title: WT_Qui_3

city: Rochester

first: Sina

last: Ghaemmaghami

state: NEW YORK

address: Hutchison Hall

department: Biology Department

institute: University of Rochester

description: Quiescent cells replicate 3

data_processing:
Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping some of them to the human reference genome (GRCh38.p2) with STAR-2.4.2a ( https://github.com/alexdobin/STAR )
cufflinks2.0.2 (cuffdiff2 - Running Cuffdiff) was used with the gencode version 23 human gene annotations to perform differential expression analysis with an FDR cutoff of 0.05 (95% confidence interval).
A Perl script was used after cuffDiff differential expression analysis to make the results files more human readable.
Supplementary_files_format_and_content: tab-delimited text files with different expressional analysis in dividing and quiescent cells

source_name: Human primary fibroblasts

growth_protocol: Eagle’s Minimum Essential Medium (ATCC) supplemented with 15% fetal bovine serum (Invitrogen), 100U/mL penicillin, 100U/mL streptomycin at 37℃ with 5% CO2. Dividing cells were collected two days after passaging, while quiescent cells were collected eight days after passaging.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations.
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

value: primary fibroblasts


title: WT_Qui_2

status: Public on Jan 01 2018

type: SRA

country: USA

description: Quiescent cells replicate 2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue


title: WT_Div_2

description: Dividing cells replicate 2


title: lung3_3

city: Brno

first: Lucia

last: Knopfova

address: Kamenice 5

department: Department of Experimental Biology

country: Czech Republic

institute: Faculty of Science, Masaryk University

data_processing:
Reads were aligned with the STAR (Dolbin A. et al., 2012) aligner with the additional options (--outFilterMatchNmin 30 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50)
Expression counts were computed using the Bioconductor package GenomicRanges (Lawrence M., 2013.).
Differential expression was computed using the Edger package (Robinson M. D. et al., 2010).
Genome_build: The mouse genome build and annotation from Ensembl (GRCm38) were used as the reference.
Supplementary_files_format_and_content: raw counts of sequencing reads for the annotated features. formatted as a matrix table, saved as a plain tab-delimited text file

organism: Mus musculus

source_name: 4T1_selected in vivo for high efficiency in lung seeding (lung3)

extract_protocol:
RNA was isolated using RNeasy Plus Mini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: mammary tumor cells

tag: transfected with

tag: in vivo passaging

value: 3x lung

tag: lung metastatic activity

value: high


title: lung3_2


title: WT_Div_1

description: Dividing cells replicate 1


title: lung3_1


title: wt_2

source_name: 4T1_wild type control

value: no

value: normal


title: MYBup_3

source_name: 4T1_Myb oncogene overexpression

value: low


title: wt_1


title: Tumor_3

city: San Francisco

first: David

last: Raleigh

state: CA

address: 555 Mission Bay Blvd South

institute: UCSF

data_processing:
Input sequences were analyzed in FASTQ format, with trimming of known adapters and low-quality regions of reads using Fastq-mcf and sequence quality control using FastQC and RSeQC
Alignment to the UCSC mm10 mouse genome assembly was performed using Bowtie 2.2.4, reads were assigned to genes using featureCounts
Gene-level counts were arrived at using Ensembl gene annotation in GTF format
EdgeR was used to calculate differential expression P-values, and p.adjust was used to calculate the false discovery rate for each P-value using the Benjamini-Hochberg method
Genome_build: mm10
Supplementary_files_format_and_content: gene level counts (Raleigh_All_Genes.xlsx)
Supplementary_files_format_and_content: p-value, FDR and fold change values for each gene (Raleigh_processed.xlsx)

source_name: Medulloblastoma

growth_protocol: Mice were aged until P35, at which point samples were collected

extract_protocol:
RNA was extracted according to the manufacturer's protocol using TRIzol (15596026, Thermo Fisher Scientific, Waltham, MA) followed by RNeasy Mini Kit cleanup (74104, QIAGEN, Valencia, CA)
Libraries were constructed according to the manfacturer's protocol using the TruSeq RNA Library Prep Kit v2 (RS-122-2001, Illumina, San Diego, CA)

tag: strain background

tag: genotype/variation

value: Math1-Cre SmoM2.c/wt

tag: Sex

value: female

value: Medulloblastoma


title: MYBup_1


title: MYBup_2


title: mock_3


title: mock_2


title: IRF4 knock out CD8 T cells-rep2

city: Xiamen

first: Yingjia

last: Shen

state: Fujian

address: A316 Jingquan Building

department: Ecology

country: China

institute: Xiamen University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mouse whole genome(mm10) using Tophat v2.0.3.
The number of reads falling in the coding region of the mouse genome were counted and differentially expression were identified by Cufflinks(v2.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: cuffdiff processed reads count

molecule: polyA RNA

source_name: IRF4 knock out CD8 T cells after 2 day in vitro activation

growth_protocol: CD8+ T cells were isolated from spleen and lymph nodes of indicated mice through MACS according to the protocol of the manufacturer (Miltoney Biotech). DCs were then mixed with CD8+ T cells (5 × 10^4) at the ratio of 1 DC:10 T cells in round-bottom 96-well plates in the presence of 0.1 μg/ml αCD3. 2 days later, RNA was extracted from the cultured cells.

extract_protocol:
RNA was extracted with Qiagen Rneasy RNA extraction kit according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8 T cells

tag: time point

value: after 2 day in vitro activation


title: mock_1


title: IRF4 knock out CD8 T cells-rep1


title: WT_Qui_1

description: Quiescent cells replicate 1


title: E6.5 epiblast input rep2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Raw FastQ sequence files were initially quality and adapter trimmed using Trim Galore v0.4.2 using default parameters (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Mapping of ChIP-Seq data was performed using Bowtie 2 v2.2.9 against the mouse GRCm38 genome assembly. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20. Mapping of RNA-Seq data was performed using HISAT2 v2.0.5 against the mouse GRCm38 genome guided by known splice sites taken from Ensembl v68. Hits were again filtered to remove mappings with MAPQ scores of <20.
For PBAT data, reads were trimmed with Trim Galore using --clip_r1 9 and --clip_r2 9. Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.16.3 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output, and methylation from single-end and paired-end mapping were merged into a single Bismark coverage report.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: "10_5_Domains_75_25_NoOverlap_NoGaps_NoInterm_NoSmall_NoGaps" file contains the GV methylated and unmethylated domains used for analyses in this study.
Supplementary_files_format_and_content: "RNAseq_groups_oocytemRNA_norep_RPKM_corrDNAcont" file contains RNA-seq quantitation for two groups: Mll2 WT oocytes and Mll2 cKO oocytes (each a replicate set of 4 single cell RNA-seq libraries).  RPKM was quantitated in SeqMonk for oocyte transcriptome mRNA annotation (Veselovska et al. 2014) excluding repetitive elements, correcting for DNA contamination
Supplementary_files_format_and_content: "ESC_oocyte_technicaloptimisation_2kbrunning_RPM_nofilters" file contains ChIP-seq quantitation for individual replicates for H3K4me3 in 1000 ESCs and 500 ESCs used for validation of the ULI-nChIP-seq method and the antibody titration for 125ng,and 62.5ng of antibody for H3K27ac and 125ng, 250ng and 500ng of H3K27me3 in GV oocytes (25-day old mice).  Reads per million was quantitated in SeqMonk for 2kb running window probes, with no filters applied.
Supplementary_files_format_and_content: "Dnmt3DKO.WT_H3K4me3_Me.Unme.domains_RPM" file contains ChIP-seq quantitation for H3K4me4 in GV oocytes (25-day old mice) from grouped Dnmt3a/b cDKO (N=4) and Dnmt3a/b WT controls (N=4).  Reads per million was quantitated in SeqMonk for GV methylated and unmethylated domains.
Supplementary_files_format_and_content: "GO_and_Mll2_peaks" file contains peak and seedpeak calls for H3K4me3 in non-growing oocytes (NGO) (5-day old mice), growing oocytes (GO) (10-day old mice), germinal vesicle (GV) oocytes (15-day old mice) and GV oocytes (25-day old mice), Mll2 WT GV oocytes (25-day old mice), and Mll2 KO GV oocytes (25-day old mice) using Chromstar peak calling program.  Temporal peak calling was done using a joint multivariate analysis (parameters: binsize = 1000bp, stepsize = 200bp, mode = differential). A cutoff of 1-10-4 was applied on the peak score (which is defined as the maximum posterior probability anywhere within a peak), to divide the resulting peak set into peaks with high H3K4me3 enrichment and seed-peaks with low H3K4me3 enrichment.
Supplementary_files_format_and_content: "bed_files_combinations_GV" file contains combinatorial peak for H3K4me3, H3K27ac, and H3K27me3 in germinal vesicle (GV) oocytes (25-day old mice) using Chromstar peak calling program.  Combinatorial chromatin states were called using a combined multivariate analysis. A cutoff of 1-10-4 was applied on the posterior probability in each bin to yield a stringent set of peaks.
Supplementary_files_format_and_content: "Epiblast_combinations_and_peaks" file contains combinatorial peak for H3K4me3, H3K27ac, and H3K27me3 in E6.5 epiblast using Chromstar peak calling program.   Combinatorial chromatin states were called using a combined multivariate analysis. A cutoff of 1-10-4 was applied on the posterior probability in each bin to yield a stringent set of peaks.
Supplementary_files_format_and_content: "bivalency_PGC_d05_d25_domains" file contains combinatorial peak for combined replicates for H3K4me3, H3K27me3 in non-growing oocytes (NGO) (5-day old mice), GV oocytes (25-day old mice), E11.5 primordial germ cells (Sachs et al. 2013).  Combinatorial chromatin states were called using a joint multivariate analysis (parameters: binsize = 1000bp, stepsize = 200bp, mode=differential).  A cutoff of 1-10-4 was applied on the peak score to select broad bivalent domains and subsequently only those domains were retained which contained clear enrichment, by applying a cutoff on the posterior probability of 1-10-4.
Supplementary_files_format_and_content: "OocyteH3K27ac_H3K27acGVpeaks_RPMcorrlength" file contains H3K27ac enrichment in grouped d5 NGOs and d25 GV oocytes for H3K27ac peaks called in GV oocytes using Chromstar.  Enrichment was quantitated as reads per million, corrected for probe length.
Supplementary_files_format_and_content: "Oocyte_H3K27ac_5kbrunning_RPM_nofilters" file contains H3K27ac enrichment in grouped d5 NGOs and d25 GV oocytes for running 5kb windows.  Enrichment was quantitated as reads per million.

molecule: genomic DNA

source_name: E6.5 epiblast input rep2

growth_protocol: Ovaries were collected from 5, 10, 15, and 25 day-old C57BL/6Babr or 21 or 25-day-old Mll2Gdf9cKO or 25-day-old Dnmt3a/bZp3cDKO mice and digested using 2mg/mL collagenase and 0.02% trypsin solution, gently agitating at 37°C for 20-30 minutes. Oocytes were hand collected and washed in M2 medium (Sigma), followed by 2 consecutive washes in PBS.

extract_protocol:
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
Cells for ChIP-seq were flash frozen in nuclear lysis buffer, cells for PBAT were flash frozen in PBS
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.

