title: Mid-maturation stage whole seed biological replicate 2

description:
B1 BR2
Whole seeds 1.1 - 1.3 cm in length and have fresh weight between 150 - 250 mg were collected.  Tip of the embryonic axis is yellow while the rest of the embryonic axis is green.

source_name: Soybean seeds containing mid-maturation (MM) stage embryos

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010).  Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (B1), and late- (AA1) maturation stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected.  For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.

extract_protocol: Harvested seeds were fixed in 3:1 (v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from ten-micron sections using a Leica LMD6000.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).  Approximately 300 nanogram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications.  We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion.  Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

value: mid-maturation stage

value: whole seed


title: HL20-2

status: Public on Dec 06 2016

type: SRA

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

country: USA

institute: University of North Texas

library_source: transcriptomic

data_processing:
Used Tophat and Bowtie for read alignment onto Arabidopsis reference genome and Cufflinks for obtaining the FPKMs and assessment of significance of fold change
Genome_build: TAIR9
Supplementary_files_format_and_content: Excel file; FPKMs for Control, 20 second light stress, and 60 second light stress

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: Plants were grown for 21 days in 9x9x6-cm3 pots covered with a fiberglass screen net at 23oC under constant low light (50 µmol m-2s-1).

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and cleaned on RNeasy Mini columns (Qiagen).
RNA-Seq

treatment_protocol: Plants were exposed to a light intensity of 1000 µmol m-2s-1 at 21oC for periods of 0, 20 and 60 sec in a growth chamber (E-30-HB, Percival Scientific). Samples were collected by immediately dipping the pots in liquid nitrogen.

tag: strain

tag: Stage

tag: treatment

value: Exposed to 20sec high light

tag: tissue

value: shoot


title: jc2662 H3K4me3 siMLL3 rep3

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description: h3k4me3_simll3-sict_input_peaks.broadPeak

library_source: genomic

data_processing:
Reads were mapped to hg19 genome using Gsnap version 2015-09-29 (Wu TD1, Nacu S., 2010).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.0.10.20131216 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
For the ChIP samples of Histones with mono and tri-methyl modifications the broad peaks were called. The peaks yielded with MACS2 q value <= 1e-5 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh37
Supplementary_files_format_and_content: bed/text

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF7 breast cancer cell line

growth_protocol: MCF-7 cells were obtained from ATCC. MCF-7 were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated foetal bovine serum (FBS), 2 mM L-glutamine, 50U/ml penicillin and 50μg/ml. All cell lines were regularly genotyped using STR profilling (Promega GenePrint 10 system). Cell lines were regularly tested for mycoplasma infection.

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275951
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.

treatment_protocol: Cells were treated either with control, MLL3 or FOXA1 siRNA prio to extraction of genomic DNA for Chip-seq analysis.

tag: cell line

tag: chip antibody

value: anti-H3K4me3 (05-1339) Millipore

tag: cell type

value: asynchonous cells

value: MLL3 siRNA


title: jc2661 H3K4me3 siMLL3 rep2


title: jc2659 H3K4me3 siCt rep4

value: Nonspecific siRNA


title: early maturation-stage seed coat

city: Los Angeles

first: Bob

last: Goldberg

state: CA

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
EM-SC
whole seed coat was captured from ten micron paraffin sections using the Leica LMD6000 system

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine. Tab-delimited text file including methylation level of each sampled cytosine. Column definitions are included in the supplementary README.txt file that is linked to the Series record.

organism: Glycine max

source_name: Laser captured seed coat from early-maturation stage   seed

growth_protocol: Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Seeds with length between 6.0 and 7.0 mm containing early maturation-stage embryos were harvested.

extract_protocol:
Harvested seeds were fixed in 3:1 (v/v) ethanol:acetic acid and embedded in paraffin (Kerk et al.,  Plant Physiol.132. 27-35 (2003)).  Seed compartment was captured from ten-micron sections using a Leica LMD6000.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA).
Approximately 300 nanogram of genomic DNA was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications.  We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion.  Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA).  BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase.  PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman).  Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.

tag: cultivar

value: Williams 82

tag: developmental stage

value: early maturation stage

value: seed coat


title: early maturation-stage embryonic cotyledons

description:
EM-COT
whole embryonic cotyledon was captured from ten micron paraffin sections using the Leica LMD6000 system

source_name: Laser captured embryonic cotyledons from early-maturation stage seed

value: embryonic cotyledon


title: jc2660 H3K4me3 siMLL3 rep1


title: jc2657 H3K4me3 siCt rep2


title: jc2656 H3K4me3 siCt rep1


title: jc1863 siMLL3 H3K4me1 Rep3

description: h3k4me1_simll3-sict_input_peaks.broadPeak

value: anti-H3K4me1 (05-1248-S) Millipore


title: CYTO_Control_7

city: Dublin

first: David

last: Henshall

address: 123 St Stephens Green

country: Ireland

institute: Royal College of Surgeons in Ireland

data_processing:
Illumina software was used for basecalling.
3’Adapter sequences were removed and the quality of sequenced reads were first checked using FASTqc software accroding to Andrews et al 2009 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Reads were then mapped to the mouse genome (Dec. 2011 (GRCm38/mmu10) assembly) using Bowtie, analysed using TopHat, Cufflinks and Cuffdiff (Trapnell et al 2009, Bioinformatics and Trapnell et al  2010, Nat Biotechnology)
Genome_build: Dec. 2011 (GRCm38/mm10) assembly
Supplementary_files_format_and_content: tab-delimited diff files include FPKM values for each sample

organism: Mus musculus

source_name: Hippocampus Cytoplasm

extract_protocol:
Hippocampai from 6 control and 6 status epilepticus mice were extracted, flash frozen on dry ice and stored at -80 degrees celcius until further processing. Control hippocampai and SE hippocampi were combined and synaptoneurosomes and cytoplasm were isolated from each pool. Upf1-bound mRNA was isolated from each sample using a Upf1 antibody (abcam ab109363). Co-precipitated RNA was isolated using Trizol. rRNA was removed from the co-precipitated RNA using the Ribo-Zero Magnetic Kit  (Illumina)
RNA libraries were prepared for sequencing according the protocol provided in the Illumina ScriptSeqTM v2 RNA-Seq Library Preparation Kit.

value: Hippocampus

tag: cell compartment

value: Cytoplasm

tag: age

value: 6-8 weeks

tag: genotype

value: WT


title: SYNAP_SE_10

source_name: Hippocampus Synaptoneurosome

value: Synaptoneurosome

value: SE


title: CYTO_SE_8


title: SYNAP_Control_9


title: jc1785 siMLL3 H3K4me1 Rep0

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275950
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: jc1789 siMLL3 H3K4me1 rep1


title: jc1859 siMLL3 H3K4me1 Rep2


title: jc1862 siCt H3K4me1 Rep3

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275949
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: 258

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

country: Australia

institute: University of Technology Sydney

data_processing:
Reads were mapped to mouse genome (UCSC, mm10) using STAR (v2.4.0).
The resulting sam files were sorted and HTSeq (v0.6.1) was used to generate counts (with options --mode=intersection-nonempty --stranded=no).
Genome_build: mm10
Supplementary_files_format_and_content: txt with raw read counts

source_name: Differentiated mouse embryonic stem cells

extract_protocol:
All RNA was extracted from sorted ES cells using RNA extraction kit and amplified using Nugen RNA amplification kit
Library construction was performed as per Illumina protocol

tag: reporter construct

value: -8/P ENG-/FDG+ HEI r3


title: jc1858 siCt H3K4me1 Rep2

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275948
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: 257

value: -8/P ENG+/FDG- HEI r3


title: jc1787 siCT H3K4me1 Rep1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275947
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: 256

value: -8/P ENG+/FDG+ HEI r3


title: 255

value: -8/P ENG-/FDG+ HEI r2


title: Mid-maturation stage whole seed biological replicate 1

description:
B1 BR1
Whole seeds 1.1 - 1.3 cm in length and have fresh weight between 150 - 250 mg were collected.  Tip of the embryonic axis is yellow while the rest of the embryonic axis is green.

data_processing:
Basecalls performed using RTA version 1.12.4.2
Original data file from the Illumina sequencing pipeline.  Each lane of sequencing is attached as an individual compressed file.  The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches.  The pre-processed reference genome consisted of sequences from the soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls)).
Genome_build: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine

value: mid-maturation stage

value: whole seed


title: jc1783 siCT H3K4me1 Rep0

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275946
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.

value: asynchonous cells

value: Nonspecific siRNA


title: jc2731 MCF7 GRHL2 3

description: grhl2_untreated-mcf7_input_peaks.narrowPeak

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275944
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.

value: anti-GRHL2 (HPA004820)  Sigma Aldrich

value: No treatment


title: 253

value: -8/P ENG+/FDG+ HEI r2


title: jc862 MCF7 GRHL2 sg

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275945
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: jc1790 FoxA1

description: foxa1_untreated-mcf7_input_peaks.narrowPeak

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275943
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.

value: anti-FOXA1 (ab5089) Abcam


title: jc2728 MCF7 GRHL2 2


title: 251


title: jc1860 siCt FOXA1 Rep3

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275942
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: jc2658 H3K4me3 siCt rep3

value: anti-H3K4me3 (05-1339) Millipore


title: 249


title: 250


title: jc1856 siCt FOXA1 Rep2

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275941
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: 112

value: -8/P ENG-/FDG+ HEI r1


title: jc1782 siCT FoxA1 Rep0

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275939
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.


title: 110

value: -8/P ENG+/FDG- HEI r1


title: 111

value: -8/P ENG+/FDG+ HEI r1


title: F. verticillioides 7600,  20 days on maize roots

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

country: Germany

institute: Technische Universität München

data_processing:
RNA-seq reads were mapped on the reference genome using tophat2 (v2.0.8).
The interval for allowed intron lengths were set to min 20 nt and max 1 kb (Kim, 2013, Trapnell et al., 2009).
Cufflinks was used  to determine the abundance of transcripts in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) and calculated differentially expressed genes using cuffdiff (Trapnell et al., ,2012, Trapnell et al., 2010).
The gene models were included as raw junctions. Genes with a minimum of fourfold increase or decrease in expression (|log2 of the FPKM values +1| ≥ 2) between the two experimental conditions were considered as regulated.
Genome_build: Zea mays: http://www.plantgdb.org/ZmGDB/ version B73_RefGen_v2, working gene set 5a.59; F. mangiferae: http://www.ebi.ac.uk/ena/data/view/PRJEB9887; F. proliferatum ET1: http://www.ebi.ac.uk/ena/data/view/PRJEB9885; F. proliferatum 62905: http://www.ebi.ac.uk/ena/data/view/PRJEB9886
Supplementary_files_format_and_content: tab-delimited text files holding FPKM values for each sample

organism: Fusarium verticillioides 7600

source_name: Maize root samples

growth_protocol: RNA was isolated from lyophilized mycelia grown before on CM agar plates for 5 days or from lyophilized infected maize roots after 4, 10 or 20 days post infection.

extract_protocol:
Total RNA was extracted using Trizol and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).
Illumina TruSeq RNA Library
Total RNA was sequenced using Illumina HiSeq 2000 technology by BGI Tech Solutions (Hong Kong) Co., Limited.

