmented from total RNA (1 µg) using oligo-T bound to magnetic beads. RNA sequencing was performed using an Illumina HiSeq 2000 (101-bp paired-end runs).


title: H3K27ac siERG ChIP-seq, rep1

description: VCaP_siERG_H3K27ac 1

source_name: VCaP prostate cancer cells, siERG, H3K27ac ChIP


title: KM4

source_name: Macrophage in Hypoxia with RANKL for 24h


title: OECs_MeDIP Seq

source_name: outgrowth endothelial cells

value: cord blood derived outgrowth endothelial cells


title: FOXA1 ChIP-seq, rep2

description:
22RV1 FOXA1 2
Processed data file: 22Rv1_FOXA1_calledpeaks.bed


title: KM1

source_name: Macrophage in Normoxia 24h


title: KM2

source_name: Macrophage in Normoxia with RANKL for 24h


title: OECs_RNA Seq


title: 3207-U-0

city: beltsvill

first: jiajie

last: sun

state: MD

address: 10300 BALTIMORE AVENUE

department: Agriculture research sevice

institute: U.S. department of agriculture

data_processing:
Total RNA was extracted from all the 6 exosomal pellets, collected from infected and control milk samples, using the TRIzol® Reagent (Life Technologies, Carlsbad, CA, USA).  RNA from these 6 exosomes was indexed and small RNA libraries were prepared using Illumina TruSeq Small RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. These six libraries were subjected to single-end sequencing to produce 36nt reads, using an Illumina Genome Analyzer II. Preliminary quality control analysis of the 8 fastq files was carried out using FASTQC software v0.10.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Subsequently, a Perl script (Adapter_trim.pl, http://122.228.158.106/mr2_dev/start_filter.php) was used to filter low quality short reads, remove polyA, trim 3'/5' adapter, and format into a non-redundant fasta file. All unique sequence tags that passed through above filtering criteria were mapped onto the bovine genome assembly (ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/bosTau6.fa.gz) using the SOAP program [19]. Uniquely mappable reference genome tags were further aligned against Rfam v11.0, miRBase v19.0, repeat database produced by RepeatMasker (http://www.repeatmasker.org) and the coding genes of the reference genome (http://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/refMrna.fa.gz). Based on their matches, these unique sequence tags were classified  under the following categories: degradation fragments of non-coding RNA, known miRNAs, genomic repeats and mRNA fragments. Sequences that were assigned to none of the above annotations but that mapped to the reference genome were classified as ‘unknown’. This approach will hereafter be referred to as ‘SOAP-method’. We also used a second approach, ‘miRDeep2-method’ with data processing steps as previously described, but with some improvements [20]. Firstly, Cutadapt v1.3 (http://code.google.com/p/cutadapt/) was used to trim 3'/5' adaptor sequences, and reads less than 18nt were discarded. Trimmed reads were then further filtered using Sickle (https://github.com/najoshi/sickle/) to remove low quality sequences that had a quality value < 20. Finally, Reads which successfully passed filtering were aligned to the bovine miRBase v19.0 using miRDeep v2.0.0.5 with a Perl script ‘quantifier.pl’.
Genome_build: bosTau6
Supplementary_files_format_and_content: Text files include count values for each identified miRNAs

organism: Bos taurus

source_name: bovine breast  milk from mid-lactation Holstein cows

extract_protocol:
Total RNA and small RNA were extracted from each of the 6 exosomal samples using the mirVanaTM miRNA Isolation Kit (Life Technologies, Carlsbad, CA, USA).  Procedures were performed according to the manufacturer’s protocol.
Then 6 indexed small RNA libraries were prepared using the ScriptMinerTM Small RNAseq Library Preparation Kit (Epicentre, Madison, WI, USA).

tag: tissue

value: bovine breast milk exosome

tag: treatment

value: prior to infection with S. uberis

tag: breed

value: US Holstein cow


title: 3207-U-2

value: 2 days post-infection with S. uberis


title: 3554-U-0


title: 3554-U-2


title: 3658-U-0


title: 3658-U-2


title: KM12

source_name: Macrophage in Hypoxia with RANKL for 24h_rep#2


title: S7HP+Snail tumor #13

status: Public on Jul 24 2017

city: Seoul

first: Simon

middle: Weonsang

last: Ro

address: Yonsei-ro 50-1

department: Institute of Gastroenterology

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: S7HP+Snail tumor #13

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: liver tumor

value: 11 weeks


title: S7HP+Snail tumor #14

source_name: S7HP+Snail tumor #14


title: S7HP+Snail tumor #15

source_name: S7HP+Snail tumor #15


title: S7HP tumor #12

source_name: S7HP tumor #12


title: S7HP tumor #11

source_name: S7HP tumor #11


title: S7HP tumor #9

source_name: S7HP tumor #9


title: LHP tumor #2

source_name: LHP tumor #2


title: LHP tumor #3

source_name: LHP tumor #3


title: LHP tumor #6

source_name: LHP tumor #6