title: ATACseq TBT rep 12

city: Irvine

first: Raquel

last: Chamorro-Garcia

address: 4351 Natural Sciences 2

institute: University of California Irvine

data_processing:
Statistical evaluation of TBT-dependent methylome and transcriptome variation in F4 male gonadal white adipose tissue was performed using R (version 3.3), and Bioconductor (version 3.3) packages MEDIPS (version 1.22), Rsubread (version 1.22), and edgeR (version 3.14). MEDIPS function MEDIPS.meth was used to estimate the statistical significance of MBD-seq reads differential coverage for GRCm38/mm10 mouse reference genomic 100-bp consecutive, non-overlapping windows with the following parameters: diff.method = edgeR, minRowSum = 10, and diffnorm = quantile. Rsubread function featureCounts was used to assigned uniquely mapped RNA-seq reads to GRCm38/mm10 mouse reference genome gene models and count reads with the following parameters: GTF.featureType = exon, GTF.attrType = gene_id, allowMultiOverlap = TRUE, nthreads = 24, and strandSpecific = 0 . edgeR functions cpm and glmQLFTest were used to estimate the number of counts per million per gene model and the statistical significance of RNA-seq reads differential coverage.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-seq_processed data.txt includes RNA-seq normalized counts per gene model for each sample, and results of the statistical analyses performed as described above.
Supplementary_files_format_and_content: MBD-seq_processed data.txt includes MBD-seq read counts, and rpkm for each sample, and results of the statistical analyses performed as described above for GRCm38/mm10 mouse reference genomic 100-bp consecutive, non-overlapping windows for which P value was lower than 0.001.
Supplementary_files_format_and_content: ATAC-seq_isochores_f3_processed data.txt and ATAC-seq_isochores_f4_processed data.txt include ATAC-seq read counts, and rpkm for each sample, and results of the statistical analyses performed as described above for GRCm38/mm10 mouse isochores obtained from isoFinder for sperm samples from F3 and F4 generations, respectively. ATAC-seq_SICER_f3_processed data.txt and ATAC-seq_SICER_f4_processed data.txt include ATAC-seq read counts, and normalized counts for each group of samples, and results of the statistical analyses performed as described above for GRCm38/mm10 mouse SICER islands for sperm samples from F3 and F4 generations, respectively.

source_name: Sperm

growth_protocol: Male (n=25) and female (n=50) C57BL/6J mice (7 weeks of age) were purchased from the Jackson Laboratory (Sacramento, CA). Mice were housed in micro-isolator cages in a temperature-controlled room (21–22°C) with a 12 hr light/dark cycle. Water and food was provided ad libitum unless otherwise indicated. Animals were treated humanely and with regard for alleviation of suffering. All procedures conducted in this study were approved by the Institutional Animal Care and Use Committee of the University of California, Irvine. All tissue harvesting was performed with the dissector blinded to which groups the animals belonged to.

extract_protocol:
Mouse sperm were isolated from 6 randomly selected, non-sibling males per generation. Epididymis and vas deferens were dissected and placed on a petri dish containing 2 mL of nucleus isolation medium (NIM) buffer (123.0 mmol/l KCl, 2.6 mmol/l NaCl, 7.8 mmol/l NaH2PO4, 1.4 mmol/l KH2PO4 and 3 mmol/l EDTA (disodium salt)). Sperm was pushed out of the tissue and media was collected and transferred to two clean microcentrifuge tubes and kept on ice. Samples were centrifuged at 13,000 xg for 5 minutes at 4ºC. Supernatant was removed and cells were resuspended in 1 mL of fresh NIM buffer.
Sperm were counted using a hemocytometer, and 50,000 sperm were suspended in 22.5 uL water containing 0.01% digitonin. The diluted sperm were immediately subjected to tagmentation by adding 25 uL Nextera tagment DNA buffer (2X reaction buffer from Illumina Nextera kit) and 2.5 uL Nextera tagment DNA enzyme (Tn5 transposon enzyme from Nextera kit) followed by incubation at 37 °C for 30 minutes. Tagmented sperm DNA was immediately purified using QIAGEN MinElute kit and subjected to PCR amplification of the tagmented DNA fragments for Illumina deep sequencing library construction as previously described. To avoid batch effects, we randomly selected one sperm specimen from each of the four treatment groups – namely, F3 DMSO, F3 TBT, F4 DMSO, and F4 TBT – and performed the ATAC-seq reaction for these four specimens as a batch on the same day. We processed six batches (total 24 sperm specimens, 6 specimens for each treatment group) as independently performed experiments. The ATAC-seq libraries were sequenced using Illumina NextSeq 500 sequencer

