title: BY3

city: Buffalo

first: Omer

last: Gokcumen

state: NY

address: 639 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

data_processing:
Alignment of raw reads to hg19 using STAR aligner, and quality control using RSeQC and Picard
Transcript quantification with Kallisto, and differential isoform expression with Sleuth
Gene quantification using featureCounts, gene annotation using Gencode, and differential expression with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files with tpm (transcript per killobase million) information or the statistics or differential expression of genes.

source_name: BJ human fibroblast

growth_protocol: BJ cells were grown in Minimum Essential Media with Earle’s salts supplemented with 2 mM L-glutamine, 10% (v/v) FBS and 1% (v/v) Penicillin-Streptomycin. Cells were grown as monolayer culture at 37 °C and 5% CO2 atmosphere under sterile conditions until they reached their proliferative capacity. BJ cells were split 1:2 or 1:4  when they reached a confluency of approximately 80-90%. Cells were routinely checked under a light microscope for changes in morphology and to monitor confluency. The cumulative population doubling was calculated from the cell count at each splitting using the formula log2 (D/D0), where D is the density of cells during harvesting and D0 is the density of cells at seeding. Cells were regularly checked for mycoplasma contamination.

extract_protocol:
Approximately two million cells were harvested as a cell pellet and total RNA was extracted using Qiagen’s RNeasy Mini kit according to manufacturer’s guidelines. An on-column DNase digestion using Qiagen’s RNase-Free DNase was carried out for RNA purification. RNA quality and yield were assessed by a Nanodrop-1000 spectrophotometer. Concentrations ranged from 50-609 ng/μL. Illumina Sequencing (150bp paired-end, ~50M/reads per sample) was performed by the New York Genome Center using three biological replicates per condition.
RNA was prepared using the KAPA Stranded RNA-Seq Kit with RiboErase.

value: Ffibroblast

tag: population doubling

value: Skin;foreskin


title: BO2

status: Public on Mar 31 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

treatment_protocol: Cells were grown as monolayer culture at 37 °C and 5% CO2 atmosphere under sterile conditions until they reached their proliferative capacity.

tag: cell type

tag: tissue


title: BY2


title: Ectoderm_NT_H3_3K4M_3 (Group6)

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

data_processing:
Fastq files processed by filtering out low-quality reads (<Q20) and low-quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to X. laevis genome 6.1 using TopHat 2.0.6.
ChIP-seq data have been aligned to X. laevis genome 6.1 using BWA 0.6.2 with default options. Duplicate reads were then removed.
Peaks were called using MACS2 2.0.9 with --broad options and q-value<0.01.
Differential analysis was conducted using EdgeR package.
The 553,960 assembled transcripts were provided by the International Xenopus Genome Project (http://www.marcottelab.org/index.php/Xenopus_Genome_Project) in October 2012. This assembly was augmented with Xenopus laevis sequences from the NCBI RefSeq database downloaded in February 2012 (30,611 sequences). The combined transcript sequences were filtered with cd-hit-est 4.5.7 (Li and Godzik, 2006) with a similarity score of 95% to remove redundant sequences. This resulted in a final set of 39,384 transcripts. To provide gene names, orthologs were found against the M. musculus proteome (downloaded in January 2013 - NCBI RefSeq) using Inparanoid 4 (Alexeyenko et al. 2006) on predicted ORFs from the Trinity Suite (Grabherr et al. 2011). The sequences were further annotated using InterProScan 4.8 (Zdobnov and Apweiler, 2001) to provide both InterPro Domains (Release 35) and Panther 7.2 ontology terms (Thomas et al. 2003). Xenopus laevis NCBI Descriptions were provided for transcripts that originated at the NCBI. The gtf file containing this information is reported as supplementary material of the previous study: PMID: 27034506, DOI: 10.1101/gr.201541.115.
Genome_build: X. laevis genome 6.1 (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.1/)
Supplementary_files_format_and_content: *.xls: Excel files contain raw counts.
Supplementary_files_format_and_content: *.bed: BED files contain coordinates of broad peaks called with MACS2 (2.0.9).

organism: Xenopus laevis

source_name: NT ectoderm cells

extract_protocol:
RNA extraction and preparation of cDNA library for sequencing: Embryonic tissues (endoderm and ectoderm, as indicated) were dissected from embryos at the respective stage and frozen at -80°C. One tissue from one embryo was processed individually. RNA extractions were performed using Qiagen RNeasy Mini kit (Qiagen, 74106) according to the manufacturer's protocol including the DNase step. RNA was eluted in 40ul of DEPC H2O and 500 ng RNA was used to generate a cDNA sequencing library with Illumina TruSeq kit (RS-122-2001), according to the manufacturer's protocol.
Library construction: Illumina TruSeq RNA sample prep kit for RNA-seq.

tag: starting material

value: single embryo

tag: developmental stage/condition

value: H3.3K4M endoderm-derived nuclear transfer embryo stage 11

value: ectoderm

tag: pairing of samples


title: Endoderm_H3K4me3_ChIP_rep1 (Group7)

description: Processed data file: Eva_HiSeq1500_2.Index15_vs_Eva_HiSeq1500_2.Index13_broad_peaks.bed

library_source: genomic

molecule: genomic DNA

source_name: Endoderm, H3K4me3 ChIP

extract_protocol:
ChIP and ChIP-seq preparation: Chromatin Immunoprecipitation (ChIP) was performed as described. Neurula (stage 18) embryos were generated by in vitro fertilization. For each ChIP experiment, 50 embryos were dissected in 1xMBS to obtain the endoderm tissue. Samples were fixed in 2 ml of 1% Formaldehyde in 0.1x MMR for 25 min at room temperature, followed by 4 washes with 1 mL 0.1xMMR and equilibration in 500 μl HEG solution (50mM Hepes-KOH pH 7.5, 1 mM EDTA, 20% Glycerol) at 4°C, then excess buffer was removed and samples were frozen at -80°C. To extract chromatin, the samples were homogenized in 2 ml buffer E1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% Glycerol, 0.5% Igepal CA-630, 0.25% Triton X-100, 1mM DTT, complete protease inhibitors (Roche)). Chromatin was collected by centrifugation for 2 min at 3500 rmp, 4°C and then washed two times with 2 ml E1, three times with 2ml buffer E2 (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, complete protease inhibitors (Roche)) and three times with 500 μl Buffer E3 (10mM Tris pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, complete protease inhibitors (Roche)). Chromatin was fragmented by sonication for 20 cycles (30s on and 30s off) using a Bioruptor (Diagenode). The samples were centrifuged at 15min, 4°C at full speed, the supernatant was collected and Triton X-100 was added to 1%. 25 μl of the solution were put aside to serve as Input for later analysis. Before ChIP, primary anti-H3K4me3 (Abcam ab8580, 0.5 μg per 50 embryos) antibodies were bound to PBS washed magnetic beads conjugated with secondary antibody (Invitrogen 11204D, 25 μl per 50 embryos) in 500 μl 1xPBS 0.1% BSA overnight at 4°C on a rotating wheel. Beads were washed 3 times with 1xPBS 0.1% BSA, added to the fragmented chromatin solution and incubated overnight at 4°C on a rotating wheel. Beads were then washed 6 times with RIPA buffer (50mM Hepes-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% Igepal CA-630, 0.7% Na-deoxycholate, complete protease inhibitors (Roche)) and twice with TEN buffer (10mM Tris pH 8.0, 1mM EDTA, 150mM NaCl, complete protease inhibitors (Roche)) for each 10 min. For crosslink reversal, the beads were resuspended in 150 μl Stop buffer (40mM Tris pH 8.0, 10mM EDTA, 1% SDS) and 125 μl Stop buffer was added to the input fraction. The samples were supplemented with Proteinase K (0.3 μg/μl), NaCl (250 mM) and incubated at 65°C overnight. RNase A (DNase free) was added to a final concentration of 200 μg/μl and DNA was Phenol/Chloroform extracted. 150 μg/μl Glycogen was added and DNA was recovered by Ethanol precipitation. The pellet was resuspended in 30 μl H2O, and half was subjected for ChIP-seq library preparation with the TruSeq DNA kit (Illumina, FC-121-2001). Two independent biological replicates were generated for each H3K4me3 ChIP experiment.
Library construction: ChIP-seq library preparation was performed using the TruSeq DNA kit (Illumina, FC-121-2001) according to the manufacturer's protocol.

value: 100 embryos

value: stage 18-21 embryo

value: endoderm

tag: chip antibody

value: H3K4me3 (Abcam ab8580, 0.5 ug per 50 embryos)


title: Ectoderm_NT_H3_3K4M_4 (Group6)


title: Late Queen Destined 4

city: Norwich

first: Matthew

last: Beckers

state: Norfolk

address: Norwich Research Park

institute: University of East Anglia

data_processing:
3' adapters were removed by matching the first 8nt of the adapter. Only sequences with trimmable matching adapters were kept for subsequent analysis. The sequences were additionally trimmed by 4nt on the 3' end to remove the multiplexed part of the HD adapter.
Trimmed sequences were filtered for low nucleotide complexity, where sequences with less than three unique nucleotides were removed, and by size, where sequences of length 16nt-30nt were kept
The filtered sequences were mapped to the reference genome using PatMaN 1.2 with no mismatches or gaps
Mapped sequences were run through miRCat, with one miRCat run per library. The results were combined to include all unique predicted miRNAs from any library.
Mapped sequences were overlapped with results from a MapMi run on the reference genome. If a predicted miRNA from miRCat overlapped a MapMi miRNA, the miRNA was assigned the relevent miRBase ID. Otherwise, new miRNAs were assigned a new ID
The resulting miRNA list was subject to a final manual curation by inspection of secondary structure and sequence mapping patterns for obvious erroneous predictions.
Genome_build: Bter2011317
Supplementary_files_format_and_content: predicted_miRNAs.csv details identified miRNAs found using miRCat using count from all libraries and MapMi predictions based on known miRNA alignments to the reference genome. MiRNA.name: assigned name of miRNA, mirbaseID: ID in miRBase of matched known miRNA (if any), Mature.sequence: mature miRNA sequence, Precursor.sequence: Prevursor miRNA sequence, seqid:reference sequence ID, strand: strand of reference sequence, pre.start: precursor sequence start, pre.end: precursor sequence end, mature.start: mature sequence start, mature.end: mature sequence end, Prediction.method: method used to predict the miRNA, EW/LW 1/2/3/4: The mature sequence count for the named library.

organism: Bombus terrestris

source_name: whole body

growth_protocol: Queen-destined and Worker-destined diploid larvae were harvested from eight Bombus terrestris colonies. These were separated into early-instar queen-destined larvae from the first and second instars of queen-destined larvae, early-instar worker-destined larvae (EW) from the first and second larval instars of worker-destined larvae, late-instar queen-destined larvae from the fourth instar of queen-destined larvae, and late-instar worker-destined larvae from the fourth larval instar of worker-destined larvae.

extract_protocol:
Whole body larvae from the same colony and developmental stage were pooled into eight samples (four for each developmental stage). They were then 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 2 ug of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols. However, instead of the Illumina 3' adaptor, a modified 3' HD adaptor with a 4bp degenerate nucleotide sequence (NNNN) on the 5' end was used during the adaptor ligation steps.

