title: REH-EpiGnome

extract_protocol:
TruSeq DNA Methylation/EpiGnome
QIAGEN All Prep protocol

value: TruSeq DNA Methylation/EpiGnome


title: E93_RNA-seq

status: Public on Oct 27 2016

type: SRA

city: Stockholm

first: Nigel

last: Kee

address: Nobels vag 3

country: Sweden

institute: LICR Stockholm

library_source: transcriptomic

data_processing:
reads were aligned to the mm10 genome using default settings of STAR v2.3.0
RPKM values were derived using rpkmforgenes, and the Ensemble v75 annotation
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and raw counts for each sample. RPKM values occupy the first half of the columns. Raw counts occupy the second half of the columns

molecule: total RNA

organism: Mus musculus

source_name: E10.5 Single Cell

extract_protocol:
Smart-seq2
Nextera XT DNA library preparation kits (FC-131-1024) using dual indexes (i5 + i7), then sequenced on an Illumina HiSeq 2000

tag: strain

value: C57BL/6 Heterozygous Lmx1a-EGFP

tag: developmental stage

tag: tissue

value: developing ventral midbrain cells


title: E94_RNA-seq


title: MOI60 Ad-AldoA, one miR-194 8-mer site, rep 2

city: South San Francisco

first: Vikram

last: Agarwal

state: CA

address: 1130 Veterans Blvd

country: USA

institute: Calico Life Sciences

description:
mRNA
MOI60_NoSite_vs_miR194_8mer.txt

data_processing:
A genome index was built for the latest build of the mouse genome (mm10) using STAR v. 2.4 (options --runMode genomeGenerate --genomeFastaFiles mm10.fa --sjdbGTFfile Ensembl72.gtf --sjdbOverhang 125 --sjdbGTFtagExonParentTranscript Parent) (Dobin et al. 2013), with “Ensembl72.gtf” referring to mouse transcript models annotated in Ensembl release 72. For ES cell libraries, the mCherry and eYFP sequences were also included in the --genomeFastaFiles parameter.
Raw reads were aligned to this genome index using STAR v. 2.4 (options --outFilterType BySJout --outFilterMultimapScoreRange 0 --readMatesLengthsIn Equal --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --outStd SAM) (Dobin et al., 2013). For ES cell libraries, reads were also mapped to mCherry and eYFP sequences, which were included in the genome index.
Pooling all biological replicates of a particular sample, differential expression analysis was performed between two samples of interest using cuffdiff v. 2.2.1 (options --library-type fr-firststrand -b mm10.fa -u --max-bundle-frags 100000000) (Trapnell et al., 2013), using mouse transcript models of protein-coding and long non-coding RNA genes annotated in Ensembl release 72. For ES cell libraries, mCherry and eYFP sequences were also quantified.
For each biological replicate, expression level data (measured in Fragments Per Kilobase Million, or FPKM) was computed using cufflinks v. 2.2.1 (options --library-type fr-firststrand -b mm10.fa -u --max-bundle-frags 100000000 --compatible) (Trapnell et al., 2010), using mouse transcript models of protein-coding and long non-coding RNA genes annotated in Ensembl release 72. For ES cell libraries, mCherry and eYFP sequences were also quantified.
For small RNA-seq data, we initially trimmed the first 8 nucleotides from the 5' end, which were added to each sequence to minimize the effect of ligation bias. We then counted the number of occurrences in which the first 20 nucleotides of the trimmed sequence matched a known mature Mus musculus miRNA sequence deposited in miRBase version 20.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing gene expression measurements (FPKM), log2(fold changes), and statistical significance values for differential expression comparisons. Separate tab-delimited text file containing gene expression measurements (FPKM) for individual biological replicates, with upper and lower confidence intervals for FPKM values. For small RNA seq data, a tab-delimited text file consisting of the name of the miRNA, the miRNA seed sequence, the observed number of reads detected, and Reads Per Million (RPM) normalized abundance measurement.

molecule: polyA RNA

source_name: Primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from liver as reported by Zhang et al. (PLoS One, 2012; also see http://www.mouselivercells.com/), grown for 4-6 hours in DMEM 1g/l glucose (1% Penicillin-Streptomycin, 1% Glutamax and 10% fetal bovine serum) and grown for 24 hours in HepatoZYME-SFM (1% Penicillin-Streptomycin and 1% Glutamax) at 300,000 cells per 6-well and lysed 30 hours post isolation.

extract_protocol:
RNA was extracted using Trizol according to the manufacturer's instructions and the RNA treated with DNase prior to library preparation.
For RNA-seq, total RNA was treated with the DNA-free Kit (Life Technologies), cleaned up with an RNAeasy MinElute Cleanup Kit (Qiagen) and the quality controlled with an Agilent 2100 Bioanalyzer. Library preparation and sequencing were performed by Fasteris SA (Switzerland) or by the Functional Genomics Centre Zürich (FGCZ), using an Illumina HiSeq 2500 machine. For small RNA-seq total RNA was size fractionated (18–35 nt), followed by ligation of 3’ preadenylated adapter (AppNNNNAGATCGGAAGAGCACACGTCTddC) and 5’ adapter (Truseq small RNA 5’ adapter RA5 + 8Ns, GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNN), reverse transcription, PCR amplification, and Solexa sequencing. The 8 and 4 random nucleotides (Ns) on the 5' and 3' ends, respectively, were added to minimize the effect of ligation bias during the quantification step.

treatment_protocol: Adenovirus were added 4-6 hours after isolation and left on the cells for 24 hours

tag: cell type

value: cells derived from liver


title: E92_RNA-seq


title: MOI80 Ad-AldoA, one let-7 8-mer site, rep 2

description: mRNA


title: F103_RNA-seq

source_name: E12.5 Single Cell


title: NA10860-SPLAT

city: Uppsala

first: Jessica

last: Nordlund

address: Academic Hospital, Entrance 70, 3rd floor

department: Medical Sciences

institute: Uppsala University

library_source: genomic

data_processing:
Base calling: RTA 1.18.61
Quality and adapter trimming; TrimGalore v0.37 --paired , --trim1
Alignment: Bismark v0.14 (bowtie2)
Deduplication: Bismark v0.14
Methylation calling: Bismark v0.14
Genome_build: GRCh37
Supplementary_files_format_and_content: bedgraph: 4th column is methylation level
Supplementary_files_format_and_content: bigWig: data value is number of reads covering position

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblastoid cell line

extract_protocol:
SPLAT
QIAGEN All Prep protocol

tag: cell line

value: lymphoblastoid cell line

tag: library preparation protocol

value: SPLAT


title: MOI60 Ad-AldoA, one miR-194 8-mer site, rep 1

description:
mRNA
MOI60_NoSite_vs_miR194_8mer.txt


title: REH-Accel

source_name: ALL cell line

extract_protocol:
Accel-NGS Methyl Seq
QIAGEN All Prep protocol

value: REH

value: ALL cell line

value: Accel-NGS Methyl Seq


title: MOI60 Ad-AldoA, no sites, rep 2

description: mRNA


title: E91_RNA-seq


title: NA10860-NEB

extract_protocol:
NEBNextUltra
QIAGEN All Prep protocol

value: NEBNextUltra


title: MOI60 Ad-AldoA, no sites, rep 1

description: mRNA


title: E9_RNA-seq


title: E89_RNA-seq


title: NA10860-EpiGnome


title: E88_RNA-seq


title: E87_RNA-seq


title: MOI63 Ad-AldoA, one miR-122 7mer site, rep 2

description:
mRNA
MOI63_NoSite_vs_miR122_7mer.txt


title: NA10860-Accel


title: E86_RNA-seq


title: E97_RNA-seq


title: MOI63 Ad-AldoA, one miR-122 7mer site, rep 1

description:
mRNA
MOI63_NoSite_vs_miR122_7mer.txt


title: E85_RNA-seq


title: E83_RNA-seq


title: MOI63 Ad-AldoA, one miR-122 6mer site, rep 2

description:
mRNA
MOI63_NoSite_vs_miR122_6mer.txt


title: MOI63 Ad-AldoA, one miR-122 6mer site, rep 1

description:
mRNA
MOI63_NoSite_vs_miR122_6mer.txt


title: E82_RNA-seq


title: RaoHuntley-2014-HIC074

city: Cambridge

first: Miriam

last: Huntley

state: MA

address: 29 Oxford Street

institute: Harvard University

data_processing:
Library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the b37 (human), mm10 (mouse), or rheMac2 (rhesus macaque).
PCR duplicates, low mapping quality and unligated reads were removed using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al, Cell 2014l)
Contact matrices were constructed at various resolutions and normalized using an in-house Hi-C analysis pipeline (see Rao, Huntley, et al, Cell 2014)
Genome_build: b37 (human), mm10 (mouse), rheMac2 (rhesus macaque)
Supplementary_files_format_and_content: Contact matrices: a text file with the raw observed contact matrix in sparse matrix notation at a given resolution. Only the upper triangle of the matrix is provided (i.e. i<=j), the matrix is symmetric, so M_i,j = M_j,i. At this stage of processing, read pairs where one or both ends do not align to the reference genome have already been removed, as well as chimeric ambiguous reads (see Section II.a.2 of the Extended Experimental Procedures of Rao, Huntley, et al., Cell 2014 for a definition of chimeric ambiguous reads). In addition, duplicate reads (reads where both ends align to within +/- 4bp of each other) have been removed as well (see Section II.a.3 of the Extended Experimental Procedures of Rao, Huntley, et al., Cell 2014 for a full description of duplicate removal). Full details of the Hi-C processing pipeline used in this study are provided in Section II.a. of the Extended Experimental Procedures of Rao, Huntley, et al., Cell 2014.
Supplementary_files_format_and_content: Normalization files: normalization vectors that can be used to transform the raw contact matrices M into normalized matrices M*.  Each file is ordered such that the first line of the normalization vector file is the norm factor for the first row/column of the corresponding raw contact matrix, the second line is the factor for the second row/column of the contact matrix, and so on. To normalize, an entry M_i,j in a *RAWobserved file, divide the entry by the corresponding norm factors for i and j. (See section II.b of the Extended Experimental Procedures of Rao, Huntley, et al., Cell, 2014 for more information about the different types of normalizations.)
Supplementary_files_format_and_content: HiCCUPS_looplist.txt files contain loop calls generated via HiCCUPS; first three fields represent the locus participating in the loop closer to the p-end of the chromosome; fields 4-6 represent the locus participating in the loop closer to the q-end of the chromosome; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 represents the observed number of counts at the loop; fields 9-12 represent the expected number of counts at the loop using four different expected models; fields 13-16 are the q-values over each of the expected values; field 17 is the number of enriched pixels that was clustered into a particular loop; field 18-19 are the centroid of the loop; field 20 is the radius of the loop
Supplementary_files_format_and_content: Arrowhead_domainlist.txt files contain domain calls generated via Arrowhead; first 6 fields represent the boundaries of the domain; field 7 represents the color used to display the feature in Juicebox (a Hi-C data visualization software, see www.aidenlab.org/juicebox); field 8 is the corner score for the domain (see Rao, Huntley, et al); fields 9-12 are the component scores used in the Arrowhead algorithm (see Rao, Huntley, et al)
Supplementary_files_format_and_content: merged_nodups.txt files contain filtered, "normal" contacts. Each line represents a single Hi-C read pair that has passed the alignment and duplicate removal stages. The format of each line of the file is: read_name, strand1, chromosome1, position1, fragment-index1, strand2, chromosome2 ,position2, fragment-index2, mapq1, mapq2
Supplementary_files_format_and_content: collisions.txt.gz files contain the contacts that have 3 or more loci.