treatment_protocol: Female C57BL/6J mice (25 females per treatment group) were randomly assigned to the different treatment groups and exposed via drinking water to 50 nM TBT or 0.1% DMSO vehicle (both diluted in 0.5% carboxymethyl cellulose in water to maximize solubility) for 7 days prior to mating. Chemicals were administered to the dams throughout pregnancy and lactation.We chose only 1 male and 2 females per litter for breeding. To randomize the breeding process as much as possible, we did not breed siblings and did not breed females from the same litter with the same male. Unexposed animals were bred to each other and TBT-exposed bred to each other. A similar approach was followed in generations F2-F4. Animals from F0-F4 were maintained on a standard diet (SD - Rodent Diet 20 5053*; PicoLab) throughout the experiment. F4 males and females (avoiding siblings within the same gender) were maintained on a higher fat diet (HFD - Mouse Diet 20 5058*; PicoLab) between weeks 19-25. Mice were subsequently returned to the SD for 8 more weeks prior to euthanasia at 33 weeks of age

value: 8 weeks

tag: generation


title: ATACseq TBT rep 10

status: Public on Nov 10 2017

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: age


title: ATACseq TBT rep 11


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_NT_sgRNA_Cas9_2 EMX1_EMX1_APE1_KO_D10A_1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA Non-transfected sgRNA Cas9 DNA replicate 2 and EMX1 EMX1 APE1 KO D10A Indel DNA replicate1

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

organism: Homo sapiens

growth_protocol: 293FT from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free. Cryopreserved human peripheral blood mononuclear cells (PBMCs) were purchased from AllCells, LLC (PB003F). CD8+ T cells were pre-enriched from the PBMCs with Easysep Human CD8+ T cell enrichment kit (19053, Stemcell Technologies) according to the manufacturer’s protocol. The cells were then activated with Dynabeads Human T-Activator CD3/CD28 (LifeTech, 11131D) for 3 days in AIM V medium (Gibco, 0870112DK) supplemented with 10% FBS. The stimulated CD8+ T cells were then cultured in AIM V medium with 10% FBS and 100 IU/ml hIL2 (200-02-100, PeproTech).

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: To determine base substitution frequencies in the genomic DNA during HDR in cell lines, cells were co-transfected with 3 μg Cas9-expressing plasmid, 1.5 μg sgRNA-expressing plasmid and 100 pmol ssODNs, dsODNs or ds-plasmid donors by electroporation (program Q-001) with Cell Line Nucleofector® Kit V (VCA-1003) on Lonza Nuclepfectoe-2b. Electroporated cells were then plated into a 60-mm dish. To determine the indels in genomic DNA in cell lines, cells were seeded in a 24-well plate at a density of 1 × 105 per well and transfected with 1 μg Cas9-variant-expressing plasmid, 0.5 μg single sgRNA-expressing plasmid and 5.4 μl LipofectamineTM 2000 (Thermo Fisher Scientific) according to the manufacture’s instructions. After 24 hrs, blasticidin was added (ant-bl-1, InvivoGen) to the media at a final concentration of 10 μg/ml. To determine base substitutions during HDR, 4x106 T cells were electroporated with 30 pmol of siRNA (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit L (Lonza, V4XP-3024) on day 4. After 24 hrs, RNP mixture with or without 100 pmol of ssODN or dsODN donor and 2x105 transfected cells were combined in a Lonza 4D strip nucleocuvette and electroporated (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit. . After another 48 hours, cells were and lysed with QuickExtract DNA Extraction Solution for HDR taq-specific PCR amplification. To determine indel formation, 4x106 T cells were electroporated with 30 pmol of siRNA (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit L (Lonza, V4XP-3024) on day 4 or day 7. After 24 hrs, 8 μg of Cas9 protein (or its variants) and 2 μg of sgRNA were mixed and incubated for 10 min to allow RNP formation. RNP mixture and 2x105 cells were combined in a Lonza 4D strip nucleocuvette and electroporated (program EO-115) by using P3 Primary Cell 4D-Nucleofector® X Kit (V4XP-3032) on day 5 and day 8. After another 48 hours, Cells were collected and lysed with QuickExtract DNA Extraction Solution for PCR amplification.

tag: cell line

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: FANCF_HDR_NT_1 VEGFA_NT_Indel_1

description: FANCF HDR Non-transfected DNA replicate 1 and VEGFA NT Indel DNA replicate 1


title: ATACseq TBT rep 9


title: ATACseq TBT rep 8


title: ATACseq TBT rep 7


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_NT_sgRNA_Cas9_1 FANCF_dn_HDR_A3Bm_ssODN_1 RNA4_dn_HDR_A3Bm_ssODN_3

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA Non-transfected sgRNA Cas9 DNA replicate 1 and FANCF downstream HDR A3Bm ssODN DNA replicate 1 and RNA4 downstream HDR A3Bm ssODN DNA replicate 3

source_name: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA Non-transfected sgRNA Cas9 DNA replicate 1 and FANCF downstream HDR A3Bm ssODN DNA replicate 1 and FANCF downstream HDR A3Bm ssODN DNA replicate 3 and RNA4 downstream HDR A3Bm ssODN DNA replicate 3


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_NT_sgRNA_2 EMX1_EMX1_APE1_KO_Cas9_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA Non-transfected sgRNA DNA replicate 2 and EMX1 EMX1 APE1 KO Cas9 Indel DNA replicate1


