title: 4_Mice_rAAV a-syn: E3

data_processing:
Low quality reads and adapters were removed using TrimGalore (v0.4.4)
Bismark (v0.17.0) was used to align bisulfite sequencing reads to a masked reference genome and the base pair specific methylation calls were extracted
Methylation calls overlapping padlock probe arms were removed using Bedtools
Methylation calls were only considered for cytosines with at least a 30× read depth. For technical replicate samples, methylation calls and counts were averaged for each site. Sites with less than 70% of samples containing methylation calls and/or sites with all samples having a methylation call of 0 were removed from further analysis.
We next explored the data using principal component analysis (PCA) of beta values defined as B = M / (M+U). PCA of all datasets was computed and sample projection onto the first two principal components was plotted, which served to identify outlying samples. Samples deviating from the center of either of the first two principal components by more than 3 standard deviations were deemed outliers and removed from further analysis. Next, the distribution of U and M read counts across experimental batches was used to determine whether sample cohort should be normalized. Normalized B values for appendix datasets were obtained from quantile normalized and rounded M and U read count matrices. Sites with stable DNA methylation calls (0%, 100%, and/or missing) in 50% or more of the samples were excluded from further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Each txt file contain the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

source_name: cecal patch

growth_protocol: Male C57BL/6J mice obtained from Jackson Labs were used in the experiment. α-Syn aggregation in neurons of the mouse cecal patch was induced by recombinant AAV (rAAV) vector-mediated overexpression of full-length human α-syn. The rAAV vector uses a pan-neuronal-specific (synapsin) promoter to express human α-syn specifically in enteric neurons. The rAAV vector also contains a separate expression cassette (with the same promoter) expressing green fluorescent protein (GFP) to allow rapid identification of transduced neurons. The negative control vector contains synapsin-promoter expressing GFP and BFP2 (to match the dual transgene system).

extract_protocol:
Genomic DNA was extracted using standard phenol-chloroform extraction methods from cecal patch of mice treated with the rAAV-α-syn vector or control vector.
DNA methylation fine-mapping was performed using the bisulfite padlock probe technique. Bisulfite conversion of gDNA and purification was done using the EZ DNA Methylation-Lightning Kit (Zymo Research) and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For each sample, the bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng) at 55ºC for 20 h. Target regions flanked by the hybridized padlock probes were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). The non-targeted, non-circularized DNA was digested using exonuclease (Exonuclease I and III; New England Biolabs). The target circularized DNA was amplified using a common linker sequence within the padlock probe. Libraries were then PCR amplified, pooled in equimolar amounts, and purified by QIAquick Gel Extraction kit (Qiagen). Libraries were quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine

treatment_protocol: At 8 weeks of age, mice were anesthetized using isoflurane and a full laparotomy was performed in order to isolate and expose the cecal patch on the cecum. Each mouse cecal patch region received two 2 µl injection at a titer of 6 x 1012 vg/ml of rAAV α-syn or control vector. Injections were performed with an automated micropump at 1 μl/s. Following the injection, the needle was left in place for an additional 10-20 s to allow the injection pressure to dissipate. All mice administered rAAV-α-syn or control vectors to the cecal patch fully recovered from surgery. Following surgery, mice remained in their home cages for a 4-week long incubation period, followed by tissue harvest.

value: cecal patch

value: m

value: GFP


title: 4_Mice_rAAV a-syn: E4

status: Public on Mar 01 2021

type: SRA

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

country: USA

institute: Van Andel Research Institute

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: subject id

tag: replicate

value: Yes

tag: Sex

tag: treatment


title: 5_OFB: OB_A26_PD3459

data_processing:
Low quality reads and adapters were removed using TrimGalore (v0.4.4)
Bismark (v0.17.0) was used to align bisulfite sequencing reads to a masked reference genome and the base pair specific methylation calls were extracted
Methylation calls overlapping padlock probe arms were removed using Bedtools
Methylation calls were only considered for cytosines with at least a 30× read depth. For technical replicate samples, methylation calls and counts were averaged for each site. Sites with less than 70% of samples containing methylation calls and/or sites with all samples having a methylation call of 0 were removed from further analysis. Sites overlapping common SNPs in the population (minor allele frequency ≥ 0.05), as identified by the 1000 Genomes Project (phase 3 v5a 20130502 release for chr1-chr22, v1b 20130502 for chrX; all populations and European populations) were also removed from further analysis
We next explored the data using principal component analysis (PCA) of beta values defined as B = M / (M+U). PCA of all datasets was computed and sample projection onto the first two principal components was plotted, which served to identify outlying samples. Samples deviating from the center of either of the first two principal components by more than 3 standard deviations were deemed outliers and removed from further analysis. Next, the distribution of U and M read counts across experimental batches was used to determine whether sample cohort should be normalized. Normalized B values for appendix datasets were obtained from quantile normalized and rounded M and U read count matrices. Sites with stable DNA methylation calls (0%, 100%, and/or missing) in 50% or more of the samples were excluded from further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Each txt file contain the following information in order: chromosome #, genomic coordinate, strand, unmethylation count, methylation count, CHH/CHG/CG context of cytosine, exact sequence of the previous context

source_name: OFB

extract_protocol:
Genomic DNA was extracted using standard phenol-chloroform extraction methods from olfactory bulb tissue of PD patients and controls.
DNA methylation fine-mapping was performed using the bisulfite padlock probe technique. Bisulfite conversion of gDNA and purification was done using the EZ DNA Methylation-Lightning Kit (Zymo Research) and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For each sample, the bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng) at 55ºC for 20 h. Target regions flanked by the hybridized padlock probes were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). The non-targeted, non-circularized DNA was digested using exonuclease (Exonuclease I and III; New England Biolabs). The target circularized DNA was amplified using a common linker sequence within the padlock probe. Libraries were then PCR amplified, pooled in equimolar amounts, and purified by QIAquick Gel Extraction kit (Qiagen). Libraries were quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine

value: olfactory bulb

value: No

tag: group

value: PD

tag: age

value: M

tag: pmi


title: 4_Mice_rAAV a-syn: E2

value: a-syn


title: SNT_TS_Pn.rrbs.rep1

city: shanghai

first: Jin

last: Sun

department: life science and technology

country: China

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
RRBS reads were firstly processed using trim_galore (0.4.2) to trim adaptor and low-quality reads by parameters --fastqc --illumina --rrbs –paired, and then aligned to a combined genome with mm10 and lambda sequence using bsmap (1.3.2) by parameters -D C-CGG -s 12 -v 0.1 -R -r 0. The methylation level of each CpG was estimated using mcall (1.3.2) by default parameters. Only the CpGs with coverage >4 in replicates were retained for later analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include methylation level and coverage for each CpG sites

organism: Mus musculus

growth_protocol: We generated embryos from 3 different sources natural fertilization (NF), somatic nuclear transfer (NT), and somatic nuclear transfer with HDACi Scriptaid treatment (SNT)

extract_protocol: For the RRBS library, we digested nuclear proteins and extracted the DNA from the nuclei of samples. Then, we add unmethylated lambda DNA (Fermentas) and took a one-tube reaction, treating the DNA with MspI digestion (Fermentas, USA), end repair, dA tailing, adaptor ligation, and bisulfite conversion using MethylCode Bisulfite Conversion Kit (Invitrogen, USA, MECOV-50). We purified the converted libraries by Agencourt AMPure XP beads (Beckman A63881, USA) and amplified using two-round PCR enrichment. Only 200–500 bp DNA fragments were reserved for sequencing.

treatment_protocol: We transferred E4.5 blastocysts onto MMC-treated ICR mouse MEFs and firstly culture in TSC medium composed 70% FCM, 30% TSM and 1 x F4H medium. Then, we collected and disaggregated outgrowths (100 μm) at 5–7 days later, and changed the TSC medium to 1.5 x F4H instead. TSC-likely colony emerged at day 12~15. Then, the medium was changed back to 1 x F4H medium.

tag: strain

tag: embryo source

value: nuclear transfer with HDACi

tag: cell type

value: TSC passage 3-4


title: SNT_TS_Pn.rrbs.rep2


title: SNT_TS_P1.rrbs.rep4

value: TSC likely colony at day 12-15


title: 4_Mice_rAAV a-syn: E1


title: SNT_TS_P1.rrbs.rep3


title: 4_Mice_rAAV a-syn: D10


title: 4_Mice_rAAV a-syn: D12


title: SNT_TS_P1.rrbs.rep2


title: SNT_TS_P1.rrbs.rep1


title: ex_vivo_tDCs_2

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

library_source: transcriptomic

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq)
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization. Cook distance cutoff filter disabled
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; htseqcounts*.rpkm files: CSV format with RPKM normalized read counts per gene;  DESeq2_genes_diffexp*.xls: XLS files with differentially expressed genes

molecule: total RNA

source_name: thymus

growth_protocol: RTOCs were generated from single-cell suspensions of thymi isolated from E14.5 to E16.5 fetuses of Foxp3hCD2 reporter mice (BALB/c background) and 0.15x106 sorted sp‑DCs or t‑DCs were added to the 0.65x106 cells from the fetal thymi before pelleting.

extract_protocol: Sp‑DCs and t‑DCs were isolated from 4-8 weeks old CD45.1xBALB/c mice by fluorescence-activated cell sorting. T‑DCs were sorted as CD49b-F4/80-CD90.2-CD45.1+CD11chi cells and sp‑DCs were sorted as CD49b-F4/80-CD3-CD19-CD45.1+CD11chi. Total RNA was isolated using the RNeasy® Mini Kit (Qiagen).

value: DCs

tag: isolation method

value: ex vivo isolated


title: SNT_outgrowth.rrbs.rep8

value: outgrowths derived in vitro at day 5-7


title: 4_Mice_rAAV a-syn: D9


title: 4_Mice_rAAV a-syn: D7


title: 4_Mice_rAAV a-syn: D8


title: 4_Mice_rAAV a-syn: D11


title: 4_Mice_rAAV a-syn: D5


title: 4_Mice_rAAV a-syn: D6


title: SNT_outgrowth.rrbs.rep5


title: SNT_outgrowth.rrbs.rep3


title: 3_Mics_DSS: E9

growth_protocol: We profiled epigenetic changes in the ALP in mice that were exposed to experimental colitis. We examined wild-type mice and a mouse model of α-synucleinopathy: hemizygous Tg(Thy1-SNCA*A30P)18Pjk mice (A30P α-syn). A30P α-syn mice express human α-syn with the A30P mutation under the neuron selective Thy1 promoter. A30P α-syn mice have been maintained on a C57BL/6 background for more than 10 generations.

extract_protocol:
Mice were anesthetized with pentobarbital and trans-cardially perfused with PBS before tissue collection. Genomic DNA was extracted using standard phenol-chloroform extraction methods from cecal patch of wild-type and A30P α-syn mice chronically treated with either DSS or water.
DNA methylation fine-mapping was performed using the bisulfite padlock probe technique. Bisulfite conversion of gDNA and purification was done using the EZ DNA Methylation-Lightning Kit (Zymo Research) and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For each sample, the bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng) at 55ºC for 20 h. Target regions flanked by the hybridized padlock probes were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). The non-targeted, non-circularized DNA was digested using exonuclease (Exonuclease I and III; New England Biolabs). The target circularized DNA was amplified using a common linker sequence within the padlock probe. Libraries were then PCR amplified, pooled in equimolar amounts, and purified by QIAquick Gel Extraction kit (Qiagen). Libraries were quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine

treatment_protocol: Colitis was induced using dextran sulfate sodium (DSS), a widely used model of ulcerative colitis. At 3 months of age, wild-type and A30P α-syn mice were exposed to a chronic DSS paradigm, consisting of 4 cycles of increasing DSS concentration from 2.5% to 3.0% to 3.5% to 4%; 1 cycle comprises 5 days of DSS followed by 2 days of water (DSS: 160110, MP Biomedicals, LLC). Non-DSS groups were administered normal drinking water. Mice were then given a 4-week long recovery period during which they received normal drinking water, followed by tissue harvest. To the extent possible, littermates were used in the experiments.