tag: development stage

value: Late

tag: caste

value: Queen


title: Late Queen Destined 3


title: Endoderm_H3K4me3_ChIP_rep2 (Group8)

description: Processed data file: IP36_H3K4me3_B_MF_vs_Input12_B_MF_broad_peaks.bed


title: BO1


title: Ectoderm_NT_H3_3K4M_2 (Group6)


title: differentiation_RNASeq.9.2

city: Bethesda

first: Bruce

middle: Hamilton

last: Howard

state: MD

address: 9000 Rockville Pike

department: Intramural Program

institute: NIH/NICHD

description:
abundance measurements (htseq) htseq*.txt files
differential expression (edgeR) de*.txt files
sample 41
See Keys_samples20-119.xls
See Keys_samples20-119.xls, raw file: 150626_EDISON_C75D4ANXX.6.10316647.bam

data_processing:
ChIP alignment: sequence reads were mapped to the human grch37 genome using Bowtie or Bowtie2 with default settings.
ChIP genome-wide coverage annotation: all mapped reads were written to znt2 annotation files by incrementing the file position value by 1 over the length of the read.
RNA-seq alignment: sequence reads were mapped to the human grch37 genome using STAR with default settings.
RNA-seq quantification was done using htseq and edgeR with default settings. FDR values were calculated with the Benjamini-Hochberg option.  Key is provided by the Sample "Title" field, where first index denotes merged data used in htseq/edgeR calculations, and second index denotes raw file replicate number (1-2 for monocytes and 1-4 for dendritic cells).
Abundance measurements (htseq) are reported in htseq*.txt files.
Differential expression (edgeR) are reported in de*.txt files.
For 'average insert size' field in paired-end experiments section median values from the bam TLEN field are provided to minimize bias from outliers related to splicing.
Genome_build: human grch37
Supplementary_files_format_and_content: ChIP-seq annotation znt2 files are binary files initialized (initially written) as short int (little endian) zeros with the length of the file in zeros equal to the number of bases in the relevant chromosome.
Supplementary_files_format_and_content: RNA-seq differentiation: differential expression files de.com.diff_cb.mono_dc.df and htseq_count.diff_cb.mono_dc.txt are derived from samples 20-31 (newborn monocyes) and samples 32-59 (newborn dendritic cells). RNA-seq differential expression files de.com.diff_ad.mono_dc.df and htseq_count.diff_ad.mono_dc.txt are derived from samples 60-75 (adult monocytes) and samples 76-119 (adult dendritic cells).
Supplementary_files_format_and_content: RNA-seq development: differential expression files de.com.dev_mono.cb_ad.df and htseq_count.dev_mono.cb_ad.txt are derived from samples 20-31 (newborn monocyes) and samples 60-71 (adult monocytes). RNA-seq differential expression files de.com.dev_dc.cb_ad.df and htseq_count.dev_dc.cb_ad.txt are derived from samples 32-59 (newborn dendritic cells) and samples 76-119 (adult dendritic cells).

molecule: polyA RNA

source_name: cord blood

growth_protocol: Cord blood and adult peripheral blood samples were enriched by Ficoll-paque gradient centrifugation (density 1.077) and pelleted twice to reduce platelet contamination. After a second lower density Ficoll-paque gradient step, monocytes were further purified by subtractive magnetic cell sorting using a monocyte isolation kit (Miltenyi, Auburn, CA) following the manufacturer’s protocol.

extract_protocol:
For ChIP-seq lysates were clarified from non-fixed Dnase I-treated nuclei and histone-DNA complexes were isolated with anti-trimethyl-Histone H3 (Lys27) antibody (Millipore catalog no. 07-449). For RNA-seq total RNA was extracted from purified monocytes or dendritic cells using RNeasy Micro kit (Qiagen). RNA integrity and concentration were measured using RNA 6000 Nano kits (Agilent) on a Agilent 2100 Bioanalyzer.
ChIP-seq libraries were prepared according to Illumina's instructions.  RNA-seq libraries were prepared following the Illumina TruSeq RNA low-throughput protocol.

treatment_protocol: Dendritic cells (DC) obtained by plating in RPMI 1640, 10% FCS, 50 ng/ml GM-CSF, 20 ng/ml IL-4. Cultures were refed every other day and DC were harvested by day 6 or 7. Purities of monocyte and DC preparations were assessed by flow cytometry (FACSCalibur;BD Biosciences, San Jose, CA) with the following antibodies: anti-CD14 FITC, anti-biotin PE (Miltenyi); anti-HLA-DR, and anti-CD86 (BD Biosciences).

value: dendritic cells

tag: developmental stage

value: newborn


title: Late Queen Destined 2


title: differentiation_RNASeq.1.2

description:
abundance measurements (htseq) htseq*.txt files
differential expression (edgeR) de*.txt files
sample 21
See Keys_samples20-119.xls
See Keys_samples20-119.xls, raw file: 140916_OPTIMUS_C5L92ANXX.2.7589005.bam

value: monocytes


title: Late Queen Destined 1


title: M_25W_embryo1_26

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

country: China

institute: Peking University

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Primordial Germ Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, after MACS and FACS purification, a single PGC or gonadal somatic cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the PGCs of the same fetal sample were pooled together and the amplified cDNA of the gonadal somatic cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 2500 platform (sequenced by Novogene).

value: 25 week gestation

tag: gender

value: male

value: Primordial Germ Cells


title: Ectoderm_NT_H3_3K4M_1 (Group6)


title: Early Queen Destined 4

value: Early


title: M_25W_embryo1_24

description: polyA RNA


title: M_25W_embryo1_107

description: polyA RNA


title: Ectoderm_NT_H3_3wt_3 (Group6)

value: H3.3wt endoderm-derived nuclear transfer embryo stage 11


title: Early Queen Destined 2


title: M_25W_embryo1_106

description: polyA RNA


title: Ectoderm_NT_H3_3wt_2 (Group6)

value: single embryo


title: Ectoderm_NT_H3_3wt_1 (Group6)


title: M_25W_embryo1_105

description: polyA RNA


title: M_25W_embryo1_104

description: polyA RNA


title: Ectoderm_IVF_3 (Group6)

source_name: IVF ectoderm cells

value: in vitro fertilized embryo stage 11


title: M_25W_embryo1_102

description: polyA RNA


title: M_25W_embryo1_101

description: polyA RNA


title: Endoderm_H3K4me3_Input_rep2 (Group8)

source_name: Endoderm, input


title: Ectoderm_IVF_2 (Group6)

value: ectoderm


title: M_21W_embryo3_17

description: polyA RNA

value: 21 week gestation


title: Early Queen Destined 3


title: M_21W_embryo3_10

description: polyA RNA


title: Ectoderm_NT_H3_3wt_4 (Group6)


title: M_21W_embryo3_10_2

description: polyA RNA


title: Endoderm_Donor_H3_3K4M_1 (Group6)

source_name: Donor endoderm cells expressing H3.3K4M

value: in vitro fertilized embryo stage 21 expressing H3.3K4M


title: cattle-lung rep1

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

description: small RNA

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Megabase of library size  were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: raw counts

organism: Bos taurus

source_name: lung

extract_protocol:
Three unrelated 2-year old adult females for both of yaks and cattle were used in this study. Two of significant hypoxia-responsive tissues (heart and lung) were rapidly separated from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen, and stored at − 80 °C until RNA extraction.
small RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: age


title: differentiation_RNASeq.11.3

description:
abundance measurements (htseq) htseq*.txt files
differential expression (edgeR) de*.txt files
sample 50
See Keys_samples20-119.xls
See Keys_samples20-119.xls, raw file: 150626_EDISON_C75D4ANXX.4.10316631.bam


title: Endoderm_Donor_H3_3wt_2 (Group6)

source_name: Donor endoderm cells expressing H3.3wt

value: in vitro fertilized embryo stage 21 expressing H3.3wt

value: endoderm


title: Ectoderm_IVF_4 (Group6)


title: panH3_Adult

city: New York

first: Federico

last: Gaiti

address: 413 East 69th St.

institute: Weill Cornell Medicine

description: Total H3_adult

data_processing:
Quality filtered paired-end Illumina sequencing reads were aligned to the Amphimedon genome (Srivastava et al. 2010) using Bowtie v1.1.2 (Langmead et al. 2009) and only uniquely mapping reads were retained. Adult histone PTM regions of enrichment relative to corresponding sequenced input DNA controls were determined using MACS2 peak caller v2.1.0 (Zhang et al. 2008) according to ENCODE and Roadmap Epigenomics consortiums guidelines (ENCODE Project Consortium 2012; Landt et al. 2012; Kellis et al. 2014; Kundaje et al. 2015). Adult RNAPII peaks were detected using the peakzilla software (Bardet et al. 2013; Schwaiger et al. 2014), using input DNA reads as control. Larva histone PTM and RNAPII regions of enrichment relative to sequenced input DNA controls were determined using MACS2 v2.1.0 (Zhang et al. 2008). The bed files are provided here.
Genome_build: Amphimedon queenslandica v1.0

organism: Amphimedon queenslandica

source_name: Adult sponge cells

growth_protocol: Amphimedon queenslandica adults and larvae were collected from Heron Island Reef, Great Barrier Reef, Queensland, Australia

extract_protocol:
Approximately a cubic centimeter of adult sponge tissue was squeezed through a fine cloth and cells were crosslinked in 2% formaldehyde for 5 min at room temperature (RT). Larvae (~350) were pooled, homogenized and crosslinked as above. A similar procedure was then adopted for both developmental stages. Crosslinking was quenched with 125 mM glycine for 5 min at RT. Cells were washed twice in filtered seawater and centrifuged at 500g for 5 min. Pelleted cells were lysed in SDS Lysis buffer (10 mM EDTA, 50 mM Tris-HCl at pH 8.0, 1% SDS, plus protease and phosphatase inhibitors), incubated for at least 10 minutes on ice, and sonicated for 12 min (12 cycles, each one 30sec “ON”, 30sec “OFF”) in a Bioruptor Sonicator (Diagenode, Seraing, Belgium) in order to generate 200-300 bp fragments. Optimal sonication conditions were previously set up by testing a range of sonication cycles (from 5 to 30), determining that 12 cycles were the optimal. Non-soluble material was removed from the lysate by centrifugation at 12,000g for 10 min at 4°C. An aliquot of the soluble material was removed for input DNA and stored at -20°C. To reduce the SDS concentration to 0.1%, the remaining soluble material was diluted 10 fold in ChIP dilution buffer (1.2 mM EDTA, 16.7 mM Tris-HCl at pH 8.0, 167 mM NaCl, 1.1% Triton X-100, 0.01% SDS, plus protease and phosphatase inhibitors). To reduce non-specific background, the diluted soluble material was pre-cleared with Dynabeads protein G beads (#10003D, ThermoFisher, Waltham, MA), and, at the same time, the antibodies were linked to Dynabeads protein G beads (#10003D, ThermoFisher), rotating for one hour at 4°C. At this point, the pre-cleared diluted soluble material was incubated with the antibody-bead mixtures, rotating at 4°C overnight. Immunoprecipitated material was washed three times with Low Salt Wash Buffer (2 mM EDTA, 20 mM Tris-HCl at pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS), three times with High Salt Wash Buffer (2 mM EDTA, 20 mM Tris-HCl at pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS), three times with LiCl Wash Buffer (1 mM EDTA, 1 mM Tris-HCl at pH 8.0, 1% DOC, 1% NP-40, 250 mM LiCl), and three times with TE buffer. DNA complexes were eluted 30 min at 65°C with TE-SDS (1X) and decrosslinked overnight at 65°C, along with input DNA, with the addition of 125 mM NaCl. Decrosslinked DNA complexes and input DNA were treated with RnaseA, and subsequently with proteinase K. Finally, immunoprecipitated and input DNA were purified with phenol:chloroform:isoamyl extraction (25:24:1), recovered by precipitation with ethanol in the presence of 300 mM NaOAc pH 5.2 and 2 μl of glycogen carrier (10 mg/ml), and resuspended in UltraPure™ DNase/RNase-Free Distilled Water (ThermoFisher) for later use.
Libraries of immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) according to the manufacturer’s protocol. The quality and profile of the libraries was analyzed using Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA) and quantified using KAPA Library Quantification Kits (#KK4824, Kapa Biosystems, Wilmington, MA). Deep sequencing (paired-end 100bp) of the adult libraries – two biological replicates for H3K4me3, H3K4me1, H3K36me3, H3K27me3, RNAPII, input DNA and no biological replicates for H3K27ac and total histone H3 – was performed by the Macrogen Oceania NGS Unit on Illumina HiSeq 2000 instrument (Illumina, San Diego, CA, United States). Deep sequencing (paired-end 40bp) of the larva libraries – no biological replicates for H3K4me3, H3K4me1, H3K27me3, H3K27ac, RNAPII, input DNA – was performed by the Central Analytical Research facility (CARF), Brisbane, Queensland, Australia, on Illumina NextSeq 500 instrument (Illumina, San Diego, CA, United States).

