title: Post LPS (time 4h; no intervention) 2


title: Pre LPS (time 0h) 6

status: Public on Aug 16 2018

type: SRA

city: Pittsburgh

first: Josiah

last: Radder

state: Pennsylvania

address: 200 Lothrop St

department: Pulmonary, Allergy, and Critical Care Medicine

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
Trimmomatic (Version 0.36)
TopHat (Version 2.1.1)
Cufflinks (Version 2.2.1)
Genome_build: GRCH37
Supplementary_files_format_and_content: Cufflinks (Version 2.2.1)

molecule: total RNA

organism: Homo sapiens

source_name: Lung parenchymal homogenate

extract_protocol:
Tissue was placed in RNA later, then RNA extracted using Qiazol
TuruSeq stranded mRNA (PolyA+)

treatment_protocol: For LPS injury, E. coli 055:B5 endotoxin was diluted in 20ml sterile PBS at 5 mg/kg ideal body weight for the donor and infused into the pulmonary arterial limb of the circuit over 5 min via automated syringe pump at T=1 hour. BC1215 was dissolved in 50ml sterile PBS and BC1215 or PBS alone was administered via a bronchoscope with 2-3 ml of solution directed into each segmental bronchus immediately following T-2 hour BAL and biopsy collection.

tag: group

value: Pre LPS


title: Pre LPS (time 0h) 3


title: Pre LPS (time 0h) 4


title: Post LPS (time 4h, BC1215 treated) 2

value: Post LPS Intervention


title: Pre LPS (time 0h) 5


title: Pre LPS (time 0h) 1


title: Post LPS (time 4h, BC1215 treated) 1


title: DHEApre_201-1

type: genomic

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

country: Israel

institute: Ariel University

hyb_protocol: Samples were randomized with respect to slide and position on arrays and all samples were hybridized and scanned concurrently to mitigate batch effects as recommended by McGill genome center using Illumina Infinum HD technology user guide.

scan_protocol: All samples scanned concurrently to mitigate batch effects as recommended by McGill genome center using Illumina Infinum HD technology user guide.

data_processing: Illumina arrays were analyzed using the ChAMP Bioconductor package in R (Morris, Butcher et al. 2014). IDAT files were used as input in the champ.load function using minfi quality control and normalization options. Raw data were filtered for probes with a detection value of P>0.01 in at least one sample. We filtered out probes on the X or Y chromosome to mitigate sex effects and probes with SNPs as identified in (Marzouka, Nordlund et al. 2016), as well as probes that align to multiple locations as identified in (Marzouka, Nordlund et al. 2016).  Batch effects were analyzed on the non-normalized data using the function champ.svd. Intra-array normalization to adjust the data for bias introduced by the Infinium type 2 probe design was performed using beta-mixture quantile normalization (BMIQ) with function champ.norm (norm="BMIQ") (Morris, Butcher et al. 2014). We corrected for batch effects after BMIQ normalization using champ.runcombat function. Differentially methylated CGs (MVP) were called using the Bioconductor package Limma (Smyth, Michaud et al. 2005) as implemented in ChAMP using “fdr” for multiple testing correction (adjusted P value (Q) of <0.05). ANOVA analysis was performed for CGs that were short listed for association with addiction using “loop_anova lmFit” function with Bonferroni adjustment for multiple testing.

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Samples were subjected to Illumina HumanMethyaltion450k BeadChip analysis. effects as recommended by McGill genome center using Illumina Infinum HD technology user guide.

extract_protocol: DNA was extracted from T cells isolated using anti-CD3 immuno-magnetic beads (Dynabed Life Technologies) and bisulfite-converted

treatment_protocol: Addicts received oral DHEA or placebo for one month. Healthy volunteers were not treated.

tag: gender

value: male

tag: tissue

value: T cells


title: Post LPS (time 4h, BC1215 treated) 3


title: Post LPS (time 4h; no intervention) 3

value: Post LPS Control


title: 0h_Schneiders_+_3%BSA_Mosq_BioRep1

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

description: sample collected in Schneider's media + 3% bovine serum albumin at 0 h at 4 C temperature

data_processing:
RNAseq reads from each sample were aligned to Plasmodium vivax reference genome (PlasmoDB version 34) and Anopheles dirus reference genome (VectorBase release VB-2018-02) using Tophat2, allowing a maximum of one mismatch per read.
The mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using Cufflinks 2.2.1. The expression level of each gene was normalized as FPKM (fragments per kilobase of exon per million mapped reads).
Genome_build: PlasmoDB-34_PvivaxP01_Genome  and Anopheles-dirus-WRAIR2_AdirW1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Anopheles dirus

source_name: Salivary Glands

extract_protocol:
For all experiments, salivary glands were dissected 14-16 days post-infected blood feed from An. dirus mosquitoes. Mosquitoes were immobilized by cold incubation (-20 C, 5 min), transferred to ice (4 C), and individually washed in a 3-step wash: 70% ethanol, 0.5 mg ml-1 penicillin- streptomycin and 1 mg ml-1 of neomycin (PSN), and 2.5 μg ml-1 FungizoneTM diluted in 1 x Dulbecco’s Phosphate Buffered Solution (DPBS). Intact, clean salivary glands were collected into 100 μl of collection media with dissection time under an hour. Salivary glands were centrifuged (1600 G, 3 min) with gland disruption using plastic pestle and manually pipetting then counted using a hemocytometer. A total of 200,000 - 2,000,000 sporozoites were collected per condition.
0.5 μg - 1.0 μg total RNA of each sample was used for library preparation. Libraries were prepared by using TruSeq Stranded mRNA kit (Illumina). Library quantification was conducted by qPCR and TapeStation (Agilent Technologies) measurements. Libraries were subsequently pooled and sequenced using 300 cycle V2 MiSeq reagent kit (Illumina)

tag: cell type

value: Salivary Glands

tag: sporozoite age

value: mosquito day 18

tag: condition

value: Schneider's + 3% BSA

tag: temperature

value: 4 C

tag: age

value: 0 h


title: 0h_Schneiders_+_3%BSA_BioRep5

organism: Plasmodium vivax

source_name: Sporozoite

value: Sporozoite

tag: mosquito

value: Anopheles dirus

tag: isolate

value: post mosquito infection day 15


title: 0h_Schneiders_BioRep5

description: sample collected in Schneider's media at 0 h at 4 C temperature

value: Schneider's


title: 0h_RPMI_Mosq_BioRep1

description: sample collected in RPMI 1640 media at 0 h at 4 C temperature

value: RPMI 1640


title: 0h_RPMI_+_3%BSA__Mosq_BioRep1

description: sample collected in RPMI 1640 media + 3% bovine serum albumin at 0 h at 4 C temperature

value: RPMI 1640 + 3% BSA


title: Pre LPS (time 0h) 2


title: 0h_Schneiders_BioRep4

value: post mosquito infection day 14


title: 0h_Schneiders_+_3%BSA_BioRep4


title: 0h_RPMI_+_3%BSA_BioRep5


title: 4h_37C_RPMI_+_3%BSA_BioRep4

description: sample collected in RPMI 1640 media + 3% bovine serum albumin at 4 h at 37 C temperature

value: 4 h


title: 0h_RPMI_BioRep5


title: 4h_37C_RPMI_BioRep4

description: sample collected in RPMI 1640 media at 4 h at 37 C temperature


title: 0h_RPMI_+_3%BSA_BioRep4


title: 4h_37C_Schneiders_+_3%BSA_BioRep4

description: sample collected in Schneider's media + 3% bovine serum albumin at 4 h at 37 C temperature


title: 0h_RPMI_BioRep4


title: T24-scrambled-rep3

type: RNA

city: Atlanta

first: Josue

last: Moran

state: GA

address: 615 Michael Street

institute: Emory University

hyb_protocol: Emory Integrated Genomics Core. Emory University, Atlanta, GA

data_processing: Gene level signal was generated by RMA normalization. Differential gene expression was determined using the samr package in R Bioconductor with 500 permutations, minimum fold change of 1.5 fold, and median FDR < 0.05.

label: biotin

source_name: T24 cell line stably expressing KRAB-dCas9-mcherry + Scrambled sgRNA

label_protocol: Lysates were placed in eppendorff tubes and manually labelled

growth_protocol: T24 Bladder cancer cell lines were obtained from American Type Culture Collection. 5637 cells were maintained in DMEM growth media supplemented with 10% FBS, 1% L-Glutamine, and 1% Penicillin-Streptomycin. Cells were cultured in a 37C incubator with humidified atmosphere of 5% CO2.   T24-scrambled-sgRNA and T24-SOX4-sgRNA were grown as previously stated with addition of 1.5ug/ml puromycin

extract_protocol: Total RNA was isolated from cultured cells using Qiagen RNAeasy kit as per manufacturer’s protocol. RNA concentrations were measured using NanoDrop Spectrophotometer (Mode # ND-1000). RNA samples were processed at the Emory Integrated Genomics Core Facility for quality control analysis and analyzed using the Affymetrix Clariom D Genechip platform.

treatment_protocol: No drug treatments were performed on cell lines

tag: cell line

tag: cell line type

value: bladder cancer


title: T24-SOX4-Knockdown-rep2

scan_protocol: Emory Integrated Genomics Core. Emory University, Atlanta, GA

source_name: T24 cell line stably expressing KRAB-dCas9-mcherry + SOX4 sgRNA


title: T24-SOX4-Knockdown-rep1


title: 4h_37C_Schneiders_+_3%BSA_BioRep3

value: post mosquito infection day 16


title: T24-SOX4-Rescue-rep2

source_name: T24 cell line stably expressing KRAB-dCas9-mcherry + SOX4 sgRNA + YFP-HA-SOX4


title: T24-scrambled-rep4


title: 4h_37C_Schneiders_BioRep3

description: sample collected in Schneider's media at 4 h at 37 C temperature


title: T24-SOX4-Rescue-rep3


title: T24-SOX4-Knockdown-rep3


title: T24-scrambled-rep2


title: 4h_37C_RPMI_+_3%BSA_BioRep3


title: 4h_37C_RPMI_BioRep3


title: T24-SOX4-Rescue-rep1


title: 4h_RT_Schneiders_BioRep3

description: sample collected in Schneider's media at 4 h at room temperature

value: room temperature


title: 4h_37C_Schneiders_BioRep4


title: 0h_Schneiders_+_3%BSA_BioRep3


title: 0h_RPMI_BioRep3


title: 4h_37C_RPMI_+_3%BSA_BioRep2


title: 4h_37C_Schneiders_BioRep2


title: T24-scrambled-rep1


title: 4h_37C_RPMI_BioRep2


title: 4h_RT_RPMI_BioRep3

description: sample collected in RPMI 1640 media at 4 h at room temperature


title: 0h_RPMI_+_3%BSA_BioRep3


title: 0h_Schneiders_BioRep3


title: 4h_RT_Schneiders_+_3%BSA_BioRep3

description: sample collected in Schneider's media + 3% bovine serum albumin at 4 h at room temperature


title: 4h_RT_RPMI_+_3%BSA_BioRep3

description: sample collected in RPMI 1640 media + 3% bovine serum albumin at 4 h at room temperature


title: 4h_RT_RPMI_BioRep2


title: 0h_Schneiders_+_3%BSA_BioRep2


title: 4h_37C_Schneiders_+_3%BSA_BioRep2


title: 0h_RPMI_BioRep2


title: 4h_RT_Schneiders_+_3%BSA_BioRep2


title: 0h_RPMI_+_3%BSA_BioRep2


title: 0h_Schneiders_BioRep2


title: 4h_37C_Schneiders_+_3%BSA_BioRep1


title: 4h_37C_RPMI_BioRep1


title: 4h_37C_Schneiders_BioRep1


title: 4h_37C_RPMI_+_3%BSA_BioRep1


title: 4h_RT_Schneiders_+_3%BSA_BioRep1


title: 4h_RT_RPMI_BioRep1


title: 4h_RT_Schneiders_BioRep1


title: 4h_RT_RPMI_+_3%BSA_BioRep1


title: 4h_RT_Schneiders_BioRep2


title: 0h_RPMI_BioRep1


title: 0h_Schneiders_+_3%BSA_BioRep1


title: 0h_RPMI_+_3%BSA_BioRep1


title: 4h_RT_RPMI_+_3%BSA_BioRep2


title: 0h_Schneiders_BioRep1


title: Large leaf - Biorep 3

city: Columbia

first: William

middle: G.

