title: Saline-treated F2 female brain Xist 2lox/2lox rep3 (N13-1)

first: Chen-Yu

last: Wang

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description: processed data file: Nestin-Cre_mice_raw_read_counts.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Custom cas and mus genome were prepared usng mm9 as genome template, combined with substitution of known SNPs and changes of known Indels and insertions reported for Mus musculus and Mus castaneus, respectively (Pinter SF, et al. (2012),Genome Biology).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to custom cas and mus genome repectively using Tophat v2.0.10 (–no-coverage-search–read-edit-dist 3 –read-mismatches 3 –read-gap-length 3 –b2-very-sensitive–mate-inner-dist 100 –mate-std-dev 100 –library-type fr-firststrand)
allelic origin of each mappable reads were then determined using in-house algorithms and the alignment coordinate of each read was adjusted to match mm9 mouse genome. Discordant pairs, multimapped reads, and PCR duplicates were discarded.
Exonic read counts of each gene were quantified using Homer v4.8 (rna mm9 -count exons -strand + -noadj -condenseGenes)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each sample

extract_protocol: Total RNA was extracted using Trizol from tissue that was snap frozen in liquid nitrogen and grinded. Ribosomal RNA was removed using RiboMinus. Strand-specific libraries were generated by performing reverse transcription with Superscript III, followed by second-strand synthesis using the NEBNext second-strand synthesis module, and then libraries were generated using the NEBNext ChIP-seq Library Preparation Kit.

treatment_protocol: Three IP injections of 100 ul per 10g of of 0.033 mg/ml in sterile saline (or just sterile saline as control) were given over the course of a week (each injection separated by 2 days) at 5 weeks of age. Age for 2 weeks after first injection.

tag: strain

value: 7 weeks

value: brain

tag: genotype

value: Xist 2lox/2lox

tag: Sex

value: female


title: Saline-treated F2 female liver Xist 2lox/2lox, Nestin-Cre +/- rep3 (N13-5)

status: Public on Jan 04 2018

type: SRA

city: Boston

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue

value: liver

value: Xist 2lox/2lox, Nestin-Cre +/-


title: Aza-treated F2 female brain Xist Δ/Δ rep3 (N13-3)

value: Xist delta/delta


title: Saline-treated F2 female brain Xist Δ/Δ rep3 (N13-2)


title: 20-3_MV_smallRNA

first: Zhiyun

last: Wei

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
Raw sequence reads were quality controlled using BGI filter pipeline with multiple filtering steps as follows: 1) removing reads with adapters; 2) removing reads in which unknown bases were more than 10%; and 3) removing reads in which more than 50% of bases had low quality (sequencing quality no more than 10). After filtering, the remaining reads were called “clean reads” and used for downstream bioinformatic analysis. Generally, 20M and 10M clean reads were generated per long RNA library and small RNA library, respectively.
For long RNA libraries, clean reads were mapped to Homo sapiens rRNA database using short read alignment software SOAPaligner/SOAP2 to remove the remaining rRNA reads. The reads left were used to perform transcriptome assembling and quantification. First, non-rRNA reads were mapped to human reference genome hg19 using an improved version of TopHat2, which can align reads across splice junction without relying on gene annotation. Then, the reads mapped to genome were assembled using Cufflinks. We performed Reference Annotation Based Transcript (RABT) assembly with the reference gene annotation to compensate incompletely assembled transcripts caused by read coverage gaps in the regions of reference gene. The set of transfrags generated was then compared with the reference transcripts to remove transfrags that were approximately equivalent to the whole or a portion of a reference transcript. After the assembling, we obtained the whole parsimonious set of transcripts. We blasted these transcripts with the NONCODE database using the filter set (identity > 0.9 and coverage > 0.8) to identify the known long non-coding RNA. Then, we aligned the rest of assembled transcripts to the reference annotation utilizing Cuffcompare. We utilized Cuffmerge to merge several assemblies from different samples together, which automatically filtered a number of transfrags that probably were artifacts and produced a single annotation file for downstream gene expression analysis. Two mismatches were allowed as default for annotation, except that only one was allowed for ERCC spike-ins. mRNA and lncRNA expression analyses were performed by cuffdiff and then normalized based on ERCC spike-in controls using cyclic loess robust local regression.
For small RNA libraries, clean reads were first aligned to carrier RNA (Enterobacteria phage MS2) of miRCURY Spike-in kit with bowtie (parameter: -v 2 -l 7). The unmapped reads were aligned against human rRNA sequences with bowtie (parameter: -v 2 -l 7) to remove the remaining rRNA reads. The rest reads were searched against the human miRNA precursors (miRBase V19) with bowtie (parameter: -v 1), and then the mature miRNAs reads and miRNA precursors reads were separated according to the mapping position. The remaining reads were then searched against spike-ins (UniSp2, UniSp4 and UniSp5; parameter: -v 1). And the remaining ones were searched against other non-coding RNA classes including tRNAs (gtRNAdb), piRNAs (RNAdb), snoRNA (snoRNA-LBME-db), scRNAs (Genbank) and others (Rfam database) (parameter: -v 2). After that, the remaining reads were then searched against the hg19 human genome, and we counted the reads mapped to exons, introns, intergenic regions and repeats (parameter: -v 0). The samtools was used to calculate the reads depth of each base position and R package barplot was used to draw the bar plot of the depth of position.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: xlsx format; fmol per ug total RNA

organism: Homo sapiens

source_name: 20/3 glioblastoma neurosphere

extract_protocol:
Approximate 100 mL conditioned media was used as input for exRNA isolation. Conditioned media was centrifuged at 300 g, 4 °C for 10 min, following by the additional centrifugation at 2,000 g, 4 °C for 15 min, to remove cells and cell debris. Five uL of SUPERase In RNase Inhibitor (Ambion) was added to the supernatants per 10 mL media. The media was then filtered sequentially through the 2 um filter (GE Healthcare, UK), 0.8 um filter (EMD Millipore, MA), and 0.22 um filter (EMD Millipore), with no/minimal pressure applied. The filtrate was split to 15 mL per sample and further filtered through the 0.02 um filter (GE Healthcare) with up to 75 psi pressure applied. To facilitate the 0.02 um filtration, a mechanical syringe pump was designed and manufactured (Fig. S2). Upon filtration, each filter was washed with 1 mL DPBS (Corning), and the corresponding fractions were lysed with 600 uL Lysis Solution of the miRCURY RNA Isolation Kit – Cell & Plant (Exiqon, Denmark). The fractions collected on 0.02 um filters were lysed with 900 uL Lysis Solution. The last flow-through fractions of 0.02 um filters were pooled together (up to 30mL) and concentrated approximately 60 times using 3 kDa Amicon Ultra Centrifugal Filters (EMD Millipore) at 4,000 g, 4 °C, for 60 min. The concentrates were collected and lysed with six volumes of the same Lysis Solution (Exiqon). Total RNA was then isolated from all fractions as recommended by miRCURY protocol, with on-column DNase treatment (Qiagen, Germany). The corresponding 1.2 mL of the source neurospheres were span down at 300 g, 4 °C for 5 min, and total cellular RNA was isolated from them and analyzed in parallel. The same protocol was carried out for RNA isolation from fresh media, with 500 mL media input. For RNA isolation from primary cells cultured in 24-wells plates, the cells were lysed with 350 uL Lysis Solution per well. The concentrations of cellular and extracellular RNA were determined using the NanoDrop 2000 Spectrophotometer and Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific), respectively. The RNA quality was examined using Agilent 2100 Bioanalyzer (Agilent, CA) and the RNA Integrity Number (RIN) estimated.
Two sets of spike-in RNAs were added to the samples prior to library preparation: ERCC RNA Spike-In Control Mixes (Ambion; 0.02 uL per one ug total RNA), and miRCURY Spike-in kit, part 1, with UniSp2’s final concentrations of 1.25 and 5.0 fmol per one ug of total RNA for cellular and extracellular RNA, respectively. Total RNA, either 40~200 ng of exRNA, or 2 ug of cellular RNA, was rRNA-depleted using the Ribo-Zero rRNA Removal Kits (Illumina, CA). One quarter of the rRNA-depleted RNA was fragmented to 100~500 nt using the 5X First-Strand Buffer (Clontech, CA), and utilized for the long RNA library construction by SMARTer Stranded RNA-Seq Kit (Clontech). The remaining 75% of the rRNA-depleted RNA was treated sequentially with Tobacco Acid Pyrophosphatase (TAP; Illumina) and T4 Polynucleotide Kinase (T4PNK; New England Biolabs, MA) to create more uniform 5’- and 3’- ends for various classes of transcripts. The RNA was then used as input for the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), with size selection of 15-65nt inserts for small RNA libraries. The quality of libraries was examined using the Agilent DNA 1000 kit at the Agilent 2100 Bioanalyzer instrument, and cDNA quantified by qRT-PCR with TaqMan Probe (Thermo Fisher Scientific). The libraries were sequenced on HiSeq 2000 (Illumina) with single read 50 cycles by Beijing Genomics Institute (BGI, China).

tag: growth protocol

value: Human low-passage (below 20) GBM cells were cultured as neurospheres in Neurobasal medium (Gibco) supplemented with 3 mM GlutaMAX (Gibco), 1x B-27 supplement (Gibco), 0.5x N-2 (Gibco), 20 ng/mL EGF (R&D systems, MN), and 20 ng/mL FGF (PEPROTECH, NJ) and passaged by NeuroCult Chemical Dissociation Kit (Mouse) (Stemcell Technologies, Canada). Approximate 0.5 million dissociated cells were seeded per 10 cm dish (Corning) in 10 mL fresh media, and 1/3 volume of fresh medium was added every 3 days. Mature neurospheres were usually formed in 7~10 days, and replated.

tag: library type

value: Small RNA library

tag: sample type


title: Aza-treated F2 female brain Xist 2lox/2lox rep3 (N13-4)


title: MGG75_Cell_smallRNA

source_name: MGG75 glioblastoma neurosphere

value: Cellular RNA


title: 20-3_Cell_smallRNA


title: Saline-treated F2 female liver Xist 2lox/2lox, Nestin-Cre +/- rep2 (N11-6)


title: Aza-treated F2 female brain Xist 2lox/2lox rep2 (N11-3)


title: Saline-treated F2 female brain Xist 2lox/2lox rep2 (N11-4)


title: Aza-treated F2 female liver Xist 2lox/2lox, Nestin-Cre +/- rep3 (N13-6)


title: GBM4_MV_smallRNA

source_name: GBM4 glioblastoma neurosphere


title: 20-3_Exo_smallRNA

value: Exosome (0,02-0.22um) RNA


title: GBM4_Cell_smallRNA


title: Saline-treated F2 female brain Xist Δ/Δ rep2 (N11-2)


title: 20-3_RNP_smallRNA

value: RNP (<0.02um) RNA


title: BPH-4

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
gene_exp.diff: BPH_3
genes.read_group_tracking: BPH_3

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--no-novel-juncs --library-type fr-firststrand) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: E7.5 implantation site

growth_protocol: Mice were raised under standard conditions

extract_protocol:
Uterine implantation sites from pregnant females at E7.5 were collected, snap frozen, and stored at -80C. Total RNA was purified using Trizol (Thermo Fisher) according to the commercial protocol. RapidOUT DNA Removal kit (Thermo Fisher) was then used to remove any co-purified genomic DNA.
RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.