value: Adult

value: panH3 (#07-690, Merck Millipore)

tag: fragmentation

value: Sonication

tag: library method

value: ChIP-seq

tag: read length

value: 100bp paired-end


title: H3K27ac_Adult

value: H3K27ac (#07-360, Merck Millipore)


title: Endoderm_Donor_H3_3wt_1 (Group6)


title: M_21W_embryo2

description: polyA RNA

value: male

value: Primordial Germ Cells


title: M_25W_embryo1_103

description: polyA RNA

value: 25 week gestation


title: Ectoderm_NT_Kdm5bwt_7 (Group5)

value: single embryo

value: Kdm5bwt endoderm-derived nuclear transfer embryo stage 11


title: Input_Adult_Rep2

description: Input_adult replicate 2


title: Ectoderm_NT_Kdm5bwt_6 (Group5)

value: ectoderm


title: Endoderm_Donor_H3_3K4M_2 (Group6)


title: RNAPII_Adult_Rep2

description: RNAPII_adult replicate 2

value: RNAPII (clone 8WG16, #05-952, Merck Millipore)


title: Ectoderm_NT_Kdm5bwt_5 (Group5)


title: Ectoderm_NT_Kdm5bci_8 (Group5)

value: Kdm5bci endoderm-derived nuclear transfer embryo stage 11


title: Input_Adult_Rep1

description: Input_adult replicate 1


title: H3K27me3_Adult_Rep2

description: H3K27me3_adult replicate 2

value: H3K27me3 (#07-449, Merck Millipore)


title: Ectoderm_NT_Kdm5bci_7 (Group5)


title: M_19W_embryo1_26

description: polyA RNA

value: 19 week gestation


title: M_19W_embryo2_102

description: polyA RNA


title: H3K27me3_Adult_Rep1

description: H3K27me3_adult replicate 1


title: Ectoderm_NT_Kdm5bci_6 (Group5)


title: M_19W_embryo1_101

description: polyA RNA


title: Ectoderm_NT_Kdm5bci_5 (Group5)


title: H3K36me3_Adult_Rep1

description: H3K36me3_adult replicate 1

value: H3K36me3 (#17-10032, Merck Millipore)


title: Early Queen Destined 1

value: Early

value: Queen


title: M_20W_embryo1

description: polyA RNA

value: 20 week gestation


title: M_19W_embryo2_104

description: polyA RNA


title: H3K36me3_Adult_Rep2

description: H3K36me3_adult replicate 2

value: Adult

value: Sonication

value: ChIP-seq


title: H3K4me1_Adult_Rep2

description: H3K4me1_adult replicate 2

value: H3K4me1 (#17-676, Merck Millipore)

value: 100bp paired-end


title: RNAPII_Adult_Rep1

description: RNAPII_adult replicate 1


title: Ectoderm_IVF_8 (Group5)

value: in vitro fertilized embryo stage 11


title: Ectoderm_IVF_7 (Group5)

value: single embryo


title: M_12W_embryo1

description: polyA RNA

value: 12 week gestation

value: male

value: Primordial Germ Cells


title: M_10W_embryo2

description: polyA RNA

value: 10 week gestation


title: H3K4me1_Adult_Rep1

description: H3K4me1_adult replicate 1


title: Ectoderm_IVF_6 (Group5)

value: ectoderm


title: M_19W_embryo1_24

description: polyA RNA

value: 19 week gestation


title: M_19W_embryo2_103

description: polyA RNA


title: H3K4me3_Adult_Rep1

description: H3K4me3_adult replicate 1

value: H3K4me3 (#07-473, Merck Millipore)


title: M_9W_embryo1

description: polyA RNA

value: 9 week gestation


title: M_10W_embryo1

description: polyA RNA


title: M_4W_embryo1_and_F_11W_embryo1

description: polyA RNA

value: 4 and 11 week gestation

value: mixed


title: Endoderm_Donor_Kdm5wt_4 (Group5)

source_name: Donor endoderm cells expressing Kdm5bwt

value: in vitro fertilized embryo stage 18 expressing Kdm5bwt

value: endoderm


title: Endoderm_Donor_Kdm5wt_3 (Group5)


title: Endoderm_Donor_Kdm5ci_4 (Group5)

source_name: Donor endoderm cells expressing Kdm5bci

value: in vitro fertilized embryo stage 18 expressing Kdm5bci


title: H3K4me3_Adult_Rep2

description: H3K4me3_adult replicate 2

value: Adult

value: Sonication

value: ChIP-seq


title: F_26W_embryo1

description: polyA RNA

value: 26 week gestation

value: female


title: F_24W_embryo2

description: polyA RNA

value: 24 week gestation


title: Endoderm_Donor_Kdm5ci_3 (Group5)

value: single embryo


title: F_24W_embryo1

description: polyA RNA

value: Primordial Germ Cells


title: Ectoderm_NT_Kdm5bwt_4 (Group4)

value: Kdm5bwt endoderm-derived nuclear transfer embryo stage 11

value: ectoderm


title: Ectoderm_NT_Kdm5bwt_2 (Group4)


title: Ectoderm_NT_Kdm5bwt_3 (Group4)


title: BY1

value: Ffibroblast

value: Skin;foreskin


title: F_23W_embryo1

description: polyA RNA

value: 23 week gestation


title: Ectoderm_NT_Kdm5bwt_1 (Group4)


title: F_20W_embryo2

description: polyA RNA

value: 20 week gestation


title: F_20W_embryo1

description: polyA RNA


title: F_23W_embryo2

description: polyA RNA


title: Ectoderm_NT_Kdm5bci_4 (Group4)

value: Kdm5bci endoderm-derived nuclear transfer embryo stage 11


title: F_18W_embryo2

description: polyA RNA

value: 18 week gestation


title: Ectoderm_NT_Kdm5bci_3 (Group4)


title: F_12W_embryo1

description: polyA RNA

value: 12 week gestation


title: Ectoderm_IVF_5 (Group5)

value: in vitro fertilized embryo stage 11


title: Ectoderm_NT_Kdm5bci_1 (Group4)


title: Ectoderm_NT_Kdm5bci_2 (Group4)


title: F_7W_embryo1

description: polyA RNA

value: 7 week gestation


title: F_5W_embryo1_and_2

description: polyA RNA

value: 5 week gestation


title: Ectoderm_IVF_2 (Group4)


title: Ectoderm_IVF_1 (Group4)


title: Ectoderm_IVF_4 (Group4)


title: Endoderm_Donor_Kdm5wt_2 (Group4)

value: in vitro fertilized embryo stage 18 expressing Kdm5bwt

value: endoderm


title: H3K27me3_ChIPSeq.18

description:
Chromatin IP against H3K27me3
sample 19

source_name: peripheral blood

value: dendritic cells

value: old adult

value: anti-trimethyl-Histone H3 (Lys27) antibody (Millipore catalog no. 07-449)


title: F_14W_embryo1_3

description: polyA RNA

value: 14 week gestation

value: female

value: Primordial Germ Cells


title: Endoderm_Donor_Kdm5ci_2 (Group4)

value: single embryo

value: in vitro fertilized embryo stage 18 expressing Kdm5bci


title: 0610_neg

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: isolated with flow cytometry from cells maintained in common condition

data_processing:
Illumina CASAVA v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: SW1990 pancreatic cancer cell line

growth_protocol: for parental line, cells were maintained in DMEM/F-12 medium plus 10% fetal bovine serum. for resistant derivative, gemctitabine was added in medium to final concentration of 100 nM

extract_protocol:
remove the medium, cells were lyzed with lysis buffer and proceeded with instruction of Absolutely RNA Nanoprep kit (Agilent Technologies, 400753)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: TRA-1-81 negative portion in parental line


title: H3K27me3_ChIPSeq.17 (130220)

description:
Chromatin IP against H3K27me3
sample 18
processed data file: exp3_olmo.chrN.znt2.tgz

value: monocytes


title: F_14W_embryo1_2

description: polyA RNA


title: Endoderm_Donor_Kdm5wt_1 (Group4)


title: F_14W_embryo1_1

description: polyA RNA


title: Endoderm_Donor_Kdm5ci_1 (Group4)


title: Ectoderm_IVF_1 (Group6)

value: ectoderm


title: H3K27me3_ChIPSeq.17 (130215)

description:
Chromatin IP against H3K27me3
sample 17
processed data file: exp3_olmo.chrN.znt2.tgz


title: Ectoderm_NT_12 (Group3)

value: endoderm-derived nuclear transfer embryo stage 11


title: 0603_neg


title: F_8W_embryo1

description: polyA RNA

value: 8 week gestation


title: BO3

value: Ffibroblast

value: Skin;foreskin


title: 0610_pos

value: TRA-1-81 positive portion in parental line


title: Ectoderm_IVF_3 (Group4)

value: in vitro fertilized embryo stage 11


title: F_18W_embryo1

description: polyA RNA

value: 18 week gestation


title: H3K27me3_ChIPSeq.16

description:
Chromatin IP against H3K27me3
sample 16

value: dendritic cells

value: young adult


title: Ectoderm_NT_11 (Group3)


title: Ectoderm_NT_10 (Group3)


title: sw_g

description: maintained in medium containing 100 nM gemcitabine

value: gemcitabine-resistant derivative


title: differentiation_RNASeq.7.4

description:
abundance measurements (htseq) htseq*.txt files
differential expression (edgeR) de*.txt files
sample 35
See Keys_samples20-119.xls
See Keys_samples20-119.xls, raw file: 150626_EDISON_C75D4ANXX.6.10316635.bam

value: newborn


title: differentiation_RNASeq.7.1

description:
abundance measurements (htseq) htseq*.txt files
differential expression (edgeR) de*.txt files
sample 32
See Keys_samples20-119.xls
See Keys_samples20-119.xls, raw file: 150626_EDISON_C75D4ANXX.5.10316635.bam


title: 0603_pos


title: Ectoderm_NT_9 (Group3)


title: H3K27me3_ChIPSeq.14

description:
Chromatin IP against H3K27me3
sample 14

value: anti-trimethyl-Histone H3 (Lys27) antibody (Millipore catalog no. 07-449)


title: F_10W_embryo1

description: polyA RNA

value: 10 week gestation

value: female

value: Primordial Germ Cells


title: sw_p

description: maintained in common condition

value: parental line


title: Ectoderm_IVF_11 (Group3)

value: single embryo

value: ectoderm


title: H3K27me3_ChIPSeq.13

description:
Chromatin IP against H3K27me3
sample 13

value: monocytes


title: H3K27me3_ChIPSeq.11

description:
Chromatin IP against H3K27me3
sample 11

value: old adult


title: H3K27me3_ChIPSeq.12

description:
Chromatin IP against H3K27me3
sample 12


title: Ectoderm_IVF_10 (Group3)


title: Ectoderm_NT_8 (Group3)

value: endoderm-derived nuclear transfer embryo stage 11


title: H3K27me3_ChIPSeq.10

description:
Chromatin IP against H3K27me3
sample 10


title: Ectoderm_IVF_9 (Group3)


title: Endoderm_Donor_3 (Group3)

source_name: Donor endoderm cells

value: in vitro fertilized embryo stage 21

value: endoderm


title: H3K27me3_ChIPSeq.8

description:
Chromatin IP against H3K27me3
sample 8


title: Ectoderm_NT_6 (Group2)