last: Spollen

state: MO

address: 113 Bond Life Sciences Center

department: Informatics Research Core Facility

institute: University of Missouri-Columbia

description: Wild grapevine ungalled control (large) leaf

data_processing:
A custom Perl script was used to parse the libraries and remove barcode sequences resulting in approximately 40.9 million reads for the ungalled library and 40.3 million reads for the galled library.
NextGENe V2.3.3.1 (SoftGenetics, LLC., State College, PA, USA) was used to quality filter the fastq data, remove reads with a median quality score of less than 22, trim reads at positions that had 3 consecutive bases with a quality score of less than 20, and remove any trimmed reads with a total length less than 40 bp.
Genome-wide syntenic analyses were performed to identify Arabidopsis thaliana – Vitis vinifera orthologs using CoGe (http://genomevolution.org/CoGe/).
Arabidopsis – Vitis orthologs were identified using reciprocal BLASTp analyses (protein database) with a 0.00001 p-value cutoff resulting in the annotation of ~86.7 % of all coding sequences in the Vitis vinifera V2 genome.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Vitis riparia

source_name: Leaf

growth_protocol: Samples were collected in the field in Rocheport (Missouri, USA; 38° 58' 16.424" N, 92° 32' 54.118" W).

extract_protocol:
Samples were dissected on ice, and flash frozen in liquid nitrogen. RNA was extracted and DNase1 treated, on column, using the Spectrum Plant Total RNA Kit (Sigma #STRN50-1KT; Sigma-Aldrich, St. Louis, MO, USA; protocol A and Appendix). The resulting RNA was further purified and concentrated with the RNeasy MinElute Cleanup Kit (Qiagen #74204; Qiagen, Hilden, Germany) and eluted with pure water. The quality of the resulting RNA was assessed using the Agilent 2100 BioAnalyzer (www.genomics.agilent.com; Agilent, Santa Clara, CA, USA), and all RNA integrity number values were found to be above 8.
The Illumina libraries were constructed using the RNA TruSeq Kit (Illumina, Inc., San Diego, CA, USA), barcoded (TACT ungalled; GTAT galled), and sequenced single-end with 100bp reads on the Illumina HiSeq-2000 platform at the University of Missouri DNA core (http://dnacore.missouri.edu ).

treatment_protocol: Ungalled control leaves vs. leaves naturally infected by Daktulosphaira vitifoliae gall-inducing insect.

tag: infection

tag: leaf size

value: Large

tag: genotype

value: Wild type


title: Bud - Biorep 2

description: Wild grapevine ungalled control Bud

source_name: Bud


title: Flower - Biorep 3

description: Wild grapevine ungalled control Bud

source_name: Flower


title: Flower - Biorep 1

description: Wild grapevine ungalled control Bud


title: Flower - Biorep 2

description: Wild grapevine ungalled control Bud


title: Large leaf - Biorep 2


title: Bud - Biorep 3

description: Wild grapevine ungalled control Bud


title: Large leaf - Biorep 1


title: Medium leaf - Biorep 2

description: Wild grapevine ungalled control (medium) leaf

value: Medium


title: Medium leaf - Biorep 1


title: Medium leaf - Biorep 3


title: Small leaf - Biorep 1

description: Wild grapevine ungalled control (small) leaf

value: Small


title: Small leaf - Biorep 3


title: Small leaf - Biorep 2


title: Gall 4 - Biorep 3

description: Phylloxera-induced gall (stage 4) on wild grapevine (large) leaf

value: Daktulosphaira vitifoliae


title: Gall 3 - Biorep 2

description: Phylloxera-induced gall (stage 3) on wild grapevine (medium) leaf


title: Bud - Biorep 1

description: Wild grapevine ungalled control Bud


title: Gall 4 - Biorep 2


title: Gall 2 - Biorep 3

description: Phylloxera-induced gall (stage 2) on wild grapevine (small) leaf


title: Gall 4 - Biorep 1


title: Gall 2 - Biorep 2


title: Gall 1 - Biorep 2

description: Phylloxera-induced gall (stage 1) on wild grapevine (small) leaf


title: Gall 3 - Biorep 1


title: Gall 1 - Biorep 3


title: Gall 1 - Biorep 1


title: WT_Log_0hrs_b_RNA

city: Boston

first: David

middle: G

last: Hendrickson

address: 725 Parsons

institute: Harvard

description:
total RNA
DATA_S2.xlsx

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq data was quantified using Salmon-0.8.1 with three separate annotation indices:     1.    open reading frames (ORFs) as defined by SGD  2.    “complex transcriptome” index created by aggregating ORFs, their longest annotated UTRs + all non-canonical and non-coding transcripts pulled from SGD (references)  3.    all features index composed of ORFs + non-coding transcripts (SGD all freatures) + genomic intergenic bins     Salmon was run using the “quant” command with the following settings:"libType": "ISR", "useVBOpt": [], "numBootstraps": "30", and "incompatPrior": "0".     Salmon quantification was prepared and processed for differential expression analysis with the Wasabi package in R for input into Sleuth. Genes changing with respect to time (generation) as opposed to batch or strain were defined as significant using: model = ~generation*strain+(batch)+(0)” and using a p < 0.05 for calculated beta values. For determining genes changing significantly across time (age) for each specific strain the model "~batch+strain+strain:generation" was specified. All test tables output from Sleuth included in Data S1 and Data S2.
Batch correction (for heatmap visualization only) was applied to the Salmon quantification output matrix with a pseudocount of 2 TPM with the COMBAT package in R [75]. Hierarchical clustering (average linkage) was performed on the batch-corrected values using the uncentered Pearson correlation as the distance metric.
Gene Ontology (GO) term enrichment analysis was performed via uploading query lists to the DAVID Bioinformatics Resources 6.8 website and running enrichment with the S. Cerevisiae species background.
ATAC-Seq Data Analysis:     Processing of raw sequencing data  Raw ATAC-seq data was processed as described in [76]. Briefly, first, the raw paired end reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, Release 64) using bwa mem version 0.7.12 with default parameters. Second, the alignments were filtered requiring that both reads in the pair are mapped, the mapping quality is greater than or equal to 30, the reads are mapping concordantly and the direction of the mapping is F1R2. Third, we converted the alignments into track of number of insertions at each position in the genome. For every aligned fragment the insertion locations are calculated by shifting the fragment ends of reads that align to ‘+’ strand by 4 nucleotides and shifting the fragment ends of reads that align to ‘-’ strand by 5 nucleotides in the 3’ direction to reflect the distance to the center of the transposase binding site [60]. To normalize for uneven sequencing depth and different amounts of rDNA in the samples, insertion counts were normalized such that the total number of insertions from unique non-rDNA, nonmitochondrial reads is constant in each sample.     Annotations  Nucleosome positions were downloaded from [62], lifted over to sacCer3 assembly and only nucleosomes with mapping score greater than 2 were used in the metagene plots. For metagene plots around promoters we defined the TSSs for each yeast gene my merging the TSS data from [77] (TIF-seq) and [78] (TSS data). If the TSS for a gene was not reported  by these two papers, we used the beginning of ORF as the TSS. TF and chromatin modifier binding data were from [65,66].     NucleoATAC   Baseline estimation of the nucleosome occupancy from ATAC-seq data could be confounded by noise in estimation of nucleosome free and nucleosomal fraction of fragments between samples. Therefore we generated a fragment size distribution that was an average fragment size distribution of all samples and ran the NucleoATAC pipeline using a constant fragment size distribution using --sizes parameter. Since occupancy estimation was sensitive to the depth of the sample, we downsampled each sample to 25 million uniquely mapped non-ribosomal reads. Finally, to limit differences due to differences in nucleosomal calling between samples, we called occupancy only on the nucleosomes from Brogaard et al that are well positioned (score > 2), located in the open chromatin part of the genome (as defined by Schep et al) and have a median occupancy of at least 0.5.      Differential accessibility  Aging slope for accessibilities was calculated as follows. We first binned the genome into non-overlapping 100 bp bins and counted number of insertions in each bin. We then performed quantile normalization for each sample separately to calculate normalization factors and supplied gene specific normalization factors as described in http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#sample-gene-dependent-normalization-factors to DESeq2 pipeline [79]. The aging slope was determined on all samples using the following model: "~ replicate + strain + ave_budscars" where ave_budscars were the average number of budscars for that time point and we looked at the bins with q-value of non-zero slope of less than 10-6. To identify bins that were specifically opening or closing in certain strains, we used the following model “replicate + strain + ave_budscars + strain:ave_budscars”.     Enrichments of regulators  We assigned each genomic bin to the gene whose gene body it intersects or to the promoter (defined as up to 400 bp upstream of TSS) of the gene that intersects. The lists of age-opening and age-closing genes were generated by looking at a genes that contained at least one opening and closing bin (with q-value < 10-6) respectively. We then intersected these lists with the list of genes that bind to transcription factor or chromatin modifier and performed a hypergeometric test to evaluate enrichment.
Genome_build: sacCer3
Supplementary_files_format_and_content: excel spreadsheet files include TPM values for each Sample at gene level and comma separated files include ATAC-seq insertion density for significantly changing genomic bins