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_A3B_sgRNA_Cas9_2 VEGFA_dC9_1 EMX1_EMX1-ON_dC9_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA A3B sgRNA Cas9 DNA replicate 2 and VEGFA dCas9 Indel DNA replicate1 and EMX1 EMX1-ON dCas9 Indel DNA replicate1


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_NT_sgRNA_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA Non-transfected sgRNA DNA replicate 1


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_A3B_sgRNA_Cas9_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA A3B sgRNA Cas9 DNA replicate 1


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_A3B_sgRNA_2 VEGFA_H8A 1 EMX1_EMX1-ON_H8A_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA A3B sgRNA DNA replicate 2 and VEGFA H840A DNA replicate1 and EMX1 EMX1-ON H840A DNA replicate1


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_A3B_sgRNA_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA A3B sgRNA DNA replicate 1


title: ATACseq TBT rep 3


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_sgRNA_Cas9_2 VEGFA_D10A_1 EMX1_EMX1-ON_D10A_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA sgRNA Cas9 DNA replicate 2 and VEGFA D10A Indel DNA replicate1 and EMX1 EMX1-ON D10A Indel DNA replicate1


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_NT_sgRNA_Cas9_1 RNA4_dn_HDR_A3B_dsODN_3

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA Non-transfected sgRNA Cas9 DNA replicate 1 and RNA4 downstream HDR A3B dsODN DNA replicate 3


title: ATACseq DMSO rep 11


title: ATACseq TBT rep 2


title: ATACseq DMSO rep 12


title: ATACseq DMSO rep 10


title: ATACseq DMSO rep 9


title: ATACseq DMSO rep 8


title: ATACseq TBT rep 6


title: BCL2L1_Dox+

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

description: mRNA from treated with Dox to induce BCL2L1 expression in hESC

library_source: transcriptomic

data_processing:
Basecalls performed by Casava using default settings
The RNA-seq reads were mapped to the human hg19 genome assembly independently by the HISAT2 software using the annotated gene structures as templates. Default parameters of HISAT2 were used except with the option “--dta-cufflinks” opening.
Reads with unique genome location were reserved for gene expression calculation using Cufflinks (version 2.0.2) with the option “--GTF”.
Fragments per Kilobase of exon per Megabase of library size (FPKM) was calculated using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks

molecule: total RNA

source_name: Treated with Dox to induce BCL2L1 expression in hESC

growth_protocol: Human ESCs were derived from human blastocysts as previously reported Thomson, Itskovitz-Eldor, Shapiro, Waknitz, Swiergiel, Marshall and Jones. Established primed human ESCs and BCL2L1/BCL2 overexpressed hESC lines were cultured in E8 medium on matrigel coated 6-well dishes. All of the stem cells were cultured at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from cultured cells by TRIzol reagent (Invitrogen). For RNA-seq library construction, The PolyA+ tailed RNA purification were performed for each sample using MicroElute RNA Clean Up Kit (OMEGA).
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed on an Illumina HiSeq 4000 sequencer with 150 bp paired-end sequencing reactions.

tag: cell type

value: primed human ESC


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_sgRNA_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA sgRNA DNA replicate 1


title: BCL2L1_Dox-

description: mRNA from untreated hESC with inducible BCL2L1

source_name: Untreated hESC with inducible BCL2L1


title: ATACseq TBT rep 5


title: ATACseq TBT rep 4


title: Kc167_spike-in gDNA reads

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Barcodes of independent low-complexity Kc167 TRIP pool used as RNA spike-in

data_processing:
Basecalling and filtering was performed using standard software of the illumina HiSeq 2500 or MiSeq. Extraction of 21 nt barcode reads from fastq files and alignment of TRIP mapping reads was performed using the TRIP script available at http://trip.nki.nl. We set a Hamming distance of 2 for removing mutated barcodes, a maximum distance of 500 nt on the forward  read  and 20 nt on the reverse read to cluster the positions during mapping and a minimum read number of 1. Spike-in library gDNA was sequenced separately to determine the spike-in barcode sequences. A list of the most abundant spike-in barcodes with over 1000 counts in gDNA was used for extracting spike-in reads from the TRIP samples. For each TRIP experiment sample, cDNA read counts per barcode were divided by the sum of cDNA read counts for all spike-in barcodes to correct for sequencing depth and standardize expression between samples. gDNA read counts were transformed to counts per million (cpm) to correct for sequencing depth. Spike-in corrected cDNA counts were then divided by gDNA cpm counts which yields the normalized expression per barcode. We set a cutoff for barcodes that had at least 100 gDNA reads in all samples to ensure that each barcode was sufficiently represented in the pool. To ensure reliable allocation of barcode integrations, we worked with a total of 1093 barcodes that fit the following criteria: (1) more than 2 reads in both forward and reverse mapping (2) 80% of forward and reverse mapping reads matched with the first mapping location and less than 10% of forward and reverse mapping reads matched with the second mapping location (3) mapq score of 10 or higher for forward and reverse mapping.
Genome_build: dm3
Supplementary_files_format_and_content: CSV files containing barcode sequences, position of integration, read counts and normalized expression for each of the samples
Supplementary_files_format_and_content: space delimited list of spike-in barcode sequences