tag: background strain

tag: time-point in reprogramming

value: embryonic day 6.5

tag: cell number

value: Epiblast

tag: antibody amount

tag: genotype


title: Wild type CD8 T cells-rep1

source_name: Wild type CD8 T cells after 2 day in vitro activation

value: WT


title: 9 control rep2

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: RDP1: NSFTV_9

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with  htseq-count
Genome_build: Oryza sativa japonica reference genome v 6
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

organism: Oryza sativa

source_name: shoot

growth_protocol: Briefly, plants were grown in a controlled environment growth chamber. Seedlings were transplanted into the pots filled with Turface (Profile Products, LLC) and were grown in tap water for two days after transplanting. For the remainder of the experiment the plants were supplemented with half strength Yoshida solution (pH 5.8). Temperatures were maintained at 28 °C and 25 °C in day and night respectively, relative humidity was maintained at 60% in both day and night. Lighting was maintained at 800 μmoles·m−2·s−1 using high pressure sodium lights.

extract_protocol:
The samples were ground with Tissuelyser II (Invitrogen) and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
96 libraries were prepared using TruSeq RNA v2 library preparation reagents. Eighteen samples were sequenced per lane.

treatment_protocol: Salinity stress (6:1 molar ratio, NaCl:CaCl2) was increased to 6 dS·m-1 gradually in two 3 dS·m-1 intervals over a period of 24h. After 24h of 6 dS·m-1, aerial parts of the seedlings were excised from the roots and frozen immediately in liquid nitrogen.

value: shoot

tag: age

value: 8 days old


title: 9 salt-stress rep1

description: RDP1: NSFTV_9


title: 9 salt-stress rep2

description: RDP1: NSFTV_9


title: E6.5 epiblast input rep1

source_name: E6.5 epiblast input rep1


title: E6.5 epiblast H3K4me3 rep2

source_name: E6.5 epiblast H3K4me3 rep2


title: 9 control rep1

description: RDP1: NSFTV_9


title: 91 salt-stress rep2

description: RDP1: NSFTV_91


title: wt_3


title: 91 salt-stress rep1

description: RDP1: NSFTV_91


title: 91 control rep2

description: RDP1: NSFTV_91


title: E6.5 epiblast H3K27me3 rep1

source_name: E6.5 epiblast H3K27me3 rep1


title: E6.5 epiblast H3K27ac rep1

source_name: E6.5 epiblast H3K27ac rep1


title: 89 salt-stress rep2

description: RDP1: NSFTV_89


title: 91 control rep1

description: RDP1: NSFTV_91


title: Mll2 WT H3K4me3 rep3

source_name: Mll2 WT H3K4me3 rep3

value: postnatal day 25

value: Germinal vesicle oocytes

value: Mll2 floxed/floxed, Gdf9 -ve


title: Mll2 WT input rep1

source_name: Mll2 WT input rep1


title: 89 control rep2

description: RDP1: NSFTV_89


title: WT_Div_3

description: Dividing cells replicate 3

value: primary fibroblasts


title: Mll2 WT H3K4me3 rep2

source_name: Mll2 WT H3K4me3 rep2


title: E6.5 epiblast H3K4me3 rep1

source_name: E6.5 epiblast H3K4me3 rep1


title: Wild type CD8 T cells-rep2


title: E6.5 epiblast H3K27me3 rep2

source_name: E6.5 epiblast H3K27me3 rep2


title: Mll2 KO H3K4me3 rep4

source_name: Mll2 KO H3K4me3 rep4

value: Mll2 floxed/floxed, Gdf9 +ve


title: Mll2 WT H3K4me3 rep1

source_name: Mll2 WT H3K4me3 rep1


title: 88 salt-stress rep1

description: RDP1: NSFTV_88


title: 89 control rep1

description: RDP1: NSFTV_89


title: 88 salt-stress rep2

description: RDP1: NSFTV_88


title: Mll2 KO H3K4me3 rep3

source_name: Mll2 KO H3K4me3 rep3


title: Mll2 KO H3K4me3 rep2

source_name: Mll2 KO H3K4me3 rep2


title: 84 salt-stress rep2

description: RDP1: NSFTV_84


title: Mll2 KO H3K4me3 rep1

source_name: Mll2 KO H3K4me3 rep1


title: E6.5 epiblast H3K27ac rep2

source_name: E6.5 epiblast H3K27ac rep2


title: Mll2 IgG control rep1

source_name: Mll2 IgG control rep1


title: 88 control rep1

description: RDP1: NSFTV_88

source_name: shoot


title: 88 control rep2

description: RDP1: NSFTV_88


title: Mll2 cKO input rep1

source_name: Mll2 cKO input rep1


title: 89 salt-stress rep1

description: RDP1: NSFTV_89


title: 84 salt-stress rep1

description: RDP1: NSFTV_84


title: Dnmt3ab WT input rep2

description: Dnmt3DKO.WT_H3K4me3_Me.Unme.domains_RPM.txt

source_name: Dnmt3ab WT input rep2

value: Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 -ve


title: 84 control rep1

description: RDP1: NSFTV_84


title: 84 control rep2

description: RDP1: NSFTV_84


title: Dnmt3ab WT input rep1

source_name: Dnmt3ab WT input rep1


title: 83 salt-stress rep2

description: RDP1: NSFTV_83


title: Dnmt3ab WT H3K4me3 rep4

source_name: Dnmt3ab WT H3K4me3 rep4


title: 83 control rep2

description: RDP1: NSFTV_83


title: Dnmt3ab DKO input rep2

source_name: Dnmt3ab DKO input rep2

value: Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve


title: 83 salt-stress rep1

description: RDP1: NSFTV_83


title: Dnmt3ab DKO input rep1

source_name: Dnmt3ab DKO input rep1


title: 83 control rep1

description: RDP1: NSFTV_83


title: Dnmt3ab DKO H3K4me3 rep4

source_name: Dnmt3ab DKO H3K4me3 rep4


title: 80 salt-stress rep1

description: RDP1: NSFTV_80


title: 80 salt-stress rep2

description: RDP1: NSFTV_80


title: d5 NGO H3K4me3 rep2

description: bivalency_PGC_d05_d25_domains.tar; GO_and_Mll2_peaks.tar

source_name: d5 NGO H3K4me3 rep2

value: postnatal day 5

value: Non-growing oocytes


title: d5 NGO Input rep2

source_name: d5 NGO Input rep2


title: d5 NGO H3K27me3 rep2

source_name: d5 NGO H3K27me3 rep2


title: 75 salt-stress rep2

description: RDP1: NSFTV_75


title: 80 control rep2

description: RDP1: NSFTV_80


title: d5 NGO H3K4me3 rep3

source_name: d5 NGO H3K4me3 rep3


title: d15 GV H3K4me3 rep2

source_name: d15 GV H3K4me3 rep2

value: postnatal day 15


title: 75 control rep1

description: RDP1: NSFTV_75


title: d10 GO input BS_2

source_name: d10 GO input BS_2

extract_protocol:
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
Cells for ChIP-seq were flash frozen in nuclear lysis buffer, cells for PBAT were flash frozen in PBS
The ChIP-seq libraries for all samples were prepared using an ultra-low input native ChIP protocol, as previously described with the several modifications.  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease in prepared digestion buffer, as per recommendations in the Brind’Amour protocol.  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using spri purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads at a 1.8:1 ratio.  Library preparation was completed using the Diagenode MicroPlex Library Preparation kit v2 using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations.
For single oocyte RNA profiling, four GV oocytes from Mll2 KO and WT mice were collected for each genotype. Cells were lysed, RNA reverse transcribed and amplified according to the protocol of SMARTer Ultra Low RNA Kit for Illumina Sequencing (Version 1, Clontech). Subsequently, samples were subjected to NEBNext Ultra DNA library preparation for Illumina using indexed adaptors (New England Biolabs). Resulting libraries were pooled in equimolar quantities for 75-bp single-read sequencing on Illumina HiSeq 2000, resulting in about 15-18 million reads per sample.
Post-bisulfite adaptor tagging (PBAT) was used to generate whole-genome bisulfite sequencing libraries using 100 collected oocytes. Briefly, cells are lysed with 0.5% SDS in EB buffer and bisulfite-treated with one-step modification procedure using the Sigma Imprint DNA Modification kit. The resulting DNA are purified using columns from Zymo EZ DNA Methylation Direct kit. First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 10 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.
ChIP-bisulfite-seq was done on MNase-digested 10% input samples from the ChIP protocol, detailed in the corresponding ChIP-seq samples.  Following DNA purification from chromatin using spri purification with Sera-Mag carboxylate-modified Magnetic SpeedBeads, samples were bisulfite converted using the Zymo EZ DNA Methylation Direct kit.  First strand synthesis is then performed using Klenow Exo- with customized, streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs of random sequences (9N). This is followed by exonuclease I treatment and binding to Dynabeads M-280 Streptavidin beads. Samples are then subjected to second strand synthesis similar to the first strand synthesis, followed by 16-20 PCR amplification cycles using Phusion High-Fidelity DNA polymerase.

value: postnatal day 10

value: Growing oocytes


title: d10 GO input BS_1

source_name: d10 GO input BS_1


title: 75 salt-stress rep1

description: RDP1: NSFTV_75


title: 75 control rep2

description: RDP1: NSFTV_75


title: 80 control rep1

description: RDP1: NSFTV_80


title: 74 salt-stress rep2

description: RDP1: NSFTV_74


title: 74 control rep2

description: RDP1: NSFTV_74


title: 74 salt-stress rep1

description: RDP1: NSFTV_74


title: tc1_testis_captureseq_rep3

city: Darlinghurst

first: Ira

middle: William

last: Deveson

state: NSW

address: 384 Victoria St

country: Australia

institute: The Garvan Institute

description: human chromosome 21 and mouse syntenic region RNA CaptureSeq

data_processing:
map PacBio reads with GMAP (see Methods)
custom filtering pipeline (see Methods)
concordance with Illumina reads (see Methods)
merge with Gencode v19
Genome_build: hg19
Supplementary_files_format_and_content: known and novel isoforms retireved with single-molecule / short read RNA CaptureSeq on Hsa21

source_name: tc1 mouse testis

extract_protocol:
For mice tissues, total RNA was extracted in TRIzol reagent (Ambion). Extraction of the aqueous phase was performed using chlorophorm and RNA precipitation was achieved with isopropanol. RNA pellets were washed in ice-cold 75% EtOH and allowed to dry before suspension in DEPC-treated H2O.
Oligonucleotide baits targeting the entire non-repetitive portion of Hsa21 (hg19) and its syntenic regions in the mouse (mm10) genome, obtained using the UCSC Genome Browser liftOver tool, were designed and synthesized by Roche/NimbleGen. In total, the array targeted 25.3 Mb comprising 0.87% of the human genome and 20.3 Mb comprising 0.77% of the mouse genome. According to procedures described previously (Mercer et al., 2014), total RNA samples were assessed for potential gDNA contamination by PCR and accordingly treated with Turbo DNAse (Ambion). Samples were spiked with ERCC RNA spike-in controls (Mix 2) (Jiang et al., 2011) to a final 1% concentration and rRNA-depleted using the Ribo-Zero rRNA removal magnetic kit (Human/Mouse/Rat, Epicentre). Capture enrichment of cDNA libraries was performed as described previously (Mercer et al., 2014). Short-read sequencing libraries were prepared with the Illumina TruSeq stranded mRNA low-template kit. Libraries were sequenced at the Garvan Institute (Sydney, NSW, Australia) on the Illumina HiSeq 2000 or Illumina HiSeq 2500 platforms, generating 2 x 101bp and 2 x 125bp paired-end sequencing, respectively.