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Aging of cells in ministats: Loaded cells were grown on ministats for desired length of time. For the dense time course, 5 ministats were loaded and an entire ministat worth of cells was collected per time point. For short mutant strain time course, cells were harvested by removing ministat from magnet (pumps off, air low, and effluent needle up) and waiting 5 minutes from mothers to disperse. Sampling of cells was done through the loading port luer-lock syringe.     Harvesting of daughter cells: Effluent tubing was diverted to a clean 50 mL Falcon tube to collect daughter cells. 5 million cells were spun down and frozen in liquid nitrogen for RNA, DNA preps or used immediately for ATAC-seq or buda scar counting as needed.  Harvesting and washing of aged mother cells:  Following removal of the ministat cap, tubing, and bubble cage (Fig. S14), the supernatant was removed using a 25 mL pipette, being careful not to disturb the magnetically-bound cells on the vessel wall.  With the vessel removed from the magnet, beaded cells were resuspended in media and placed back on the magnet for 5-10 minutes. This was repeated for a minimum of 4 washes or until the cells were of desired purity as assessed by microscopy.  Final beaded cells were resuspended in 1 mL of media and 5E6 cells were spun down and frozen in liquid nitrogen for RNA, DNA preps or used immediately for ATAC-seq or bud scar counting as needed.

extract_protocol:
mRNA extraction:  Frozen cell pellets were resuspended in 200 µL of Lysis buffer (10mM Tris [pH 8.0], 0.5% SDS, 10 mM EDTA). Following the addition of 200 µL Acid Phenol [pH 4.3], samples were vortexed for 30 seconds.  Samples were incubated at 65oC for 1 hour in a Thermomixer with intermittent shaking (2000 RPM for 1 minute every 15 minutes). 400 µL of ethanol was then added and the RNA was purified using the Direct-zolTMRNA Miniprep Plus kit (Zymo research) according to the manufacturer’s protocol including the optional DNase digestion step. RNA integrity was confirmed using an Agilent Bioanalyzer.
RNA-Seq Library Preparation: RNA-seq libraries were prepared first by removing rRNA with the Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina Cat #MRZY1324 and eluted in 30 µL. After rRNA removal, RNA was bound to AGENCOURT RNACLEAN XP beads (Beckman coulter cat#A66514) using a 2X bead volume (60 µL) followed by washing and elution as per vendor’s protocol (except that RNA was eluted in Fragment, Prime, Finish Mix from the TruSeq Stranded mRNA Library Prep [Illumina cat# 20020595]). Subsequent steps were carried out as per the protocol for the TruSeq Stranded mRNA Library Prep. Libraries were indexed using either Illumina barcode kit cat#s 20020492, 20020493 or 20019792). Libraries were sequenced on a hISEQ4000 (with 150x150 paired-end reads). ATAC-Seq Sample Preparation: 5 million cells were spun down (1200 rcf / 4 min. / room temperature) and resuspended in 250 mL media.  Propidium Monoazide (PMA, Qiagen 296015) was added to a concentration of 50 mM, the cells were incubated in the dark at room temperature for 10 min. and then illuminated in the BLU-V system (Qiagen 9002300) for 20 minutes at 4oC.  Cells were spun down, washed twice with SB buffer (1M Sorbitol, 40 mM HEPES [pH7.5], 10 mM MgCl2) and then resuspended in 190 mL SB Buffer. 10 µL of 10 mg/mL Zymolyase-100T was added and the cells were incubated at 30oC for 30 min. with light shaking (600 RPM) in a thermomixer (Eppendorf). Spheroplasts were spun down (1500 rcf / 5 min. / room temperature) and washed twice with SB Buffer, resuspended in 50 mL Tagmentation Mix (25 mL Nextera Tagment DNA Buffer, 22.5 mL H2O, 2.5 mL  Nextera Tagment DNA Enzyme I) and incubated at 37oC for 30min.  DNA was purified over DNA Clean & ConcentratorTM-5 kit (Zymo Research) following the manufacturer’s protocol, eluted in 11ml H2O and stored at -20oC until ready for PCR.          PCR reactions were set up using Nextera Index i5 and i7 series PCR primers (Illumina).  Mixed 25ml NEBNext Hi-Fidelity 2x PCR Master Mix, 7.5ml H2O, 6.25ml i5 primer (10 mM), 6.25ml i7 primer (10 mM) and 5 mL tagmented DNA from above such that each sample has a unique barcoded primer pair. Ran PCR amplification (1 cycle: 72ºC for 5 min.; 1 cycle: 98ºC for 30 sec.; 8 cycles: 98ºC for 10 sec., 63ºC for 30 sec., 72ºC for 1 min.; hold at 4ºC).  PCR reactions were cleaned up using the Agencourt AMPure XP system (Beckman Coulter) 1st by negatively selecting against large DNA fragments using 0.4x volume of beads and then by positively selecting for the desired fragments using 1.5x volume of beads.  The final solution was re-purified over DNA Clean & ConcentratorTM-5 columns to eliminate primers, eluted in 22 µL H2O and analyzed on the BioAnalyzer.

treatment_protocol: for pma: 5 million cells were spun down (1200 rcf / 4 min. / room temperature) and resuspended in 250 mL media.  Propidium Monoazide (PMA, Qiagen 296015) was added to a concentration of 50 mM, the cells were incubated in the dark at room temperature for 10 min. and then illuminated in the BLU-V system (Qiagen 9002300) for 20 minutes at 4oC.  Cells were spun down, washed twice with SB buffer

tag: strain

tag: class

value: Log

tag: age in hours

tag: batch

value: b

tag: treatment


title: SIR2_mother_40hrs_a_RNA

description:
total RNA
DATA_S2.xlsx

value: mother

value: a


title: FOB1_mother_40hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_mother_40hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_mother_20hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_Log_0hrs_d_RNA

description:
total RNA
DATA_S2.xlsx

value: d


title: UBR2_Log_0hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_Log_0hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_Log_0hrs_d_RNA

description:
total RNA
DATA_S2.xlsx


title: SIR2_mother_20hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_mother_40hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_mother_20hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_mother_20hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_Log_0hrs_d_RNA

description:
total RNA
DATA_S2.xlsx


title: Gall 3 - Biorep 3


title: WT_mother_40hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: Gall 2 - Biorep 1


title: FOB1_mother_40hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_Log_0hrs_c_RNA

description:
total RNA
DATA_S2.xlsx

value: c


title: SIR2_Log_0hrs_d_RNA

description:
total RNA
DATA_S2.xlsx


title: SIR2_Log_0hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_mother_40hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_mother_20hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_mother_20hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: SIR2_Log_0hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_mother_20hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_Log_0hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_Log_0hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: SIR2_mother_20hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_mother_20hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: SIR2_mother_40hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_mother_40hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_mother_20hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_mother_20hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_mother_40hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: FOB1_mother_40hrs_c_RNA

description:
total RNA
DATA_S2.xlsx


title: WT_mother_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv

library_source: genomic


title: SIR2_mother_40hrs_b_RNA

description:
total RNA
DATA_S2.xlsx


title: SIR2_mother_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_mother_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_daughter_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv

value: daughter


title: WT_mother_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_mother_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_mother_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_Log_0hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_daughter_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: SIR2_daughter_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: SIR2_mother_20hrs_a_RNA

description:
total RNA
DATA_S2.xlsx


title: UBR2_Log_0hrs_d_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_Log_0hrs_d_ATACseq

description:
DNA
DATA_S3.csv


title: WT_daughter_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_mother_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: WT_mother_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_mother_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_mother_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_Log_0hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: WT_daughter_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: 0h_Schneiders_Mosq_BioRep1

description: sample collected in Schneider's media at 0 h at 4 C temperature

tag: cell type

value: Salivary Glands

value: mosquito day 18

value: Schneider's

value: 4 C

value: 0 h


title: UBR2_daughter_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: SIR2_daughter_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: WT_daughter_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: SIR2_Log_0hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_daughter_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: mouse_liver_VEGFDko_rep4

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description:
VEGFDko_rep4_RPKM
VEGF-D knock-out sample - replicate 4

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the mm9 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression values (RPKM, log2 fold changes and FDRs) and UCSC Bedgraphs are provided

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
RNA was extracted from mouse livers using RNeasy Lipid Tissue Mini Kit (Qiagen) and enriched for Poly(A)-RNA with Dynabeads Oligo (dT)25 beads (Invitrogen).
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: All mice were on high-fat diet for 12 weeks.

tag: tissue

value: liver

tag: replicate

value: biological replicate #4


title: mouse_liver_VEGFDko_rep3

description:
VEGFDko_rep3_RPKM
VEGF-D knock-out sample - replicate 3

value: biological replicate #3


title: mouse_liver_VEGFDko_rep2

description:
VEGFDko_rep2_RPKM
VEGF-D knock-out sample - replicate 2

value: biological replicate #2


title: mouse_liver_VEGFDko_rep1

description:
VEGFDko_rep1_RPKM
VEGF-D knock-out sample - replicate 1

value: biological replicate #1


title: SIR2_daughter_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: SIR2_mother_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: SIR2_mother_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: mouse_liver_control_rep3

description:
ctrl_rep3_RPKM
control sample - replicate 3


title: WT_Log_0hrs_c_ATACseq

description:
DNA
DATA_S3.csv

value: Log


title: FOB1_mother_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: mouse_liver_control_rep2

description:
ctrl_rep2_RPKM
control sample - replicate 2


title: SIR2_mother_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv

value: b


title: mouse_liver_control_rep1

description:
ctrl_rep1_RPKM
control sample - replicate 1


title: mouse_liver_control_rep4

description:
ctrl_rep4_RPKM
control sample - replicate 4


title: PVG_naive_biological rep3

city: Nedlands

first: Anya

last: Jones

state: Western Australia

address: Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue

country: Australia

institute: Telethon Kids Institute, The University of Western Australia

hyb_protocol: Hybridisation was carried at the core facility according to the manufacturers instructions.

scan_protocol: cDNA was hybridised to Affymetrix Rat Gene 2.1 ST 24-Array Plate.

data_processing: The raw expression data was analysed in the R statistical programming language. The robust multi-array average (RMA) algorithm as used for background correction, log2 transformation and quantile normalisation. A custom chip description file (ragene21strnentrezgcdf, Version 19) was employed to annotate probe sets to genes based on updated genome and transcriptome information. The data was filtered with the PVAC algorithm and probe sets of low quality were removed. Differentially expressed genes were identified employing moderated t-statistics LIMMA with a false discovery rate (FDR) control for multiple testing.

organism: Rattus norvegicus

source_name: Rat BAL cells_PVG_naive

label_protocol: Total RNA samples (n=12) were labelled according to the manufacturers instructions at the core facility.

extract_protocol: Total RNA was extracted from BAL cells with TRIzol followed by RNAeasy.

treatment_protocol: 8-12 week old male BN and PVG rats were infected with attentuated mengovirus (vMC0) via intranasal administration with 100μl of 107 plaque-forming units (PFU) of vMC0. The inflammatory response was assessed at day 1 post-infection and compared to naive rats (no virus). Bronchoalveolar lavage (BAL) was performed with 8 mL GKN/5%FCS.