title: GBM4_Exo_smallRNA


title: Aza-treated F2 female brain Xist Δ/Δ rep2 (N11-1)


title: Aza-treated F2 female liver Xist 2lox/2lox, Nestin-Cre +/- rep2 (N11-5)


title: C57-3

description:
gene_exp.diff: C57_2
genes.read_group_tracking: C57_2

value: wildtype


title: C57-4

description:
gene_exp.diff: C57_3
genes.read_group_tracking: C57_3


title: C57-2

description:
gene_exp.diff: C57_1
genes.read_group_tracking: C57_1


title: C57-1

description:
gene_exp.diff: C57_0
genes.read_group_tracking: C57_0


title: BPH-2

description:
gene_exp.diff: BPH_1
genes.read_group_tracking: BPH_1


title: BPH-3

description:
gene_exp.diff: BPH_2
genes.read_group_tracking: BPH_2


title: BPH-1

description:
gene_exp.diff: BPH_0
genes.read_group_tracking: BPH_0


title: CoW4_RNAseq

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

description: PolyA RNA

data_processing:
Mapping with STAR 2.3.1, allowing for two mismatches. SAMtools 0.1.185 was used to sort the aligned reads. Gene level quantification was performed with HTSeq-0.5.4 using -- mode=union -- stranded=no, using Ensembl version 71 as gene annotation database
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: .xls peak files were generated by MACS2 on ChIP-seq data.
Supplementary_files_format_and_content: .bed files were generated by extending MACS2 peaks to 2kb regions.
Supplementary_files_format_and_content: .tdf files were generated for viewing in genome browser such as IGV.
Supplementary_files_format_and_content: .txt files containing readcounts were generated using HTSeq-0.5.4 and Ensembl version 71 on RNA-seq data.
Supplementary_files_format_and_content: .txt files containing RPKM were generated by calculating reads per kilobase million based on readcounts files.

source_name: Circle of Willis blood vessel

extract_protocol:
Frozen in liquid nitrogen, RNA extraction.
Illumina TruSeq DNA library protocol.

value: Circle of Willis

tag: sample id

tag: gender

value: Male

tag: Cause of death

value: Aortic aneurysm

tag: postmortem delay

value: 9:00 hours


title: CoW2_RNAseq

description: PolyA RNA

value: Female

value: Euthanasia (metastasized non-small cell lung carcinoma)

value: 8:25 hours


title: Aza-treated F2 female brain Xist 2lox/2lox (N4-6)

data_processing:
Illumina Casava1.8 software used for basecalling.
Custom cas and mus genome were prepared usng mm9 as genome template, combined with substitution of known SNPs and changes of known Indels and insertions reported for Mus musculus and Mus castaneus, respectively (Pinter SF, et al. (2012),Genome Biology).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to custom cas and mus genome repectively using Tophat v2.0.10 (–no-coverage-search–read-edit-dist 3 –read-mismatches 3 –read-gap-length 3 –b2-very-sensitive–mate-inner-dist 100 –mate-std-dev 100 –library-type fr-firststrand)
allelic origin of each mappable reads were then determined using in-house algorithms and the alignment coordinate of each read was adjusted to match mm9 mouse genome. Discordant pairs, multimapped reads, and PCR duplicates were discarded.
Exonic read counts of each gene were quantified using Homer v4.8 (rna mm9 -count exons -strand + -noadj -condenseGenes)
Genome_build: Custom cas and mus genomes were prepared based on mm9
Supplementary_files_format_and_content: tab-delimited text files include raw read count for each sample. We used an allele-specific pipeline that allow us to deduce the allele (cas or mus) where a read in coming from.  For the fibroblast read counts, the .cas column contains the number of cas-specific reads, the .mus column contains the number of mus-specific reads and the .comp column contains the total number of reads (cas-specific reads, mus-spefic reads, and reads that do not have allele-specific information).  In contrast to the fibroblasts, the mice are not from cas/mus hybrid background. We processed the mouse tissue reads using the same allele-specific analysis pipeline but only used the .comp reads for analysis and in generating the read count table.

value: 7 weeks

value: brain

value: Xist 2lox/2lox

value: female


title: Aza-treated F2 female brain Xist Δ/Δ (N4-2)

value: Xist delta/delta


title: Srambled LNA treated fibroblast rep1 (F1-1)

description: processed data file: Fibroblasts_raw_read_counts.txt

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

extract_protocol: Total RNA was extracted using Trizol from PBS rinsed cells. Ribosomal RNA was removed using RiboMinus. Strand-specific libraries were generated by performing reverse transcription with Superscript III, followed by second-strand synthesis using the NEBNext second-strand synthesis module, and then libraries were generated using the NEBNext ChIP-seq Library Preparation Kit.

treatment_protocol: 800K cells were plated in 6-well plate plate at 37C, and treated with 20 nM LNA (transfected with lipofectamine) and 0.5 uM Aza (in some cases). Let grow 72h.

tag: passage

value: passage 15-20

value: embryonic fibroblasts


title: Saline-treated F2 female brain Xist Δ/Δ (N4-4)


title: Xist LNA and Aza treated fibroblast rep1 (F1-3)


title: Scrambled LNA and Aza treated fibroblast rep1 (F1-2)


title: CoW1_RNAseq

description: PolyA RNA

value: Acute renal failure

value: 8:00 hours


title: Untreated F1 female brain Xist Δ/+ (N10-1)

value: 75 weeks

value: Xist delta/+


title: Saline-treated F2 female liver Xist 2lox/2lox, Nestin-Cre +/- (N4-5)

value: liver

value: Xist 2lox/2lox, Nestin-Cre +/-


title: Untreated F2 female brain Xist 2lox/2lox (N10-8)

value: 91 weeks


title: LNCaP treated with 2uM iBET for 8 hours_1

city: Sutton, London

first: Wei

last: Yuan

address: 15 Cotswold Road

country: United Kingdom

institute: Institute of Cancer Research

data_processing:
FASTQ file generation and de-multiplexing using CASAVA
Alignment with tophat2
Generation of normalized abundance measurements
Genome_build: hg19
Supplementary_files_format_and_content: [gtf] normalized abundance measurements

source_name: LNCaP treated with 2uM iBET for 8 hours

extract_protocol:
Agilent Bioanalyzer RNA Nano kit
Illumina's TruSeq Stranded,The quality of the libraries was confirmed using the Agilent Bioanalyzer High Sensitivity DNA Assay (Santa Clara, CA). The libraries were quantified and normalized by qPCR using KAPA Library Quantification Kit (ABI Prism®)(Wilmington, Massachusetts). Library clustering was performed on a cBot with Illumina HiSeq PE Cluster kit v3 (San Diego, CA). The libraries were sequenced as paired-end 101 base pair reads on an Illumina HiSeq 2500 (San Diego, CA) with an Illumina HiSeq SBS kit v3 (San Diego, CA).

tag: cell line

value: Prostate Cancer Cell line LNCaP

tag: agent

value: iBET

tag: dose


title: LNCaP treated with 0.5uM iBET for 8 hours_1


title: LNCaP treated with DMSO for 8 hours_2

source_name: LNCaP treated with DMSO for 8 hours

value: control


title: LNCaP treated with 0.5uM iBET for 8 hours_2


title: LNCaP treated with DMSO for 8 hours_1


title: WGBS naive hESC T28KO rep2

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

library_source: genomic

data_processing:
Bisulfite-seq reads were aligned using BS Seeker2
Generate a CG methylation level track from methylation level files (CGmap)
Genome_build: hg19
Supplementary_files_format_and_content: Coverage track is BigWig format

molecule: genomic DNA

source_name: embryonic stem cell

growth_protocol: hESCs are cultured in conventional human ESC culture medium which contains KSR and bFGF.

extract_protocol:
RNA-seq: RNA was extracted using the RNeasy Micro Kit (Qiagen).
RNA-seq: The RNA was subsequently amplified through the use of the Ovation RNA-Seq System V2 kit (Nugen), and bar codes were added using the Rapid DR Library Systems kit (Nugen).
ATAC-seq: home made lysis buffer
ATAC-seq: Nextera DNA library prep kit + NEBNext® High-Fidelity 2X PCR Master Mix
Bisulfite-seq: genomic DNA was extracted by the Zymo Quick DNA miniprep kit
Bisulfite-seq: libraries were constructed by Ovation Ultralow Methyl-Seq Library System kit (Nugen)

tag: cell type

value: naive embryonic stem cell


title: ATAC Library CM Rep 1

city: Seattle

first: Charles

last: Murry

state: WA

address: 850 Republican St

department: Institute for Stem Cell and Regenerative Medicine

institute: University of Washington

description: CM Rep 1

data_processing:
Sequenced reads were mapped with BWA-MEM (version 0.7.13) to hg38 with default parameters for paired end reads. Mapped reads were filtered for their primary mapping location and a MAPQ score greater than 30. Duplicate reads were removed with Picard Tools (available at http://broadinstitute.github.io/picard/). Hotspots were called with MACS2 (version 2.1.0) using the parameters “--nomodel -q 0.01 --shift -100 --extsize 200”. Bigwigs were generated with bedtools (version 2.26.0) normalizing to reads per million.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak file in BED6+4 format output from MACS2 for peak calls of ATAC-seq data.
Supplementary_files_format_and_content: BigWig file for ATAC data from bedtools for gene tracks of reads per million normalized signal.

source_name: ATAC Library CM

growth_protocol: RUES2 hESCs were maintained on lamin-521 matrix (Biolamina) at 0.5mg/cm2 with Essential 8 (E8) media (ThermoFisher).For differentiation, 4x106 cells in E8 with 10mM Y-27632 (Tocris) were seeded per well of a 12-well dish that was pre-coated with 2mg/cm2 lamin-521. After 24 hours media was changed to E8 with 1mM CHIR-99021 (Cayman), denoted day -1. On day 0 media was changed to RPMI (ThermoFisher) with BSA (500mg/ml) (Sigma, A9418) + ascorbic acid (213mg/ml) (Sigma, A8960), denoted RBA media, supplemented with 3mM CHIR-99021. Samples for day 0 were collected prior to media change. Day 2 samples were collected 48 hours later. Wells for further differentiation were left unchanged until day 3, when media was changed to RBA plus 1mM Xav-939 (Tocris). Day 5, samples were either collected or changed to RBA without inhibitors. On day 7 media was changed to RPMI plus B27 (Thermo Fisher, 17504044), with further media changes every other day until day 14 samples were collected.

extract_protocol:
ATAC-seq was performed according to the protocol from Buenrostro et al. (2015). Briefly cells were harvested from cell culture and lysed in lysis buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630, 1x Protease inhibitor, Sigma).
After lysis 5x10^4 nuclei were washed in lysis buffer and resuspended in 25ml TD buffer, 24ml Lysis buffer, 1ml TDE1 enzyme from the Nextera DNA Prep kit (Illumina FC-121-1030). The reaction was incubated for 30min at 55° and DNA was then extracted with a MinElute PCR Purfication kit (Qiagen 28004). DNA was amplified for using NEBNext High-Fidelity 2x Master Mix (M0541L) and quantified with a Qubit. All samples were pooled with Nextera primers and sequenced on an Illumina NEXTSEQ.

treatment_protocol: Cells were collected fresh with TrypLE prior to lysis for ATAC-seq.

value: cardiomyocyte (CM)

tag: time point

value: Day 14 of differentiation


title: ATAC Library CM Rep 2

description: CM Rep 2


title: ATAC Library CP Rep 2

description: CP Rep 2

source_name: ATAC Library CP

value: cardiac progenitor (CP)

value: Day 5 of differentiation


title: Untreated F1 female brain Xist 2lox/+ (N10-2)

tag: strain

value: brain

tag: genotype

value: Xist 2lox/+

value: female


title: CoW1_ChIPseq_H3K4me1

data_processing:
Mapping Illumina: Bowtie (1.1.0), parameters: -l 45 -n 1 --phred64-quals -- best --strata --chunkmbs 512 -m 1 -S. Peak calling: MACS2 (2.1.0), parameters: callpeak -p 1e-5 -g hs -B --nomodel --extsize 400 --llocal 100000
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: .xls peak files were generated by MACS2 on ChIP-seq data.
Supplementary_files_format_and_content: .bed files were generated by extending MACS2 peaks to 2kb regions.
Supplementary_files_format_and_content: .tdf files were generated for viewing in genome browser such as IGV.
Supplementary_files_format_and_content: .txt files containing readcounts were generated using HTSeq-0.5.4 and Ensembl version 71 on RNA-seq data.
Supplementary_files_format_and_content: .txt files containing RPKM were generated by calculating reads per kilobase million based on readcounts files.

extract_protocol:
Frozen in liquid nitrogen, Crosslinked, Lysed and Immunoprecipitated.
Illumina TruSeq DNA library protocol.