value: wild type

tag: dpi


title: F. verticillioides 7600,  4 days on maize roots


title: 23


title: F. verticillioides 7600,  10 days on maize roots


title: 254

value: -8/P ENG+/FDG- HEI r2


title: 24


title: WT_EZH2

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
ChIP-Seq reads were trimmed using Trim Galore v0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the human GRCh38 genome assembly using Bowtie 2 v2.2.5 using default parameters. BAM files were imported to Seqmonk and reads were extended by 200bp at their 5’ end to approximate the true insert size.
Processed data files format and content: Quantitated ChIP-Seq data file is tab delimited and shows log2 RPM data for -/+2.5kb surrounding each TSS: (1) mRNA transcript associated with TSS (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Associated gene name (Ensembl) (7) mRNA ID (Ensembl); (8) Description (Ensembl); (9-29) log2 RPM value
Libraries were sequenced on the Illumina HiSeq1000/2500 platforms using the default RTA analysis software.
Genome_build: GRCh38

extract_protocol:
Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100μl RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Life Technologies) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. Crosslinked ChIP for profiling EZH2 occupancy was performed using iDeal ChIP-Seq kit for Transcription Factors (Diagenode).
Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB).

value: embryonic stem cell (ESC)

tag: genotype/variation


title: B10_rx3_strong_ZT09

status: Public on Dec 05 2016

city: Eggenstein-Leopoldshafen

first: Thomas

last: Dickmeis

address: Hermann-von-Helmholtz-Platz 1

department: ITG

institute: KIT

data_processing:
raw counts
Genome_build: Zv9

organism: Danio rerio

source_name: Larvae Total RNA

growth_protocol: 30  rx3 mutant and wildtype sibling embryos (1 dpf) from pooled clutches were separated and transferred into cell culture flasks containing E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 0.1% methylene blue). Embryos/larvae were kept at 28°C in an incubator under a 12 h light:12 h dark (LD) exposure.

extract_protocol:
Larvae were sampled in liquid nitrogen and stored at -80°C until further processing. RNA was extracted with TRIzol (Life Technologies) following the manufacturer’s instructions with minor modifications: 30 larvae were sampled in a volume of 1.5 ml TRIzol reagent. Samples were kept at least overnight at -80°C. In order to disrupt the cell membranes, the samples were passed four times through a syringe with a diameter of 0.45 mm.
The cDNA libraries for Sample 1-12 (untreated) were generated using the directional mRNA-seq sample preparation kit (#15018460, Rev.A, October 2010, Illumina) following the manufacturer’s protocol.  mRNAseq libraries of samples 13-20 (treated) were generated following the TruSeq mRNA kit protocol (Illumina). The size and concentration of the generated libraries were evaluated with a Bioanalyzer 2100 and adjusted to a concentration of 10 pM. Cluster and sequencing reactions were performed with the TruSeq SBS kit v3-HS and the paired-end cluster v3-cBot-HS kit.

treatment_protocol: For glucocorticoid treatment, the E3 medium was supplemented with 25 μM dexamethasone (DEX) solved in 0.1% DMSO

value: mixed TU, AB, WIK

value: untreated

value: 5 dpf

tag: zeitgeber time

value: rx3 strong mutant


title: B12_rx3_strong_ZT21


title: 252


title: B09_rx3_strong_ZT03


title: B11_rx3_strong_ZT15


title: B08_rx3_weak_ZT21

value: rx3 weak mutant


title: B07_rx3_weak_ZT15


title: B06_rx3_weak_ZT09


title: B05_rx3_weak_ZT03


title: E4-ORF1-3

city: New York

first: natasha

last: chaudhary

state: NY

address: 1300 York Avenue

department: Biochemistry

institute: Weill Cornell Medicine

data_processing:
Illumina bcl2fastq-1.8.4/RTA ver 1.18.64 was used for basecalling.
Due to no evidence of adapter contamination and very high Phred quality scores no pre-processing of reads was necessary.
The sequences were directly aligned to the mouse reference genome (GRCm38p4) using STAR (ver v2.4.2a), a universal RNA-seq aligner. Ref: Dobin A et al., Bioinfomatics, 2013
To improve accuracy of the mapping, the genome was created with a splice junction database based on Gencode vM6 basic annotation, Ref: Harrow  J et al., Genome Research, 2012.
Reads per gene were calculated using featureCounts (v1.4.6-p4) with default parameters
Genome_build: GRCm38p4
Supplementary_files_format_and_content: tab-delimited text files include raw read counts values for each sample

growth_protocol: Both control and E4-ORF1 stably expressing 3T3-L1 cells were differentiated and day 10 adipocytes were used.

extract_protocol:
RNA was harvested from control and E4-ORF1 stably expressing adipocytes by using Qiagen Rneasy Mini kit. 1ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina TruSeq (polyA+) protocols

treatment_protocol: Adipocytes were starved for 2 hours prior RNA extraction

value: E4-ORF1 expressing adipocyte

tag: differentiation stage

value: Day 10


title: B02_wild-type_ZT09

tag: strain

value: Wild type


title: E4-ORF1-1


title: jc1786 siCT FoxA1 Rep1

extract_protocol:
ChIPseq, Schmidt et al, 2009. PMID: 19275940
After amplification, DNA was extracted using QIAgen MinElute gel extraction kit.

value: asynchonous cells

value: Nonspecific siRNA


title: E4-ORF1-2


title: Control-3

value: Control adipocyte


title: Control-2


title: F. verticillioides 7600, CM

source_name: liquid culture, complete media


title: single cell from blastocyst [KO_64C_CB_10]

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Quality control: Reads characterized by at least one of the following criteria were discarded from the analysis i) >50% of low quality bases (Phred score <5) ii) >5% of N bases iii) >80% of AT rate iv) ≥30% of continuous A and/or T
Genome reconstruction: The VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf) reporting all SNP sites from 36 mouse strains based on mm10 was downloaded from the Sanger database. Using SNPsplit tool (v0.3.0), these SNPs were filtered based on their quality values (FI value) and used to reconstruct the Cast genome from mm10 genome assembly.
Mapping: Single-end reads were then aligned to the mouse mm10 and Cast/EiJ genomes using the TopHat2 software (v2.1.0). Only random best alignments with less than 2 mismatches were reported for downstream analyses. The resulting mapping files for both parental genomes were then merged for each sample.
Allelic Ratio: The SAMtools mpileup utility (v1.1) was then used to extract base-pair information at each genomic position from the merged alignment file. At each SNP position, the number of paternal and maternal allele was counted. The allele-specific origin of the transcripts (or allelic ratio) has been measured by the total number of reads mapped on the paternal genome divided by the total number of reads for each gene: allelic ratio = paternal reads / (paternal+maternal) reads.
Estimation of gene expression levels: To estimate the transcript abundance, count tables of gene expression were generated using HTSeq v0.6.1 software. Read counts are then normalized based on the amplification size of each transcript (RPRT for Reads Per Retro-Transcribed length per million mapped reads)
Genome_build: mm10

source_name: pre-implantation embryo

growth_protocol: natural matings, no embryo culture

extract_protocol:
PolyA+ mRNA extracted from each single cell was reverse transcribed from the 3’UTR and amplified following the Tang et al protocol. Care was taken to process only embryos and single blastomeres of the highest quality based on morphology, number of cells and on amplification yield. A total of 72 BC and 110 CB single blastomeres have been processed and passed quality controls.
Illumina manufacturer protocol
50 bp single end

treatment_protocol: single cell cDNA amplification (Tang et al, 2010)

value: Xist wt/ko

tag: Sex

value: Male


title: single cell from blastocyst [KO_64C_CB_14]


title: single cell from blastocyst [KO_64C_CB_9]


title: single cell from blastocyst [KO_64C_CB_7]


title: single cell from blastocyst [KO_64C_CB_3]


title: single cell from blastocyst [KO_64C_CB_78]

value: Female


title: single cell from blastocyst [KO_64C_CB_75]


title: single cell from blastocyst [KO_64C_CB_74]


title: B03_wild-type_ZT15

tag: treatment


title: single cell from blastocyst [KO_64C_CB_70]


title: B04_wild-type_ZT21


title: single cell from blastocyst [KO_64C_CB_65]


title: B01_wild-type_ZT03


title: single cell from blastocyst [KO_64C_CB_69]


title: single cell from blastocyst [KO_64C_CB_68]


title: single cell from blastocyst [KO_64C_CB_67]


title: single cell from blastocyst [KO_64C_CB_76]


title: single cell from blastocyst [KO_64C_CB_55]


title: single cell from blastocyst [KO_64C_CB_66]


title: single cell from blastocyst [KO_64C_CB_51]


title: single cell from blastocyst [KO_64C_CB_50]


title: single cell from blastocyst [KO_64C_CB_37]


title: Control-1


title: single cell from blastocyst [KO_64C_CB_36]


title: single cell from blastocyst [KO_64C_CB_54]


title: single cell from blastocyst [KO_64C_CB_35]


title: single cell from blastocyst [KO_64C_CB_49]


title: single cell from blastocyst [KO_64C_CB_33]


title: single cell from blastocyst [KO_64C_CB_34]


title: single cell from blastocyst [KO_64C_CB_13]


title: single cell from blastocyst [KO_64C_CB_16]


title: single cell from blastocyst [KO_64C_CB_8]


title: single cell from blastocyst [KO_64C_CB_73]


title: single cell from 32-cell stage embryo [KO_32C_CB_1]


title: single cell from blastocyst [KO_64C_CB_12]


title: single cell from 32-cell stage embryo [KO_32C_CB_4]


title: single cell from 32-cell stage embryo [KO_32C_CB_51]


title: single cell from 32-cell stage embryo [KO_32C_CB_2]


title: single cell from 32-cell stage embryo [KO_32C_CB_49]


title: single cell from 32-cell stage embryo [KO_32C_CB_50]


title: single cell from 32-cell stage embryo [KO_32C_CB_46]


title: single cell from 32-cell stage embryo [KO_32C_CB_48]


title: single cell from 32-cell stage embryo [KO_32C_CB_45]


title: single cell from 32-cell stage embryo [KO_32C_CB_42]


title: single cell from 32-cell stage embryo [KO_32C_CB_47]


title: single cell from 32-cell stage embryo [KO_32C_CB_40]


title: single cell from 32-cell stage embryo [KO_32C_CB_8]


title: single cell from 32-cell stage embryo [KO_32C_CB_43]


title: single cell from 32-cell stage embryo [KO_32C_CB_44]


title: single cell from 32-cell stage embryo [KO_32C_CB_7]


title: single cell from 32-cell stage embryo [KO_32C_CB_5]


title: single cell from 16-cell stage embryo [KO_16C_CB_41]


title: single cell from 32-cell stage embryo [KO_32C_CB_6]


title: single cell from 16-cell stage embryo [KO_16C_CB_36]


title: single cell from 16-cell stage embryo [KO_16C_CB_37]


title: single cell from 32-cell stage embryo [KO_32C_CB_3]


title: single cell from 16-cell stage embryo [KO_16C_CB_35]


title: single cell from 16-cell stage embryo [KO_16C_CB_33]


title: single cell from 16-cell stage embryo [KO_16C_CB_30]


title: single cell from 16-cell stage embryo [KO_16C_CB_31]


title: single cell from 16-cell stage embryo [KO_16C_CB_28]


title: single cell from 8-cell stage embryo [KO_8C_CB_10]


title: single cell from 32-cell stage embryo [KO_32C_CB_41]


title: single cell from 8-cell stage embryo [KO_8C_CB_7]


title: single cell from 8-cell stage embryo [KO_8C_CB_9]


title: single cell from 16-cell stage embryo [KO_16C_CB_29]


title: single cell from 8-cell stage embryo [KO_8C_CB_2]


title: single cell from 8-cell stage embryo [KO_8C_CB_1]


title: single cell from 8-cell stage embryo [KO_8C_CB_3]


title: single cell from blastocyst [64C_CB_58]

value: Xist wt/wt


title: single cell from blastocyst [64C_CB_60]


title: single cell from blastocyst [64C_BC_26]


title: single cell from 16-cell stage embryo [KO_16C_CB_39]


title: genomic DNA from 15 days' conidia of Metarhizium robertsii

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

data_processing:
bisulfite-converted DNA
The resultant DNAs were applied to paired-end sequencing using an ultrahigh-throughput Illumina Genetic Analyzer (GA2)
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle
All clean BS-Seq reads were mapped to the genome using the BSMAP aligner
Genome_build: ARSEF 23
Supplementary_files_format_and_content: wig files were generated using bsmap, and Scores represent mean count of reads mapping to the genome
Supplementary_files_format_and_content: Four wig files per sample representing the total mC, mCG, mCHG, and mCHH in the genome (H represents A, T, G)

organism: Metarhizium robertsii

extract_protocol:
Metarhizium robertsii fungus were ground into powder in liquid nitrogen,Powder was used to isolate nuclear proteins with EpiQuik™ Nuclear Extraction Kit I
DNA was fragmented by sonication with a Diagenome sonicator to a mean size of approximately 250 bp, followed by DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptors according to the manufacturer’s instructions (Illumina).

