title: ChIP-seq_H3K27me3_WT_rods_rep2

description: processed data files: ChIP-seq_H3K27me3_WT_rods_SICER_peaks.gz

source_name: Rods from WT mouse retina

extract_protocol:
The retina was rapidly dissected from 1-2 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

tag: strain background

tag: genotype/variation

value: LMOPC1-Cre; R26-LSL-CAG-Sun1-GFP-myc

tag: age

value: 8 to 11 weeks

tag: Sex

value: male

value: retina

value: WT rod photoreceptors

tag: chip antibody

value: rabbit anti-H3K27me3 (Millipore 07-449)


title: ChIP-seq_H3K27me3_WT_rods_rep1

status: Public on Mar 07 2016

type: SRA

city: Baltimore

first: Alisa

last: Mo

state: MD

address: 725 N. Wolfe St. PCTB805

department: Molecular Biology and Genetics

country: USA

institute: Johns Hopkins University School of Medicine

library_source: genomic

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2015 (in submission)
RNA-seq: Five base pairs were trimmed from the 5'-end of all reads to remove possible adaptor contamination (seqtk trimfq -b 5)
RNA-seq: Trimmed reads were aligned to the mm10/ERCC92 combined index using TOPHAT v1.4.0 (--GTF --no-novel-juncs) guided by protein coding gene annotation from iGenomes
RNA-seq: Gene expression levels were estimated using RSEM v1.1.20 (--fragment-length-mean 250 --fragment-length-sd 50)
RNA-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.15.0 genomeCoverageBed -split -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).

MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/) for alignment and mC calling
MethylC-seq: DMRs were identified using DSS [Feng H. et al. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 42, e69 (2014)].
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.

ATAC-seq: Adapter sequences were trimmed from ATAC reads (cutadapt v1.3 -a CTGTCTCTTATACACATCT -q 30 --minimum-length 36 --paired-output)
ATAC-seq: Trimmed reads were aligned to the mm10 genome (BOWTIE2 v2.1.0 -t -X2000 --no-mixed --no-discordant)
ATAC-seq: Redundant reads were removed (picard MarkDuplicates).
ATAC-seq: Peaks were called with MACS2 [Zhang Y. et al. Model-based analysis of ChIP-Seq. Genome Biol. 9, R137 (2008)] (macs2 2.1.0.20140616 callpeak -p 0.00001 --call-summits --nomodel --shift -50 --extsize 100) using sub-nucleosomal (<100bp) fragments. File format is MACS2 narrowPeak.
ATAC-seq: Visualization tracks were generated by counting genome-wide coverage of all fragments (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).

ChIP-seq: Reads were aligned to the mm10 genome, keeping only uniquely aligning reads (BOWTIE v0.12.7 -m 1)
ChIP-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).
ChIP-seq: Peaks were called with SICER_V1.1 (redundancy threshold = 1; fragment size=150; W=200, G=200 for H3K27ac, H3K4me1, and H3K4me3; W=200, G=1000 for H3K27me3). Overlapping peaks from the 2 replicates were merged (BEDTOOLS merge) to generate 1 set of peaks for each histone modification.

Genome_build: mm10

Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq, ATAC-seq, and ChIP-seq datasets
tab delimited text files of gene expression levels estimated using RSEM v1.1.20
tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category
tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
tab delimited text files of ATAC-seq peaks; columns in peak files are: column 1 - chromosome; column 2 - start; column 3 - end
tab delimited text files of ChIP-seq peaks; columns in peak files are: column 1 - chromosome; column 2 - start; column 3 - end

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

tag: tissue

tag: cell type


title: ChIP-seq_input_WT_rods_rep3

value: none (input)


title: ChIP-seq_input_WT_rods_rep2


title: ChIP-seq_H3K4me3_WT_rods_rep1

description: processed data files: ChIP-seq_H3K4me3_WT_rods_SICER_peaks.gz

value: rabbit anti-H3K4me3 (Abcam ab8580)


title: ChIP-seq_input_WT_rods_rep1


title: ChIP-seq_H3K4me1_WT_rods_rep1

description: processed data files: ChIP-seq_H3K4me1_WT_rods_SICER_peaks.gz

value: rabbit anti-H3K4me1 (Abcam ab8895)


title: ChIP-seq_H3K4me1_WT_rods_rep2


title: ChIP-seq_H3K27ac_WT_rods_rep1

description: processed data files: ChIP-seq_H3K27ac_WT_rods_SICER_peaks.gz

value: rabbit anti-H3K27ac (Abcam ab4729)


title: NSF1_o67-9-2

city: Raleigh

first: Vincent

middle: L

last: Chiang

state: NC

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

library_source: transcriptomic

data_processing:
Six to twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for Illumina GAIIx or HiSeq 2000 sequencing
68 to 100 bp average read lengths were obtained.  After removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: Populus trichocarpa gene model name (version 3)
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts

molecule: total RNA

organism: Populus trichocarpa

source_name: Stem differentiating xylem

growth_protocol: P. trichocarpa Wild type and transgenic trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 6 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation. Due to limited greenhouse space, different batch of transgenic trees with respective wild type were planted in soil and harvest at different time, there are total six batch trees were labeled with NSF1 to NSF6

extract_protocol:
Stem defferentiating xylem were scraped from the surface of the debark stem using a single-edge razor into liquid nitrogen immediately. collected tissues were ground into powder and stored in liquid nitrogen. Total RNA of SDX sample were extracted by uing Qiagen RNeasy Mini Kit (Invitrogen/Life Technologies, Grand Island, NY) with DNase I treatment option as suggested by kit manunal.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Agrobacterium mediated transformation of binary vector to knockdown or overexpression target genes driven by xylem specific promoter of 4-coumarate:CoA ligase gene[EU603323]

tag: gene perturbation type

value: overexpression of CAD2

tag: batch of trees

value: Stem differentiating xylem


title: ATAC-seq_NrlKO_retina_rep1

source_name: Nrl KO mouse retina

extract_protocol:
The retina was rapidly dissected from 1 adult mouse on ice.
Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described [Buenrostro J.D. et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013)], with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

value: Nrl-/-

value: 3 to 3.5 weeks

value: Nrl-/-retina


title: ATAC-seq_NrlKO_retina_rep2


title: NSF1_o67-9-3


title: ATAC-seq_rd7_retina_rep2

source_name: rd7 mouse retina

value: Nr2e3rd7/rd7 retina


title: ChIP-seq_H3K27ac_WT_rods_rep2


title: ChIP-seq_H3K4me3_WT_rods_rep2


title: WT_077

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
RNA-seq reads were aligned to the GRCm37/mm9 build of the Mus musculus genome using the Subread aligner. Mapping quality score was used to break the tie when more than one best location was found for a read.
Genewise counts were obtained using featureCounts. Only reads overlapping with the last 3000 exonic bases (located at 3’ end) of each gene were counted because only these bases in the genes were sequenced in this experiment. All exonic bases will be used for read counting if a gene has a total exon length of less than 3000 bases. NCBI RefSeq mouse annotation build 37.2 was used in the analysis.
Genes were filtered from downstream analysis if they failed to achieve a RPKM (reads per kilobase of exon length per million mapped reads) value of at least 0.5 in at least two libraries. Differential expression analysis was performed using Biconductor R package edgeR. A negative binomial generalized log-linear model was fitted to each gene, and likelihood ratio tests were performed to assess differential expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 or less and also had at least 8 RPKMs in one or both of the two cell types being compared.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including log2-RPKM values for genes in each sample