source_name: Erythroleukemia

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Specific protocols and there descriptions are indicated as additional columns in the SAMPLES section
Standard Illumina library construction protocol was performed, and libraries were sequenced on the HiSeq X Ten/NextSeq/HiSeq2500 following the manufacturer's protocols.

tag: protocol

value: in situ Hi-C


title: E90_RNA-seq


title: MOI63 Ad-AldoA, one miR-122 8mer site, rep 2

description:
mRNA
MOI63_NoSite_vs_miR122_8mer.txt


title: E8_RNA-seq


title: E79_RNA-seq


title: RaoHuntley-2014-HIC072


title: E81_RNA-seq


title: RaoHuntley-2014-HIC070


title: E84_RNA-seq


title: E78_RNA-seq


title: MOI63 Ad-AldoA, no mir-122 site, rep 2

description: mRNA


title: RaoHuntley-2014-HIC071


title: E75_RNA-seq


title: E77_RNA-seq


title: E73_RNA-seq


title: RaoHuntley-2014-HIC069


title: E72_RNA-seq


title: MOI63 Ad-AldoA, no mir-122 site, rep 1

description: mRNA


title: E71_RNA-seq


title: RaoHuntley-2014-HIC067

source_name: Epidermal Keratinocytes


title: MOI20 Ad-AldoA, one miR-122 7mer site, rep 2

description:
mRNA
MOI20_NoSite_vs_miR122_7mer.txt


title: RaoHuntley-2014-HIC066


title: E80_RNA-seq


title: E7_RNA-seq


title: MOI20 Ad-AldoA, one miR-122 7mer site, rep 1

description:
mRNA
MOI20_NoSite_vs_miR122_7mer.txt


title: MOI63 Ad-AldoA, one miR-122 8mer site, rep 1

description:
mRNA
MOI63_NoSite_vs_miR122_8mer.txt


title: RaoHuntley-2014-HIC073


title: RaoHuntley-2014-HIC065


title: E67_RNA-seq


title: E68_RNA-seq


title: MOI20 Ad-AldoA, one miR-122 6mer site, rep 2

description:
mRNA
MOI20_NoSite_vs_miR122_6mer.txt


title: RaoHuntley-2014-HIC063

source_name: Mammary Epithelial Cells


title: E65_RNA-seq


title: E66_RNA-seq


title: E64_RNA-seq


title: E62_RNA-seq


title: E63_RNA-seq


title: RaoHuntley-2014-HIC062


title: RaoHuntley-2014-HIC061


title: E61_RNA-seq


title: MOI20 Ad-AldoA, one let-7 8mer site, rep 2

description:
mRNA
MOI20_NoSite_vs_let7_8mer.txt


title: E60_RNA-seq


title: MOI20 Ad-AldoA, one miR-122 8mer site, rep 2

description:
mRNA
MOI20_NoSite_vs_miR122_8mer.txt


title: E6_RNA-seq


title: RaoHuntley-2014-HIC060


title: E70_RNA-seq


title: MOI20 Ad-AldoA, one let-7 8mer site, rep 1

description:
mRNA
MOI20_NoSite_vs_let7_8mer.txt


title: E59_RNA-seq


title: MOI20 Ad-AldoA, one miR-122 8mer site, rep 1

description:
mRNA
MOI20_NoSite_vs_miR122_8mer.txt


title: E69_RNA-seq


title: MOI20 Ad-AldoA, one miR-122 6mer site, rep 1

description:
mRNA
MOI20_NoSite_vs_miR122_6mer.txt


title: E58_RNA-seq


title: RaoHuntley-2014-HIC058


title: E57_RNA-seq


title: E56_RNA-seq


title: E54_RNA-seq


title: MOI20 Ad-AldoA, no mir-122 site, rep 2

description: mRNA


title: RaoHuntley-2014-HIC056

source_name: Lung Fibroblasts


title: E55_RNA-seq


title: MOI20 Ad-AldoA, no mir-122 site, rep 1

description: mRNA


title: E52_RNA-seq


title: RaoHuntley-2014-HIC055


title: E51_RNA-seq


title: MOI11 Ad-AldoA, one miR-122 7mer site, rep 2

description:
mRNA
MOI11_NoSite_vs_miR122_7mer.txt


title: RaoHuntley-2014-HIC059


title: E50_RNA-seq


title: RaoHuntley-2014-HIC054


title: E5_RNA-seq


title: MOI11 Ad-AldoA, one miR-122 7mer site, rep 1

description:
mRNA
MOI11_NoSite_vs_miR122_7mer.txt


title: E49_RNA-seq


title: E48_RNA-seq


title: MOI11 Ad-AldoA, one miR-122 6mer site, rep 2

description:
mRNA
MOI11_NoSite_vs_miR122_6mer.txt


title: E47_RNA-seq


title: RaoHuntley-2014-HIC053


title: MOI11 Ad-AldoA, one miR-122 6mer site, rep 1

description:
mRNA
MOI11_NoSite_vs_miR122_6mer.txt


title: RaoHuntley-2014-HIC052


title: RaoHuntley-2014-HIC051


title: E45_RNA-seq


title: MOI11 Ad-AldoA, one let-7 8mer site, rep 2

description:
mRNA
MOI11_NoSite_vs_let7_8mer.txt


title: E44_RNA-seq


title: RaoHuntley-2014-HIC050


title: MOI11 Ad-AldoA, one let-7 8mer site, rep 1

description:
mRNA
MOI11_NoSite_vs_let7_8mer.txt


title: E42_RNA-seq


title: MOI11 Ad-AldoA, one miR-122 8mer site, rep 2

description:
mRNA
MOI11_NoSite_vs_miR122_8mer.txt


title: RaoHuntley-2014-HIC049

source_name: B-lymphoblastoids


title: E40_RNA-seq


title: E39_RNA-seq


title: MOI11 Ad-AldoA, one miR-122 8mer site, rep 1

description:
mRNA
MOI11_NoSite_vs_miR122_8mer.txt


title: E4_RNA-seq


title: E38_RNA-seq


title: MOI11 Ad-AldoA, no sites, rep 2

description: mRNA


title: RaoHuntley-2014-HIC048


title: E37_RNA-seq


title: RaoHuntley-2014-HIC047

value: agar in situ Hi-C - no crosslinking


title: E46_RNA-seq


title: E34_RNA-seq


title: MOI11 Ad-AldoA, no sites, rep 1

description: mRNA


title: E3_RNA-seq


title: E29_RNA-seq


title: RaoHuntley-2014-HIC046


title: E28_RNA-seq


title: E43_RNA-seq


title: E27_RNA-seq


title: RaoHuntley-2014-HIC045


title: RaoHuntley-2014-HIC044


title: WT_E6.5_Epiblast_2

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

description:
mRNA with polyA tail
Epiblast_E6.5_nCount.txt.gz

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling.
Adaptor contamination and low-quality reads were discarded from the raw data.
For RNA-Seq Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and nCount values were generated by HTSeq(version 0.6.1) and then normalized by DESeq2(version 1.6.1).
For PBAT DNA illumina paired-end reads,Bismark(version 0.7.6) were use for sequence alignment, and SingleC data were generated by SAMtools(version 0.1.19-44428cd)
Reference sequence and transcript annotation files were from UCSC genome assembly mm9.
Genome_build: mm9
Supplementary_files_format_and_content: nCount data were generated by DESeq2

source_name: Epiblast of E6.5

growth_protocol: For embryo preparation, mice were maintained on a 12/12 h light/dark cycle. After mating, the morning of appearance of a vaginal plug was designated as embryonic day 0.5 (E0.5). On day 7 of pregnancy, corresponding to E6.5, embryos were recovered carefully from uteri and isolated from decidua using fine forceps and a needle under a dissecting microscope. After incubation in PBS with 0.25% pancreatin (Sigma, P7545) and 0.05% trypsin (Gibco, 27250-018) for 10 minutes at 4 °C, embryos were transferred to Dulbecco's Modified Eagle Medium (DMEM) (Invitrogen) supplemented with 10% FBS and then the visceral endoderm layer was detached from embryos by being gently aspirated through a mouth pipette several times. The epiblast was separated from the extraembryonic ectoderm using a fine tungsten needle. The visceral endoderm layer or the extraembryonic ectoderm was used for genotyping.

extract_protocol:
Total RNA was purified from isolated epiblasts by using the Qiagen AllPrep DNA/RNA Mini Kit, treated with DNase.
About 1 ng of extracted RNA was first amplified 18 cycles according to the protocol for single-cell RNA-seq published previously. Briefly, 1 ng of extracted RNA was reverse translated into cDNA, then the free primers were removed by the ExoSAP-IT. TdT was used to add PolyA to the 3’ end of cDNA, the second strand were synthesized, and the double-stranded DNA product were amplified 18 cycles to obtain enough product for DNA library construction. The amplified DNA product was purified by DNA Clean & Concentrator™-5 (Zymo Research), and further purified by Zymoclean™ Gel DNA Recovery Kit (Zymo Research) for the 0.5-8 kb size DNA products. The gel purified products were sheared by Covaris S2 for the generation of fragments about 250 bp in length, and purified with DNA Clean & Concentrator™-5 (Zymo Research). Then NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, Catalog #E7370L) was used to construct a cDNA library, with reagent amount reduced to half of the reactions. The cDNA libraries were sequenced on Illumina HiSeq 2500 instrument with 100-bp reads and paired-end parameter.
single cell RNA-seq

treatment_protocol: A pool of 8 WT and 9 Tet-null fresh epiblasts were disrupted and homogenized in Buffer RLT Plus respectively, then snap-frozen in liquid nitrogen and stored at -80 ºC.

value: Epiblast

tag: age

value: Embryonic day 6.5

tag: genotype


title: WT_E6.5_Epiblast_3


title: E24_RNA-seq


title: RaoHuntley-2014-HIC043

value: in situ Hi-C - no crosslinking


title: E21_RNA-seq


title: E25_RNA-seq


title: WT_E6.5_Epiblast_1


title: RaoHuntley-2014-HIC042


title: RaoHuntley-2014-HIC041


title: E20_RNA-seq


title: E2_RNA-seq


title: E30_RNA-seq


title: Tet_TKO_E6.5_Epiblast_2


title: RaoHuntley-2014-HIC040


title: E175_RNA-seq


title: Tet_TKO_E6.5_Epiblast_1


title: E18_RNA-seq


title: E176_RNA-seq


title: RaoHuntley-2014-HIC039


title: E17_RNA-seq


title: RaoHuntley-2014-HIC033

value: supernatant Hi-C


title: RaoHuntley-2014-HIC038


title: E169_RNA-seq


title: E168_RNA-seq


title: E165_RNA-seq


title: E164_RNA-seq


title: RaoHuntley-2014-HIC031

value: agar in situ Hi-C


title: E163_RNA-seq


title: E162_RNA-seq


title: E19_RNA-seq


title: E161_RNA-seq


title: RaoHuntley-2014-HIC029


title: E172_RNA-seq


title: E157_RNA-seq


title: E16_RNA-seq


title: RaoHuntley-2014-HIC028


title: NDGA5_degradome

city: Hangzhou

first: Dongdong

last: Li

state: Zhejiang

address: Yuhangtang Road

department: Food Science and Nutrition

institute: Zhejiang University

data_processing:
Raw reads were filtered before assembly to exclude low quality reads, including adaptors, low quality sequences (reads with more than 5% ambiguous bases) and reads with a Phred quality score Q ≤ 20 using the NGS QC toolkit (Patel & Jain 2012). The resulting clean reads were assembled with Trinity program (Grabherr et al. 2011). Assembled unigenes, which can not be extended on either end, were aligned against the NCBI non-redundant (NR) protein database using the BLASTx with an E-value cut-off of 10−5. All the unigenes also compared with protein databases of Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), euKaryotic Ortholog Groups (KOG) and Pfam using the BLASTx algorithm with E-value cut-off of 10−5. Gene expression levels in each sample were normalized with the read counts per kilobase of exon model per million reads (RPKM) method (Mortazavi et al. 2008). Differential expressed genes (DEGs, P <0.05) were analysed among groups according to the method described by Yu et al. (2012).
sRNA sequencing data were processed as described previously by Li et al. (2013). In addition, the recently released miRbase v 21.0 was applied to indentify conserved miRNAs in strawberry. The differential expression levels of miRNAs based on normalized deep-sequencing counts, was analyzed by Chi-squared nXn test among groups.
The CleaveLand 3.0 software package and the ACGT301-DGE v1.0 program (LC Sciences, Houston, TX, USA) were used for analyzing degradome sequencing data (Addo-Quaye et al. 2009).
Genome_build: n/a
Supplementary_files_format_and_content: counts

organism: Fragaria x ananassa

source_name: strawberry fruit

growth_protocol: Octaploid strawberry plants (Fragaria ananassa ‘Toyonoka’) were planted in a greenhouse (60%-80% relative humidity) with cycles of 14 h light at 25 oC followed by 10 h dark at 20 oC.