title: H3K27me3_ChIPSeq.7

description:
Chromatin IP against H3K27me3
sample 7


title: H3K27me3_ChIPSeq.9

description:
Chromatin IP against H3K27me3
sample 9


title: Ectoderm_NT_7 (Group2)


title: H3K27me3_ChIPSeq.6

description:
Chromatin IP against H3K27me3
sample 6


title: H3K27me3_ChIPSeq.5

description:
Chromatin IP against H3K27me3
sample 5


title: H3K27me3_ChIPSeq.15

description:
Chromatin IP against H3K27me3
sample 15


title: Ectoderm_NT_5 (Group2)


title: H3K27me3_ChIPSeq.4

description:
Chromatin IP against H3K27me3
sample 4


title: Ectoderm_IVF_8 (Group2)

value: in vitro fertilized embryo stage 11


title: Ectoderm_NT_4 (Group2)


title: H3K27me3_ChIPSeq.3

description:
Chromatin IP against H3K27me3
sample 3


title: H3K27me3_ChIPSeq.1

description:
Chromatin IP against H3K27me3
sample 1


title: H3K27me3_ChIPSeq.2

description:
Chromatin IP against H3K27me3
sample 2

value: dendritic cells


title: Ectoderm_IVF_7 (Group2)


title: Ectoderm_IVF_5 (Group2)


title: AH3

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

data_processing:
RNA-seq data was analyzed with Partek Flow version 4 (Partek Inc., St. Louis, MO).  Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses).  Trimmed reads were then mapped to the mouse genome mm10 using Tophat version 2.0.5 (14) with default parameter settings and using Gencode M2 annotation (15) as guidance.  Gencode M2 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.  Finally, read counts per gene/transcript in all samples were normalized using Upper Quartile normalization (16) and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).  The differentially expressed gene (DEG) lists were generated for each comparison using the cutoff of FDR<0.05 and fold changes greater than 2 either direction.  Hierarchical clustering of samples based on DEG lists was carried out using Partek Genomic Suite version 5 (Partek Inc., St. Louis, MO).  Downstream functional analysis of the DEG lists were carried out using Ingenuity Pathway System (Qiagen, Redwood City CA).
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses).
Trimmed reads were then mapped to the mouse genome mm10 using Tophat version 2.0.5 with default parameter settings and using Gencode M2 annotation as guidance.
Gencode M2 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
Finally, read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
The differentially expressed gene (DEG) lists were generated for each comparison using the cutoff of FDR<0.05 and fold changes greater than 2 either direction.
Supplementary_files_format_and_content: raw reads

organism: Mus musculus

source_name: liver

growth_protocol: Male C57BL/6j were grown in normal breeding conditions.

extract_protocol:
Total RNA was extracted from liver tissues using Direct-zol RNA MiniPrep Kit (Zymo Research).
RNA samples were provided to the USC Genomics Core for library construction and sequencing.  RNA integrity was verified by Bio-Rad Experion analysis.  Library construction was carried out using the Illumina TruSeq RNA Sample Prep kit per manufacturer's protocol.  Libraries were visualized on the Agilent Bioanalzyer and quantified using the Kapa Biosystems Library Quantification Kit according to manufacturer’s instructions.  Libraries were applied to an Illumina flow cell and run on the Illumina HiSeq 2000 as a single-end read for 50 cycles with total raw reads per sample averaged around 22 millions.

treatment_protocol: C57BL/6j mice had 2 weeks of ad libitum feeding of regular chow or solid diet high in cholesterol and saturated fat (HCFD) (Dyets Inc. #180529), surgical implantation of intragatric (iG) catheter, 1 week acclimatization with iG feeding of a control high fat diet (corn oil, 36%Cal) for 60% of daily caloric requirement and ad libitum feeding of HCFD or chow for the remaining 40%Cal, and switching to an ethanol high fat diet with incrementally increasing ethanol concentration over a 8 wk period for ethanol-fed mice. This hybrid feeding regimen produces chronic ASH, and superimposition of weekly ethanol binge shifts liver pathology to AH.  For this AH model, ethanol binge was given weekly from the 2nd week by withdrawing ethanol infusion for 5-6 hours before and after the binge and administering an equivalent amount of ethanol withdrawn as a bolus in a concentrated solution (4~5g/kg). For control mice, isocaloric dextrose was given as a bolus in the identical manner.

tag: strain

tag: disease state

value: AH


title: Ectoderm_IVF_6 (Group2)

tag: cell type


title: AH2


title: AH1


title: ASH3

value: ASH


title: Ectoderm_NT_1 (Group1)

source_name: NT ectoderm cells


title: Ectoderm_NT_2 (Group1)


title: Ectoderm_NT_3 (Group1)


title: ASH2


title: Endoderm_Donor_2 (Group2)


title: ASH1


title: control4

value: control


title: Ectoderm_IVF_2 (Group1)


title: control3


title: yak-heart rep1

description: small RNA

organism: Bos grunniens

source_name: heart

tag: tissue

value: heart


title: control2


title: Ectoderm_IVF_4 (Group1)

tag: starting material


title: M_21W_embryo1

description: polyA RNA

value: 21 week gestation

value: male


title: yak-heart rep2

description: small RNA


title: Endoderm_Donor_1 (Group1)

tag: developmental stage/condition


title: yak-lung rep3

description: small RNA

value: lung


title: Ectoderm_IVF_1 (Group1)

tag: pairing of samples


title: yak-lung rep2

description: small RNA


title: Ectoderm_IVF_3 (Group1)


title: yak-lung rep1

description: small RNA


title: F16  RS947

city: Saint Lucia, Brisbane

first: Tony

last: Vuocolo

state: Queensland

address: 306 Carmody Road

country: Australia

institute: CSIRO

data_processing:
Reads were mapped to the Oarv3.1 reference genome using STAR RNA-Seq aligner (v 2.5.0b) with the following parameters --outFilterMultimapNmax 1 --outFilterMismatchNmax 10 --readMatesLengthsIn Equal --alignIntronMax 100000 --outSAMstrandField intronMotif --outReadsUnmapped Fastx
SNPs were called using the UnifiedGenotyper tool in the Genome Analysis ToolKit (GATK, version 3.4-46-gbc02625), with the following parameters -nt 7 -l ERROR -glm SNP -nda -out_mode EMIT_VARIANTS_ONLY -gt_mode DISCOVERY -stand_call_conf 30 -stand_emit_conf 10 -dt NONE -U ALLOW_N_CIGAR_READS
Filter 1: We removed SNPs that were present in known repeat regions, as described by the UCSC Simple Repeats track (downloaded on 21 February 2014)
Filter 2: SNPs were retained if at least five of the 18 samples had 10 or more reads for both the reference and alternate alleles.
Reads mapping to each  SNP were measured and this data used for statistical analysis to identify allele specific expression.
Genome_build: OARv3.1.74
Supplementary_files_format_and_content: tab-delimited text file.
Supplementary_files_format_and_content: Column Descriptor Key:
Supplementary_files_format_and_content: Gene: Gene SNP associated with
Supplementary_files_format_and_content: SNP:  SNP coordinate
Supplementary_files_format_and_content: SNPConsequence: DNA consequence of SNP
Supplementary_files_format_and_content: chi_stat: chi test statistic significance of SNP
Supplementary_files_format_and_content: p_val: significance score of SNP
Supplementary_files_format_and_content: HigherAllele: dominantly expressed allele
Supplementary_files_format_and_content: ProportionReadsToRef: proportion of reads mapping to reference genome
Supplementary_files_format_and_content: *_ref : read count for that sample for reference allele
Supplementary_files_format_and_content: *_alt : read count for that sample for alternate allele
Supplementary_files_format_and_content: *_geno : genotype for that sample and SNP as called by GATK

organism: Ovis aries

source_name: perirenal adipose tissue

growth_protocol: Tissues for this study were provided by Janna L Morrison and Isabella C McMillen from the Sansom Institute for Health Research, The University of South Australia, Adelaide, 4001, SA, Australia.  All procedures involving animals were carried out with approval from the University of Adelaide Animal Ethics Committee.  Animals were maintained on 100% maintenance energy requirement diets and  cared for humanely as a research flock according to strict animal ethics guidelines. The pregnant ewes  were housed from 110 days post conception (dpc); term, 150 d) in pens for two weeks before sampling. The pregnant ewes were maintained on a diet that provided 100% of their maintenance energy requirements. The pregnant ewes were humanely euthanased with an intravenous overdose of sodium pentobarbitone (8.2 g Lethobarb, Virbac Pty ltd, Peakhurst, NSW, Australia), the uterus removed and fetal tissue collected at 132±1 dpc.

extract_protocol:
Perirenal adipose tissue was removed from animals within 10 minutes of euthanasia, flash frozen in liquid nitrogen, stored on dry ice and then stored at -80 degrees Celcius.  RNA was extracted using Trizol reagent (Life Technologies) and further purified using RNeasy purification (QIAGEN) and treated with DNase1 to remove any contaminating DNA. RNA quantity and integrity were assessed using the Bioanalyzer 2100 (RIN scores >9; Agilent, Santa Clara, USA).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of paired end read sequencing libraries.
Paired end 100 bp read libraries for the 18 samples were 6-fold multiplexed and run on three flowcells of an Illumina HiSeq2000 sequencing platform.  A mean number of reads of ~75.6 (+/-9.8m) million reads was obtained from each library.

treatment_protocol: No treatment was applied to the  animals.

tag: breed

value: pure bred merino

value: 132 day old fetus

tag: Sex

value: f

value: perirenal adipose

tag: genotype

value: wild type


title: F18  RS969

tag: developmental stage


title: F15  RS943


title: control1


title: F11  RS930


title: F14  RS940


title: F13  RS937


title: F10  RS929


title: F8  RS920


title: F7  RS919


title: F5  RS917


title: F4  RS905


title: Jinding rep8

city: Yangzhou

first: tao

middle: zhi

last: yun

address: Cangjie road NO.58

institute: jinagsu lnstitute of Poultry Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: BGI_duck_1.0 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.fna.gz)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Anas platyrhynchos

source_name: ovary

growth_protocol: Jinding ducks were obtained from Jiangsu Gaoyou Duck Group, Yangzhou, Jiangsu, China. These ducks were chosen from half-sib family, of same age and feeding condition. The ducks were raised to 340 days.

extract_protocol:
Ducks ovaries were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit (Illumina,USA) was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The number of eggs of each duck was recorded daily. The laying rate of ducks higher than 99% was defined as high egg production group(HEP), and the laying rate of ducks lower than 85% was defined as low egg production group(LEP).