value: testis

tag: Stage

value: adult

tag: type


title: tc1_testis_captureseq_rep2

tag: tissue


title: tc1_testis_captureseq_rep1


title: tc1_kidney_captureseq_rep3

source_name: tc1 mouse kidney

value: kidney


title: tc1_kidney_captureseq_rep2


title: 74 control rep1

description: RDP1: NSFTV_74

source_name: shoot

value: shoot


title: tc1_kidney_captureseq_rep1


title: tc1_brain_captureseq_rep3

source_name: tc1 mouse brain

value: brain


title: 72 salt-stress rep1

description: RDP1: NSFTV_72

value: 8 days old


title: tc1_brain_captureseq_rep2


title: 72 control rep2

description: RDP1: NSFTV_72


title: 72 control rep1

description: RDP1: NSFTV_72


title: tc1_brain_captureseq_rep1


title: 70 salt-stress rep2

description: RDP1: NSFTV_70


title: mmu_testis_captureseq_rep1

description: mouse syntenic regions RNA CaptureSeq

source_name: mouse testis

value: wild type


title: 70 control rep2

description: RDP1: NSFTV_70


title: 70 control rep1

description: RDP1: NSFTV_70


title: mmu_kidney_captureseq_rep3

description: mouse syntenic regions RNA CaptureSeq

source_name: mouse kidney


title: mmu_testis_captureseq_rep2

description: mouse syntenic regions RNA CaptureSeq


title: 70 salt-stress rep1

description: RDP1: NSFTV_70


title: mmu_kidney_captureseq_rep1

description: mouse syntenic regions RNA CaptureSeq


title: 66 salt-stress rep1

description: RDP1: NSFTV_66


title: mmu_brain_captureseq_rep2

description: mouse syntenic regions RNA CaptureSeq

source_name: mouse brain


title: mmu_brain_captureseq_rep1

description: mouse syntenic regions RNA CaptureSeq


title: 72 salt-stress rep2

description: RDP1: NSFTV_72


title: 66 control rep2

description: RDP1: NSFTV_66


title: 66 control rep1

description: RDP1: NSFTV_66


title: 620 control rep2

description: RDP1: NSFTV_620


title: 620 salt-stress rep1

description: RDP1: NSFTV_620


title: 620 salt-stress rep2

description: RDP1: NSFTV_620


title: 620 control rep1

description: RDP1: NSFTV_620


title: 168FARN rep2 (3'-seq)

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Down-regulated_IPA_168FARN_vs_4T1.txt
Up-regulated_IPA_168FARN_vs_4T1.txt
Down-regulated_IPA_168FARN_vs_4T07.txt
Up-regulated_IPA_168FARN_vs_4T07.txt
A162T4.R1_q20_peaks_filt.bed
3'-seq

data_processing:
Raw reads were trimmed in their 5’ and 3’ ends to remove uninformative nucleotides due to primer sequences, nucleotides added by SMART Scribe RT enzyme and polyA tail of mRNAs.
Trimmed reads of 25 bp or more were aligned on the Mouse reference genome (mm9) using Bowtie2 (version 2.2.5; Langmead 2012). Only reads with a mapping quality score (MAPQ) of 20 or more were retained (Samtools version 1.1) for downstream analysis.
Reads were then clustered along the genome using Bedtools (version 2.17.0; Aaron 2010) allowing a maximum distance of 170 bp (max library fragment length (300bp) – min fragment length (60bp) – read length (50bp) – oligodT length (25bp)) and a minimum number of 5 reads per peak.
Peaks with a stretch of 6 consecutive As (or 8 As out of 9 nucleotides) within 150 bp downstream were filtered out, as they are likely due to internal priming of oligo-dT.
Overlapping peaks from all analyzed samples were merged to define a common set of genomic windows corresponding to polyA sites.
To annotate peak location within genes, gene coordinates were obtained on the basis of overlapping Refseq transcripts with the same gene symbol. Peaks overlapping any intronic region of a gene were classified as intronic polyA (IPA) peaks. Peaks overlapping the last exon of a gene were classified as LE peaks.
Differential analyses between two conditions were done using two independent biological replicates per condition. To compare the regulation of each IPA to the regulation of the gene’s last exon (taken as the sum of the peaks in this exon), we used DESeq2 (version 1.4.5; Love 2014) and the following statistical model: Y ij = μ + L i + C j + (LC) ij + E ij where Y ij is the normalized counts of peak i in biological condition j, μ is the mean, L i is the peak localization (IPA or LE), C j is the biological condition, (LC)ij is the interaction between peak localization and biological condition, and Eij is the residual. Adjusted P-values (Benjamini-Hochberg) were calculated.
Genome_build: mm9
Supplementary_files_format_and_content: .bed peak files, tab-delimited text files representing regulated IPA peaks were generated after the MAPQ filter

source_name: Mouse mammary tumor cell line

growth_protocol: Cell lines  kindly provided by F. Miller (Michigan Cancer Foundation, Detroit, Michigan, USA) were cultured in DMEM GlutaMax media (Life Technologies) supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Life Technologies). After DNAse I treatment (TURBO DNA-free, Ambion) the RNA was quantified using a NanoDrop 2000 instrument (Thermo Scientific).
5 µg of total RNA was used for poly(A)+ RNA purification with MicroPoly(A)Purist™ Kit (Ambion). Poly(A)+ RNA was fragmented at 70°C for 10 min in  RNA Fragmentation buffer (Ambion). After ethanol precipitation, RNA was reverse transcribed using anchored oligo-dT and SMART Scribe RT enzyme (Clontech) allowing to add adapter sequences to the 5’ and 3’ ends of RNA fragments. Libraries were amplified by 13 cycles of PCR with Phusion polymerase (New England Biolabs). A size selection step was done using Agencourt AMPure XP (Beckman Coulter) magnetic beads to obtain fragments of 200–300 bp. Purified libraries were subjected to sequencing using the HiSeq 2000 machine (Illumina). 50 bp reads were obtained by single-end sequencing with P5 Illumina primers.

treatment_protocol: For 4T1-U1-ASO samples, antisense morpholino oligonucleotides coupled to an Endo Porter (6 µl/mL) delivery reagent (Gene Tools, LLC) were added to cell culture media.

tag: invasive status

value: non-invasive tumor cells


title: mmu_testis_captureseq_rep3

description: mouse syntenic regions RNA CaptureSeq


title: 168FARN rep1 (3'-seq)

description:
Down-regulated_IPA_168FARN_vs_4T1.txt
Up-regulated_IPA_168FARN_vs_4T1.txt
Down-regulated_IPA_168FARN_vs_4T07.txt
Up-regulated_IPA_168FARN_vs_4T07.txt
A162T3.R1_q20_peaks_filt.bed
3'-seq


title: 4T07 rep2 (3'-seq)

description:
Down-regulated_IPA_168FARN_vs_4T07.txt
Up-regulated_IPA_168FARN_vs_4T07.txt
Down-regulated_IPA_67NR_vs_4T07.txt
Up-regulated_IPA_67NR_vs_4T07.txt
A162T6.R1_q20_peaks_filt.bed
3'-seq

value: invasive tumor cells


title: mmu_brain_captureseq_rep3

description: mouse syntenic regions RNA CaptureSeq


title: 66 salt-stress rep2

description: RDP1: NSFTV_66


title: 4T07 rep1 (3'-seq)

description:
Down-regulated_IPA_168FARN_vs_4T07.txt
Up-regulated_IPA_168FARN_vs_4T07.txt
Down-regulated_IPA_67NR_vs_4T07.txt
Up-regulated_IPA_67NR_vs_4T07.txt
A162T5.R1_q20_peaks_filt.bed
3'-seq


title: 619 salt-stress rep1

description: RDP1: NSFTV_619


title: 619 control rep2

description: RDP1: NSFTV_619


title: 67NR rep1 (3'-seq)

description:
Down-regulated_IPA_67NR_vs_4T1.txt
Up-regulated_IPA_67NR_vs_4T1.txt
Down-regulated_IPA_67NR_vs_4T07.txt
Up-regulated_IPA_67NR_vs_4T07.txt
A162T1.R1_q20_peaks_filt.bed
3'-seq


title: 67NR rep2 (3'-seq)

description:
Down-regulated_IPA_67NR_vs_4T1.txt
Up-regulated_IPA_67NR_vs_4T1.txt
Down-regulated_IPA_67NR_vs_4T07.txt
Up-regulated_IPA_67NR_vs_4T07.txt
A162T2.R1_q20_peaks_filt.bed
3'-seq


title: 619 control rep1

description: RDP1: NSFTV_619


title: 4T1 rep2 (3'-seq)

description:
Down-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
Up-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
Down-regulated_IPA_67NR_vs_4T1.txt
Up-regulated_IPA_67NR_vs_4T1.txt
Down-regulated_IPA_168FARN_vs_4T1.txt
A162T8.R1_q20_peaks_filt.bed
3'-seq


title: 60 salt-stress rep1

description: RDP1: NSFTV_60


title: 60 control rep2

description: RDP1: NSFTV_60


title: 5 salt-stress rep2

description: RDP1: NSFTV_5


title: 60 control rep1

description: RDP1: NSFTV_60


title: 5 salt-stress rep1

description: RDP1: NSFTV_5


title: 4T1-U1-ASO rep1 (3'-seq)

description:
Down-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
Up-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
A162T9.R1_q20_peaks_filt.bed
3'-seq

tag: treatment

value: transfected with antisense oligo targeting U1 snRNA


title: 5 control rep2

description: RDP1: NSFTV_5


title: 4T1 rep1 (3'-seq)

description:
Down-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
Up-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
Down-regulated_IPA_67NR_vs_4T1.txt
Up-regulated_IPA_67NR_vs_4T1.txt
Down-regulated_IPA_168FARN_vs_4T1.txt
A162T7.R1_q20_peaks_filt.bed
3'-seq


title: TIA1 rep3 (CLIP-seq)

description: immunoprecipitated RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt software version 1.8.2 with this parameter -m 19
CLIP-seq reads were aligned to the mm9 genome assembly using TopHat version 2.1.1 with the following configurations -N 2 –read-edit-dist 2 -x 1 -g 1
Data were filtered with MAPQ ≥ 20 and remove duplicated reads
Peaks were called using Piranha version 1.2.1 with the following setting: -s -v -b 50 -a 0.95
To annotate peak location within genes, gene coordinates were obtained on the basis of overlapping RefSeq transcripts with the same gene symbol
Only peaks found (or overlapping) in at least 2 of 3 replicates are keeped. We remove peaks present in several genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files were generated after the annotation peaks (raw count)
Supplementary_files_format_and_content: A tab-delimited text file of merged peaks was generated keeping only the peaks found (or overlapping) in at least 2 of 3 replicates

growth_protocol: 4T1 cells  kindly provided by F. Miller (Michigan Cancer Foundation, Detroit, Michigan, USA) were cultured in DMEM GlutaMax media (Life Technologies) supplemented with 10% FBS.

extract_protocol:
For CLIP, after UV light crosslinking (400 mJ/cm2 at 254nm, Stratalinker 1800) to covalently bind proteins to RNA molecules, cells were lysed using PLX buffer (1X PBS, 0.1% SDS, 0.5% NP40, 0.5% sodium deoxycholate). Endogenous TIA1-RNA complexes were immunoprecipitated overnight at 4°C using rabbit monoclonal TIA1 antibody (clone EPR9304) or goat anti-TIA1 (Santa Cruz, C20, sc-1751 for CLIP-seq) coupled to Dynabeads® Protein G (Novex). 10% of the initial extract was kept as input. Two extensive washes were performed with RIPA-S (50 mM Tris-HCl pH 7.5, 0.1% SDS, 0.5% NP40, 1% sodium deoxycholate, 5 mM EDTA, 1 M NaCl, 2 M Urea) and PNK buffer (50 mM Tris-HCl pH 7.5, 0.5% NP40, 5 mM MgCl2). For CLIP-seq, the RNA was radioactively labelled on beads. After gel electrophoresis and nitrocellulose membrane transfer, protein-RNA complexes were visualized by autoradiogram. The RNA was recovered by proteinase K digestion.
The libraries were prepared by the TruSeq Small RNA Library prep (Illumina) according to the manufacturer’s instructions. Purified libraries were sequenced using the HiSeq 2500 machine (Illumina). 50 bp reads were obtained by single-end sequencing with P5 Illumina primers.