source_name: Wildtype (WT) Bone marrow

extract_protocol:
NP366+ CD8+ T cells were purified by flow cytometric sorting from day 9 HKx31-infected PR8-primed mixed bone marrow chimeras. Total RNA was prepared using a Qiagen RNeasy Plus Mini Kit (Qiagen) according to the manufacturers instructions. RNA-seq was carried out based on a previously published single-cell protocol (Tang, F. et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nature protocols 5, 516-535, 2010). Samples were sequenced on a Solexa 1G Genome Analyzer instrument (Illumina) at the National Heart Lung and Blood Institute.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: CD8+ T cells

tag: reporter

tag: mrna extraction

value: Single-cell


title: NSF1_o67-3-2


title: NSF1_o67-9-1


title: NSF1_o67-3-3


title: NSF1_o67-15-3


title: NSF1_o67-3-1


title: ATAC-seq_WT_retina_rep1

source_name: WT mouse retina

value: WT

value: WT retina


title: ATAC-seq_rd7_retina_rep1

value: male

value: retina


title: ATAC-seq_WT_cones_rep1

source_name: Cones from WT mouse retina

extract_protocol:
The retina was rapidly dissected from 2-4 adult mice on ice, and the INTACT method was used to affinity purify GFP+ nuclei.
Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described [Buenrostro J.D. et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013)], with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

value: HRGP-Cre; R26-LSL-CAG-Sun1-GFP-myc

value: 8 to 11 weeks

value: WT cone photoreceptors


title: ATAC-seq_WT_cones_rep2


title: ATAC-seq_WT_retina_rep2


title: ATAC-seq_WT_rods_rep2

extract_protocol:
The retina was rapidly dissected from 1 adult mouse on ice, and the INTACT method was used to affinity purify GFP+ nuclei.
Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described [Buenrostro J.D. et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013)], with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

value: LMOPC1-Cre; R26-LSL-CAG-Sun1-GFP-myc

value: WT rod photoreceptors


title: NSF1_i7-8-3

value: knockdown of PAL2,PAL4,PAL5


title: NSF1_i7-8-1

value: Stem differentiating xylem


title: NSF1_o67-15-2

value: overexpression of CAD2


title: NSF1_i7-8-2


title: NSF1_i7-2-2


title: ATAC-seq_WT_rods_rep1


title: NSF1_i7-2-3


title: aortic valve from hypertensive mice, replicate 3

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

data_processing:
The quality of the sequence reads was assessed using the FastQC program (version 0.11.2).
Paired-end reads (50-bp) were then aligned to the mouse transcriptome (UCSC known genes, genome build mm10, Dec. 2011) with the bowtie program (version 1.0.1) using default parameters.
The samtools program (version 0.1.9) was used to parse the BAM alignment files in order to calculate the total count of sequence reads per UCSC known gene transcript.   Using information from the UCSC kgXref table, reads per transcript were combined to generate read counts per gene.
The resulting counts file was imported into edgeR (an R/Bioconductor package, version 2.6.0, R version x64 2.15.1), which was used to normalize counts between samples and to generate pairwise comparisons between the different groups.
Expression of the ApoE gene was used to confirm the loss of ApoE in the ApoE -/- mice.  Expression of the X inactive specific transcript (Xist) gene (only widely expressed in females) was used to verify the sex of the sample source (both males and females were used in the study).
A p-value less than 0.01 was used to filter the list of candidate genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file of normalized read counts per gene

source_name: aortic valve_hypertensive mice

extract_protocol:
Total RNA from aortic valves was extracted using the Trizol method and purified using the Qiagen RNeasy column.  A DNase digestion was performed to remove genomic DNA.
The Nugen Ovation RNA-Seq System v2 (San Carlos, CA) was used to generate cDNA from 1 ng of total RNA by using the manufacturer’s suggested protocol. Indexed sequencing libraries were generated with the KAPA hyper prep kit  (Wilmington, MA) according to the manufacturer’s suggested protocol.

value: M

tag: mouse group

value: hypertensive mice

value: aortic valve


title: NSF1_i7-6-1


title: aortic valve from hypertensive mice, replicate 4


title: RNA-seq_WT_rods_rep1

extract_protocol:
The retina was rapidly dissected from 1 adult mouse on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

tag: molecule subtype

value: nuclear RNA


title: RNA-seq_rd7_rods_rep2

source_name: Rods from rd7 mouse retina

value: rd7 rod photoreceptors


title: RNA-seq_rd7_rods_rep1


title: NSF1_o67-15-1


title: NSF1_i7-2-1


title: RNA-seq_WT_cones_rep2

extract_protocol:
The retina was rapidly dissected from 2-4 adult mice on ice, and GFP+ nuclei were obtained by flow cytometry. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.


title: RNA-seq_WT_rods_rep2


title: NSF1_i7-10-3


title: NSF1_i7-6-3


title: NSF1_i7-10-2


title: RNA-seq_WT_cones_rep1


title: aortic valve from control mice, replicate 4

source_name: aortic valve_control mice

value: control mice


title: NSF1_i7-10-1


title: aortic valve from hypertensive mice, replicate 1

value: F


title: aortic valve from control mice, replicate 3


title: aortic valve from hypertensive mice, replicate 2


title: NSF1_a2-8-3

value: knockdown of PAL3


title: NSF1_i7-6-2


title: NSF1_a2-1-2


title: aortic valve from control mice, replicate 2


title: aortic valve from control mice, replicate 1


title: aortic valve from high cholesterol/hypertensive model, replicate 4

source_name: aortic valve_high cholesterol/hypertensive model

value: high cholesterol/hypertensive model


title: aortic valve from high cholesterol/hypertensive model, replicate 3


title: NSF1_a1-3-1

value: knockdown of PAL1


title: NSF1_a1-1-3


title: NSF1_a1-1-1


title: aortic valve from high cholesterol/hypertensive model, replicate 2


title: aortic valve from high cholesterol/hypertensive model, replicate 1


title: aortic valve from high cholesterol model, replicate 4

source_name: aortic valve_high cholesterol model

value: high cholesterol model


title: aortic valve from high cholesterol model, replicate 3


title: aortic valve from high cholesterol model, replicate 2


title: Root Control 120 rep 2

status: Public on Mar 06 2016

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Small RNA

data_processing:
Q20 Quality triming
Adaptor trimming
Size trimming (<18)
Read alignment to rice genome (using Bowtie2 aligner)
Reads aligning with Rfam v11.0 were removed
Read alignment to miRNA database (miRBase v21)
Total read library normalization
Genome_build: Oryza sativa, version 7.0
Supplementary_files_format_and_content: text file with reads and abundances for each detected miRNA

organism: Oryza sativa

growth_protocol: Rice plants were grown for 2 week at 28ºC ans 16h/8h light/dark conditions

extract_protocol:
total RNA was extracted with Trizol (Invitrogen) following manufacturer's instructions
TruSeq protocol (Illumina)

treatment_protocol: Plants were treated with Margaporthe oryzae elicitors for 30 min and 2 hours