value: Jinding

value: ovary

value: 340 days

tag: egg production

value: low


title: F6  RS918

value: m


title: F3  RS903


title: Jinding rep5

tag: age


title: Jinding rep4

value: high


title: F17  RS953


title: Jinding rep7


title: Input_Larva

source_name: Larva sponge cells

value: Larva

tag: fragmentation

value: Sonication

value: ChIP-seq

value: 40bp paired-end


title: Jinding rep1


title: Jinding rep2


title: H3K27ac_Larva

tag: chip antibody

value: H3K27ac (Millipore, 07-360)

tag: library method


title: F2  RS902


title: F1  RS910


title: F12  RS933


title: H3K27me3_Larva

value: H3K27me3 (Millipore, 07-449)

tag: read length


title: 1F4 Ab. passaged virus

city: Cambridge

first: Benjamin

middle: Robert

last: tenOever

state: MA

address: 7 Divinity Avenue

department: MCB

institute: Harvard University

description: reads.csv

data_processing:
Libraries were run on an Illumina MiSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using Bowtie aligners on BaseSpace.
Genome_build: All sequenced were aligned to mouse adapted B/Malaysia/2506/04
Supplementary_files_format_and_content: counts per segment of virus

organism: Influenza B virus (B/Malaysia/2506/2004)

source_name: Allantoic fluid

extract_protocol:
Total RNA was extracted from supernatant or allontoic fluid using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: host for culture

value: Gallus gallus

tag: monoclonal antibody

value: 1F4 Ab


title: 4B2 Ab. passaged virus

description: reads.csv

source_name: MDCK Cells

value: Canis lupus

value: 4B2 Ab


title: F9  RS926

value: pure bred merino

value: 132 day old fetus

value: f

value: perirenal adipose

value: wild type


title: 4F11 Ab. passaged virus

description: reads.csv

value: 4F11 Ab


title: H3K4me1_Larva

value: H3K4me1 (Millipore, 17-676)


title: 1F2 Ab. passaged virus

description: reads.csv

value: 1F2 Ab


title: H3K4me3_Larva

value: Larva

value: H3K4me3 (Millipore, 07-473)

value: Sonication


title: 3G1 Ab. passaged virus

description: reads.csv

value: 3G1 Ab


title: Input_S2

status: Public on Mar 30 2017

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: control for Nup98_S2 and Nup98_S2_OE

data_processing:
Raw fastq files were trimmed to remove low quality base calls using Trimmomatic, with parameter "LEADING:3 TRAILING:3 SLIDINGWINDOW:3:3 MINLEN:30".
Trimmed reads were aligned to dm3 using Bowtie2, allowing for only uniquely aligned reads (MAPQ > 10) to be reported.
Duplicate reads and mitochondria reads were removed using Samtools and Bedtools.
Significant peaks were called using MACS2, with parameter "--qvalue 0.05 -m 2 50".
Bedgraphs were generated using the command "bedtools genomecov", library sizes were normalized to 10 million reads per sample.
BigWig files were then converted from bedgraph files using command "bedGraphToBigWig".
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files were converted from bedgraph files, which were generated using Bedtools. Scores were normalized to 10 million reads per sample.

organism: Drosophila melanogaster

source_name: embryonic cells

extract_protocol:
Lysates from embryonic cells or 3rd instar brains were clarified from sonicated nuclei and histone-DNA or Nup-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for NextSeq® 500/550 High Output Kit v2 (FC-404-2005).

value: embryo

tag: strain

tag: cell type

value: embryonic cells

tag: genotype/variation


title: 0-2 hr embryo Rnase R

city: Singapore

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: rRNA-depleted Rnase treated total RNA

data_processing:
Sequenced and aligned reads were passed through a Perl filtering algorithm to determine if they were internal to an intron or overlapped with the 5' or 3' junction of each intron in the Drosophila melanogaster (dm3) genome. Each intron was indexed and reads that aligned to the index were parsed and counted to determine molecule size. Sequence information was then extracted for each putative molecule, and pairwise aligned using Blast (43). Positive Blast hits were then aligned with Clustalw2 to determine actual sequence alignment for further downstream analysis (44).
Genome_build: dm3

source_name: 0-2 hr embryo Rnase R

extract_protocol:
RNA was extraction in accordance to Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: y w


title: Nup98_S2_OE

value: Nup98 (Capelson et al., (2010))

value: Nup98 overexpression


title: Nup98_S2


title: Wound_ATACseq

first: Yejing

last: Ge

address: 1230 York Ave

institute: The Rockefeller University

description: tagged DNA library made from genomic DNA

data_processing:
50-bp paired-end reads were aligned to mm10 using bowtie with the parameters –X 2000 and –m 1.
Duplicates were removed using Picard.
Peaks were called using MACS2 (2.1.1.20160309) (Zhang et al., 2008) with the parameter –keep-dup all.
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: Skin

growth_protocol: Samples 1-2: adult P50 backskin; Sample 3: grafted SCC-SCs; Sample 4: skin full-thickness and partial-thickness wounds

extract_protocol:
ATAC protocol from Buenrostro et al 2013 Nat Method
ATAC protocol from Buenrostro et al 2013 Nat Method
Pair-end Read Clustering and 51 Cycles Sequencing (per lane)

tag: gender

value: female

value: CD1/B6 mixed

tag: cell types

value: wounded stem cells from adult skin epithelia

tag: sort markers

value: Integrin A6Pos, Sca1Pos


title: RNAPII_Larva

value: RNAPII (Millipore, 05-952)

value: ChIP-seq

value: 40bp paired-end


title: EpdSC_ATACseq

value: adult skin epithelia

value: Integrin A6Hi, CD34Neg, Sca1Pos


title: HFSC_ATACseq

value: Integrin A6Hi, CD34Pos, Sca1Neg


title: Clark18a_k1_yellowsectors_BR3

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description:
Bio Repeat 3
R158_rC18a4B_k1yellowsectors

data_processing:
Alignments of mRNA sequences to all 88,647 Glyma models, including splice variants, from the Williams 82 a.2 reference genome of Glycine max (Phytozome, Joint Genome Institutes) were performed using the Bowtie program v.1 (Langmead et al., 2009) with up to 3 mismatches and up to 25 alignments allowed. Data presented as reads per million mapped reads per kb of  transcript (RPKM).
Genome_build: Williams 82 a.2
Supplementary_files_format_and_content: text file with RPKM values.

organism: Glycine max

source_name: yellow region of immature seed coat

growth_protocol: Plants were grown in optimal greenhouse conditions. Seed were harvested at stated mg fresh weight of the whole seed.

extract_protocol:
Extraction of total RNA from seed coats tissues required the use of a modified extraction protocol which prevents procyanidins produced in pigmented seed genotypes from binding the RNA. Procedure is from Wang, Todd and Vodkin Plant Physiology, 1994.
Transcriptome libraries and high throughput sequencing (RNA-Seq) were performed with the HiSeq‑2000 (Illumina, San Diego, CA) by the Keck Center (University of Illinois, Urbana, IL) using standard Illumina protocol.

treatment_protocol: Immature seed coats were dissected from cotyledons and into regions destined to become either the black saddle or yellow sections of the chimeric seed coats.

tag: cultivar (pi #)

tag: tissue

value: immature seed coat

tag: seed region

value: yellow region of immature seed coat

tag: seed weight

value: 100-200 mg fresh seed weight

tag: preservation

value: lyophilized


title: Clark18a_k1_blacksaddle_BR3

description:
Bio Repeat 3
R159_rC18a4H_k1blacksaddle

source_name: black saddle of immature seed coat

value: black saddle of immature seed coat


title: Clark8_K1_blacksaddle_BR3

description:
Bio Repeat 3
R161_rC8H3_K1blacksaddle


title: Clark18a_k1_blacksaddle_BR1

description:
Bio Repeat 1
R54_rc18a2h_k1blacksaddle


title: Clark18a_k1_yellowsectors_BR2

description:
Bio Repeat 2
R56_rc18a3b_k1yellowsectors


title: Clark8_K1_yellowsectors_BR2

description:
Bio Repeat 2
R75_rC8B2_K1yellowsectors


title: Clark18a_k1_blacksaddle_BR2

description:
Bio Repeat 2
R57_rc18a3h_k1blacksaddle


title: Clark8_K1_yellowsectors_BR1

description:
Bio Repeat 1
R74_rC8B1_K1yellowsectors


title: Clark8_K1_blacksaddle_BR1

description:
Bio Repeat 1
R72_rC8H1_K1blacksaddle


title: Clark8_K1_blacksaddle_BR2

description:
Bio Repeat 2
R73_rC8H2_K1blacksaddle


title: D50_C18aB_BR2

description: small RNA

data_processing:
Adapter trimming was performed using Illumina’s Flicker pipeline which finds the presence of the adapter in each read by finding the best alignment of the adapter to the read, and removing it from the read.
After the seqeunces are trimmed, sequences are counted with excluding any sequences shorter than 16bp. Counting is the process of compressing a file of reads by listing reads uniquely together with a number representing how many times it occurred in the file.
Supplementary_files_format_and_content: Fasta files include counts of reads.

source_name: Non-pigmented seed coat

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated days after flowering or mg fresh weight. Whole seeds were divided by hand into cotyledons and seed coats and dissected to separate pigemented and non-pigmented parts.

extract_protocol:
Proanthocyanidins bind to the RNA in the pigmented seed coat regions of these three soybean varieties. The modified RNA isolation method was designed specifically to overcome this problem (Wang and Vodkin, 1994).
smRNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq 2000.

tag: cultivar

value: Clark isoline with i-i, k1 alleles, PI 547439 (L67-3479)

tag: Stage

value: 100-200mg fresh weight

tag: purification

value: seed coat

tag: pigmentation

value: non-pigmented


title: D64_C8B_BR1

description: small RNA

value: Clark isoline with i-k, K1 alleles, PI 547450 (L70-4204)


title: D67_C8H_BR2

description: small RNA

source_name: Pigmented seed coat (saddle)

value: seed coat (saddle)

value: pigmented


title: D49_C18aH_BR2

description: small RNA


title: D38_C18aH_BR1

description: small RNA


title: D39_C18aB_BR1

description: small RNA


title: D65_C8B_BR2

description: small RNA


title: D66_C8H_BR1

description: small RNA


title: D108_50_100WM43B_BR2

description: small RNA

source_name: Non-pigmented seed coat without hilum

value: Williams, PI548631

value: 50-100mg fresh weight

value: seed coat without hilum


title: Tumor_ATACseq

value: female

value: CD1/B6 mixed

value: tumor-initiating stem cells from oncogenic HRas-induced SCCs

value: Integrin A6Hi, B1Hi, GFPpos


title: D47_50_100WM43H_BR1

description: small RNA

source_name: Pigmented hilum

value: hilum


title: D48_50_100WM43B_BR1

description: small RNA

value: lyophilized


title: D109_50_100WM43H_BR2

description: small RNA


title: Clark8_K1_yellowsectors_BR3

description:
Bio Repeat 3
R160_rC8B3_K1yellowsectors

value: immature seed coat

value: yellow region of immature seed coat

value: 100-200 mg fresh seed weight


title: Clark18a_k1_yellowsectors_BR1

description:
Bio Repeat 1
R55_rc18a2b_k1yellowsectors


title: D107_25_50WM43H_BR2

description: small RNA

value: 25-50mg fresh weight


title: D37_25_50WM43B_BR1

description: small RNA

value: non-pigmented


title: D36_25_50WM43H_BR1

description: small RNA


title: T8.D.9840761

city: Montreal

first: Juan Pablo

last: Lopez

state: Quebec

address: 6875 La Salle Blvd

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
All sequencing data were processed using CASAVA 1.8+34 and extracted from FASTQ files. The Fastx_toolkit was used to trim the Illumina adapter sequences. Additional filtering based on defined cut-offs was applied in order to obtain high quality data. These filters included: 1) Phred quality (Q) mean scores higher than 30, 2) reads between 15-40nt in length, 3) adapter detection based on perfect-10nt match, and 4) removal of reads without detected adapter. Additionally, we used Bowtie 35 to align reads to the human genome (GRCh37)36 and ncPRO-seq37 in combination with miRBase (V20) to match them to known miRNA sequences38,39. We used a detection threshold of 10 counts per miRNA (present at least in 80% of libraries tested). A total of 281 miRNAs survived our criteria and were included in the analysis. All small RNA sequencing data was normalized with the Bioconductor – DESeq2 package using the Variance Stabilizing Transformation (VST) method40. To identify significant microRNAs based on differential expression changes across time, we used significance analysis of microarrays method, adapted for small RNA sequencing data (SAMSeq)41. SAMSeq was implemented using a two-class paired model which accounts for changes not only between groups, but also within subjects as there is a one-to-one pairing between subjects across time. We used the Benjamini–Hochberg, false discovery rate (FDR) correction for multiple testing set at 5%, which corrects for the proportion of miRNAs likely to have been identified by chance as being significant (adjusted P values < 0.05). We also tested for potential confounding effects of age, gender, race, and RNA integrity (RIN) but found no significant differences across groups or time.
Genome_build: Human genome (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text file includes miRNA count values for each sample

source_name: Whole-blood

extract_protocol:
Peripheral blood samples were collected in PAXgene blood RNA tubes (PreAnalytix). PAXgene tubes were frozen using a sequential freezing process: tubes were stored at room temperature for 3hrs, transferred to 4°C overnight, followed by 6-8 hrs at -20°C, then final storage at -80°C. Total RNA (including the miRNA fraction) was isolated from whole-blood using the PAXgene Blood miRNA Kit (Qiagen, Canada), according to manufacturer’s instructions. RNA and miRNA yield and quality were determined using the Nanodrop 1000 (Thermo Scientific, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
All libraries were prepared using the Illumina TruSeq Small RNA protocol following the manufacturer's instructions with 12 cycles of PCR amplification after ligation of the 3' and 5' adapters, as described elsewhere5. Libraries were purified using biotinylated magnetic AMPure beads that allow for selection of specified cDNA products bound to streptavidin. A total of 50µl of amplified cDNA were mixed and purified twice with AMPure XP beads at a 1.8:1 ratio (beads:sample). This ratio allows for optimal selection of all products higher than 100nt. Library qualities were assessed using an Agilent 2100 Bioanalyzer High Sensitivity DNA chip, as well as qRT-PCR with the KAPA library quantification kit (Kapa Biosystems, USA). Samples were sequenced at the McGill University and Genome Quebec Innovation Centre (Montreal, Canada) using the HiSeq2500 Illumina sequencer with 50nt single-end reads.