value: ARSEF 23

value: asexual developmental stage


title: single cell from blastocyst [64C_BC_21]


title: genomic DNA from 9 days' conidia of Metarhizium robertsii


title: single cell from blastocyst [64C_BC_11]


title: single cell from blastocyst [64C_BC_23]


title: single cell from blastocyst [64C_BC_9]


title: single cell from 16-cell stage embryo [KO_16C_CB_32]


title: single cell from 16-cell stage embryo [KO_16C_CB_22]


title: genomic DNA from mycelium of Metarhizium robertsii


title: YMD3271_exponential_Sau3AI

city: Stanford

first: Seungsoo

last: Kim

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description:
Y12xDBVPG6044.32000.bed
mismapped.bed

data_processing:
Library strategy: Hi-C-seq
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20) trimmed of adapter sequences and then trimmed up to the ligation junction (if present), excluding read pairs in which either read was shorter than 20 bp after trimming.
Reads were independently mapped using bowtie2 2.2.3 using the parameter set --very-sensitive. For interspecific hybrids, reads were mapped to a combined reference containing both species references, where if secondary mappings were present the best alignment must have a score ≥ 10 greater than the next best alignment. For intraspecific S. cerevisiae hybrids, reads were mapped separately to both strain references, keeping only read pairs mapping to both—perfectly to one reference and with ≥ 2 mutations including ≥ 1 substitution to the other. In both cases, only read pairs in which both reads mapped with MAPQ ≥ 30 were used.
PCR duplicates (with identical fragment start and end positions) were removed, as were read pairs mapping within 1 kb of each other or in the same restriction fragment, which represent either unligated or invalid ligation products.
The genome was then binned into 32 kb fragments (except the last fragment of each chromosome), and the number of read pairs mapping to each 32 kb genomic bin was counted based on the position of the restriction sites that were ligated together. Due to gaps in the reference genomes of S. uvarum, some repetitive sequences were only represented once and therefore artifactually mapped uniquely; therefore, reads mapping to annotated repetitive sequences were masked from further analysis. Similarly, gaps in the S. paradoxus reference led to mismapping of reads to the corresponding S. cerevisiae sequence; therefore, for S. cerevisiae x S. paradoxus libraries we masked regions in the S. cerevisiae genome where > 1 read from a S. paradoxus Hi-C library mapped, and vice versa. We took a similar approach to mask regions of the Y12 and DBVPG6044 references that were prone to mismapping, as estimated by haploid Y12 and DBVPG6044 Hi-C libraries. For knock-in experiments, the HAS1pr-TDA1pr region was masked to account for its altered genomic location. The resulting matrices were then normalized by excluding the diagonal (interactions within the same genomic bin), filtering out rows/columns with an average of less than 1 read per bin, and then multiplying each entry by the total number of read pairs divided by the column and row sums.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD and Saccharomyces cerevisiae and Saccharomyces uvarum (bayanus var. uvarum) from saccharomycessensustricto.org, with minor modifications; Y12 and DBVPG6044 references generated by Pacbio sequencing
Supplementary_files_format_and_content: tab-delimited text files ending in "matrix.txt" include the raw read counts and normalized interaction frequencies for each pair of 32 kb genomic bins; those ending in "rowsums.txt" include the raw sums across each row of these matrices. BED files include either the genomic regions included in each matrix bin or those masked from the matrices.

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown overnight, shaking at 30C (room temperature for S. uvarum) in YPD media (1% yeast extract, 2% peptone, 2% dextrose), or for "raffinose" cultures, YP + 2% raffinose, or for "galactose" cultures, YP + 2% galactose. For non-saturated cultures, fresh cultures were inoculated to OD600=0.1 in the same media and grown until OD600 = 0.6-0.8.

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme Sau3AI or HindIII, gap-filled in using biotinylated dCTP, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
Libraries were prepared according to manufacturer's instructions using the KAPA Hyper Prep kit.

treatment_protocol: Cells were crosslinked by resuspension and incubation in 1% formaldehyde in PBS for 20 minutes at room temperature, and then quenched by addition of 1% solid glycine, incubation for 20 minutes, and a PBS wash. For nocodazole culture, media was supplemented with 15 ug/ml nocodazole and grown for an additional 2 hours prior to crosslinking.

tag: growth conditions

value: exponential

tag: growth medium

value: YPD

tag: growth phase

tag: growth temperature

tag: restriction enzyme


title: YMD3271_saturated_Sau3AI

description:
Y12xDBVPG6044.32000.bed
mismapped.bed

value: saturated


title: single cell from blastocyst [64C_CB_52]

tag: developmental stage


title: single cell from blastocyst [64C_CB_56]


title: single cell from blastocyst [64C_CB_54]


title: single cell from 8-cell stage embryo [KO_8C_CB_5]


title: single cell from blastocyst [64C_CB_51]


title: Y12_DBVPG6044_exponential_Sau3AI

description:
Y12xDBVPG6044.32000.bed
mismapped.bed


title: single cell from blastocyst [64C_CB_49]


title: Y12_exponential_Sau3AI


title: DBVPG6044_exponential_Sau3AI


title: single cell from blastocyst [64C_CB_50]


title: single cell from blastocyst [64C_BC_24]


title: single cell from blastocyst [64C_BC_64]


title: wt 24h rep3 (siRNA-Seq)

city: Charlestown

first: Richard

last: Joh

state: MA

department: Center for Cancer Research

institute: Mass General Hospital

description: Ago1-associated RNA

data_processing:
Remove adapter with Cutadapt
Map go S pombe genome with Bowtie2 2.1.0
Select reads that starts with "U"
Select reads between 18 and 25nt
Quantify the number of reads per transcript by HTSeq 0.6.1
Genome_build: S. pombe ASM294v2.22
Supplementary_files_format_and_content: Number of reads per transcript. Txt file

organism: Schizosaccharomyces pombe

growth_protocol: Cells grown in EMM 225ug/ml adenine/histidine/leucine/lysine/uracil (OD~1) at 32C, and were washed twice with EMM -N.  Cells were resuspended in EMM -N and incubated at 32C.

extract_protocol:
Ago1-bound sRNAs were isolated and sequenced using the protocol described in Holoch and Moazed (Holoch and Moazed, 2015b).  Briefly, cell pellets from freshly grown proliferative and quiescent cells were frozen as droplets in liquid nitrogen. Cells were lysed by grinding in Retsch Cryomill (pre-chilled in liquid nitrogen) using Tissue Lyser II (5x 2 min at 30Hz). Lysed cells were thawed at room temperature for 10 min and then resuspended in 1ml of IP buffer (50 mM HEPES, pH 7.4, 5mM Magnesium acetate, 1mM EDTA, 1mM EGTA, 300mM Sodium acetate, 5% glycerol, 0.5% CHAPS, 1 mM PMSF and Roche complete EDTA-free protease-inhibitor cocktail) per gram of lysed cells. The lysate was clarified by centrifugation and the supernatant was incubated with pre-equilibrated anti-DYKDDDDK magnetic microbeads (Medna Bio # P8101ML1) for 4 h at 4 °C. Beads were washed 3x 1 ml lysis buffer, resuspended in 500 μl of nuclease free water, subjected to Phenol/chloroform extraction followed by ethanol precipitation. The RNA samples were resuspended in nuclease free water, electrophoresed on 17.5% Polyacrylamide/7M Urea gel and RNA species between 20-30 nucleotides were gel-extracted. Gel slices were crushed and resuspended in 0.4M sodium acetate (pH = 5.2) overnight at 4 deg C. Extracted siRNAs were ethanol precipitated and resuspended in nuclease-free water. These purified siRNAs were used for library preparation as described previously (Holoch and Moazed, 2015b).
Custom library based on Holoch and Moazed, 2015b

value: N starvation

tag: time

value: 24h after -N

tag: ip antibody

value: FLAG Magnetic bead (Medna Bio P8101ML1)


title: single cell from blastocyst [64C_BC_75]

tag: genotype


title: wt 0h rep3 (siRNA-Seq)

description: Ago1-associated RNA

value: control

value: 0h after -N


title: single cell from blastocyst [64C_BC_40]


title: wt 24h rep2 (siRNA-Seq)

description: Ago1-associated RNA


title: wt 0h rep2 (siRNA-Seq)

description: Ago1-associated RNA


title: single cell from blastocyst [64C_BC_36]


title: wt 24h rep1 (siRNA-Seq)

description: Ago1-associated RNA


title: single cell from blastocyst [64C_BC_35]


title: wt 0h rep1 (siRNA-Seq)

description: Ago1-associated RNA


title: single cell from blastocyst [64C_BC_19]


title: single cell from 32-cell stage embryo [32C_CB_84]


title: clr4D 24h rep2 (RNA-seq)

description: rRNA-depleted RNA

data_processing:
Map to rRNA by TopHat 2.0.8
Convert unmapped reads into fastq
Remapp to S pombe genome with TopHat 2.0.8
Quantify the number of reads per transcript by HTSeq 0.6.1
Genome_build: S. pombe ASM294v2.22
Supplementary_files_format_and_content: Number of reads per transcript. Txt file

extract_protocol:
RNA from cell pellets was extracted by the hot phenol RNA exraction method (Leeds et al 1991), and further processed with the Rneasy Mini kit (Quagen 74104) and DNaseI (Roche)
rRNA was removed by Ribo-Zero Bold rRNA Removal Kit Yeast (Illumina MRZY1306), and libraries were constructed by NEBNext Ultra Directional RNA Librayr Prep Kit for Illumina (NEB E7420L)

value: clr4D (975 h+ clr4D::NatMX6)


title: clr4D 10h rep2 (RNA-seq)

description: rRNA-depleted RNA

value: 10h after -N


title: clr4D 4h rep2 (RNA-seq)

description: rRNA-depleted RNA

value: 4h after -N


title: single cell from 32-cell stage embryo [32C_CB_80]


title: single cell from 32-cell stage embryo [32C_CB_73]


title: YMD1797_raffinose_Sau3AI

description:
ScSu.32000.bed
ScSp.32000.bed

value: raffinose

value: YP+raffinose


title: single cell from 32-cell stage embryo [32C_CB_72]