tag: gender

value: male

value: Piebald-Virol-Glaxo (PVG)

value: naïve

value: 8-12 weeks of age

value: Bronchoalveolar lavage cells


title: FOB1_mother_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv

value: mother

value: c


title: WT_daughter_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv

value: daughter

value: a


title: SIR2_daughter_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_daughter_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_mother_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_daughter_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_daughter_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_Log_0hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: BN_naive_biological rep3

source_name: Rat BAL cells_BN_naive

value: Brown Norway (BN)

tag: age


title: BN_naive_biological rep1


title: PVG_naive_biological rep2


title: shGFP-Dox_r2

city: Miami

first: Kerry

last: Burnstein

department: Molecular and Cellular Pharmacology

institute: University of Miami

hyb_protocol: Samples were hybridized to HuGene.ST.1.0.v1 microarrays according to the manufacturer's instructions (Affymetrix)

scan_protocol: According to the manufacturer's instructions (Affymetrix)

data_processing: Microarrays were read into R (3.3.1, https://cran.r-project.org/), the Bioconductor suite (https://www.bioconductor.org/), and the oligo package (1.36.1). Arrays were rma normalized. Limma (3.28.21) was used to calaculate differential gene expression upon doxycycline induced knock-down.

source_name: 22Rv1 cell line, shGFP, - dox

label_protocol: Total RNA was labeling with the WT kit according to the manufacturer's instructions (Affymetrix)

extract_protocol: RNA was isolated using Trizol reagent according to manufacturers protocol

treatment_protocol: 22Rv1 cells were grown in androgen depleted conditions (10% CSS) plus or minus doxycycline for 3 days

value: prostate cancer


title: shGFP-Dox_r3


title: PVG_virus24h_biological rep2

source_name: Rat BAL cells_PVG_virus24h


title: BN_naive_biological rep2


title: PVG_virus24h_biological rep3


title: shGFP+Dox_r2

source_name: 22Rv1 cell line, shGFP, + dox


title: shGFP+Dox_r3


title: BN_virus24h_biological rep2

source_name: Rat BAL cells_BN_virus24h


title: SIR2_mother_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: WT_Log_0hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: WT_mother_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_daughter_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: PVG_naive_biological rep1


title: shGFP-Dox_r1


title: BN_virus24h_biological rep3


title: shGFP+Dox_r1


title: PVG_virus24h_biological rep1


title: shVAV3-Dox_r3

source_name: 22Rv1 cell line, shVAV3, - dox


title: shVAV3-Dox_r2


title: WT_mother_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_Log_0hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: FOB1_mother_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: UBR2_daughter_20hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: shVAV3-Dox_r1


title: BN_virus24h_biological rep1


title: UBR2_mother_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: shVAV3+Dox_r3

source_name: 22Rv1 cell line, shVAV3, + dox


title: shAR3-Dox_r3

source_name: 22Rv1 cell line, shAR3, - dox


title: WT_Log_0hrs_d_ATACseq

description:
DNA
DATA_S3.csv

value: d


title: FOB1_daughter_20hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: shVAV3+Dox_r2


title: shAR3-Dox_r2


title: shVAV3+Dox_r1


title: shAR3-Dox_r1


title: UBR2_mother_40hrs_a_ATACseq

description:
DNA
DATA_S3.csv


title: shAR3+Dox_r2

source_name: 22Rv1 cell line, shAR3, + dox


title: SIR2_Log_0hrs_d_ATACseq

description:
DNA
DATA_S3.csv


title: Dnd1-KD-ESC_rep2

city: Sendai

first: Kei

last: Otsuka

state: miyagi

address: 4-1 Seiryomachi Aoba-ku

department: Institute of Development, Aging and Cancer

country: Japan

institute: Tohoku university

data_processing:
Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.64, Illumina).
For gene expression analysis, reads were mapped to the mouse genome (UCSC mm10 genome assembly and NCBI RefSeq database) using TopHat2 and Bowtie.
Cufflinks was used to estimate gene expression levels based on reads per kilobase of exon per million mapped reads (RPKM) normalization.
Differentially expressed genes (DEGs) were extracted from the Cuffdiff results with statistical significance (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: text files include RPKM values for each Sample

source_name: Embryonic stem cells

growth_protocol: All cells were grown in serum/LIF containing DMEM.

extract_protocol:
Total RNA was purified  by RNeasy Plus Mini Kit or RNeasy Micro Kit (QIAGEN).
RNA-seq libraries were prepared with TruSeq RNA sample prep kit v2 (Illumina).

tag: passages

value: WT

tag: sample type


title: Klf9 OE PGC

data_processing:
Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.64, Illumina).
For gene expression analysis, reads were mapped to the mouse genome (UCSC mm10 genome assembly and NCBI RefSeq database) using TopHat2 and Bowtie.
Cufflinks was used to estimate gene expression levels based on reads per kilobase of exon per million mapped reads (RPKM) normalization.
Differentially expressed genes (DEGs) were extracted from the Cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: text files include RPKM values for each Sample

source_name: primordial germ cell

growth_protocol: PGCs were cultured for one day in bFGF containing GS medium.

extract_protocol:
Total RNA was purified  by RNeasy Micro Kit (QIAGEN).
RNA-seq libraries were prepared with TruSeq RNA sample prep kit v2 (Illumina).

treatment_protocol: Control or Klf9-OE lenti-virus vector was infected at MOI5

value: primordial germ cell

tag: lentivirus


title: SIR2_Log_0hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: shAR3+Dox_r1

tag: cell line


title: SIR2_mother_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: Dnd1-KD-ESC_rep1


title: Control PGC

value: control


title: control ESC_rep2


title: WT_daughter_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: shAR3+Dox_r3


title: SIR2_daughter_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: WT_mother_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: 2012CM7F040p05ar154bMN15

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 411 Borlaug Hall, 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

description: Fast-neutron mutant/ wild-type parent comparison

hyb_protocol: Arrays are hybridized at 67C for approximately 72 hours at a rotation speed of 20rpm. Arrays are washed in Wash Buffer 1 for 5 minutes at room temperature, Wash Buffer 2 for 1.5 minutes at 37C, followed by a 1minute wash in room temperature Acetonitrile. All other processing follow Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

scan_protocol: Arrays are immediately and individually scanned using Agilent Technologies G2505C SureScan Microarray Scanner using Agilent Scan Control vA.8.5.1 acquisition software. The scan resolution is set at 2 microns, Gain PMT at 100% for both channels and the image is saved as a single 16 bit Tiff file.

data_processing: Image extraction and grid alignment is done using Agilent Feature Extraction (FE) 12.0.0.7.  The CGH module portion of Agilent Genomic Workbench (AWB) 7.0.4.0 software is used to generate data.  Analysis settings include: Aberration Algorithm is ADM-2, Threshold is 6.0, Fuzzy Zero is selected, GC correction is selected with a window size of 2 Kb, Legacy is selected with a bin size of 10, Diploid Peak is deselected, Manually Reassign Peaks is deselected and Combine Intra-Array Replicates is selected. The Aberration Filter is set to call amplification or deletion as having 2 consecutive probes with an absolute log ratio greater or equal to +/- 1.

organism: Glycine max

label_protocol: Individual reactions with 500ng of Soybean DNA are labeled with Cy3 and Cy5 following Agilent Protocol version 7.3 March 2014 entitled “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis”.

extract_protocol: Soybean DNA is extracted from approximately 90 mg of fresh, young tissue disrupted with mortar and pestle and liquid nitrogen. The tissue is processed using Qiagen DNeasy Plant Mini Kit catalog number 69106. The Qiagen protocol is followed with 2 elution’s of DNA from the column using 60uL – 50% AE / 50% Water.

tag: genotype/variation

value: fast neutron mutant

value: Leaf

value: wildtype


title: 2R29C14Ccar39aMN15


title: UBR2_daughter_40hrs_b_ATACseq

description:
DNA
DATA_S3.csv

value: b


title: 2R29C14Cladacr233cMN15


title: control ESC_rep1


title: CDGC6-P5-6_rep2

source_name: pluripotent stem cells


title: R32C17Dccbbcdar223bMN15


title: WT_daughter_20hrs_b_ATACseq

description:
DNA
DATA_S3.csv


title: R60C28p35c02br177aMN15


title: P1016CaBr505dBMN15


title: CDGC6-P5-6_rep1


title: FOB1_daughter_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: CDGC1-P3-9_rep2


title: SIR2_daughter_40hrs_c_ATACseq

description:
DNA
DATA_S3.csv


title: CDGC1-P3-9_rep1


title: mini_stat_55hrs_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv

value: 50 mM Propidium Monoazide


title: siSET8 Replicate4

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Raw paired-end reads were trimmed for Nextera transposase adapter sequences using Trimmomatic (v0.32) in palindrome mode with default settings except ILLUMINACLIP:2:30:10:1:true MINLEN:25.
Trimmed PE reads were mapped to the hg19 assembly (canonical chromosomes only) using bowtie2 v.2.2.9 with default settings except -k 2 -X 2000 --no-mixed --no-discordant.
Sorting (SortSam) and labeling duplicates (MarkDuplicates) was done with Picard tools (v. 2.6.0-27-g915ffa7-SNAPSHOT).
A NH tag (number of reported alignments) was added using custom code.
Filtering to exclude unmapped, multimapping and mitochondrial reads was done using samtools view -f 2 -F 4 and a custom filter.
Wig files were generated by importing bam-files in EaSeq (http://easeq.net) and exporting as wig-files using default settings
Genome_build: hg19
Supplementary_files_format_and_content: Fixed-step wig file

source_name: Osteosarcoma cell line

growth_protocol: U2OS cells cultured in DMEM high glucose supplemented with 10% FBS and 1% PS

extract_protocol:
Nuclei were prepared and processed with Tn5 transposase cutting as described in Buenrostro J et al; 2015.
Illumina Nextera DNA library prep

treatment_protocol: Double thymidine synchronized

value: Osteosarcoma cell line

tag: sirna transfection


title: mini_stat_44hrs_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv


title: P1016Cbar505dBMN15

scan_protocol: Nine of the arrays (FNMN0022, FNMN0008, FNMN0036, FNMN0005, FNMN0014, FNMN0016, FNMN0027, FNMN0001, FNMN0069) were immediately and individually scanned using Roche NimbleGen MS200 array scanner using NimbleGen MS200 v1.2 acquisition software. The arrays were inserted “active side up” with a Scan Resolution of 2micons, Gain at 100% for both channels, Laser Intensity at 100% for both channels, Autogain was deselected and a Multi Tiff File Setting. Ten of the arrays (FNMN0030, FNMN0039, FNMN0041, FNMN0048, FNMN0061, FNMN0065, FNMN0077, FNMN0066, FNMN0046, FNMN0085) were immediately and individually scanned using Agilent Technologies G2505C SureScan Microarray Scanner using Agilent Scan Control vA.8.5.1 acquisition software. The scan resolution was set at 2 microns, Gain PMT at 100% for both channels and the image was saved as a single 16 bit Tiff file.