tag: genotype

value: wt/wt

value: DSS


title: 3_Mics_DSS: E8

value: cecal patch

value: TG/wt


title: SNT_outgrowth.rrbs.rep6


title: 3_Mics_DSS: E6

value: m

value: Water


title: SNT_outgrowth.rrbs.rep4


title: SNT_outgrowth.rrbs.rep7


title: SNT_outgrowth.rrbs.rep1


title: SNT_outgrowth.rrbs.rep2


title: SNT_TE4.5.rrbs.rep4

value: E4.5 blastocysts trophoectoderm


title: SNT_TE4.5.rrbs.rep2


title: SNT_TE4.5.rrbs.rep3


title: 3_Mics_DSS: E5

value: Yes


title: 3_Mics_DSS: D4

value: No

value: f


title: 3_Mics_DSS: D3


title: 3_Mics_DSS: D2


title: SNT_TE3.5.rrbs.rep3

value: E3.5 blastocysts trophoectoderm


title: 3_Mics_DSS: D1


title: 3_Mics_DSS: C12


title: 3_Mics_DSS: C11


title: SNT_TE3.5.rrbs.rep2

value: nuclear transfer with HDACi


title: SNT_TE3.5.rrbs.rep1


title: NT_TS_P1.rrbs.rep2

value: nuclear transfer


title: NT_TS_Pn.rrbs.rep1

value: TSC passage 3-4


title: 3_Mics_DSS: C9


title: 3_Mics_DSS: E7


title: 3_Mics_DSS: C10


title: NT_outgrowth.rrbs.rep6


title: 3_Mics_DSS: C8


title: 3_Mics_DSS: C6


title: NT_TS_P1.rrbs.rep1

value: TSC likely colony at day 12-15


title: 3_Mics_DSS: C4


title: NT_outgrowth.rrbs.rep5


title: NT_outgrowth.rrbs.rep4


title: NT_outgrowth.rrbs.rep3


title: NT_outgrowth.rrbs.rep1


title: 3_Mics_DSS: C2


title: NT_outgrowth.rrbs.rep2


title: 3_Mics_DSS: C3


title: 3_Mics_DSS: C1


title: SNT_TE4.5.rrbs.rep1


title: NT_TE4.5.rrbs.rep2


title: 3_Mics_DSS: C7


title: 3_Mics_DSS: B12


title: NT_outgrowth.rrbs.rep7


title: NT_TE4.5.rrbs.rep1


title: 3_Mics_DSS: C5


title: 3_Mics_DSS: B10


title: NT_TE3.5.rrbs.rep2


title: NT_TE3.5.rrbs.rep3


title: 3_Mics_DSS: B8


title: NT_TE3.5.rrbs.rep1


title: 3_Mics_DSS: B7


title: 3_Mics_DSS: B9


title: NF_ICM.rrbs.rep1

value: natural fertilization

value: E3.5 blastocysts inner cell mass


title: 3_Mics_DSS: B5

value: wt/wt


title: NF_ICM.rrbs.rep3


title: 3_Mics_DSS: B3

value: DSS


title: NT_TE4.5.rrbs.rep3


title: NF_EXE.rrbs.rep3

value: E6.5 extraembryonic ectoderm


title: NF_ICM.rrbs.rep2


title: 3_Mics_DSS: B2

value: cecal patch

value: TG/wt


title: NF_EXE.rrbs.rep1


title: 3_Mics_DSS: B1

value: Water


title: 3_Mics_DSS: A12


title: 3_Mics_DSS: B11


title: NF_EXE.rrbs.rep2


title: NF_EPI.rrbs.rep2

value: E6.5 epiblast


title: 3_Mics_DSS: A10

value: m


title: 3_Mics_DSS: A11

value: Yes


title: 3_Mics_DSS: A9

value: No


title: NF_TS_Pn.rrbs.rep1


title: 3_Mics_DSS: A8


title: NF_TS_P1.rrbs.rep11


title: 3_Mics_DSS: A7


title: 3_Mics_DSS: B6


title: NF_TS_P1.rrbs.rep10


title: 3_Mics_DSS: B4


title: NF_EXE.rrbs.rep4


title: NF_TS_P1.rrbs.rep9


title: 3_Mics_DSS: A6


title: 3_Mics_DSS: A5


title: NF_TS_P1.rrbs.rep7


title: NF_TS_P1.rrbs.rep8


title: 3_Mics_DSS: A4


title: 3_Mics_DSS: A2


title: NF_TS_P1.rrbs.rep5


title: 3_Mics_DSS: A1


title: 3_Mics_DSS: A3


title: NF_TS_P1.rrbs.rep4


title: NF_TS_P1.rrbs.rep3


title: 1_PD_Appendix: 3649-R1

source_name: Appendix

extract_protocol:
Genomic DNA was extracted using standard phenol-chloroform extraction methods from appendix tissue of PD patients and controls.
DNA methylation fine-mapping was performed using the bisulfite padlock probe technique. Bisulfite conversion of gDNA and purification was done using the EZ DNA Methylation-Lightning Kit (Zymo Research) and quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). For each sample, the bisulfite-converted DNA (200 ng) was hybridized to the padlock probes (1.5 ng) at 55ºC for 20 h. Target regions flanked by the hybridized padlock probes were extended using PfuTurbo Cx (Agilent Technologies) and circularization was completed using Ampligase (Epicentre). The non-targeted, non-circularized DNA was digested using exonuclease (Exonuclease I and III; New England Biolabs). The target circularized DNA was amplified using a common linker sequence within the padlock probe. Libraries were then PCR amplified, pooled in equimolar amounts, and purified by QIAquick Gel Extraction kit (Qiagen). Libraries were quantified by qPCR (Kapa Biosystems) on a ViiA 7 Real-time PCR system (Applied Biosystems). Next-generation sequencing of the libraries was performed on an Illumina HiSeq 2500 machine

value: Appendix

value: M

tag: diagnosis

value: Control

tag: batch

tag: aginganalysis

tag: pdvscontrolanalysis


title: NF_TS_Pn.rrbs.rep2

value: TSC passage 3-4


title: NF_EPI.rrbs.rep1


title: 1_PD_Appendix: 3649-R2

tag: tissue


title: NF_TS_P1.rrbs.rep1

value: TSC likely colony at day 12-15


title: 1_PD_Appendix: 3649

tag: subject id


title: NF_outgrowth.rrbs.rep7

value: natural fertilization

value: outgrowths derived in vitro at day 5-7


title: 1_PD_Appendix: 3656

tag: replicate

value: F

value: PD


title: 1_PD_Appendix: 3645

tag: Sex


title: NF_outgrowth.rrbs.rep6


title: NF_outgrowth.rrbs.rep5


title: NF_outgrowth.rrbs.rep4


title: NF_outgrowth.rrbs.rep3


title: 1_PD_Appendix: 3628


title: 1_PD_Appendix: 3610


title: NF_TS_P1.rrbs.rep6


title: 1_PD_Appendix: 3623


title: 1_PD_Appendix: 3625


title: NF_outgrowth.rrbs.rep2


title: NF_outgrowth.rrbs.rep1


title: 1_PD_Appendix: 3599


title: NF_TE4.5.rrbs.rep2

value: E4.5 blastocysts trophoectoderm


title: 1_PD_Appendix: G9


title: 1_PD_Appendix: 3544


title: 1_PD_Appendix: G8


title: NF_TE3.5.rrbs.rep3

value: E3.5 blastocysts trophoectoderm


title: NF_TE4.5.rrbs.rep1


title: 1_PD_Appendix: G7


title: NF_TS_P1.rrbs.rep2


title: 1_PD_Appendix: G6


title: CC.rrbs.rep3

value: donor (cumulus cells)


title: NF_TE3.5.rrbs.rep1


title: 1_PD_Appendix: G5


title: CC.rrbs.rep2


title: SNT_TS_Pn_rep3

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were removed adaptor and low-quality reads using cutadapt (1.11) by parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 50 -q 20, and then aligned to mm10 transcript genome using STAR (020201) by parameters --readFilesCommand zcat --runThreadN 8 --outFilterMismatchNmax 3. Uniquely mapped reads were subsequently assembled into known transcripts (iGenome mm10) with featureCounts (v1.6.1).  The reads count of genes were normalized by library size using edgeR and differential expressed genes were defined by the cutoff log2foldchange >2 and padj<0.01 using by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include log2(CPM) of all samples

extract_protocol:
For RNA-seq, we performed reverse transcription directly on the cytoplasmic lysate and used terminal deoxynucleotidyl transferase to add a poly(A) tail to the 3' end of the first-strand cDNAs. We amplified the total cDNA library by 18-20 cycles. Afterward, we fragmented the amplified cDNA by Covaris sonicator (Covaris S220, USA) and used the TruSeq Library Prep Pooling kit (Illumina 15042173, USA) to generate the RNA sequence libraries.
Illumina HiSeq 2500