tag: time point (weeks)

tag: treatment

value: Duloxetine 60 mg

tag: response

value: NRES


title: T0.D.9840761


title: T8.D.9840733

value: RES


title: T8.D.9840702


title: T0.D.9840733


title: T8.D.9840723


title: T0.D.9840702


title: T8.D.9840700


title: T8.P.9840672

value: Placebo


title: T0.D.9840700


title: T0.D.9840723


title: T8.P.9840577


title: T0.P.9840591


title: T0.P.9840610


title: T0.P.9840672


title: T0.P.9840577


title: T8.P.9840591


title: T0.P.9840568


title: T8.P.9840610


title: T8.D.9840566


title: T8.D.9840541


title: T0.D.9840541


title: D106_25_50WM43B_BR2

description: small RNA

value: Williams, PI548631


title: T0.D.9840566


title: T8.D.9840449


title: T0.P.9840448


title: T0.D.9840449


title: T8.P.9840448


title: T8.D.9840447


title: T0.D.9840447


title: T8.D.9840428


title: T0.P.9840395


title: T8.P.9840392


title: T0.P.9840392


title: T8.P.9840568


title: T8.P.9840395


title: T8.D.9840383


title: T0.D.9840383


title: T0.D.9840388


title: T8.P.9840344


title: T8.D.9840324


title: T0.P.9840344


title: T0.D.9840324


title: T8.P.9840263


title: T8.D.9840254


title: T0.D.9840300


title: T0.P.9840263


title: T8.D.9840300


title: T0.D.9840254


title: T8.D.9840248


title: T8.D.9840253


title: T0.D.9840253


title: T0.D.9840248


title: T0.D.9840428


title: T0.P.9840237


title: T0.D.9840203


title: T8.D.9840388


title: T8.D.9840203


title: T8.P.9840237


title: T8.D.9840199


title: T8.P.9840198


title: T8.D.9840188


title: T0.P.9840198


title: T0.D.9840188


title: T8.P.9840172


title: T0.P.9840133


title: T0.P.9840172


title: T0.P.9840183


title: T8.P.9840133


title: T8.P.9840183


title: T0.P.9840159


title: T8.P.9840107


title: T0.P.9840107


title: T8.P.9840064


title: T8.P.9840078


title: T0.D.9840199


title: T8.D.9840044


title: T0.P.9840026


title: T8.P.9840026


title: T8.D.9180586


title: T8.P.9180563


title: T0.D.9180586


title: T0.D.9840044


title: T0.P.9180637


title: T8.P.9180637


title: T8.P.9840159


title: T8.D.9180539


title: T0.P.9180563


title: T0.D.9180539


title: T8.P.9180465


title: T0.P.9840078


title: T8.P.9840104


title: T0.P.9840064


title: T0.P.9180465


title: T0.P.9180331


title: T0.P.9840104


title: T0.P.9180382


title: T0.D.9180316


title: T8.P.9180382


title: T8.D.9180316


title: T0.P.9180284


title: T8.P.9180331


title: T8.P.9180270


title: T8.P.9180284


title: T8.D.9180262


title: T0.P.9180254


title: T8.P.9180254


title: T8.P.9180208


title: T0.D.9180262


title: T8.D.9180181


title: T0.D.9180181


title: T8.P.9180172


title: T8.D.9180164


title: T0.D.9180164


title: T0.D.9180145


title: T8.D.9180093


title: T0.P.9180270


title: T8.P.9180083


title: T0.D.9180093


title: T0.P.9180083


title: T8.P.9180082


title: T0.P.9180082


title: T0.P.9180208


title: T0.P.9180081


title: T8.P.9180081


title: T0.D.9180020


title: T8.D.9180075


title: T8.D.9180020


title: T0.P.2670598


title: T8.D.9180019


title: T8.P.2670606


title: T8.D.2670594


title: T0.P.2670606


title: T0.P.9180172


title: T0.D.2670594


title: T0.D.2670593


title: T8.P.2670592


title: T0.D.9180075


title: T8.D.9180145


title: T8.P.2670598


title: T8.P.2670578


title: T0.P.2670592


title: T8.D.2670593


title: T8.P.2670574


title: T0.D.9180019


title: T0.P.2670574


title: T0.P.2670573


title: T8.P.2670573


title: T8.P.2670572


title: T8.D.2670558


title: T8.P.2670562


title: T0.P.2670562


title: T0.D.2670558


title: T8.P.2670546


title: T0.P.2670546


title: T8.P.2670541


title: T8.D.2670543


title: T0.D.2670543


title: T8.P.2670533


title: T0.P.2670533


title: T8.P.2670539


title: T8.P.2670521


title: T8.D.2670532


title: T0.P.2670541


title: T8.D.2670525


title: T0.P.2670539


title: T0.D.2670532


title: T8.P.2670520


title: T0.P.2670521


title: T0.D.2670525


title: T0.P.2670572


title: T8.P.2670518


title: T0.P.2670578


title: T0.P.2670518


title: T8.D.2670516


title: T0.D.2670516


title: T8.D.2670519


title: T0.D.2670519


title: T0.P.2670510


title: T0.D.2670511


title: T0.P.2670520


title: T8.P.2670510


title: T0.D.2670509


title: T8.D.2670505


title: T8.P.2670508


title: T8.D.2670509


title: T0.D.2670505


title: T8.D.2670504


title: T0.P.2670501


title: T0.D.2670504


title: T0.P.2670491


title: T0.D.2670490


title: T8.P.2670501


title: T8.D.2670489


title: T8.D.2670490


title: T8.P.2670491


title: T8.P.2670483


title: T0.D.2670485


title: T0.D.2670489


title: T8.D.2670482


title: T0.P.2670483


title: T0.D.2670482


title: T8.D.2670485


title: T8.D.2670511


title: T0.P.2670508


title: T0.P.2670480


title: T0.P.2670481


title: T8.P.2670475


title: T8.P.2670480


title: T0.P.2670500


title: T8.P.2670500


title: T8.D.2670471


title: T0.D.2670471


title: T8.P.2670469


title: T0.P.2670469


title: T8.D.2670463


title: T8.D.2670455


title: T0.D.2670448


title: T0.D.2670463


title: T0.P.2670438


title: T8.P.2670438


title: T0.D.2670455


title: T8.D.2670448


title: T8.P.2670433


title: T0.P.2670433


title: T8.P.2670429


title: T0.P.2670429


title: T8.D.2670412


title: T0.D.2670428


title: T8.D.2670428


title: T8.P.2670481


title: T0.P.2670475


title: T0.D.2670422


title: T8.P.2670407


title: T0.D.2670412


title: T8.D.2670422


title: T8.D.2670403


title: T0.P.2670407


title: T8.P.2670402


title: T0.D.2670403


title: T8.P.2670393


title: T0.D.2670399


title: T0.P.2670402


title: T0.P.2670393


title: T8.D.2670399


title: T0.D.2670391


title: T8.D.2670391


title: T0.P.2670388


title: T8.D.2670387


title: T8.D.2670384


title: T0.D.2670387


title: T8.P.2670388


title: T8.P.2670382


title: T0.P.2670382


title: T8.D.2670379


title: T8.D.2670375


title: T0.D.2670379


title: T8.D.2670370


title: T0.P.2670369


title: T0.D.2670367


title: T0.D.2670370


title: T8.P.2670374


title: T8.P.2670369


title: T0.P.2670364


title: T0.P.2670362


title: T0.P.2670374


title: T0.P.2670372


title: T0.P.2670365


title: T0.D.2670375


title: T8.P.2670372


title: T8.D.2670367


title: T8.P.2670360


title: T0.P.2670360


title: T0.D.2670361


title: T8.D.2670354


title: T8.P.2670362


title: T0.D.2670384


title: T0.P.2670346


title: T8.P.2670346


title: T0.D.2670354


title: T8.P.2670341


title: T0.P.2670341


title: T8.P.2670365


title: T8.P.2670364


title: T8.D.2670361


title: T8.P.2670337


title: T0.P.2670339


title: T8.D.2670331


title: T0.P.2670337


title: T0.D.2670331


title: T8.D.2670326


title: T8.P.2670339


title: T0.P.2670307


title: T8.P.2670307


title: T8.D.2670330


title: T0.D.2670330


title: T0.P.2670306


title: T0.P.2670296


title: T0.D.2670304


title: T8.P.2670295


title: T0.P.2670295


title: T8.D.2670304


title: T0.D.2670292


title: T8.P.2670291


title: T8.D.2670292


title: T0.P.2670291


title: T8.P.2670290


title: T8.D.2670285


title: T0.P.2670290


title: T0.D.2670285


title: T8.D.2670284


title: T8.P.2670306


title: T0.D.2670284


title: T8.P.2670296


title: T0.P.2670283


title: T8.D.2670275


title: T8.D.2670276


title: T8.P.2670283


title: T0.D.2670276


title: T0.D.2670270


title: T8.D.2670270


title: T8.P.2670273


title: T0.P.2670273


title: T8.D.2670268


title: T0.D.2670275


title: T0.D.2670268


title: T0.P.2670264


title: T0.P.2670258


title: T8.P.2670256


title: T8.P.2670264


title: T0.P.2670260


title: T8.P.2670258


title: T0.P.2670256


title: T8.P.2670250


title: T0.D.2670251


title: T0.P.2670250


title: T8.D.2670251


title: T8.P.2670248


title: T0.P.2670248


title: T0.P.2670243


title: T8.P.2670243


title: T8.P.2670240


title: T8.P.2670260


title: T0.P.2670240


title: T0.P.2670238


title: T0.D.2670232


title: T8.P.2670238


title: T8.D.2670232


title: T0.P.2670229


title: T8.P.2670229


title: T8.D.2670224


title: T0.D.2670231


title: T8.D.2670215


title: T8.P.2670205


title: T0.D.2670212


title: T8.D.2670212


title: T8.P.2670222


title: T8.D.2670204


title: T8.D.2670231


title: T0.D.2670207


title: T0.D.2670204


title: T0.P.2670225


title: T8.D.2670207


title: T0.D.2670224


title: T0.P.2670222


title: T0.P.2670202


title: T8.P.2670200


title: T8.P.2670199


title: T0.P.2670200


title: T0.P.2670199


title: T8.P.2670192


title: T0.P.2670192


title: T8.D.2670188


title: T8.P.2670225


title: T0.D.2670215


title: T8.P.2670202


title: T0.D.2670188


title: T0.P.2670205


title: T8.P.2670187


title: T0.P.2670187


title: T8.P.2670186


title: T0.D.2670183


title: T8.D.2670177


title: T8.P.2670180


title: T8.P.2670173


title: T0.D.2670177


title: T8.D.2670168


title: T0.P.2670173


title: T0.D.2670168


title: T8.D.2670162


title: T0.P.2670161


title: T8.P.2670161


title: T8.D.2670160


title: T0.D.2670160


title: T8.P.2670157


title: T0.P.2670157


title: T8.D.2670153


title: T0.P.2670180


title: T8.P.2670152


title: T0.D.2670153


title: T0.P.2670186


title: T0.P.2670152


title: T8.D.2670147


title: T0.D.2670147


title: T8.D.2670183


title: T8.P.2670145


title: T0.P.2670142


title: T0.P.2670145


title: T0.P.2670139


title: T0.D.2670136


title: T0.D.2670162


title: T8.D.2670136


title: T8.P.2670139


title: T8.D.2670129


title: T0.D.2670129


title: T0.D.2670128


title: T0.D.2670122


title: T8.D.2670124


title: T0.D.2670124


title: T8.D.2670122


title: T0.D.2670118


title: T8.P.2670142


title: T8.P.2670117


title: T0.D.2670119


title: T8.D.2670118


title: T0.P.2670117


title: T8.P.2670116


title: T0.P.2670116


title: T8.P.2670134


title: T8.D.2670108