value: Fast-neutron mutant


title: R15C01P33a02ar168bMN15


title: 5R10C28Decfbar241aMN15 [2]


title: 5R16C01Dacar261bMN15


title: siSET8 Replicate3


title: siSET8 Replicate2


title: R29C32DSaeccdr240bMN15


title: mini_stat_20hrs_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv

value: mother


title: RP13DM7r450MN15


title: siControl Replicate4

value: siControl


title: siSET8 Replicate1


title: Adipose Cachexia 6

city: Shanghai

first: LEI

last: SHEN

state: State...

address: Feng lin road 180

department: Department of General Surgery

country: China

institute: Zhongshan Hospital, Fudan University

description: littermate control

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).1. Assemble the slides into an slide holder. Place assembled slide holders into scanner carousel. Verify scan settings for one-color scans. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: adipose tissue, cachexia

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA was extracted from each sample using TRIzol Reagent (Life Technologies, USA) according to the protocol from manufacturer. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).

treatment_protocol: Colon-26 adenocarcinoma (C26) cells were subcutaneously inoculated into the flank of 6 syngeneic BALB/c mice to build CAC models. As a control group, 6 non-tumor-bearing littermate mice received the vehicle (PBS) only. All mice were euthanized at day 21 and dissected to harvest adipose tissue.

value: BALB/c

value: Male

value: 6 weeks

tag: inoculated cells

value: colon-26 adenocarcinoma cells

tag: inoculation site

value: Lateral abdominal subcutaneous

tag: sampling time

value: day 21

value: inguinal white adipose tissue


title: Adipose Cachexia 5

description: littermate control

tag: strain


title: mini_stat_10hrs_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv

tag: class

tag: age in hours

tag: batch


title: Adipose Cachexia 4

description: littermate control

tag: tissue


title: siControl Replicate3


title: mini_stat_30hrs_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv

tag: treatment


title: 5R10C28Decfbar241aMN15


title: Adipose Cachexia 2

description: littermate control

tag: gender


title: Adipose Cachexia 3

description: littermate control

tag: age


title: 1R19C77Ccbbbcar278MN15


title: mini_stat_55hrs_long_timecourse_ATACseq

description:
DNA
DATA_S3.csv


title: siControl Replicate1


title: mini_stat_44hrs_long_timecourse_ATACseq

description:
DNA
DATA_S3.csv


title: 6R39C93Daacdcar355MN15


title: 3R22C02Dbaar389MN15


title: germination_stage3 rep3

city: East Lansing

first: Wonyong

last: Kim

state: Michigan

address: 612 Wilson Road, Room 166

department: Plant Biology

institute: Michigan State University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 High Output flow cell (v4) using Illumina HiSeq SBS reagents (v4) in a 1x50bp paired end format. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.
Poor quality reads were trimmed and/or filtered out, and adapters and homopolymers were trimmed from raw reads, using the ngsShoRT program v2.2, with parameters -lqs 12 -tera_avg 20 -5a_mp 98 -rmHP_ml 10
Filtered reads were mapped to the repeat-masked genome (Ensembl version 32), using the HISAT2 program v2.0.4, with default parameters
Reads Per Kilobase of transcript per Million mapped reads (RPKM) values were calculated using the StringTie program v1.3.0, and transcripts with a variance of RPKM values less than one were removed, using the Ballgown R package v2.4.2.
Genome_build: Fusarium graminearum str. PH-1 Ensembl Genomes 32
Supplementary_files_format_and_content: tab-delimited text file include a matrix of RPKM values for all samples and the associated gtf file

organism: Fusarium graminearum

extract_protocol:
Asexual spores (macro conidia) were spread on Bird agar media (Metzenberg, 2004 Fungal Genet Newsl 51: Article 8) overlaid with a cellophane membrane, and sampled at the indicated spore germination stages and frozen in liquid nitrogen. Total RNA was isolated using the standard Trizol extraction protocol with additional extraction steps.
The KAPA Stranded RNA-Seq Library Preparation Kit was used with 1 ug of total RNA for the construction of cDNA libraries.
Stranded RNA-seq with poly-A captured RNA samples

value: hyphal branching


title: 5R24C26Dbaar416MN15


title: Adipose Cachexia 1

description: littermate control


title: mini_stat_30hrs_long_timecourse_ATACseq

description:
DNA
DATA_S3.csv


title: 3R45C15Ddcar395MN15


title: RNA-seq_Nontarget_Sp_KRAB_rep2

city: Stanford

first: Daniel

middle: R

last: Fuentes

state: CA

address: 265 Campus Drive, G3065

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Base calling was performed using CASAVA 1.8
Reads were trimmed of adapter sequences with cutadapt 1.8.1: "cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 30 -o $trimmed_read1.fastq.bz2 -p $trimmed_read2.fastq.bz2 $read1.fastq.bz2 $read2.fastq.bz2"
Reads were aligned to hg38 transcriptome with hisat2 2.1.0: "hisat2 -q -p $threads -t --no-mixed --no-discordant -x hg38_tran -1 $read1 -2 $read2 -S aligned.sam"
Reads were assigned to gene models with featureCounts v1.4.6-p2: "featureCounts -t exon -g gene_name -Q 10 --primary -T $threads -a $.gtf -p -B -C -o $counts $.sam"
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes read count values for each sample for each gene

growth_protocol: NCCIT cells were obtained from ATCC. NCCIT cells were grown in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA, USA), supplemented with 10% FBS (Omega Scientific, Tarzana, CA, USA), 1x Glutamax (Thermo Fisher Scientific), 1x non-essential amino acids (Thermo Fisher Scientific), and 1x antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
Cells for RT-qPCR and RNA-seq were homogenized in Trizol (Thermo Fisher Scientific), then RNA was extracted using Direct-zol RNA columns (Zymo Research, Irvine, CA, USA), with DNase treatment on-column, and eluted in water.
Total RNA (10 ug) from two independent biological replicates was subjected to oligo-dT purification using Dynabeads oligo(dT) (Thermo Fisher Scientific), then fragmented with 10x fragmentation buffer (Thermo Fisher Scientific). Fragmented RNA was used for first strand cDNA synthesis with Superscript II (Thermo Fisher Scientific) and random hexamer primers (Thermo Fisher Scientific). Second strand cDNA synthesis was performed using RNase H (Thermo Fisher scientific) and DNA polymerase I (New England Biolabs). The resulting double-stranded cDNA was used for Illumina library preparation as described for ChIP-seq experiments, but was size-selected on acrylamide gels, and pooled and sequenced on a NextSeq 500 (Illumina) at the Stanford Functional Genomics Facility, using 2x150 sequencing with index read.

treatment_protocol: NCCIT cells were treated with doxycycline for four days before extraction to induce dCas9 expression

value: NCCIT (ATCC CRL-2073)

tag: cell type

value: Human embryonal carcinoma

tag: grna target

value: nontarget

tag: grna scaffold species

value: S. pyogenes

tag: dcas9 fusions

tag: experimental replicate

value: Replicate 2


title: Adipose Control 6

description: littermate control

source_name: adipose tissue, control

value: PBS


title: Log_Phase_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv

source_name: Saccharomyces cerevisiae

value: Log

value: 50 mM Propidium Monoazide


title: germination_stage3 rep2


title: RNA-seq_LTR5HS_Sa_KRAB_rep2

tag: cell line

value: S. aureus


title: mini_stat_20hrs_long_timecourse_ATACseq

description:
DNA
DATA_S3.csv

value: mother


title: Adipose Control 5

description: littermate control

value: BALB/c

value: Male

tag: inoculated cells


title: germination_stage3 rep1


title: mini_stat_14hrs_long_timecourse_ATACseq

description:
DNA
DATA_S3.csv


title: RNA-seq_LTR5HS_Sp_KRAB_rep2


title: 1R28C85Cdafdcar219MN15

tag: genotype/variation

value: Fast-neutron mutant

value: Leaf

value: wildtype


title: germination_stage2 rep3

value: doubling of long axis


title: Adipose Control 4

description: littermate control

value: 6 weeks

tag: inoculation site

value: Lateral abdominal subcutaneous

tag: sampling time

value: day 21

value: inguinal white adipose tissue


title: mini_stat_10hrs_long_timecourse_ATACseq

description:
DNA
DATA_S3.csv

tag: strain

tag: class


title: mini_stat_14hrs_long_timecourse_ATACseq_plus_PMA_plus_PMA

description:
DNA
DATA_S3.csv

tag: age in hours

tag: batch


title: RNA-seq_LTR5HS_Sa_VPR_rep2

value: NCCIT (ATCC CRL-2073)

value: Human embryonal carcinoma


title: Adipose Control 3

description: littermate control

value: PBS

tag: tissue


title: germination_stage2 rep2


title: Log_Phase_long_timecourse_ATACseq

description:
DNA
DATA_S1.xlsx

value: Log

tag: treatment


title: Adipose Control 2

description: littermate control

tag: gender

tag: age


title: RNA-seq_LTR5HS_Sp_VPR_rep2

tag: cell type

tag: grna target

value: S. pyogenes

value: Replicate 2


title: germination_stage2 rep1


title: sexual_stage4 rep3_∆xrn1

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 High Output flow cell (v4) using Illumina HiSeq SBS reagents (v4) in a 1x50bp paired end format. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.
Poor quality reads were trimmed and/or filtered out, and adapters and homopolymers were trimmed from raw reads, using the ngsShoRT program v2.2, with parameters -lqs 12 -tera_avg 20 -5a_mp 98 -rmHP_ml 10
Filtered reads were mapped to the repeat-masked genome (Ensembl version 32), using the HISAT2 program v2.0.4, with default parameters
De novo transcript assembly was performed using the StringTie program v1.3.0, with default parameters
Read counts for gene loci in the de novo annotations were calculated using the htseq-count program v0.6.1. Gene expression levels in counts-per-million (CPM) value were computed and normalized by effective library size estimated by trimmed mean of M values, using the edgeR R package v3.14.0.
Genome_build: Fusarium graminearum str. PH-1 Ensembl Genomes 32
Supplementary_files_format_and_content: tab-delimited text file include a matrix of log2-CPM values for all samples and the associated GTF file

source_name: sexual_stage4 ∆xrn1

extract_protocol:
Fungal hyphae were scraped out from carrot agar culture and frozen in liquid nitrogen, and total RNA was isolated using the standard Trizol extraction protocol with additional extraction steps.
The KAPA Stranded RNA-Seq Library Preparation Kit was used with 2 ug of total RNA for the construction of cDNA libraries.
Stranded RNA-seq with poly-A captured RNA samples