value: nuclear transfer with HDACi


title: 1_PD_Appendix: G2


title: 1_PD_Appendix: G1


title: SNT_TS_Pn_rep2


title: 1_PD_Appendix: 3604


title: 1_PD_Appendix: G4


title: SNT_TS_Pn_rep1


title: SNT_TS_P1_rep3


title: SNT_TS_P1_rep2


title: 1_PD_Appendix: G3


title: 1_PD_Appendix: F11


title: 1_PD_Appendix: F12


title: NF_TE3.5.rrbs.rep2


title: SNT_TS_P1_rep1


title: SNT_outgrowth_rep3


title: SNT_outgrowth_rep2


title: SNT_outgrowth_rep1


title: SNT_TE4.5_rep2


title: 1_PD_Appendix: F3


title: CC.rrbs.rep1


title: 1_PD_Appendix: F2


title: 1_PD_Appendix: F6


title: 5_OFB: OB_A14_PD3518

value: olfactory bulb


title: 1_PD_Appendix: F5


title: 1_PD_Appendix: F10


title: 1_PD_Appendix: E11


title: 1_PD_Appendix: F1


title: SNT_TE3.5_rep1


title: 1_PD_Appendix: E10


title: SNT_TE3.5_rep2


title: SNT_TE3.5_rep4


title: SNT_TE3.5_rep3


title: NT_TS_Pn_rep4

value: nuclear transfer


title: 1_PD_Appendix: E9

value: Yes


title: 1_PD_Appendix: F9


title: 1_PD_Appendix: F7

value: No


title: NT_TS_Pn_rep3


title: 1_PD_Appendix: E8

value: Appendix


title: SNT_TE4.5_rep1


title: 1_PD_Appendix: E7

value: M


title: 1_PD_Appendix: E6

value: Control


title: NT_TS_Pn_rep2

value: TSC passage 3-4


title: NT_TS_Pn_rep1


title: NT_TS_P1_rep3

value: TSC likely colony at day 12-15


title: 1_PD_Appendix: E5


title: 1_PD_Appendix: E4


title: NT_TS_P1_rep2


title: NT_outgrowth_rep4


title: NT_TS_P1_rep1


title: 1_PD_Appendix: E3


title: 1_PD_Appendix: E2


title: NT_TS_Pn_rep5


title: NT_outgrowth_rep3


title: NT_TE4.5_rep2


title: NT_outgrowth_rep2


title: NT_outgrowth_rep1


title: 1_PD_Appendix: D10


title: 1_PD_Appendix: D12


title: 1_PD_Appendix: D11


title: NT_TE3.5_rep3


title: NT_TE3.5_rep2


title: 1_PD_Appendix: D9


title: NT_TE3.5_rep1


title: 1_PD_Appendix: D6


title: 1_PD_Appendix: D5


title: NF_EXE_rep5

value: E6.5 extraembryonic ectoderm

value: natural fertilization


title: 1_PD_Appendix: D4


title: NF_EXE_rep4


title: 1_PD_Appendix: D2

value: F


title: NF_EXE_rep2


title: NF_EXE_rep3


title: 1_PD_Appendix: C12


title: NF_EXE_rep1


title: 1_PD_Appendix: D1


title: NT_TE4.5_rep1


title: NF_TS_Pn_rep3


title: 1_PD_Appendix: C11


title: 1_PD_Appendix: D8


title: NF_TS_Pn_rep2


title: 1_PD_Appendix: D7


title: 1_PD_Appendix: C8


title: NF_TS_Pn_rep1


title: 1_PD_Appendix: C10


title: 1_PD_Appendix: C9


title: NF_TS_P1_rep3


title: 1_PD_Appendix: C7


title: 1_PD_Appendix: D3


title: 1_PD_Appendix: C6

value: PD


title: NF_TS_P1_rep1


title: NF_TS_P1_rep2


title: NF_outgrowth_rep5

value: outgrowths derived in vitro at day 5-7


title: 1_PD_Appendix: C5


title: 1_PD_Appendix: F4


title: NF_outgrowth_rep4


title: 1_PD_Appendix: C4


title: 1_PD_Appendix: C3


title: 1_PD_Appendix: C2


title: NF_outgrowth_rep3


title: NF_outgrowth_rep2


title: NF_TS_P1_rep4


title: NF_outgrowth_rep1


title: 1_PD_Appendix: B11


title: NF_TE4.5_rep4

value: E4.5 blastocyst trophoectoderm


title: NF_TE4.5_rep5


title: 1_PD_Appendix: B12


title: 1_PD_Appendix: B10


title: NF_TE4.5_rep3


title: 1_PD_Appendix: B9


title: NF_TE4.5_rep2


title: 1_PD_Appendix: B7


title: 1_PD_Appendix: B5


title: NF_TE3.5_rep2

value: E3.5 blastocysts trophoectoderm


title: 1_PD_Appendix: B4


title: NF_TE4.5_rep1


title: NF_TE3.5_rep3


title: NF_TE3.5_rep4


title: 1_PD_Appendix: B3


title: 1_PD_Appendix: B2


title: 1_PD_Appendix: B8


title: 1_PD_Appendix: A12


title: 1_PD_Appendix: C1


title: splenic B cells, WT3

city: La Jolla

first: Numana

last: Bhat

email: numana.bhat@gmail.com, nbhat@sbp.edu

state: California

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys  Medical Discovery Institute

description: WT or Regnase-1+/+ hCD20TamCre

data_processing:
Casava1.7 software for basecalling
Sequenced reads trimmed to minimum 35bp
mapped to mm10 reference genome using tophat
RefSeq annotation from UCSC genome browser
RPKM calculated after alignment to mm10
obtained HTSeq counts; DESeq2 normalization
Genome_build: mm10
Supplementary_files_format_and_content: Htseq counts of all samples

source_name: Spleen

extract_protocol:
splenic B cells were isolated by negative selection by CD43 beads, cells were lysed with the TRIzol reagent from Invitrogen and RNA was isolated using chloroform and isopropanol. RNA was cleaned with ethanol, and passed through the Qiagen RNA clean-up kit for further purification.
RNA sequencing was done at the La Jolla Institute of Immunology sequencing core facility using Hiseq2500 technology from Illumina.

value: Spleen

value: primary splenic B cells

tag: developmental stage

value: naive

tag: treatment

value: untreated

value: wild type


title: splenic B cells, WT4

description: WT or Regnase-1+/+ hCD20TamCre


title: splenic B cells, WT3_BCR

description: WT-BCR or BCR-Regnase-1+/+ hCD20TamCre

value: BCR stimulated

value: anti-IgM F(ab')2 treated for 4 hours


title: 1_PD_Appendix: A11

value: Appendix

value: No

tag: age

value: M

value: Yes


title: splenic B cells, WT2_BCR

description: WT-BCR or BCR-Regnase-1+/+ hCD20TamCre


title: 1_PD_Appendix: A10

tag: pmi


title: splenic B cells, WT2

description: WT or Regnase-1+/+ hCD20TamCre


title: splenic B cells, WT1_BCR

description: WT-BCR or BCR-Regnase-1+/+ hCD20TamCre


title: 1_PD_Appendix: A8

value: Control


title: 1_PD_Appendix: B6

value: F


title: splenic B cells, WT1

description: WT or Regnase-1+/+ hCD20TamCre


title: 1_PD_Appendix: A6


title: 1_PD_Appendix: A7

value: PD


title: 1_PD_Appendix: A9


title: splenic B cells, KO3

description: KO or Regnase-1f/f hCD20TamCre

value: Regnase-1 f/f


title: 1_PD_Appendix: A5


title: NF_TE3.5_rep1

tag: strain

value: natural fertilization


title: splenic B cells, KO3_BCR

description: KO-BCR or BCR-Regnase-1f/f hCD20TamCre


title: splenic B cells, KO2_BCR

description: KO-BCR or BCR-Regnase-1f/f hCD20TamCre


title: 1_PD_Appendix: A4


title: 1_PD_Appendix: A2


title: 1_PD_Appendix: A1


title: splenic B cells, KO1

description: KO or Regnase-1f/f hCD20TamCre


title: splenic B cells, KO1_BCR

description: KO-BCR or BCR-Regnase-1f/f hCD20TamCre


title: 1_PD_Appendix: A3


title: splenic B cells, KO2

description: KO or Regnase-1f/f hCD20TamCre


title: RDEBSCC70_TGFb1_rep3

city: Minneapolis

first: Jakub

last: Tolar

state: Minnesota

address: 2001 6th St SE

department: Pediatrics

institute: University of Minnesota - Twin Cities

data_processing:
FastQC v0.11.8 - generates sequence quality plots
Trimmomatic v0.39 - removes sequence adapters and low quality bases
FastQC v0.11.8 - generates sequence quality plots for filtered fastq files
HISAT2 v2.1.0 - aligns reads to the genome, creating a bam file that is then sorted and indexed
Picard v2.18.10 - calculates insert size metrics
SubRead v1.6.2 - featureCounts program in SubRead package is used to generate a transcript abundance file
Cufflinks v2.2.1 - Cuffquant program in the Cufflinks package is used to generate a .cxb transcript abundance file
Cufflinks v2.2.1 - Cuffnorm program in the Cufflinks package is used to generate FPKM data
Genome_build: hg38
Supplementary_files_format_and_content: xlsx spreadsheet in matrix form, where each row corresponds to a gene, each column corresponds to a sample, with raw read counts in the individual cells

source_name: cell line derived from cutaneous squamous cell carcinoma tumor in patient with recessive dystrophic epidermolysis bullosa

growth_protocol: 500,000 cells plated in 10cm dishes with EpiLife media (see above for specific experimental treatments) for 24 hours

extract_protocol:
Total RNA was harvested after 24 hours in culture using the RNeasy Micro Kit (Qiagen). RNA concentration and quality were determined using RiboGreen quantitation and Agilent 2100 Bioanalyzer
Libraries were prepared using the Illumina TruSeq Stranded mRNA LT kit. Libraries were analyzed using PicoGreen, DNA Agilent, and KAPA to determine concentration, size, and functionality

treatment_protocol: EpiLife Medium with 1% EpiLife Defined Growth Supplement (EDGS) and 0.2% Gentamicin/Amphotericin solution (Gibco/Thermo Fisher Scientific)

tag: cell line number


title: RDEBSCC70_TGFb1+inhibitor_rep3

tag: cell type

value: cell line derived from cutaneous squamous cell carcinoma tumor in patient with recessive dystrophic epidermolysis bullosa

value: TGFb1 + inhibitor


title: RDEBSCC70_TGFb1_rep2


title: RDEBSCC70_TGFb1+inhibitor_rep2


title: RDEBSCC70_TGFb1+inhibitor_rep1


title: RDEBSCC70_TGFb1_rep1


title: RDEBSCC70_untreated2


title: RDEBSCC4_TGFb1+inhibitor_rep3


title: shh1-1_Ov_RNA_rep2

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Mapping: mRNA-seq reads were mapped to the TAIR10 reference genome using STAR (v2.5.0c) with the following options: “--outFilterMismatchNmax 2”, to allow 2 mismatches, and “--outFilterMultimapNmax 1”, to include only uniquely mapped reads. The sorted bam files were then used to generate Tag Directories using the HOMER makeTagDirectory script with the “-mis 2 and -unique” options and UCSC format tracks were generated using the makeUCSCfile script with the “tair10 -fragLength given and -style rnaseq” options.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: unfertilized ovules (Ov)

growth_protocol: Growth conditions and tissue collection for 15 day old rosettes (Rs) and 25 day old leaves (Lv) for all genotypes were as follows: seeds were sterilized with bleach and plated on half strength Linsmaier and Skoog medium (1/2 LS) supplemented with 1% agar. After three days stratification in the dark at 4 ℃, plants were grown in a Percival growth chamber (GCU-36L5) under 16h-light and 8h-dark cycle at 22 ℃ for 7 days and were then transplanted onto soil in a Salk greenhouse with long day conditions. At day 15 and day 25 of total growth, rosette tissue (whole seedling without roots) or the first and second true leaves (without petioles) were collected from ~45 plants as the rosette (Rs) and leaf (Lv) samples, respectively.  These samples were immediately frozen in liquid nitrogen, and kept at -80 °C until use. Growth conditions and tissue collection for mature, unfertilized ovules (Ov) were as follows: seeds were grown on soil in a Salk greenhouse with long day conditions and un-opened flower buds (stage 10-12) were dissected using tweezers to obtain carpels. The carpels were then fixed on a glass slide with double-side tape and opened using dissection microscope with a straight sewing pin.  The ovules were collected with the vacuum-based micro-aspiration device as detailed below. After collection, ovules for RNA extraction were quickly mixed with 100 µL Trizol (Invitrogen, Cat# 15596018), flash frozen in liquid nitrogen and preserved at -80 ℃ until use, while ovules for DNA preparation were flash frozen in liquid nitrogen and preserved at -80 ℃ without Trizol. For each genotype, > 300 carpels were dissected and over 10,000 ovules were collected.

extract_protocol:
Total RNA from rosettes and leaf tissue was isolated using the Quick-RNA MiniPrep kit (Zymo Research, Cat# R1055), while total RNA from ovules was isolated using the Direct-zol RNA Microprep Kits (Zymo Research, Cat# R2061).
1.0 μg total RNA (0.1-0.5 μg for ovule tissue) was used to generate mRNA-seq libraries using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Cat# E7775). Sera-Mag Magnetic SpeedBeads (Thermo Scientific, Cat# 65152105050250) were used for all size selection and clean-up steps and the resulting libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

tag: ecotype

value: Columbia

tag: tissues

value: unfertilized ovules (Ov)


title: nrpd1-4_Ov_RNA_rep1

tag: genotype


title: shh1-1_Ov_RNA_rep1


title: RDEBSCC4_TGFb1+inhibitor_rep1


title: RDEBSCC70_untreated3

value: untreated


title: RDEBSCC4_TGFb1+inhibitor_rep2


title: nrpd1-4_Ov_RNA_rep2


title: RDEBSCC4_TGFb1_rep3


title: clsy1-7_2-2_3-1_4-1_Ov_RNA_rep2


title: RDEBSCC4_TGFb1_rep2


title: clsy3-1_4-1_Ov_RNA_rep2


title: RDEBSCC4_untreated3


title: RDEBSCC4_untreated2


title: clsy1-7_2-2_3-1_4-1_Ov_RNA_rep1


title: RDEBSCC4_untreated1


title: RDEBSCC4_TGFb1_rep1


title: clsy1-7_2-2_Ov_RNA_rep2


title: clsy1-7_2-2_Ov_RNA_rep1


title: clsy3-1_4-1_Ov_RNA_rep1


title: clsy4-1_Ov_RNA_rep2


title: RDEBSCC2_TGFb1+inhibitor_rep1


title: RDEBSCC2_TGFb1+inhibitor_rep3


title: clsy3-1_Ov_RNA_rep2


title: clsy4-1_Ov_RNA_rep1


title: RDEBSCC2_TGFb1_rep3


title: RDEBSCC70_untreated1


title: RDEBSCC2_TGFb1_rep1


title: clsy3-1_Ov_RNA_rep1


title: clsy2-2_Ov_RNA_rep4


title: clsy2-2_Ov_RNA_rep3


title: RDEBSCC2_untreated_rep2


title: RDEBSCC2_untreated_rep3


title: RDEBSCC2_untreated_rep1


title: WT_3_Ov_RNA_rep2

value: wild-type


title: MUHT35_2: Mutant  HvMADS1 at high temperature during W3.5 replicate 2

city: Shanghai

last: Shi

address: 800 Dongchuan Rd

department: Life Science and technology Department

institute: Shanghai Jiaotong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Morex genome using Hisat2 with the highest alignment rate and mismatch is set to 2.
HTSeq software was used to analyze the gene expression levels in this experiment, using the union mode.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a custom script.
Genome_build: Hordeum vulgare subsp. vulgare (domesticated barley)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Hordeum vulgare

source_name: inflorescence

growth_protocol: Barley grains were set in cocopeat soil, germinated, and grown at 15 °C light, 10 °C dark conditions (standard temperature) with a 16 h photoperiod at 50% humidity in growth chambers. In all experiments, night (dark) temperature was 5 °C below the day (light) temperature.