treatment_protocol: No treatment.

tag: cell line

value: 4T1 - Mouse mammary tumor cell line

tag: ip antibody

value: TIA1 antibody


title: 59 salt-stress rep2

description: RDP1: NSFTV_59


title: 5 control rep1

description: RDP1: NSFTV_5


title: TIA1 rep1 (CLIP-seq)

description: immunoprecipitated RNA


title: 59 salt-stress rep1

description: RDP1: NSFTV_59


title: HU09: Homeostasis  H2AK119ub replicate3

city: Madrid

first: Monica

last: Franch

address: Darwin 3

department: BioinfoGP

country: Spain

institute: National Center for Biotechnology-CSIC

description: Homeostasis  H2AK119ub

data_processing:
Chip-seq reads were aligned to Mouse genome (Ensembl version GRCm38.85) using Bowtie2 software with default parameters
Data was transformed into a independent plataform using makeTagDirectory function with parameter mapq 1 from HOMER version 4.8
Peaks were called using HOMER’s findpeaks function version 4.8 using by default parameters (FDR < 0.001)
Genome_build: Mouse genome (Ensembl version GRCm38.85)
Supplementary_files_format_and_content: Standard bed files containing peak coordinates, detected as described in “data processing”

source_name: Sca1+CD45- cardiac cells

growth_protocol: Cardiac cells from 6-8 weeks-old mice were enriched in Sca1+CD45- population by magnetic cell sorting. Sca1+CD45- cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM, Invitrogen) containing 10% fetal bovine serum (ESCell FBS, Gibco), 100 U/ml penicillin, 100 mg/ml streptomycin and 2 mM L-glutamine (all from Invitrogen), 103 units ESGRO Supplement (Millipore), 10 ng/ml EGF (epidermal growth factor; Sigma) and 20 ng/ml FGF (fibroblast growth factor; Peprotech) (37°C, 3% O2, 5% CO2).

extract_protocol:
After isolating the Sca1+CD45- cardiac population, we added formaldehyde directly to the cell suspension (final concentration 1%) and incubated cells on a shaking platform (10 min, RT).  Crosslinking was terminated by adding glycine (0.125 M; 5 min).  Crosslinked cells were washed twice with cold PBS and lysed at a density of 5 × 106 cells ml−1 in 1% SDS, 50 mM Tris-HCl (pH 8.0) and 10 mM EDTA, with protease inhibitors (15 min, 4°C).  Lysates were sonicated lysates to obtain chromatin fragments <1 kb, then centrifuged (15 min, RT), lysate diluted 1:10 with 1.1% Triton-X100, 2 mM EDTA, 150 mM NaCl and 20 mM Tris-HCl (pH 8.0) containing protease inhibitors, precleared with 50% salmon sperm DNA and protein A agarose slurry (Upstate).  Antibodies were added (O/N, 4ºC) (for antibodies used, see Appendix S2).  We then added salmon sperm DNA and protein A agarose beads (60 l) and incubated (1 h, 4ºC).  Samples were centrifuged and immunoprecipitated pellets washed with 0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl (once); 0.1% SDS, 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl (once); 0.25 M LiCl, 1% Nonidet P-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.0) (once); and 10 mM Tris-HCl (pH 8.0), 1 mM EDTA(twice).  Chromatin was eluted from beads twice by incubation with 250 l 1% SDS, 0.1 M NaHCO3 with rotation (15 min, RT).  Crosslinking was reversed by adding 20 l 5 M NaCl (4 h, 65°C).  Samples were supplemented with 20 l 1 M Tris-HCl (pH 6.5), 10 l 0.5 M EDTA, 20 g RNase A and 40 g proteinase K and incubated (1 h, 45°C), followed by DNA isolation using a kit (MO BIO).
Libraries were prepared using the NEBNext Ultra DNA Library Prep for Illumina kit (E7370; New England Biolabs).  Briefly, from 1 to 5 ng of input and ChIP-enriched DNA were subjected to end repair and addition of “A” bases to 3′ ends, ligation of adapters and USER excision.  All purification steps were performed using AgenCourt AMPure XP beads (A63881, Qiagen).  Libraries were amplified by PCR using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1; E7335 or Index Primers Set 2; E7500).  Final libraries were analyzed using Agilent High Sensitivity chip to estimate quantity and confirm size distribution, and then quantified by qPCR using the KAPA Library Quantification Kit (KK4835, KapaBiosystems) prior to amplification with Illumina cBot.  Libraries were loaded at a 1.42 pM concentration onto the flow cell and were sequenced 1 x 50 on Illumina HiSeq 2500.

treatment_protocol: For “Damaged” samples, each mouse received a single dose of 20 mg/kg Paraquat (i.p.) dissolved in PBS. For “Homeostasis” samples, mice only received PBS.

tag: strain

value: Sca1+CD45- cardiac cells

value: Homeostasis

tag: chip-protein


title: INP1: Input 1

description: Input

value: not treated


title: HU05: Homeostasis  H2AK119ub replicate2

description: Homeostasis  H2AK119ub


title: 59 control rep2

description: RDP1: NSFTV_59


title: INP2: Input 2

description: Input


title: mmu_kidney_captureseq_rep2

description: mouse syntenic regions RNA CaptureSeq


title: 57 salt-stress rep2

description: RDP1: NSFTV_57


title: HU03: Homeostasis  H2AK119ub replicate1

description: Homeostasis  H2AK119ub


title: 4T1-U1-ASO rep2 (3'-seq)

description:
Down-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
Up-regulated_IPA_4T1-U1-ASO_vs_4T1.txt
A162T12.R1_q20_peaks_filt.bed
3'-seq


title: HB06: Homeostasis BMI1 replicate2

description: Homeostasis BMI1


title: 60 salt-stress rep2

description: RDP1: NSFTV_60


title: 57 salt-stress rep1

description: RDP1: NSFTV_57


title: 57 control rep2

description: RDP1: NSFTV_57


title: TIA1 rep2 (CLIP-seq)

description: immunoprecipitated RNA


title: DU03: Damage H2AK119ub replicate3

description: Damage H2AK119ub

value: Damaged


title: HB01: Homeostasis BMI1 replicate1

description: Homeostasis BMI1


title: DU02: Damage H2AK119ub replicate2

description: Damage H2AK119ub


title: DU01: Damage H2AK119ub replicate1

description: Damage H2AK119ub


title: 55 salt-stress rep2

description: RDP1: NSFTV_55


title: 57 control rep1

description: RDP1: NSFTV_57


title: 55 salt-stress rep1

description: RDP1: NSFTV_55


title: 55 control rep2

description: RDP1: NSFTV_55


title: DB02: Damage BMI1 replicate2

description: Damage BMI1


title: DB03: Damage BMI1 replicate3

description: Damage BMI1


title: 55 control rep1

description: RDP1: NSFTV_55


title: DB01: Damage BMI1 replicate1

description: Damage BMI1


title: 59 control rep1

description: RDP1: NSFTV_59


title: 4 salt-stress rep1

description: RDP1: NSFTV_4


title: 4 control rep2

description: RDP1: NSFTV_4


title: 4 salt-stress rep2

description: RDP1: NSFTV_4


title: RNP granule fraction arsenite treated sample replicate 1

city: Ithaca

first: Hojoong

last: Kwak

state: NY

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

description:
Ins_AS_Rep1
readcounts.rep1.txt

data_processing:
Read alignment using TopHat with default parameters
Read count calculation using bedtools coverage with -s (strand specific) and -split (calculate from exons) options and mm10 refSeq annotation bed file
Genome_build: mm10
Supplementary_files_format_and_content: Text delimited file containing read count tables

molecule: cytoplasmic RNA

extract_protocol:
RNA extraction using Trizol
rRNA depletion using Illumina RiboZero kit followd by strand specific RNA-seq library preparation using BIOO scientific NextFlex directional RNA-seq library kit