organism: Drosophila melanogaster

source_name: Kc167_spike-in gDNA reads

growth_protocol: Kc167 cells were cultured at 23.5°C in Shields and Sang M3 Insect Medium (Sigma-Aldrich) with 0.25% Bacto Peptone (BD), 0.1% Yeast Extract (BD), 5% heat-inactivated FBS (Thermo Scientific) and 1% Penicillin/Streptomycin (Thermo Scientific). For pMT induction, sterile-filtered CuSO4 (Sigma-Aldrich) dissolved in H2O was added to 0.5mM final concentration

extract_protocol: To map the reporter integrations, gDNA was extracted from 20*106 cells using ISOLATE II Genomic DNA Kit (Bioline) and digested with NlaIII (40 U, NEB) in buffer 4 supplemented with BSA in a total volume of 100 µl for 2 h at 37°C. The reaction was terminated by heat inactivation for 20 min at 65°C. Fragments were circularized over night at 12°C using T4 Ligase (100 U, NEB) in T4 Ligase buffer in a total volume of 1600 µl. Products were precipitated with ethanol and purified with ISOLATE II PCR and Gel kit (Bioline). Unligated fragments were removed by digestion with Plasmid-Safe DNase (20 U, Epicentre) with added ATP (final concentration 1 mM) in the manufacturer-supplied reaction buffer in a total volume of 100 µl for 5 h at 37°C. The reaction was terminated by heat-inactivation for 30 min at 70°C and purified using ISOLATE II PCR and Gel kit (Bioline). To eliminate any remaining unintegrated plasmid , products were digested with I-CeuI (5 U, NEB) in buffer 4 supplemented with BSA in s total volume of 60 µl for 2 h at 37°C. The reaction was terminated by heat-inactivation for 20 min at 65°C and purified using ISOLATE II PCR and Gel kit (Bioline). Products containing barcodes and flaking gDNA were amplified in two rounds by inverse PCR to add Illumina adapters for Illumina paired-end sequencing. For cDNA reads, RNA from 10*106 transfected cells isolated by FACS sorting was extracted with Chloroform from TRIsure-resuspended samples (Bioline). The polyadenylated fraction was isolated using the Oligotex kit (Qiagen). RNA samples were treated with RNase-free DNase I (2 U, Roche) in DNase buffer in a total volume of 20 µl for 30 min at 37°C. The reaction was terminated by adding 1 µl of 25 mM EDTA and incubation at 70°C  for 15 min. cDNA was generated using Tetro cDNA Synthesis Kit (Bioline) according to the manufacturer’s instructions with a GFP-specific primer instead of OligoDT. 1/4 of total cDNA was used in a PCR reaction to add adapters for Illumina single-end sequencing. The appropriate PCR cycle number was determined by qPCR to avoid overamplification. For gDNA reads, gDNA was isolated from 10*106 unsorted TRIP cells using ISOLATE II Genomic DNA Kit (Bioline). 500 ng were used in a PCR reaction to add adapters for Illumina single-end sequencing and amplified over 25 cycles.

treatment_protocol: To establish the pool of cells harboring reporter constructs, 1 million Kc167 cells were transfected with 1 µg barcoded 5xGal4UAS-pMT-GFP plasmid library and 1 µg plasmid encoding Sleeping Beauty transposase (Addgene #65487) by electroporation. Transposase expression was induced by four heat shock treatments of 2.5 h at 37°C distributed over 36 h. Transfected cells were expanded until Sleeping Beauty expression was lost. For the resulting TRIP pool, we determined the number of integrations to be 0.3 per cell based on qPCR on gDNA for GFP integrations compared to a cell line with a single integration. A subpool of 30,000 cells was taken from the TRIP pool and expanded to  limit the library complexity to a maximum of 10,000 integrations before gDNA was isolated for mapping of integrations. For assessing the effect of recruiting ACF1 to integrated reporters, GFP expression was induced by adding 0.5 mM CuSO4 two days before the TRIP pool was transiently transfected with plasmids encoding either pAc5-Gal4DBD-V5-ACF1-T2A-mCherry or control plasmids encoding Gal4DBD-V5 or V5-ACF1 or  Gal4DBD-V5-HP1a instead of Gal4DBD-V5-ACF1. For assessing reporter expression by day two after transfection, cells were sorted for mCherry expression before gDNA and cDNA were isolated for further analysis. To be able to compare bulk expression changes between cDNA samples, an independent TRIP pool with a complexity of approximately 200 barcodes was suspended in TRIsure (Bioline) and added to TRIP cells to an amount of 2.5% based on cell counts before RNA extraction.