extract_protocol:
Total RNA was extracted from 15–20 spikes for each of three biological replicates using TRIzol (Invitrogen) and purified using a RNeasy Micro Kit (Qiagen, Germany) following manufacturer’s instructions.
Library preparation was performed using 1 μg of high integrity total RNA (RIN > 8) using the TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2101 and RS-122-2001), following manufacturer’s instructions

treatment_protocol: low temperature treament is controlled at 15 ℃/10 ℃  (day/night), while high temperature treatment is controlled at 25 ℃/20 ℃ (day/night)

value: Golden Promise

value: inflorescence

value: HvMADS1 mutant

value: high temperature treatment(replicate 2)


title: MUHT35_3: Mutant  HvMADS1 at high temperature during W3.5 replicate 3

value: high temperature treatment(replicate 3)


title: clsy1-7_Ov_RNA_rep1


title: clsy1-7_Ov_RNA_rep2


title: WT_2_Ov_RNA_rep4


title: MUHT25_2: Mutant  HvMADS1 at high temperature during W2.5 replicate 2


title: WT_3_Ov_RNA_rep1


title: MUHT25_3: Mutant  HvMADS1 at high temperature during W2.5 replicate 3


title: MUHT25_1: Mutant  HvMADS1 at high temperature during W2.5 replicate 1

value: high temperature treatment(replicate 1)


title: MUHT35_1: Mutant  HvMADS1 at high temperature during W3.5 replicate 1


title: GPHT35_1: WT at  high temperature during W3.5 replicate 1

value: WT


title: WT_2_Ov_RNA_rep3


title: GPHT35_2: WT at  high temperature during W3.5 replicate 2


title: WT_2_Ov_RNA_rep2


title: GPHT25_2: WT at  high temperature during W2.5 replicate 2


title: GPHT25_3: WT at  high temperature during W2.5 replicate 3


title: 1_PD_Appendix: E12

value: Appendix

value: No

value: M

tag: diagnosis

value: Control

tag: batch

value: Yes


title: Stage2_2

city: Guangzhou

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mulberry transcriptome (NCBI accession no. SRP026705)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Morus alba var. atropurpurea

source_name: fruit

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

tag: disease

value: treated


title: GPHT25_1: WT at  high temperature during W2.5 replicate 1

tag: tissue


title: Stage2_1

department: The Sericulture and Agri-Food Research Institute

institute: Guangdong Academy of Agricultural Sciences


title: WT_2_Ov_RNA_rep1

value: Columbia


title: Stage1_2


title: MULT35_3: Mutant  HvMADS1 at low temperature during W3.5 replicate 3

value: low temperature treatment(replicate 3)


title: MULT35_2: Mutant  HvMADS1 at low temperature during W3.5 replicate 2

value: low temperature treatment(replicate 2)


title: Stage1_1


title: WT_1_Ov_RNA_rep2

value: unfertilized ovules (Ov)

value: wild-type


title: HuCCT1-KO 1

type: RNA

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: ARID1A-knockout human cholangiocarcinoma cell line HuCCT1

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

label: biotin

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Human cholangiocarcinoma cell line HuCCT1 was purchased from the RIKEN CELL Bank, and then grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. Oligoes targeting ARID1A (5'-TGAGCGAGACTGAGCAACAC-3') were cloned into the lentiCRISPR v2 vector, and lentivirus was produced from Lenti-X 293T cells (TaKaRa) were transfected with the vector by using polyethyenimine for lentivirus production. Cells were infected with the lentivirus, and then treated with puromycin (Thermo Fisher Scientific). ARID1A-konckout clones were obtained by limiting dilution.

tag: cancer

value: Cholangiocarcinoma

tag: cell line


title: GPHT35_3: WT at  high temperature during W3.5 replicate 3

value: Golden Promise

value: inflorescence


title: HuCCT1-WT 2

description: ARID1A wild-type human cholangiocarcinoma cell line HuCCT1


title: HuCCT1-KO 2

source_name: ARID1A-knockout human cholangiocarcinoma cell line HuCCT1


title: HuCCT1-WT 1

source_name: ARID1A wild-type human cholangiocarcinoma cell line HuCCT1


title: MULT25_3: Mutant  HvMADS1 at low temperature during W2.5 replicate 3

value: HvMADS1 mutant


title: Control_2

value: non-treated


title: Control_1


title: WT_1_Ov_RNA_rep1


title: nrpd1-4_Lv_RNA_rep4

source_name: 25 day old leaves (Lv)

value: 25 day old leaves (Lv)


title: GPLT35_3: WT at  low temperature during W3.5 replicate 3

value: WT


title: MULT25_2: Mutant  HvMADS1 at low temperature during W2.5 replicate 2


title: MULT25_1: Mutant  HvMADS1 at low temperature during W2.5 replicate 1

value: low temperature treatment(replicate 1)


title: GPLT35_2: WT at  low temperature during W3.5 replicate 2


title: nrpd1-4_Lv_RNA_rep3


title: GPLT35_1: WT at  low temperature during W3.5 replicate 1


title: GPLT25_3: WT at  low temperature during W2.5 replicate 3


title: IAA_IN_6h_YKR1895

city: Planegg-Martinsried

first: Martina

last: Peritore

state: Bayern

address: Am Klopferspitz 18

institute: MPIB

data_processing:
Sequecing reads were mapped to the S. cerevisiae genome using Bowtie2  (version 2.2.9) with default parameters
Multiple mapping reads were filtered with SAMtools.
Genome_build: LYZE00000000.1, sacCer3
Supplementary_files_format_and_content: All files were generated with R. Bed files contain aligned reads, bedGraph files represent read coverage

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown in YP-media containing 2% raffinose at 30°C. Exponentially  growing cells (OD600 0.5-0.7) were synchronized in M phase with 5 μg/ml  nocodazole for 2-3 hours. Cell cycle arrest was assessed via microscopy and  DNA content measured by flow cytometry.

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to  fragments of 200-500 bp. 40% of the chromatin extract was used for  immunoprecipitation, the purified complexes were treated with proteinase K and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol  precipitation.
Strand-specific ChIP-seq libraries were prepared starting from 1-3 ng of DNA using Accel-NGS® 1S Plus Library Kit following manufacturer instructions and 10-12 cycles were used for library amplification. Clean-up steps were performed with SPRIselect beads.

treatment_protocol: Site-specific DSBs were introduced  inducing the HO endonuclease or the AsiSI restriction enzyme via the galactose  promoter, adding galactose to the cultures to a final concentration of 2%. Cells  were crosslinked at the indicated time points with 1% formaldehyde for 16  minutes at room temperature and the reaction quenched with glycine (final concentration 400 mM). Cells were harvested by centrifugation (3500xg at  4°C), washed with cold PBS and the pellet flash frozen in liquid nitrogen.

tag: genome used for alignment


title: nrpd1-4_Lv_RNA_rep1


title: GPLT25_1: WT at  low temperature during W2.5 replicate 1

value: low temperature  treatment(replicate 1)


title: IAA_IN_4h_YKR1895


title: MULT35_1: Mutant  HvMADS1 at low temperature during W3.5 replicate 1


title: shh1-1_Lv_RNA_rep2


title: SMAskeletalmuscle3

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

data_processing:
Raw paired-end sequencing reads were aligned to the mouse reference genome (mm10) using MapSplice version 2.2.1.
Gene read counts against UCSC mouse gene models (obtained on February 21, 2016) were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s no
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: sample_gene_counts.txt – tab-delimited text file of gene raw counts for all samples
Supplementary_files_format_and_content: sample_gene_normalized_counts.txt – tab-delimited text file of gene normalized counts (DESeq2 size factor normalization) for all samples

extract_protocol:
Total RNA from skeletal muscle tissue was isolated using the RNeasy Fibrous Mini Kit from Qiagen.  RNA integrity was assessed using the AATI Fragment Analyzer for RIN > 7.
Total RNA input of 200 ng was used for library preparation using the TruSeq Stranded mRNA Library Preparation Kit.  The sequencing libraries were quantified by quantitative PCR using a KAPA Library Quantification Kit for NGS (Kapa Biosystems) on a Roche Light Cycler 480 Instrument II and the size distribution was assessed with a Fragment Analyzer.
The sequencing libraries were pooled and sequenced on a HiSeq 3000 Sequencer (Illumina) after clustering on a cBot2 (Illumina) and using a HiSeq 3000/4000 PE Cluster Kit and SBS Kit (150) cycles with paired-end reads of 75 bp in length.

tag: strain background

value: FVB/N

tag: genotype/variation

value: Spinal motor atrophy mice (SMN delta 7 mice)

value: hindlimb skeletal muscle


title: SMAskeletalmuscle4


title: SMAskeletalmuscle2


title: WTskeletalmuscle4

value: wild type


title: IAA_IN_2h_YKR1895


title: WTskeletalmuscle5


title: SMAskeletalmuscle1


title: IAA_IN_0h_YKR1895


title: CTR_IN_4h_YKR1895


title: WTskeletalmuscle2


title: WTskeletalmuscle3


title: CTR_IN_2h_YKR1895


title: shh1-1_Lv_RNA_rep1

value: Columbia


title: nrpd1-4_Lv_RNA_rep2


title: wt Low rep2

city: Los Angeles

first: Haruko

last: Nakano

address: 615 Charles E. Young Dr. South

department: MCDB

institute: University of California, Los Angele

description:
MY_Ht_9_Low_510
wild type cardiomyocyte with lower mitotracker signal

data_processing:
Raw sequencing reads were assessed for quality using FastQC, then low-quality bases with a Phred quality value lower than 20 were trimmed off the read ends.
The RNA Sequencing reads were mapped to mouse genome assembly UCSC mm10 using the HISAT2 with default settings. UCSC annotation release mm10 was used to identify genes for feature counting.
Read counts for genes were determined as counts mapped to the union of all exons for all transcript isoforms of a given gene using HTSeq.
Differential expression analysis and generation of the corresponding data plots were performed using DESeq2 using default settings.
NA
Genome_build: mouse genome assembly UCSC mm10
Supplementary_files_format_and_content: gene IDs and read counts in tabular file

source_name: wt Low_heart

extract_protocol:
heart tiussue was dissected, flash frozen in liquid nitrogen, collected in Tri-reagent.  RNA was extracted with Qiagen kit
Illumina HiSeq mRNA kit

tag: age

value: Postnatal Day 1

value: Heart

value: cardiomyocyte


title: GPLT25_2: WT at  low temperature during W2.5 replicate 2

tag: treatment

value: low temperature treatment(replicate 2)


title: wt Low rep1

description:
MY_Ht_9_Low_59
wild type cardiomyocyte with lower mitotracker signal