value: Male


title: single cell from 32-cell stage embryo [32C_CB_58]

value: Xist wt/wt


title: single cell from 32-cell stage embryo [32C_BC_36]


title: single cell from 32-cell stage embryo [32C_CB_57]


title: wt 24h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: wt 4h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: wt 10h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_BC_31]


title: single cell from 32-cell stage embryo [32C_BC_33]


title: single cell from 32-cell stage embryo [32C_BC_35]


title: wt 2h rep2 (RNA-seq)

description: rRNA-depleted RNA

value: 2h after -N


title: single cell from 32-cell stage embryo [32C_BC_30]


title: wt 1h rep2 (RNA-seq)

description: rRNA-depleted RNA

value: 1h after -N


title: wt 0h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: clr4D 24h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_BC_29]


title: single cell from 32-cell stage embryo [32C_CB_6E]

value: Female


title: single cell from 32-cell stage embryo [32C_CB_6C]


title: clr4D 10h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: clr4D 2h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_CB_6B]


title: clr4D 4h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_CB_2G]


title: single cell from 32-cell stage embryo [32C_CB_2F]


title: clr4D 1h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_CB_2E]


title: clr4D 2h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: wt 24h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_CB_2C]


title: clr4D 1h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: wt 10h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: wt 4h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_CB_2B]


title: single cell from 32-cell stage embryo [32C_BC_28]


title: single cell from 32-cell stage embryo [32C_CB_2A]


title: wt 1h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: clr4D 0h rep2 (RNA-seq)

description: rRNA-depleted RNA


title: single cell from 32-cell stage embryo [32C_BC_27]


title: wt 0h rep1 (RNA-seq)

description: rRNA-depleted RNA


title: Input for S2 cells treated with GFP RNAi

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Sequencing reads were mapped to dm3 using bowtie.
Peaks were called using MACS14  with default settings.
Peak overlap analysis was done using bedtools
differentially bound peaks were calculated with HOMER
Genome_build: dm3
Supplementary_files_format_and_content: bed files containing peak intervals detected by Macs14

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Kc and S2 cells were grown in schneider's media supplemented with 10% FBS and incubated at 25 C

extract_protocol:
Kc cells were washed with PBS and croslinked with formaldehyde (1%). Formaldehyde was quenched with glycine. Cells were washed twice with ice-cold PBS. Nuclei were exrtacted with IP buffer . Nuclei were sheared and incubated with antibody overnight. immunocomplexes were collected by agarose A/G beads. DNA was purified with Chelex-100 beads.
Libraries were prepared according to Illumina's instructions

treatment_protocol: Kc and S2 cells were treated with GFP or CP190 dsRNA  (90 ug/6 million cells)

value: GFP dsRNA treated S2 cells

tag: antibody

tag: cell type

value: S2 cells


title: single cell from 32-cell stage embryo [32C_BC_21]


title: Gcn5 ChIP-Seq in S2 cells treated with GFP RNAi

value: Gcn5 rabbit polyclonal antibody (5 ug/IP)


title: single cell from 32-cell stage embryo [32C_BC_19]


title: Input for Kc cells treated with GFP RNAi

source_name: Kc cells

value: GFP dsRNA treated Kc cells

value: Kc cells


title: single cell from 16-cell stage embryo [16C_CB_37]


title: Input for Kc cells treated with CP190 RNAi

value: CP190 dsRNA treated Kc cells


title: single cell from 16-cell stage embryo [16C_BC_5]


title: single cell from 16-cell stage embryo [16C_BC_19]


title: clr4D 0h rep1 (RNA-seq)

description: rRNA-depleted RNA

value: control

value: 0h after -N


title: Gcn5 ChIP-Seq in Kc cells treated with GFP RNAi


title: Gcn5 ChIP-Seq in Kc cells treated with CP190 RNAi


title: single cell from 16-cell stage embryo [16C_BC_3]


title: single cell from 16-cell stage embryo [16C_CB_49]


title: Gcn5-depleted cells_R1

data_processing:
sequencing reads were mapped to dm3 using Tophat.
data is normalized using FPKM
Differentially expressed genes were calculated by cuffdiff
Genome_build: Drosophila_melanogaster_UCSC_dm3
Supplementary_files_format_and_content: Cuffdiff output txt file includes fold change expression and statistics (contains three different contrasts)

molecule: polyA RNA

growth_protocol: S2 cells were grown in Schneider's media supplemented with 10% FBS and incubated at 25 C

extract_protocol:
RNA was isolated using TRIZOL extraction method.
After polyA-mRNA purification libraries were prepared using ScriptSeq v2 according to the manufacturer's instructions

treatment_protocol: S2 cells were treated with GFP or CP190 dsRNA  (90 ug/6 million cells)

value: Gcn5 dsRNA


title: single cell from 16-cell stage embryo [16C_CB_47]


title: CP190-depleted cells_R2

value: CP190 dsRNA


title: Gcn5-depleted cells_R2


title: wt 2h rep1 (RNA-seq)

description: rRNA-depleted RNA

value: N starvation


title: CP190-depleted cells_R1


title: GFP-treated cells_R2

value: GFP dsRNA


title: single cell from 16-cell stage embryo [16C_BC_65]


title: single cell from 16-cell stage embryo [16C_BC_68]


title: single cell from 32-cell stage embryo [32C_BC_20]


title: single cell from 16-cell stage embryo [16C_BC_64]


title: BB24 embryo (R1555s2 BB24)

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

department: Biology

country: Israel

institute: Technion

description:
R1555s2 BB24
first 3 nucleotides are a GGG barcode
processed data file: genescount-R155s2_BB4_RDE1_E_GGG_col.fastq.sam-genes.csv_allgenecount.gz

data_processing:
mRNA sequences were aligned to gene transcripts using bowtie.
DEseq package in R (http://www.r-project.org) was used from the data obtained from bowtie to identify differentially expressed genes.
Genome_build: WS220
Supplementary_files_format_and_content: [.xlsx] DEseq output
Supplementary_files_format_and_content: [.txt] abundance measurements

organism: Caenorhabditis elegans

source_name: BB24 embryo

growth_protocol: All strains were raised at 20°C on enriched NGM with OP50 as food

extract_protocol:
RNA in high and low molecular weight fractions was extracted by mirVana kit (ambion).
RNA Sample Preparation kit automated by Agilent Bravo Automated Liquid Handling Platform. The resulting libraries were sequences with an Illumina HiSeq 2500

tag: genotype/variation

value: ADAR mutant and RNAi mutant

value: Embryo

tag: tissue

value: whole worm


title: BB23 embryo (R154 BB23)

description:
R154 BB23
first 3 nucleotides are a CCC barcode
processed data file: genescount-R154_BB4_RDE1_E_101028_KOJAK_00018_FC62P3V_L3_pf_CCC_col.fastq.sam-genes.csv_allgenecount.gz

source_name: BB23 embryo


title: BB21 L4

description:
29 BB21_L4_04.01.16
processed data file: genescount-BB21_L4_04_01_16_CTTGTA_L004_R1.fastq.uniq.sam-genes.csv_allgenecount.gz

source_name: BB21 L4

value: ADAR mutant


title: single cell from 16-cell stage embryo [16C_BC_62]

value: Xist wt/wt

value: Female


title: GFP-treated cells_R1

value: S2 cells


title: single cell from 16-cell stage embryo [16C_BC_61]


title: BB21 Embryo mRNA 3

description:
29 BB21_Emb_04.01.16
processed data file: genescount-BB21_Emb_04_01_16_GCCAAT_L004_R1.fastq.uniq.sam-genes.csv_allgenecount.gz

source_name: BB21 Embryo


title: N2 L4 mRNA 6

description:
27 N2 _L4 (26/04)_10 lane 2
processed data file: genescount-N2_L4_26_04__10_CCGTCC.fastq.uniq.sam-genes.csv_allgenecount.gz

source_name: N2 L4

value: wildtype


title: N2 L4 mRNA 4 (27 N2 _L4 (24/03)_9 lane 2)

description:
27 N2 _L4 (24/03)_9 lane 2
processed data file: genescount-N2_L4_24_03__9_CAGATC.fastq.uniq.sam-genes.csv_allgenecount.gz


title: N2 L4 mRNA 5

description:
27 N2 _L4 (26/04)_10 lane 1
processed data file: genescount-N2_L4_26_04__10_CCGTCC.fastq.uniq.sam-genes.csv_allgenecount.gz


title: N2 L4 mRNA 3 (27 N2 _L4 (24/03)_9 lane 1)

description:
27 N2 _L4 (24/03)_9 lane 1
processed data file: genescount-N2_L4_24_03__9_CAGATC.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 16-cell stage embryo [16C_BC_59]


title: single cell from 8-cell stage embryo [8C_CB_23]

value: Male


title: single cell from 8-cell stage embryo [8C_BC_51]


title: single cell from 16-cell stage embryo [16C_CB_46]


title: N2 Embryo mRNA 7

description:
27 N2_embryo (09/09)_8 lane 2
processed data file: genescount-N2_embryo_09_09__8_TGACCA.fastq.uniq.sam-genes.csv_allgenecount.gz

source_name: N2 Embryo


title: single cell from 8-cell stage embryo [8C_BC_49]


title: single cell from 8-cell stage embryo [8C_BC_48]


title: N2 Embryo mRNA 6

description:
27 N2_embryo (09/09)_8 lane 1
processed data file: genescount-N2_embryo_09_09__8_TGACCA.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 16-cell stage embryo [16C_BC_71]


title: N2 Embryo mRNA 5

description:
27 N2_ embryo (30/06)_7 lane 2
processed data file: genescount-N2_embryo_30_06__7_CGATGT.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_BC_46]


title: single cell from 8-cell stage embryo [8C_BC_14]


title: N2 Embryo mRNA 4

description:
27 N2_ embryo (30/06)_7 lane 1
processed data file: genescount-N2_embryo_30_06__7_CGATGT.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_CB_21]


title: BB21 L4 3

description:
27 BB21_L4 (17/09)_6 lane 2
processed data file: genescount-BB21_L4_17_09__6_GTGAAA.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_CB_20]


title: BB21 Embryo mRNA 2

description:
27 BB21_embryo (17/09)_5 lane 1
processed data file: genescount-BB21_embryo_17_09__5_CTTGTA.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_CB_19]


title: BB21 L4 2

description:
27 BB21_L4 (17/09)_6 lane 1
processed data file: genescount-BB21_L4_17_09__6_GTGAAA.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_CB_17]


title: N2 L4 mRNA 4 (27 N2_L4 (23/08)_4 lane 2)

description:
27 N2_L4 (23/08)_4 lane 2
processed data file: genescount-N2_L4_23_08__4_GCCAAT.fastq.uniq.sam-genes.csv_allgenecount.gz


title: N2 L4 mRNA 3 (27 N2_L4 (23/08)_4 lane 1)

description:
27 N2_L4 (23/08)_4 lane 1
processed data file: genescount-N2_L4_23_08__4_GCCAAT.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 16-cell stage embryo [16C_BC_57]


title: single cell from 8-cell stage embryo [8C_BC_44]


title: N2 Embryo mRNA 3

description:
27 N2_embryo (16/08)_3 lane 2
processed data file: genescount-N2_embryo_16_08__3_ACAGTG.fastq.uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_BC_45]