value: drosophila melanogaster dorsal closure stage embryonal cell line


title: ATACseq DMSO rep 4


title: ATACseq DMSO rep 5


title: Yeast Total RNA replicate 3

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

description:
Total3Yeast
Total RNA was extracted after NaN3 stress

data_processing:
Mammaliean RNA-seq data Processing:
Illumina adaptors were trimmed using Trimmomatic 0.32 in paired end (PE) mode
An index genome was acquired from NCBI, build 37.2
Reads were aligned using Tophat2 (version and Bowtie2
Reads mapping to each gene were counted using HTSeq with parametes –t gene –I Name –f sam –s reverse, using the R64-1-1 annotation file
Differential expression analysis was perfomed using Cuffdiff
Yeast RNA-Seq data Processing:
Illumina adaptors were trimmed using Trimmomatic 0.32 in single end (SE) mode
An index genome was built with Bowtie 0.12.7 using the ‘build’ command and the S288C reference genome version (R64-1-1 .fasta file), which was acquired through Saccharomyces Genome Database (SGD)
Reads were aligned using Bowtie 0.12.7 using the following options: -S -v 2 -m 3 –best
Reads mapping to each gene were counted using HTSeq with parametes –t gene –I Name –f sam –s reverse, using the R64-1-1 annotation file
Normalization and differential expression analysis were then performed using DESeq 1.22.1
Genome_build: SCG R64-1-1; NCBI build 37.2
Supplementary_files_format_and_content: U2OSSGcuffdiff.txt contains Cuffdiff output (.txt)
Supplementary_files_format_and_content: yeastSGnormTable.txt contains DESeq output and normalized reads for each sample(.txt)

organism: Saccharomyces cerevisiae

source_name: Yeast Total RNA

growth_protocol:
U-2 OS cells expressing G3BP1-GFP were grown to 85% confluency in three 500 cm2 square TC-treated culture dishes
Yeast samples: We grew a 2.4L culture of Pab1-GFP expressing yeast cells in YEPD and stressed them with Sodium Azide (NaN3) for 30min, prior to lysis

extract_protocol:
The isolation of SG cores was adapted from Jain et al., 2016 and Wheeler et al. 2017.  Stress granules were purified through a series of differential centrigutation step, bound to ani-GFP antibody, and purified by binding to Protein A dynabeads. The beads were resuspended in a Protease K solution and incubated for 15 mins at 37°C.  Trizol LS reagent was added to the samples and RNA was extracted following the manufacturers protocol. Following isopropanol precipitation, the RNA pellet was re-suspended in 20 µL RNase-free H2O.  RNA was then Ribzeroed and DNAse treated.
Yeast sample: RNA was phenol:chloroform extracted, Ribzeroed, and DNAse treated
cDNA libraries were prepared following manufacturer’s protocol from three replicates of 10 ng ribosomal-depleted RNA from cells and SG cores using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina
Yeast samples: Libraries were constructed using the Bio Scientific NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kit.

treatment_protocol:
Cells were treated with .5 mM NaAsO2 for one hour at 37°C/5% CO2. After stress, cells were washed once with media, transferred to falcon tubes, and pelleted at 1,500 x g for 3 mins. Upon aspirating the media, the pellets were immediately flash-frozen in liquid N2 and stored at -80°C until isolation of mammalian SG cores was performed.
Yeast samples: Total cellular RNA (TotalRNA) and RNA from stress granule cores (SGRNA) was isolated from this culture.  A stress granule enriched fraction was obtained as outlined in Jain et al. 2016.  Stress granules were purified from this fraction with anti-GFP antibody, which was the bound to Protein A dynabeads.

tag: strain background

tag: genotype/variation

value: Pab-GFP

tag: stress

value: NaN3 stress

tag: molecule subtype

value: Total RNA


title: ATACseq DMSO rep 6


title: BCL2_Dox+

description: mRNA from treated with Dox to induce BCL2 expression in hESC

source_name: Treated with Dox to induce BCL2 expression in hESC


title: ATACseq DMSO rep 3


title: ATACseq TBT rep 1


title: HDAC1 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
Samples were aligned by bwa v0.7.10 using default parameters.
Bam files were generated and indexed with samtools v0.1.19 using default parameters.
Tag directories were generated with homer v4.2 makeTagDirectory using -checkGC parameter.
Region calling for histone ChIP-seq samples was done with homer v4.2 findPeaks using -center -size 1000 -minDist 2500 parameters.
Peak calling for ATAC-seq and factor ChIP-seq samples was done with macs2 2.0.10 using -B --SPMR parameters.
mm10 ENCODE blacklist were subtracted from the peak lists.
Annotation was created with homer v4.2 annotatePeaks.pl using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: annotation file

source_name: bone marrow

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP.
Libraries were prepared either with Ovation Ultralow Library Systems (Nugen) or TruSeq ChIP library systems (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Mouse bone marrow-derived macrophages were treated with (1) IL-4 (20 ng/ml; 1, 6 or 24 hours) as indicated or (2) were pretreated with IL-4 (20 ng/ml) for 24 hours then LPS (100ng/ml) were added for 1 hours.