tag: cultivar

value: Nipponbare

value: Root

value: 15 days old

tag: time point

value: 120 minutes


title: Root Elicitor 30 rep 3

description: Small RNA

value: 30 minutes


title: Root Elicitor 30 rep 2

description: Small RNA


title: Leaf Elicitor 30

description: degradome analysis

data_processing:
Q20 Quality triming
Adaptor trimming
Size trimming
Read alignment to rice genome (using Bowtie2 aligner)
Degradome analysis using PARE-snip pipeline
Genome_build: Oryza sativa, version 7.0
Supplementary_files_format_and_content: text file with targets for miRNA

value: Leaf

tag: timepoint

value: 30 min


title: Leaf Elicitor 120

description: degradome analysis

value: 120 min


title: Leaf Control 120

description: degradome analysis


title: Root Elicitor 30 rep 1

description: Small RNA


title: Root Control 30 rep 3

description: Small RNA


title: Root Elicitor 120 rep 3

description: Small RNA


title: Leaf Control 30

description: degradome analysis


title: Root Elicitor 120 rep 2

description: Small RNA


title: Root Elicitor 120 rep 1

description: Small RNA


title: Root Control 120 rep 1

description: Small RNA


title: Leaf Elicitor 120 rep 2

description: Small RNA


title: Root Control 30 rep 1

description: Small RNA


title: NSF1_a1-1-2

value: Stem differentiating xylem


title: aortic valve from high cholesterol model, replicate 1

tag: strain background

value: aortic valve


title: Leaf Elicitor 120 rep 3

description: Small RNA


title: Root Control 30 rep 2

description: Small RNA


title: Leaf Elicitor 120 rep 1

description: Small RNA


title: Leaf Elicitor 30 rep 3

description: Small RNA


title: Leaf Control 120 rep 3

description: Small RNA


title: Leaf Control 120 rep 2

description: Small RNA


title: Leaf Elicitor 30 rep 2

description: Small RNA


title: Root Control 120 rep 3

description: Small RNA


title: Leaf Control 120 rep 1

description: Small RNA


title: Leaf Elicitor 30 rep 1

description: Small RNA


title: Leaf Control 30 rep 3

description: Small RNA


title: PCK over

city: Bucheon

first: Hyojung

last: Lee

address: Rm 718 Dasol Bd., 43 Jibong-ro, Wonmi-gu

department: Biotechnology

country: South Korea

institute: The Catholic University of Korea

data_processing:
Xpression (https://depts.washington.edu/cshlab/html/rnaseq.html) was used for RNA-Seq data processing.
Xpression was used for filtering and trimming reads.
Reference files for the genome sequence being queried, Escherichia coli BL21(DE3) genome (NC_012971) were uploaded.
Raw sequencing reads (FASTQ)were processed by Xpression and only the uniquely mapped reads were subjected to further analysis.
The number of reads overlapping each gene was recorded and normalized based on reads per kilobase per million (RPKM) uniquely mapped reads.
Genome_build: gi|387825439

organism: Escherichia coli BL21(DE3)

source_name: bacterial cells

growth_protocol: Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g/L glucose, 0.1 mM IPTG, and 50 μg/mL antibiotics. The fermentors were operated at 37 °C and 250 rpm with  aeration (200 mL/min). Flow rate was 1.162ml/min(dilution rate 0,7/h). The pellets were used for RNA.

extract_protocol:
Total RNA was harvested from C. glutamicum cells using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) and NucleoSpin® (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions with the following modifications. Cells were harvested by centrifugation, resuspended in TRIzol® reagent, and transferred to a vial containing Lysing Matrix B® (MP Biomedicals, Solon, OH, USA) for lysis. The suspension was centrifuged, and the supernatant was applied to a NucleoSpin® RNA II kit for purification.
First and second strand cDNA synthesis was carried out using the Ovation® Prokaryotic RNA-Seq System (NuGEN Technologies Inc., San Carlos, CA, USA), and NuGEN’s Encore NGS Library System was applied to construct the cDNA library for the IlluminaHiSeq platform.

tag: genotype

value: Pck over-expressed

tag: condition

value: LB+3g/L Glc +0.1mM IPTG + 50μg/ml Amp


title: Leaf Control 30 rep 2

description: Small RNA

tag: age


title: Leaf Control 30 rep 1

description: Small RNA


title: wt_mloti_B

status: Public on Mar 05 2016

city: Aarhus

first: Jens

last: Stougaard

address: Gustav Wieds Vej 10

department: Department of Molecular Biology and Genetics

country: Denmark

institute: Centre for Carbohydrate Recognition and Signalling, Aarhus University

description: Processed data file: ShortranOutput_cut10.xlsx

data_processing:
Sequence analysis steps were followed as described in Gupta et al., 2012 (PMID: 22914220, doi: 10.1093/bioinformatics/bts496) using the shortran pipeline.
Briefly, after trimming the adapter and barcode sequences, inserts were k-mer corrected using ECHO (Kao et al., 2011; doi: 10.1101/gr.111351.110). Sequences with less than 10 counts across the four libraries were disregarded. For the remaining sequences, counts were normalized to the largest library. Size fractions containing 19-24 nt long sequences were used for onward analysis and mapped to the genomes of L. japonicus v2.5 (Sato et al., 2008; doi: 10.1093/dnares/dsn008) and M. loti MAFF303099 (Kaneko et al., 2000; doi: 10.1093/dnares/7.6.331) using Bowtie (Langmead et al., 2009; doi: 10.1186/gb-2009-10-3-r25), allowing for 2 mismatches. As the L. japonicus genome is currently still incomplete, we retained sequences for further analysis irrespective of whether mapping positions were assigned. Sequences were further mapped to the TIGR plant repeat database v2.0.0 (Fabaceae phylogeny branch) (Ouyang & Buell, 2004; doi: 10.1093/nar/gkh099) (http://plantrepeats.plantbiology.msu.edu/), and to identify sequences corresponding to previously annotated miRNAs, to miRBase v19 (Kozomara & Griffiths-Jones, 2011; doi: 10.1093/nar/gkq1027) using the same software and allowing for 2 and 3 mismatches, respectively. Spearman Rank Correlation Coefficients were calculated using The R Project for Statistical Computing (R-2.13.0) (http://www.r-project.org/). Expression and comparative data were extracted from the shortran output database using custom MySQL queries. All scripts used are available from the authors upon request.
Genome_build: Lotus japonicus v2.5 (Sato et al., 2008; doi: 10.1093/dnares/dsn008)
Genome_build: Mesorhizobium loti MAFF303099 (Kaneko et al., 2000; doi: 10.1093/dnares/7.6.331)
Supplementary_files_format_and_content: ShortranOutput_cut10.xlsx: The processed data file contains the entire data output of the shortdan pipeline run for all four sRNA libraries. Filtering and mapping steps were as described above. Raw and normalized sequence counts, as well as mapping data, are included.

organism: Lotus japonicus

source_name: root, wt, M. loti infected

growth_protocol: Seedlings were grown on square plastic dishes with wedged 1/2 strength Broughton and Dilworth medium (Broughton and Dilworth, 1971) supplemented with 1 mM KNO3 at 21°C (16 h light, 8 h dark). Roots were shielded from light access.