title: clsy1-7_2-2_3-1_4-1_Lv_RNA_rep1


title: Glut1 O/E Low rep3

description:
G1MY_Ht_5_Low
Glut1 O/E cardiomyocyte with lower mitotracker signal

source_name: Glut1 O/E Low_heart

value: aMHC-hGLUT1tg;aMHC-Cre tg; R26+/YFP reporter


title: IAA_IN_6h_YKR1894

tag: strain


title: Glut1 O/E Low rep2

description:
G1MY_Ht_4_Low
Glut1 O/E cardiomyocyte with lower mitotracker signal


title: CTR_IN_6h_YKR1895


title: IAA_IN_4h_YKR1894


title: clsy1-7_2-2_3-1_4-1_Lv_RNA_rep4


title: clsy3-1_4-1_Lv_RNA_rep3


title: clsy1-7_2-2_3-1_4-1_Lv_RNA_rep3


title: wt High rep1

description:
MY_Ht_9_High_59
wild type cardiomyocyte with higher mitotracker signal

source_name: wt High_heart


title: Glut1 O/E High rep4

description:
G1MY_Ht_8_High
Glut1 O/E cardiomyocyte with higher mitotracker signal

source_name: Glut1 O/E High_heart


title: wt High rep2

description:
MY_Ht_9_High_510
wild type cardiomyocyte with higher mitotracker signal


title: clsy1-7_2-2_Lv_RNA_rep2


title: IAA_IN_0h_YKR1894


title: WTskeletalmuscle1


title: Glut1 O/E High rep3

description:
G1MY_Ht_5_High
Glut1 O/E cardiomyocyte with higher mitotracker signal


title: Glut1 O/E High rep2

description:
G1MY_Ht_4_High
Glut1 O/E cardiomyocyte with higher mitotracker signal


title: IAA_IN_2h_YKR1894


title: Glut1 O/E High rep1

description:
G1MY_Ht_3_High
Glut1 O/E cardiomyocyte with higher mitotracker signal


title: CTR_IN_6h_YKR1894


title: clsy4-1_Lv_RNA_rep2


title: CTR_IN_0h_YKR1895


title: Glut1 O/E Low rep4

description:
G1MY_Ht_8_Low
Glut1 O/E cardiomyocyte with lower mitotracker signal


title: clsy3-1_4-1_Lv_RNA_rep4


title: clsy1-7_2-2_3-1_4-1_Lv_RNA_rep2


title: CTR_IN_4h_YKR1894


title: clsy4-1_Lv_RNA_rep1


title: day2 MCH-treat rep 2

city: Brockport

first: Rongkun

last: Shen

state: New York

address: 350 New Campus Dr

department: Biology

institute: SUNY Brockport

data_processing:
alignment by STAR v2.5.2a
Reads count by HTSEQ v0.11.2
filtering out low-expressed genes
DESeq2 v1.24.0
Genome_build: mm10
Supplementary_files_format_and_content: reads count data, Excel .xlsx file format

source_name: Cell culture

growth_protocol: Cell line standard culture protocol based on ATCC

extract_protocol:
RNA extracted using Rneasy Mini Kit(Qiagen)
WaferGen PrepXTM mRNA Strand-Specific Library Preparation Protocol (WaferGen Biosystems)
Illumina mulitplex indexed single-end

treatment_protocol: Insulin-induced differentiation and MCH treatment

value: 3T3-L1 preadipocytes


title: Glut1 O/E Low rep1

description:
G1MY_Ht_3_Low
Glut1 O/E cardiomyocyte with lower mitotracker signal


title: day2 rep 3


title: clsy3-1_Lv_RNA_rep2


title: CTR_IN_2h_YKR1894


title: day2 rep 2


title: CTR_IN_0h_YKR1894


title: day2 rep 1


title: day0 MCH-treat rep 2


title: day0 MCH-treat rep 3


title: clsy3-1_Lv_RNA_rep1


title: clsy2-2_Lv_RNA_rep2


title: day2 MCH-treat rep 3


title: clsy1-7_2-2_Lv_RNA_rep1


title: day0 MCH-treat rep 1


title: IN_6h_MNase2


title: day0 rep 2


title: IN_4h_MNase2


title: IN_2h_MNase2


title: clsy1-7_Lv_RNA_rep2


title: clsy2-2_Lv_RNA_rep1


title: day2 MCH-treat rep 1


title: clsy1-7_Lv_RNA_rep1


title: IN_6h_MNase1


title: WT_3_Lv_RNA_rep4

value: wild-type


title: IN_4h_MNase1


title: WT_3_Lv_RNA_rep3


title: IN_2h_MNase1


title: day0 rep 3


title: day0 rep 1


title: IN_0h_MNase1


title: lthsc_young_rep4

city: Augsburg

first: Stephen

last: Krämer

address: Alter Postweg 101

institute: University of Augsberg

data_processing:
Sequence alignment was performed using the workflow published in (Wang et al., Nat. Prot., 2013). The workflow was implemented as a Roddy Workflow (https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
Alignment was performed against the mm10 reference genome extended with the PhiX and lambda phage sequences. Briefly, before alignment, trimmomatic was used for adapter trimming and reads were in silico converted (C>T for the first read in the pair, G>A for the second).
Alignments of the individual libraries were performed against the concatenated C>T and G>A in silico converted reference genomes using a patched version of bwa mem with default parameters.
After alignment, reads were converted back to their original state. PCR duplicate removal was performed per library using Picard MarkDuplicates before merging reads from all libraries.
At each cytosine position, reads that maintain the cytosine status were considered methylated, and the reads that have cytosine converted to thymine were considered unmethylated.
Only bases with Phred-scaled quality score of ≥20 were considered. The first 9 bp of the second read and last 9 bp before the adapter in the first read were excluded from methylation calling.
The in silico conversion and methylation calling steps were performed using methylctools (https://github.com/hovestadt/methylCtools).
Genome_build: mm10
Supplementary_files_format_and_content: CpG methylation calls in MOABS-like format (PMID: 24565500) indicating in order i) #chrom, start, end: CpG coordinates as BED-like, i.e. 0-based, left-closed, right-open intervals; ii) ratio, totalC, methC, strand, next: average methylation, total number of reads, number of methylated reads, covered strands (B=both, +, -), next base (here: always G); iii) Plus, totalC, methC: number of reads on the plus strand; iv) Minus, totalC, methC: number of reads on the minus strand; v) snpScore: methylCtools-based SNP score (https://github.com/hovestadt/methylCtools)

extract_protocol:
LT-HSCs were sorted from lineage-depleted hematopoietic mononuclear cells (10,000 cells per replicate). Cells were cultured overnight without growth factors at 3% O2 and washed twice with PBS before genomic DNA was isolated using the QIAamp DNA Micro Kit (Qiagen, Germany) and polyacryl precipitation carrier (Molecular Research Center Inc., Cincinnati, OH, USA).
Tagmentation-based whole-genome bisulfite sequencing (T-WGBS) was performed as published in (Wang et al., Nat. Prot., 2013). We used 8-30 ng genomic mouse DNA as input.

value: young

value: primary murine hematopoietic stem cells

tag: cell subtype

value: LT-HSC (LSK CD34- Flk2- )

tag: molecule subtype

value: bisulfite converted genomic DNA


title: WT_3_Lv_RNA_rep2

tag: ecotype

value: 25 day old leaves (Lv)


title: WT_2_Lv_RNA_rep4

tag: tissues


title: WT_3_Lv_RNA_rep1

tag: genotype


title: WT_2_Lv_RNA_rep3


title: IN_0h_MNase2


title: HO_long_IN_4h


title: HO_long_IN_10h


title: HO_long_IN_0h


title: LNCaP siHDAC2 (rep2)

city: Heidelberg

first: Simone

last: Bauer

address: INF 460

institute: DKFZ

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LNCaP cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: LNCaP cells (ATCC) were cultivated according to the manufacurers instructions in RPMI 1640 full growth medium supplemented with 10 % FBS.

extract_protocol: RNA was extracted using the miRNasy Kit (Qiagen), including Dnase digest.

treatment_protocol: HDAC1 siRNA (Qiagen) or a scrambled control (AllStars siRNA, Qiagen) were transfected to a final concentration of 20 nM using Lipofectamine (Thermo Fisher Scientific) for 72 h.

value: LNCaP

value: prostate cancer cell line


title: LNCaP siHDAC3 (rep3)

description: replicate 3


title: LNCaP AllStars (rep1)

description: replicate 1


title: LNCaP AllStars (rep3)

description: replicate 3


title: lthsc_young_rep2

tag: cell type


title: lthsc_aged_rep1

value: aged


title: WT_2_Lv_RNA_rep2


title: lthsc_young_rep1


title: Nd1_replicate_2

city: Charlestown

first: Mark

middle: W.

last: Albers

state: MA

address: 114 16th Street, 2nd Fl

department: Neurology

institute: Massachusetts General Hospital

data_processing:
Sequenced reads were mapped to mm9 using Bowtie VN:0.12.5 by the Massachusetts General Hospital Nextgeneration Sequencing Core
Cuffcompare v1.3.0 software was used to track transcripts across experiments
Cuffdiff v1.3.0 software was used to generate a list of differential transcripts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: polyA RNA

source_name: mature olfactory sensory neurons

extract_protocol:
Freshly dissected olfactory epithelia were minced to ~1mm3 cubes with a razor blade on a glass slide on ice, and placed in a scintillation vial for dissociation. To isolate individual cells we used the Papain Dissociation System (catalog # LK003150, Worthington Biochemical Corporation, Lakewood, NJ), with the following modifications: 1) we incubated olfactory epithelia in papain solution for only 15 minutes versus the recommended time without an appreciable loss of cells, 2) after trituration, the cell suspension was filtered through a 40 μm mesh strainer (catalog # 352340, BD Bioscience, San Jose, CA). Dissociated cells were resuspended in 1ml ice-cold 1x Hank’s balanced salt solution (HBSS) (catalog # 14025 , Life Technologies, Grand Island NY) and then sorted. Each OE was prepared and sorted within 1.5 hours. Samples were visually inspected under a microscope.
Illumina TruSeq RNA sample preparation protocol

value: olfactory epithelium

value: 87 days old

value: Nd1+/-; OMP-IRES-tTA+/-:OMP-IRES-GFP+/-


title: lthsc_aged_rep3


title: lthsc_aged_rep5


title: Nd1_replicate_1

value: 212 days old


title: LNCaP siHDAC1 (rep1)

description: replicate 1


title: lthsc_aged_rep2


title: WT_2_Lv_RNA_rep1

value: Columbia


title: LNCaP AllStars (rep2)

description: replicate 2


title: Control_replicate_2

value: Nd1-/-; OMP-IRES-tTA+/-:OMP-IRES-GFP+/-


title: WT_1_Lv_RNA_rep4


title: lthsc_young_rep3


title: lthsc_aged_rep4


title: Control_replicate_1

value: Nd1+/-; OMP-IRES-tTA-/-:OMP-IRES-GFP+/-


title: HO_Dpb11_1_4h

tag: chip antibody

value: anti-FLAG beads (RRID:AB_2637089)


title: ESC_WT_FBS_repeat3

first: Jing

last: Huang

institute: National Cancer Institute

data_processing:
Bascalling: RTA 1.12.4.2
Alignment: Illumina Casava 1.8.2
FPKM was calculated using cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing FPKM for each sample

source_name: embryonic stem cells

growth_protocol: The 2i medium contains a base medium made from a 1:1 mix of DMEM/F12 (Life technologies, 11032-033) and Neurobasal medium (Life Technologies, 21103-049) including N2 supplement (Life Technologies, 17502-048, 1:100 dilution), B27 supplement (Life Technologies (Life Technologies, 17504-044, 1:50 dilution), 0.1 mM 2-mercaptoethanol, 1,000 units/mL of LIF, 3 µM of CHIR99021 (Cayman Chemical) and 1 µM of PD0325901 (Cayman Chemical). FBS medium contains high glucose DMEM (Cellgro, 10-013-CM), 15% FBS (Atlanta Biologicals, Inc.), 100 mM MEM nonessential amino acids (Life Technologies), 0.1 mM 2-mercaptoethanol (Sigma), 2 mM L-glutamine (Life Technologies), 1× penicillin/streptomycin (Life Technologies), and 1,000 units/mL of LIF (Gemini, 400-495).