tag: treatment

value: cells differentiated in the presence of MCSF (ctrl)

value: 8-12 weeks

tag: tissue

value: bone marrow-derived macrophages

tag: chip antibody


title: ATACseq DMSO rep 2


title: Yeast Total RNA replicate 2

description:
Total2Yeast
Total RNA was extracted after NaN3 stress


title: CDKN2A-6,EMX1,FANCF,RAG1-E,VEGFA_sgRNA_2 VEGFA_Cas9_1 EMX1_EMX1-ON_Cas9_1

description: CDKN2A-6, EMX1, FANCF, RAG1-E, VEGFA sgRNA DNA replicate 2 and VEGFA Cas9 Indel DNA replicate1 and EMX1 EMX1-ON Cas9 Indel DNA replicate1


title: ATACseq DMSO rep 1


title: Yeast Total RNA replicate 1

description:
Total1Yeast
Total RNA was extracted after NaN3 stress


title: Yeast SG RNA replicate 3

description:
SG3Yeast
RNA was extracted from purified stress granules after NaN3 stress

source_name: Yeast SG RNA

value: Stress granule RNA purification


title: MBDseq TBT rep 4

description: MBD-seq_processed data.txt

source_name: Gonadal adipose tissue

extract_protocol:
Genomic DNA (gDNA) and RNA were isolated from male white gonadal adipose tissue using ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research) of animals sacrificed at 33 weeks of age (after the diet challenge). Nucleic acid samples from 4 randomly selected mice from control or TBT groups were submitted for DNA methylome and transcriptome analyses
Sonicated gDNA (100-200 bp, 500 ng) was subjected to methylated DNA enrichment using the MethylMiner kit (Life Technologies), followed by deep sequencing library construction using the NEBNext Ultra kit (New England Biolabs). Sonicated gDNA without methylation enrichment was used as input control. Following the ENCODE recommendation for ChIP-seq, we aimed for 20 million mapped reads (75 nt single) for each gDNA sample

value: 33 weeks


title: Yeast SG RNA replicate 1

description:
SG1Yeast
RNA was extracted from purified stress granules after NaN3 stress


title: Yeast SG RNA replicate 2

description:
SG2Yeast
RNA was extracted from purified stress granules after NaN3 stress


title: MBDseq TBT rep 3

description: MBD-seq_processed data.txt


title: MBDseq TBT rep 2

description: MBD-seq_processed data.txt


title: ATACseq DMSO rep 7


title: MBDseq TBT rep 1

description: MBD-seq_processed data.txt


title: gDNA reads, Gal4-HP1, repl 2

description:
4453_15_plb032_Gal4HP1_r2_gDNA_AGTGGT_S15_L003
gDNA_Gal4HP1_r2
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by two days after transfection.  Replicate 2 of 2

source_name: Kc167_gDNA reads_Gal4-HP1

tag: transfected protein


title: gDNA reads, ACF1, repl 2

description:
4453_14_pAS09_Acf1_r2_gDNA_CAATGT_S14_L003
gDNA_Acf1_r2
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with ACF1 collected by two days after transfection.  Replicate 2 of 2

source_name: Kc167_gDNA reads_ACF1


title: gDNA reads, Gal4-HP1, repl 1

description:
4453_11_plb032_Gal4HP1_r1_gDNA_GGCTAC_S6_L003
gDNA_Gal4HP1_r1
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a collected by two days after transfection.  Replicate 1 of 2


title: MBDseq DMSO rep 3

description: MBD-seq_processed data.txt


title: BCL2_Dox-

description: mRNA from untreated hESC with inducible BCL2

source_name: Untreated hESC with inducible BCL2


title: MBDseq DMSO rep 2

description: MBD-seq_processed data.txt


title: MBDseq DMSO rep 4

description: MBD-seq_processed data.txt


title: gDNA reads, ACF1, repl 1

description:
4453_10_pAS09_Acf1_r1_gDNA_TAGCTT_S3_L003
gDNA_Acf1_r1
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with ACF1 collected by two days after transfection.  Replicate 1 of 2


title: MBDseq DMSO rep 1

description: MBD-seq_processed data.txt


title: RNAseq TBT rep 4

description: RNA-seq_processed data.txt

extract_protocol:
Genomic DNA (gDNA) and RNA were isolated from male white gonadal adipose tissue using ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research) of animals sacrificed at 33 weeks of age (after the diet challenge). Nucleic acid samples from 4 randomly selected mice from control or TBT groups were submitted for DNA methylome and transcriptome analyses
Directional RNA-seq libraries were synthesized from ribosomal RNA-depleted samples using the TruSeq RNA-seq kit (Illumina).


title: gDNA reads, Gal4, repl 2

description:
4453_16_Plb033_Gal4_r2_gDNA_CACGTT_S16_L003
gDNA_Gal4_r2
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by two days after transfection.  Replicate 2 of 2

source_name: Kc167_gDNA reads_Gal4


title: gDNA reads, Gal4-ACF1, repl 1

description:
4453_9_pAS05_Gal4Acf1_r1_gDNA_GATCAG_S1_L003
gDNA_Gal4Acf1_r1
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-ACF1 collected by two days after transfection.  Replicate 1 of 2

source_name: Kc167_gDNA reads_Gal4-ACF1


title: gDNA reads, Gal4-ACF1, repl 2

description:
4453_13_pAS05_Gal4Acf1_r2_gDNA_ATGTTT_S13_L003
gDNA_Gal4Acf1_r2
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-ACF1 collected by two days after transfection.  Replicate 2 of 2