value: AS

tag: fraction

value: RNP granule


title: 4 control rep1

description: RDP1: NSFTV_4


title: RNP granule fraction arsenite treated sample replicate 2

description:
Ins_AS_Rep2
readcounts.rep2.txt


title: HB07: Homeostasis BMI1 replicate3

description: Homeostasis BMI1


title: Cytoplasmic arsenite treated sample replicate 2

description:
Cyt_AS_Rep2
readcounts.rep2.txt

source_name: Cytoplasmic arsenite treated sample

value: Cytoplasm


title: Cytoplasmic arsenite treated sample replicate 1

description:
Cyt_AS_Rep1
readcounts.rep1.txt


title: 46 salt-stress rep2

description: RDP1: NSFTV_46


title: RNP granule fraction heat shock treated sample replicate 2

description:
Ins_HS_Rep2
readcounts.rep2.txt

value: HS


title: RNP granule fraction heat shock treated sample replicate 1

description:
Ins_HS_Rep1
readcounts.rep1.txt


title: 46 salt-stress rep1

description: RDP1: NSFTV_46

value: shoot


title: 46 control rep1

description: RDP1: NSFTV_46


title: Cytoplasmic heat shock treated sample replicate 1

description:
Cyt_HS_Rep1
readcounts.rep1.txt

source_name: Cytoplasmic heat shock treated sample


title: 44 salt-stress rep2

description: RDP1: NSFTV_44


title: Cytoplasmic heat shock treated sample replicate 2

description:
Cyt_HS_Rep2
readcounts.rep2.txt


title: 44 salt-stress rep1

description: RDP1: NSFTV_44


title: RNP granule fraction H2O treated sample replicate 1

description:
Ins_CO_Rep1
readcounts.rep1.txt

source_name: RNP granule fraction H2O treated sample


title: Cytoplasmic H2O treated sample replicate 1

description:
Cyt_CO_Rep1
readcounts.rep1.txt

source_name: Cytoplasmic H2O treated sample


title: 44 control rep2

description: RDP1: NSFTV_44


title: Cytoplasmic H2O treated sample replicate 2

description:
Cyt_CO_Rep2
readcounts.rep2.txt


title: 40 salt-stress rep2

description: RDP1: NSFTV_40


title: 44 control rep1

description: RDP1: NSFTV_44


title: 40 control rep2

description: RDP1: NSFTV_40


title: 40 salt-stress rep1

description: RDP1: NSFTV_40


title: RNP granule fraction Thapsigargin treated sample replicate 1

description:
Ins_THAP_Rep1
readcounts.rep1.txt

value: THAP


title: RNP granule fraction Thapsigargin treated sample replicate 2

description:
Ins_THAP_Rep2
readcounts.rep2.txt


title: Cytoplasmic Thapsigargin treated sample replicate 3

description:
Cyt_THAP_Rep3
readcounts.rep3.txt

source_name: Cytoplasmic Thapsigargin treated sample


title: RNP granule fraction Thapsigargin treated sample replicate 3

description:
Ins_THAP_Rep3
readcounts.rep3.txt


title: 39 salt-stress rep2

description: RDP1: NSFTV_39

value: 8 days old


title: 40 control rep1

description: RDP1: NSFTV_40


title: Cytoplasmic Thapsigargin treated sample replicate 1

description:
Cyt_THAP_Rep1
readcounts.rep1.txt


title: 39 salt-stress rep1

description: RDP1: NSFTV_39


title: Cytoplasmic Thapsigargin treated sample replicate 2

description:
Cyt_THAP_Rep2
readcounts.rep2.txt


title: RNP granule fraction DMSO treated sample replicate 3

description:
Ins_DMSO_Rep3
readcounts.rep3.txt

value: DMSO


title: 39 control rep1

description: RDP1: NSFTV_39


title: 39 control rep2

description: RDP1: NSFTV_39


title: 46 control rep2

description: RDP1: NSFTV_46


title: RNP granule fraction DMSO treated sample replicate 2

description:
Ins_DMSO_Rep2
readcounts.rep2.txt


title: 395 salt-stress rep2

description: RDP1: NSFTV_395


title: RNP granule fraction H2O treated sample replicate 2

description:
Ins_CO_Rep2
readcounts.rep2.txt


title: 395 control rep2

description: RDP1: NSFTV_395


title: Cytoplasmic DMSO treated sample replicate 3

description:
Cyt_DMSO_Rep3
readcounts.rep3.txt

source_name: Cytoplasmic DMSO treated sample


title: RNP granule fraction DMSO treated sample replicate 1

description:
Ins_DMSO_Rep1
readcounts.rep1.txt


title: Cytoplasmic DMSO treated sample replicate 1

description:
Cyt_DMSO_Rep1
readcounts.rep1.txt


title: 395 control rep1

description: RDP1: NSFTV_395


title: Cytoplasmic DMSO treated sample replicate 2

description:
Cyt_DMSO_Rep2
readcounts.rep2.txt


title: 381 salt-stress rep2

description: RDP1: NSFTV_381


title: 381 salt-stress rep1

description: RDP1: NSFTV_381


title: 381 control rep1

description: RDP1: NSFTV_381


title: 381 control rep2

description: RDP1: NSFTV_381


title: CSF3RT618I

city: Cincinnati

first: Mohammad

last: Azam

state: OH

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

institute: Cincinnati Childrens Hospital and Medical Center

data_processing:
RNA-Seq analysis is based on the TopHat/Cufflinks pipeline.  First, sequences were aligned to the reference genome with TopHat, which efficiently aligns reads spanning known or novel splice junctions.  Each sample is then independently processed with Cufflinks2 in order to generate an initial transcriptome.  We then used the Cuffmerge tool to merge the private transcriptomes into a single reference, and at the same time annotate known genes and extend partial transcripts.  This common transcriptome was then  used in a second pass with Cufflinks, which  quantified each transcript and gene (known or novel) in each sample.  The reference annotation used is based on the UCSC knownGenes table and includes the long non-coding RNAs.
Genome_build: mm10
Supplementary_files_format_and_content: Gene matrix Spread sheet

source_name: Kit+ Bone marrow cells

growth_protocol: Kit+ cells from the bonemarrow of WT mice were isolated using the CD117 MicroBead Kit (Miltenyi biotec) according to their instructions. These cells were incubated overnight in IMDM media supplemented with 10% FBS and cytokine cocktail of FLT3, IL-6, IL-3, and mSCF(complete IMDM).

extract_protocol:
Total RNA was isolated using miRNA easy Mini Kit according to the manufacturers protocol. (Qiagen)
TruSeq Stranded mRNA library preparation method.  The protocol was followed as per the manufacturer.

treatment_protocol: After 12 hours of stimulation cells were transduced with  control vector or CSF3R mutant retro virus using retronectin (Takara). One to two million positive cells (isolated by FACS) from each group were grown overnight in complete IMDM

tag: genotype/variation


title: 37 salt-stress rep1

description: RDP1: NSFTV_37


title: CSF3RT618IW791


title: 37 salt-stress rep2

description: RDP1: NSFTV_37


title: Vector_control


title: CSF3RQ741


title: CSF3RW791


title: 37 control rep1

description: RDP1: NSFTV_37


title: 37 control rep2

description: RDP1: NSFTV_37


title: EZH1 HET AGM count

city: Boston

first: Melissa

last: Kinney

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.1 –o 10)
Then, the cleaned reads were aligned to the human genome/transcriptome (hg19 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (--library-type=fr-unstranded --min-intron-length=10 --no-coverage-search --microexon-search --min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene using a htseq-count tool with the following parameters (--stranded=no --idattr=gene_id -t exon -i gene_name).
Genome_build: hg19
Supplementary_files_format_and_content: .txt files containing read counts from htseq-count

source_name: Mouse VE-cadherin+cKit+CD45+CD41+ AGM cells

growth_protocol: Human CD34- and MSC-iPS cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Dox was added at 2 μg/ml (Sigma) and puromycin was added at 0.35 ug/mL (ThermoFisher). Media were changed every 3-4 days. RNA was harvested from bulk day 4 samples, or from sorted CD34+CD38- day 28 samples.  Mouse AGM and YS were microdissected from E10.5 embryos and dissociated to single cells. Cells were then sorted for immunophenotypic markers cKit+VE-Cadherin+CD45+CD41+.

extract_protocol: For 5F cells, we used the NEB ultradirectional kit with 50 ng of input RNA. For mouse YS and AGM cells, we used the Clontech smarterseq kit with 10 ng input RNA.

treatment_protocol: 5F cells were transfected with 2x shRNAs targeting the luciferase (shRNAs F8 and C11) and EZH1(shRNAs D4 and D6) genes. mRNA was collected 4 and 28 days after transfection

tag: cell type

value: Hematopoietic cells


title: wt AGM count


title: 379 salt-stress rep1

description: RDP1: NSFTV_379


title: EZH1 HET YS count

source_name: Mouse VE-cadherin+cKit+CD45+CD41+ YS cells


title: EZH1 KO AGM count


title: 379 salt-stress rep2

description: RDP1: NSFTV_379


title: 379 control rep2

description: RDP1: NSFTV_379


title: 379 control rep1

description: RDP1: NSFTV_379


title: 395 salt-stress rep1

description: RDP1: NSFTV_395


title: MBD_Ctrl_HFD_rep_6

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

description: MBD.xlsx

data_processing:
supplementary files format and content: An excel sheet containing the promoters, gene exons, CpG island and CpG shores differentially methylated in response to exercise. The CpG islands/shores are annotated with their nearest gene
Reads were preprocessed using trimmomatic using the parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15 and trimmed for Illumina primers
The preprocessed reads were aligned to the mm10 genome using bowtie2 with the --very-sensitive setting
Picard-tools markDuplicates were used to remove duplicates
The read coverage of CpG islands, CpG shores, RefSeq promoters defined as +/- 1000 bp from transcription start site and RefSeq exons were computed with featureCounts (25), extending reads to 253bp; the median length estimated by Bioanalyzer
Regions surviving a 1 RPKM in more than 12 samples inclusion criterion were tested for differential expression with edgeR using the glmFit/glmLRT functions and tagwise dispersion.
Basecalls performed using CASAVA version 1.8.2
Genome_build: mm10

source_name: satellite cells

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen), and quantified using Qubit dsDNA HS kit (Life Technologies). Purified DNA was sonicated to achieve fragments between 100-1000 bp in size.
Methylated DNA was captured using MethylMiner (Invitrogen). Methylated DNA was captured by beads conjugated with methyl-binding-domains (MBD). Captured DNA was eluted using a high-salt buffer, followed by ethanol precipitation. Recovered DNA was prepared for sequencing by adenylation using dATP and Klenow DNA polymerase (3’ to 5’ exo minus) (New England Biolabs) followed by ligation to TruSeq adapters (Illumina). Ligation products were purified using AMPure Beads, subjected to an ethanol-based cleanup and amplified by PCR (30s 98°C; (10s 98°C, 30s 60°C; 30s 72°C) x 18-25 cycles; 5 min 72°C) using Phusion DNA Polymerase (New England Biolabs). PCR products were purified using AMPure Beads (Beckman Coulter). Libraries were quality-controlled using a Bioanalyzer instrument (Agilent)

tag: radiation

value: Ctrl

tag: diet

value: HFD


title: EZH1 KO YS count


title: 371 salt-stress rep2

description: RDP1: NSFTV_371

source_name: shoot


title: CSF3RT618IQ741


title: 371 control rep2

description: RDP1: NSFTV_371


title: MBD_Ctrl_Chow_rep_6

description: MBD.xlsx

value: Chow


title: 36 salt-stress rep2

description: RDP1: NSFTV_36


title: 36 control rep1

description: RDP1: NSFTV_36


title: 36 control rep2

description: RDP1: NSFTV_36


title: MBD_Irr_HFD_rep_5

description: MBD.xlsx

value: Irr


title: 371 control rep1

description: RDP1: NSFTV_371


title: 356 control rep1

description: RDP1: NSFTV_356


title: 356 control rep2

description: RDP1: NSFTV_356


title: MBD_Irr_Chow_rep_4

description: MBD.xlsx


title: MBD_Irr_HFD_rep_4

description: MBD.xlsx


title: wt YS count


title: MBD_Ctrl_HFD_rep_4

description: MBD.xlsx


title: 356 salt-stress rep2

description: RDP1: NSFTV_356


title: 349 salt-stress rep2

description: RDP1: NSFTV_349


title: MBD_Irr_HFD_rep_3

description: MBD.xlsx


title: MBD_Ctrl_Chow_rep_4

description: MBD.xlsx


title: 371 salt-stress rep1

description: RDP1: NSFTV_371


title: MBD_Ctrl_HFD_rep_3

description: MBD.xlsx


title: 349 salt-stress rep1

description: RDP1: NSFTV_349


title: MBD_Irr_Chow_rep_6

description: MBD.xlsx


title: 349 control rep2

description: RDP1: NSFTV_349


title: MBD_Irr_Chow_rep_3

description: MBD.xlsx


title: 36 salt-stress rep1

description: RDP1: NSFTV_36


title: MBD_Ctrl_Chow_rep_5

description: MBD.xlsx


title: 349 control rep1

description: RDP1: NSFTV_349


title: 619 salt-stress rep2

description: RDP1: NSFTV_619


title: MBD_Ctrl_HFD_rep_5

description: MBD.xlsx


title: MBD_Irr_HFD_rep_6

description: MBD.xlsx


title: MBD_Ctrl_Chow_rep_3

description: MBD.xlsx


title: MBD_Irr_Chow_rep_5

description: MBD.xlsx


title: 348 salt-stress rep2

description: RDP1: NSFTV_348


title: MBD_Ctrl_HFD_rep_2

description: MBD.xlsx


title: MBD_Ctrl_Chow_rep_2

description: MBD.xlsx


title: 348 control rep2

description: RDP1: NSFTV_348


title: MBD_Ctrl_HFD_rep_1

description: MBD.xlsx


title: MBD_Irr_HFD_rep_2

description: MBD.xlsx


title: 348 control rep1

description: RDP1: NSFTV_348


title: MBD_Irr_Chow_rep_2

description: MBD.xlsx


title: 347 salt-stress rep2

description: RDP1: NSFTV_347


title: 347 salt-stress rep1

description: RDP1: NSFTV_347


title: MBD_Ctrl_Chow_rep_1

description: MBD.xlsx


title: MBD_Irr_Chow_rep_1

description: MBD.xlsx


title: 33 salt-stress rep2

description: RDP1: NSFTV_33


title: RNA_Ctrl_HFD_rep_6

description: RNA.xlsx

data_processing:
supplementary files format and content: An excel sheet with the main effect of radiation, the effect of radiation in high-fat diet fed mice, the effect of radiation in CHOW fed mice and the effect of high-fat diet in radiated mice.
Files were preprocessed with trim_galore v0.4.0
Preprocessed reads were aligned to mm10 using tophat2 with the --very-sensitive setting
Exonic read coverage was computed with featureCounts
Tests for differential gene expression was conducted using edgeR followed by correction for multiple testing with the Benjamini-Hochberg method.
Basecalls performed using CASAVA version 1.8.2
Genome_build: mm10