extract_protocol:
Transcriptome: Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies, USA) according to the manufacturer’s instructions. RNA samples were treated with RNase free DNase I (Takara, Japan) to avoid genomic DNA contamination. For each group, samples from 10 individual fruits were randomly selected and RNA was extracted separately. Before equal amount pooling, the total RNA quantity and concentration were tested on Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RNA integrity number (RIN) higher than 8.0.
Transcriptome: Paired-end Illumina mRNA libraries were generated in accordance with the manufacturer’s instructions for mRNA-Seq Sample Preparation (Illumina Inc., San Diego, CA, USA). The 7 libraries were subjected to sequencing on an Illumina Hiseq 2000 platform and 100 bp paired-end reads were generated.
miRNA: Seven small RNA libraries of samples as mentioned above were prepared for sRNA analysis according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).
miRNA: Single end sequencing (36 bp) was performed on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.
degradome:7 degradome cDNA libraries were constructed following the procedures previously described by German et al. (2008).

treatment_protocol: 100 μL chemical solutions of ABA (1 μM), ABA biosynthesis blocker nordihydroguaiaretic acid (NDGA, 100 μM) or distilled water (served as control) were injected into each fruit receptacle core through the pedicel with a sterile 100 μL microsyringe.

tag: cultivar

value: Toyonoka

value: Strawberry receptacle

tag: treatment

value: fruit 5 days later after treatment with NDGA on day 0


title: E156_RNA-seq

value: C57BL/6 Heterozygous Lmx1a-EGFP

value: developing ventral midbrain cells


title: NDGA8_degradome

value: fruit 8 days later after treatment with NDGA on day 0


title: E152_RNA-seq


title: RaoHuntley-2014-HIC013


title: E154_RNA-seq


title: E166_RNA-seq


title: E151_RNA-seq


title: E167_RNA-seq


title: E150_RNA-seq


title: RaoHuntley-2014-HIC032

value: pellet in situ Hi-C


title: RaoHuntley-2014-HIC011


title: ABA5_degradome

value: fruit 5 days later after treatment with ABA on day 0


title: E15_RNA-seq


title: CK8_degradome

value: fruit treated with water on day 8


title: RaoHuntley-2014-HIC010


title: E149_RNA-seq


title: RaoHuntley-2014-HIC009


title: E146_RNA-seq


title: CK5_degradome

value: fruit treated with water on day 5


title: ABA8_degradome

value: fruit 8 days later after treatment with ABA on day 0


title: E140_RNA-seq


title: E144_RNA-seq


title: CK0_degradome

value: fruit treated with water two weeks after athesis, set as day 0


title: RaoHuntley-2014-HIC008

value: in situ Hi-C


title: E141_RNA-seq


title: RaoHuntley-2014-HIC004


title: NDGA8_miRNA


title: E14_RNA-seq


title: HTBE_H1N1_MOI5_24h_2

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the human hg38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples

source_name: Human Tracheobronchial Epithelial Cells

growth_protocol: HTBE cells (Lonza) were maintained in PneumaCult-Ex Medium (Stemcell Technologies) according to the manufacturer’s recommendations.

extract_protocol:
1 ml Trizol was added to 5-10 x 10^6 cells and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: 24 hours before infection, HTBE cells (Lonza, Donor 4F1289J) were plated at a density of 2 x 10^6 cells in a 10 cm dish. For infection, growth medium was replaced with virus diluted to the appropriate concentration in Pneumacult-Ex complete medium at a total volume of 2 mL. Dishes were incubated in a cell culture incubator with gentle rocking every 15 minutes. After 60 minutes, the inoculum was removed and cells were washed twice washed gently with 5 mL Pneumacult-Ex. 10 mL of Pneumacult-Ex was added and cells were incubated for the specified length of time.

value: Human Tracheobronchial Epithelial Cells

tag: infection

value: A/California/04/09 (H1N1), MOI 5

tag: time point

tag: biological replicate


title: NDGA5_miRNA


title: E129_RNA-seq


title: ABA8_miRNA


title: E137_RNA-seq


title: HTBE_H1N1_MOI5_24h_1


title: E124_RNA-seq


title: E13_RNA-seq


title: E121_RNA-seq


title: E147_RNA-seq


title: E120_RNA-seq


title: ABA5_miRNA


title: E12_RNA-seq


title: HTBE_H1N1_MOI5_18h_1


title: E118_RNA-seq


title: E117_RNA-seq


title: CK5_miRNA


title: HTBE_H1N1_MOI0_18h_2

value: uninfected (mock control)


title: CK0_miRNA


title: E116_RNA-seq


title: E112_RNA-seq


title: E111_RNA-seq


title: HTBE_H1N1_MOI5_12h_2


title: HTBE_H1N1_MOI0_18h_1


title: HTBE_H1N1_MOI5_18h_2


title: E11_RNA-seq


title: NDGA8_transcriptome


title: ABA8_transcriptome


title: HTBE_H1N1_MOI0_24h_1


title: E113_RNA-seq


title: HTBE_H1N1_MOI5_12h_1


title: E110_RNA-seq


title: E119_RNA-seq


title: NDGA5_transcriptome


title: CK8_miRNA


title: E41_RNA-seq


title: E115_RNA-seq


title: ABA5_transcriptome


title: E114_RNA-seq


title: HTBE_H1N1_MOI0_12h_2


title: CK8_transcriptome


title: E106_RNA-seq


title: HTBE_H1N1_MOI0_12h_1


title: E105_RNA-seq


title: E103_RNA-seq


title: CK5_transcriptome


title: HTBE_H1N1_MOI5_06h_2


title: E101_RNA-seq


title: CK0_transcriptome


title: HTBE_H1N1_MOI5_06h_1


title: E102_RNA-seq


title: E100_RNA-seq


title: E10_RNA-seq


title: HTBE_H1N1_MOI0_06h_2


title: E104_RNA-seq


title: E1_RNA-seq


title: HTBE_H1N1_MOI0_06h_1


title: C9_RNA-seq


title: E108_RNA-seq


title: C8_RNA-seq


title: C72_RNA-seq


title: HTBE_H1N1_MOI5_03h_2


title: RaoHuntley-2014-HIC030

value: agar in situ Hi-C


title: C70_RNA-seq


title: Tet_TKO_E6.5_Epiblast_3

value: Epiblast

value: Embryonic day 6.5


title: E107_RNA-seq


title: C71_RNA-seq


title: HTBE_H1N1_MOI5_03h_1


title: HTBE_H1N1_MOI0_03h_2


title: C7_RNA-seq


title: C67_RNA-seq


title: C69_RNA-seq


title: HTBE_H1N1_MOI0_03h_1


title: C66_RNA-seq


title: C63_RNA-seq


title: C6_RNA-seq


title: HTBE_H5N1_MOI5_18h_1

value: A/Vietnam/1203/04 (H5N1) HALo, MOI 5


title: C62_RNA-seq

value: C57BL/6 Heterozygous Lmx1a-EGFP


title: C59_RNA-seq

value: developing ventral midbrain cells


title: HTBE_H5N1_MOI5_18h_2


title: C64_RNA-seq


title: C57_RNA-seq


title: HTBE_H5N1_MOI0_18h_2


title: C56_RNA-seq


title: HTBE_H5N1_MOI0_18h_1


title: C58_RNA-seq


title: HTBE_H5N1_MOI5_12h_2


title: E170_RNA-seq


title: C54_RNA-seq


title: C51_RNA-seq


title: C68_RNA-seq


title: HTBE_H5N1_MOI0_12h_2


title: HTBE_H5N1_MOI5_12h_1


title: C53_RNA-seq


title: C52_RNA-seq


title: C5_RNA-seq


title: HTBE_H5N1_MOI5_06h_2


title: C60_RNA-seq


title: C43_RNA-seq


title: C47_RNA-seq


title: C42_RNA-seq


title: HTBE_H5N1_MOI5_06h_1


title: C4_RNA-seq


title: C41_RNA-seq


title: C40_RNA-seq


title: HTBE_H5N1_MOI0_06h_1


title: C38_RNA-seq


title: C36_RNA-seq


title: C37_RNA-seq


title: C35_RNA-seq


title: HTBE_H5N1_MOI5_03h_2


title: HTBE_H1N1_MOI0_24h_2


title: HTBE_H5N1_MOI5_03h_1


title: C34_RNA-seq


title: C33_RNA-seq


title: HTBE_H5N1_MOI0_03h_2


title: HTBE_H5N1_MOI0_12h_1


title: C32_RNA-seq


title: C30_RNA-seq


title: C46_RNA-seq


title: C3_RNA-seq


title: HTBE_H5N1_MOI0_03h_1


title: RaoHuntley-2014-HIC068

value: dilution Hi-C


title: C29_RNA-seq


title: C27_RNA-seq


title: HTBE_H5N1_MOI0_06h_2


title: RaoHuntley-2014-HIC064


title: HTBE_H3N2_MOI5_18h_2

value: A/Wyoming/03/03 (H3N2), MOI 5


title: C25_RNA-seq


title: C24_RNA-seq


title: C26_RNA-seq


title: C48_RNA-seq


title: HTBE_H3N2_MOI0_18h_2


title: C23_RNA-seq


title: RaoHuntley-2014-HIC057


title: C39_RNA-seq


title: C22_RNA-seq


title: C21_RNA-seq


title: RaoHuntley-2014-HIC037


title: C20_RNA-seq


title: HTBE_H3N2_MOI0_18h_1


title: C2_RNA-seq


title: C19_RNA-seq


title: RaoHuntley-2014-HIC036


title: HTBE_H3N2_MOI5_12h_2


title: RaoHuntley-2014-HIC035


title: HTBE_H3N2_MOI5_12h_1


title: C18_RNA-seq


title: RaoHuntley-2014-HIC034


title: C16_RNA-seq


title: HTBE_H3N2_MOI0_12h_2


title: C17_RNA-seq


title: HTBE_H3N2_MOI5_18h_1


title: C15_RNA-seq


title: HTBE_H3N2_MOI0_12h_1


title: HTBE_H3N2_MOI5_06h_2


title: RaoHuntley-2014-HIC026


title: C12_RNA-seq


title: RaoHuntley-2014-HIC027


title: RaoHuntley-2014-HIC025


title: C10_RNA-seq


title: HTBE_H3N2_MOI5_06h_1


title: RaoHuntley-2014-HIC024


title: C1_RNA-seq


title: HTBE_H3N2_MOI0_06h_2


title: HTBE_H3N2_MOI0_06h_1


title: 518_ctrl_10w

city: Freiburg

first: Dominica

last: Willmann

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

data_processing:
We aligned these reads to the mm10 build of the mouse genome using TopHat version 2
The aligned reads were counted with the homer software (analyzeRNA) and DEG’s were identified using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: normalized read counts in txt format