title: RNAseq TBT rep 3

description: RNA-seq_processed data.txt


title: cDNA reads, Gal4-HP1a, repl 2

description:
4453_7_plb032_Gal4HP1_r2_cDNA_CAGATC_S10_L003
cDNA_Gal4HP1_r2
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2

molecule: polyA RNA

source_name: Kc167_cDNA reads_Gal4-HP1a


title: RNAseq TBT rep 2

description: RNA-seq_processed data.txt


title: RNAseq DMSO rep 4

description: RNA-seq_processed data.txt


title: RNAseq TBT rep 1

description: RNA-seq_processed data.txt


title: RNAseq DMSO rep 3

description: RNA-seq_processed data.txt


title: cDNA reads, ACF1, repl 2

description:
4453_6_pAS09_Acf1_r2_cDNA_GCCAAT_S7_L003
cDNA_Acf1_r2
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with ACF1, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2

source_name: Kc167_cDNA reads_ACF1


title: cDNA reads, ACF1, repl 1

description:
4453_2_pAS09_Acf1_r1_cDNA_CGATGT_S5_L003
cDNA_Acf1_r1
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with ACF1, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2


title: cDNA reads, Gal4, repl 1

description:
4453_4_Plb033_Gal4_r1_cDNA_TGACCA_S8_L003
cDNA_Gal4_r1
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2

source_name: Kc167_cDNA reads_Gal4


title: cDNA reads, Gal4, repl 2

description:
4453_8_Plb033_Gal4_r2_cDNA_ACTTGA_S11_L003
cDNA_Gal4_r2
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2


title: U-2 OS Total RNA replicate 3

description:
T3R1; T3R2
Total RNA was extracted after arsenite stress

source_name: U-2 OS Total RNA

value: osteosarcoma (OS) cells

value: arsenite stress


title: RNAseq DMSO rep 2

description: RNA-seq_processed data.txt


title: RNAseq DMSO rep 1

description: RNA-seq_processed data.txt


title: cDNA reads, Gal4-ACF1, repl 2

description:
4453_5_pAS05_Gal4Acf1_r2_cDNA_ACAGTG_S9_L003
cDNA_Gal4Acf1_r2
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-ACF1, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 2 of 2

source_name: Kc167_cDNA reads_Gal4-ACF1


title: U-2 OS Total RNA replicate 2

description:
T2R2; T2R2
Total RNA was extracted after arsenite stress


title: U-2 OS Total RNA replicate 1

description:
T1R1; T1R2
Total RNA was extracted after arsenite stress


title: gDNA reads, Gal4, repl 1

description:
4453_12_Plb033_Gal4_r1_gDNA_CTTGTA_S12_L003
gDNA_Gal4_r1
processed data: TRIP_ACF1.csv
gDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD collected by two days after transfection.  Replicate 1 of 2


title: WT day 30 rep3

city: WEST LAFAYETTE

first: Vikki

last: Weake

state: INDIANA

address: 175 S. University St.

department: Biochemisty

institute: Purdue University

data_processing:
Sanger / Illumina 1.9 used for basecalling.
Paired-end sequenced reads were trimmed using Trimmomatic with settings -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment to Ensemble Drosophila genome release 86 using Tophat with commands  --library-type fr-secondstrand --max-intron-length 141628 --mate-inner-dist 150 -p 8 --GTF
Sorting by read name using samtools sort with command -n
Read counting using HTSeq with commands --stranded=yes --format=bam
Differential expression analysis and counts per million (CPM) calculations done using edgeR
Genome_build: BDGP6
Supplementary_files_format_and_content: Comma separated value (CSV) file of raw and filtered gene counts, and normalized filtered counts (cpm) for each sample.

molecule: nuclear RNA

source_name: Retina

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10, 20, 25, 30, and 40 days with transfer to new food each 3 days.

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted from isolated GFP-tagged photoreceptor nuclei using previously described method by Ma J. and Weake V.M., J Vis Exp 2014 with minor modifications: nuclei were washed with PBS+300 mM NaCl following affinity purification.
Libraries were prepared using NuGen Ovation Drosophila RNA seq system. rRNA was depleted using InDA-C technology.

value: photoreceptor neurons

value: adult retina

value: 30 day old post eclosion

tag: Sex

value: male


title: WT day 10 pre3

data_processing:
CASAVA version 2.18.0.12 used for basecalling.
Single-end sequenced reads were trimmed using Trimmomatic SE -phred33 ILLUMINACLIP:Our_hiscan_vector_file:2:40:10 LEADING:20 TRAILING:20 MINLEN:14
Alignment to Ensemble Drosophila genome release 86 using Tophat with commands --library-type fr-secondstrand
Sorting by read name using samtools sort with command -n
Read counting using HTSeq with commands --stranded=yes
Differential expression analysis and counts per million (CPM) calculations done using edgeR
Genome_build: BDGP6
Supplementary_files_format_and_content: Comma separated value (CSV) file of raw and filtered gene counts, and normalized filtered counts (cpm) for each sample.

source_name: head

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10 days with transfer to new food each 3 days.