extract_protocol:
Total RNA was extracted from 10-15 independent root systems per sample using mirVana (Ambion, Life Technologies, Naerum, Denmark) kit materials and following the supplier's recommendations. RNA was eluted in DEPC-treated water before being quality checked on an Agilent 2100 Bioanalyzer.
10 μg of total RNA per sample were used for purifying circa 18-28 nt small RNA fractions on denaturing 15% acrylamide gels. Small RNA preparation and sequencing were performed by Fasteris (Genève, Switzerland) following a modified Illumina (Madison, WI, USA) protocol for sRNA library construction and sequencing (Chrysalis 36 cycles v4.0). Briefly, single-stranded RNA adapters were sequentially ligated to 3' and 5' ends of sequences using T4 RNA ligase in the presence or absence of ATP, respectively. Following a second gel purification step, cDNA was generated and PCR-amplified (12 cycles). Aliquots were cloned, sequenced and mapped to the L. japonicus genome v2.5 for quality control purposes.

treatment_protocol: Plants were inoculated at day 7 days post germination. For inoculation, liquid cultures of M. loti MAFF303099 expressing DsRed (Maekawa et al., 2009) were grown for 2 days and harvested by centrifuging for 10 minutes at 3000 g. The bacterial pellet was washed twice in 1/2 strength Broughton and Dilworth medium (1 mM KNO3) and diluted to an optical density at λ=600 of 0.01. 100 µl bacterial suspension was applied directly to each root. Mock roots were treated with an equal amount of sterile medium. Roots were harvested and shock-frozen in nitrogen 10 days post germination.

tag: genotype/variation

value: wild type

value: root

tag: treatment

value: Mesorhizobium loti infection

value: 3 dpi

tag: biological replicate

value: B


title: BL21_2

value: wild-type

value: LB+3g/L Glc +0.1mM IPTG


title: BL21_1


title: Z938_13_5R

city: san diego

first: Marwa

last: Khater

address: 11990 cypress valley dr

institute: UCSD

data_processing:
illumina
FASTQC followed by trimming to remove 10 nucleotides on each end, and removal of reads with a paired read quality score < 30
STAR mapping to hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Annotated using Human reference genome version Ensembl GRCh37
Genes without at least one sample with at least ten reads were removed from the analysis
2 Putamen samples with low reads were removed
The count data for the remaining samples were normalized using the R package DESeq2
One-way ANOVA (analysis of variance) with post-hoc Tukey HSD (honestly significant difference) was performed
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file containing normalized read counts and metrics used to perform the comparison for each brain region separately: ("low cell dose" AND "high cell dose") to "buffer injection". These metrics include: average counts per comparison group, q-value, and fold-change.

organism: Chlorocebus sabaeus

source_name: brain

extract_protocol:
RNA was extracted using the miRVANA miRNA Isolation Kit (Life Tecnhnologies) using the total RNA protocol
RNAseq libraries were constructed using the TruSeq Stranded Total RNA Library Prep Kit (Illumina)

tag: mptp treatment

value: MPTP treated

tag: transplant type

value: High cell dose

tag: monkey id

tag: brain region

value: Putamen

tag: tissue

value: brain


title: Z938_11_5R

value: Caudate


title: K231_13_5R

description: Wild Type

value: untreated

value: No transplant procedure


title: K231_11_5R

description: Wild Type


title: wt_mock_B

source_name: root, wt, mock infected

value: mock infection


title: K231_41R

description: Wild Type

value: Substantia Nigra


title: Z937_11_5R

value: Low cell dose


title: Z914_41R


title: Z938_41R


title: MeDIP result

city: Ann Arbor

first: Yibin

last: Chen

state: MI

address: 1115 w medical drive

institute: university of Michigan

description: TGACCA

data_processing:
The read quality of each sample was determined by FastQC software. After prefiltering the raw data by removing sequenced adapters and low quality reads, the tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Parameter settings were as follows: -v, 3 (reported alignments with at most 3 mismatches), -5, 3 and -3, 3 (trim3 bases from 5’ and 3’ end to remove low-quality bases). Peak detection was performed using MACS software from Galaxy browser (www.galaxy.psu.edu). Parameters settings were as follows: tag size with 25bp, band width with 300bp, P-value cutoff for peak detection was set to 1e-05. The peaks obtained from ChIP sequencing were matched to the annotated reference genome (mouse mm9) using Cisgenome 2.0
Genome_build: MM9
Supplementary_files_format_and_content: The tags were mapped to the mouse genome (assembly mm9) by Bowtie software. Peak detection was performed using MACS software from Galaxy browser.

source_name: Mouse ES cells

growth_protocol: All procedures are to be done under sterile conditions in a laminar flow hood using sterile instruments and detergent-free glassware. Dulbecco’s modified Eagle’s media (DMEM)  is pared for ES cell medium.

extract_protocol:
Mouse ES cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 10^8 cells and fragmented to 200 to 400 bp by sonication. For MeDIP, we sonicated genomic DNA to produce random fragments ranging in size from 100 to 400 bp.
DNA were repaired to blunt ends by T4 DNA polymerase and phosphorylated with T4 polynucleotide kinase using the END-IT kit (Epicentre). A single “A” base was added to 3’ end with Klenow. Double-stranded adaptors were ligated to the fragments with DNA ligase. Ligation products between 200 and 600 bp were gel purified on 2% agarose to remove unligated adaptors and subjected to 20 PCR cycles. For MeDIP, The DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3’-A base used for adaptor ligation. Following ligation of a pair of adaptors to the repaired ends, the fragments around 160 bp to 370 bp isolated from agarose gel.We used 1 ug of fragmented DNA for a standard MeDIP assay as described. Following denaturation at 95°C for 10 min, immunoprecipitation was carried at 4°C for 1 hr using 1 μg of monoclonal antibody against 5-methylcytidine  in a final volume of 500 μl IP buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100) and incubate at 4 C for 12 hours. And we added the mixture with 40 μl of Protein A/G beads (20421, Pierce) and Rabbit anti-mouse IgG (315-005-008, Jackson Immunoresearch) for 2 hr at 4°C and washed it for times with 700 μl of IP buffer. We then treated the beads with proteinase K for 2 hr at 50°C and recovered the methylated DNA by phenol-chloroform extraction followed by ethanol precipitation. Then the MeDIP-enriched DNA was amplified using the adaptor primers for 15 cycles and the fragments around 220 bp to 420 bp were isolated from agarose gel.

treatment_protocol: Mouse ES cells were cultured in LIF alone without a feeder layer before harvest.