value: Circle of Willis

value: Female

tag: age

value: Acute renal failure

value: 8:00 hours

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: WGBS naive hESC T28KO rep1


title: WGBS naive hESC Ctrl rep2

value: wild type


title: ATAC Library CP Rep 1

description: CP Rep 1


title: CoW3_RNAseq

description: PolyA RNA

tag: tissue

value: Unknown

value: 5:50 hours


title: Aza-treated F2 female liver Xist 2lox/2lox, Nestin-Cre +/- (N4-3)

value: 7 weeks

value: liver

value: Xist 2lox/2lox, Nestin-Cre +/-

tag: Sex


title: ATAC Library MES Rep 2

description: MES Rep 2

source_name: ATAC Library MES

value: mesodermal cells (MES)

value: Day 2 of differentiation


title: Untreated F2 female brain Xist Δ/Δ (N10-7)

value: 91 weeks

value: Xist delta/delta


title: WGBS naive hESC Ctrl rep1

value: naive embryonic stem cell


title: WGBS primed hESC T28KO rep2

value: primed embryonic stem cell


title: ATAC Library MES Rep 1

description: MES Rep 1


title: ATAC Library ESC Rep 2

description: ESC Rep 2

source_name: ATAC Library ESC

value: Embryonic stem cells (ESC)

value: Day 0 of differentiation


title: ATAC Library ESC Rep 1

description: ESC Rep 1


title: WGBS primed hESC T28KO rep1


title: RNA Library Fetal Heart Rep 1

data_processing:
Reads were mapped to hg38 using STAR (version 2.5.2b) with default parameters and then quantified and processed through the Cufflinks suite (version 2.2.1), using cuffquant (CXB file), cuffnorm (fpkm and counts tables) and cuffdiff (differentiall expression.
Genome_build: hg38
Supplementary_files_format_and_content: gene_exp.diff is the differential expression between samples, applicable to all samples, from cuffdiff output.
Supplementary_files_format_and_content: genes.fpkm_table and genes.count_table are the fpkm and counts, applicable to all samples, from cuffnorm output.

source_name: RNA Library Fetal Heart

growth_protocol: RUES2 hESCs were maintained on lamin-521 matrix (Biolamina) at 0.5mg/cm2 with Essential 8 (E8) media (ThermoFisher).For differentiation, 4x106 cells in E8 with 10mM Y-27632 (Tocris) were seeded per well of a 12-well dish that was pre-coated with 2mg/cm2 lamin-521. After 24 hours media was changed to E8 with 1mM CHIR-99021 (Cayman), denoted day -1. On day 0 media was changed to RPMI (ThermoFisher) with BSA (500mg/ml) (Sigma, A9418) + ascorbic acid (213mg/ml) (Sigma, A8960), denoted RBA media, supplemented with 3mM CHIR-99021. Samples for day 0 were collected prior to media change. Day 2 samples were collected 48 hours later. Wells for further differentiation were left unchanged until day 3, when media was changed to RBA plus 1mM Xav-939 (Tocris). Day 5, samples were either collected or changed to RBA without inhibitors. On day 7 media was changed to RPMI plus B27 (Thermo Fisher, 17504044), with further media changes every other day until day 14 samples were collected. Fetal Heart samples were collected by the Laboratory of Developmental Biology at the University of Washington (UW), in accordance with IRB approval from the UW. Collected hearts were washed in PBS and flash frozen in liquid N2 and stored at -80 prior to further analysis.

extract_protocol:
Samples for RNA were collected in RLT and lysed with a Qiashredder (Qiagen) and then RNA was purified with a Qiagen RNeasy kit. For RNA from whole hearts, samples were extracted with Qiagen RNeasy Fibrous Tissue Kit.
RNA-seq libraries were prepared from total RNA using the TruSeq Stranded Total RNA Ribo-Zero H/M/R kit (Illumina RS-122-2201). Samples were barcoded together for sequencing. RNA-seq libraries were sequenced on the NEXTSEQ.

value: Whole Fetal Heart

tag: developmental stage

value: Gestational Age 67 days


title: RNA Library CM Rep 2

source_name: RNA Library CM

value: cardiomyocyte (CM)

value: Day 14 of differentiation


title: WGBS primed hESC Ctrl rep2

value: wild type


title: ATAC primed hESC T28KO rep3

data_processing:
ATAC-seq alignment using Bowtie 2 version 2.2.6 with default parameters
Generate a normalized coverage track using bamCoverage from deepTools package (version 2.0) with parameter -normalizeUsingRPKM
Genome_build: hg19
Supplementary_files_format_and_content: Coverage track is BigWig format


title: ATAC primed hESC T28KO rep2


title: RNA Library CM Rep 1


title: WGBS primed hESC Ctrl rep1


title: RNA Library CP Rep 2

source_name: RNA Library CP

value: cardiac progenitor (CP)

value: Day 5 of differentiation


title: ATAC primed hESC T28KO rep1


title: RNA Library CP Rep 1


title: ATAC primed hESC Ctrl rep2


title: RNA Library MES Rep 2

source_name: RNA Library MES


title: RNA naive hESC T28KO rep3

description: Processed data in Series supplementary file RPKM_table_trim28.xlsx

data_processing:
RNA-seq alignment using Tophat 2.1.0 with default parameters
Calculate RPKM of genes by using cuffdiff (cufflinks-2.2.1) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values for WT and Trim28 KO samples

molecule: polyA RNA


title: RNA Library MES Rep 1


title: ATAC primed hESC Ctrl rep1


title: Bulk Hi-C Library RUES2 Fetal Heart Rep 2

description: Fetal Heart Rep 2

data_processing:
Reads were mapped with BWA-MEM version 0.7.13 to hg38 using default parameters. Secondary mappings were filtered out with samtools.
Primary mappings were processed using HIC-PRO version 2.7.6, excluding pairs less than 1KB apart and excluding MAPQ scores <30, to generate validPairs files and ICED normalized counts, outputed as a bed file of bins and a three column file of bins and contact counts.
validPair files were used as input for HOMER version 4.7 at 500KB resolution to generate PC1 values (A/B compartment calls).
TADs were determined using the Directionality Index (DI) method and domain call pipeline at 40kb resolution from Dixon et al. 2012.
Genome_build: hg38
Supplementary_files_format_and_content: validPairs file is processed output from HiC-Pro and contains read name and mapping location for the two reads after passing distance and quality threshold
Supplementary_files_format_and_content: bins.bed file is the bed file plus bin name for use with the corresponding 3 column Hi-C data at 500KB resolution, output from HiC-Pro.
Supplementary_files_format_and_content: ICED.matrix file is the 3 column counts matrix (Bin1, Bin2, counts) corresponding to the bins.bed file at 500KB resolution, output from HiC-Pro.
Supplementary_files_format_and_content: PC1.bedGraph files are the ouput from HOMER on the processed Hi-C data, representing the A/B compartment calls, in bedGraph format (coordinates and score)
Supplementary_files_format_and_content: DI_TADs.bed are the bed files of the TAD calls using the directionality index on samples individually and the merged replicates (single file for both replicates), called at 40KB resolution.

source_name: Bulk Hi-C Library Fetal Heart

extract_protocol:
Cells are lysed using 10mM Tris-HCl, pH 8.0, 10mM NaCl, 0.2% Igepal CA-630, 1x Protease Inhibitor in ddH2O
Library prep was carried out using a similar protocol to the insitu DNase Hi-C protocols (V. Ramani et al. Nat Protoc. 2016). Samples were barcoded during final library PCR and samples were demultiplexed prior to downstream analysis.

treatment_protocol: Cells were fixed using 2% formaldehyde for 10 minutes. For fetal hearts samples were first treated with a dismembrator for 1 min at 2000 rpm and then fixed in 1% formaldehyde for 25 minutes.

value: Gestational Age 57 days


title: RNA Library ESC Rep 2

source_name: RNA Library ESC


title: RNA Library ESC Rep 1


title: LNCaP treated with 2uM iBET for 8 hours_2

value: Prostate Cancer Cell line LNCaP

value: iBET


title: Bulk Hi-C Library RUES2 CM Rep 2

description:
CM Rep 2
processed data file:
CM_Merged_DI_TADs.bed.gz

source_name: Bulk Hi-C Library CM


title: RNA Library Fetal Heart Rep 2


title: RNA naive hESC Ctrl rep2


title: RNA naive hESC Ctrl rep3


title: RNA naive hESC T28KO rep1


title: Bulk Hi-C Library RUES2 CM Rep 1

description:
CM Rep 1
processed data file:
CM_Merged_DI_TADs.bed.gz


title: Bulk Hi-C Library RUES2 Fetal Heart Rep 1

description: Fetal Heart Rep 1


title: RNA primed hESC T28KO rep2


title: RNA primed hESC T28KO rep3


title: RNA primed hESC Ctrl rep2


title: Bulk Hi-C Library RUES2 MES Rep 1

description:
MES Rep 1
processed data file:
MES_Merged_DI_TADs.bed.gz

source_name: Bulk Hi-C Library MES

value: mesodermal cells (MES)

value: Day 2 of differentiation


title: RNA naive hESC Ctrl rep1


title: Bulk Hi-C Library RUES2 MES Rep 2

description:
MES Rep 2
processed data file:
MES_Merged_DI_TADs.bed.gz


title: ATAC primed hESC Ctrl rep3


title: Bulk Hi-C Library RUES2 CP Rep 2

description:
CP Rep 2
processed data file:
CP_Merged_DI_TADs.bed.gz

source_name: Bulk Hi-C Library CP


title: RNA naive hESC T28KO rep2


title: RNA primed hESC Ctrl rep1


title: Bulk Hi-C Library RUES2 ESC Rep 1

description:
ESC Rep 1
processed data file:
ESC_Merged_DI_TADs.bed.gz

source_name: Bulk Hi-C Library ESC


title: Input 0 Gy Acetyl Histone H4

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Basecalling was done using bcl2fastq/2.17
Fastq files were trimmed for quality and adapters using fastq-mcf (ea-utils/1.1.2-806)
Fastq files were mapped to hg19 (UCSC) using bowtie/2.2.3
Reads with mapping quality less than 10 were removed using samtools/1.2-2-gf8a6274
Duplicates were removed using picard-tools/1.127
Normalized bigwig files were made using homer/v4.8.3
Peak calling was done using MACS/2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain normalized read coverage, Reads per 10 million
tab delimited files contain annotated narrowPeak files

source_name: Input LNCaP non-radiated control cells

growth_protocol: RPMI 1640 medium supplemented with 10% (vol/vol) FBS in a 5% CO2 incubator at 37 °C

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturer's protocol (Diagenode). ChIP DNA was isolated and purified (IPure Kit, Diagenode) from samples.
Next- generation sequencing library preparation using KAPA Hyper Prep kit (KAPA Biosystems) using TruSeq adapters (Integrated DNA Technologies). A quality check of the purified libraries was carried out using the Bioanalyzer 2100 (Agilent).

treatment_protocol: LNCaP cells were radiated with 5 Gy, fixed in formaldehyde four hours post-radiation, and processed to carry out ChIP-seq using acetyl histone H4 antibody (06-598, Millipore)

value: LNCaP

tag: stress

value: control


title: GROseq.SRSF2WTCtr_rep1

city: Nanjing

first: Jia-Yu

state: CA

address: No 163 of XianlinAvenue, Qixia District

department: School of Life Sciences

country: China

institute: Nanjing University

description:
GROseq.SRSF2WTCtr_rep1_e100s2_rev.bw
GROseq.SRSF2WTCtr_rep1_e100s2_fwd.bw

data_processing:
R-ChIP and GRO-seq sequence reads were mapped to the human genome (hg18) via default --local mode of Bowtie2
Repeatedly-mapped reads, reads with low mapping quality (-q 30 for R-ChIP and -q 2 for GRO-seq) and PCR duplicates were discarded according to Samtools
R-ChIP reads were extended to 150 nt (which corresponds to the average size of gel-isolated DNA fragments). We randomly sampled 2M reads for each replicate of each sample and then combined together to call a unified set of R-loop regions by MACS2. Only confident R-loop peaks with ≥5 folds enrichment and with q-value ≤ 0.001 over background were kept for subsequent analyses. GRO-seq reads were extended to 100 nt and were used to estimate the travelling ratio.
Genome_build: hg18
Supplementary_files_format_and_content: bigWig file, narrowPeak file