title: N2 Embryo mRNA 2

description:
27 N2_embryo (16/08)_3 lane 1
processed data file: genescount-N2_embryo_16_08__3_ACAGTG.fastq.uniq.sam-genes.csv_allgenecount.gz


title: BB21 L4 1

description:
21 BB21 L4 TruSeq
processed data file: genescount-BB21L4_Truseq_CAGATC_L003_R1.Trim-collapse.sam-genes.csv_allgenecount.gz


title: BB24 embryo (20 BB24_embryo_2)

description:
20 BB24_embryo_2
processed data file: genescount-BB24_embryo_2_GTGAAA_L001_R1_trim_uniq.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_BC_41]


title: single cell from 8-cell stage embryo [8C_BC_42]


title: BB23 embryo (20 BB23_embryo_1)

description:
20 BB23_embryo_1
processed data file: genescount-BB23_embryo_1_ACAGTG_L001_R1.Trim-collapse.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_BC_40]


title: single cell from 8-cell stage embryo [8C_BC_39]


title: ChIP_seq_H3K27ac_day4_rep2

first: Hynek

last: Wichterle

address: 630 West 168th Street

department: Departments of Pathology and Cell Biology, Neurology, and Neuroscience

institute: Columbia University Medical Center

data_processing:
ChIP-seq sequencing reads were aligned to the mm9 genome assembly using Bowtie (version 0.12.7).
Peaks were called using the Genome Positioning System (GPS) and the GeneTrack to identify regions enriched by TFs over background.
For ChIP-seq H3K27ac data sets, peaks were called using Model-based Analysis of ChIP-Seq (MACS).
For ATAC-seq data, peaks were called using Homer software (v4.7.2).
For DNase-seq data, peaks were called using the GeneTrack peak finding algorithms (Albert et al., 2008).
RNA-seq sequencing reads were aligned to the mouse genome using RNA-seq alignment algorithm in the STAR (Spliced Transcripts Alignment to a Reference) software.
To assemble transcripts and estimate the relative abundances of these transcripts
The FPKM (Fragments Per Kilobase of exon per Million fragments mapped) was calculated per individual gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include: FPKM values for RNA-seq samples; GPS peak calls and GeneTrack peak calls for TF ChIP-exo and ChIP-seq data.  BED format files include: MACS peak calls for histone modification; Homer peak calls for ATAC-seq.

source_name: Motor neurons progenitors day 4

growth_protocol: Motor neuron differentiation of ESCs was performed as described previously (Wichterle et al., 2002) with some modification. Briefly, ESCs were trypsinized and seeded at 5 x 10^4 cells per mL (day 0). 1 uM RA and 0.25 uM SAG were added to the medium on day 2. 5 uM DAPT was added on days 4 and 5. For inducible Ngn2 and NIL lines, 3 ug/ml of doxycycline (Dox) was added on day 3 and day 2, respectively.

extract_protocol:
For ChIP-seq and ChIP-exo experiments, cells were lysed, and chromatin pellets were isolated and then solubilized and fragmented by sonication. Fragmented chromatin was then subject to immunoprecipitation using antibodies against protein of interest. RNA was extracted using TRIzol reagent (Thermo 15596026). Illumina Ribo-Zero rRNA Removal Kit (MRZH116) was used with DNase-treated total RNA sample to remove ribosomal RNA.
ChIP-seq libraries were prepared according to standard Illumina's instructions for HiSeq2000. Briefly, DNA was end-repaired, and ligated to sequencing adaptors, then PCR amplified and gel purified. The purified DNA libraries were sequenced following the manufacturer's protocols. For ChIP-exo libraries, while immunoprecipitates were still on the beads, samples were end-repaired, and ligated to a first sequencing adaptor, and subjected to lambda exonuclease digestion. Samples were then eluted from the beads and converted to double-stranded DNA by primer annealing and extension. A second sequencing adaptor was then ligated to exonuclease treated ends, then DNA was PCR amplified, gel purified, and sequenced. ATAC-seq libraries were prepared as described previously (Buenrostro et al., 2013). Briefly, cells were lysed and spun down. The pellet was resuspended in 50 ul of the transposase reaction mix containing 2.5 μL Tn5 transposase and sequencing adaptors (Illumina DNA Library Preparation Kit, FC-121-1030), and incubated for 30 min at 37 °C. The purified DNA was PCR amplified and sequenced. RNA-seq libraries were prepared for sequencing using standard Illumina protocols. DNase-seq libraries were prepared as described previously (He et al., 2014). Briefly, cells were lysed and spun down. The pellet was resuspended in 500 uL pre-warmed 15 mM Tris buffer A (pH8.0) containing 15 mM NaCl, 60 mM KCl, and 0.5 mM spermidine, and then add different amounts (0, 25, 50, and 75U) of DNase I (Roche, 04716728001) for 5 min at 37C. The reactions were terminated by 500 uL Stop buffer containing 0.5 mM spermidine and 1 ug of RNase, and incubated at 55C for 15 min. The purified DNA was sequenced by following standard Illumina protocols.

value: Ainv15 ES cell-derived spinal motor neuron progenitors

value: day 4

tag: growth protocol

value: iCre; RA, SAG on day 2

tag: chip antibody

value: H3K27ac (Abcam, catalog# ab4729, lot# GR00563-2)


title: N2 L4 mRNA 2

description:
9 N2 L4 illumina
processed data file: genescount-N2_L4_illumina_CTTGTA_L007_R1.Trim-collapse.sam-genes.csv_allgenecount.gz

tag: strain


title: RNA_seq_day6_fwd

description:
rRNA depleted total RNA
processed data file: RNAseq_FPKM_ES_to_MN.txt

source_name: Postmitotic motor neurons day 6

value: Ainv15 ES cell-derived spinal motor neurons

value: day 6

value: iCre; RA, SAG on day 2; DAPT on days 4,5


title: RNA_seq_day5_fwd

source_name: Postmitotic motor neurons day 5

value: day 5

value: iCre; RA, SAG on day 2; DAPT on day 4


title: ChIP_seq_H3K27ac_day4_rep1


title: RNA_seq_day4_fwd

value: Ainv15 ES cell-derived motor neuron progenitors

value: HBG3; RA, SAG on day 2


title: single cell from 8-cell stage embryo [8C_BC_38]

tag: Sex


title: BB4 L4 mRNA

description:
7 BB4L4
processed data file: genescount-BB4L4_CAGATC_L003_R1_all.Trim-collapse.sam-genes.csv_allgenecount.gz

source_name: BB4 L4

value: ADAR mutant

value: whole worm


title: RNA_seq_day0_fwd

source_name: Embryonic stem cells day 0

value: Ainv15 ES cell

value: day 0


title: DNase_seq_day0_fwd

description: DNase-seq

value: HBG3; none


title: single cell from 8-cell stage embryo [8C_BC_33]

value: Xist wt/wt

value: Female


title: N2 L4 mRNA 1

description:
6 N2L4
processed data file: genescount-N2L4_CGATGT_L003_R1_all.Trim-collapse.sam-genes.csv_allgenecount.gz

value: wildtype


title: ATAC_seq_day6

description: library strategy: ATAC-seq


title: BB21 Embryo mRNA 1

description:
5 BB21_E
processed data file: genescount-Bb21_ACTGAT_L004_R1.Trim-collapse.sam-genes.csv_allgenecount.gz

value: Embryo


title: single cell from 8-cell stage embryo [8C_BC_43]


title: ATAC_seq_day5

description: library strategy: ATAC-seq


title: ATAC_seq_day4

description: library strategy: ATAC-seq

value: day 4

value: iCre; RA, SAG on day 2


title: ATAC_seq_day2

description: library strategy: ATAC-seq

source_name: Primitive ectodermal cells day 2

value: Ainv15 ES cell-derived primitive ectodermal cells

value: day 2

value: iCre; none


title: ChIP_seq_p300_day6

value: Ainv15 ES cell-derived spinal motor neurons

value: day 6

value: iCre; RA, SAG on day 2; DAPT on days 4,5

value: p300 (Santa Cruz, catalog# sc-584, lot# I2712)


title: BB4 Embryo mRNA

description:
4 BB4_E
processed data file: genescount-Bb4_GATCAG_L004_R1.Trim-collapse.sam-genes.csv_allgenecount.gz

source_name: BB4 Embryo

value: ADAR mutant

value: whole worm


title: ChIP_seq_p300_day5

value: day 5

value: iCre; RA, SAG on day 2; DAPT on day 4


title: single cell from 8-cell stage embryo [8C_BC_11]

source_name: pre-implantation embryo

value: Xist wt/wt


title: N2 Embryo mRNA 1

description:
3 N2_E
processed data file: genescount-N2_TTAGGC_L004_R1.Trim-collapse.sam-genes.csv_allgenecount.gz


title: single cell from 8-cell stage embryo [8C_BC_9]

value: Female


title: ChIP_seq_H3K27ac_day6

value: H3K27ac (Abcam, catalog# ab4729, lot# GR00563-2)


title: single cell from 8-cell stage embryo [8C_BC_8]


title: ChIP_seq_H3K27ac_day5


title: Control_rep3

description: ChIP-exo

value: none (WCE)


title: ChIP_seq_iNgn2_day4

value: Ainv15 ES cell-derived motor neuron progenitors

value: day 4

value: iCre; RA, SAG on day 2; Dox on day 3

value: V5 (Invitrogen, catalog# R960, lot# 1652168)


title: Control_rep2

description: ChIP-exo

value: IgG (R&D, catalog# AB-108-C, lot# ES3411101)


title: single cell from 8-cell stage embryo [8C_BC_5]


title: Control_rep1

description: ChIP-exo

value: Ainv15 ES cell-derived spinal motor neurons


title: ChIP_exo_Lhx3_iNIL

description: ChIP-exo

source_name: Postmitotic motor neurons day 4

value: iCre; RA, Dox on day 2


title: ChIP_exo_Onecut1_day6

description: ChIP-exo

value: day 6

value: iCre; RA, SAG on day 2; DAPT on days 4,5

value: Onecut1 (Santa Cruz, catalog# sc-13050, lot# J0405)


title: ChIP_exo_Onecut1_day5

description: ChIP-exo


title: single cell from 8-cell stage embryo [8C_BC_4]


title: single cell from 8-cell stage embryo [8C_BC_32]


title: ChIP_exo_Isl1_day6_rep2

description: ChIP-exo

value: Isl1 (gifts from T. Jessell)


title: ChIP_exo_Isl1_day5_rep2

description: ChIP-exo

value: day 5


title: single cell from 8-cell stage embryo [8C_BC_3]


title: single cell from 8-cell stage embryo [8C_BC_1]


title: single cell from 8-cell stage embryo [8C_BC_2]


title: single cell from 4-cell stage embryo [4C_BC_51C]

value: Male


title: single cell from 4-cell stage embryo [4C_CB_33]

value: Xist wt/wt


title: ChIP_exo_Isl1_day5_rep1

description: ChIP-exo

value: iCre; RA, SAG on day 2; DAPT on day 4


title: single cell from 8-cell stage embryo [8C_BC_31]

value: Female


title: single cell from 4-cell stage embryo [4C_CB_32]


title: single cell from 4-cell stage embryo [4C_CB_29]


title: single cell from 4-cell stage embryo [4C_BC_51A]


title: single cell from 4-cell stage embryo [4C_BC_50A]


title: Sox2R75EOct4_coopseq (unbound)

city: St. Louis

first: Gary

middle: D.

last: Stormo

state: MO

address: 4515 McKinley Ave. Room 4208.