extract_protocol:
Total RNA was isolated with TRIzol reagent (Life Technologies) or Qiagen’s Allprep DNA/RNA/miRNA Universal Kit according to the manufacturer’s protocols
Sequencing was performed according to Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol. mRNA was depleted for ribosomal RNA, fragmented and cDNA was synthesized cDNA using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was subjected to a cleanup using AMPure beads (Beckman Coulter) and adenylated to prime for adapter ligation. After a cleanup using AMPure beads DNA fragments were amplified using PCR with the following settings: (30s 98°C; (10s 98°C, 30s 60°C; 30s 72°C) x 9-13 cycles; 5 min 72°C) followed by a final cleanup


title: 347 control rep1

description: RDP1: NSFTV_347


title: RNA_Ctrl_ch_rep_6

description: RNA.xlsx


title: MBD_Irr_HFD_rep_1

description: MBD.xlsx


title: 33 salt-stress rep1

description: RDP1: NSFTV_33


title: 339 salt-stress rep2

description: RDP1: NSFTV_339


title: RNA_Irr_HFD_rep_6

description: RNA.xlsx


title: RNA_Ctrl_ch_rep_5

description: RNA.xlsx


title: 33 control rep2

description: RDP1: NSFTV_33


title: RNA_Irr_ch_rep_6

description: RNA.xlsx


title: 33 control rep1

description: RDP1: NSFTV_33


title: 348 salt-stress rep1

description: RDP1: NSFTV_348


title: 339 control rep2

description: RDP1: NSFTV_339


title: 339 control rep1

description: RDP1: NSFTV_339


title: RNA_Irr_ch_rep_5

description: RNA.xlsx


title: 347 control rep2

description: RDP1: NSFTV_347


title: 335 salt-stress rep2

description: RDP1: NSFTV_335


title: RNA_Irr_HFD_rep_4

description: RNA.xlsx


title: 335 salt-stress rep1

description: RDP1: NSFTV_335


title: 356 salt-stress rep1

description: RDP1: NSFTV_356


title: RNA_Irr_ch_rep_4

description: RNA.xlsx


title: 335 control rep2

description: RDP1: NSFTV_335


title: 335 control rep1

description: RDP1: NSFTV_335


title: 329 salt-stress rep2

description: RDP1: NSFTV_329


title: RNA_Ctrl_ch_rep_4

description: RNA.xlsx


title: RNA_Ctrl_HFD_rep_4

description: RNA.xlsx


title: 329 control rep2

description: RDP1: NSFTV_329


title: 329 salt-stress rep1

description: RDP1: NSFTV_329


title: 339 salt-stress rep1

description: RDP1: NSFTV_339


title: RNA_Irr_ch_rep_3

description: RNA.xlsx


title: 329 control rep1

description: RDP1: NSFTV_329


title: RNA_Irr_HFD_rep_5

description: RNA.xlsx


title: RNA_Ctrl_ch_rep_3

description: RNA.xlsx


title: 315 salt-stress rep1

description: RDP1: NSFTV_315


title: RNA_Ctrl_HFD_rep_5

description: RNA.xlsx


title: RNA_Ctrl_HFD_rep_2

description: RNA.xlsx


title: 315 control rep2

description: RDP1: NSFTV_315


title: RNA_Ctrl_ch_rep_2

description: RNA.xlsx


title: RNA_Irr_HFD_rep_2

description: RNA.xlsx


title: RNA_Irr_ch_rep_2

description: RNA.xlsx


title: 315 control rep1

description: RDP1: NSFTV_315


title: 311 salt-stress rep2

description: RDP1: NSFTV_311


title: 311 salt-stress rep1

description: RDP1: NSFTV_311


title: RNA_Ctrl_ch_rep_1

description: RNA.xlsx


title: RNA_Ctrl_HFD_rep_3

description: RNA.xlsx


title: 311 control rep1

description: RDP1: NSFTV_311


title: 311 control rep2

description: RDP1: NSFTV_311


title: RNA_Irr_ch_rep_1

description: RNA.xlsx


title: RRBS_SC_Ctrl_HFD_rep_6

data_processing:
supplementary files format and content: Two xlsx files with DMRs, median change in methylation and annotation with nearest gene
Files were prerpcessed with trim_galore v0.4.0 and the parameter --rrbs, and with Cutadapt v1.8.3
Preprocessed reads were aligned to mm10 using Bismark v0.14.4 using standard setting, and with bowtie2 v2.2.6
Aligned reads were processed using BiSeq v1.10 using the settings suggested in the documentation, except that the parameters perc.samples = 3/6 and min.sites = 5 were used
The model used was formula = ~ Radiation*Diet | Radiation + Diet. Final trimmed clusters were detected with a false discovery rate (FDR) cutoff of 0.1
Basecalls performed using CASAVA version 1.8.2
Genome_build: mm10

extract_protocol:
Genomic DNA was extracted with the Nucleon™ BACC Genomic DNA Extraction Kit (GE Healthcare, Life Sciences).
Reduced Representation Bisulfite Sequencing libraries were constructed as previously described (Boyle et al., 2012, Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome biology 13, R92). Briefly, 200 ng of genomic DNA was digested with 40 U of MspI enzymes (New England Biolabs) and ligated to TruSeq (Illumina) sequencing adaptors. Bisulfite conversion was conducted once with the EpiTecht bisulfite kit (Qiagen) in accordance with the manufacturer’s instructions, and the converted DNA was amplified by PCR and sequenced on a HiSeq Illumina instrument.


title: RRBS_SC_Ctrl_Chow_rep_6


title: RRBS_SC_Irr_HFD_rep_6


title: RRBS_SC_Ctrl_Chow_rep_5


title: 303 salt-stress rep2

description: RDP1: NSFTV_303


title: 306 control rep2

description: RDP1: NSFTV_306


title: 303 salt-stress rep1

description: RDP1: NSFTV_303


title: 306 control rep1

description: RDP1: NSFTV_306


title: RNA_Irr_HFD_rep_3

description: RNA.xlsx


title: RRBS_SC_Ctrl_HFD_rep_5


title: 303 control rep1

description: RDP1: NSFTV_303


title: 302 salt-stress rep2

description: RDP1: NSFTV_302


title: 303 control rep2

description: RDP1: NSFTV_303


title: 315 salt-stress rep2

description: RDP1: NSFTV_315


title: RNA_Irr_HFD_rep_1

description: RNA.xlsx


title: RRBS_SC_Irr_Chow_rep_5


title: RRBS_SC_Irr_HFD_rep_4


title: RRBS_SC_Ctrl_HFD_rep_4


title: RRBS_SC_Ctrl_Chow_rep_4


title: 306 salt-stress rep2

description: RDP1: NSFTV_306


title: 302 control rep1

description: RDP1: NSFTV_302


title: RRBS_SC_Ctrl_HFD_rep_3


title: 306 salt-stress rep1

description: RDP1: NSFTV_306


title: RRBS_SC_Irr_Chow_rep_6


title: 295 salt-stress rep1

description: RDP1: NSFTV_295


title: RRBS_SC_Irr_HFD_rep_5


title: RRBS_SC_Irr_HFD_rep_3


title: RRBS_SC_Irr_Chow_rep_3


title: RRBS_SC_Ctrl_HFD_rep_2


title: 295 control rep1

description: RDP1: NSFTV_295


title: 293 salt-stress rep2

description: RDP1: NSFTV_293


title: 293 salt-stress rep1

description: RDP1: NSFTV_293


title: RRBS_SC_Ctrl_Chow_rep_3


title: RRBS_SC_Irr_HFD_rep_2


title: 302 control rep2

description: RDP1: NSFTV_302


title: RRBS_SC_Irr_Chow_rep_2


title: 293 control rep2

description: RDP1: NSFTV_293


title: 293 control rep1

description: RDP1: NSFTV_293


title: RRBS_SC_Ctrl_Chow_rep_1


title: 271 salt-stress rep1

description: RDP1: NSFTV_271


title: RRBS_SC_Irr_HFD_rep_1


title: 271 control rep2

description: RDP1: NSFTV_271


title: 295 salt-stress rep2

description: RDP1: NSFTV_295


title: 271 control rep1

description: RDP1: NSFTV_271


title: RRBS_SVF_Irr_Chow_rep_4

source_name: Stromal vascular fraction


title: RRBS_SC_Irr_Chow_rep_1


title: 270 salt-stress rep1

description: RDP1: NSFTV_270


title: RRBS_SC_Ctrl_HFD_rep_1


title: RRBS_SVF_Ctrl_Chow_rep_6


title: 295 control rep2

description: RDP1: NSFTV_295


title: RRBS_SVF_Ctrl_HFD_rep_7


title: RRBS_SVF_Ctrl_Chow_rep_5


title: RRBS_SC_Irr_Chow_rep_4


title: RRBS_SC_Ctrl_Chow_rep_2


title: 268 salt-stress rep2

description: RDP1: NSFTV_268


title: 268 salt-stress rep1

description: RDP1: NSFTV_268


title: RRBS_SVF_Irr_HFD_rep_7


title: 270 control rep2

description: RDP1: NSFTV_270


title: 270 control rep1

description: RDP1: NSFTV_270


title: 270 salt-stress rep2

description: RDP1: NSFTV_270


title: 268 control rep2

description: RDP1: NSFTV_268


title: RRBS_SVF_Ctrl_HFD_rep_6


title: 266 salt-stress rep1

description: RDP1: NSFTV_266


title: 266 control rep2

description: RDP1: NSFTV_266


title: 268 control rep1

description: RDP1: NSFTV_268


title: RRBS_SVF_Irr_HFD_rep_6


title: RRBS_SVF_Irr_Chow_rep_3


title: 266 salt-stress rep2

description: RDP1: NSFTV_266


title: RRBS_SVF_Irr_HFD_rep_5


title: 271 salt-stress rep2

description: RDP1: NSFTV_271


title: RRBS_SVF_Ctrl_Chow_rep_4


title: RRBS_SVF_Ctrl_HFD_rep_5


title: RRBS_SVF_Irr_HFD_rep_4


title: 262 salt-stress rep2

description: RDP1: NSFTV_262


title: RRBS_SVF_Ctrl_HFD_rep_4


title: 266 control rep1

description: RDP1: NSFTV_266


title: 262 salt-stress rep1

description: RDP1: NSFTV_262


title: RNA_Ctrl_HFD_rep_1

description: RNA.xlsx


title: RRBS_SVF_Ctrl_HFD_rep_3


title: 262 control rep1

description: RDP1: NSFTV_262


title: RRBS_SVF_Ctrl_HFD_rep_2


title: RRBS_SVF_Ctrl_Chow_rep_3


title: 262 control rep2

description: RDP1: NSFTV_262


title: 25 salt-stress rep1

description: RDP1: NSFTV_25


title: RRBS_SVF_Irr_Chow_rep_2


title: 302 salt-stress rep1

description: RDP1: NSFTV_302


title: RRBS_SVF_Irr_HFD_rep_2


title: 25 control rep2

description: RDP1: NSFTV_25


title: RRBS_SVF_Ctrl_Chow_rep_2


title: RRBS_SVF_Irr_HFD_rep_3


title: RRBS_SVF_Ctrl_HFD_rep_1


title: RRBS_SVF_Irr_Chow_rep_1


title: RRBS_SVF_Irr_HFD_rep_1


title: 256 salt-stress rep2

description: RDP1: NSFTV_256


title: 25 control rep1

description: RDP1: NSFTV_25


title: 258 control rep2

description: RDP1: NSFTV_258


title: 258 salt-stress rep2

description: RDP1: NSFTV_258


title: 258 salt-stress rep1

description: RDP1: NSFTV_258


title: 256 control rep1

description: RDP1: NSFTV_256


title: 256 salt-stress rep1

description: RDP1: NSFTV_256


title: Single_TE_4

city: Beijing

first: YangLu

last: Yang

state: Beijing

address: Beijing Xicheng District Yongan Road NO.95

institute: Beijing Friendship Hospital, Capital Medical University

description:
sequenced on Illumina
Sample 67

data_processing:
library strategy: MAST-seq (Measure a single cell twice by RNA-Seq)
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling. For data from Ion Proton, base calls were collected using Ion Torrent Suite v4.3 software.
Adaptor contamination and low-quality reads were discarded from the raw data.
For Illumina paired-end reads, TopHat (version 2.0.10) were used for sequence alignment, and FPKM values were generated by Cufflinks (version 2.1.1). For Ion Proton RNA-Seq reads, 2-step alignment method which combined STAR (version 2.3.0) and bowtie2 (version 2.1.0) was applied. Unmapped reads produced by STAR were re-mapped with bowtie2 in the “very-sensitive-local” mode, and merged bam files were taken as input by Cufflinks.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly mm10.
Supplementary_files_format_and_content: FPKM table generated by cufflinks