tag: cell type

value: mouse ES cells

tag: antibody information

value: mouse anti-5-Methylcytosine (Clone 33D3)


title: H2ABbd ChIP-seq result

description: CAGATC

value: rabbit anti-mH2ABbd (home-made)


title: Z911_11_5R

value: Buffer injection


title: Z899_41R


title: Z899_13_5R

description: outlier removed


title: Z911_13_5R


title: Z899_11_5R


title: Z914_11_5R


title: Z914_13_5R


title: Z887_41R


title: Z887_13_5R


title: Z887_11_5R


title: Z859_41R


title: Z937_41R


title: Z937_13_5R


title: Z841_11_5R


title: Z911_41R


title: Z859_11_5R


title: Z841_13_5R


title: Z802_11_5R


title: Z836_11_5R


title: Z836_13_5R

description: outlier removed


title: Z841_41R


title: Z836_41R


title: Z802_13_5R


title: Tumor_9

city: Indianapolis

first: Milan

last: Radovich

state: Indiana

address: 980 W. Walnut St, Room C312

institute: Indiana University School of Medicine

data_processing:
Basecalling performed using SOLiD system.  Output (.csfasta and .qual) files were converted to XSQ Files.
Reads were mapped to hg19 using LifeScope 2.5.1
RPKM values were generated using ParTek Genomics Suite v6.6
Genome_build: hg19
Supplementary_files_format_and_content: genic RPKM values in tab-delimited text file

organism: Homo sapiens

source_name: Tumor

extract_protocol:
RNA samples isolated at OriGene
SOLiD Whole Transcriptome Analysis Kit

tag: gender

value: female

value: Breast Carcinoma

tag: tissue type

value: triple-negative breast cancer


title: Tumor_10


title: Tumor_6


title: wt_mloti_A

value: wild type

value: root

value: Mesorhizobium loti infection

tag: time point

value: 3 dpi

value: A


title: Tumor_4


title: Tumor_5


title: Z761_13_5R

value: MPTP treated

value: Putamen

value: brain


title: Z802_41R

value: Substantia Nigra


title: wt_mock_A

value: mock infection


title: Z761_41R

value: Low cell dose


title: Tumor_2


title: Tumor_3


title: Z859_13_5R

value: High cell dose


title: Pbx wo Meis1_ChIPSeq

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Basecalls were performed using CASAVA version 1.4.
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND (Illumina).
Peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).

source_name: Hoxa9 only AML

growth_protocol: AML cells are maintained in IMDM supplemented with 10% FBS and 10 ng/ml IL3

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

treatment_protocol: Meis1 was deleted by 4-hydroxy-tamoxifen treatment that induces expression of Cre recombinase

value: Hoxa9 single expressing murine AML cells

tag: strain

tag: chip antibody

value: Pbx1/2/3 (Santa Cruz, sc-888, lot J157)


title: Input DNA

source_name: Hoxa9/Meis1 AML

value: Hoxa9-and Meis1-co-expressing murine AML cells


title: Tumor_1

value: female

value: Breast Carcinoma


title: Tumor_8

value: triple-negative breast cancer


title: pre-osteoblasts + vehicle replicate 2

city: Madrid

first: Ozge

last: Uluckan

address: calle melchor fernandez almagro, 3

country: Spain

institute: CNIO

description: Isolation of poly A+ RNA from total RNA

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned with the mouse genome (GRCm38/mm10) with TopHat-2.0.4 (using Bowtie 0.12.7 and Samtools 0.1.16), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Transcripts annotations used were Mus musculus GRCm38/mm10 from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

source_name: Osteoblasts from bone marrow

growth_protocol: WT bone marrow was plated overnight in AMEM+20% FBS for 5 days.  The adherent cells were counted and plated into 6 well plates at 5x10^5 cells/ml with b-glycerolphosphate and ascorbic acid (osteogenic media) as in standard osteoblast differentiation protocols.  50 ng/ml IL-17A was added at the time of plating with osteogenic media.

extract_protocol:
RNA was extracted from the wells after 7 days with Trizol.
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 9.7 to 10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation V2  Part # 15026495 Rev. B February 2012). Adapter-ligated library was completed by 8 cycles of PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: vehicle or 50 ng/ml IL-17A

value: osteoblasts

value: vehicle


title: Tumor_7


title: pre-osteoblasts + IL-17A replicate 2

description: Isolation of poly A+ RNA from total RNA

value: 50 ng/ml IL-17A


title: Hoxa9 wo Meis1_ChIPSeq


title: Z761_11_5R

value: Caudate


title: pre-osteoblasts + IL-17A replicate 1

description: Isolation of poly A+ RNA from total RNA


title: Pbx_ChIPSeq


title: Meis1_ChIPSeq


title: pre-osteoblasts + vehicle replicate 1

description: Isolation of poly A+ RNA from total RNA


title: BirA

status: Public on Mar 04 2016

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

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

institute: University of Texas at Austin

description: Control of Yap1_OE sample

data_processing:
Sequenced reads were mapped to mm9 whole genome using Tophat2 with default setting
FPKM values were calculated using Cuffdiff with default setting
Genome_build: mm9
Supplementary_files_format_and_content: text file include FPKM values for each Sample. Genes with FPKM value 0 all across the samples are excluded.

molecule: polyA RNA

source_name: J1 ES cell_control

extract_protocol:
RNAs were extracted using Qiagen Rneasy plus mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic stem cells

tag: passages


title: Yap1_KO1

source_name: J1 ES cell_Yap1_knockout


title: Yap1_KD1

source_name: J1 ES cell_Yap1_knockdown


title: dESC_control

description: Control of dESC_Yap1 KD sample

source_name: J1 ES cell_differentiated_control


title: ESC

description: Control of Yap1 KO samples


title: Control

description: Control of Yap1 KD sample


title: dESC_Yap1_KD1


title: Yap1_KO2


title: Yap1_OE

source_name: J1 ES cell_Yap1_overexpression


title: Input DNA P19

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

data_processing:
SCL-exo fastq files were filtered using SolexaQA to retain high-quality reads only (Q=20, l=17) before being mapped to mouse mm8 (P19 cells) and mm9 (E14 ES cells) genome assemblies, forward and reverse strands separately, using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0 [32]. Resulting .wig files were filtered to remove UCSC blacklisted regions as well as few regions showing a very high signal (above 100x coverage) and not included in the blacklist.
SCL-exo data reads for which a single CpG was found within 10 bases from their 5’ end were selected to build a single-CpG resolution .wig file in which signal at id CpGs corresponds to the sum of the reads covering both Cs (two strands) at each given CpG.
Genome_build: mm8 for P19 cells, mm9 for E14 ES cells
Supplementary_files_format_and_content: wig files

source_name: RA-treated P19 EC cells

growth_protocol: P19 EC cells were routinely grown in DMEM complemented with 10% fetal calf serum. To obtain neural precursor cells, P19 EC cells were treated with 10-6 M retinoic acid for 48 hrs. Cells were either collected without crosslinking for genomic DNA extraction or fixed with 1% formaldehyde for chromatin immunoprecipitation. E14 ES cells were grown in the presence of serum and collected without prior fixation for genomic DNA extraction.