department: Genetics

institute: Washington University School of Medicine

description:
Contains unbound for downstream processing. Contains raw data from 2 replicates.
Processed data file: coopseq_Chang_allData.txt

data_processing:
Library strategy: Coop-seq
Extracting binding sites sequence from raw reads. Each read follows the format of GAGTCGTCTCGTCAGCAC-binding site-CCGTAGAGCACTCAGGTC.
Count read numbers for each variant, classified by dimer bound, Sox bound, POU bound, or unbound in coopseq and classfied by bound or unbound in specseq.
For specseq, calculate the bound/unbound ratio for each variant, then rank variants according to their relative affinities.
For coopseq, the cooperativity, omega, is calculated by (Dimer bound x unbound)/(Sox bound x POU bound).
Supplementary_files_format_and_content: Tab delimited text files.  See Processed_data_description.txt.

molecule: other

organism: synthetic construct

source_name: Synthesized DNA

extract_protocol:
All EMSA were done with Sox and Oct proteins in 1X NEB Cutsmart buffer (50mM Potassium Acetate, 20mM Tris-acetate, 10mM Magnesium Acetate, 100μg/ml BSA, pH 7.9@25°C) supplemented with 10% glycerol with 1mM of dsDNA and were incubated for 30 minutes on ice. Electrophoresis mobility assay (EMSA) were done using native 12% PAGE prepared as Tris/Glycine (25mM Tris pH 8.3; 192mM glycine) mini-gels. These gels were first pre-run using 1X Tris/Glycine buffer (25mM Tris pH 8.3; 192mM glycine) at 200V for 30 minutes, then samples were loaded for an additional run of 60 minutes at 200 V at 4°C. After EMSA, the gels were stained with ethidium bromide and visualized using Biorad gel imager. Each band detected in the EMSA were excised with a plastic tool and the DNA in the gel extracted by incubating for 30 mins at 50°C in 50ml acrylamide gel extraction buffer (500mM Ammonium acetate, 10mM Magnesium Acetate, 1mM EDTA, 0.1% SDS). 0.01 pmole of PCR Control DNA with the sequence of GAGTCGTCTCGTCAGCACCGGCGGCGGTTCCCGGAAAGACCGTAGAGCACTCAGGTC (primer binding sites underlined) were added to each extracted sample. Sample in the extraction buffer were purified with QIAquick Nucleotide Removal Kit (Qiagen) following the manufacturer’s instructions. Each fraction of DNA was barcoded and amplified using HotStart PCR Master Mix (Lambda Biotech). DNA was denatured at 94°C for 30 seconds, annealed at 55°C for 30 seconds and extend at 72°C for 45 seconds per round for 12 to 20 rounds with modified Indexed-Illumina primers (PE1-Genetics1/2, PE2.0). The PCR product was then purified again using QIAquick Nucleotide Removal Kit.
DNA library was constructed by mixing the following oligos GAGTCGTCTCGTCAGCACCGGCCATTGTNTGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGGCATTGTNNTGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGCATTGTNGNTGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCCATTGTNGGNTGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTNGGCNTGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTNGGCGNTGCTAATGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTNGGCGGNTGCTAATACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTNGGCGGCNTGCTAATCCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGGCATTGTTATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGCATTGTTNATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCCATTGTTNNATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTTNGNATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTTNGGNATGCTAATGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGGCATTGTTATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGCATTGTTNATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCCATTGTTNNATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTTNGNATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCATTGTTNGGNATTAGCATGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGGAACAATGATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGAACAATGNATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCAACAATGNNATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACAACAATGNGNATGCTAATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACAACAATGNGGNATGCTAATGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGGAACAATGATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCGAACAATGNATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACCAACAATGNNATTAGCATAGACCGTAGAGCACTCAGGTC, GAGTCGTCTCGTCAGCACAACAATGNGNATTAGCATAGACCGTAGAGCACTCAGGTC, and GAGTCGTCTCGTCAGCACAACAATGNGGNATTAGCATGACCGTAGAGCACTCAGGTC. DNA library was designed by flanking the degenerate sequences of interest with sequences GAGTCGTCTCGTCAGCAC and CCGTAGAGCACTCAGGTC for downstream processing. To make double-stranded DNA (dsDNA) libraries, 100 pmole single-strand degenerate template sequences were mixed with an equal amount of reverse complement primer (GACCTGAGTGCTCTACGG). In the presence of Taq Polymerase, brief 10-sec denaturing followed by 10 min of 55 degree annealing/extension is sufficient to make dsDNA libraries. Because any unextended single-stranded DNA (ssDNA) could contaminate the unbound band, the reaction mix was digested by 1 ml NEB Exo I exo- nuclease (New England Biolabs, Beverly, MA) for 30 min. All final dsDNA products were purified by QIAGEN (Valencia, CA) PCR purification columns.

tag: library

value: DNA target oligos

tag: transcription factor(s)


title: single cell from 4-cell stage embryo [4C_BC_5]


title: single cell from 4-cell stage embryo [4C_BC_3]


title: Sox2K57EOct4_coopseq (unbound)


title: single cell from 2-cell stage embryo [2C_CB_4]


title: Sox2R75EOct4_coopseq (POU bound)

description:
Contains monomer bound for downstream processing. Contains raw data from 2 replicates.
Processed data file: coopseq_Chang_allData.txt


title: Sox2E46LK57EOct4_coopseq (Sox bound)

description:
Contains monomer bound for downstream processing. Contains raw data from 3 replicates.
Processed data file: coopseq_Chang_allData.txt


title: single cell from 4-cell stage embryo [4C_BC_2]


title: single cell from 2-cell stage embryo [2C_CB_2]


title: ChIP_exo_Isl1_day6_rep1

description: ChIP-exo


title: single cell from 4-cell stage embryo [4C_BC_50C]


title: Sox2K57EOct4_coopseq (POU bound)


title: Sox2E46LK57EOct4_coopseq (POU bound)


title: Sox2R75EOct4_coopseq (Sox bound)


title: Sox17_specseq (unbound)

description:
Contains unbound reads needed to calculate the relative binding energy.
Processed data file: Sox17_specseq_processed.txt

data_processing:
Library strategy: Spec-seq
Extracting binding sites sequence from raw reads. Each read follows the format of GAGTCGTCTCGTCAGCAC-binding site-CCGTAGAGCACTCAGGTC.
Count read numbers for each variant, classified by dimer bound, Sox bound, POU bound, or unbound in coopseq and classfied by bound or unbound in specseq.
For specseq, calculate the bound/unbound ratio for each variant, then rank variants according to their relative affinities.
For coopseq, the cooperativity, omega, is calculated by (Dimer bound x unbound)/(Sox bound x POU bound).
Supplementary_files_format_and_content: Tab delimited text files.  See Processed_data_description.txt.


title: Sox2E46LK57EOct4_coopseq (unbound)

description:
Contains unbound for downstream processing. Contains raw data from 3 replicates.
Processed data file: coopseq_Chang_allData.txt


title: Oct4_specseq (unbound)

description:
Contains unbound reads needed to calculate the relative binding energy.
Processed data file: Oct4_specseq_processed.txt


title: Sox2_specseq (unbound)

description:
Contains unbound reads needed to calculate the relative binding energy.
Processed data file: Sox2_specseq_processed.txt


title: Sox2R75EOct4_coopseq (dimer bound)

description:
Contains dimer bound for downstream processing. Contains raw data from 2 replicates.
Processed data file: coopseq_Chang_allData.txt


title: single cell from 2-cell stage embryo [2C_BC_11]


title: Sox2K57EOct4_coopseq (Sox bound)


title: Sox2E46LK57EOct4_coopseq (dimer bound)

description:
Contains dimer bound for downstream processing. Contains raw data from 3 replicates.
Processed data file: coopseq_Chang_allData.txt


title: Sox2K57EOct4_coopseq (dimer bound)


title: single cell from 2-cell stage embryo [2C_CB_6]


title: single cell from 2-cell stage embryo [2C_BC_10]


title: Sox17_specseq (bound)

description:
Contains bound reads needed to calculate the relative binding energy.
Processed data file: Sox17_specseq_processed.txt


title: Oct4_specseq (bound)

description:
Contains bound reads needed to calculate the relative binding energy.
Processed data file: Oct4_specseq_processed.txt


title: Oocyte Cast [Oo_Cast_12]

source_name: oocyte

value: Cast/EiJ

value: Oocyte


title: nuclearRNAseq_control5_3

description:
RNAseq_PCM1plus_vsPCM1minus.txt
nuclear RNA

data_processing:
All reads were aligned using Bowtie against the rat genome (build 3.4) using settings  -n 1 -m 1 --strata --best (i.e. requiring at most one unique mapping per read, allowing one mismatch).  Results were converted to the BAM file format using SAMtools. Annotations of functional genomic features and their coordinates were obtained from Ensembl (Release 69). ChIP-seq reads were extended in silico to 150 bp, for them to correspond to the average length of the mononucleosomal DNA fragments observed upon 2100 Bioanalyzer measurements. Read counts of genomic features of interest were determined using the SeqMonk Mapped Sequence Data Analyser (Version 0.22.0; www.bioinformatics.babraham.ac.uk/projects/seqmonk/), and further processed using R version 2.15.1.
Analysis of gene expression was based on strand-specific read counts, with only reads mapping to the strand opposite of the annotated gene orientation being counted. To assess issues related to strand-specificity of the RNA-seq, we assessed the fraction of all reads per gene mapping to the opposite strand. Differential RNA expression was assessed based on differences between each treatment and control sample, paired per experiment, using a Chi-squared test. The average read number per million reads was determined, as well as the median of the resulting P value per gene from 4 independent experiments was calculated, and corrected for multiple testing. Differential expression in read counts from PCM1-positive and -negative samples was determined using EdgeR.
Except for cluster analyses, histone methylation was always assessed in autosomal 10 kb windows, with a 10 kb step size. Windows with no or poor mapping (resp. gaps in the genome build or highly repetitive sequences) were not considered. Such windows were identified as having read counts that were over 6 times the third interquartile range different from the median input read counts. Read counts for input samples were highly concordant (average Pearson’s r = 0.994) and failed to show significant differences between H3K9me2 and H3K27me3, or between the different treatments (q-value exceeding 0.5 for all). All input samples were therefore binned and treated as one dataset in subsequent analyses. To identify regions of estimated equal H3K9me2 or H3K27me3 levels, circular binary segmentation was applied on the combined control datasets using the DNAcopy package using default parameters. Circular binary segmentation was applied using the segment function, using the hybrid approach for the computation of the P-value of the maximal t-statistic, requiring a significance level lower than 0.01 to accept change-points, and a minimum of 5 probes per segment.
Differences in ChIP-seq read density between these segments between paired treated and control samples were assessed using a paired t-test on the 10kb window read counts. Counts were normalized in SeqMonk by adjusting them to have a matched distribution across all samples. Average histone methylation levels per segment were required to differ at least 20%, and to differ in at least 3 out of 4 paired treatment-control experiments in the same direction. P-values from student t-tests were corrected for multiple testing, and segments were only considered significantly different if q-values were below 0.1.
Genome_build: rn3.4
Supplementary_files_format_and_content: Quantitated ChIP-Seq data files are tab-delimited and contain the following 7 columns: position of chromosome segments as identified by CBS (1) Chromosome, (2) Start and (3) End; (4-5) log2 reads per million
Supplementary_files_format_and_content: Quantitated RNA-Seq data files for hypertrophic vs control are tab-delimited and contain the following 4 columns: (1) gene name (Ensembl); (2-3) log2 reads per million; (4) FDR-adjusted P-value
Supplementary_files_format_and_content: Quantitated RNA-Seq data files for PCM1+ vs - are tab-delimited and contain the following 4 columns: (1) gene name (Ensembl); (2) log2 fold change; (3) log2 counts per million; (4) FDR-adjusted P-value