title: T0.D.2670108


title: T8.P.2670107


title: T0.D.2670115


title: T8.D.2670128


title: T0.P.2670107


title: T8.D.2670101


title: T0.D.2670103


title: T8.D.2670100


title: T0.D.2670100


title: T8.D.2670099


title: T8.D.2670119


title: T0.P.2670098


title: T0.D.2670099


title: T8.D.2670097


title: T8.P.2670098


title: T8.D.2670115


title: T0.D.2670097


title: T0.P.2670093


title: T0.D.2670086


title: T8.P.2670088


title: T8.D.2670086


title: T8.P.2670093


title: T0.P.2670088


title: T0.P.2670134


title: T8.D.2670103


title: T0.P.2670085


title: T8.P.2670085


title: T0.D.2670084


title: T0.D.2670101


title: T8.P.2670075


title: T0.D.2670076


title: T8.D.2670076


title: T8.D.2670084


title: T0.P.2670073


title: T0.P.2670075


title: T8.P.2670073


title: T8.D.2670072


title: T8.P.2670068


title: T0.P.2670068


title: T0.P.2670067


title: T0.D.2670066


title: T8.D.2670066


title: T8.D.2670062


title: T0.D.2670062


title: T0.D.2670061


title: T8.P.2670060


title: T0.D.2670042


title: T8.D.2670042


title: T8.P.2670045


title: T0.P.2670060


title: T0.P.2670045


title: T0.P.2670037


title: T8.P.2670036


title: T0.D.2670038


title: T8.D.2670038


title: T0.D.2670072


title: T0.P.2670033


title: T0.P.2670031


title: T8.P.2670033


title: T0.P.2670036


title: T0.D.2670029


title: T8.D.2670029


title: T8.P.2670031


title: T8.P.2670067


title: T0.D.2670027


title: T0.D.2670028


title: T8.D.2670061


title: T8.D.2670028


title: T0.P.2670026


title: T8.P.2670026


title: T8.D.2670024


title: T0.D.2670024


title: T8.P.2670037


title: T0.D.2670019


title: T8.D.2670012


title: T0.D.2670022


title: T8.D.2670001


title: T8.P.2670011


title: T8.P.2670004


title: T0.P.2670004


title: T0.D.2670012


title: T0.P.2670011


title: T0.D.2670001


title: T8.D.2670027


title: T8.D.2670019


title: ET1_JQ1_2

city: San Francisco

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

description: Cells were pre-treated with JQ1 (100uM) for 3 hours before ET-1 (10nM) stimulation for 18 hours

data_processing:
Adapters and barcodes were trimmed, and low-quality reads were filtered using Fastq-mcf
High quality sequences were aligned to hg38 (human) with Tophat 2.0.13 and assigned to Ensembl genes and counted using "featureCounts" part of the Subread suite
Raw counts were used as inputs to DESeq (v.1.25.0)
Genome_build: hg38
Supplementary_files_format_and_content: text file with read counts

source_name: human derived iPS cardiomyocytes

growth_protocol: iPS cardiomyocytes were cultured in conditions recommended by the manufactuer  (Cellular Dynamics)

extract_protocol:
Total RNA was isolated using Trizol reagent and the Aurum purification kit (BioRad, 732-6830)
Paired-end libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold rRNA depletion (Illumina)

treatment_protocol: iPS cardiomyocytes were pre-treated with JQ1 (100uM) vs. DMSO for 3 hours followed by stimulation with ET-1 (10nM) for 18 hours before RNA was harvested

value: ET1 JQ1


title: ET1_JQ1_4


title: ET1_JQ1_1


title: Baseline_DMSO_2

description: Cells were pre-treated with DMSO for 3 hours and were not stimulated with ET-1

value: baseline DMSO


title: Baseline_DMSO_4


title: ET1_DMSO_1

description: Cells were pre-treated with DMSO for 3 hours and were then stimulated with ET-1 (10nM) for 18 hours

value: ET1 DMSO


title: ET1_DMSO_3


title: Baseline_DMSO_3


title: ET1_DMSO_2


title: T8.D.2670022

tag: time point


title: Baseline_DMSO_1


title: IgG_shUHRF1

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

description:
IgG library of Y79 cells lentivirally transduced with UHRF1 shRNA construct
null

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 hg19 whole genome using bowtie v2.2.5 with default parameter for single end and paired end reads seperately
Unique mapped reads were extracted for further analysis, DMR(Differential Methylation Region) analysis were performed by using  SICER.sh and SICER-df.sh script from SICER software v1.1 with parameter -W 200 -G 800 -FDR 0.05
Candidate peaks were annoted by annotedPeaks.pl from  HOMER v4.8.3
Genome_build: hg19
Supplementary_files_format_and_content: SCICER output format as descripted below: 'Sample1_single-W200-G800-islands-summary' contains sample 1-sourced candidate islands against sample 3 (control library) identified by SICER.sh in SICER tool packages, while ‘Sample2_single-W200-G800-islands-summary’ contains the similar comparison result in sample 2 using sample 4 as control library. The above two files are tab-delimited format with 7 columns : chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, and FDR_threshold. Additionally, the other 3 processed file were generated by SICER-df.sh script provided by SICER package. File name of each result presents the comparison relationship during each analysis, for example, “Sample8-and-Sample5-W200-G800-summary”stored comparison between sample 8 and sample 5 by taking sample 8 as KO (knock out) sample and sample 5 as WT (wild type) sample. Readers should also notice that the control file of KO samples like sample 8,9,10 is sample 12 and corresponding control file of WT samples including sample 5,6,7 is sample 11. For format of 3 file, they are tab-delimited 13 columns files with header information: Chrom, start, end, Readcount_KO, Normalized_Readcount_KO, Readcount_WT, Normalized_Readcount_WT, Fc_KO_vs_WT, pvalue_KO_vs_WT, FDR_KO_vs_WT, Fc_WT_vs_KO, pvalue_WT_vs_KO, FDR_WT_vs_KO. The detailed format information could be found at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152844/

source_name: Retina

extract_protocol:
After lentiviral gene knockdown, genomic DNA from each sample was isolated and fragmented for adapter ligation followed by immunoprecipitation with a 5meC antibody
Fragmented genomic DNA was subjected to adapter ligation using KAPA LTP Library preparation kit (KAPABiosystems) according to the manufacturer’s instructions

tag: cell type

value: Y79 retinoblastoma cell line (ATCC HTB18)

tag: medip antibody

value: IgG

tag: transduction

value: control shRNA


title: ET1_DMSO_4


title: 100M-83 Wild-type 8DAP

city: College Station

first: John

last: Mullet

address: 300 Olsen Boulevard

institute: Texas A&M University

data_processing:
The sequence reads were aligned with the sorghum transcript sequence Sbicolor-v2.1_255 version (Phytozome) using CLC Main Workbench Version 7 (CLC Inc., Aarhus, Denmark).
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
RNA-seq datasets were analyzed using the Edge statistical test in the CLC Main Workbench Version 7 (CLC Inc., Aarhus, Denmark).
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample …

organism: Sorghum bicolor

source_name: tiller buds

growth_protocol: PhyB-1 and wild-type plants were grown in the growth chamber and buds in the the first leaf axil were sampled (three biological replicates for each sample) at 6 DAP (Days After Planting), 7 DAP and 8 DAP.

extract_protocol:
RNAs were extracted from tiller buds using TRIzol (Invitrogen)
RNA-seq libraries were prepared using the TruSeq™ RNA Sample Prep Kit v2 (Illumina, Inc.), following the recommended protocol.

tag: strain

value: tiller bud

value: First leaf axil

tag: age

value: 8 Days After Planting

tag: genotype

value: wild type


title: 100M-82 Wild-type 8DAP

tag: tissue


title: 100M-81 Wild-type 8DAP


title: MeDIP_shUHRF1-3

description:
Experimental MeDIP library 3 of three biological replicates, lentiviral transduction of UHRF1 shRNA construct into Y79 retinoblastoma cell line
Sample10-and-Sample7-W200-G800-summary.txt

value: 5meC (Diagenode, C15200081)

value: UHRF1 shRNA


title: IgG_shCTL

description:
IgG library of Y79 cells lentivirally transduced with control shRNA construct
null


title: MeDIP_shCTL-2

description:
Control MeDIP library 2 of three biological repilcates, lentiviral transduction of control shRNA construct into Y79 retinoblastoma cell line
Sample9-and-Sample6-W200-G800-summary.txt


title: 100M-73 Wild-type 7DAP

value: 7 Days After Planting


title: MeDIP_shUHRF1-1

description:
Experimental MeDIP library 1 of three biological replicates, lentiviral transduction of UHRF1 shRNA construct into Y79 retinoblastoma cell line
Sample8-and-Sample5-W200-G800-summary.txt


title: ET1_JQ1_3


title: 100M-72 Wild-type 7DAP


title: 100M-71 Wild-type 7DAP


title: MeDIP_shUHRF1-2

description:
Experimental MeDIP library 2 of three biological replicates, lentiviral transduction of UHRF1 shRNA construct into Y79 retinoblastoma cell line
Sample9-and-Sample6-W200-G800-summary.txt


title: MeDIP_shCTL-1

description:
Control MeDIP library 1 of three biological repilcates, lentiviral transduction of control shRNA construct into Y79 retinoblastoma cell line
Sample8-and-Sample5-W200-G800-summary.txt


title: MeDIP_shCTL-3

description:
Control MeDIP library 3 of three biological repilcates, lentiviral transduction of control shRNA construct into Y79 retinoblastoma cell line
Sample10-and-Sample7-W200-G800-summary.txt


title: 100M-62 Wild-type 6DAP

value: 6 Days After Planting


title: 100M-63 Wild-type 6DAP


title: Input_Y79

description:
Input library of genomic DNA from Y79 retinoblastoma cell line
Sample2_single-W200-G800-islands-summary.txt


title: 100M-61 Wild-type 6DAP


title: Input_NR

description:
Input library of genomic DNA from normal retina (NR)
Sample1_single-W200-G800-islands-summary.txt

value: normal retina (12 years old)


title: MeDIP_Y79

description:
MeDIP library of Y79 retinoblastoma cell line
Sample2_single-W200-G800-islands-summary.txt