extract_protocol:
Use Trizol
IlluminaTruSeq, protocol: FC-122-1001

treatment_protocol: No treatment

value: Wild type

tag: growth condition

value: grown in FBS containing medium

tag: repeat


title: HO_Dpb11_1_2h


title: ESC_WT_FBS_repeat2


title: HO_Dpb11_1_0h


title: WT_1_Lv_RNA_rep3

value: wild-type


title: ESC_WT_FBS_repeat1


title: ESC_KO_2i_repeat4

value: Tfcp2l1 knockout

value: grown in 2i medium


title: HO_Ddc1_1_4h


title: HO_Ddc1_1_2h


title: ESC_KO_2i_repeat2


title: ESC_WT_2i_repeat4


title: ESC_WT_2i_repeat3


title: ESC_KO_2i_repeat1


title: HO_Ddc1_1_0h


title: WT_1_Lv_RNA_rep1

value: 25 day old leaves (Lv)


title: WT_1_Lv_RNA_rep2


title: ESC_WT_2i_repeat1


title: ESC_WT_2i_repeat2


title: shh1-1_Rs_RNA_rep2

source_name: 15 day old aerial rosettes (Rs)

value: 15 day old aerial rosettes (Rs)


title: nrpd1-4_Rs_RNA_rep1


title: Lpcat3 KOMac 1

city: dijon

first: david

last: masson

address: 7 boulevard jeanne d'arc

country: France

institute: INSERM

description: no treatment

data_processing:
Libraries were sequenced with 2x150bp paired-end reads on an Illumina HiSeq.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Kupffer cells

growth_protocol: Mice fed a 16 week high fat diet (60% fat diet, D12492, Ssniff, Germany) and livers were digested using a two-step collagenase perfusion. Homogenate were centrifugated at 30g during 3 minutes and F4/80 positive cells contained in supernatant were isolated using MACS (Anti-F4/80 MicroBeads UltraPure, mouse, Miltenyi)

extract_protocol:
Total RNAs were extracted using RNeasy Mini Kit (Qiagen, Hilden,Germany) according to the manufacturer's instructions.
mRNA purification from total RNA and library preparation were performed with the NEBNext Ultra RNA Library Preparation Kit with poly-A selection according to the manufacturer protocols.

value: Lpcat3 KOMac

tag: differentiation

value: Kupffer cells isolated from mouse liver

tag: donor

value: Mouse fed high fat diet

value: No  treatment


title: WT3

description: no treatment

value: WT


title: Lpcat3 KOMac 2

description: no treatment


title: Lpcat3 KOMac 3

description: no treatment


title: arp8_mut2_H3_0h

value: anti-H3 antibody (RRID:AB_2687473)

tag: genome used for alignment


title: arp8_mut2_H3_4h


title: WT2

description: no treatment


title: arp8_mut2_H3_2h


title: arp8_mut2_H3_6h


title: clsy1-7_2-2_3-1_4-1_Rs_RNA_rep2

value: Columbia


title: ESC_KO_2i_repeat3


title: clsy1-7_2-2_3-1_4-1_Rs_RNA_rep1


title: WT1

description: no treatment


title: nrpd1-4_Rs_RNA_rep2


title: arp8_mut1_H3_4h


title: arp8_mut1_H3_6h


title: shh1-1_Rs_RNA_rep1


title: arp8_mut1_H3_2h


title: clsy3-1_4-1_Rs_RNA_rep2


title: clsy3-1_4-1_Rs_RNA_rep1


title: arp8_mut1_H3_0h


title: DNAm_Subject_3400521

type: genomic

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Raw idat files were loaded into R using the R package minfi
Samples were evaluated for potential sex mismatch, and probes were removed if they had detection p-values < .1 in more than 10% of samples
Raw data were normalized using functional normalization and normal-exponential out-of-band background correction using the R package minfi
Normalized data were corrected for batch effects using ComBat from the R package sva
Beta values are provided as a .csv, post normalization and QC

source_name: Placenta of infants born at low gestational age

label_protocol: Extracted DNA was bisulphate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA), followed by quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA).

extract_protocol: Recruited patients from the ELGAN cohort that were scheduled to give birth at participating institutions between 2002 to 2004. Patients involved in the study comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation.  Maternal, demographic, and clinical assessments were taken before and after delivery. Each infant's anthropometric measures were recorded throughout hospitalization and at follow-up. Placenta samples were collected immediately after surgery and stored at -80 degrees C until further analysis.  DNA molecules with 18 nucleotides or greater were extraced with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). and extracted DNA was bisulphate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA), followed by quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA)

tag: tissue

value: placenta

tag: birthweight (grams)

tag: infant sex

value: Male

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: DNAm_Subject_3400741

value: Female


title: DNAm_Subject_3400571


title: DNAm_Subject_3400672


title: DNAm_Subject_3400661


title: DNAm_Subject_3400531


title: arp8_ctr_H3_6h

tag: strain


title: DNAm_Subject_3400321


title: DNAm_Subject_3400362


title: DNAm_Subject_3400371


title: DNAm_Subject_3400361


title: DNAm_Subject_3400401


title: clsy1-7_2-2_Rs_RNA_rep1


title: arp8_ctr_H3_4h


title: DNAm_Subject_3400341


title: DNAm_Subject_3400291


title: clsy4-1_Rs_RNA_rep1


title: arp8_ctr_H3_0h


title: DNAm_Subject_3400301


title: DNAm_Subject_3400211


title: clsy3-1_Rs_RNA_rep2


title: DNAm_Subject_3400201


title: arp8_ctr_H3_2h


title: clsy1-7_2-2_Rs_RNA_rep2


title: DNAm_Subject_3301331


title: DNAm_Subject_3301321


title: S24 A549 cells

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked by FastQC | version: 0.11.5
Trimed adapter by TrimGalore-0.4.5
Reads were mapped to the Homo_sapiens.GRCh38.98 reference genome using STAR | version 2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes gencode.v25.annotation.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10
Genome_build: Homo_sapiens.GRCh38.dna.chromosome
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: A549 cells

growth_protocol: P. californicus (stock IS) were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769).  P. californicus derived from about 60 ancestors collected between 1979 and 1987 in Santa Monica Mts., CA.

extract_protocol:
Total RNA was extracted from A549 cells using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)

treatment_protocol: A549 cells were treated with the serum collected from bonded, bond-disrupted, and virgin male mice.

tag: culture

value: DMEM and Fetal bovine serum (FBS)


title: clsy4-1_Rs_RNA_rep2

tag: ecotype


title: clsy2-2_Rs_RNA_rep2

tag: tissues


title: DNAm_Subject_3301242


title: DNAm_Subject_3301301


title: S22 A549 cells


title: S23 A549 cells


title: clsy3-1_Rs_RNA_rep1

tag: genotype


title: DNAm_Subject_3301191


title: S21 A549 cells


title: clsy2-2_Rs_RNA_rep1


title: S20 A549 cells


title: DNAm_Subject_3301241


title: clsy1-7_Rs_RNA_rep2


title: DNAm_Subject_3301081


title: clsy1-7_Rs_RNA_rep1


title: S19 A549 cells


title: DNAm_Subject_3301021


title: DNAm_Subject_3301011


title: DNAm_Subject_3301001


title: WT_3_Rs_RNA_rep2


title: DNAm_Subject_3300981


title: DNAm_Subject_3300991


title: S18 A549 cells

tag: age of serum donors

value: 15 months

value: DMEM and serum from virgin P. californicus_male_7475


title: WT_3_Rs_RNA_rep1

value: wild-type


title: DNAm_Subject_3300911


title: DNAm_Subject_3300901


title: WT_2_Rs_RNA_rep2


title: DNAm_Subject_3301201


title: WT_2_Rs_RNA_rep1


title: DNAm_Subject_3300861


title: DNAm_Subject_3300761


title: DNAm_Subject_3300841


title: S15 A549 cells

value: 16 months

value: DMEM and serum from virgin P. californicus_male_7422


title: S16 A549 cells

value: DMEM and serum from virgin P. californicus_male_7484


title: DNAm_Subject_3301202


title: DNAm_Subject_3300721


title: S14 A549 cells

value: 17 months


title: DNAm_Subject_3300711


title: WT_1_Rs_RNA_rep2

value: 15 day old aerial rosettes (Rs)


title: DNAm_Subject_3300732


title: WT_1_Rs_RNA_rep1


title: DNAm_Subject_3300611


title: DNAm_Subject_3300641


title: DNAm_Subject_3300602


title: S12 A549 cells

value: DMEM and serum from bond-disrupted P. californicus_male_7449


title: S17 A549 cells

value: 14 months

value: DMEM and serum from virgin P. californicus_male_7496


title: DNAm_Subject_3300601


title: S11 A549 cells

value: DMEM and serum from bond-disrupted P. californicus_male_7418


title: DNAm_Subject_3300592


title: shh1-1_Ov_smRNA-seq

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering, Mapping, and cluster calling: The adapters were removed from the de-multiplexed reads using cutadapt (v1.9.1) and trimmed reads longer that 15nt were mapped to the TAIR10 genome using ShortStack (v3.8.1) with the following options: --mismatches 1 and either --mmap f, to include multi-mapping reads, or --mmap n, to include only unique mapping reads. Only perfectly matched read or reads with a single 3’ mismatch were used to call smRNA clusters using ShortStack with the --mincov 20, --pad 100, --dicermin 21 and dicermax 24 options, to generate Tag Directories using the using the makeTagDirectory script from the HOMER with the -format sam -mis 1 and -keepAll options, and to make genome browser tracks specifically for the 24nt sized smRNAs using the makeUCSCfile script from HOMER with the -fragLength 24 and -norm 10000000 options.
TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: unfertilized ovules (Ov)

extract_protocol:
Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. 2.0 µg of total RNA from rosette and leaf tissues, or ~0.5ug of total RNA from Ov tissue, were used for smRNA enrichment through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The small RNAs were used for library preparation with the NEBnext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat# E7300) following the user’s manual. The final library products were further purified using an 8% polyacrylamide gel to excise 130-160nt products relative to the pBR322 DNA-MspI Digest ladder (New England Biolabs, Cat# E7323AA). The purified libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

value: Columbia

value: unfertilized ovules (Ov)


title: clsy1-7_2-2_3-1_4-1_Ov_smRNA-seq


title: DNAm_Subject_3300591

value: placenta


title: S10 A549 cells

value: DMEM and serum from bond-disrupted P. californicus_male_7464


title: DNAm_Subject_3300531

value: Female


title: clsy3-1_4-1_Ov_smRNA-seq


title: DNAm_Subject_3300501


title: DNAm_Subject_3300411


title: S09 A549 cells

value: 18 months

value: DMEM and serum from bond-disrupted P. californicus_male_7404


title: DNAm_Subject_3300401


title: DNAm_Subject_3300381


title: DNAm_Subject_3300361

value: Male


title: DNAm_Subject_3300371


title: clsy1-7_2-2_Ov_smRNA-seq


title: S13 A549 cells

value: 15 months

value: DMEM and serum from virgin P. californicus_male_7472


title: S07 A549 cells

value: DMEM and serum from bond-disrupted P. californicus_male_7432


title: S08 A549 cells

value: DMEM and serum from bond-disrupted P. californicus_male_7400


title: clsy4-1_Ov_smRNA-seq


title: nrpd1-4_Ov_smRNA-seq


title: clsy3-1_Ov_smRNA-seq


title: DNAm_Subject_3200721


title: DNAm_Subject_3300211


title: S05 A549 cells

value: 17 months

value: DMEM and serum from bonded P. californicus_male_7437


title: DNAm_Subject_3200612


title: clsy2-2_Ov_smRNA-seq


title: DNAm_Subject_3200651


title: DNAm_Subject_3200611


title: S06 A549 cells

value: 16 months

value: DMEM and serum from bonded P. californicus_male_7438


title: clsy1-7_Ov_smRNA-seq


title: S04 A549 cells

value: DMEM and serum from bonded P. californicus_male_7427


title: WT_3_Ov_smRNA-seq

value: Columbia

value: wild-type


title: DNAm_Subject_3200531

value: placenta


title: DNAm_Subject_3200541


title: S03 A549 cells

value: DMEM and serum from bonded P. californicus_male_7449


title: S02 A549 cells

value: DMEM and serum from bonded P. californicus_male_7418


title: DNAm_Subject_3200342

value: Female


title: DNAm_Subject_3200521


title: DNAm_Subject_3200461


title: WT_2_Ov_smRNA-seq

value: unfertilized ovules (Ov)


title: DNAm_Subject_3200431

value: Male


title: DNAm_Subject_3200241


title: S01 A549 cells

value: 18 months

value: DMEM and serum from bonded P. californicus_male_7400


title: DNAm_Subject_3200231


title: WT_1_Ov_smRNA-seq


title: DNAm_Subject_3200171


title: nrp1-4_Lv_smRNA-seq

value: 25 day old leaves (Lv)


title: DNAm_Subject_3200141


title: ESC_WT_FBS_repeat4

value: Wild type

value: grown in FBS containing medium


title: shh1-1_Lv_smRNA-seq


title: DNAm_Subject_3200022


title: DNAm_Subject_3200023


title: clsy1-7_2-2_3-1_4-1_Lv_smRNA-seq


title: dm_groseq6

first: Arnold

middle: J

last: Berk

address: 611 Charles E. Young Dr.