extract_protocol:
Cells were scraped in phosphate buffered saline 48 hours after RA addition and were pelleted at 100 g before genomic DNA extraction using a DNeasy Blood and Tissue kit (Qiagen, France).
Twenty micrograms of DNA in 300 ml of TE buffer (Tris 10 mM, EDTA 0.1 mM, pH 8.0) were sonicated with a Bioruptor (Diagenode, Belgium) to yield 200 to 500 bp fragments. Each glucosylation and biotinylation reaction was run using reagents from the Hydroxymethyl Collector kit (ref. 55013, Active Motif, Belgium) and 500 ng of sonicated DNA. For SCL-seq, 16 reactions were captured on streptavidin-coated magnetic beads (ref. 11205D, Invitrogen). After 5 washes and elution from the beads according to the manufacturer’s protocol, the captured DNA was purified, precipitated and pooled for sequencing library preparation using the TruSeq ChIP Sample Prep Kit (Illumina, ref. IP-202-1012). For SCL-exo, after 6 washes in RIPA buffer (50 mM HEPES pH 7.6; 1 mM EDTA; 0.7% Na-Deoxycholate; 1% NP-40; 0.5 M LiCl) and 2 washes in Tris 10 mM pH 8, the DNA-beads complex was processed as previously described [19]: end polishing, ligation of the P7 exo-adapter, nick repair, lambda and RecJf exonuclease digestion, elution, P7 primer extension, ligation of the P5 exo-adapter, PCR amplification, and finally gel-size selection. The exonuclease-digested DNA was eluted from the beads by incubation in 100 ml of Elution Buffer (95% formamide, 10 mM EDTA) at 90 ⁰C for 5 min, followed by DNA precipitation and resuspension in 20 ml of water. The SCL-seq and SCL-exo libraries were quantified using the KAPA library quantification kit for Illumina sequencing platforms (KAPA Biosystems, KK4824) and 40 bp single-end sequenced in a single lane of a HiSeq 2000 (Illumina) following the manufacturer’s protocol.

value: EC-derived neural progenitor cells

tag: cell line


title: SCL-seq P19

data_processing:
Library strategy: SCL-exo_seq
SCL-exo fastq files were filtered using SolexaQA to retain high-quality reads only (Q=20, l=17) before being mapped to mouse mm8 (P19 cells) and mm9 (E14 ES cells) genome assemblies, forward and reverse strands separately, using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0 [32]. Resulting .wig files were filtered to remove UCSC blacklisted regions as well as few regions showing a very high signal (above 100x coverage) and not included in the blacklist.
SCL-exo data reads for which a single CpG was found within 10 bases from their 5’ end were selected to build a single-CpG resolution .wig file in which signal at id CpGs corresponds to the sum of the reads covering both Cs (two strands) at each given CpG.
Genome_build: mm8 for P19 cells, mm9 for E14 ES cells
Supplementary_files_format_and_content: wig files


title: H3K27ac ChIP-seq P19

description: antibody: Abcam, ab4729, lot # GR132150-1


title: H3K4me1 ChIP-seq P19

description: antibody: Abcam, ab8895, lot # GR149140-1


title: SCL-exo technical replicate 2 P19


title: HCC

city: Shanghai

first: Chunyang

last: Bao

state: Shanghai

address: Shanghai Medical College, Fudan University 1207 Rm., 2# Bldg., 270 Dong An Rd.

department: Fudan University Shanghai Cancer Center

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using TopHat v2.1.0 with default parameters.
Back-spliced reads were calculated using a protocol from Memczak et al., Nature, 2013. Briefly, the unmapped reads were processed to 20-nucleotide anchors from both ends of the read. Anchors that aligned in the reversed orientation (head-to-tail) indicated a back-spliced junction. Anchor alignments were extended such that the complete read aligns and the breakpoints were flanked by GT/AG splice sites. To estimate the relative expression of a circular RNA, denoted as spliced reads per billion mapped reads (SRPBM), we counted the total number of reads mapped to the human reference genome in each sample and normalized the number of reads spanning the back-spliced junction to the total number of mapped reads (units in billion) and read length. To  estimate the relative expression of mRNA, fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using Cufflinks with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include SRPBM values for each Sample and tab-delimited text files include FPKM values for each Sample

source_name: Hepatocellular carcinoma

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries.
Strand-specific RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.

value: Hepatocellular carcinoma


title: SCL-exo technical replicate 1 P19


title: PRAD

source_name: Prostate cancer

value: Prostate cancer


title: KCA

source_name: Clear cell carcinoma

value: Clear cell carcinoma


title: Hoxa9_ChIPSeq


title: CRC

source_name: Colorectal cancer

value: Colorectal cancer


title: GC

source_name: Gastric cancer

value: Gastric cancer


title: BRCA

source_name: Breast cancer

value: Breast cancer


title: CRC_NT

source_name: Normal tissue adjacent to colorectal cancer


title: GC_NT

source_name: Normal tissue adjacent to gastric cancer


title: PRAD_NT

source_name: Normal tissue adjacent to prostate cancer


title: BRCA_NT

source_name: Normal tissue adjacent to breast cancer

value: Normal tissue adjacent to breast cancer


title: KCA_NT

source_name: Normal tissue adjacent to clear cell carcinoma


title: SCL-exo technical replicate 3 P19


title: HCC_NT

source_name: Normal tissue adjacent to hepatocellular carcinoma


title: Stomach_rep2

source_name: Stomach

value: Stomach


title: Lung_rep2

source_name: Lung

value: Lung


title: BLCA_NT

source_name: Normal tissue adjacent to bladder urothelial carcinoma


title: Heart_rep2

source_name: Heart

value: Heart


title: Liver_rep2

source_name: Liver

value: Liver


title: BICR31_K27ac

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

data_processing:
BWA alignment
MACS Peak-calling
Genome_build: hg19
Supplementary_files_format_and_content: bed; DNA coordinates of regions significantly associated with H3K27ac

source_name: Cancer cell line

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FBS

extract_protocol:
Chromatin-IP
Following NEB ChIP-seq library preparation kit (E6200S)

treatment_protocol: No treatment

tag: tumor type

value: Lung adenocarcinomas

tag: antibody


title: Colon_rep2

source_name: Colon

value: Colon


title: Brain_rep2

source_name: Brain

value: Brain


title: Heart_rep1


title: Liver_rep1


title: ZIKV2-1

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned using tophat v2.0.13 and differential RPKM expression values were extracted using cuffdiff v2.2.1
genome build: hg19
Supplementary_files_format_and_content: text file with abundance values for combined replicates and statistical test for differential expression.

source_name: human Neural Progenitor cells

growth_protocol: Human iPSC lines (C1-2 and D3-2) were previously generated from skin biopsy samples and they had been fully characterized and passaged on MEF feeder layers (Wen et al., 2014). H9 hESCs (WA09 from WiCell) and iPSC line (DF19-9-11T.H.) were cultured on feeder free condition. All studies followed institutional IRB and ISCRO protocols approved by Johns Hopkins University School of Medicine and Florida State University. Human iPSCs (C1 and D3-2) were differentiated into forebrain specific hNPCs and immature neurons following previous protocols (Wen et al., 2014). Briefly, hiPSCs colonies were detached from the feeder layer with 1 mg/ml collagenase treatment for 1 hr and suspended in embryonic body (EB) medium, consisting of FGF-2-free iPSC medium supplemented with 2 µM Dorsomorphin and 2 µM A-83, in non-treated polystyrene plates for 4 days with a daily medium change. After 4 days, EB medium was replaced by neural induction medium (NPC medium) consisting of DMEM/F12, N2 supplement, NEAA, 2 µg/ml heparin and 2 µM cyclopamine. The floating EBs were then transferred to matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with NPC medium change every other day. On day 22, the rosettes were picked mechanically and transferred to low attachment plates (Corning) to form neurospheres in NPC medium containing B27. The neurospheres were then dissociated with Accutase at 37⁰C for 10 min and placed onto matrigel-coated 6-well plates at day 24 to form monolayer NPCs in hNPC medium containing B27. These hNPCs expressed markers for forebrain-specific progenitor markers, including NESTIN, PAX6, EMX-1, FOXG1 and OTX2 (Wen et al., 2014). For neuronal differentiation, monolayer hNPCs were dissociated with Accutase at 37⁰C for 10 min and placed onto Poly-D-Lysine/laminin-coated coverslips in the neuronal culture medium, consisting of Neurobasal medium supplemented with 2 mM L-glutamine, B27, cAMP (1 µM), L‐Ascorbic Acid (200 ng/ml), BDNF (10 ng/ml) and GDNF (10 ng/ml).