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1X penicillin-streptomycin

extract_protocol:
For R-ChIP, cells expressing mutant RNASEH1(D210N) were fixed followed by nuclei extraction. Chromatin DNA was sheared to 250-600 bp in size by sonication followed by incubation with magnetic beads conjugated with anti-V5 antibody overnight at 4°C. Beads were sequentially washed in high salt buffers to remove non-specifically bound protein and chromtin complexes. The enriched RNASEH1-RNA/DNA complex was eluted and decrosslinked overnight at 65°C. After sequential RNase A and Proteinase K treatment, the precipitated hybrid was cleaned by phenol and phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. The recovered fragment was subjected to library construction. For GRO-seq, the intact nuclei were extracted and mixed with run-on reaction buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 300 mM KCl, 1 mM DTT, 200 U/ml RNaseOut, 1% Sarkosyl, 500 μM ATP, 500 μM GTP, 500 μM Br-UTP and 2 μM CTP) for in vitro run-on reaction and Br-U labeling for 5 min at 30°C. The reaction was stopped by adding TRIzol LS reagent (Thermo Fisher). RNA was then extracted followed by treatment wtih DNase I (Promega) and antarctic phosphatase (NEB). For immunopurification, equilibrated and blocked anti-BrdU agarose beads (Santa Cruz) were mixed with RNA for 1 hr at 4°C. After binding, beads were thoroughly washed and BrU-incorporated RNAs were eluted. The BrU-RNA end was repaired by T4 PNK (NEB) and then subjected to poly-A tailing reaction. Tailed RNAs were reverse transcribed into cDNA by using superscript III (Thermo Fisher) and the GRO-seq RT primer (5’-pAGATCGGAAGAGCGTCGTGTAG;GCAGAAGACGGCATACGAGATTTTTTTTTTTTTTTTTTTTVN-3’), where p indicates 5’ phosphate; ‘;’ indicates the abasic dSpacer furan, and VN indicates degenerate nucleotides. The cDNA products were treated with Exonuclease I (NEB) for 1 hr at 37°C to eliminate excessive primer. The resultant cDNA was resolved in 10% polyacrylamide TBE-urea gel and the fraction in the size range of 100-400 bp was excised and recovered.
For R-ChIP library construction, DNA from precipitated RNA/DNA hybrids was used as the template to generate dsDNA by random priming using a tail-containing N9 primer (5’- /invddt/CAAGCAGAAGACGGCATACGAGNNNNNNNNN-3’). An “A” base was then added to the 3’ end and the standard Illumina adaptor was ligated to one end of the resultant dsDNA. After purification,PCR were performed and the libraries in the size range of 130-350 bp were gel-isolated and purified. For GRO-seq library construction, cDNA was circularized and re-linearized. the libraries were amplified by PCR reaction. the final products were resolved in a non-denaturing 10% polyacrylamide TBE gel and libraries with the size 130-250 bp were recovered.
R-ChIP and GRO-seq

treatment_protocol: Dox (1 μg/ml)

tag: sample type

value: RNA


title: ChIP-seq 0 Gy Acetyl Histone H4

source_name: ChIP-seq LNCaP non-radiated control cells

value: anti-acetyl histone H4 antibody (Millipore, catalog# 06-598, lot# 2605373)


title: ChIP-seq 5 Gy Acetyl Histone H4 RT

source_name: ChIP-seq LNCaP Radiated cells

value: radiated


title: GROseq.SRSF2WT5h_rep2

description:
GROseq.SRSF2WT5h_rep2_e100s2_rev.bw
GROseq.SRSF2WT5h_rep2_e100s2_fwd.bw

tag: treatment

value: Dox


title: Input 5 Gy Acetyl Histone H4 RT

source_name: Input LNCaP Radiated cells


title: GROseq.U2AF35S34FDOX_rep1

description:
GROseq.S34FDOX_rep1_e100s2_rev.bw
GROseq.S34FDOX_rep1_e100s2_fwd.bw


title: Bulk Hi-C Library RUES2 CP Rep 1

description:
CP Rep 1
processed data file:
CP_Merged_DI_TADs.bed.gz


title: ChIPseq_AGO1_brm-4_ChIP

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

institute: Tsinghua University

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C)

data_processing:
Reads were mapped with Bowtie for all data; Peaks were called with MACS2 for ChIP-seq; Gene expressions were calculated with Cuffdiff for RNA-seq; GRO-seq data was analysed by HOMER software; sRNA-seq data was analysed by in house PERL scripts.
Genome_build: TAIR 10
Supplementary_files_format_and_content: bedgraph for ChIP-seq; expression matrix for RNA-seq; bigwig for GRO-seq; Raw read counts for sRNA-seq

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C). Other growth conditions for specific tissues/organs are in the DESCRIPTION column of the SAMPLES section.

extract_protocol:
ChIP assays were performed as previously described (Fang et al., 2015), using antibodies against AGO1 (Qi et al., 2005), myc (Abcam,ab32), Pol II (Abcam,ab817), Pol II Ser2P (Abcam,ab5095), Pol II Ser5P (Abcam,ab5131), or IgG (Abmart, B30011). For GRO-seq, ~5X10^6 nuclei were run on for 5 min at 30 °C. The reactions were stopped by addition of Trizol and RNAs were extracted. After digestion with Terminator exonuclease (Epicentre) and fragmentation, nascent RNAs were enriched twice for 5-bromo-UTP (BrUTP) by immunoprecipitation. For RNA-seq, total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN).For sRNA-seq，nuclei were isolated from 10-day-old Col-0 and coi1-1 seedlings without or with MeJA treatment as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008). To characterize nuclear AGO1-associated sRNAs, sRNAs were extracted from the immunoprecipitates as described (Mi et al., 2008)
Libraries for ChIP-seq were generated using the NEXTflex ChIP-seq Kit (Bioo Scientific) according to the manufacturer’s instructions; Libraries for GRO-seq were performed as described (Wang et al., 2011a). Libraries for RNA-seq were generated using NEXTflex RNA-Seq Kit (Bioo Scientific) or NEBNext Ultra Directional RNA Library Prep Kit for Illumina(NEB)according to the manufacturer’s instructions;Libraries for sRNA-seq were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB)

treatment_protocol: Ten-day-old seedlings were exposed to one of the following treatments: 50 μM of MeJA for 1 h, 10 μM of flg22 for 3 h, 40 μM of BTH for 24 h and 4 °C (cold) for 6 h. For IAA treatment, 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days. Then they were grown on 1/2 MS containing 20 μM IAA for 1 h.Plants grown under the same condition were treated with the buffers and served as controls.

tag: ecotype/background

tag: genotype/variation

value: seedling

value: 10 days

tag: substrate


title: RNA primed hESC Ctrl rep3

source_name: embryonic stem cell

value: primed embryonic stem cell


title: ChIPseq_AGO1_WT-control2swi3bandbrm_ChIP

value: WT


title: GROseq.U2AF35S34FCtr_rep2

description:
GROseq.S34FCtr_rep2_e100s2_rev.bw
GROseq.S34FCtr_rep2_e100s2_fwd.bw


title: ChIPseq_AGO1_swi3b_ChIP


title: RNA primed hESC T28KO rep1


title: Bulk Hi-C Library RUES2 ESC Rep 2

description:
ESC Rep 2
processed data file:
ESC_Merged_DI_TADs.bed.gz

tag: cell line

value: Embryonic stem cells (ESC)

value: Day 0 of differentiation


title: IP_GFP-AGO1ΔNES_rep2

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.38 ; RTA 1.18.61.0 ; CASAVA-1.8.2
FASTQ file generation and demultiplexing and adapter removal was done by Fasteris.
15-to-35-nt reads with identical sequence were grouped using the processReads function from the ncPRO-seq pipeline and aligned against A.thaliana’s genome (TAIR10) using bowtie2.
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, tab-delimited text files including distinct sequences and reads count values after genomic mapping.

source_name: Inflorescences

growth_protocol: Plants were grown for 2 weeks in soil in a 12-h-light/12-h-dark regimen, then moved into a 16 h/8 h chamber

extract_protocol:
For each GFP-AGO1 allele, two independent pools of ~10 different lines were frozen and ground in liquid nitrogen. Supernatants were precleared and incubated with GFP-Trap_MA (ChromoTek). The beads were removed magnetically and RNA was then phenol-extracted and precipitated in sodium acetate, ethanol, and glycogen, washed in ethanol 80% and re-suspended in RNase-free water.
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq sequencer

tag: ecotype

tag: expressing

value: Inflorescences

tag: development stage

value: Unopened flower buds


title: IP_GFP-AGO1ΔNES_rep1


title: GROseq.U2AF35Q157PDOX_rep1

description:
GROseq.Q157PDOX_rep1_e100s2_rev.bw
GROseq.Q157PDOX_rep1_e100s2_fwd.bw


title: GROseq.U2AF35Q157PDOX_rep2

description:
GROseq.Q157PDOX_rep2_e100s2_rev.bw
GROseq.Q157PDOX_rep2_e100s2_fwd.bw


title: IP_GFP-AGO1_rep2


title: GROseq.U2AF35Q157PCtr_rep2

description:
GROseq.Q157PCtr_rep2_e100s2_rev.bw
GROseq.Q157PCtr_rep2_e100s2_fwd.bw


title: GROseq.U2AF35Q157PCtr_rep1

description:
GROseq.Q157PCtr_rep1_e100s2_rev.bw
GROseq.Q157PCtr_rep1_e100s2_fwd.bw


title: GROseq.SRSF2WTCtr_rep2

description:
GROseq.SRSF2WTCtr_rep2_e100s2_rev.bw
GROseq.SRSF2WTCtr_rep2_e100s2_fwd.bw


title: sRNAseq_NuclAGO1_WT_rep2

description:
Small RNA; sRNA-Seq
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Nuclei were isolated from 10-day-old Col-0 seedlings as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008).sRNAs were extracted from the immunoprecipitates and subjected to library construction as described (Mi et al., 2008).

data_processing:
Reads were mapped with Bowtie for all data; Peaks were called with MACS2 for ChIP-seq; Gene expressions were calculated with Cuffdiff for RNA-seq; GRO-seq data was analysed by HOMER software.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph for ChIP-seq; expression matrix for RNA-seq; bigwig for GRO-seq; raw read counts for sRNA-seq.

source_name: seedling, WT, untreated

growth_protocol: Plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C). Other growth conditions for specific tissues/organs are in the 'description' field.

extract_protocol:
ChIP assays were performed as previously described (Fang et al., 2015), using antibodies against AGO1 (Qi et al., 2005), myc (Abcam, ab32), Pol II (Abcam, ab817), Pol II Ser2P (Abcam, ab5095), Pol II Ser5P (Abcam, ab5131), or IgG (Abmart, B30011). For GRO-seq, ~5X10^6 nuclei were run on for 5 min at 30 °C. The reactions were stopped by addition of Trizol and RNAs were extracted. After digestion with Terminator exonuclease (Epicentre) and fragmentation, nascent RNAs were enriched twice for 5-bromo-UTP (BrUTP) by immunoprecipitation. For RNA-seq, total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN). For sRNA-seq, nuclei were isolated from 10-day-old Col-0 and coi1-1 seedlings without or with MeJA treatment as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008). To characterize nuclear AGO1-associated sRNAs, sRNAs were extracted from the immunoprecipitates as described (Mi et al., 2008).
Libraries for ChIP-seq were generated using the NEXTflex ChIP-seq Kit (Bioo Scientific) according to the manufacturer's instructions; Libraries for GRO-seq were performed as described (Wang et al., 2011a); Libraries for RNA-seq were generated using NEXTflex RNA-Seq Kit (Bioo Scientific) or NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions; Libraries for sRNA-seq were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB).

treatment_protocol: Ten-day-old seedlings were exposed to one of the following treatments: 50 μM of MeJA for 1 h, 10 μM of flg22 for 3 h, 40 μM of BTH for 24 h and 4 °C (cold) for 6 h. For IAA treatment, 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days. Then they were grown on 1/2 MS containing 20 μM IAA for 1 h. Plants grown under the same condition were treated with the buffers and served as controls.


title: IP_GFP-AGO1_rep1


title: GROseq.SRSF2P95HCtr_rep2

description:
GROseq.P95HCtr_rep2_e100s2_rev.bw
GROseq.P95HCtr_rep2_e100s2_fwd.bw


title: sRNAseq_NuclAGO1_WT_JAtreat

description:
Small RNA; sRNA-Seq
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Nuclei were isolated from 10-day-old Col-0 seedlings with MeJA treatment as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008).sRNAs were extracted from the immunoprecipitates and subjected to library construction as described (Mi et al., 2008).