institute: UCLA

description: nascent RNA

data_processing:
GRO-seq reads were aligned with HISTAT2 software to Ad5 and human (hg19) genomes and normalized to the number of reads aligned to hg19.
Pause indexes (TSS to +200 counts)/(+201 to TTS counts) were calculated using HTSeq software.
Bedgraph and wiggle files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: hg19 human genome, Adenovirus 5 genome

source_name: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

growth_protocol: Human Bronchial/Tracheal Epithelial Cells (HBTEC, Lifeline Cell Technology Cat# FC-0035; lot# 02196) were grown at 37°C in BronchiaLife Medium Complete Kit (Lifeline Cell Technology catalog number: LL-0023) in a 5% CO2 incubator

extract_protocol:
1x10^7 low-passage HBTEC were infected with indicated Ad vector 3 days after reaching confluence. 12h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and the indicated antibody. 50uL of protein A/G dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
GRO-seq libraries were constructed using the Illumina Truseq Small RNA Library Prep Kit
GRO-seq

treatment_protocol: HBTEC were grown until they reached confluence. Cells were then incubated 3 days more without addition of fresh media and were Infected with the indicated Ad5-based vectors for 12h, followed by the indicated treatment (DMSO or A-485) for 2h.

tag: cell type

tag: passage

tag: Sex

tag: ad5 mutant

value: DM E1A

tag: treatment


title: wt_dl312_groseq6

description: nascent RNA

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

value: wt E1A


title: clsy3-1_4-1_Lv_smRNA-seq


title: dm_groseq5

description: nascent RNA


title: DNAm_Subject_3200021


title: wt_dl312_groseq5

description: nascent RNA


title: DNAm_Subject_3101411


title: DNAm_Subject_3101401


title: clsy1-7_2-2_Lv_smRNA-seq


title: DNAm_Subject_3101372


title: dm_groseq4

description: nascent RNA


title: DNAm_Subject_3101331


title: wt_dl312_groseq4

description: nascent RNA


title: DNAm_Subject_3101241


title: clsy4-1_Lv_smRNA-seq


title: DNAm_Subject_3101163


title: clsy2-2_Lv_smRNA-seq


title: DNAm_Subject_3101181


title: DNAm_Subject_3101341


title: clsy3-1_Lv_smRNA-seq


title: DNAm_Subject_3101141


title: DNAm_Subject_3101232


title: dmso_enl

description: genomic DNA and viral DNA

data_processing:
Reads were mapped to the adenovirus 5 or hg19 human genome reference using Bowtie2 software. Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis. Duplicate reads that mapped to the same exact location in the genome were counted only once to reduce clonal amplification effects.
A custom algorithm executed by MATLAB was used for further processing. The genome was tiled into 50 base pair windows and each read was extended by 150 bases and was counted as one read to each window to which it partially or fully matched. The total counts of the input and ChIP samples were normalized to each other.
Bedgraph and wiggle files were generated using a custom algorithm and present the data as normalized tag density.
Genome_build: hg19 human genome, Adenovirus 5 genome

extract_protocol:
1x10^7 low-passage HBTEC were infected with indicated Ad vector 3 days after reaching confluence. 12h p.i. cells were cross-linked for 1% formaldehyde for 10 minutes at room temperature on rotator. Formaldehyde crosslinking was quenched with 0.14M glycine for 30 minutes at room temperature on rotator. Cells were washed with PBS and scraped from plates in PBS with Roche protease inhibitor cocktail. Cells were pelleted and lysed in 400uL lysis buffer (1% SDS, 50mM Tris-HCl pH8, 20mM EDTA, Roche complete protease inhibitors) and sonicated at 4°C using the Qsonica Q800R2 at 20% amplitude 10s on 30s off until DNA fragments from sheared chromatin were mostly between the sizes of 200-600 base pairs. 100uL of sonicated chromatin was diluted in 10X lysis dilution buffer (16.7 mM Tris-HCl, 1.1% Triton X-100, 1.2mM EDTA, 167mM NaCl) and precleared for 1h 4°C with 30uL of protein A dynabeads washed 10X lysis dilution buffer on nutator. IPs were performed O/N at 4°C on nutator with precleared chromatin and the indicated antibody. 50uL of protein A/G dynabeads were added for 4h on nutator at 4°C. Bead-immunocomplexes were washed for 5min 2X with each of the following buffers in order: wash buffer A (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 140mM NaCl), wash buffer B (50mM Hepes pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1mM EDTA, 500mM NaCl), LiCl buffer (20mM Tris-HCl pH8, 0.5% NP-40, 0.5% Deoxycholate, 1mM EDTA, 250mM LiCl), TE (50mM Tris-HCl pH8, 1mM EDTA). Elution was performed in 150uL of elution buffer (50mM Tris HCl pH8, 1mM EDTA, 1% SDS) then ChIP samples and inputs (10uL of precleared chromatin lysis plus 140uL elution buffer) were reverse crosslinked O/N at 65°C. Samples were RNase A treated for 1h at 37°C and DNA was purified and extracted with phenol/chloroform and ethanol precipitated. DNA pellets were resuspended in 12uL of TE and measured using Qubit fluorometer.
ChIP sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the KAPA Hyper Prep Kit from KAPA Biosystems and NEXTflex ChIP-Seq barcodes purchased from Bioo Scientific.

value: DMSO

tag: chip antibody

value: Rabbit monoclonal anti-ENL/MLLT1 Cell Signaling Cat#14893S


title: clsy1-7_Lv_smRNA-seq

value: Columbia


title: DNAm_Subject_3101131

tag: tissue

value: placenta


title: a485_enl

description: genomic DNA and viral DNA


title: DNAm_Subject_3101471

tag: birthweight (grams)


title: dmso_af9

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-AF9 Genetex Cat#GTX102835


title: DNAm_Subject_3101096

tag: infant sex


title: WT_3_Lv_smRNA-seq

value: wild-type


title: DNAm_Subject_3101071

value: Female

tag: mage (age of mother) (years)


title: a485_af9

description: genomic DNA and viral DNA


title: WT_1_Lv_smRNA-seq


title: DNAm_Subject_3101081

tag: bmi (body mass index)


title: DNAm_Subject_3101051


title: a485_k18

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-H3K18ac (814) Grunstein/Kurdistani laboratories (Suka et al., 2001)


title: DNAm_Subject_3101061


title: DNAm_Subject_3100991


title: DNAm_Subject_3100981

value: Male


title: DNAm_Subject_3101161


title: DNAm_Subject_3100972


title: dm_brd4

description: genomic DNA and viral DNA

value: Rabbit polyclonal anti-BRD4 Bethyl Cat#A301-985A50


title: DNAm_Subject_3100971


title: shh1-1_Rs_smRNA-seq

value: 15 day old aerial rosettes (Rs)


title: DNAm_Subject_3100931


title: nrpd1-4_Rs_smRNA-seq


title: DNAm_Subject_3100891


title: DNAm_Subject_3100863


title: WT_2_Lv_smRNA-seq

value: 25 day old leaves (Lv)


title: DNAm_Subject_3100852


title: wt_dl312_enl

description: genomic DNA and viral DNA


title: DNAm_Subject_3100501


title: clsy3-1_4-1_Rs_smRNA-seq


title: dm_enl

description: genomic DNA and viral DNA


title: dm_af9

description: genomic DNA and viral DNA


title: dmso_k18

description: genomic DNA and viral DNA


title: wt_dl312_af9

description: genomic DNA and viral DNA


title: clsy4-1_Rs_smRNA-seq


title: DNAm_Subject_3100573


title: clsy1-7_2-2_Rs_smRNA-seq


title: DNAm_Subject_3100481


title: clsy3-1_Rs_smRNA-seq


title: dm_nelf

description: genomic DNA and viral DNA

value: Rabbit monoclonal anti-NELF TH1L Cell Signaling Cat#12265S


title: DNAm_Subject_3100461


title: DNAm_Subject_3100431


title: wt_brd4

description: genomic DNA and viral DNA


title: clsy1-7_2-2_3-1_4-1_Rs_smRNA-seq


title: clsy2-2_Rs_smRNA-seq


title: DNAm_Subject_3100421


title: DNAm_Subject_3100371


title: wt_dl312_nelf

description: genomic DNA and viral DNA


title: clsy1-7_Rs_smRNA-seq


title: DNAm_Subject_3100851


title: DNAm_Subject_3100381


title: DNAm_Subject_3100351


title: wt_dl312_cdk9

description: genomic DNA and viral DNA

value: Rabbit monoclonal anti-CDK9 Cell Signaling Cat#2316


title: DNAm_Subject_3100491


title: WT_2_Rs_smRNA-seq


title: DNAm_Subject_3100271


title: DNAm_Subject_3100261


title: DNAm_Subject_3100041


title: DNAm_Subject_2302211


title: dm_ser2

description: genomic DNA and viral DNA

value: DM E1A

value: Rabbit monoclonal anti-Pol2 Ser2-P Cell Signaling Cat#13499


title: wt_dl312_ser2

description: genomic DNA and viral DNA

value: Primary Human Bronchial/Tracheal Epithelial Cells (HBTEC)

value: wt E1A


title: dm_ser5

description: genomic DNA and viral DNA

value: Rabbit monoclonal anti-Pol2 Ser5-P Cell Signaling Cat#13523


title: shh1-1_Ov_BS-seq

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: MethylC-seq reads were mapped and processed using BS-Seeker2. Briefly, reads were mapped with the bs_seeker2-align.py script allowing 2 mismatches, clonal reads were removed using the MarkDuplicates function within picard tools (http://broadinstitute.github.io/picard/), and methylation levels at each cytosine covered by at least 4 reads were determined using the bs_seeker2-call_methylation.py script.
Methylation levels: For visualization of methylation levels in each sequence context or in all contexts together, wig files were generated using a custom perl script (BSseeker2_2_wiggleV2_CG_CHG_CHH_allmC.pl) based on the BS-Seeker2 CGmap output files. Information regarding the mapability, coverage, global percent CG, CHG, and CHH methylation levels, and non-conversion rates are presented in Table S3.
DMR calling: DMRs in the CG, CHG or CHH contexts were identified in 100 bp non-overlapping bins based on either pair-wise comparisons between each mutant and three independent wild-type data sets, or between all three wild-type data sets from one tissue and all three wild-type datasets from another tissue. To be designated a DMR, the following criteria were required: (1) the 100 bp bins must to contain ≥ 4 cytosines in the specified context, (2) the bins must have sufficient coverage in both genotypes being compared (i.e. ≥ 4 reads over the required 4 cytosines in the specific context), and (3) the bins must show a fold change of 40%, 20% or 10% methylation in the CG, CHG, and CHH contexts, respectively, with an adjusted p value of ≤0.01. After these pairwise DMR calling, the final set of DMRs were determined for each mutant by taking the overlap between the DMRs called relative to each wild-type control (Table S12). For the DMRs between tissues, a more stringent approach was taken, requiring the DMR to be present in across all 9 pair-wise comparisons to be included (e.g. “WT_Rs_CG_hyperDMR_vs_Fl” Table S7). These wild-type (WT) versus WT DMRs were subsequently combined to generate a set of 100 bp hyper and hypo DMRs amongst all pairwise tissue comparisons (e.g. “WTvsWT all tissues hypo” DMRs; Table S7 and Fig. S3A).
Genome_build: TAIR10
Supplementary_files_format_and_content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation