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files).

tag: strain background

value: C57BL/6 N

value: 10 weeks

tag: genotype/variation

value: Lsd1 floxed; Control

value: Brown adipose tissue (BAT)


title: 517_ctrl_10w


title: 516_KO_10w

value: Lsd1knock-out; KO


title: RaoHuntley-2014-HIC022

value: in situ Hi-C


title: HTBE_H3N2_MOI5_03h_2

value: Human Tracheobronchial Epithelial Cells


title: 514_ctrl_10w


title: LSD1_ChIPseq BAT

data_processing:
peak finding algorithm MACS 1.41
All peaks with FDR greater than 1 % were excluded from further analysis
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
Genome_build: mm10
Supplementary_files_format_and_content: wiggle files and peak files: wig, bed

source_name: Differentiated primary brown adipocytes

growth_protocol: Mouse primary brown adipocytes were maintained in Dulbecco’s modified Eagle’s medium (DMEM) High Glucose containing 20 % fetal bovine serum (FBS) and 10 mL of 1 M Hepes buffer in dishes coated with collagen.

extract_protocol:
PMID: 26704968
Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
PMID: 19261174

treatment_protocol: Differentiation of primary brown adipocytes was induced by treatment of confluent cells with an adipogenic mixture consisting of 850 nM insulin (Gibco), 1 µM dexamethasone (Calbiochem), 1 µM rosiglitazone (Cayman), 125 nM Indomethacin (Sigma), 1 nM T3 (Sigma), and 500 µM isobutylmethylxanthine (Serva)

value: Control

value: differentiated primary brown adipocytes

tag: passages

tag: chip antibody

value: LSD1 (20752, homemade, Schüle lab)


title: 515_KO_10w


title: C14_RNA-seq

tag: strain

tag: developmental stage


title: 513_KO_10w

tag: tissue


title: RaoHuntley-2014-HIC021

tag: cell line


title: C13_RNA-seq


title: HTBE_H3N2_MOI0_03h_2

tag: cell type

value: uninfected (mock control)


title: HTBE_H3N2_MOI5_03h_1


title: RaoHuntley-2014-HIC020

tag: protocol


title: RaoHuntley-2014-HIC019

value: tethered in situ Hi-C


title: 512_KO_10w

tag: age


title: RaoHuntley-2014-HIC017


title: RaoHuntley-2014-HIC018


title: HTBE_H3N2_MOI0_03h_1


title: dim-5_polyA-mRNAseq

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

data_processing:
Paired-end reads were demultiplexed, trimmed to 50bp (if needed)
Hi-C contact maps were produced according to Imakaev et al. (Imakaev et al. 2012). Briefly, an attempt was made to uniquely map the first 15 base pairs (bp) of each read to the Neurospora genome. If a unique match was not found, the read was extended 5 bp and another attempt was made. This process continued until a unique match was found or the end of the read reached (50 bp).
Read pairs were then assessed using a number of quality control filters, typically removing reads that covered unligated products (Dangling Ends), products that were too close to the restriction site, Self-circles, and extremely large or small fragments.
Read pairs passing all filters (typically 10% of total read pairs) were used to build uncorrected contact maps (arrays) that were then corrected to account for the unequal representation of genomic loci in HiC datasets. Corrected maps were used in all subsequent analyses
To calculate the ratio of observed contacts to expected contacts, the median contact frequency was calculated at each genomic distance (up to a distance of ~3.5 Mb at which point contact frequency had reached background levels) and used as the expected contact frequency at each respective distance.
To directly compare datasets, a fixed number of reads (prior to filtering) were sampled with the program seqtk, such that the sampled number of raw reads from each dataset produced approximately equal numbers of reads that passed the filtering steps.
To make ChIPseq enrichment files across 10kb bins to use for Circos plots, .bcf files were produced using samtools' mpileup function from ChIPseq .bam files, the .bcf files were "fixed" to replace empty positions with zeros, and processed with a custom script to report the ChIP-seq enrichment over 10kb bins (the resulting seven files were catenated into one file).
All python scripts (".py" files) used for Hi-C data processing are available as supplemental information in the manuscript Galazka et al, 2016, Genome Research, except for the modified scripts, plotIntraTelomeres.py and plotInterTelomeres.py, which were used to calculate intra and inter telomeric enrichment in our Hi-C datasets. In addition, the python script K9-K27Quant.py counts the number of Hi-C links originating from a H3K9me3-marked 10kb bin and end in a bin marked by H3K27me2/3, while the python script K9-K27only_Quant.py counts the number of Hi-C links originating from a H3K9me3-marked 10kb bin and end in a bin marked ONLY by H3K27me2/3 (and not H3K9me3). The program count_links_K27marked.py counts the number of Hi-C links in each 10Kb bin marked by H3K27me2/3. The program hicEigenvectorAnalysis.py derives the number of principle components for the whole genome specified using non-iteratively corrected Hi-C .hdf5 datasets. The program hicEigenvector_singleLG.py extracts the Eigenvector of a single Linkage Group from the whole genome data derived from the "hicEigenvectorAnalysis.py" script. The program hicPearsonCorrelationHeatmap.py calculates the Pearson Correlation between all genomic regions and displays them as a heatmap for a specific Linkage Group. These scripts are provided here.
To determine differences in the genome organization caused by mutants, mutants were compared to the WT Hi-C data (NMF39 [GSM1825702] within the GEO dataset GSE71024)
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows. Output file was a .tdf file, displayable on IGV.
For Poly-A mRNA seq, high quality, adapter-less reads were identified (Stacks); Kmer filtering reduced sequencing errors. Reads were mapped (TopHat) to the modified Neurospora genome assembly 12, and sorted (SAMTools), and directionality-preserved read numbers were calculated at each gene ID (HTSeq), adding one read count to prevent abnormal fold changes. Differential gene expression analysis (DESeq) examined replicate differences and pair-wise analyses between WT and mutants. Output .bed files of genes with log2 ≥ 2 or log2 ≤ -2 expression and adjusted p-values ≤ 0.05 were modified as .txt files for Circos plot display.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.
Supplementary_files_format_and_content: For RNA-seq files: the .txt files were generated by the program HTseq (using sequencing reads aligned to the Neurospora crassa assembly 12 Fixed genome with the program samtools). These HTseq.txt files report read number counts per gene for each replicate sample (two replicates total) from our four strains (WT N3752, delta set-7 N4718 and N4730, delta npf N4721, delta set-7;delta dim-5 N5916). The three Dataset.xls files were produced using the replicate HTseq.txt files in the program DESeq to determine genes that were differentially expressed > four fold and were significant (p < 0.05) in each mutant strain when compared to the WT N3752 reference expression datasets.

organism: Neurospora crassa

growth_protocol: 2.5x10^8 conidia were grown in cultures of 50mL 1xVogels, 1.5% Sucrose medium for 3-4 hours at 30oC with shaking at 200rpm (At this time, >70% of the conidia for all strains had germination tubes >4x their original size, as roughly measured by light microscopy)

extract_protocol:
protocol for mRNA isolation and library preparation: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were harvested and added to a tube containing ~300uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 10 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was added to 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed with 70% EtOH, and resuspended in DEPC-treated dH2O.RNA was treated with DNAse (DNA-free™ DNA Removal Kit, Thermo Fisher Scientific), cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter), and RNA-seq libraries were prepared (KAPA Stranded mRNA-seq kit, KAPA Biosystems)
protocol for histone modification ChIPseq: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP.  Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit  and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 8 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.
Indexed paired-end HiC libraries were pooled and sequenced either on an Illumina HiSeq 2500 as a 50nt paired end sequencing run, or a NextSeq500 as either 37nt or 75nt paired-end sequencing run at the University of Oregon Genomics Core Facility. ChIP-seq or RNA-seq samples were sequenced on a NextSeq500 as a single-end 75nt run.

treatment_protocol: 2.6 mL of methanol-free formaldehyde (20%) was added to a final concentration of 1%. After a 10 minute room temperature (RT) incubation with shaking at 100 RPM, crosslinking reactions were quenched by adding 3.4 mL of 2 M Tris-HCl [pH 8 @ 25 °C] to a final concentration of 125 mM and incubating at room temperature (RT) for another 10 minutes with shaking at 100 RPM. Conidia were harvested by centrifugation (3000 RPM, 5 minutes) and resuspended gently in 40 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4  [pH 7.5]) plus 30 mM β-mercaptoethanol, pelleted again (3000 RPM, 5 minutes) and resuspended in 40 mL spheroplasting buffer. 200 mg of VinoTaste Pro (Novozymes) was added and strains were spheroplasted for 60 minutes at 30°C with shaking at 100 RPM. Spheroplasts were harvested by centrifugation (2000 RPM, 5 minutes) and washed 3x with 20 mL HindIII buffer (50 mM NaCl, 10 mM Tris-HCl [pH 7.9 @ 25°C], 10 mM MgCl2, 100 μg/mL bovine serum albumin (BSA)). Washed pellets were resuspended in 6 mL HindIII buffer, split into 1 mL aliquots in 1.7 mL eppendorf tubes. Spheroplasts were pelleted (1500 g, 5 minutes) and the supernatant was aspirated away. Aliquots were frozen in liquid nitrogen and stored at -80°C.

value: delta dim-5

value: germinated conidia


title: dim-3_H3K27me2me3_ChIPseq

value: delta dim-3

value: H3K27me2me3 (ActiveMotif; cat# 39535)


title: 18month

city: DAEGU

first: keetae

last: kim

address: 333 TECHNO0 JUNGANG-DAERO

department: NEW BIOLOGY

country: South Korea

institute: DGIST

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with in-house script, and Adaptor trimming processed is done to eliminate the adaptor sequences that exist in the read which were attached to the miRNA during the smRNA library construction process. If a read matches more than at least first 8 bp of 3' adapter sequence, it was regarded the sequence truly is adapter sequence, and then trimmed from the read. Trimmed reads should be at the minimum of 15 bp in order to be considered reliable for analysis.
To minimize the sequence uniqueness and computational intensity, adaptor sequence trimmed reads are gathered and form a cluster. This cluster contains reads that are 100% match to the sequence identity and read length and are given its temporary cluster ID and the number of reads it holds.
These reads were then aligned mouse matured miRNAs obtained from miRBase v18. Uniquely clustered reads are then aligned to non-coding RNA database Rfam 9.1 to identify known miRNAs and other type of RNA.
Raw data (the reads for each miRNA) were normalized by the total reads of each individual sample as the standardized to reads per million (RPM, miRNA counts / total counts of each sample x 1 million).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read count for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the Hippocampal tissue using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions.Length of 18–30 nt small RNAs were isolated from total RNA using 15% denaturing polyacrylamide gel electrophoresis.
The RNA isolated from each sample was used to construct sequencing libraries with the Illumina TruSeq Small RNA Sample Prep Kit, following the manufacturer's protocol. Briefly, 3′ and 5′ adapters were sequentially ligated to small RNA molecules and the obtained ligation products were subjected to a reverse transcription reaction to create single stranded cDNA. To selectively enrich those fragments that have adapter molecules on both ends, the cDNA was amplified with 15 PCR cycles using a common primer and a primer containing an index tag; this allows multiplexing and sequencing of different samples in a single lane of a flowcell. The amplified cDNA constructs were gel purified, and validated by checking the size, purity, and concentration of the amplicons on the Agilent Bioanalyzer. The libraries were pooled in equimolar amounts, and sequenced on an Illumina HiSeq 2000 instrument to generate 50 base reads. Image decomposition and quality values calculation were performed using the modules of the Illumina pipeline.