source_name: seedling, WT, MeJA

value: MeJA


title: GROseq.U2AF35S34FDOX_rep2

description:
GROseq.S34FDOX_rep2_e100s2_rev.bw
GROseq.S34FDOX_rep2_e100s2_fwd.bw


title: GROseq.SRSF2P95HCtr_rep1

description:
GROseq.P95HCtr_rep1_e100s2_rev.bw
GROseq.P95HCtr_rep1_e100s2_fwd.bw


title: sRNAseq_NuclAGO1_coi1_JAtreat

description:
Small RNA; sRNA-Seq
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Nuclei were isolated from 10-day-old coi1-1 seedlings with MeJA treatment as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008).sRNAs were extracted from the immunoprecipitates and subjected to library construction as described (Mi et al., 2008).

source_name: seedling, coi1, MeJA


title: GROseq.SRSF2P95H5h_rep2

description:
GROseq.P95H5h_rep2_e100s2_rev.bw
GROseq.P95H5h_rep2_e100s2_fwd.bw


title: RNAseq_WT_JAtreat_rep3_mate1

description:
PolyA RNA
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN).Library generation and Illumina sequencing were performed by Bionova Biotech (Beijing).
Processed data file: RNAseq_WT_JA_control_treat_gene_expression.matrix.gz


title: chipseq.U2AF35S34F_input

description:
Combined_Control_Sampling.m.bw
Combined_Control_Sampling.p.bw

tag: rnaseh mutant

value: DNA


title: GROseq.U2AF35S34FCtr_rep1

description:
GROseq.S34FCtr_rep1_e100s2_rev.bw
GROseq.S34FCtr_rep1_e100s2_fwd.bw


title: GROseq.SRSF2P95H5h_rep1

description:
GROseq.P95H5h_rep1_e100s2_rev.bw
GROseq.P95H5h_rep1_e100s2_fwd.bw


title: RNAseq_WT_JAtreat_rep2_mate1


title: RNAseq_WT_JAcontrol_rep2_mate1

source_name: seedling, WT, MeJA control

value: MeJA control


title: chipseq.U2AF35S34FCtr_V5_rep2

description:
Combined_Treat_Sampling.m.bw
Combined_Treat_Sampling.p.bw

tag: antibody

value: RNA-DNA hybird


title: chipseq.U2AF35S34F5h_V5_rep2


title: RNAseq_WT_JAcontrol_rep1_mate1

tag: age


title: chipseq.U2AF35S34FCtr_V5_rep1


title: chipseq.U2AF35S34F5h_V5_rep1


title: RNAseq_ago1-36_rep2

description:
PolyA RNA
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN).Library generation and Illumina sequencing were performed by Bionova Biotech (Beijing).
Processed data file: RNAseq_WT_ago1-36_gene_expression.matrix.gz

source_name: seedling, ago1-36, untreated


title: RNAseq_WT_JAcontrol_rep3_mate1


title: RNAseq_WT_JAtreat_rep1_mate1


title: chipseq.U2AF35WTCtr_input


title: RNAseq_ago1-36_JAtreat_rep3_mate1

description:
PolyA RNA
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN).Library generation and Illumina sequencing were performed by Bionova Biotech (Beijing).
Processed data file: RNAseq_ago1-36_JA_control_treat_gene_expression.matrix.gz

source_name: seedling, ago1-36, MeJA


title: chipseq.U2AF35WTCtr_V5_rep2


title: RNAseq_ago1-36_JAtreat_rep1_mate1


title: RNAseq_ago1-36_JAtreat_rep2_mate1


title: sRNAseq_NuclAGO1_WT_JAcontrol

description:
Small RNA; sRNA-Seq
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Nuclei were isolated from 10-day-old Col-0 seedlings without MeJA treatment as described (Wang et al., 2011). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008).sRNAs were extracted from the immunoprecipitates and subjected to library construction as described (Mi et al., 2008).


title: chipseq.U2AF35WT5h_V5_rep1


title: chipseq.U2AF35Q157PCtr_V5_rep2


title: RNAseq_ago1-36_JAcontrol_rep3_mate1

source_name: seedling, ago1-36, MeJA control


title: chipseq.U2AF35Q157PCtr_V5_rep1


title: RNAseq_ago1-36_JAcontrol_rep2_mate1


title: RNAseq_ago1-36_JAcontrol_rep1_mate1


title: chipseq.U2AF35Q157PCtr_input


title: GROseq_WT_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); GRO-seq was performed as described (Wang et al., 2011a), except that nuclei were isolated from 10-day-old seedlings as described (Wang et al., 2011b).

data_processing:
Library strategy: GRO-Seq
Reads were mapped with Bowtie for all data; Peaks were called with MACS2 for ChIP-seq; Gene expressions were calculated with Cuffdiff for RNA-seq; GRO-seq data was analysed by HOMER software.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph for ChIP-seq; expression matrix for RNA-seq; bigwig for GRO-seq; raw read counts for sRNA-seq.


title: GROseq_WT_rep1


title: chipseq.U2AF35Q157P5h_V5_rep2


title: RNAseq_ago1-36_rep1


title: chipseq.U2AF35Q157P5h_V5_rep1


title: chipseq.U2AF35WTCtr_V5_rep1


title: chipseq.SRSF2WTCtr_V5_rep2


title: chipseq.SRSF2WTCtr_input_rep2


title: chipseq.SRSF2WTCtr_V5_rep1


title: GROseq_ago1-36_rep1


title: ChIPseq_PolIISer5P_ago1-36_input

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C).

tag: chip antibody


title: GROseq_ago1-36_rep2

tag: tissue


title: chipseq.U2AF35WT5h_V5_rep2


title: chipseq.SRSF2WT5h_V5_rep2


title: ChIPseq_PolIISer5P_ago1-36_ChIP


title: ChIPseq_PolIISer5P_WT_input


title: ChIPseq_PolIISer5P_WT_ChIP


title: chipseq.SRSF2WTCtr_input_rep1


title: ChIPseq_PolIISer2P_ago1-36_input


title: ChIPseq_PolIISer2P_WT_input


title: chipseq.SRSF2WT5h_input_rep2


title: ChIPseq_PolIISer2P_WT_ChIP


title: chipseq.SRSF2WT5h_input_rep1


title: ChIPseq_PolIISer2P_ago1-36_ChIP


title: chipseq.SRSF2P95HCtr_V5_rep2


title: chipseq.SRSF2P95HCtr_input_rep2


title: chipseq.SRSF2P95HCtr_V5_rep1


title: chipseq.SRSF2P95HCtr_input_rep1


title: mBEC_Cell_smallRNA

data_processing:
Raw sequence reads were quality controlled using BGI filter pipeline with multiple filtering steps as follows: 1) removing reads with adapters; 2) removing reads in which unknown bases were more than 10%; and 3) removing reads in which more than 50% of bases had low quality (sequencing quality no more than 10). After filtering, the remaining reads were called “clean reads” and used for downstream bioinformatic analysis. Generally, 20M and 10M clean reads were generated per long RNA library and small RNA library, respectively.
For long RNA libraries, clean reads were mapped to Homo sapiens rRNA database using short read alignment software SOAPaligner/SOAP2 to remove the remaining rRNA reads. The reads left were used to perform transcriptome assembling and quantification. First, non-rRNA reads were mapped to human reference genome hg19 using an improved version of TopHat2, which can align reads across splice junction without relying on gene annotation. Then, the reads mapped to genome were assembled using Cufflinks. We performed Reference Annotation Based Transcript (RABT) assembly with the reference gene annotation to compensate incompletely assembled transcripts caused by read coverage gaps in the regions of reference gene. The set of transfrags generated was then compared with the reference transcripts to remove transfrags that were approximately equivalent to the whole or a portion of a reference transcript. After the assembling, we obtained the whole parsimonious set of transcripts. We blasted these transcripts with the NONCODE database using the filter set (identity > 0.9 and coverage > 0.8) to identify the known long non-coding RNA. Then, we aligned the rest of assembled transcripts to the reference annotation utilizing Cuffcompare. We utilized Cuffmerge to merge several assemblies from different samples together, which automatically filtered a number of transfrags that probably were artifacts and produced a single annotation file for downstream gene expression analysis. Two mismatches were allowed as default for annotation, except that only one was allowed for ERCC spike-ins. mRNA and lncRNA expression analyses were performed by cuffdiff and then normalized based on ERCC spike-in controls using cyclic loess robust local regression.
For small RNA libraries, clean reads were first aligned to carrier RNA (Enterobacteria phage MS2) of miRCURY Spike-in kit with bowtie (parameter: -v 2 -l 7). The unmapped reads were aligned against human rRNA sequences with bowtie (parameter: -v 2 -l 7) to remove the remaining rRNA reads. The rest reads were searched against the human miRNA precursors (miRBase V19) with bowtie (parameter: -v 1), and then the mature miRNAs reads and miRNA precursors reads were separated according to the mapping position. The remaining reads were then searched against spike-ins (UniSp2, UniSp4 and UniSp5; parameter: -v 1). And the remaining ones were searched against other non-coding RNA classes including tRNAs (gtRNAdb), piRNAs (RNAdb), snoRNA (snoRNA-LBME-db), scRNAs (Genbank) and others (Rfam database) (parameter: -v 2). After that, the remaining reads were then searched against the hg19 human genome, and we counted the reads mapped to exons, introns, intergenic regions and repeats (parameter: -v 0). The samtools was used to calculate the reads depth of each base position and R package barplot was used to draw the bar plot of the depth of position.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: xlsx format; fmol per ug total RNA

source_name: mouse primary brain endothelial cells

tag: growth protocol

value: Primary neurons, astrocytes, and microglia were cultured as described previously [Absalon S. et al., J Neurosci 2013; Tamashiro T.T. et al., J Vis Exp 2012]. Briefly, cortical tissues of E18 and P1 C57BL/6 mice were dissected for primary cultures of neurons and glial cells, respectively. The tissues were dissociated with 0.25 % Trypsin (Gibco) and 0.1 mg/mL DNaseI (Roche) for 15 min at 37 °C. The cells were plated in poly-D-lysine coated T25 flasks or 24-well plates at ∼80,000 cells per cm2, in the seeding medium consisting of DMEM-F12 (Gibco), 10% FBS (Gibco), and 1% Antibiotic-Antimycotic Solution (Corning). For neuronal cultures, the media was exchanged to Neurobasal (Gibco), 2% B-27 (Gibco), 1% Antibiotic-Antimycotic Solution (Corning) and 0.5 mM Glutamax (Gibco) one day after plating. Mature neurons at 21 days in culture have been utilized for the RNAseq. For glial cultures, the flasks were shaken (200 rpm at 37 °C) three times overnight to remove microglia, and astrocytes trypsinized and further cultured in 24-well plates. For microglia cultures, the media was supplemented with the recombinant M-CSF mouse protein (10 ng/mL; Gibco). Floating microglial cells were collected from the conditioned media by gentle spin (300 g, 10 min), and re-plated in 24-well poly-D-lysine coated plates at ∼100,000 cells per cm2. For human primary neuroglial cultures, fetal cortical tissues (gestational age 18 weeks) were provided by Advanced Bioscience Resources, Inc. (Alameda CA), dissociated with papain (12 U/ml; Worthington), and cultured as previously described [Wang Y. et al., Neurobiology of Aging, in press]. Mature neuronal cultures at 30 days in vitro have been utilized for the RNAseq. Human (HBEC) and mouse (MBEC) primary brain microvascular endothelial cells were purchased from Cell Biologics, IL (Catalog# H-6023; Lot# 021514F14 and Catalog# C57-6023; Lot# 070613T2MP, respectively) and cultured accordingly to the manufacturer.

tag: library type

value: Small RNA library

value: Cellular RNA


title: ChIPseq_AGO1_WT_JAtreat_input_rep2


title: mAstrocyte_Cell_smallRNA

source_name: mouse primary astrocyte


title: mMicroglia_Cell_smallRNA

source_name: mouse primary microglia


title: chipseq.SRSF2P95H5h_V5_rep2


title: ChIPseq_AGO1_WT_JAcontrol_input_rep2


title: ChIPseq_AGO1_WT_JAtreat_ChIP_rep2


title: chipseq.SRSF2WT5h_V5_rep1


title: ChIPseq_AGO1_WT_IAAtreat_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days, then they were grown on 1/2 MS containing 20 μM IAA for 1h.