title: patient_15_gastric_tissue

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

country: Germany

institute: Christian-Albrechts-University of Kiel

description: small RNA

data_processing:
Trimming of adapter sequences: cutadapt -b TGGAATTCTCGGGTGCCAAGG -m 18 -q 30 –discard-untrimmed (cutadapt v1.9.dev6)
Filtering of reads mapped to viral genome (RefSeq), human tRNAs, rRNAs, snRNAs and sRNAs (Rfam) : blastn  -word_size=18 (BLASTN v2.2.30)
Quantification of miRNAs: miraligner -sub 1 -trim 3 -add 3 -s hsa -i $reads -db miRBase_v21 -o "isomir_$sample" -freq (SeqBuster)
Supplementary_files_format_and_content: tab-delimited text files include miRNA and iso-miRNA counts for each sample

source_name: gastric tissue

extract_protocol:
The RNA extraction was performed using standard protocol of commercial miRNeasy FFPE Kit miRNeasy FFPE Kit by QIAGEN
Small RNA libraries were prepared using standard protocol of TruSeq Small RNA Sample Preparation Kit by Illumina

tag: gender

value: Male


title: 58M-82 PhyB-1  8DAP


title: 58M-83 PhyB-1  8DAP


title: T0.D.2670326

value: Duloxetine 60 mg

value: RES


title: patient_15_gastric_GIST

description: small RNA

source_name: gastric GIST

tag: cd117 staining

value: Positive

value: Epithelioid

tag: risk grade

value: High


title: 58M-81 PhyB-1  8DAP


title: MeDIP_NR

description:
MeDIP library of normal retina (NR)
Sample1_single-W200-G800-islands-summary.txt


title: 58M-71 PhyB-1 7DAP


title: patient_14_gastric_GIST

description: small RNA

value: Female

value: Spindle

value: Low


title: 58M-62 PhyB-1 6DAP

value: tiller bud

value: First leaf axil


title: patient_13_gastric_tissue

description: small RNA


title: 58M-61 PhyB-1 6DAP


title: patient_13_gastric_GIST

description: small RNA

value: Negative

value: Intermediate


title: patient_12_gastric_tissue

description: small RNA


title: 58M-72 PhyB-1 7DAP


title: 58M-63 PhyB-1 6DAP


title: patient_12_gastric_GIST

description: small RNA


title: patient_11_gastric_tissue

description: small RNA


title: patient_10_gastric_tissue

description: small RNA


title: patient_10_gastric_GIST

description: small RNA


title: patient_11_gastric_GIST

description: small RNA


title: patient_9_gastric_tissue

description: small RNA


title: patient_8_gastric_GIST

description: small RNA


title: patient_9_gastric_GIST

description: small RNA


title: patient_14_gastric_tissue

description: small RNA


title: patient_7_gastric_tissue

description: small RNA


title: patient_7_gastric_GIST

description: small RNA


title: patient_6_gastric_tissue

description: small RNA


title: patient_6_gastric_GIST

description: small RNA


title: BF2 ovary (RNA-seq)

city: ShenZhen

first: Jinmin

last: Lian

address: Building No.11, Beishan Industrial Zone, Yantian District

institute: BGI-ShenZhen

data_processing:
TopHat (v1.4.1) was employed to map the RNA-seq reads to the naked mole rat reference genome (Heter_glaber.v1.7.fa.gz from http://mr.genomics.org.cn) with a segment length of 25 bp. Two mismatches were allowed in each segment. Only RNA-seq reads that were uniquely mapped to the genome and overlapped with annotated exons (gene-reads) in the naked mole rat gene set were kept. Gene expression levels were measured by RPKM (reads per kilobase per million mapped exonic reads). RPKMs in all the sequenced samples were adjusted by a scaling normalization method based on TMM (trimmed mean of M values).
MeDIP-seq reads were aligned to the naked mole rat reference genome using BWA (v0.5.9-r16), allowing two mismatches and one indel. Multiple reads mapping to the same position were regarded as PCR duplicates, and only one of them was kept. Reads mapping to more than one position were discarded. Differentially methylated regions (DMRs) between breeders and subordinates of the same sex were detected using edgeR integrated in the Bioconductor package MEDIPS (v.1.10.0) with a window size of 200 bp and default settings. P-values were adjusted for multiple testing by applying FDR, and windows with adjusted p-values < 0.05 were considered as DMRs. Differentially methylated genes (DMGs) were defined as genes containing DMRs in their putative promoter regions (TSS -2 kb to +500 bp) or gene body regions (exons + introns).
Genome_build: Heter_glaber.v1.7.fa.gz from http://mr.genomics.org.cn
Supplementary_files_format_and_content: Tab-delimited text file includes gene expression levels in terms of RPKM and gene annotations for each samples.

organism: Heterocephalus glaber

source_name: breeding female

growth_protocol: Naked mole rats were housed in the laboratory of Rochelle Buffenstein.

extract_protocol:
For RNA-seq library construction, 2 μg total RNA per sample was treated with DNase I (New England BioLabs) to remove possible contamination with genomic DNA. Then poly (A+) mRNA was purified from the total RNA using the Dynabeads mRNA Purification Kit (Invitrogen), followed by fragmentation using the RNA fragmentation kit (Ambion). Next, the first cDNA strand was synthesized using random hexamer primers and reverse transcriptase (Invitrogen), and second-strand cDNA was synthesized using DNA polymerase I (New England BioLabs). After that, the synthetic double-stranded cDNA was end repaired, followed by 3’-end addition of dA, adapter ligation and size selection according to Illumina’s protocols. Finally, the selected products were amplified by 15 PCR cycles to yield the RNA-seq libraries.
All RNA-seq libraries were subjected to 90 bp paired-end sequencing on an Illumina HiSeq 2000 platform.
We analyzed brains from all eight individuals separately, but female ovaries were only large enough for individual analysis in breeders, whereas subordinate ovaries were so small that 3–5 of them had to be pooled for gene expression analyses. The testes of breeding and non-breeding males were not visually different, but breeder status was known because these males had previously sired pups. RNA and DNA were isolated as described in Kim, et al. Nature (2011).

treatment_protocol: Tissues were obtained from male (n = 2) and female (n = 2) breeders as well as male (n = 2) and female (n = 2) non-breeders (subordinates).

tag: age (year)

value: ovary

value: female


title: BF1 ovary (RNA-seq)


title: SM1 testis (RNA-seq)

source_name: subordinate male

value: testis

value: male


title: SF-mix2 ovary (RNA-seq)

source_name: subordinate female (mix of 3 individuals)


title: SF-mix1 ovary (RNA-seq)

source_name: subordinate female (mix of 5 individuals)

value: unknown


title: BM1 testis (RNA-seq)

source_name: breeding male


title: patient_5_gastric_GIST

description: small RNA


title: SM2 testis (RNA-seq)


title: SM2 brain (MeDIP-seq)

extract_protocol:
For MeDIP-seq libraries construction, 5 μg DNA was cut into 100 - 500 bp fragments with a Bioruptor sonicator (Diagenode), followed by end repair, 3’-end addition of dA, and adapter ligation according to Illumina’s protocols. Adaptor-ligated DNA was then immunoprecipitated by a monoclonal anti-methylcytidine antibody. The specificity of the enrichment was confirmed by qPCR using SYBR green mastermix (Applied Biosystems) with primers for positive and negative internal control DNA of non-human samples supplied in the Magnetic Methylated DNA Immunoprecipitation kit (Diagenode). The enriched fragments were purified on ZYMO DNA Clean & Concentrator-5 columns following the manufacturer’s instructions, followed by amplification via 10 adaptor mediated PCR cycles to yield the MeDIP-seq libraries.
All MeDIP-seq libraries were subjected to 50 bp paired-end sequencing on an Illumina HiSeq 2000 platform.
We analyzed brains from all eight individuals separately, but female ovaries were only large enough for individual analysis in breeders, whereas subordinate ovaries were so small that 3–5 of them had to be pooled for gene expression analyses. The testes of breeding and non-breeding males were not visually different, but breeder status was known because these males had previously sired pups. RNA and DNA were isolated as described in Kim, et al. Nature (2011).

value: brain


title: SM1 brain (MeDIP-seq)


title: patient_4_gastric_GIST

description: small RNA

value: Male


title: BM2 brain (MeDIP-seq)


title: SM2 brain (RNA-seq)


title: patient_4_gastric_tissue

description: small RNA


title: patient_8_gastric_tissue

description: small RNA


title: BM2 testis (RNA-seq)


title: patient_3_gastric_GIST

description: small RNA

value: Positive


title: 58M-73 PhyB-1 7DAP

value: 7 Days After Planting


title: patient_2_gastric_tissue

description: small RNA


title: SM1 brain (RNA-seq)


title: patient_5_gastric_tissue

description: small RNA


title: patient_2_gastric_GIST

description: small RNA

value: Epithelioid


title: BM1 brain (MeDIP-seq)


title: patient_1_gastric_GIST

description: small RNA

value: Female

value: High


title: SF2 brain (MeDIP-seq)

source_name: subordinate female


title: SF2 brain (RNA-seq)


title: SF1 brain (MeDIP-seq)


title: BF2 brain (MeDIP-seq)


title: 4tU-seq 4.5h Rep2

city: Boston

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
Paired-end 50 base reads with additional 6 base reads of barcodes were obtained in replicates for all samples.
Reads were demultiplexed and mapped with STAR 2.3.0  to the concatenated S.pombe genome and external spike-in sequences with maximum one mismatch (--outFilterMismatchNmax 2) allowing for only one mapping position (--outFilterMultimapScoreRange 0).
SAM files were filtered using Samtools  for alignments with MAPQ of at least 7 (-q 7) and only proper pairs (-f99, -f149, -f84, -f163) were selected.
PicardTools (version 1.118) CollectInsertSizeMetrics was used to determine average insert size and standard deviation with default settings: Deviations: 10.0; Minimum percentage: 0.05, Metric Accumulation Level: All reads
Genome_build: ASM294v2
Supplementary_files_format_and_content: tab-delimited files containing fragment counts per sample, based on the annotation of Eser et al, MSB 2016, calculated by the "summarizeOverlaps" function in the "GenomicAlignments" R/Bioconductor package (with parameters: ignore.strand=FALSE, singleEnd=FALSE, mode="IntersectionStrict").  For TU info, see TU_details_msb156526-sup-0003-DatasetEV1.txt.
Supplementary_files_format_and_content: bigwig files contain strand specific read coverages

organism: Schizosaccharomyces pombe

source_name: 4tU-seq 4.5h, ASP167

growth_protocol: Streak out ASP167 (h- spt5::hphMX6-Pnmt81-spt5+-V5-IAA17-kanMX6 ade6::ade6+-Padh15-skp1-OsTIR1-natMX6-Padh15-skp1-AtTIR1-2NLS-9myc ura4-D18) from glycerol stock onto an EMM plate. Inoculate single colonies of ASP167 into 5 ml EMM cultures and grow overnight at 30oC. The next evening, measure the OD600 and dilute the culture into 370 ml EMM so that the culture will be at OD600 = 0.4 the next morning. At OD 0.4 (0 hr time point) add thiamine and NAA. Collect samples after 2.5 hr and 4.5 hr.

extract_protocol:
4tU-labeled RNAs were purified as described in Sun et al, 2013
Libraries were constructed using the Ovation Universal RNA-Seq-System (NuGen).

treatment_protocol: At time point 0hr, 2.5hr and 4.5 hr cells were labeled with 4thiouracil (final concentration 5mM) for 10 min, spin immediately at 30°C at 3500 rpm for 1 min.

value: thiamine + 1-Napthaleneacetic acid (NAA)

tag: treatment time

tag: labeled with


title: BF2 brain (RNA-seq)


title: patient_3_gastric_tissue

description: small RNA


title: 4tU-seq 4.5h Rep1


title: 4tU-seq 2.5h Rep1

source_name: 4tU-seq 2.5h, ASP167


title: 4tU-seq 2.5h Rep2


title: BM2 brain (RNA-seq)


title: 4tU-seq 0h Rep2

source_name: 4tU-seq 0h, ASP167

value: 0 hr


title: 4tU-seq 0h Rep1