extract_protocol:
~0.1 g of tissue from either 15 day old rosettes or leaves, and >5,000 unfertilized ovules were collected for genomic DNA isolation using the DNeasy Plant Mini Kit (Qiagen, Cat# 69104).
MethylC-seq libraries were generated using 2.0 μg of DNA from rosettes and leaves, and 0.5-1.0 μg of DNA from ovules as described in Li et al. (2017). The libraries were then pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

value: Columbia

value: unfertilized ovules (Ov)


title: DNAm_Subject_2301791

value: placenta


title: dm_cdk9

description: genomic DNA and viral DNA


title: clsy1-7_2-2_3-1_4-1_Ov_BS-seq


title: WT_3_Rs_smRNA-seq

value: wild-type


title: clsy3-1_4-1_Ov_BS-seq


title: DNAm_Subject_2301671


title: DNAm_Subject_3100341

value: Female


title: DNAm_Subject_3100171


title: DNAm_Subject_2301592


title: clsy1-7_2-2_Ov_BS-seq


title: DNAm_Subject_2301591


title: SA05712_S53

first: Yu-Ling

last: Chang

address: 10833 Le Conte Ave

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

data_processing:
Read quality was checked using FastQC (version 0.11.7)
Reads with the adaptors and the terminal CG were trimmed using the trimmomatic software (v0.38)
Reads aligned using BS-Seeker2 pipeline with the aligner bowtie (v1.2.2)
Genome_build: cohort1(Hg19); cohort2(Hg38)
Supplementary_files_format_and_content: [CGfinal files] chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency;  [CGmap] Columns are: 1. chromosome, 2. nucleotide on Watson (+) strand, 3. position, 4. context (CG/CHG/CHH), 5. dinucleotide context (CA/CC/CG/CT), 6. methylation-level = #_of_C/ (#_of_C + #_of_T), 7. #_of_C (methylated C, the count of reads showing C here), 8. #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).

source_name: Peripheral blood

extract_protocol:
Genomic DNA was extracted from whole blood samples using QIAGEN’s QIAamp DNA Blood Midi/Maxi Kit, performed at Duke. The purified genomic DNA was shipped on ice to University of California, Los Angeles (UCLA) for RRBS library preparation. Genomic DNA was first quantified by Qubit dsDNA BR Assay Kit (ThermoFisher cat. Q32850). The RRBS libraries were prepared as described(52) with the following conditions. For each sample, 100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and adenylation tailing were performed by the addition of Klenow Fragment 3ʹ->5ʹ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP, and d5meCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 1 µl of Quick T4 DNA Ligase (NEB cat# M2200L). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 400 bp. Bisulfite treatment was performed using EpiTect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer’s protocol, except that two consecutive rounds of conversion were performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30 s; 12 cycles of 98°C for 15 s, 60°C for 30 s, 72°C for 30 s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers.
The sequencing data were first demultiplexed based on the barcodes of each sample pooled in the lanes. The data were subjected to a quality control step using FastQC (version 0.11.7), where the low quality reads were discarded from further analysis based on the per base sequence quality and per sequence quality score using the default criteria setting in FastQC(53). Sequencing data were trimmed to remove the adaptors and the terminal CG using the trimmomatic software (v0.38) (54). The reads were aligned to the human genome GRCh38/hg38 (release 93, downloaded from Ensembl) and DNA methylation levels were determined using the BS-Seeker2 pipeline(55) with the aligner bowtie (v1.2.2) and the default settings for the fragment length (20 for lower bound, 500 for upper bound). Samples with less than 5 M total raw reads (3 samples) were excluded from further analyses. On average each sample generated about 36 M total raw reads with 73.7% mappability. Within the study, sequencing data were generated from two sequencing runs, termed batch.

tag: disease state

value: ARMB

tag: batch

value: TBS-seq


title: SA05820_S54

value: APMB


title: SA05682_S52


title: nrpd1-4_Ov_BS-seq

last: Law

institute: The Salk Institute for Biological Studies

tag: ecotype


title: WT_1_Rs_smRNA-seq

tag: tissues

value: 15 day old aerial rosettes (Rs)


title: DNAm_Subject_2301941


title: DNAm_Subject_2301391


title: DNAm_Subject_2301542

value: Male


title: clsy4-1_Ov_BS-seq

tag: genotype


title: DNAm_Subject_2301521


title: SA05572_S51


title: DNAm_Subject_2301891


title: SA05567_S50


title: wt_dl312_ser5

description: genomic DNA and viral DNA


title: DNAm_Subject_2301751


title: DNAm_Subject_2301781


title: DNAm_Subject_2301281


title: DNAm_Subject_2301251


title: DNAm_Subject_2301151


title: clsy2-2_Ov_BS-seq


title: SA05537_S49


title: DNAm_Subject_2301631


title: DNAm_Subject_2301061


title: clsy1-7_Ov_BS-seq


title: SA05526_S48


title: DNAm_Subject_2301021


title: DNAm_Subject_2300901


title: WT_3_Ov_BS-seq


title: SA05525_S47


title: DNAm_Subject_2300871


title: SA05519_S46


title: WT_2_Ov_BS-seq


title: clsy3-1_Ov_BS-seq


title: DNAm_Subject_2300851


title: DNAm_Subject_2300861


title: SA05500_S45


title: nrp1-4_Lv_BS-seq

source_name: 25 day old leaves (Lv)

value: 25 day old leaves (Lv)


title: WT_1_Ov_BS-seq


title: DNAm_Subject_2300891


title: SA05467_S44


title: DNAm_Subject_2300852


title: DNAm_Subject_2300761


title: shh1-1_Lv_BS-seq


title: DNAm_Subject_2300741


title: SA05444_S43


title: DNAm_Subject_2300701


title: DNAm_Subject_2300692


title: DNAm_Subject_2300691


title: DNAm_Subject_2300921


title: clsy3-1_4-1_Lv_BS-seq


title: SA05432_S42


title: DNAm_Subject_2300662


title: clsy1-7_2-2_3-1_4-1_Lv_BS-seq


title: DNAm_Subject_2300651


title: DNAm_Subject_2300661


title: DNAm_Subject_2300601


title: SA05315_S40


title: SA05423_S41


title: DNAm_Subject_2300591


title: clsy1-7_2-2_Lv_BS-seq


title: SA05300_S39


title: clsy4-1_Lv_BS-seq


title: DNAm_Subject_2300571


title: SA05272_S38


title: DNAm_Subject_2300521


title: DNAm_Subject_2300522


title: DNAm_Subject_2300491


title: SA05238_S37


title: DNAm_Subject_2300481


title: clsy2-2_Lv_BS-seq


title: SA05208_S36


title: DNAm_Subject_2300461


title: DNAm_Subject_2300441


title: WT_3_Lv_BS-seq


title: SA05170_S35


title: DNAm_Subject_2300431


title: DNAm_Subject_2200821


title: WT_2_Lv_BS-seq


title: SA05121_S34


title: DNAm_Subject_2200811


title: DNAm_Subject_2200681


title: WT_1_Lv_BS-seq


title: DNAm_Subject_2200661


title: clsy3-1_Lv_BS-seq


title: DNAm_Subject_2300551


title: DNAm_Subject_2200582


title: SA05101_S33


title: clsy1-7_Lv_BS-seq


title: nrpd1-4_Rs_BS-seq


title: DNAm_Subject_2200562


title: SA05073_S32


title: DNAm_Subject_2200481


title: clsy1-7_2-2_3-1_4-1_Rs_BS-seq


title: DNAm_Subject_2200421


title: DNAm_Subject_2200371


title: shh1-1_Rs_BS-seq


title: DNAm_Subject_2200511


title: SA05030_S30


title: DNAm_Subject_2200331


title: SA05019_S29


title: DNAm_Subject_2200301


title: clsy3-1_4-1_Rs_BS-seq


title: DNAm_Subject_2200241


title: SA05004_S28


title: DNAm_Subject_2200211


title: clsy4-1_Rs_BS-seq


title: DNAm_Subject_2200221


title: DNAm_Subject_2200171


title: DNAm_Subject_2200041


title: SA04942_S27


title: SA04915_S26


title: DNAm_Subject_2101562


title: SA05051_S31


title: clsy3-1_Rs_BS-seq


title: clsy2-2_Rs_BS-seq


title: SA04908_S25


title: clsy1-7_Rs_BS-seq


title: DNAm_Subject_2101531


title: DNAm_Subject_2101501


title: DNAm_Subject_2101561


title: DNAm_Subject_2101391


title: DNAm_Subject_2101491


title: DNAm_Subject_2101461


title: WT_2_Rs_BS-seq


title: DNAm_Subject_2101521


title: SA04886_S24


title: DNAm_Subject_2101431


title: clsy1-7_2-2_Rs_BS-seq


title: SA04873_S22


title: SA04878_S23


title: WT_1_Rs_BS-seq


title: DNAm_Subject_2101332


title: SA04864_S21


title: WT_3_Rs_BS-seq


title: DNAm_Subject_2101321


title: CLSY3-3xFLAG_Fl_IP

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Mapping:  The ChIP-seq data was aligned to TAIR10 reference genome using bowtie (v1.1.0) using the “-m 1 -v 2 --all –best and –strata” options to allow 2 mismatches and including only uniquely mapping reads.
Data processing: TagDirectories and UCSC genome browser tracks from ChIP-seq data were generated with the makeTagDirectory and makeUCSCfile scripts from HOMER using the “format sam -mis 2 and -unique” or “none -fragLength given and -norm 10000000” options, respectively.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: stage 12 and younger flower buds (Fl)

growth_protocol: Growth conditions and tissue collection were as follows: seeds were grown from soil in a Salk greenhouse with long day conditions and un-opened flower buds (stage 10-12) were collected.

extract_protocol:
~2.0 g of un-opened flower buds (stage 12 and younger) was collected, ground in liquid nitrogen, and in vitro crosslinked with 1% formaldehyde (20 minutes at RT; Sigma, Cat# F8775). The chromatin was then fragmented to ~500bp by sonication, incubated with anti-Flag M2 Magnetic beads (4 °C for 2 h; Sigma, Cat# M8823), washed 5 times and then eluted with 3xFLAG peptide ([0.1 mg/mL]; Sigma, Cat# F4799). The crosslinking was reversed overnight at 65 °C overnight and purified DNA (Thermo Scientific, Cat# 17908) was used to generate libraries with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, Cat# 7645).
The libraries were sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

value: stage 12 and younger flower buds (Fl)

value: CLSY1-3xFLAG in clsy3-1

tag: antibody

value: anti-Flag M2


title: DNAm_Subject_2101301


title: SA04862_S20


title: WT_Fl_IP


title: DNAm_Subject_2101281


title: DNAm_Subject_2101282


title: DNAm_Subject_2101221


title: WT_Fl_input


title: SA04859_S19


title: SA04821_S64


title: DNAm_Subject_2101201


title: DNAm_Subject_2101171