source_name: seedling, WT, IAA

value: IAA


title: Lsk1as_CDK9as_3MBPP1r2

first: Gregory

middle: Thomas

last: Booth

state: New York

address: 526 Campus Road

department: Molecular Biology and Genetics

description:
Nascent RNA
ePROseq_Pombe_Lsk1asCDK9as_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_Lsk1asCDK9as_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

data_processing:
Library strategy: PRO-seq
Adaptor sequences were clipped from read 3' ends.  In cases where inline barcodes were used, they were clipped from 5' ends.  Sequences were trimmed to a maximum length of 36 (minimum = 15).  The reverse complement of reads was generated for alignment.
Using Bowtie (version 1.0) Reads were first aligned to ribosomal DNA genomes of both S. cerevisiae and S. pombe.  Any reads that failed to align to ribosomal DNA were then aligned to a combinded genome of S. cerevisiae and S. pombe. We allowed for a maximum of 2 mismatches Only uniquely aligning reads were used for downstream analysis.
Unique reads were parsed based on their species of origin.  Bedgraph files were created by recording only the most 3' base of each read (which represents the position of the Pol II active site).  The counts at each position in a bedgraph file were normalized as counts per million mappable spike-in reads.  Normalized bedgraphs were then converted to bigwig formated files.
Genome_build: S. pombe: ASM294v2;  S. cerevisiae: S288C_reference_genome_R64-1-1_20110203
Supplementary_files_format_and_content: processed files are in bigwig format. There are two bigwig files for each sample, one for each strand. Each bigwig file contains normalized counts of read 3'-ends.

organism: Schizosaccharomyces pombe

growth_protocol: S. pombe cultures were grown in YES media from a starting OD600 of 0.2 to a final OD600 = 0.5 before treatment.

extract_protocol:
Immediately prior to treatments, a fixed amount of spike-in culture (i.e.  S. cerevisaie samples) was added to each sample culture for PRO-seq experiment.  After treatment, cultures were then spun down and washed once in ice-cold water.  Samples were then spun again and resuspended in ice-cold permeabilization buffer (0.05% sarkosyl) and left on ice for 20 minutes.  Permeabilized cells were then spun down at 400XG for 5 minutes.  Permeabilized cell pellets were resuspeneded in 120 uL 2.5X transcription buffer (50 mM Tris-HCl, pH 7.7, 500 mM KCl, 12.5 mM MgCl2).  To the reaction buffer we then added 3.75 uL of each biotin-11-NTP (epicentre), 6 uL .1M DTT, 3 uL SUPERase Inhibitor (invitrogen) and 141 uL DEPC treated water.  The run-on was then performed by adding 15 uL 10% sarkosyl and placing samples at 30°C for 5 minutes.  After the run-on, samples were spun and the reaction buffer was removed.  RNA was then isolated using the hot acid phenol extraction protocol followed by ethanol precipitation.
PRO-seq libraries were prepared according to Mahat et al. Nature Protocols (2016).

treatment_protocol: 10 mL cultures were placed into 15 mL falcon tubes, treated with 10 μM 3-MB-PP1 or an equivalent volume of 100% DMSO.  Treated cultures were left shaking at 30 °C for specified amount of time.  Treatments were terminated by pouring cultures into 30 mL ice cold water and then immediately pelleting cells.

value: cdk9as lsk1as:cdk9T120G::hphMX6 lsk1F353G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+

tag: treatment duration

value: 5 minutes


title: ChIPseq_AGO1_WT_IAAtreat_input_rep1

value: seedling

value: 10 days


title: ChIPseq_AGO1_WT_IAAtreat_ChIP_rep1

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days; 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days, then they were grown on 1/2 MS containing 20 μM IAA for 1h.

value: WT


title: chipseq.SRSF2P95H5h_input_rep2

value: Dox

tag: sample type


title: mNeuron_Cell_smallRNA

source_name: mouse primary neuron


title: ChIPseq_AGO1_WT_JAcontrol_ChIP_rep2

tag: treatment


title: chipseq.SRSF2P95H5h_V5_rep1


title: chipseq.SRSF2P95H5h_input_rep1


title: ChIPseq_AGO1_WT_IAAcontrol_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days.

source_name: seedling, WT, IAA control

tag: ecotype/background

value: IAA control


title: Cdk9as_20min_10uM_3MBPP1_rep2

description:
Nascent RNA
ePROseq_Pombe_CDK9as_20min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_20min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

tag: genotype/variation

value: cdk9as:cdk9T120G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+

value: 20 minutes


title: Lsk1as_CDK9as_DMSOr1

description:
Nascent RNA
ePROseq_Pombe_Lsk1asCDK9as_DMSO_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_Lsk1asCDK9as_DMSO_COMBINED_pombe_SpikeNormed_minus.bw

value: DMSO


title: ChIPseq_AGO1_WT_IAAcontrol_input_rep1

tag: substrate


title: ChIPseq_AGO1_WT_IAAcontrol_ChIP_rep2


title: Lsk1as_CDK9as_DMSOr2


title: Cdk9as_20min_10uM_3MBPP1_rep1


title: Cdk9as_10min_10uM_3MBPP1_rep1

description:
Nascent RNA
ePROseq_Pombe_CDK9as_10min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_10min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

value: 10 minutes


title: Cdk9as_7.5min_10uM_3MBPP1_rep1

description:
Nascent RNA
ePROseq_Pombe_CDK9as_7min30sec_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_7min30sec_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

value: 7.5 minutes


title: Cdk9as_7.5min_10uM_3MBPP1_rep2


title: ChIPseq_IgG_ago1-36

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C)

growth_protocol: Plants (all in Col-0 background) were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C). Other growth conditions for specific tissues/organs are in the DESCRIPTION column of the SAMPLES section.

extract_protocol:
ChIP assays were performed as previously described (Fang et al., 2015),using antibodies against AGO1 (Qi et al., 2005), myc (Abcam,ab32), Pol II (Abcam,ab817), Pol II Ser2P (Abcam,ab5095), Pol II Ser5P (Abcam,ab5131), or IgG (Abmart, B30011). For GRO-seq, ~5X106 nuclei were run on for 5 min at 30 °C. The reactions were stopped by addition of Trizol and RNAs were extracted. After digestion with Terminator exonuclease (Epicentre) and fragmentation, nascent RNAs were enriched twice for 5-bromo-UTP (BrUTP) by immunoprecipitation. For RNA-seq, total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN).For sRNA-seq，nuclei were isolated from 10-day-old Col-0 and coi1-1 seedlings without or with MeJA treatment as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008). To characterize nuclear AGO1-associated sRNAs, sRNAs were extracted from the immunoprecipitates as described (Mi et al., 2008)
Libraries for ChIP-seq were generated using the NEXTflex ChIP-seq Kit (Bioo Scientific) according to the manufacturer’s instructions; Libraries for GRO-seq were performed as described (Wang et al., 2011a). Libraries for RNA-seq were generated using NEXTflex RNA-Seq Kit (Bioo Scientific) or NEBNext Ultra Directional RNA Library Prep Kit for Illumina(NEB)according to the manufacturer’s instructions;Libraries for sRNA-seq were generated using NEBNext Small RNA Library Prep Set for Illumina (NEB)

value: IgG


title: ChIPseq_AGO1_WT_IAAtreat_ChIP_rep2


title: ChIPseq_AGO1_WT_IAAcontrol_ChIP_rep1

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); 6-day-old seedlings were transferred to new 1/2 MS media and placed vertically for 4 days, then they were grown on new 1/2 MS media for 1h.


title: ChIPseq_AGO1_WT_Flg22treat_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were treat with10 μM of flg22 for 3h.

source_name: seedling, WT, Flg22


title: Lsk1as_CDK9as_3MBPP1r1


title: Cdk9as_5min_10uM_3MBPP1_rep1

description:
Nascent RNA
ePROseq_Pombe_CDK9as_5min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_5min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw


title: ChIPseq_AGO1_WT_Flg22treat_input_rep1


title: ChIPseq_IgG_WT

source_name: seedling


title: RNAseq_WT_rep2

description:
PolyA RNA
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Total RNA was purified from 10-day-old seedlings using RNeasy Plant Mini Kit (QIAGEN).Library generation and Illumina sequencing were performed by Bionova Biotech (Beijing).
Processed data file: RNAseq_WT_ago1-36_gene_expression.matrix.gz


title: Cdk9as_5min_10uM_3MBPP1_rep2


title: Cdk9as_10min_10uM_3MBPP1_rep2


title: Cdk9as_2.5min_10uM_3MBPP1_rep1

description:
Nascent RNA
ePROseq_Pombe_CDK9as_2min30sec_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_2min30sec_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

value: 2.5 minutes


title: Cdk9as_2.5min_10uM_3MBPP1_rep2


title: Cdk9as_0.5min_10uM_3MBPP1_rep2

description:
Nascent RNA
ePROseq_Pombe_CDK9as_30sec_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_30sec_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

value: 0.5 minutes


title: Cdk9as_0.5min_10uM_3MBPP1_rep1


title: Cdk9as_1min_10uM_3MBPP1_rep2

description:
Nascent RNA
ePROseq_Pombe_CDK9as_1min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_1min_3MBPP1_10uM_COMBINED_pombe_SpikeNormed_minus.bw

value: 1 minute


title: ChIPseq_AGO1_WT_Flg22treat_ChIP_rep1


title: sRNAseq_NuclAGO1_WT_rep1

description:
Small RNA; sRNA-Seq
Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Nuclei were isolated from 10-day-old Col-0 seedlings as described (Wang et al., 2011b). Nuclear lysates were used for immunopurification of AGO1 complexes as described (Mi et al., 2008).sRNAs were extracted from the immunoprecipitates and subjected to library construction as described (Mi et al., 2008).


title: Cdk9as_1min_10uM_3MBPP1_rep1


title: Mcs6as_CDK9as_3MBPP1r2

description:
Nascent RNA
6713_7157_31626_HWV7YBGXX_pombe_Mcs6as_CDK9as_3MB-PP1_COMBINED_TGACCA_R1ChrFix_spikeNormed_plus.bw
6713_7157_31626_HWV7YBGXX_pombe_Mcs6as_CDK9as_3MB-PP1_COMBINED_TGACCA_R1ChrFix_spikeNormed_minus.bw

value: cdk9as mcs6as5:cdk9T120G::hphMX6 mcs6N84T-L87G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h-


title: ChIPseq_AGO1_WT_Flg22control_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were treat with water for 3h.

source_name: seedling, WT, Flg22 control

value: Flg22 control


title: RNAseq_WT_rep1


title: ChIPseq_PolII_WT_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C).


title: ChIPseq_PolII_WT_input_rep1


title: ChIPseq_AGO1_WT_Flg22treat_ChIP_rep2


title: Isk1as_3MBPP1r2

description:
Nascent RNA
6713_7157_31630_HWV7YBGXX_pombe_Isk1as_3MB-PP1_COMBINED_ACTTGA_R1ChrFix_spikeNormed_plus.bw
6713_7157_31630_HWV7YBGXX_pombe_Isk1as_3MB-PP1_COMBINED_ACTTGA_R1ChrFix_spikeNormed_minus.bw

value: lsk1as:lsk1F353G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M216 h-

value: 5 minutes


title: Mcs6as_CDK9as_DMSOr1

description:
Nascent RNA
6713_7157_31625_HWV7YBGXX_pombe_Mcs6as_CDK9as_DMSO_COMBINED_TTAGGC_R1ChrFix_spikeNormed_plus.bw
6713_7157_31625_HWV7YBGXX_pombe_Mcs6as_CDK9as_DMSO_COMBINED_TTAGGC_R1ChrFix_spikeNormed_minus.bw


title: ChIPseq_AGO1_WT_Flg22control_input_rep1

value: seedling

value: 10 days


title: Mcs6as_CDK9as_DMSOr2


title: Isk1as_3MBPP1r1


title: Cdk9as_0min_DMSO_rep2

description:
Nascent RNA
ePROseq_Pombe_CDK9as_0min_DMSO_COMBINED_pombe_SpikeNormed_plus.bw
ePROseq_Pombe_CDK9as_0min_DMSO_COMBINED_pombe_SpikeNormed_minus.bw


title: ChIPseq_PolII_WT_ChIP_rep1

value: WT

value: PolII


title: ChIPseq_AGO1_WT_Flg22control_ChIP_rep1


title: CDK9_3MBPP1r2

description:
Nascent RNA
5993_7157_26982_HJ72CBGXX_pombe_CDK9as_COMBINED_3MB-PPI_CTTGTA_R1ChrFix_spikeNormed_plus.bw
5993_7157_26982_HJ72CBGXX_pombe_CDK9as_COMBINED_3MB-PPI_CTTGTA_R1ChrFix_spikeNormed_minus.bw

value: cdk9as:cdk9T120G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+


title: ChIPseq_AGO1_WT_Coldtreat_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were grown under 4 °C (cold) for 6h.