value: hippocampus

tag: genotype

value: wild type


title: N4718_set7_HiC

description:
genomic DNA HiC libraries
library strategy: HiC

data_processing:
Paired-end reads were demultiplexed, trimmed to 50bp (if needed)
Hi-C contact maps were produced according to Imakaev et al. (Imakaev et al. 2012). Briefly, an attempt was made to uniquely map the first 15 base pairs (bp) of each read to the Neurospora genome. If a unique match was not found, the read was extended 5 bp and another attempt was made. This process continued until a unique match was found or the end of the read reached (50 bp).
Read pairs were then assessed using a number of quality control filters, typically removing reads that covered unligated products (Dangling Ends), products that were too close to the restriction site, Self-circles, and extremely large or small fragments.
Read pairs passing all filters (typically 10% of total read pairs) were used to build uncorrected contact maps (arrays) that were then corrected to account for the unequal representation of genomic loci in HiC datasets. Corrected maps were used in all subsequent analyses
To calculate the ratio of observed contacts to expected contacts, the median contact frequency was calculated at each genomic distance (up to a distance of ~3.5 Mb at which point contact frequency had reached background levels) and used as the expected contact frequency at each respective distance.
To directly compare datasets, a fixed number of reads (prior to filtering) were sampled with the program seqtk, such that the sampled number of raw reads from each dataset produced approximately equal numbers of reads that passed the filtering steps.
To make ChIPseq enrichment files across 10kb bins to use for Circos plots, .bcf files were produced using samtools' mpileup function from ChIPseq .bam files, the .bcf files were "fixed" to replace empty positions with zeros, and processed with a custom script to report the ChIP-seq enrichment over 10kb bins (the resulting seven files were catenated into one file).
All python scripts (".py" files) used for Hi-C data processing are available as supplemental information in the manuscript Galazka et al, 2016, Genome Research, except for the modified scripts, plotIntraTelomeres.py and plotInterTelomeres.py, which were used to calculate intra and inter telomeric enrichment in our Hi-C datasets. In addition, the python script K9-K27Quant.py counts the number of Hi-C links originating from a H3K9me3-marked 10kb bin and end in a bin marked by H3K27me2/3, while the python script K9-K27only_Quant.py counts the number of Hi-C links originating from a H3K9me3-marked 10kb bin and end in a bin marked ONLY by H3K27me2/3 (and not H3K9me3). The program count_links_K27marked.py counts the number of Hi-C links in each 10Kb bin marked by H3K27me2/3. The program hicEigenvectorAnalysis.py derives the number of principle components for the whole genome specified using non-iteratively corrected Hi-C .hdf5 datasets. The program hicEigenvector_singleLG.py extracts the Eigenvector of a single Linkage Group from the whole genome data derived from the "hicEigenvectorAnalysis.py" script. The program hicPearsonCorrelationHeatmap.py calculates the Pearson Correlation between all genomic regions and displays them as a heatmap for a specific Linkage Group. These scripts are provided here.
To determine differences in the genome organization caused by mutants, mutants were compared to the WT Hi-C data (NMF39 [GSM1825702] within the GEO dataset GSE71024). See GSM2186732 in this GSE82222 dataset.
To make ChIPseq enrichment files for display in Integrative Genomics Viewer (IGV, Robinson et al, 2011, Nat. Biotechnol.), .bam files (and the corresponding .bai index files) were counted with the "Count" command of igvtools, using the mean window function and 200bp windows. Output file was a .tdf file, displayable on IGV.
For Poly-A mRNA seq, high quality, adapter-less reads were identified (Stacks); Kmer filtering reduced sequencing errors. Reads were mapped (TopHat) to the modified Neurospora genome assembly 12, and sorted (SAMTools), and directionality-preserved read numbers were calculated at each gene ID (HTSeq), adding one read count to prevent abnormal fold changes. Differential gene expression analysis (DESeq) examined replicate differences and pair-wise analyses between WT and mutants. Output .bed files of genes with log2 ≥ 2 or log2 ≤ -2 expression and adjusted p-values ≤ 0.05 were modified as .txt files for Circos plot display.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf)
Supplementary_files_format_and_content: for Hi-C files: "...array.txt" files are the generated tab-delininated files with raw counts (on a log2 scale) for each bin (the entire genome is divided into 40kb, 50kb, or 10kb segments, and a bin indicates the intersection of two of these segments in an array format) across the genome. "...observed_expected.txt" is a file where the above array file containing observed interactions in our HiC dataset was normalized by the "expected" interaction if interactions were locally strong and stochastically decreased as genomic distance increased.
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011), using a window size of 200bp (.tdf files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV). The bcf files were produced from bam files (mapped to the Neurospora crassa assembly 12 Fixed by samtools), and report enrichment values.
Supplementary_files_format_and_content: For RNA-seq files: the .txt files were generated by the program HTseq (using sequencing reads aligned to the Neurospora crassa assembly 12 Fixed genome with the program samtools). These HTseq.txt files report read number counts per gene for each replicate sample (two replicates total) from our four strains (WT N3752, delta set-7 N4718 and N4730, delta npf N4721, delta set-7;delta dim-5 N5916). The three Dataset.xls files were produced using the replicate HTseq.txt files in the program DESeq to determine genes that were differentially expressed > four fold and were significant (p < 0.05) in each mutant strain when compared to the WT N3752 reference expression datasets.

source_name: germinated conidia

extract_protocol:
[HiC] To determine the concentration of genomic DNA (gDNA) per aliquot of spheroplasts, 1 aliquot per replicate was resuspended in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM Na Ethylenediaminetetraacetic acid (Na-EDTA), 0.5% (w/v) sodium dodecyl sulfate (SDS)) plus 100 mg proteinase K and incubated at 65 °C overnight. The next day, the volume was brought to 500 uL with TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA) plus 40 mg RNase A and aliquots were incubated at 37°C for 30 minutes. gDNA was then extracted twice with a 1:1 mixture of buffered phenol (pH 8) and chloroform, and once with chloroform. gDNA was precipitated by adding 1/10 volume of Na acetate (pH 5.2) and 1 volume of isopropanol. DNA pellets were washed 3x with 70% (v/v) ethanol, dried at RT for 10 minutes and resuspended in 50 μL TE. The DNA concentration was determined from the absorbance at 260 nm. Spheroplasts corresponding to 3.5 μg of gDNA were resuspended in 270 μL of HindIII buffer and 30 μL of 10% (w/v) SDS was added to a final concentration of 0.1% (w/v). Spheroplasts were then lightly decrosslinked by incubation at 65°C for 10 minutes and then placed immediately on ice. 33 μL of 10% (v/v) Triton X-100 and 8.3 μL of 10x HindIII buffer was added and gDNA digested with 400 U (20 μL of 20 U/μL from NEB) HindIII for 16 hours at 37 °C while nutating. The next day, samples were placed on ice and split into two aliquots. To construct HiC libraries, one aliquot of HindIII digested chromatin was labeled with biotin-14-dCTP in a 210 μL reaction consisting of 30 μM dATP, 30 μM dTTP, 30 μM dGTP, 30 μM biotin-14-dCTP and 25 U of Klenow (large fragment). This reaction was incubated at 37 °C for 45 minutes with nutating. Klenow (large fragment) and HindIII was then inactivated by the addition of SDS to 1.5% (w/v) and incubation at 65°C for 30 minutes. This chromatin was then used in a 3.5 mL ligation reaction consisting of 50 mM Tris-HCl [pH 7.5 @ 25 °C], 10 mM MgCl2, 0.9% (v/v) Triton X-100, 10 mM Dithiothrireitol (DTT), 100 μg/mL BSA, 1 mM adenosine triphosphate (ATP) and 1675 U T4 DNA ligase (4.2 μL of 400,000 U/mL T4 DNA ligase from NEB). This reaction was incubated at 16°C for 4 hours. At the end of the 4 hour 3C and HiC ligation reactions, 250 mg of proteinase K was added and all reactions were allowed to decrosslink at 65°C overnight. The next day, another 250 mg of proteinase K was added and samples were decrosslinked at 65°C for another 2 hours. Samples were cooled to ~25°C on ice, and extracted with 5 mL of phenol (pH 8) by vortexing for 2 minutes. After centrifugation (3500 RPM, 10 minutes), the aqueous phase was removed and extracted with 5 mL of phenol (pH 8):chloroform (1:1) by vortexing for 2 min. After centrifugation (3500 RPM, 10 minutes), the aqueous phase was removed and brought to a volume of 5 mL with TE. DNA was precipitated by the addition of 0.5 mL 3 M Na Acetate [pH 5.2], 50 mg glycogen, 12.5 mL 95% ethanol and incubation at -80°C for 1 hour. DNA was pelleted by centrifugation (20,000 g, 20 minutes, 4°C), the supernatant decanted and DNA resuspended in 450 μL TE by vortexing. DNA was again extracted with 1 volume of phenol (pH 8):chloroform (1:1) and then chloroform as before. DNA was then ethanol precipitated as before and resuspended in 25 μL of TE/10 buffer (10 mM Tris-HCl [pH 8 @ 25°C], 0.1 mM Na-EDTA). To remove biotin-dCTP from unligated ends, the HiC libraries were digested for 2 hours at 12°C in a 50 μL reaction consisting of 5 μL of NEB buffer 2, 100 μg/mL BSA, 100 μM dATP, 100 μM dGTP and 5 U of T4 DNA polymerase. These reactions were quenched by adding Na-EDTA to 10 mM and DNA extracted with 1 volume of phenol (pH 8):chloroform and then with 1 volume of chloroform. DNA was ethanol precipitated, resuspeneded in 500 μL of TE and sheared by sonication (duty cycle 80, power 1.2, 10 s, 5x with 1 minute rest on ice between pulses). Sheared, biotinylated DNA was captured by adding 25 μL of streptavidin beads (Invitrogen) that had been equilibrated in BW buffer (5 mM Tris-HCl [pH 8 @ 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% (v/v) Tween-20) and incubating for 30 minutes with shaking. Beads were washed 2x with BW buffer, 2x with TE/10 buffer and resuspended in 25 μL TE/10 buffer.
[HiC] To prepare HiC libraries for Illumina sequencing, either Illumina TruSeq kits was used according to the manufacturers’ protocol, or essentially a “homemade version” of that protocol was used. In the homemade version, DNA ends were repaired in reactions consisting of 25 μL of HiC libraries on streptavidin beads, 5 μL of T4 DNA ligase buffer, 2 μL 10 mM (each) dNTPs, 0.5 μL end repair enzyme mix (0.5 U T4 DNA polymerase, 0.25 U Klenow Fragment, 2.25 U T4 DNA Polynucleotide Kinase) in a final volume of 50 μL and incubated at 20°C for 30 minutes. Beads were washes 2x with BW buffer and 2x with TE/10, resuspended in 16.5 μl TE/10. A-tailing was performed by adding 2 ul 10x NEB Buffer #2, 1 ul 4 mM dATP, 0.5 ul Klenow 3’ to 5’ exo minus (5 U/ul) and incubating at 37 C for 30 minutes, mixing every 10 minutes. Beads were again washed with BW and TE/10 buffers as above and resuspended in 20 ul TE/10. Indexed adaptors were ligated by adding 25 ul 2x ligase buffer (132 mM Tris-HCl [pH 7.6], 20 mM MgCl2, 2 mM DTT, 2 mM ATP, 15% (w/v) PEG 6000), 2.5 ul T4 DNA ligase (400 U/ul) and 2.5 ul Illumina TruSeq DNA adapters diluted 1:10 and incubating at RT for 20 minutes, mixing every 10 minutes. Ligation reactions were quenched with 5 ul of 0.5 M Na-EDTA [pH 8] and beads washed 3x with BW buffer and 2x with TE/10. Beads were then resuspended in 50 ul TE/10 and HiC libraries amplified in 50 ul PCR reactions using the Phusion polymerase and the following cycle: 45 s at 98°C; 18 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C; 1 minute at 72°C. The PCR product was separated from the beads, cleaned with Ampure XP beads, and resuspended in 25 ul TE/10. Library quality was assessed by gel electrophoresis before deeps sequencing.
[ChIP] Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde for histone modification ChIP.  Tissue added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A or Protein G slurry (agarose or magnetic beads) was added to bind the antibody, incubated for 3 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC.  Samples (IP and input) were decrosslinked at 65oC overnight.  The next day, samples were proteinase K treated for 2 hours at 50oC, and DNA was purified using the QIAquick PCR purification kit  and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the Illumina Tru-Seq kits A and B (Illumina, IP-202-1012 and IP-202-1024) according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98 °C for 30 sec, 8 cycles at 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec and a final extension at 72 °C for 5 min.
[RNA] Cultures were grown in Vogels m