value: asci

tag: genotype


title: mini_stat_55hrs_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx

value: mother


title: RNA-seq_Nontarget_Sp_KRAB_rep1

value: nontarget

tag: grna scaffold species

tag: dcas9 fusions

tag: experimental replicate

value: Replicate 1


title: germination_stage1 rep3

value: polar growth


title: mini_stat_44hrs_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx


title: sexual_stage4 rep2_∆xrn1


title: RNA-seq_Nontarget_Sp_VPR_rep2

tag: cell line


title: germination_stage1 rep2


title: RNA-seq_LTR5HS_Sa_KRAB_rep1

value: S. aureus


title: mini_stat_30hrs_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx


title: 4R47C81Caar16MN15

tag: genotype/variation

value: Fast-neutron mutant

value: Leaf

value: wildtype


title: 5R15C12Daddbar301MN15


title: Adipose Control 1

description: littermate control

value: BALB/c

value: Male

value: 6 weeks

tag: inoculated cells

tag: inoculation site

value: Lateral abdominal subcutaneous

tag: sampling time

value: day 21


title: 1R26C94Cbadbr360MN15


title: sexual_stage4 rep1_∆xrn1

tag: strain


title: germination_stage1 rep1


title: RNA-seq_LTR5HS_Sp_KRAB_rep1

value: NCCIT (ATCC CRL-2073)

value: Human embryonal carcinoma


title: sexual_stage0 rep3_∆xrn1

source_name: sexual_stage0 ∆xrn1

value: vegetative hyphae


title: germination_stage0 rep3

value: fresh spore


title: 2012CM8F030p02


title: RNA-seq_LTR5HS_Sa_VPR_rep1


title: germination_stage0 rep2


title: mini_stat_14hrs_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx

tag: class

value: mother

tag: age in hours

tag: batch


title: sexual_stage0 rep1_∆xrn1

tag: tissue


title: sexual_stage0 rep2_∆xrn1


title: RNA-seq_LTR5HS_Sp_VPR_rep1

value: S. pyogenes


title: germination_stage0 rep1


title: 1R25C64Cbaaxar247MN15


title: Log_Phase_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx

value: Log

tag: treatment


title: R18C55Dhhaajar131MN15


title: mini_stat_10hrs_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx


title: P2358Caar551BMN15


title: control muscle

status: Public on Aug 15 2018

city: Kennesaw

first: Anton

last: Bryantsev

address: 370 Paulding Ave.

institute: Kennesaw State University

description: driver only

data_processing:
Aligned and counted with the Salmon algorythm, using whole referenced D.melanogaster transcriptome and genome of 6.21 release
Salmon produced consolidated transcript counts for each Drosophila gene in the ‘transcripts per million’ (TPM) metric.
Analysis of gene expression differences between control and bs KD samples was performed with the DEseq2 method
Genome_build: 6.21
Supplementary_files_format_and_content: xlsx

organism: Drosophila melanogaster

source_name: normal indirect flight muscles

extract_protocol:
Qiagen Rneasy minispin kit, total RNA
Standard Illumina Protocol

value: indirect flight muscles

tag: age

value: 3 days


title: R15C01p33a02ar168bMN15

value: Fast-neutron mutant


title: bs RNAi knockdown

description: driver driving RNAi knockdown of the gene blistered (bs)

source_name: indirect flight muscle with bs knockdown


title: PBMC Cell 17_hickit

city: Cambridge

first: Longzhi

last: Tan

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

data_processing:
please see 00README.md.txt on series record.
Genome_build: hg19
Supplementary_files_format_and_content: contact file: the .pairs format (and its index .px2) of the 4DN project; 3d genome file (3dg): five columns (chromosome, bead starting position, x, y, z, and fraction of CpG in 100kb window around the bead)

source_name: blood

extract_protocol: Dip-C

tag: cell type

value: peripheral blood mononuclear cell (PBMC)


title: PBMC Cell 18_hickit


title: PBMC Cell 16_hickit


title: PBMC Cell 13_hickit


title: 3R40C69Ccaabar91MN15

value: Leaf

value: wildtype


title: PBMC Cell 9_hickit


title: PBMC Cell 10_hickit


title: PBMC Cell 12_hickit


title: PBMC Cell 7_hickit


title: PBMC Cell 14_hickit


title: PBMC Cell 11_hickit


title: siControl Replicate2

value: Osteosarcoma cell line

tag: sirna transfection

value: siControl


title: PBMC Cell 6_hickit


title: PBMC Cell 5_hickit


title: PBMC Cell 8_hickit


title: PBMC Cell 15_hickit


title: PBMC Cell 2_hickit


title: PBMC Cell 4_hickit


title: PBMC Cell 1_hickit


title: PBMC Cell 3_hickit


title: GM12878 Cell 15_hickit

source_name: lymphoblastoid cell line

value: lymphoblastoid cell line


title: GM12878 Cell 17_hickit


title: GM12878 Cell 16_hickit

description: No processed data available. Sample failed quality control.


title: GM12878 Cell 14_hickit


title: GM12878 Cell 9_hickit


title: GM12878 Cell 10_hickit


title: GM12878 Cell 11_hickit


title: GM12878 Cell 12_hickit


title: GM12878 Cell 13_hickit


title: GM12878 Cell 5_hickit


title: GM12878 Cell 1_hickit


title: PBMC Cell 17-2

data_processing:
contact identification from alignment files (BAM): raw.con.gz
removal of duplicates: dedup.con.gz
removal of bad regions (bad.reg) and non-chromosomal contigs, followed by haplotype assignment in haploid regions (hap.reg): reg.con.gz
removal of 3C/Hi-C artifacts: clean.con.gz
2D imputation of haplotypes: impute.con.gz
draft 3D genome: impute.3dg
3D imputation of haplotypes after 4 rounds: impute3.round4.con.gz
final 3D genome: impute3.round4.3dg
removal of contact-poor regions (such as centromeres): impute3.round4.clean.3dg
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: contact file (con): two columns of "chromosome,coordinate,haplotype" separated by a tab; 3d genome file (3dg): five tab-delimited columns (chromosome/homolog, coordiante, x, y, z, respectively)

value: PBMC


title: GM12878 Cell 6_hickit


title: GM12878 Cell 7_hickit


title: GM12878 Cell 4_hickit


title: GM12878 Cell 2_hickit


title: GM12878 Cell 8_hickit


title: PBMC Cell 18-2


title: PBMC Cell 16-2


title: 2012CM8F030p09


title: PBMC Cell 18-1


title: PBMC Cell 15-2


title: PBMC Cell 17-1


title: PBMC Cell 16-1


title: GM12878 Cell 3_hickit


title: PBMC Cell 14-2


title: 252DaTinput

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

data_processing:
Adapters were trimmed from the raw reads using Scythe (https://github.com/vsbuffalo/scythe).
The raw reads were aligned to the  GRCm38 genome using Hisat2 v2.1.0 using default parameters.
MACS2 v2.1.1.20160309 was used to call peaks by comparing immunoprecipitated samples to input using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig from MACS2 bedgraph files.

source_name: Input DNA

extract_protocol: According to previously published ultra-low input native ChIP-seq protocol (Brind'Amour J, Liu S, Hudson M, Chen C, Karimi MM, Lorincz MC. An ultra-low-input native ChIP-seq protocol for genome wide profiling of rare cell populations. Nature Communications, 2015; 6:6033).

value: CBA/J

tag: Sex

value: female

value: Lung

value: CD11c+ dendritic cells

value: 6-8 weeks

tag: condition

value: Day 14 post intratracheal Cryptococcus neoformans 10^4 CFU

value: anti-TNFalpha antibody 14 days prior to cell isolation

tag: chip antibody


title: 352DaTH3K4me3

value: H3K4me3 (Abcam ab8580)


title: 352DaTinput


title: 252DaTH3K4me3


title: PBMC Cell 11-2


title: PBMC Cell 15-1


title: PBMC Cell 12-1


title: PBMC Cell 13-1


title: 252Dinput


title: 352DH3K4me3


title: RNA-seq_Nontarget_Sp_VPR_rep1

tag: cell line

value: NCCIT (ATCC CRL-2073)

value: Human embryonal carcinoma

tag: grna target

value: nontarget

tag: grna scaffold species

value: S. pyogenes

tag: dcas9 fusions

tag: experimental replicate

value: Replicate 1


title: PBMC Cell 12-2


title: PBMC Cell 10-1


title: PBMC Cell 13-2


title: 152Dinput

tag: strain


title: PBMC Cell 9-2


title: 252DH3K4me3


title: PBMC Cell 10-2


title: 152DaTH3K4me3


title: 3NaTH3K4me3

value: Naïve


title: PBMC Cell 11-1


title: 152DH3K4me3


title: 3NaTinput


title: PBMC Cell 14-1


title: PBMC Cell 9-1


title: 152DaTinput


title: 352Dinput


title: 2NaTinput


title: PBMC Cell 7-1


title: PBMC Cell 8-1


title: 2NaTH3K4me3


title: PBMC Cell 8-2


title: 1NaTinput


title: PBMC Cell 6-2


title: 1NaTH3K4me3


title: PBMC Cell 5-2


title: PBMC Cell 5-1


title: 2NH3K4me3


title: PBMC Cell 4-1


title: PBMC Cell 6-1


title: 1Ninput


title: 1NH3K4me3


title: PBMC Cell 3-2


title: PBMC Cell 2-2


title: PBMC Cell 3-1


title: PBMC Cell 7-2


title: 3Ninput


title: day6_eb

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

data_processing:
We used CellRanger verision 2.0
Demultiplexing was performed based on the 8 bp sample index read to generate FASTQs for the Read1 and Read2 paired-end reads.
Reads were aligned using STAR.
Barcodes and UMIs were filtered.
PCR duplicates were marked if two sets of read pairs shared a barcode sequence, a UMI tag, and a gene ID (Ensembl).
Previously described processing is according to: Zheng et. al. 2017.
[citations] van Dijk, D., Nainys, J., Sharma, R., Kathail, P., Carr, A.J., Moon, K.R., Mazztis, L., Wolf, G., Krishnaswamy, S., Pe'er, D., 2017. MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. bioRxiv.
Genome_build: mm10 with added exogenous genes including green fluorescent protein
Supplementary_files_format_and_content: Processed data files are csv files with the rows as genes and the columns as cells (labeled by cell barcode).  They are expression matrices that were corrected for dropout using the MAGIC algorithm (van Dijk et al. 2017), downsampled then normalized.

growth_protocol: Bry-GFP mESCs were maintained on mouse embryonic feeder (mEF) cells in Dulbecco’s Modified Eagles’ Medium (DMEM; Gibco) containing 15% FBS (Sigma-Aldrich), 1%PSG (Gibco), LIF (MTI Global Stem; 1,000 U/mL), and 2-mercaptoethanol (Sigma; 0.1 mM). mESCs were passaged every other day via trypsinization (TrypLE; Gibco) and complete dissociation of colonies by pipetting.