growth_protocol: Isolation of zygotes, 2-cell, 4-cell, 8-cell embryos, inner cell mass (ICM) and trophectoderm (TE). 6- to 8-weeks old ICR female mice were injected with 7.5IU human chorionic gonadotropin (hCG) 46~48h after injection of 7.5IU pregnant mare serum gonadotrophin (PMSG). 2-cell, 4-cell and 8-cell stage embryos were collected from the oviduct of mated mice at 48, 56 and 70h post-hCG, respectively. The embryos were treated with Acid Tyrode’s solution to remove the zona pellucida and then were transferred to trypsin-EDTA and incubated at 37°C for 5 minutes. Then the embryos were washed with PBS-BSA buffer gently to dissociate the embryos into individual blastomeres. ICM and TE were isolated from mouse E3.5 blastocysts (Yan et al. 2013). The trophectoderm was isolated from the blastocysts with zona pellucida removed under a microscope by mechanically cut using a 30G needle. The exposed ICM was gently scraped from the trophectoderm. These two types of cells were then treated with Accutase or 0.005% trypsin at 37 °C for dissociated into single cell. Cell lines. Mouse embryonic fibroblast (MEF) was derived from E13.5 embryos of ICR strain. Mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatinized tissue culture plates and were passaged every two days.

extract_protocol:
The RNA of single mESC was extracted by the MAST-Seq protocol which was developed from the single cell RNA-Seq technique we previously developed (Tang et al. 2010b).
For the library constructed for Illumina sequencing platform, 10-100ng amplified cDNA was fragmentized to about 200bp fragments by Covaris S2, and purified with DNA Clean & Concentrator™-5. Then NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, Catalog #E7370L) was used to construct the cDNA library. The cDNA libraries were sequenced on Illumina HiSeq 2000 and 2500 instrument with 100bp reads and pair-end parameter. For the libraries constructed for Thermo Fisher Proton sequence platform, First, 10-100ng amplified cDNA was fragmentized to about 250bp fragments by Covaris S2, and purified with DNA Clean & Concentrator™-5. The Ion XpressTM Plus Fragment Library Kit (ThermoFisher, cat. no. 4471269) and Ion XpressTM Barcode Adapters 1-16 Kit (Thermo Fisher, cat. No. 4471250) were used to construct the library. Then, sequencing was performed using PI chips with the Ion PI Sequencing 200 kit v3 on Ion PI Proton system.