extract_protocol:
Total RNA was extracted from mESCs by RNeasy (Qiagen), and 1 μg total RNA was primed with Oligo(dT)20 primers (Invitrogen) for cDNA synthesis.
ZIKV infected hNPCs at 56 hrs and mock infected parallel cultures were used for global transcriptome analysis. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. An Agilent 2100 BioAnalyzer was used to quantify amplified cDNA and qPCR was applied to accurately quantify library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle pair-end sequencings were performed using Illumina MISeq. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq reads were aligned using tophat v2.0.8 (Trapnell et al., 2012) and differential RPKM expression values were extracted using cuffdiff v2.2.1 (Trapnell et al., 2012). Statistical significance were determined by cuffdiff in duplicated samples per condition. Gene Ontology analyses were on biological process (BP) performed by The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (Huang da et al., 2009).

treatment_protocol: A ZIKV stock with the titer of 1x105 TCID/ml in the form of culture fluid from an infected rhesus Macaca cell line, LLC-MK2, were originally obtained from ZeptoMetrix (Buffalo, NY). This virus stock was then used to infect the Aedes C3/C36 cells at a MOI of 0.02. Supernatant from the infected mosquito cells were collected 4-7 days post-infection and frozen in aliquots for both titering and infection of human cells. Infections of different cell types were performed at a low multiplicity of infection (MOI; MOI < 0.1) and the virus inoculum was removed after a 2-hour incubation with the cells. To determine whether infected hNPCs produce more infectious ZIKV particles, supernatant from hNPC cultures 72 hour after infection were added to Vero cells for 48 hours.

value: Neural Progenitor cells

tag: infection status

value: Zika infected


title: Colon_rep1


title: ZIKV1-1


title: Brain_rep1


title: Mock2-1

value: mock infected


title: BLCA

source_name: Bladder urothelial carcinoma

value: Bladder urothelial carcinoma


title: healthy_iPSC_50days_neuron

city: Memphis

first: Xiaolong

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

description: HDF D50

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat v2.0.13 with default parameters
Fragment Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a Cufflinks v1.3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: healthy human neuron after 50 days of differentiation from iPSC

growth_protocol: Induced pluripotent stem (iPS) cells were generated and maintained in DMEM/F12 (Invitrogen), supplemented with 2mM L-glutamine (Invitrogen), 1mM β-mercaptoethanol, 1x non-essential amino acids (NEAA), 20% knock-out serum replacement (KSR, Invitrogen), 100 U/mL penicillin, 100 μg/mL streptomycin (Invitrogen)) on irradiated MEF cells.

extract_protocol:
Cell samples of HDF2-iPS and SC128 were collected at four stages during the neuronal differentiation，i.e., iPSC (day0) , IA (day6), NE (day 18), mature neuron (day50). RNA was extracted with TRIzol Reagent(Ambion) according to the manufacturer’s protocol.
We constructed RNA-seq libraries following the protocol described in Illumina TruSeqTM RNA Sample Preparation Guide. Briefly, we started with 400 ng of total RNA. We then purified poly-A containing mRNA molecules by poly-T oligo-attached magnetic beads. After RT and complementary cDNA strand synthesis, we did end-repair and adapter ligation. Finally we amplified the cDNA by 15-cycle PCR. The concentration of the amplified product was determined by Qubit Fluorometer (Invitrogen).

treatment_protocol: iPS colonies were enzymatically lifted (CollagenaseIV,1mg/ ml) and grown in suspension to create floating iPS cell aggregates (IA). IA were grown for 6 days: 4 days in DMEM:F12 (Invitrogen) containing 20% KSR (Invitrogen), 1% Glutamax (Invitrogen), 1% NEAA (Invitrogen); and 2 days in neural induction medium(NIM) composed of DMEM:F12 (Invitrogen) containing 1% N2 (Invitrogen), 1% Glutamax (Invitrogen), 1% NEAA (Invitrogen) and heparin (1 mg/ml, Sigma); IA were reseeded onto laminin (20 mg/ml, Gibco) coated 6-well plate and cultured in NIM for 11 days, until they developed into the definitive neural epithelia(NE) containing neural tube-like rosettes. NE were detached by gentle pipetting leaving the peripheral flat cells attached and further grown in suspension medium (NIM supplemented with 1% B27 to create neural epithelia aggregates (NA) for 8 days. At day25, NA were mechanically digested by accutase/trypsin (1:1) and plated on glass coverslips (Fisher Scientific) coated with poly-L-Ornithine /laminin (Sigma, at a final concentration of 10 mg/ml and 20 mg/ml, respectively). Plated cells were grown in neural differentiation medium (NDM) composed of neurobasal medium (Invitrogen) supplemented with 1% N2 (Invitrogen), 1% B27 (without Vitamin A, Invitrogen), 1% Glutamax (Invitrogen), 1% NEAA (Invitrogen), plus BDNF, GDNF and IGF-1 (Peprotech, all at a final concentration of 10ng/ml). Following NS final plating, postmitotic neurons were developed within 10 days. Fully developed neurons were observed 25 days post-plating.

value: male

tag: genotype

value: wild type

value: neuron


title: FXS_patient_iPSC D0

description: SC128 D0

source_name: FXS patient MEF derived iPSC

value: FXS patient

value: iPSC


title: FXS_patient_iPSC_50days_neuron

description: SC128 D50

source_name: FXS patient neuron after 50 days of differentiation from iPSC


title: healthy_iPSC D0

description: HDF D0

source_name: healthy human MEF derived iPSC


title: healthy_iPSC_6days_iPSC aggregates

description: HDF D6

source_name: healthy human iPSC aggregates after 6 days of differentiation from iPSC

value: iPSC aggregates


title: FXS_patient_iPSC_6days_iPSC aggregates

description: SC128 D6

source_name: FXS patient iPSC aggregates after 6 days of differentiation from iPSC


title: HEK293-FLP cells

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
miRNAs were aligned using Mirdeep2's mapper.pl script to Mirbase's version 21 database of miRNAs using options -d -e -h -i -j -l 18 -m
Known miRNAs were quantified using Mirdeep2's quantifier.pl script using the option -d
Genome_build: mm9
Supplementary_files_format_and_content: Text file with each miRNA, its total read counts, its precursor miRNA, its total read counts, its read counts in the two replicates, and its read per million values in the two replicates

source_name: HEK293-FLP cells

growth_protocol: HEK293-FLP cells were maintained in DMEM supplemented with 10% FBS, 1% penicillin/streptomycin, and 100 μg/mL zeocin

extract_protocol:
Total RNA
1 μg of total RNA was used with the Illumina TruSeq Small RNA Sample Preparation kitkit. Libraries were sequenced on a Hi-Seq 2000, generating 50 bp reads.