extract_protocol:
Single-cell samples were prepared by dissociating incubating them in TrypLE for 2 minutes at 37C and then vortexing them briefly. Cells were then strained them with a 30 µm cell strainer (Miltenyi Biotec). The strained cells were washed twice with dPBS containing 0.04% bovine serum albumin (BSA, Sigma) and then counted.  The concentration of the cells was adjusted to 450-500 cells/uL and then 10,000 cells from each sample underwent library preparation.
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 30 Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) as indicated in Zheng et al 2017) .
[citations] Zheng, G.X.Y., Terry, J.M., Belgrader, P., Ryvkin, P., Bent, Z.W., Wilson, R., Ziraldo, S.B., Wheeler, T.D., McDermott, G.P., Zhu, J., Gregory, M.T., Shuga, J., Montesclaros, L., Underwood, J.G., Masquelier, D.A., Nishimura, S.Y., Schnall-Levin, M., Wyatt, P.W., Hindson, C.M., Bharadwaj, R., Wong, A., Ness, K.D., Beppu, L.W., Deeg, H.J., McFarland, C., Loeb, K.R., Valente, W.J., Ericson, N.G., Stevens, E.A., Radich, J.P., Mikkelsen, T.S., Hindson, B.J., Bielas, J.H., 2017. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8.

treatment_protocol: To begin differentiation (day 0), cells were trypsinized, removed from feeder cells, and cultured in suspension in serum-free differentiation media (SFD; Craft et al. 2013) at a density of 75,000 cells/mL for 48 hours to form embryoid bodies (EBs). At this point (day 2), we induced primitive streak (PS) formation by culturing cells in SFD containing the following growth factors and inhibitors: Noggin (150ng/mL), Wnt3a (25ng/mL), and Activin A (9ng/mL). After, the 48-hour PS induction (day 4), cells were removed from primitive streak-inducing factors and cultured as cell aggregates in SFD containing bFGF (10ng/mL) for an additional 48 hours.

value: cells from ES-derived embryoid body

tag: time


title: 3NH3K4me3


title: day4_eb


title: 2Ninput


title: PBMC Cell 2-1


title: PBMC Cell 1-2


title: mini_stat_20hrs_long_timecourse_RNA

description:
total RNA
DATA_S1.xlsx

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq data was quantified using Salmon-0.8.1 with three separate annotation indices:     1.    open reading frames (ORFs) as defined by SGD  2.    “complex transcriptome” index created by aggregating ORFs, their longest annotated UTRs + all non-canonical and non-coding transcripts pulled from SGD (references)  3.    all features index composed of ORFs + non-coding transcripts (SGD all freatures) + genomic intergenic bins     Salmon was run using the “quant” command with the following settings:"libType": "ISR", "useVBOpt": [], "numBootstraps": "30", and "incompatPrior": "0".     Salmon quantification was prepared and processed for differential expression analysis with the Wasabi package in R for input into Sleuth. Genes changing with respect to time (generation) as opposed to batch or strain were defined as significant using: model = ~generation*strain+(batch)+(0)” and using a p < 0.05 for calculated beta values. For determining genes changing significantly across time (age) for each specific strain the model "~batch+strain+strain:generation" was specified. All test tables output from Sleuth included in Data S1 and Data S2.
Batch correction (for heatmap visualization only) was applied to the Salmon quantification output matrix with a pseudocount of 2 TPM with the COMBAT package in R [75]. Hierarchical clustering (average linkage) was performed on the batch-corrected values using the uncentered Pearson correlation as the distance metric.
Gene Ontology (GO) term enrichment analysis was performed via uploading query lists to the DAVID Bioinformatics Resources 6.8 website and running enrichment with the S. Cerevisiae species background.
ATAC-Seq Data Analysis:     Processing of raw sequencing data  Raw ATAC-seq data was processed as described in [76]. Briefly, first, the raw paired end reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, Release 64) using bwa mem version 0.7.12 with default parameters. Second, the alignments were filtered requiring that both reads in the pair are mapped, the mapping quality is greater than or equal to 30, the reads are mapping concordantly and the direction of the mapping is F1R2. Third, we converted the alignments into track of number of insertions at each position in the genome. For every aligned fragment the insertion locations are calculated by shifting the fragment ends of reads that align to ‘+’ strand by 4 nucleotides and shifting the fragment ends of reads that align to ‘-’ strand by 5 nucleotides in the 3’ direction to reflect the distance to the center of the transposase binding site [60]. To normalize for uneven sequencing depth and different amounts of rDNA in the samples, insertion counts were normalized such that the total number of insertions from unique non-rDNA, nonmitochondrial reads is constant in each sample.     Annotations  Nucleosome positions were downloaded from [62], lifted over to sacCer3 assembly and only nucleosomes with mapping score greater than 2 were used in the metagene plots. For metagene plots around promoters we defined the TSSs for each yeast gene my merging the TSS data from [77] (TIF-seq) and [78] (TSS data). If the TSS for a gene was not reported  by these two papers, we used the beginning of ORF as the TSS. TF and chromatin modifier binding data were from [65,66].     NucleoATAC   Baseline estimation of the nucleosome occupancy from ATAC-seq data could be confounded by noise in estimation of nucleosome free and nucleosomal fraction of fragments between samples. Therefore we generated a fragment size distribution that was an average fragment size distribution of all samples and ran the NucleoATAC pipeline using a constant fragment size distribution using --sizes parameter. Since occupancy estimation was sensitive to the depth of the sample, we downsampled each sample to 25 million uniquely mapped non-ribosomal reads. Finally, to limit differences due to differences in nucleosomal calling between samples, we called occupancy only on the nucleosomes from Brogaard et al that are well positioned (score > 2), located in the open chromatin part of the genome (as defined by Schep et al) and have a median occupancy of at least 0.5.      Differential accessibility  Aging slope for accessibilities was calculated as follows. We first binned the genome into non-overlapping 100 bp bins and counted number of insertions in each bin. We then performed quantile normalization for each sample separately to calculate normalization factors and supplied gene specific normalization factors as described in http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#sample-gene-dependent-normalization-factors to DESeq2 pipeline [79]. The aging slope was determined on all samples using the following model: "~ replicate + strain + ave_budscars" where ave_budscars were the average number of budscars for that time point and we looked at the bins with q-value of non-zero slope of less than 10-6. To identify bins that were specifically opening or closing in certain strains, we used the following model “replicate + strain + ave_budscars + strain:ave_budscars”.     Enrichments of regulators  We assigned each genomic bin to the gene whose gene body it intersects or to the promoter (defined as up to 400 bp upstream of TSS) of the gene that intersects. The lists of age-opening and age-closing genes were generated by looking at a genes that contained at least one opening and closing bin (with q-value < 10-6) respectively. We then intersected these lists with the list of genes that bind to transcription factor or chromatin modifier and performed a hypergeometric test to evaluate enrichment.
Genome_build: sacCer3
Supplementary_files_format_and_content: excel spreadsheet files include TPM values for each Sample at gene level and comma separated files include ATAC-seq insertion density for significantly changing genomic bins

tag: class

value: mother

tag: age in hours


title: PBMC Cell 4-2

value: PBMC


title: low growth factor, +DAPT

city: Pasadena

first: Nagarajan

last: Nandagopal

address: 1200 E. California Blvd, M/C 114-96

institute: California Institute of Technology

description: low growth factor, +DAPT

data_processing:
All data processing was perfomed using the Galaxy tools and servers (https://usegalaxy.org) Fastq files from the same samples were concatenated.
Single-end reads were aligned to the mm10 mouse genome using RNA star
Gene expression levels (FKPM, Frequency per Kilobase of exon Per Megabase of reads) was calculated using Cufflinks and appropriate mm10 gene model file.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files with FKPM values

source_name: Neural progenitor cells

growth_protocol: Prior to treatment, cells were cultured in neurobasal medium supplemented with 20 ng/ml recombinant EGF, 20 ng/ml recombinant FGF, and 5 ug/ml Heparin

extract_protocol:
Cells were lysed on the plate and RNA was extracted using the Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were plated in high (20 ng/ml EGF and FGF) or low growth factor conditions (0.5 ng/ml EGF, 5 ug/ml Heparin) with or with 10 uM DAPT treatment

tag: tissue of origin

value: E14.5 mouse cortex

tag: source of cells

value: EMD Millipore, Catalog No. SCR029


title: CASE, maternal placenta (C24_car)

city: Freising

first: Krzysztof

last: Flisikowski

address: Liesel-Beckmannstr. 1

department: Livestock Biotechnology

country: Germany

institute: Technical University of Munich

data_processing:
The first step was to detect and remove adapter sequences with the tool FastqMcf
The quality of Fastq files was checked before and after adapter clipping with FastQC
Each adapter-clipped FastQ file was collapsed into the sequence and the number of appearances (using the tool “Collapse” - FastxTools http://hannonlab.cshl.edu/fastx_toolkit/) ranked by the counts
The final count table contained only the sequences and the number of reads per sample
Genome_build: bta3.1
Supplementary_files_format_and_content: Excel files include abundance measurements

organism: Bos taurus

source_name: CASE, maternal placenta

extract_protocol:
Total RNA was extracted using Zymo Direct-zol RNA MiniPrep kit
TruSeq Small RNA Library Prep Kit (Illumina)

tag: breed

value: Finnish Ayshire

tag: genotype

tag: tissue

value: maternal placenta


title: CONTROL, maternal placenta (C23_car)

source_name: CONTROL, maternal placenta

value: wild-type


title: CONTROL, maternal placenta (C20_car)


title: CONTROL, maternal placenta (C26_car)


title: CONTROL, maternal placenta (C22_car)


title: CASE, maternal placenta (C25_car)


title: low growth factor, no DAPT

description: low growth factor, no DAPT


title: BMSCs from 18 month mice, biological rep3

city: changsha

first: CHANGJUN

last: LI

address: 87# Xiangya Road

department: Department of Endocrinology, Endocrinology Research Center

institute: Xiangya Hospital of Central South University

description: Gene expression data from BMSCs from 18 month mice,

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mouse BMSCs from 18-month-old mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The sorted mouse Sca-1+ CD29+ CD45− CD11b− BMSCs were cultured to reach 80%–85% confluence. Then, first-passage BMSCs were detached and seeded in culture flasks for the enrichment of cell populations.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Femurs of mice were collected and crushed with a mortar and pestle. The bone was then digested with collagenase A (Sigma) to obtain a single-cell suspension. Cells within the supernatant were collected and incubated with phycoerythrin (PE)-, FITC-, peridinin chlorophyll protein (PerCP)- and allophycocyanin (APC)-conjugated antibodies that recognized mouse Sca-1 (Cat. No. 108108, BioLegend), CD29 (Cat. No. 102206, BioLegend), CD45 (Cat. No. 103132, BioLegend), and CD11b (Cat. No. 101226, BioLegend) for 20 min at 4°C. The acquisition was performed on a fluorescence-activated cell sorting (FACS) Aria model (BD Biosciences), and the analysis was performed using FACS DIVE software version 6.1.3 (BD Biosciences).