treatment_protocol: [HiC] 2.6 mL of methanol-free formaldehyde (20%) was added to a final concentration of 1%. After a 10 minute room temperature (RT) incubation with shaking at 100 RPM, crosslinking reactions were quenched by adding 3.4 mL of 2 M Tris-HCl [pH 8 @ 25 °C] to a final concentration of 125 mM and incubating at room temperature (RT) for another 10 minutes with shaking at 100 RPM. Conidia were harvested by centrifugation (3000 RPM, 5 minutes) and resuspended gently in 40 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4  [pH 7.5]) plus 30 mM β-mercaptoethanol, pelleted again (3000 RPM, 5 minutes) and resuspended in 40 mL spheroplasting buffer. 200 mg of VinoTaste Pro (Novozymes) was added and strains were spheroplasted for 60 minutes at 30°C with shaking at 100 RPM. Spheroplasts were harvested by centrifugation (2000 RPM, 5 minutes) and washed 3x with 20 mL HindIII buffer (50 mM NaCl, 10 mM Tris-HCl [pH 7.9 @ 25°C], 10 mM MgCl2, 100 μg/mL bovine serum albumin (BSA)). Washed pellets were resuspended in 6 mL HindIII buffer, split into 1 mL aliquots in 1.7 mL eppendorf tubes. Spheroplasts were pelleted (1500 g, 5 minutes) and the supernatant was aspirated away. Aliquots were frozen in liquid nitrogen and stored at -80°C.

value: delta set-7

value: spheroplasts


title: 6month


title: 511_ctrl_10w

value: C57BL/6 N

value: 10 weeks

value: Lsd1 floxed; Control

value: Brown adipose tissue (BAT)


title: NMF39_WildType_HiC (reanalyzed)


title: C11_RNA-seq

value: C57BL/6 Heterozygous Lmx1a-EGFP

value: developing ventral midbrain cells


title: Tet-MII-WT2

description: processed data file: MII_ncount.txt.gz

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling.
Adaptor contamination and low-quality reads were discarded from the raw data.
For RNA-Seq Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and nCount values were generated by HTSeq(version 0.6.1) and then normalized by DESeq2(version 1.6.1).
For PBAT DNA illumina paired-end reads,Bismark(version 0.7.6) were use for sequence alignment, and SingleC data were generated by SAMtools(version 0.1.19-44428cd)
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly mm9. Bisulfite conversion rate was estimated by the lambda genome, which was built as the extra chromosome.
Supplementary_files_format_and_content: nCount data were generated by DESeq2 and SingleC data were generated by SAMtools (version 0.1.19-44428cd)

source_name: Tet-MII-WT

growth_protocol:
For collection of mature oocytes, oviducts were removed from the female mice 13–15h after human chorionic gonadotropin injection. Cumulus–oocyte complexes were released into HCZB containing 0.1% bovine testicular hyaluronidase (300 USP units per mg; ICN Biomedicals Inc.).
Cavitated E3.5 blastocysts were flushed from the uteri of naturally mated mice into M2 or DMEM followed by sequential washing in KSOM.

extract_protocol:
Total RNA was extracted using Rneasy Micro Kit (QIAGEN, Cat No. 74004), and treated with Rnase-Free Dnase Set (QIAGEN, Cat No. 79254).
Total RNA was purified from isolated blastocysts by using the Qiagen AllPrep DNA/RNA Mini Kit, treated with DNase.
Then libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat No. E7530L) following the manual. Then libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat No. E7530L) following the manual.
About 1 ng of extracted RNA was first amplified 18 cycles according to the protocol for single-cell RNA-seq published previously. Briefly, 1 ng of extracted RNA was reverse translated into cDNA, then the free primers were removed by the ExoSAP-IT. TdT was used to add PolyA to the 3’ end of cDNA, the second strand were synthesized, and the double-stranded DNA product were amplified 18 cycles to obtain enough product for DNA library construction. The amplified DNA product was purified by DNA Clean & Concentrator™-5 (Zymo Research), and further purified by Zymoclean™ Gel DNA Recovery Kit (Zymo Research) for the 0.5-8 kb size DNA products. The gel purified products were sheared by Covaris S2 for the generation of fragments about 250 bp in length, and purified with DNA Clean & Concentrator™-5 (Zymo Research). Then NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, Catalog #E7370L) was used to construct a cDNA library, with reagent amount reduced to half of the reactions. The cDNA libraries were sequenced on Illumina HiSeq 2500 instrument with 100-bp reads and paired-end parameter.

treatment_protocol:
A pool of 200 (x 2) WT and 200 (x 2) Tet-null fresh oocytes were disrupted and homogenized in Buffer RLT Plus respectively, then snap-frozen in liquid nitrogen and stored at -80 ºC.
A pool of 46 WT and 46 Tet-null fresh blastocysts were disrupted and homogenized in Buffer RLT Plus respectively, then snap-frozen in liquid nitrogen and stored at -80 ºC.

value: MII oocyte

value: oocyte


title: set7dim5_polyA-mRNA_rep2

description:
polyA_mRNAseq_libraries
Dataset_S3_4X-changed-genes_WT-v-set7dim5.xlsx

value: delta set-7;delta dim-5

value: mycelia


title: RaoHuntley-2014-HIC016

value: in situ Hi-C


title: N5542_set7dim5_HiC


title: Tet-MII-TKO2

description: processed data file: MII_ncount.txt.gz

source_name: Tet-MII-TKO


title: RaoHuntley-2014-HIC015


title: npf_polyA-mRNA_rep2

description:
polyA_mRNAseq_libraries
Dataset_S2_4X-changed-genes_WT-v-npf.xlsx

value: delta npf


title: Tet-MII-TKO1

description: processed data file: MII_ncount.txt.gz


title: Input_BAT

value: Control

value: differentiated primary brown adipocytes


title: Tet-MII-WT1

description: processed data file: MII_ncount.txt.gz


title: 2month

value: hippocampus

value: wild type


title: RaoHuntley-2014-HIC014


title: Matched Breast Normal

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

data_processing:
Trimming raw sequence reads smaller than 100-bp long out of a fastq file with a custome-made Python script
Mapping raw sequence reads to a custome-made database containing bisulfite-converted AluY sequences using Bowtie2
Grouping a number of sequence reads to each AluY5/Yb8 locus using a custome-made Perl script
Trimming out raw sequence reads for a given Alu locus that do not have a sufficient sequence coverage for DNA methylation analyses
Running a batch analysis of BiQanalyzerHT for DNA methylation levels of AluYa5/Yb8 with a custom-made Perl script
Genome_build: hg19
Supplementary_files_format_and_content: BED files showing methylation level of each sequenced locus

source_name: Normal breast

extract_protocol:
Genomic DNA was isolated from the fibroblast cell stock using phenol-chloroform extraction protocol, precipitated using ethanol precipitation protocol and resuspended in 1X TE buffer.
In brief, genomic DNA were fractionated by sonication, ligated to an adaptor and modified with bisulfite conversion protocol. It was then amplified with a PCR scheme designed to enrich AluYa5 and AluYb8, and finally size-fractionated using the E-gel Precast Agarose Electrophoresis System (Life Technologies). The prepared libraries were sequenced on the Ion-Torrent PGM platform.

value: normal breast

tag: Sex

value: Female

value: Adult


title: Matched Breast Primary Tumor

source_name: Invasive ductal carcinoma

value: Invasive ductal carcinoma


title: Fibroblast

source_name: Fibroblast

value: fibroblast

value: Male

value: Fetal


title: RaoHuntley-2014-HIC012


title: RaoHuntley-2014-HIC007


title: npf_polyA-mRNA_rep1


title: RaoHuntley-2014-HIC023


title: set7_polyA-mRNA_rep2

description:
polyA_mRNAseq_libraries
Dataset_S1_4X-changed-genes_WT-v-set7.xlsx

value: delta set-7


title: set7_polyA-mRNA_rep1


title: RaoHuntley-2014-HIC003


title: WT2_E6.6_Epiblast_PBAT

data_processing:
library strategy: whole-genome bisulfite sequencing by post-bisulfite adaptor tagging (PBAT)
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling.
Adaptor contamination and low-quality reads were discarded from the raw data.
For RNA-Seq Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and nCount values were generated by HTSeq(version 0.6.1) and then normalized by DESeq2(version 1.6.1).
For PBAT DNA illumina paired-end reads,Bismark(version 0.7.6) were use for sequence alignment, and SingleC data were generated by SAMtools(version 0.1.19-44428cd)
Bisulfite conversion rate was estimated by the lambda genome, which was built as the extra chromosome.
Genome_build: mm9, J02459.1
Supplementary_files_format_and_content: SingleC data were generated by SAMtools(version 0.1.19-44428cd)

extract_protocol:
DNA was extracted from isolated epiblasts by using the Qiagen AllPrep DNA/RNA Mini Kit.
About 5 ng genomic DNA were used to construct the PBAT library using the protocol slightly modified from previously published. Briefly, the isolated genomic DNAs, together with 1% unmethylated lambda DNA (Thermo Scientific), were converted and purified with MethylCode Bisulfite Conversion kit (Invitrogen) following the manufacturer’s instructions. Then random nonamer primers with a 5’ biotin tag and a truncated Illumina P5 adaptor (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of Klenow polymerase (3’ to 5’ exo-, NEB) were used to amplify the bisulfite-converted templates linearly. The excess primers remained in last reaction were removed using 40U Exonuclease I (NEB) before amplified products were purified with 0.8 x Agencourt Ampure XP beads (Beckman Coulter). The newly synthesized DNA strands with biotin were captured with Dynabeads M280 Streptavidin (Invitrogen), and the original bisulfite-treated DNA templates were washed away by 0.1 N NaOH. The second strands were synthesized using 50 units Klenow polymerase with random nonamer primers containing a truncated P7 Illumina adaptor (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads with double strand DNA products were further collected and washed several times, and the libraries were generated with 5-6 cycles of PCR amplifications using 1 unit KAPA HiFi HS DNA Polymerase (KAPA Biosystems), together with 0.4 μM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 μM pre-indexed Illumina Reverse primer (5’- CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates the index sequences). Amplified libraries were purified with 0.8 x Agencourt Ampure XP beads twice and were assessed with the Fragment Analyzer (Advanced analytical) and quantified with a standard curve-based qPCR assay (Roche). The final quality-ensured libraries were pooled and sequenced on the Illumina X Ten sequencer for 150 bp paired-end sequencing.
whole-genome bisulfite sequencing by post-bisulfite adaptor tagging (PBAT)

treatment_protocol: A pool of 23 WT and 26 Tet-null fresh epiblasts were disrupted and homogenized in Buffer RLT Plus respectively, then snap-frozen in liquid nitrogen and stored at -80 ºC.