value: HEK293-FLP cells


title: Main_screen_RNA

description: Has a sequencing library with a custom library for cells that are GFP+

data_processing:
Reads were filtered out if they did not contain a barcode sequence, if the Phred scores for the barcode were <20, if the read lacked sequences specific to the genomic locus, and if the region containing the variable 8mer had Phred scores <20
Reads that passed were partioned into barcodes, and the number of times each 8mer was present was counted
Supplementary_files_format_and_content: Text file with read counts for each 8mer in each sequenced sample

source_name: HEK-293 FLP cells

growth_protocol: HEK293-FLP cells were stably transfected using the FLP/FRT system with GFP/dsRed reporter constructs

extract_protocol:
Genomic DNA was isolated with a Qiagen Blood and Cell Culture Midi Kit; total RNA was isolated using the Trizol protocol
The genomic locus containing the reporter construct was amplified using PCR. Custom barcodes and Illumina sequencing adapters were added in subsequent PCRs.

treatment_protocol: Cells were sorted using fluorescence activated cell sorting to isolate different subsets of GFP expression, then maintained

tag: screen

value: main

tag: 8mers tested

value: selected 3918


title: healthy_iPSC_18days_neuroepithelia aggregates

description: HDF D18

source_name: healthy human neuroepithelia aggregates after 18 days of differentiation from iPSC

value: neuroepithelia aggregates


title: FXS_patient_iPSC_18days_neuroepithelia aggregates

description: SC128 D18

source_name: FXS patient neuroepithelia aggregates after 18 days of differentiation from iPSC


title: Main_screen_DNA

description: Includes sequencing libraries with custom adapters for cells that are GFP+ and cells in the following GFP+ subsets: 0-10%, 20-30% 40-60%, 70-80%, 90-100%


title: Mock1-1


title: Lung_rep1

source_name: Lung

value: Lung


title: Stomach_rep1

source_name: Stomach

value: Stomach


title: dat-Lateral-1 midbrain dopamine neurons

city: New York

first: Mary

middle: Alanna

last: Hynes

address: 1230 York Ave

institute: Rockefeller University

description:
(DAT or Slc6a3 JD1640, JAX #905444)
ribosomal tagged mRNA

data_processing:
Reads were mapped to the mm10 mus musculus genome using STAR
genes in Gencode vM2 were quantified with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts output

source_name: midbrain dopamine neurons

growth_protocol: Normal BacTrap embryos were dissected at E15. E18 midbrain was dissected at E15 and aged in vitro for 3 days to assure identical dissections.

extract_protocol: First strand cDNA was initially amplified by long-distance PCR (LD-PCR) using hot-start amplification. 2-7 ng cDNA was sonicated (Covaris S2; Covaris Inc., Woburn, MA, USA) and  ~200 bp fragments end-repaired following adapter ligation, and enriched with 10 cycles of PCR for HiSeq 2500 technology (Ilumina Inc., San Diego, CA) using TruSeq DNA Sample kit (FC-121-2001, Illumina) following manufacturer`s instructions, and sequenced as 100 bp single reads at the RU Genomics Resource Center. The quality and quantity of the libraries were validated using Agilent’s High Sensitivity DNA Chip (Agilent) for the Agilent 2100 Bioanalyzer

value: midbrain

tag: transporter

value: dopamine


title: Pilot_screen

description: Includes sequencing libraries with custom adapters for unsorted cells, cells with low GFP, and cells with high GFP

value: pilot

value: random


title: datM4-2 midbrain neurons

tag: tissue


title: Input DNA E14

source_name: E14 ES cells

extract_protocol:
Cells were scraped in phosphate buffered saline and were pelleted at 100 g before genomic DNA extraction using a DNeasy Blood and Tissue kit (Qiagen, France).
Twenty micrograms of DNA in 300 ml of TE buffer (Tris 10 mM, EDTA 0.1 mM, pH 8.0) were sonicated with a Bioruptor (Diagenode, Belgium) to yield 200 to 500 bp fragments. Each glucosylation and biotinylation reaction was run using reagents from the Hydroxymethyl Collector kit (ref. 55013, Active Motif, Belgium) and 500 ng of sonicated DNA. For SCL-seq, 16 reactions were captured on streptavidin-coated magnetic beads (ref. 11205D, Invitrogen). After 5 washes and elution from the beads according to the manufacturer’s protocol, the captured DNA was purified, precipitated and pooled for sequencing library preparation using the TruSeq ChIP Sample Prep Kit (Illumina, ref. IP-202-1012). For SCL-exo, after 6 washes in RIPA buffer (50 mM HEPES pH 7.6; 1 mM EDTA; 0.7% Na-Deoxycholate; 1% NP-40; 0.5 M LiCl) and 2 washes in Tris 10 mM pH 8, the DNA-beads complex was processed as previously described [19]: end polishing, ligation of the P7 exo-adapter, nick repair, lambda and RecJf exonuclease digestion, elution, P7 primer extension, ligation of the P5 exo-adapter, PCR amplification, and finally gel-size selection. The exonuclease-digested DNA was eluted from the beads by incubation in 100 ml of Elution Buffer (95% formamide, 10 mM EDTA) at 90 ⁰C for 5 min, followed by DNA precipitation and resuspension in 20 ml of water. The SCL-seq and SCL-exo libraries were quantified using the KAPA library quantification kit for Illumina sequencing platforms (KAPA Biosystems, KK4824) and 40 bp single-end sequenced in a single lane of a HiSeq 2000 (Illumina) following the manufacturer’s protocol.

tag: cell type

value: embryonic stem cells


title: dat-Medial-1 midbrain dopamine neurons


title: 5ht-R2 hindbrain serotonin neurons

source_name: hindbrain serotonin neurons

value: hindbrain

value: serotonin


title: datL4-1 midbrain neurons


title: SCL-exo technical replicate 2 E14


title: SCL-exo technical replicate 3 E14


title: SCL-exo technical replicate 1 E14


title: Soybean leaf dcl1a-ho_dcl1b-ho

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Soybean leaf, dcl1a-ho_dcl1b-ho

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: JGI glyma v2
Supplementary_files_format_and_content: tag count file

organism: Glycine max

source_name: Soybean leaf

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed using the Illumina TruSeq Small RNA sample preparation kit RS-200-0012 and RNA-Seq libraries were prepared using the Illumina TruSeq RNA sample preparation kit RS-122-2001.

value: Soybean leaf

tag: genotype/variation

value: mutant


title: Soybean leaf dcl1a rep2-2

description: Soybean leaf, dcl1a rep2-2


title: Soybean leaf dcl1a rep2-1

description: Soybean leaf, dcl1a rep2-1


title: 5ht-R1 hindbrain serotonin neurons


title: Soybean leaf WT rep2

description: Soybean leaf, wildtype rep2

value: wildtype


title: Soybean leaf dcl1b rep1-2

description: Soybean leaf, dcl1b rep1-2


title: Soybean dcl1a/dcl1b-2.2

description: Soybean leaf, dcl1a/dcl1b-2.2


title: Soybean leaf dcl1b rep1-1

description: Soybean leaf, dcl1b rep1-1


title: Soybean leaf dcl1a rep1-2

description: Soybean leaf, dcl1a rep1-2


title: Soybean dcl1a/dcl1b-2.1

description: Soybean leaf, dcl1a/dcl1b-2.1


title: Soybean leaf dcl1a-ho_dcl1b-he

description: Soybean leaf, dcl1a-ho_dcl1b-he