organism: Rattus norvegicus

source_name: control 5

extract_protocol:
End repair or second strand synthesis reactions were purified using Agencourt AMPure XP (Beckman Coulter) and eluted in 15 µL dA-tailing mix (NEBNext dA-Tailing Module; New England Biolabs). This mix was incubated at 37 °C for 30 min, purified using Agencourt AMPure XP (Beckman Coulter) and eluted in 14 µL of pre-annealed barcoded adapters at a 20× molar amount relative to the estimated amount of dA-tailed DNA. Next, 4 µL 5× Ligation Buffer and 2 µL Quick Ligase (NEBnext Quick Ligation Module; New England Biolabs) were added, and the reaction was incubated for 15 min at 37 °C.  These reactions were again purified using Agencourt AMPure XP (Beckman Coulter) and eluted in 50 µL water for ChIP sequencing, or 49 µL TE buffer and 1 µL USER enzyme mix (New England Biolabs) for nuclear RNA sequencing. The latter mix was incubated at 37 °C for 30 min and at 95 °C for 5 min. To amplify these libraries, 50 µL Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific, Loughborough, UK) was added to each sample, together with primer 1 and 2 oligonucleotides to a final concentration of 500 nM. Each reactions was distributed between 4 PCR tubes and PCR was performed in a thermal cycler using the following program: initial denaturation at 98°C for 30 seconds, amplification over 18 cycles of 98 °C, 65 °C and 72 °C for respectively 10, 30 and 30 seconds, and a final extention at 72 °C for 7 min. PCR reactions were purified using the QIAquick PCR purification kit, eluted in 25 µL, mixed with 10 µL loading buffer (200 mg/mL Ficoll 400, 15 mg/mL Orange G and 2× Tris/Borate/EDTA buffer) and loaded on a 1.7% TBE agarose gel, prestained with SYBR safe DNA gel stain (Life Technologies). DNA was separated by electrophoresis at 4V/cm for 2 hours at 4 °C, and 200 to 400 bp fragments were excised and purified using the QIAquick Gel Extraction Kit (QIAGEN) as per the manufacturer’s instructions. DNA fragment size was verified on a 2100 Bioanalyzer Instrument using a High Sensitivity DNA Analysis Kit (both from Agilent Technologies Inc., Santa Clara, USA), and DNA concentration was verified using the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).
nuclei sorting protocol: To minimize handling times and to control potential inter-experimental artefacts, nuclei were isolated and sorted from 2 left ventricular wall samples per experiment, one hypertrophic sample and one corresponding control sample. Methods for nuclear isolation were based on a previously described method.To minimize handling times and to control potential inter-experimental artefacts, nuclei were isolated and sorted from 2 left ventricular wall samples per experiment, one hypertrophic sample and one corresponding control sample. Methods for nuclear isolation were based on a previously described method. All buffers were precooled, supplemented with dithiothreitol (1 µM), actinomycin D (1mg/L), cOmplete protease inhibitor (PI) cocktail (Roche; 0.5 µL/mL) and SUPERase.In (Ambion; 200 U/mL), and buffered with 10 mM Tris-HCl to pH 8.0. Frozen hearts where thawed in 10 mL lysis buffer (0.32 M sucrose, 5 mM CaCl2, 5 mM EDTA, 0.5 mM EGTA, 3 mM Mg(CH3COO)2) and homogenized using an IKA ultra-Turrax (20,000 RPM, 15 sec). After addition of 30 mL lysis buffer, the homogenate was dounced 10× on ice, filtered consecutively over mesh, a 100 µm and a 70 µm cell strainer and spun for 10 minutes (700×G; 4°C). The resulting pellet was dissolved in 10 mL centrifuge buffer (2.1 M sucrose, 3 mM Mg(CH3COO)2, and 5 mM EDTA), and superimposed upon 5 mL centrifuge buffer in an autoclaved Thinwall Ultra-Clear Tube (Beckman Coulter, High Wycombe, UK). Tubes were loaded in a precooled rotor (SW32.1Ti) and spun for 60 minutes (26,000×G; 4°C) in an OPTIMA MAX Ultracentrifuge (both from Beckman Coulter). The resulting pellet was dissolved in 1.5 mL sorting buffer (0.43 M sucrose, 70 mM KCl, 2 mM MgCl2 and 5 mM EDTA) and labelled for 1 hour on ice using 3 µL anti-PCM1 antibody (HPA023374) that was pre-incubated for 15 minutes with 2 µL Alexa Fluor 488 Goat Anti-Rabbit IgG (H+L) Antibody (Life Technologies). Nuclei were sorted on an Influx streaming air high-speed cell sorter (BD Biosciences, Oxford, UK), into Protein LoBind tubes (Eppendorf, Stevenage, UK) on a cooled tube holder. For comparison of unsorted and sorted nuclei, the input samples corresponded to a 350 µL aliquot of the original homogenized sample, and the nuclear samples corresponded to 400,000 nuclei not gated for PCM1 staining.  All buffers were precooled, supplemented with dithiothreitol (1 µM), actinomycin D (1mg/L), cOmplete protease inhibitor (PI) cocktail (Roche; 0.5 µL/mL) and SUPERaseIn (Ambion; 200 U/mL), and buffered with 10 mM Tris-HCl to pH 8.0. Frozen hearts where thawed in 10 mL lysis buffer (0.32 M sucrose, 5 mM CaCl2, 5 mM EDTA, 0.5 mM EGTA, 3 mM Mg(CH3COO)2) and homogenized using an IKA ultra-Turrax (20,000 RPM, 15 sec). After addition of 30 mL lysis buffer, the homogenate was dounced 10× on ice, filtered consecutively over mesh, a 100 µm and a 70 µm cell strainer and spun for 10 minutes (700×G; 4°C). The resulting pellet was dissolved in 10 mL centrifuge buffer (2.1 M sucrose, 3 mM Mg(CH3COO)2, and 5 mM EDTA), and superimposed upon 5 mL centrifuge buffer in an autoclaved Thinwall Ultra-Clear Tube (Beckman Coulter, High Wycombe, UK). Tubes were loaded in a precooled rotor (SW32.1Ti) and spun for 60 minutes (26,000×G; 4°C) in an OPTIMA MAX Ultracentrifuge (both from Beckman Coulter). The resulting pellet was dissolved in 1.5 mL sorting buffer (0.43 M sucrose, 70 mM KCl, 2 mM MgCl2 and 5 mM EDTA) and labelled for 1 hour on ice using 3 µL anti-PCM1 antibody (HPA023374) that was pre-incubated for 15 minutes with 2 µL Alexa Fluor 488 Goat Anti-Rabbit IgG (H+L) Antibody (Life Technologies). Nuclei were sorted on an Influx streaming air high-speed cell sorter (BD Biosciences, Oxford, UK) using a gating strategy as described.15 Post-sorting flow cytometric analyses were done using FlowJo (v9.6.3) and Bioconductor’s flowCore package.52 Nuclei were sorted into Protein LoBind tubes (Eppendorf, Stevenage, UK) on a cooled tube holder. For comparison of unsorted and sorted nuclei, the input samples corresponded to a 350 µL aliquot of the original homogenized sample, and the nuclear samples corresponded to 400,000 nuclei not gated for PCM1 staining.
DNA libraries were sequenced on an Illumina HiSeq 1000 (Illumina, Essex, UK) using either the default RTA software, or a custom program that consisted of annealing of Illumina Read 1 sequencing primer, 4 dark cycles, 46 light cycles, denaturation, annealing of Illumina Read 1 sequencing primer and 5 light cycles to read the indexing barcode. The latter modification was introduced because the low complexity of the first bases from the indexing barcode yielded incorrect cluster definitions and consequently lowered the number of high quality reads.

value: nuclei from left ventricle of the heart, sorted but not gated for PCM1

value: Sprague Dawley

tag: hypertrophy induction

value: Male Sprague Dawley rats of ~280 g not assigned to the exercise protocol were used as control.

tag: isolation of material from sorted nuclei

value: A solution of at least 100000 sorted nuclei was mixed with 3× its volume of TRIzol LS reagent (Life Technologies) and 2 µL glycogen (Life Technologies), and stored for at most one month at -80°C until further processing according to manufacturer's instructions. Genomic DNA was removed using the TURBO DNA-free kit (Life Technologies) as per the kit’s instructions. RNA was subsequently reverse transcribed using SuperScript III Reverse Transcriptase (Life Technologies) as follows:3 µg Random Primers (mostly hexamers; Life Technologies) were added to 10 µL RNA and 8 µL 5× First-Strand Buffer. This mixture was heated to 94 °C for 3 minutes for RNA fragmentation, and incubated on ice for at least 1 minute. Next 2 µL dNTP Mix (10 mM) (Life Technologies) were added, as well as 4 µl DTT (100 mM), 40U SUPERase.In, 400U SuperScript™ III Reverse Transcriptase and 8 µg Actinomycin D. Water was added to make up the volume to 40 µL, and the sample was incubated at 25 °C for 5 min 50 °C for 30 minutes and inactivated at 70 °C for 15 min. cDNA-RNA duplexes were purified using 72 µL Agencourt AMPure XP (Beckman Coulter) and eluted in 20 µL of the following second-strand synthesis reaction mix:0.33 mM dATP, dCTP and dGTP (Life Technologies), 0.33 mM dUTP (Sigma Aldrich), 0.25 U Ribonuclease H (Life Technologies) and 10 U DNA polymerase I (New England Biolabs). The reaction was allowed to proceed for 2.5 hours at 16°C.


title: ribo_minus_RNAseq_control1

source_name: control 1

value: left ventricle of the heart

value: 250 µL of homogenized tissue solution (200 mg/10mL) of was mixed with 3× its volume of TRIzol LS reagent (Life Technologies) and 2 µL glycogen (Life Technologies), and stored for at most one month at -80°C until further processing according to manufacturer's instructions. RNA was depleted of ribosomal RNA using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Life Technologies) as instructed by the kit. Genomic DNA was removed using the TURBO DNA-free kit (Life Technologies) as per the kit’s instructions. RNA was subsequently reverse transcribed using SuperScript III Reverse Transcriptase (Life Technologies) as follows:3 µg Random Primers (mostly hexamers; Life Technologies) were added to 10 µL RNA and 8 µL 5× First-Strand Buffer. This mixture was heated to 94 °C for 3 minutes for RNA fragmentation, and incubated on ice for at least 1 minute. Next 2 µL dNTP Mix (10 mM) (Life Technologies) were added, as well as 4 µl DTT (100 mM), 40U SUPERase.In, 400U SuperScript™ III Reverse Transcriptase and 8 µg Actinomycin D. Water was added to make up the volume to 40 µL, and the sample was incubated at 25 °C for 5 min 50 °C for 30 minutes and inactivated at 70 °C for 15 min. cDNA-RNA duplexes were purified using 72 µL Agencourt AMPure XP (Beckman Coulter) and eluted in 20 µL of the following second-strand synthesis reaction mix:0.33 mM dATP, dCTP and dGTP (Life Technologies), 0.33 mM dUTP (Sigma Aldrich), 0.25 U Ribonuclease H (Life Technologies) and 10 U DNA polymerase I (New England Biolabs). The reaction was allowed to proceed for 2.5 hours at 16°C.