value: Epiblast

value: Embryonic day 6.5


title: Sample_13A_PnD39_DSTP

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

data_processing:
Primary sequencing data that produced by Illumina Hiseq 2000, called as raw reads, were subjected to quality control to determine if resequencing step is needed. After QC, raw readere were filtered into clean reads which were then aligned to reference sequence Streptococcus  pneumoniae GenBank file: AF026471 (NC_008533.1) with SOAPaligner/SOAP2 v2.20 [Li. R, Yu,C., LiY et al  Bioinformatics :Doi:10.1093/bioinformatics/btp336.  259(15)1966-1967]. the alignment data were utilized to calculate distribution of reads on reference genes and perform coverage analysis. Upon QC pass, down stream analysis including gene expression, novel transcript prediction and annotation were done. gene ontology enrichment analysis were used for pathway enrichment analysis. In order to assess the effectiveness of selected mapping tool, the comparative analysis between SOAPAligner/SOAP2 and other popular-alignment tool BOWTIE [Langmead B. et al (2009)genome biology 10:25-34/ http://Bowtie-bio.sourceforge.net/index.shtml].  because the SOAPaligner/SOAP2 performed better, quantification analysis of gene expression was done with SOAPaligner/SOAP2.For significance of didgital gene expression profile alogorithms as published [ Audic et al (1997) Gemome Res. 7:986-985].. We used FDR< 0.001 [benjamini and Yekutieli(2001)Ann Statistics29:1165-1188] and the absolute value Log2 ratio > 1 as the threshold to judge the significance of gene expression difference. KEGG was used to perform Pathway enrichment analysis. For gene refinement, transcripts reads were assemble by using CUFFLINK software [Roberts et al Bioinformatics: doi:10.1093/bioinformatics. btr355].
Genome_build: NC_007297.1
Supplementary_files_format_and_content: DEGS and RPKM, Pvalue and FDR; Details provided in the *readme_en.txt files.

organism: Streptococcus pneumoniae

growth_protocol: All pneumococcal cultures were grown in Todd Hewitt broth supplemented with 0.5% yeast extract. Cultures were grown at 37oC till O.D. reached at 0.8. (wt) mutant (0.6) i.e. till late log phase. The cultures were then centrifuges at 4oC  and washed once with sterile autoclaved PBS. The cell were then resuspended in PBS in the 1/50th of the starting culture volume.

extract_protocol:
Total RNA was extracted using  Norgen RNA isolation kit (canada).
The high quality total RNA samples were obtained by DNase treatment. The samples were then sent to BGI Americas. rRNA was removed from the total RNA samples.cDNA was then made using mRNA as template. Short fragments were made by heat treatment and the they  were purified and resolved  with EB buffer for endrepairation and single nucleotide A ( adenine) addition. Short fragments were then connected to adapters. Subsequently, following agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification. All quality control (QC) steps i.e. for quatification and quality of sample library ABI bioanalyzer and ABI StepOnePlus realtime PCR system were used. Library were sequenced using IlluminaHiseq 2000.

treatment_protocol: Using  Janus cassette [Sung et al (2001) Appl. Environ. Microbiol. 67:5190-5196], S. pneumoniae D39-derived  mutant lacking the ser/thr phosphatase encoding gene phpP (stp) gene was derived as described previously [ Agarwal et al (2012) Infect. Immun. 80:1361-1372]. The washed concentrated bacterial pellet suspension was treated with mutanolysin (lysozyme 1:10 diluted 20mg/ml) to lyse the bacterial cells.

value: mutant lacking the phpP gene

tag: growth phase

value: Late-log phase culture


title: WT1_E6.5_Epiblast_PBAT


title: Tet_TKO1_E6.5_Epiblast_PBAT


title: Tet_TKO2_E6.6_Epiblast_PBAT


title: RaoHuntley-2014-HIC002

value: tethered in situ Hi-C


title: RaoHuntley-2014-HIC001


title: npf_N4721_H3K27me3_ChIPseq

description: genomic DNA ChIPseq libraries

value: delta npf

tag: antibody used

value: H3K27me3 (Millipore, catalog# 07-449, lot# 2607758)

value: mycelia


title: Sample_13B_PnD39_DSTP


title: WT_N3752_H3K27me3_ChIPseq

description: genomic DNA ChIPseq libraries

value: wild type


title: H3 rep1

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control and trimming were performed using CLC Genomics Workbench 6.5.1.
High-quality reads were mapped to the reference human genome GRCh37 and exon–exon junctions were identified using Tophat2 (v2.0.13) (mapping parameters: maximum of two mismatches, only uniquely mapped reads were allowed)
Normalization of read counts provided by DESeq method.
Genome_build: GRCh37
Supplementary_files_format_and_content: comma-separated text file include normalized read counts for each sample

source_name: Skeletal muscle

extract_protocol:
Samples from the vastus lateralis muscle were taken using a microbiopsy technique and were frozen in liquid nitrogen; RNA was extracted from the samples using an RNeasy mini kit (Qiagen). TruSeq RNA sample kit v2 (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A warm-up (5 min, 50% V'о2max) and exercise session (65 min, 70% or 50% V'о2max) started 1 h 45 min after the breakfast. Two hours after the exercise session, the participants ate a standardized lunch.

tag: treatment

value: cycling session (70 min, 70% V’о 2max )

value: vastus lateralis muscle

tag: time point

value: 8 hours after exercise


title: H3 rep2


title: sample_12A_PnD39_WT

tag: strain background

value: wild-type; Intact SP-PTP


title: set7dim5_polyA-mRNA_rep1

tag: genotype/variation

value: delta set-7;delta dim-5


title: N4721_npf_HiC

value: spheroplasts


title: Mycobacterium smegmatis infected with mycobacteriophage  MichelleMyBell for 2 hours 30 minutes (Late)

city: Pittsburgh

first: Travis

last: Mavrich

state: Pennsylvania

address: 4249 Fifth Avenue

institute: University of Pittsburgh

description: Mycobacteriophage MichelleMyBell

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.2.6
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.2
BAM format was converted to BED format using bedtools version 2.25.0
Expression levels were computed as reads mapped per base pair per strand ("top" and "bottom") using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: KC576783.1 (Butters)
Genome_build: JN256079.1 (Charlie)
Genome_build: KF986246.1 (MichelleMyBell)
Genome_build: KU935727.1 (Panchino)
Genome_build: KU935731.1 (Phrann)
Genome_build: JN624851.1 (Redi)
Genome_build: KU935728.1 (Xeno)
Genome_build: KU935726.1 (Xerxes)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage MichelleMyBell

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using Ribo-Zero (Illumina)
Libraries were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina)

tag: host strain

value: Mycobacterium smegmatis mc2155

tag: phage

value: Mycobacteriophage MichelleMyBell

tag: infection timepoint

value: 2 hours 30 minutes


title: Mycobacteriophage Panchino lysogen

description: Mycobacteriophage Panchino lysogen

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Panchino

value: Mycobacteriophage Panchino

value: no exogenous phage added


title: RaoHuntley-2014-HIC006

value: in situ Hi-C


title: H2 rep2

value: 4 hours after exercise


title: Mycobacterium smegmatis infected with mycobacteriophage Charlie for 2 hours 30 minutes (Late)

description: Mycobacteriophage Charlie

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Charlie

value: Mycobacteriophage Charlie


title: RaoHuntley-2014-HIC005


title: Mycobacteriophage Xeno lysogen

description: Mycobacteriophage Xeno lysogen

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Xeno

value: Mycobacteriophage Xeno


title: H2 rep1


title: sample_12B_PnD39_WT

value: Late-log phase culture


title: Mycobacterium smegmatis infected with mycobacteriophage Charlie for 30 minutes (Early)

description: Mycobacteriophage Charlie

value: 30 minutes


title: H0 rep2

value: before


title: H0 rep1

value: vastus lateralis muscle


title: hs63I3_1,KO13

status: Public on Oct 26 2016

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

data_processing:
The RNA-seq reads were aligned to the mouse genome mm9 using Bowtie2 with ultrasensitive parameters. Because the number of assignable reads in the samples ranged from 11x106 to 38x106, Homer (http://homer.salk.edu) was used to randomly select an equal number of reads from each sample. RNA-seq reads were counted over gene exons and reads for the same exons were combined allowing only two exact duplicate tags in any one position. Genes with less than eight tags per kilobase were filtered out. EdgeR software (www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/ edgeRUsersGuide.pdf) was used for statistical analysis, set with a p-value ≤ 0.01 and a minimum fold-change of 1.5 either up or down. Pairwise comparisons of each control to each knockout sample were used to generate correlation plots that identified genes with a consistent pattern of differential expression in control vs. knockout pituitaries.
Genome_build: mm9
Supplementary_files_format_and_content: differential expression values in tab-delimited text format

source_name: pituitary

extract_protocol:
Total RNA from separate biological replicates of three control and two knockout pituitaries was isolated using Trizol (Life Technologies), chloroform extraction, and isopropanol precipitation. Ribosomal RNA was removed using a Ribo-Zero Magnetic Kit (Epicentre).
Strand-specific libraries were constructed with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre).
RNA-seq deep sequencing was carried out on an Illumina HiSeq 2000.

value: epithelial pituitary cells

tag: embryonic day

value: Itgb1 f/f; Pitx1-cre

tag: mouse strain


title: Mycobacteriophage Phrann lysogen

description: Mycobacteriophage Phrann lysogen

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Phrann

value: Mycobacteriophage Phrann


title: hs63I3_3,KO16


title: Mycobacteriophage MichelleMyBell lysogen


title: Mycobacteriophage Butters lysogen

description: Mycobacteriophage Butters lysogen

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Butters

value: Mycobacteriophage Butters


title: Mycobacteriophage Charlie lysogen

description: Mycobacteriophage Charlie lysogen

value: Mycobacterium smegmatis mc2155


title: hs63I3_5,WT10

value: Itgb1 f/f


title: hs63I3_6,WT12


title: hs63I3_4, WT9


title: Mycobacteriophage Xerxes lysogen

description: Mycobacteriophage Xerxes lysogen

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Xerxes

value: Mycobacteriophage Xerxes


title: OE-RBM25-2

city: Stanford

first: Or

last: Gozani

address: 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Raw FASTQ paired-end reads were mapped against gencode v24 GRCh38 chromosomes only with HISAT2 v2.0.3
SAM files were converted to BAM using samtools v0.1.19
BAM files were used to quantify alternative splicing events using JuncBASE v1.2 (default parameters)
Genome_build: gencode v24 GRCh38
Supplementary_files_format_and_content: Excel file containing output from JuncBASE. Values indicate "Percent Spliced In" for each splicing event.