value: ICR

tag: tissue/cell type

value: mouse trophectoderm


title: 256 control rep2

description: RDP1: NSFTV_256

tag: genotype


title: Single_TE_3

description:
sequenced on Illumina
Sample 66


title: Single_TE_5

description:
sequenced on Illumina
Sample 68


title: Single_TE_2

description:
sequenced on Illumina
Sample 65


title: 255 salt-stress rep2

description: RDP1: NSFTV_255

tag: age


title: Single_TE_1

description:
sequenced on Illumina
Sample 64


title: 25 salt-stress rep2

description: RDP1: NSFTV_25


title: 255 salt-stress rep1

description: RDP1: NSFTV_255


title: 255 control rep2

description: RDP1: NSFTV_255


title: Single_ICM_4

description:
sequenced on Illumina
Sample 62

value: mouse inner cell mass


title: Single_ICM_3

description:
sequenced on Illumina
Sample 61


title: Single_ICM_5

description:
sequenced on Illumina
Sample 63


title: 254 salt-stress rep2

description: RDP1: NSFTV_254


title: 254 salt-stress rep1

description: RDP1: NSFTV_254


title: Single_ICM_2

description:
sequenced on Illumina
Sample 60


title: RRBS_SVF_Ctrl_Chow_rep_1


title: Single_ICM_1

description:
sequenced on Illumina
Sample 59


title: 258 control rep1

description: RDP1: NSFTV_258


title: 254 control rep1

description: RDP1: NSFTV_254


title: 8-cell_embryo_Pool/split_1h

description:
sequenced on Illumina
Sample 42

value: mouse 8-cell embryo


title: 253 salt-stress rep2

description: RDP1: NSFTV_253


title: 8-cell_embryo_Pool/split_1e

description:
sequenced on Illumina
Sample 39


title: 8-cell_embryo_Pool/split_1g

description:
sequenced on Illumina
Sample 41


title: 8-cell_embryo_Pool/split_1d

description:
sequenced on Illumina
Sample 38


title: 253 salt-stress rep1

description: RDP1: NSFTV_253


title: 243 salt-stress rep2

description: RDP1: NSFTV_243


title: 243 salt-stress rep1

description: RDP1: NSFTV_243


title: 253 control rep2

description: RDP1: NSFTV_253


title: 8-cell_embryo_Pool/split_1c

description:
sequenced on Illumina
Sample 37


title: 8-cell_embryo_Pool/split_1b

description:
sequenced on Illumina
Sample 36


title: 243 control rep2

description: RDP1: NSFTV_243


title: 253 control rep1

description: RDP1: NSFTV_253


title: MEF_2a

description:
sequenced on Illumina
Sample 33

value: mouse embryonic fibroblast


title: MEF_2b

description:
sequenced on Illumina
Sample 34


title: 8-cell_embryo_Pool/split_1a

description:
sequenced on Illumina
Sample 35


title: 255 control rep1

description: RDP1: NSFTV_255


title: 241 salt-stress rep2

description: RDP1: NSFTV_241


title: 254 control rep2

description: RDP1: NSFTV_254


title: 243 control rep1

description: RDP1: NSFTV_243


title: 241 control rep1

description: RDP1: NSFTV_241


title: 241 control rep2

description: RDP1: NSFTV_241


title: ESC_2b

description:
sequenced on Illumina
Sample 30

value: mouse embryonic stem cell


title: 241 salt-stress rep1

description: RDP1: NSFTV_241


title: MEF_1a

description:
sequenced on Illumina
Sample 31


title: MEF_1b

description:
sequenced on Illumina
Sample 32


title: 8-cell_embryo_Pool/split_1f

description:
sequenced on Illumina
Sample 40


title: 231 control rep2

description: RDP1: NSFTV_231


title: 231 salt-stress rep1

description: RDP1: NSFTV_231


title: ESC_1a

description:
sequenced on Illumina
Sample 27


title: ESC_1b

description:
sequenced on Illumina
Sample 28


title: Single_mESC_10

description:
sequenced on Illumina
Sample 10


title: 228 salt-stress rep1

description: RDP1: NSFTV_228


title: Single_mESC_7

description:
sequenced on Illumina
Sample 7


title: Single_mESC_9

description:
sequenced on Illumina
Sample 9


title: Single_mESC_8

description:
sequenced on Illumina
Sample 8


title: 231 salt-stress rep2

description: RDP1: NSFTV_231


title: 228 salt-stress rep2

description: RDP1: NSFTV_228


title: 228 control rep2

description: RDP1: NSFTV_228


title: ESC_2a

description:
sequenced on Illumina
Sample 29


title: 231 control rep1

description: RDP1: NSFTV_231


title: 209 control rep2

description: RDP1: NSFTV_209


title: 21 salt-stress rep1

description: RDP1: NSFTV_21


title: 209 salt-stress rep1

description: RDP1: NSFTV_209


title: 21 control rep1

description: RDP1: NSFTV_21


title: 217 control rep2

description: RDP1: NSFTV_217


title: 217 salt-stress rep1

description: RDP1: NSFTV_217


title: 214 control rep1

description: RDP1: NSFTV_214


title: 214 salt-stress rep2

description: RDP1: NSFTV_214


title: 226 control rep1

description: RDP1: NSFTV_226


title: 226 control rep2

description: RDP1: NSFTV_226


title: 21 control rep2

description: RDP1: NSFTV_21


title: 21 salt-stress rep2

description: RDP1: NSFTV_21


title: 201 salt-stress rep1

description: RDP1: NSFTV_201


title: 226 salt-stress rep2

description: RDP1: NSFTV_226


title: 217 control rep1

description: RDP1: NSFTV_217


title: 201 salt-stress rep2

description: RDP1: NSFTV_201


title: 214 control rep2

description: RDP1: NSFTV_214


title: 217 salt-stress rep2

description: RDP1: NSFTV_217


title: 214 salt-stress rep1

description: RDP1: NSFTV_214


title: 225 salt-stress rep1

description: RDP1: NSFTV_225


title: 201 control rep2

description: RDP1: NSFTV_201


title: 225 control rep2

description: RDP1: NSFTV_225


title: 209 salt-stress rep2

description: RDP1: NSFTV_209


title: 209 control rep1

description: RDP1: NSFTV_209


title: 226 salt-stress rep1

description: RDP1: NSFTV_226


title: 225 control rep1

description: RDP1: NSFTV_225


title: 228 control rep1

description: RDP1: NSFTV_228


title: 225 salt-stress rep2

description: RDP1: NSFTV_225


title: 201 control rep1

description: RDP1: NSFTV_201


title: 192 salt-stress rep2

description: RDP1: NSFTV_192


title: 188 control rep1

description: RDP1: NSFTV_188


title: 188 control rep2

description: RDP1: NSFTV_188


title: 192 salt-stress rep1

description: RDP1: NSFTV_192


title: 188 salt-stress rep1

description: RDP1: NSFTV_188


title: 187 control rep2

description: RDP1: NSFTV_187


title: 189 salt-stress rep2

description: RDP1: NSFTV_189


title: 179 salt-stress rep2

description: RDP1: NSFTV_179


title: 192 control rep2

description: RDP1: NSFTV_192


title: 189 control rep1

description: RDP1: NSFTV_189


title: 192 control rep1

description: RDP1: NSFTV_192


title: 189 control rep2

description: RDP1: NSFTV_189


title: 187 salt-stress rep1

description: RDP1: NSFTV_187


title: 189 salt-stress rep1

description: RDP1: NSFTV_189


title: 187 salt-stress rep2

description: RDP1: NSFTV_187


title: 179 salt-stress rep1

description: RDP1: NSFTV_179


title: 187 control rep1

description: RDP1: NSFTV_187


title: 179 control rep2

description: RDP1: NSFTV_179


title: 188 salt-stress rep2

description: RDP1: NSFTV_188


title: 177 control rep2

description: RDP1: NSFTV_177


title: 177 salt-stress rep1

description: RDP1: NSFTV_177


title: 177 salt-stress rep2

description: RDP1: NSFTV_177


title: 179 control rep1

description: RDP1: NSFTV_179


title: 171 salt-stress rep2

description: RDP1: NSFTV_171


title: 172 salt-stress rep2

description: RDP1: NSFTV_172


title: 172 salt-stress rep1

description: RDP1: NSFTV_172


title: 171 salt-stress rep1

description: RDP1: NSFTV_171


title: 171 control rep2

description: RDP1: NSFTV_171


title: 172 control rep2

description: RDP1: NSFTV_172


title: 177 control rep1

description: RDP1: NSFTV_177


title: 16 salt-stress rep2

description: RDP1: NSFTV_16


title: 171 control rep1

description: RDP1: NSFTV_171


title: 16 salt-stress rep1

description: RDP1: NSFTV_16


title: 162 salt-stress rep1

description: RDP1: NSFTV_162


title: 162 control rep2

description: RDP1: NSFTV_162


title: 162 salt-stress rep2

description: RDP1: NSFTV_162


title: 172 control rep1

description: RDP1: NSFTV_172


title: 162 control rep1

description: RDP1: NSFTV_162


title: 16 control rep1

description: RDP1: NSFTV_16


title: 16 control rep2

description: RDP1: NSFTV_16


title: 157 salt-stress rep2

description: RDP1: NSFTV_157


title: R 2 Hr  Epithelial Injury

city: St. Augustine

first: Rachel

last: Sanford

state: FL

address: 9505 Oceanshore Blvd

institute: University of Florida

description:
EpiInj_RPKM.xlsx
total RNA

data_processing:
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed by CLCbio Genomic Workbench 7.5
Quantification to produce Reads per Kilobase Per Million Mapped Reads (RPKMs) and statistical analysis perfromed by Partek Genomic Suite 6.6
Supplementary_files_format_and_content: EU_RPKM.xlsx This is a file of the RPKMs produced by Partek. This is a measure of abundance of each gene or transcript in each project. These are the project which were treated with the chemical EU, so they are the nascent RNA.
Supplementary_files_format_and_content: EpiInj_RPKM. This is a file of the RPKMs produced by Partke. This is a measure of abundance of each gene in each project. These are the projects not treated with EU, so they are the total RNA.

organism: Mnemiopsis leidyi

source_name: Epithelial Tissue

extract_protocol:
Tissue dissected and RNA isolated with QIAGEN Rneasy
cDNA constructed with reverse transcriptase, cDNA library made using NEB NEXT Ultra Library Construction for Illumina Protocol

value: 2 Hr Regenerationg Tissue


title: U 30 Min Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA

value: 30 Min Regenenerating Tissue


title: P 1 Hr Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA

value: 1 Hr Regenerating Tissue


title: O 1 Hr Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: W Cont Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA

value: Control Tissue


title: S 2 Hr Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: T 2 Hr Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: 154 salt-stress rep2

description: RDP1: NSFTV_154

value: shoot

value: 8 days old


title: 156 control rep1

description: RDP1: NSFTV_156


title: 157 salt-stress rep1

description: RDP1: NSFTV_157


title: 156 salt-stress rep1

description: RDP1: NSFTV_156


title: 157 control rep1

description: RDP1: NSFTV_157


title: 154 salt-stress rep1

description: RDP1: NSFTV_154


title: 156 salt-stress rep2

description: RDP1: NSFTV_156


title: 154 control rep2

description: RDP1: NSFTV_154


title: 156 control rep2

description: RDP1: NSFTV_156


title: X Cont Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: 157 control rep2

description: RDP1: NSFTV_157


title: N 30 Min Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: M 30 Min Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: DM_RES_Rep1

city: Houston

first: srikanth

last: appikonda

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
RNA-Seq data was generated at the Institute of Applied Cancer Science of the UT MD Anderson cancer center. The data were processed with CASAVA pipeline. The sequences in the FASTQ files were aligned to the Hg19/GRCh37 assembly of Human genome using Bowtie aligner.
Bioconductor package easyRNASeq was used to quantitate the expression using the genes.gtf annotations provided by ENSEMBL.
The data were filtered, normalized and differential expression was obtained with edgeR Bioconductor package.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: Tabl delimited text file for raw count data (raw_data_matrix_6samples.txt) and filtered, normalized data with annotations (filtered_normalized_counts_6samples.txt).

extract_protocol:
RNA was extracted according to Illumina's instructions
Libraries were constructed using Illumina's standard protocoles.
RNA-Seq with poly-A selection

tag: shRNA

value: SUMO DM rescue


title: Q 1 Hr Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: DM_RES_Rep2


title: L 30 Min Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA

source_name: Epithelial and Combs


title: WT_RES_Rep2

value: wild type rescue


title: DM_RES_Rep3


title: K Cont Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: 150 salt-stress rep2

description: RDP1: NSFTV_150


title: WT_RES_Rep3


title: I Cont Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: H 1 Hr Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: G 2 Hr Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: WT_RES_Rep1


title: E 1 Hr Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: V Cont Epithelial Injury

description:
EpiInj_RPKM.xlsx
total RNA


title: J Cont Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: 132 salt-stress rep2

description: RDP1: NSFTV_132


title: F 2 Hr Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: D 2 Hr Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: B 30 Min Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: C 30 Min Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: A 1 Hr Epithelial and Combs Injury Nascent

description:
EU_RPKM.xlsx
nascent RNA


title: Dnmt3ab KO input BS_3

source_name: Dnmt3ab KO input BS_3

tag: background strain

tag: time-point in reprogramming

value: postnatal day 25

tag: cell number

value: Germinal vesicle oocytes

tag: antibody amount

value: Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve


title: 150 salt-stress rep1

description: RDP1: NSFTV_150

tag: tissue


title: Dnmt3ab WT input BS_1

source_name: Dnmt3ab WT input BS_1

value: Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 -ve


title: Dnmt3ab WT input BS_2

source_name: Dnmt3ab WT input BS_2


title: 150 control rep2

description: RDP1: NSFTV_150


title: 150 control rep1

description: RDP1: NSFTV_150


title: 154 control rep1

description: RDP1: NSFTV_154


title: 5m

city: Saint Louis

first: Bo

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Reads were aligned to Mus_musculus reference build Ensembl_R76 with STAR (v2.4.0b).
Unambiguous uniquely aligned reads were quantified using Subreads featureCount
Genome_build: Mus_musculus reference build Ensembl_R76
Supplementary_files_format_and_content: Gene level CPM normalized counts matrix

source_name: Right Atrium

extract_protocol:
RNA was isolated from right atria using Trizol.
RNA libraries were made using Illumina protocols

treatment_protocol: Littermate control  and iNICD mice at 2-3 months of age were administered doxycyline chow for 3 weeks with no washout prior to tissue harvest.

value: Heart

value: Adult

value: iNICD


title: 6m


title: 132 control rep2

description: RDP1: NSFTV_132


title: Dnmt3ab KO input BS_1

source_name: Dnmt3ab KO input BS_1


title: 4m


title: d5 NGO input BS_1

source_name: d5 NGO input BS_1

value: postnatal day 5

value: Non-growing oocytes


title: Dnmt3ab KO input BS_2

source_name: Dnmt3ab KO input BS_2


title: 3m


title: 132 control rep1

description: RDP1: NSFTV_132


title: d25 GV input BS_1

source_name: d25 GV input BS_1


title: 6c

value: Control


title: d15 GV input BS_1

source_name: d15 GV input BS_1

value: postnatal day 15


title: 4c


title: 131 salt-stress rep2

description: RDP1: NSFTV_131


title: 3c


title: Uhrf1 cKO

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

country: Japan

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

description: Genomic DNA enriched using MBD2 protein

data_processing:
Sequence data were mapped on the mouse genome (mm10) using CLC Genomics Workbench v8.
Peaks were called using MACS version 1.4.2 with the following setting: band width = 300, pvalue cutoff = 1.00e-10, control
Genome_build: mm10
Supplementary_files_format_and_content: A tabbular file containing information about fold enrichment (control: "Uhrf1 cKO", treat: "Control")

source_name: Primary chondrocytes

growth_protocol: Knee cartilage obtained from post natal day 3 was sequentially digested by Collagenase D.

extract_protocol:
Genomic DNA was extracted with DNeasy spin column kit (Qiagen, USA). Extracted DNA was sonicated with a Covaris sonicator (Covaris Inc.) to obtain ~300 bp fragments. MBD2-mediated enrichment of methylated DNA was performed using the methylated DNA enrichment kit, EpiXplore (TAKARA, Japan) according to the manufacturer’s instructions.
MBD-Seq libraries were prepared using DNA SMART ChIP-Seq Kit (TAKARA, Japan) according to the manufacturer’s instructions and validated for an average size of about 300-700 bp using a TapeStation and the Agilent High Sensitivity D1000 ScreenTape kit.

treatment_protocol: Confluent cells were treated with 100 ng/ml of rhBMP-2 for 24 hours.

tag: strain background

value: Uhrf1 cKO

value: post natal day 3

value: knee cartilage

value: Primary chondrocytes


title: 131 control rep2

description: RDP1: NSFTV_131

extract_protocol:
The samples were ground with Tissuelyser II (Invitrogen) and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
96 libraries were prepared using TruSeq RNA v2 library preparation reagents. Eighteen samples were sequenced per lane.

value: shoot

value: 8 days old


title: 131 salt-stress rep1

description: RDP1: NSFTV_131


title: 1c


title: 2c


title: 132 salt-stress rep1

description: RDP1: NSFTV_132


title: Control

description: Genomic DNA enriched using MBD2 protein


title: 130 salt-stress rep2

description: RDP1: NSFTV_130


title: 130 salt-stress rep1

description: RDP1: NSFTV_130


title: 131 control rep1

description: RDP1: NSFTV_131


title: 130 control rep2

description: RDP1: NSFTV_130


title: mESC [re-analysis]

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

description:
WT OG2ES
GSM1229023

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.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9

source_name: mouse embryonic stem cells(mESCs)

extract_protocol:
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)

tag: time

tag: tag


title: 130 control rep1

description: RDP1: NSFTV_130

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with  htseq-count
Genome_build: Oryza sativa japonica reference genome v 6
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts


title: MEF [re-analysis]

description:
WT MEF
GSM1229026

source_name: mouse embryonic fibroblasts (MEFs)

value: OG2 transgenic mouse embryonic fibroblasts (MEFs)


title: 128 control rep2

description: RDP1: NSFTV_128


title: 2m


title: 128 salt-stress rep1

description: RDP1: NSFTV_128


title: 128 salt-stress rep2

description: RDP1: NSFTV_128


title: 5c


title: 1m


title: 122 salt-stress rep1

description: RDP1: NSFTV_122


title: 122 salt-stress rep2

description: RDP1: NSFTV_122


title: 120 salt-stress rep2

description: RDP1: NSFTV_120


title: 122 control rep1

description: RDP1: NSFTV_122


title: 122 control rep2

description: RDP1: NSFTV_122


title: 120 salt-stress rep1

description: RDP1: NSFTV_120


title: 120 control rep1

description: RDP1: NSFTV_120


title: 117 salt-stress rep1

description: RDP1: NSFTV_117


title: 128 control rep1

description: RDP1: NSFTV_128


title: 117 control rep2

description: RDP1: NSFTV_117


title: 109 salt-stress rep1

description: RDP1: NSFTV_109


title: 117 control rep1

description: RDP1: NSFTV_117


title: 109 salt-stress rep2

description: RDP1: NSFTV_109


title: 109 control rep2

description: RDP1: NSFTV_109


title: 107 salt-stress rep2

description: RDP1: NSFTV_107


title: 109 control rep1

description: RDP1: NSFTV_109