tag: cell type


title: BMSCs from 3 month mice, biological rep3

description: Gene expression data from BMSCs from 3 month mice,

source_name: Mouse BMSCs from 3-month-old mice


title: CASE, maternal placenta (C18_car)


title: BMSCs from 18 month mice, biological rep2


title: BMSCs from 18 month mice, biological rep1


title: BMSCs from 3 month mice, biological rep2


title: PBMC Cell 1-1


title: BMSCs from 3 month mice, biological rep1


title: GM12878 Cell 17-2

source_name: lymphoblastloid cell line


title: CONTROL, maternal placenta (C19_car)


title: CASE, maternal placenta (C15_car)


title: CONTROL, maternal placenta (C13_car)


title: high growth factor, +DAPT

description: high growth factor, +DAPT


title: CASE, maternal placenta (C17_car)


title: GM12878 Cell 16-2


title: high growth factor, no DAPT

description: high growth factor, no DAPT


title: GM12878 Cell 15-2


title: CONTROL, fetal placenta (C19_cot)

source_name: CONTROL, fetal placenta

value: fetal placenta


title: CONTROL, fetal placenta (C20_cot)


title: CASE, fetal placenta (C24_cot)

source_name: CASE, fetal placenta


title: CONTROL, fetal placenta (C26_cot)


title: GM12878 Cell 15-1


title: GM12878 Cell 14-2


title: CONTROL, fetal placenta (C22_cot)


title: GM12878 Cell 13-2


title: CONTROL, maternal placenta (C14_car)


title: CONTROL, fetal placenta (C14_cot)


title: CASE, fetal placenta (C17_cot)


title: GM12878 Cell 17-1


title: CASE, fetal placenta (C25_cot)


title: CONTROL, fetal placenta (C23_cot)


title: IgG_ChIP-seq, TPA-treated HL-60 cells

city: Seoul

first: Jiyoung

last: KIM

address: 84 Heuk Seok-Dong, Dong jak -Gu

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Peak callings were performed using Homer.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: HL-60 cell

growth_protocol: HL-60 cells were grown in RPMI-1640 containing 10% heat-inactivated fetal bovine serum and 0.05% penicillin-streptomycin at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The construction of library was performed using TruSeq ChIP Library Preparation Kits according to the manufacturer’s instructions.

treatment_protocol: For differentiation, HL-60 cells were seeded in 100 mm plate with 2 × 107 numbers and treated with 32 nM TPA or DMSO.

value: Human promyelocytic leukemia cells

tag: treatment

value: 32 nM TPA

tag: passages

value: Rabbit IgG (Millipore [12-370])


title: CONTROL, fetal placenta (C13_cot)


title: CASE, fetal placenta (C18_cot)


title: Rax_E95_rep2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
library strategy: 4C-seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Danio rerio (danRer6 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
A running 51 bins-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: Amphioxus Bl71nemr (Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession), danRer10, mm10
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 2Mb around each viewpoint that can be directly uploaded to UCSC for visualization.

organism: Danio rerio

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Rax

growth_protocol: CBA/Ca×C57Bl/10 crosses. Embryos taken at 9.5dpc, taking the day in which the plug was found as 0.5dpc.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

tag: developmental

value: whole embryo


title: Shh_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Shh


title: GM12878 Cell 13-1

tag: cell line


title: H3K27me3_ChIP-seq, TPA-treated HL-60 cells

tag: chip antibody


title: Rax_E95_rep1


title: Pax7_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Pax7


title: GM12878 Cell 12-2


title: GM12878 Cell 12-1


title: CASE, fetal placenta (C15_cot)


title: Pax6_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Pax6


title: HDAC2_ChIP-seq, TPA-treated HL-60 cells

value: HDAC2 (Abcam [ab12169])


title: GM12878 Cell 16-1


title: RNA PolII_ChIP-seq, TPA-treated HL-60 cells

value: RNA Pol II (Santa Cruz [sc-899 X])


title: Pax7_E95_rep2


title: AcH3_ChIP-seq, TPA-treated HL-60 cells

value: AcH3 (Abcam [ab47915])


title: Pax5_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Pax5


title: Pax5_E95_rep2


title: Meox1_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Meox1


title: Gbx2_E95_rep2

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Gbx2


title: Ihh_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Ihh


title: Pax3_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Pax3


title: GM12878 Cell 14-1


title: Gbx2_E95_rep1


title: GM12878 Cell 10-2


title: IgG_ChIP-seq, DMSO-treated HL-60 cells

value: DMSO


title: GM12878 Cell 11-2


title: H3K27me3_ChIP-seq, DMSO-treated HL-60 cells


title: GM12878 Cell 11-1


title: GM12878 Cell 10-1


title: FoxA2_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of FoxA2


title: RNA PolII_ChIP-seq, DMSO-treated HL-60 cells


title: FoxA1_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of FoxA1


title: AcH3_ChIP-seq, DMSO-treated HL-60 cells


title: GM12878 Cell 8


title: GM12878 Cell 9


title: GM12878 Cell 7


title: En1_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of En1


title: Dlx6_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dlx6


title: En2_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of En2


title: En2_E95_rep2


title: HDAC2_ChIP-seq, DMSO-treated HL-60 cells


title: Dlx3_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dlx3


title: FoxA2_E95_rep2


title: GM12878 Cell 6

source_name: lymphoblastloid cell line


title: Dlx4_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dlx4


title: Dlx2_E95_rep2

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dlx2


title: Dlx2_E95_rep1


title: GM12878 Cell 4


title: GM12878 Cell 5


title: Dlx1_E95_rep2

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dlx1


title: Dlx1_E95_rep1


title: Dhh_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dhh


title: Rax_8hpf_rep1

source_name: 4Cseq in 8hh amphioxus embryos from the promoter of Rax

growth_protocol: Embryos were cultivated at 19°C in filtered seawater until desired developmental stage


title: GM12878 Cell 3


title: Rax_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Rax


title: Dlx5_E95_rep1

source_name: 4Cseq in E9.5 mouse embryos fromm the promoter of Dlx5


title: Pax4.6_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Pax4.6


title: GM12878 Cell 1


title: Pax3.7_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Pax3.7


title: Pax2.5.8_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Pax2.5.8


title: MDA-MB-231,MKC-8866 treated, 1% O2, 24 hours, biological rep3

city: Galway

first: Afshin

last: Samali

address: Newcastle Road, Dangan

department: Biomedical Sciences

country: Ireland

institute: Apoptosis Research Centre

hyb_protocol: Labeled, fragmented cDNA (5.5ug) (AffymetrixGeneChip® WT Terminal Labeling and Controls Kit, catalogue number 901524) was hybridized to Human Gene 2.0 arrays for 16 hours at 45°C (at 60 rpm) (Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, catalogue number 900720).

scan_protocol: Arrays were washed and stained using the Affymetrix Fluidics Station 450, and scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring (Agilent technologies) software using Affymetrix default analysis settings and Robust Multichip Average (RMA) algorithm as normalization method.

label: Biotin

source_name: Human triple negative breast cancer cell line MDA-MB-231 from ATCC (HTB-26)

label_protocol: Human RNA samples (450ng) were processed and labeled for array hybridization using the Ambion WT Expression kit (Life Technologies, catalogue number 4411974).

growth_protocol: MDA-MB 231 cells were maintained at 37C in 5% CO2, in DMEM High Glucose (4,500 mg/ml), supplemented with 10% FBS and 2mM L-glutamine

extract_protocol: RNA was extracted from cells using a combination of Trizol extraction and Rneasy Columns from Qiagen.

treatment_protocol: MDA-MB 231 cells at passage 16 (repeat 1), 17 (repeat 2) 19, (repeat 3) were seeded at 500,000 cells/T25 flask. The next day the media on cells was replaced with media containing DMSO or MKC-8866 (20 μM). In parallel cells were placed in a hypoxic glovebox (1% O2, Coy Laborartoy) and the media was replaced with hypoxia pre-conditioned media (i.e. media left in hypoxia overnight) containing DMSO or MKC-8866 (20 μM). At appropriate time-points cells were scraped from the flasks, pelleted and resuspended in 1mL Trizol.

value: MKC-8866 treated, 1% O2, 24 hours


title: Pax2.5.8_8hpf_rep1

source_name: 4Cseq in 8h amphioxus embryos from the promoter of Pax2.5.8


title: Meox_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Meox


title: MDA-MB-231,MKC-8866 treated, 1% O2, 24 hours, biological rep2


title: Meox_15hpf_rep2


title: MDA-MB-231,MKC-8866 treated, 1% O2, 24 hours, biological rep1


title: Hh_8hpf_rep1

source_name: 4Cseq in 8h amphioxus embryos from the promoter of Hh


title: Gbx_8hpf_rep1

source_name: 4Cseq in 8h amphioxus embryos from the promoter of Gbx


title: Hh_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Hh


title: GM12878 Cell 2

source_name: lymphoblastloid cell line


title: FoxAa_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of FoxAa


title: Fezf_8hpf_rep1

source_name: 4Cseq in 8h amphioxus embryos from the promoter of Fezf


title: Fezf_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Fezf


title: En_8hpf_rep1

source_name: 4Cseq in 8h amphioxus embryos from the promoter of En


title: MDA-MB-231,MKC-8866 treated, 1% O2, 4 hours, biological rep3

value: MKC-8866 treated, 1% O2, 4 hours


title: MDA-MB-231,MKC-8866 treated, 1% O2, 4 hours, biological rep1


title: En_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of En


title: MDA-MB-231,MKC-8866 treated, 1% O2, 4 hours, biological rep2


title: MDA-MB-231, DMSO treated, 1% O2, 4 hours, biological rep2

value: DMSO treated, 1% O2, 4 hours


title: MDA-MB-231,MKC-8866 treated, 24 hours, biological rep3

value: MKC-8866 treated, 24 hours


title: MDA-MB-231, DMSO treated, 1% O2, 4 hours, biological rep3


title: MDA-MB-231, DMSO treated, 1% O2, 4 hours, biological rep1


title: MDA-MB-231,MKC-8866 treated, 24 hours, biological rep2


title: Gbx_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Gbx


title: MDA-MB-231,MKC-8866 treated, 4 hours, biological rep3

value: MKC-8866 treated, 4 hours


title: shhb_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of shhb

growth_protocol: Embryos were raised at 28ºC untill they reached the desired developmental stage. They were dechorionated with pronase before fixation.


title: shhb_24hpf_rep1


title: Dlx_15hpf_rep1

source_name: 4Cseq in 15h amphioxus embryos from the promoter of Dlx


title: shha_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of shha


title: MDA-MB-231,MKC-8866 treated, 24 hours, biological rep1


title: rx3_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of rx3


title: shha_24hpf_rep2


title: pax7b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax7b


title: pax6b_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax6b


title: pax6a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax6a


title: pax7a_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax7a


title: pax2b_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax2b


title: pax5_24hpf_rep1

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax5


title: pax2b_24hpf_rep1


title: pax2a_24hpf_rep2

source_name: 4Cseq in 24hpf zebrafish embryos from the promoter of pax2a


title: MDA-MB-231,MKC-8866 treated, 4 hours, biological rep1

source_name: Human triple negative breast cancer cell line MDA-MB-231 from ATCC (HTB-26)


title: MDA-MB-231, DMSO treated, 4 hours, biological rep3

value: DMSO treated, 4 hours