source_name: seedling, WT, Cold

value: Cold


title: Isk1as_DMSOr2

description:
Nascent RNA
6713_7157_31629_HWV7YBGXX_pombe_Isk1as_DMSO_COMBINED_CAGATC_R1ChrFix_spikeNormed_plus.bw
6713_7157_31629_HWV7YBGXX_pombe_Isk1as_DMSO_COMBINED_CAGATC_R1ChrFix_spikeNormed_minus.bw

value: DMSO


title: ChIPseq_PolII_ago1-36_input_rep2


title: Isk1as_DMSOr1


title: ChIPseq_AGO1_WT_Coldtreat_input_rep1


title: ChIPseq_PolII_ago1-36_input_rep1


title: Cdk9as_0min_DMSO_rep1

value: 20 minutes


title: CDK9_3MBPP1r1


title: ChIPseq_AGO1_WT_Coldtreat_ChIP_rep2


title: ChIPseq_PolII_ago1-36_ChIP_rep1


title: mcs6_3MBPP1r1

description:
Nascent RNA
5993_7157_26980_HJ72CBGXX_pombe_mcs6as_COMBINED_3MB-PPI_TAGCTT_R1ChrFix_spikeNormed_plus.bw
5993_7157_26980_HJ72CBGXX_pombe_mcs6as_COMBINED_3MB-PPI_TAGCTT_R1ChrFix_spikeNormed_minus.bw

value: mcs6as5:mcs6N84T -L87G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h+


title: CDK9_DMSOr1

description:
Nascent RNA
5993_7157_26981_HJ72CBGXX_pombe_CDK9as_COMBINED_DMSO_GGCTAC_R1ChrFix_spikeNormed_plus.bw
5993_7157_26981_HJ72CBGXX_pombe_CDK9as_COMBINED_DMSO_GGCTAC_R1ChrFix_spikeNormed_minus.bw


title: CDK9_DMSOr2


title: mcs6_3MBPP1r2


title: ChIPseq_AGO1_WT_Flg22control_ChIP_rep2


title: ChIPseq_AGO1_WT_Coldcontrol_input_rep2

source_name: seedling, WT, Cold control

value: Cold control


title: ChIPseq_AGO1_WT_JAtreat_input_rep1

source_name: seedling, WT, MeJA

value: MeJA


title: mcs6_DMSOr2

description:
Nascent RNA
5993_7157_26979_HJ72CBGXX_pombe_mcs6as_COMBINED_DMSO_GATCAG_R1ChrFix_spikeNormed_plus.bw
5993_7157_26979_HJ72CBGXX_pombe_mcs6as_COMBINED_DMSO_GATCAG_R1ChrFix_spikeNormed_minus.bw


title: ChIPseq_AGO1_WT_Coldtreat_ChIP_rep1


title: mcs6_DMSOr1


title: WT_3MBPP1r2

description:
Nascent RNA
5993_7157_26978_HJ72CBGXX_pombe_WT_COMBINED_3MB-PPI_ACTTGA_R1ChrFix_spikeNormed_plus.bw
5993_7157_26978_HJ72CBGXX_pombe_WT_COMBINED_3MB-PPI_ACTTGA_R1ChrFix_spikeNormed_minus.bw

value: wt:leu1-32 ura4-D18 his3-D1 ade6-M210 h+


title: ChIPseq_AGO1_WT_JAtreat_ChIP_rep1


title: WT_3MBPP1r1


title: ChIPseq_AGO1_WT_JAcontrol_ChIP_rep1

value: MeJA control


title: ChIPseq_AGO1_WT_Coldcontrol_ChIP_rep1


title: ChIPseq_AGO1_WT_Coldcontrol_input_rep1


title: Male RLX treated Rat 7 -24 months old

city: Pittsburgh

first: Brian

last: Martin

state: Pennsylvania

address: 3550 Terrace St

department: Bioengineering

institute: University of Pittsburgh

description:
processed data file header: GS10
processed data file: Male_24_month_Control_and_RLX_treated.xlsx

data_processing:
Fastq files were uploaded into Biomedical Genomics Workbench, v.3.0.1
Base pair reads were matched to the rat reference sequence (rattus_norvegicus_ensembl_v79)
Gene expression changes were based on total count differences between groups.
Comparisons between groups were performed on Biomedical Genomics Workbench 3.0.1 between young and aged male ctrls, aged RLX treated and aged ctrl males, young and aged female ctrls, aged RLX treated and aged ctrl females
For data imported into Ingenuity Pathway Analysis, filters were applied to include only genes with absolute fold changes greater than 1.5 and an FDR < 0.05.
Genome_build: rattus_norvegicus_ensembl_v79
Supplementary_files_format_and_content: Female 24 month and 9 month Controls: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
Supplementary_files_format_and_content: Female 24 month Control and RLX treated: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
Supplementary_files_format_and_content: Male 24 month and 9 month Controls: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
Supplementary_files_format_and_content: Male 24 month Control and RLX treated: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.

organism: Rattus norvegicus

source_name: Left Ventricle

extract_protocol:
Preparation was performed using TruSEQ Standard Total RNA Sample Preparation Kit (Illumia, San Diego, CA) according to manufactuers instructions.
Following removal of ribosomal sequences, RNA was fragmented for 8 minutes and reverse transcription performed. Double stranded cDNA was subjected to 3’ adenylation and ligation of sequencing adapters. Sequencing was carried out on a NextSeq 500 (Illumina) for 2 x 75 bp paired end reads. Loading concentration was 1.2-1.4 pM.

treatment_protocol: Rats were treated with control (Sodium Acetate) or RLX (400 ug/kg/day) for 14 days via subcutaneous osmotic mini pumps.

tag: strain

value: F-344 Brown/Norway Rat

value: Left Ventricle

value: 24 months

tag: Sex

value: Male

value: RLX


title: Male CTRL Rat 4 -9months old

description:
processed data file header: GS13
processed data file: Male_24_month_and_9_month_Controls.xlsx

value: 9 months

value: CTRL


title: ChIPseq_AGO1_WT_Coldcontrol_ChIP_rep2

value: WT

value: seedling

value: 10 days


title: Male CTRL Rat 2 -9 months old

description:
processed data file header: GS12
processed data file: Male_24_month_and_9_month_Controls.xlsx


title: Male RLX treated Rat 3 -24 months old

description:
processed data file header: GS8
processed data file: Male_24_month_Control_and_RLX_treated.xlsx


title: GROseq.SRSF2WT5h_rep1

description:
GROseq.SRSF2WT5h_rep1_e100s2_rev.bw
GROseq.SRSF2WT5h_rep1_e100s2_fwd.bw

value: Dox

value: RNA


title: ChIPseq_PolII_ago1-36_ChIP_rep2

value: PolII


title: WT_DMSOr1

description:
Nascent RNA
5993_7157_26977_HJ72CBGXX_pombe_WT_COMBINED_DMSO_CAGATC_R1ChrFix_spikeNormed_plus.bw
5993_7157_26977_HJ72CBGXX_pombe_WT_COMBINED_DMSO_CAGATC_R1ChrFix_spikeNormed_minus.bw

value: DMSO

value: 5 minutes


title: WT_DMSOr2

value: wt:leu1-32 ura4-D18 his3-D1 ade6-M210 h+


title: ChIPseq_AGO1_WT_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C).

source_name: seedling, WT, untreated


title: Male RLX treated Rat 2 -24 months old

description:
processed data file header: GS7
processed data file: Male_24_month_Control_and_RLX_treated.xlsx


title: Male CTRL Rat 11 -24 months old

description:
processed data file header: GS6
processed data file: Male_24_month_and_9_month_Controls.xlsx
processed data file: Male_24_month_Control_and_RLX_treated.xlsx


title: ChIPseq_AGO1_WT_input_rep1


title: ChIPseq_AGO1_WT_BTHtreat_input_rep1

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were treat with 40 μM of BTH for 24h.

source_name: seedling, WT, BTH

value: BTH


title: Male CTRL Rat 3 -9 months old

description:
processed data file header: GS1
processed data file: Male_24_month_and_9_month_Controls.xlsx

value: F-344 Brown/Norway Rat


title: ChIPseq_PolII_WT_ChIP_rep2


title: Male CTRL Rat 8 -24 months old

description:
processed data file header: GS4
processed data file: Male_24_month_and_9_month_Controls.xlsx
processed data file: Male_24_month_Control_and_RLX_treated.xlsx

value: Left Ventricle


title: ChIPseq_AGO1_WT_BTHtreat_ChIP_rep2


title: ChIPseq_AGO1_WT_BTHtreat_ChIP_rep1


title: ChIPseq_AGO1_WT_JAcontrol_input_rep1

source_name: seedling, WT, MeJA control

value: MeJA control


title: Female CTRL Rat 5 -9 months old

description:
processed data file header: GS32
processed data file: Female_24_month_and_9_month_Controls.xlsx

value: Female


title: Female CTRL Rat 4 -9 months old

description:
processed data file header: GS31
processed data file: Female_24_month_and_9_month_Controls.xlsx


title: Female CTRL Rat 3 -9 months old

description:
processed data file header: GS30
processed data file: Female_24_month_and_9_month_Controls.xlsx


title: Female CTRL Rat 1 -9 months old

description:
processed data file header: GS29
processed data file: Female_24_month_and_9_month_Controls.xlsx


title: Mcs6as_CDK9as_3MBPP1r1

description:
Nascent RNA
6713_7157_31626_HWV7YBGXX_pombe_Mcs6as_CDK9as_3MB-PP1_COMBINED_TGACCA_R1ChrFix_spikeNormed_plus.bw
6713_7157_31626_HWV7YBGXX_pombe_Mcs6as_CDK9as_3MB-PP1_COMBINED_TGACCA_R1ChrFix_spikeNormed_minus.bw

value: cdk9as mcs6as5:cdk9T120G::hphMX6 mcs6N84T-L87G::kanMX6 leu1-32 ura4-D18 his3-D1 ade6-M210 h-


title: ChIPseq_AGO1_WT_ChIP_rep2


title: ChIPseq_AGO1_WT_BTHcontrol_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were treat with water for 24h.