source_name: 293T cell culture

growth_protocol: 293T cells grown in DMEM+10% FBS.

extract_protocol:
Qiagen Rneasy Plus Mini kit
Oligo(dT) enrichment and cDNA synthesis with random hexamers, followed by standard preparation for Illumina sequencing.

treatment_protocol: Gene knock-down by CRISPR/Cas9 for four days, or stable over-expression of GFP, RBM25 or RBM25 K77R mutant.

tag: knock-down

tag: over-expression


title: Mycobacterium smegmatis infected with mycobacteriophage MichelleMyBell for 30 minutes (Early)

description: Mycobacteriophage MichelleMyBell

value: Mycobacteriophage MichelleMyBell


title: OE-RBM25-1


title: OE-K77R-1


title: KO-RBM25-1


title: KO-Control-1

value: control


title: KO-RBM25-2


title: OE-K77R-2


title: OE-GFP-2

value: GFP


title: KO-Control-2


title: MCF10A/PHF8-TGFβ1-48hr rep2

city: Iowa City

first: Noah

middle: S

last: Butler

state: IA

address: 4-350 BSB, 51 Newton Road

department: Department of Microbiology and Immunology

institute: University of Iowa

description:
secondary round of RNA-seq
Sample 15

data_processing:
The paired-end raw reads were aligned against the hg19 assembly of the human genome using the TopHat (v2.0.13) program (Kim et al., 2013). Counts were generated using featureCounts from the Subread package (Release 1.4.6) (Liao et al., 2013), and the initial differential expression was assessed with DESeq2 (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements by DESeq2

source_name: MCF10A cells overexpressing PHF8

growth_protocol: MCF10A cells were cultured in DMEM-F12 supplemented with 20 ng/ml Epidermal Growth Factor (EGF) (Sigma), 100 ng/ml cholera toxin (Sigma), 10 µg/ml insulin (Sigma), 500 ng/ml hydrocortisone (Sigma), and 5% horse serum.

extract_protocol:
Total RNA without rRNA was extracted using the RNeasy Plus Mini Kit (Qiagen).
RNA-seq libraries were made using the TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero™ Human/Mouse/Rat, RS-122-2201) and multiplexed with Illumina barcodes.50-bp paired-end reads were generated. More than 20 Mb reads were produced for each library.

treatment_protocol: TGF-β1 (Calbiochem) was added into the medium directly, at 5 ng/ml.

tag: cell line

value: 48 hours


title: MCF10A/PHF8-TGFβ1-72hr rep2

description:
secondary round of RNA-seq
Sample 16

value: 72 hours


title: Mycobacteriophage Redi lysogen

description: Mycobacteriophage Redi lysogen

organism:
Mycolicibacterium smegmatis MC2 155
Mycobacterium phage Redi

value: Mycobacteriophage Redi

value: no exogenous phage added


title: MCF10A/PHF8-TGFβ1-24hr rep2

description:
secondary round of RNA-seq
Sample 14

value: 24 hours


title: MCF10A/PHF8-NC rep2

description:
secondary round of RNA-seq
Sample 13

value: without treatment


title: MCF10A/Mock-TGFβ1-72hr rep2

description:
secondary round of RNA-seq
Sample 12

source_name: MCF10A cells overexpressing empty vector

value: Mock


title: MCF10A/Mock-TGFβ1-48hr rep2

description:
secondary round of RNA-seq
Sample 11


title: MCF10A/Mock-TGFβ1-24hr rep2

description:
secondary round of RNA-seq
Sample 10


title: MCF10A/Mock-NC rep2

description:
secondary round of RNA-seq
Sample 9


title: MCF10A/PHF8-TGFβ1-72hr rep1

description:
fist round of RNA-seq
Sample 8


title: MCF10A/PHF8-TGFβ1-24hr rep1

description:
fist round of RNA-seq
Sample 6


title: MCF10A/PHF8-NC rep1

description:
fist round of RNA-seq
Sample 5


title: MCF10A/Mock-NC rep1

description:
fist round of RNA-seq
Sample 1


title: OE-GFP-1


title: MCF10A/Mock-TGFβ1-72hr rep1

description:
fist round of RNA-seq
Sample 4


title: MCF10A/Mock-TGFβ1-48hr rep1

description:
fist round of RNA-seq
Sample 3


title: miRNA-control

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

description:
Control-VS-ETOH_Fly_Head_known_miR_DiffExp.txt
Control-VS-ETOH_Fly_Head_novel_miR_DiffExp.txt

data_processing:
RNA-seq reads were aligned and mapped to the Drosophila reference genome (BDGP Release 5) using SOAPaligner/SOAP2, allowing no more than 5 bp mismatches. Low-quality reads (containing adapters or high content of unknown bases) were filtered out. Known miRNAs were identified by alignment to miRBase21.0.
Expression levels for miRNAs were calculated using the CLC Genomics Workbench (CLC bio, Boston, MA). Differential expression analysis was conducted using Cluster 3.0, and Java TreeView software (Eisen et al., 1998; Saldanha, 2004) and expressed as log2 Ratios (EtOH/Ctrl). We used FDR ≤ 0.0001 and an absolute value of log2 Ratio ≥ 1 as the threshold to judge the significance of expression difference.
The following criteria was used to identify novel miRNAs. After removing the known miRNAs, RNA sequences with a length of 19 to 26 nucleotides were examined further. Those that matched the sense strand of a mRNA, rRNA, tRNA, snoRNA, or a snRNA gene were filtered out. The remaining RNAs were mapped to the genome and the mirReap algorithm was used to show that a stem-loop structure of the appropriate loop size, without any internal bulges, could be formed by a transcript produced by the genomic locus. The putative hairpin structure of a possible precursor is relatively stable with an energy of hybridization less than or equal to -18 kcal/mol. Each predicted precursor has a 3 n depth for the Drosha/Dicer cutting site. All putative miRNAs also must have an arbitrary cutoff count of no fewer than 5 reads per million.
Genome_build: DM3
Supplementary_files_format_and_content: Text files include raw count and normalized values for each sample, and differential expression between the two samples for (1) all known miRNAs, and (2) novel miRNAs detected.

organism: Drosophila melanogaster

source_name: heads

growth_protocol: All flies were maintained on a standard cornmeal/molasses/agar medium under 12:12 light:dark conditions

extract_protocol:
Approximately 180 adult female flies were used per sample. Flies were transferred to a 50 ml conical tube and snap frozen in liquid nitrogen. Heads were snapped off from the body by briefly vortexing the tubes. The frozen heads were sorted from the bodies using a series of cooled metal mesh sieves. Total RNA was isolated from the heads using the guanidinium thiocyanate single-step method (Ausubel, 1994). After isolation, RNA was treated with DNAse I (Life Technologies, Grand Island, NY) and purified by acid-phenol/chloroform extraction and ethanol precipitation. RNA concentration and quality was assessed using a 2100 Bioanalyzer RNA 6000 Pico Chip (Agilent Technologies, Inc., Santa Clara, CA). RIN values for the control and ethanol-treated samples were 6.80 and 6.40, respectively.
Small RNAs (18-30 nuclotides) were isolated by PAGE size fractionation.Small RNA libraries were generated from each RNA sample using Illumina Small RNA Sample Preparation kit according to the manufacturer’s instructions and sequenced with the Illumina HiSeq 2000 at the Beijing Genomics Institute (Shenzhen, China).

treatment_protocol: The ethanol treated group was exposed to an ethanol-saturated air stream until all flies were sedated (15 minutes), followed by a 30 minute ethanol-free air stream. For the untreated control group, flies were exposed to an ethanol-free air stream for the entire 45 minutes.

tag: strain

value: Canton-S

tag: developmental stage

value: Adult

tag: age

value: 3-5 days

tag: tissue

value: head


title: MCF7+EtOH ChIP-seq input

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
For ChIP-seq, Sole-Search (alpha=0.0001, FDR=0.0001, peakmergedistance=0, histoneblurlength=1200) was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, tab-delimited text files include location of peaks

source_name: MCF7+EtOH ChIP-seq input

growth_protocol: The human breast cancer MCF7 cells (ATCC # HTB-22) were grown in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
For ChIP-seq, cells were crosslinked using 1% formaldehyde and lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).

treatment_protocol: For vehicle experiment, instead of estradiol, EtOH was added.

tag: cell type

value: Human breast cancer cell line

tag: treated with

value: ethanol (vehicle)


title: miRNA-EtOH_30min

tag: treatment

value: 15 min ethanol vapor, 30 minute air


title: H3K27Ac ChIP-seq MCF7+EtOH rep2

source_name: H3K27Ac ChIP-seq MCF7+EtOH

tag: chip antibody

value: H3K27Ac Abcam ab4729


title: H3K27Ac ChIP-seq MCF7+EtOH rep1


title: MCF7+E2 ChIP-seq input

source_name: MCF7+E2 ChIP-seq input

treatment_protocol: For estradiol stimulation, cells were grown in phenol red free medium with charcoal stripped serum for several days and treated with 100nM of estradiol for 45 min.

value: 100nM of estradiol for 45 min


title: MCF10A ChIP-seq input

source_name: MCF10A ChIP-seq input

growth_protocol: The immortalized human normal breast cell line MCF10A (ATCC # CRL-10317) was maintained in DMEM/F12 with 5% horse serum, 100units/ml penicillin, 0.1mg/ml streptomycin, 0.5ug/ml hydrocortisone, 100ng/ml cholera toxin, 10ug/ml insulin, and 20ng/ml epidermal growth factor (EGF).

value: Human breast cell line


title: H3K27Ac ChIP-seq MCF7+E2 rep1

source_name: H3K27Ac ChIP-seq MCF7+E2


title: H3K27Ac ChIP-seq MCF10A rep2

source_name: H3K27Ac ChIP-seq MCF10A


title: MCF10A FAIRE-seq input

data_processing:
FAIRE-seq reads were aligned to hg19 genome assembly using bwa.
For FAIRE-seq, Sole-Search (TF parameter, alpha value: 0.001, fdr: 0.001) was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: For FAIRE-seq, tab-delimited text files include location of peaks

source_name: MCF10A FAIRE-seq input

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


title: FAIRE-seq MCF10A rep2

source_name: FAIRE-seq MCF10A


title: FAIRE-seq MCF10A rep1


title: ChIP-seq Input RWPE1 rep2

source_name: Human prostate cell line RWPE1

growth_protocol: RWPE1 cells were grown in medium following ATCC recommended conditions: Keratinocyte Serum Free Medium (K-SFM), Kit Catalog Number 17005-042 (GIBCO) which supplies bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF).

tag: antibody


title: H3K27Ac ChIP-seq MCF10A rep1


title: ChIP-seq Input RWPE1 rep1


title: H3K27Ac ChIP-seq RWPE1 rep2

tag: antibody vendor/catalog#


title: H3K27Ac ChIP-seq C42B rep2

source_name: Human prostate cancer cell line C42B

growth_protocol: C42B cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum.


title: H3K27Ac ChIP-seq RWPE1 rep1


title: ChIP-seq Input C42B rep1


title: MCF10A/Mock-TGFβ1-24hr rep1

description:
fist round of RNA-seq
Sample 2

tag: genotype/variation

tag: time point


title: MCF10A/PHF8-TGFβ1-48hr rep1

description:
fist round of RNA-seq
Sample 7

value: 48 hours