title: ribo_minus_RNAseq_control2


title: nuclearRNAseq_control1_2


title: Oocyte Cast [Oo_Cast_11]


title: Oocyte B6 [Oo_B6_21]


title: Oocyte Cast [Oo_Cast_10]


title: nuclearRNAseq_control5_2

value: PCM1-negative nuclei from left ventricle of the heart


title: nuclearRNAseq_control1_1


title: ChIPseq_input_control

description:
H3K9me2_normalized_RPM_in_CBS_bins_SHAM_AB.txt
H3K27me3_normalized_RPM_in_CBS_bins_CTRL_RUN.txt
nuclear RNA

source_name: control

value: PCM1-positive nuclei from left ventricle of the heart

value: A solution of at least 100000 freshly sorted nuclei for nucleosome extraction was topped up with MNase buffer (0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2 and 1 µL/mL cOmplete PI cocktail) to a final volume of 1.5 mL and spun for 10 minutes (1,000×G, 4°C). All but 100 µL supernatant was removed, and nuclei were gently suspended in an additional 1.4 mL MNase buffer and spun for 10 minutes (1,000×G, 4°C). All but 100 µL supernatant was again removed, and the pelleted nuclei were suspended to a concentration of 4,000 nuclei (as counted by flow cytometry) per µL in MNase buffer. Micrococcal nuclease (Affymetrix USB, Staufen, Germany) was subsequently added (20 U/mL) to the nuclei suspension. In order to digest the chromatin to a predominantly mononucleosomal resolution, the reaction was stopped after 8 minutes of incubation at 37°C by transfer on ice and by the addition of ½ volume of nucleosome extraction buffer (15 mM EDTA, 0.3% Triton X-100, 10 mM Na2HPO4, 3.5 mM KH2PO4, 1.5 M NaCl, 20 µg/mL and 3 µL/mL cOmplete PI cocktail at pH 7.4). Nucleosomes were subsequently extracted at 4°C overnight on a vertical rotor (30 RPM). The next day, nuclear debris was removed by centrifugation for 10 minutes (21,000×G, 4°C), after which 50 µL was used as input. These solutions were kept overnight on a vertical rotor at 4 °C (5 RPM). Proteinase K (2 mg) was subsequently added to each tube (including input fractions), and after incubation at 42°C for 30 minutes, DNA was extracted using the QIAquick PCR purification kit (QIAGEN, Manchester, UK) as follows:binding buffer PB with pH indicator was added directly to the suspension, pH adjusted using Na(CH3COO) and after an incubation of 10 minutes, the DNA binding, washing and elution in 50 µL water was done as per the kit’s instructions. Purified DNA was rendered blunt ended using the NEBnext End Repair Module (New England Biolabs) as per the manufacturer’s instructions.


title: ChIPseq_input_exercise

source_name: exercise

value: Male Sprague Dawley rats of ~280 g were assigned to interval training on a treadmill (Columbus Instruments, OH, US) with 25 degree inclination, with 5 days of acclimatization with running velocity for 6 m/min for 30, 45, 60, 75, 90 and 120 min. Thereafter interval training was performed 6 days a week with 12 x 8 min intervals with 2 min resting period (6 m/min) after a warm-up period at 10 m/min. Exercise training was performed over six weeks at a running speed of 15 m/min increasing with 2 m/min each week. Rats not able to fulfill the exercise protocol were withdrawn from the study.


title: Oocyte B6 [Oo_B6_20]


title: Oocyte B6 [Oo_B6_4]


title: ChIPseq_input_sham_operated

source_name: sham-operated

value: Male Sprague Dawley rats of ~170 g were anesthetized and ventilated through endotracheal intubation with a mixture of 69% N2O, 29% O2 and 2% isoflurane. Sham-operated animals underwent the same surgical procedure as those receiving aortic banding, except tightening the silk suture around the ascending aorta proximal to the brachiocephalic trunk. Buprenorphine was given as postoperative analgesia.


title: nuclearRNAseq_sham_operated4

description:
Sample 48
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: sham-operated 4


title: nuclearRNAseq_sham_operated3

description:
Sample 47
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: sham-operated 3


title: HA-Input_rep2

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

description: Replicate 2 for Input for SKM early cells (HA tag on ATFs)

data_processing:
Illumina Casava 1.8.2 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using Bowtie2 version 2.2.5.
Output sam files were converted to bam files, sorted, and indexed with Samtools 1.3.
Differential peak signals were determined by DiffBind 1.16.2 for H3K27ac and H3K9me3 histone marks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include peaks called by MACS; comma separated files for pairwise comparisons

source_name: mouse embryonic fibroblasts

growth_protocol: Transduced MEFs were grown in knock-out DMEM supplemented with 15% fetal bovine serum, 1% nonessential amino acids, 2 mM L-glutamine, 1 x 10^3 units/mL leukemia inhibitory factor, 1 mM sodium pyruvate, and 100 µM beta-mercaptoethanol on 0.1% gelatin. iPS cells were treated with 100 nM 4-hydroxytamoxifen to induce expression of the Oct4-MerCreMer; Tomato/GFP reporter. Cells were maintained in a humidified 37°C incubator with 5% CO2.

extract_protocol:
For histone marks, 6 x 10^6 cells were harvested, and for ATFs, 2.5 x 10^7 cells were harvested. Cells were fixed in 1.5% formaldehyde, then flash frozen. Cells were lysed with a series of 3 buffers: LB1, LB2, and LB3. LB1 consisted of 10 mM HEPES, 10 mM EDTA, 0.5 mM EGTA, and 0.25% Triton X-100. LB2 consisted of 200 mM NaCl, 10 mM HEPES, 1 mM EDTA, and 0.5 mM EGTA. LB3 consisted of 50 mM Tris-HCl, 10 mM EDTA, 0.5% Empigen BB, and 1% SDS. Samples were sonicated in a Misonix sonicator (S-4000) at 60% power, 10 sec on and 10 off, for a total of 32 min total pulse time. Samples were cleared by centrifugation 17,000 x g for 10 min. For preclearing, samples were incubated with magnetic Protein G beads (Life Technologies #10003D) for 1 hour at 4°C. After preclearing, 1% of sample was saved as input. Samples were incubated with the appropriate antibody, H3K27ac antibody (Abcam #ab4729), H3K9me3 antibody (Abcam #ab8898), or HA antibody (Abcam #ab9110), overnight at 4°C with IP Buffer (2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, and 1% Triton X-100). Protein-DNA complexes on magnetic beads were washed in WB1 once, WB2, once, WB3 once, and TE Buffer twice. WB1 consisted of 2 mM EDTA, 20 mM Tris-HCl, 0.1% SDS, 1% Triton X-100, 150 mM NaCl). WB2 consisted of 2 mM EDTA, 20 mM Tris-HCl, 0.1% SDS, 1% Triton X-100, and 500 mM NaCl. WB3 consisted of 1 mM EDTA, 10 mM Tris-HCl, 250 mM LiCl, 1% deoxycholate, and 1% NP-40. DNA was eluted in 0.1 M NaHCO3, 0.2 M NaCl, and 1% SDS. Protein-DNA complexes were reverse crosslinked by incubation at 65°C for 6 hours. DNA was treated with RNase A and Proteinase K. Captured DNA was column purified (Epoch Life Sciences #1920-250).
Samples were prepared for sequencing with the TruSeq ChIP Sample Preparation Kit (Illumina #IP-202-1012) as per the manufacturer instructions and quantified with a Qubit fluorometer (Life Technologies #Q32866). Three, four or six TruSeq indexed ChIP samples were pooled per lane. All samples were loaded at a final concentration of 8 pM and sequenced as single reads on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: MEF-derived cells

tag: transduction

value: ZFATF1, ZFATF2, ZFATF3, Sox2, Klf4, c-Myc/Empty, Sox2, Klf4, c-Myc

value: none (input)


title: Sox2_specseq (bound)

description:
Contains bound reads needed to calculate the relative binding energy.
Processed data file: Sox2_specseq_processed.txt

value: DNA target oligos


title: nuclearRNAseq_banded_aorta3

description:
Sample 43
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: banded aorta 3

value: Male Sprague Dawley rats of ~170 g were anesthetized and ventilated through endotracheal intubation with a mixture of 69% N2O, 29% O2 and 2% isoflurane. A silk suture 3-0 was tightened around the ascending aorta proximal to the brachiocephalic trunk. Buprenorphine was given as postoperative analgesia. After 6 weeks, only those rats were retained, that had non-failing hearts with detectable hypertrophy, defined as increased posterior wall thickness in diastole (>1.9 mm), increased left ventricular weight (>0.75 g) and preserved lung weight (<2.0 g).


title: nuclearRNAseq_banded_aorta4

description:
Sample 44
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: banded aorta 4


title: nuclearRNAseq_sham_operated1

description:
Sample 45
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: sham-operated 1


title: single cell from 2-cell stage embryo [2C_BC_9]

tag: developmental stage

value: Xist wt/wt

value: Female


title: nuclearRNAseq_banded_aorta1

description:
Sample 41
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: banded aorta 1

value: Sprague Dawley


title: HA-Input_rep1

description: Replicate 1 for Input for SKM early cells (HA tag on ATFs)


title: nuclearRNAseq_banded_aorta2

description:
Sample 42
RNAseq_normalizedRPM_SHAM_AB.txt
RNAseq_raw_read_counts_SHAM_AB.txt
nuclear RNA

source_name: banded aorta 2


title: nuclearRNAseq_control4

description:
Sample 40
RNAseq_normalizedRPM_CTRLRUN.txt
RNAseq_raw_read_counts_CTRL_RUN.txt
nuclear RNA

source_name: control 4

value: Male Sprague Dawley rats of ~280 g not assigned to the exercise protocol were used as control.


title: nuclearRNAseq_control5_1

value: A solution of at least 100000 sorted nuclei was mixed with 3× its volume of TRIzol LS reagent (Life Technologies) and 2 µL glycogen (Life Technologies), and stored for at most one month at -80°C until further processing according to manufacturer's instructions. Genomic DNA was removed using the TURBO DNA-free kit (Life Technologies) as per the kit’s instructions. RNA was subsequently reverse transcribed using SuperScript III Reverse Transcriptase (Life Technologies) as follows:3 µg Random Primers (mostly hexamers; Life Technologies) were added to 10 µL RNA and 8 µL 5× First-Strand Buffer. This mixture was heated to 94 °C for 3 minutes for RNA fragmentation, and incubated on ice for at least 1 minute. Next 2 µL dNTP Mix (10 mM) (Life Technologies) were added, as well as 4 µl DTT (100 mM), 40U SUPERase.In, 400U SuperScript™ III Reverse Transcriptase and 8 µg Actinomycin D. Water was added to make up the volume to 40 µL, and the sample was incubated at 25 °C for 5 min 50 °C for 30 minutes and inactivated at 70 °C for 15 min. cDNA-RNA duplexes were purified using 72 µL Agencourt AMPure XP (Beckman Coulter) and eluted in 20 µL of the following second-strand synthesis reaction mix:0.33 mM dATP, dCTP and dGTP (Life Technologies), 0.33 mM dUTP (Sigma Aldrich), 0.25 U Ribonuclease H (Life Technologies) and 10 U DNA polymerase I (New England Biolabs). The reaction was allowed to proceed for 2.5 hours at 16°C.