source_name: seedling, WT, BTH control

value: BTH control


title: Female CTRL Rat 6- 24 months old

description:
processed data file header: GS24
processed data file: Female_24_month_and_9_month_Controls.xlsx
processed data file: Female_24_month_Control_and_RLX_treated.xlsx

value: 24 months

value: CTRL


title: ChIPseq_AGO1_WT_BTHcontrol_input_rep1

value: WT

value: seedling


title: ChIPseq_AGO1_WT_BTHcontrol_ChIP_rep2

value: 10 days


title: ChIPseq_AGO1_ago1-36_ChIP_rep2

source_name: seedling, ago1-36, untreated


title: ChIPseq_AGO1_WT_BTHcontrol_ChIP_rep1


title: ChIPseq_AGO1_ago1-36_input_rep1


title: ChIPseq_AGO1_ago1-36_ChIP_rep1


title: ChIPseq_AGO1_ago1-36_input_rep2


title: Female CTRL Rat 5- 24 months old

description:
processed data file header: GS23
processed data file: Female_24_month_and_9_month_Controls.xlsx
processed data file: Female_24_month_Control_and_RLX_treated.xlsx


title: Female CTRL Rat 4- 24 months old

description:
processed data file header: GS22
processed data file: Female_24_month_and_9_month_Controls.xlsx
processed data file: Female_24_month_Control_and_RLX_treated.xlsx


title: FreshMedia_RNP_longRNA

organism: other sequences

source_name: Fresh media

extract_protocol:
Approximate 100 mL conditioned media was used as input for exRNA isolation. Conditioned media was centrifuged at 300 g, 4 °C for 10 min, following by the additional centrifugation at 2,000 g, 4 °C for 15 min, to remove cells and cell debris. Five uL of SUPERase In RNase Inhibitor (Ambion) was added to the supernatants per 10 mL media. The media was then filtered sequentially through the 2 um filter (GE Healthcare, UK), 0.8 um filter (EMD Millipore, MA), and 0.22 um filter (EMD Millipore), with no/minimal pressure applied. The filtrate was split to 15 mL per sample and further filtered through the 0.02 um filter (GE Healthcare) with up to 75 psi pressure applied. To facilitate the 0.02 um filtration, a mechanical syringe pump was designed and manufactured (Fig. S2). Upon filtration, each filter was washed with 1 mL DPBS (Corning), and the corresponding fractions were lysed with 600 uL Lysis Solution of the miRCURY RNA Isolation Kit – Cell & Plant (Exiqon, Denmark). The fractions collected on 0.02 um filters were lysed with 900 uL Lysis Solution. The last flow-through fractions of 0.02 um filters were pooled together (up to 30mL) and concentrated approximately 60 times using 3 kDa Amicon Ultra Centrifugal Filters (EMD Millipore) at 4,000 g, 4 °C, for 60 min. The concentrates were collected and lysed with six volumes of the same Lysis Solution (Exiqon). Total RNA was then isolated from all fractions as recommended by miRCURY protocol, with on-column DNase treatment (Qiagen, Germany). The corresponding 1.2 mL of the source neurospheres were span down at 300 g, 4 °C for 5 min, and total cellular RNA was isolated from them and analyzed in parallel. The same protocol was carried out for RNA isolation from fresh media, with 500 mL media input. For RNA isolation from primary cells cultured in 24-wells plates, the cells were lysed with 350 uL Lysis Solution per well. The concentrations of cellular and extracellular RNA were determined using the NanoDrop 2000 Spectrophotometer and Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific), respectively. The RNA quality was examined using Agilent 2100 Bioanalyzer (Agilent, CA) and the RNA Integrity Number (RIN) estimated.
Two sets of spike-in RNAs were added to the samples prior to library preparation: ERCC RNA Spike-In Control Mixes (Ambion; 0.02 uL per one ug total RNA), and miRCURY Spike-in kit, part 1, with UniSp2’s final concentrations of 1.25 and 5.0 fmol per one ug of total RNA for cellular and extracellular RNA, respectively. Total RNA, either 40~200 ng of exRNA, or 2 ug of cellular RNA, was rRNA-depleted using the Ribo-Zero rRNA Removal Kits (Illumina, CA). One quarter of the rRNA-depleted RNA was fragmented to 100~500 nt using the 5X First-Strand Buffer (Clontech, CA), and utilized for the long RNA library construction by SMARTer Stranded RNA-Seq Kit (Clontech). The remaining 75% of the rRNA-depleted RNA was treated sequentially with Tobacco Acid Pyrophosphatase (TAP; Illumina) and T4 Polynucleotide Kinase (T4PNK; New England Biolabs, MA) to create more uniform 5’- and 3’- ends for various classes of transcripts. The RNA was then used as input for the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), with size selection of 15-65nt inserts for small RNA libraries. The quality of libraries was examined using the Agilent DNA 1000 kit at the Agilent 2100 Bioanalyzer instrument, and cDNA quantified by qRT-PCR with TaqMan Probe (Thermo Fisher Scientific). The libraries were sequenced on HiSeq 2000 (Illumina) with single read 50 cycles by Beijing Genomics Institute (BGI, China).

value: Long RNA library

value: RNP (<0.02um) RNA


title: Female CTRL Rat 2- 24 months old

description:
processed data file header: GS21
processed data file: Female_24_month_and_9_month_Controls.xlsx
processed data file: Female_24_month_Control_and_RLX_treated.xlsx


title: Male CTRL Rat 12 -24 months old

description:
processed data file header: GS2
processed data file: Male_24_month_and_9_month_Controls.xlsx
processed data file: Male_24_month_Control_and_RLX_treated.xlsx

value: Male


title: FreshMedia_Exo_longRNA

value: Exosome (0,02-0.22um) RNA


title: FreshMedia_MV_longRNA


title: Female RLX treated Rat 4- 24 months old

description:
processed data file header: GS19
processed data file: Female_24_month_Control_and_RLX_treated.xlsx

value: RLX


title: ChIPseq_AGO1_WT_ChIP_rep1

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C).


title: Female RLX treated Rat 1- 24 months old

description:
processed data file header: GS17
processed data file: Female_24_month_Control_and_RLX_treated.xlsx


title: FreshMedia_Exo_smallRNA

value: Small RNA library


title: Female RLX treated Rat 2- 24 months old

description:
processed data file header: GS18
processed data file: Female_24_month_Control_and_RLX_treated.xlsx

value: F-344 Brown/Norway Rat


title: FreshMedia_MV_smallRNA


title: FreshMedia_RNP_smallRNA


title: 3110_IPTG2

status: Public on Jan 03 2018

city: Austin

first: Bryan

last: Davies

state: TX

address: 2506 Speedway

institute: University of Texas at Austin

description:
processed data file:
2016_12_3110_medium_full_library_partial_properties.xlsx

data_processing:
We used ustacks to consolidate and then trimmed reads that originated from a particular nucleotide sequence.
We translated the nucleotide sequences for each nucleotide sequence into an amino acid sequence with a custom python script using the Biopython library, and then summed the total reads for each unique peptide.
A file containing each peptide sequence and the total number of reads in each library was then used as input for the DESeq2 R/Bioconductor package. We used a standard DESeq2 workflow, which includes read count normalization, peptide dispersion estimates, and Wald tests for significance of differential abundance.  For each peptide, we compared the total abundance (normalized reads) in the induced (IPTG) libraries to the abundance in the input libraries, resulting in a log2 FoldChange (log2FC) and p-value for each peptide.  P-values were adjusted (padj) for multiple testing using Benjamini-Hochberg correction as part of the standard DESeq2 workflow detailed in the package manual  (available here: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf). Generally, peptides that were selected for further experimental validation had a log2FC < -1 and padj < .05.
Supplementary_files_format_and_content: PeplibV3_Hiseq_properties_cory.csv: Comma-separated text file contains nucleotide and corresponding peptide sequences for the massive random library. We provide the full 20-mer sequence as well as sequences truncated by stop codons. Hydrophobicity, charge, lfcMLE, adjusted p-value, and read counts (input and output) are provided for each sequence.

organism: Escherichia coli str. K-12 substr. W3110

growth_protocol: An aliquot of the frozen library was thawed and added to 10ml of LB supplemented with carbenicillin 75mg/ml for growth, shaking at 37°C for about 1 hour. The culture was then back diluted into 5ml LB/carb75 to OD600nm 0.01 supplemented with 0.1mM IPTG. The remaining culture was collected as the “Input” sample. Induced cultures were allowed to grow, shaking at 37°C. Cells were harvested after 2, 3, 4 and 5 hours for the defined peptide library and harvest after 4 hours for the random peptide library.

extract_protocol:
Plasmid DNA was isolated using the Zyppy Miniprep Kit in accordance with the prescribed protocol provided with the kit.
Custom primers were used to ligate adaptors to regions flanking the peptide nucleotide sequence. Products were gel-extracted and cleaned using the Zymoclean Gel DNA Recovery Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 0.1mM IPTG was used for induction.

tag: induced with

value: 0.1mM IPTG for 4hrs

tag: molecule subtype

value: plasmid DNA


title: 3110_IPTG1


title: 3110_Input2

value: none (input)


title: Runx3 deficient replicate 2

city: Jupiter

first: Adam

last: Getzler

state: FL

address: 130 Scripps Way

institute: TSRI-FL

description:
Exp64_16
Processed data file: Total_RNA_Seq_Raw_Counts.csv

data_processing:
Bowties2
HT-Seq Count
DESEQ2
Genome_build: UCSC mm9 (MGSCv37)
Supplementary_files_format_and_content: Total_RNA_Seq_Raw_Counts.csv: Comma-separated text file; HT-Seq Count raw counts.

source_name: Day 6 100U IL2 CD8+ T-cells

extract_protocol:
Total RNA was extracted in TRIZoL reagent.
Strand-specific paired-end libraries were made using the TruSeq stranded total RNA kit. Samples were DNaseI treated and rRNA depleted.

tag: strain/background

value: C57BL/6 Runx3fl/fl

tag: retrovirus

value: pMigR-Cre

tag: cell type

value: CD8+ T-cells


title: Runx3 Overexpression replicate 2

description:
Exp64_13
Processed data file: Total_RNA_Seq_Raw_Counts.csv

value: pMigR-Runx3 cDNA


title: Wildtype replicate 1

description:
Exp64_6
Processed data file: Total_RNA_Seq_Raw_Counts.csv

value: PMigR-Empty


title: Runx3 deficient replicate 1

description:
Exp64_8
Processed data file: Total_RNA_Seq_Raw_Counts.csv


title: Runx3 Overexpression replicate 1

description:
Exp64_5
Processed data file: Total_RNA_Seq_Raw_Counts.csv


title: Wildtype replicate 2

description:
Exp64_14
Processed data file: Total_RNA_Seq_Raw_Counts.csv


title: Female RLX treated Rat 6- 24 months old

description:
processed data file header: GS20
processed data file: Female_24_month_Control_and_RLX_treated.xlsx

value: Left Ventricle

tag: age

value: 24 months

value: Female


title: Mouse_dermis_rep2

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

description:
protocol: SMART-seq2
processed data file: Mouse_TPM.txt

data_processing:
Sequenced reads were mapped to Ensembl v.87 transcriptomes of Mus musculus (mm10) and Rattus norvegicus (Rnor_6.0) using bowtie v1.0.0 with parameters: -S --offrate 1 -a -m 200 --best -p 8 -v 2
Transcripts per million (TPM) measurements for rat and mouse samples were obtained using read alignments to Ensembl v87 transcriptomes and rsem v1.2.31
Genome_build: mm10 or Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for mouse samples and rat samples separately.

source_name: Mouse wound dermis

extract_protocol:
Whole tissue was homogenized using Precellys in RLT buffer supplemented with beta-mercapto ethanol to preserve RNA integrity. Total RNA was isolated using Rneasy micro kit as per manufacturer's suggestions (Qiagen), including DNAse treatment. Total RNA was eluted in molecular grade water. RNAs with optimal RIN scores were considered for library preparation.
SMART-seq2 was performed on total RNA as described by Picelli et al. Briefly, 10 ng and 100 ng total RNA was used for RT. Resulting cDNA was pre-amplified for 12 and 10 cycles, respectively and tagmentation  performed on 18 ng and 20 ng cDNA using the Nextera DNA Sample Preparation Kit (Illumina). Fragments were amplified for 8 continuous cycles. Libraries sequenced as single-end (86bp and 43bp) on a NextSeq 500 Illumina Sequencing Platform (Illumina).

tag: tissue

value: skin

tag: tissue compartment

value: dermis

tag: skin status

value: Skin wound

tag: Stage

value: Scab detachment day 1


title: ChIPseq_AGO1_WT_BTHtreat_input_rep2

description: Plants were grown in 1/2 X MS containing 1% sucrose under long-day conditions (16 h of light/8 h of darkness, 22°C); Ten-day-old seedlings were treat with 40 μM of BTH for 24h.

value: WT

value: seedling

value: 10 days

value: BTH

tag: chip antibody


title: Rat_IFE_rep5

description:
protocol: SMART-seq2
processed data file: Rat_TPM.txt

source_name: Rat inter-follicular epidermis

value: epidermis

value: Normal skin

value: Adult


title: Rat_IFE_rep4


title: Mouse_epidermis_rep2

source_name: Mouse wound epidermis


title: Rat_IFE_rep3


title: Mouse_dermis_rep1


title: Mouse_dermis_rep3


title: Mouse_epidermis_rep1


title: Mouse_epidermis_rep3