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted from isolated GFP-tagged photoreceptor nuclei using previously described method by Ma J. and Weake V.M., J Vis Exp 2014 with minor modifications: nuclei were washed with PBS (supplemented to final salt concentration of 300 mM NaCl) following affinity purification.
Libraries were prepared using NuGen Ovation Drosophila RNA seq system. rRNA was depleted using InDA-C technology.

value: head

tag: biological replicate (paired)

value: adult head

value: 10 day old post eclosion


title: Per3 KO 2

city: Palo Alto

first: Brian

last: Feldman

state: CA

address: SIM1 Lokey Building

institute: Stanford University

data_processing:
The samples were subjected to Illumina HiSeq2000 analysis (Otogenetics, Inc.)
Sequencing analysis generated about 40 million paired-end reads of 100 bp in length for each sample.
Using DNANexus pipeline, the raw RNASeq reads (Fastq files) for each sample are aligned to the reference genome mm9 using STAR v2.4.0 (Dobin et al. 2013) with default parameters.
After alignment, estimation of transcript abundance measures as fragments per kilobase of exon per million aligned fragments (FPKM) values is performed using Cufflinks in the Tuxedo protocol (Trapnell et al. 2012).
For comparative expression analysis,cufflinks.cuffdiff 2.2.1 was used
Genome_build: mm9
Supplementary_files_format_and_content: Individual excel files for each sample with RPKM values

source_name: APCs

growth_protocol: APCs (defined by Sca1+ CD45- CD31- staining) from WT and Per3 KO mice were fresly isolated

extract_protocol:
Samples were immediately lysed for total RNA extraction using RNeasy micro kit (Qiagen).
Libraries of cDNA were generated using oligo d(T) priming

tag: genotype

value: Per3 KO

value: adipose

value: Adipocyte precursor cells

tag: cell markers

tag: tissue source

value: Primary


title: Per3 KO 1

tag: strain


title: U-2 OS Stress Granule RNA replicate 1

description:
SG1R1; SG1R2
RNA was extracted from purified stress granules after arsenite stress

source_name: U-2 OS Stress Granule RNA

tag: cell line


title: WT day 10 pre2

tag: age


title: U-2 OS Stress Granule RNA replicate 2

description:
SG2R1; SG2R2
RNA was extracted from purified stress granules after arsenite stress

tag: cell type


title: WT 2

value: wildtype


title: WT day 10 post3


title: WT day 10 pre1


title: Kc167_mapping reads

description: mapping of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations by iPCR, paired-end reads

source_name: Kc167_mapping reads

value: drosophila melanogaster dorsal closure stage embryonal cell line


title: WT day 10 post1


title: WT day 10 post2


title: cDNA reads, Gal4-HP1a, repl 1

description:
4453_3_plb032_Gal4HP1_r1_cDNA_TTAGGC_S4_L003
cDNA_Gal4HP1_r1
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-HP1a, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2


title: Mouse 3_control ear

city: Frederick

first: Vladimir

last: Majerciak

state: MD

address: 1050 Boyles Street

department: National Cancer Institute

institute: NIH

data_processing:
Illumina RTA 1.18.64 software used for basecalling and Bcl2fastq 1.8.4 for demultiplexed allowing 1 mismatch.
Sequenced reads were trimmed for adaptor sequence, then mapped to circularly permuted MmuPV1 genome using STAR 2.4.2a with default parameters
Reads from antisense transcripts were selected from the bam files
Bedgraphs were calculated by bedtools (v2.25.0) with parameters genomecov -bg -split
Note that our raw data contains only viral mapped reads.
Genome_build: MmupV1 (NC_014326; GI:301173443) with start site at nt 7088
Supplementary_files_format_and_content: bedgraph

organism: Mus musculus papillomavirus type 1

source_name: normal tissue

growth_protocol: The tissues were observed 6 months for tumor formation after virus innoculation.

extract_protocol:
Total RNA from frozen tissues was extracted after homogenization using TriPure Isolation reagent (Roche) and treated with TURBO DNA-free™ Kit (Thermo Fisher Scientific).
cDNA libraries were prepared on ribo-depleted total RNA using Illumina Stranded Total RNA (Illumina, RS-122-2201, San Diego, CA) protocol with TruSeq V4 chemistry and sequenced in the Sequencing Facility of NCI on Illumina HiSeq 2500 with 2×125 nts modality and depth of 100 million reads per sample.

value: Ear (Control)

tag: mouse source

value: Mouse 3


title: WT day 40 rep2

description: htseq_weake_aging.csv column: 40_1

data_processing:
Sanger / Illumina 1.9 used for basecalling.
Paired-end sequenced reads were trimmed using Trimmomatic with settings -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignment to Ensemble Drosophila genome release 86 using Tophat with commands  --library-type fr-secondstrand --max-intron-length 141628 --mate-inner-dist 150 -p 8 --GTF
Sorting by read name using samtools sort with command -n
Read counting using HTSeq with commands --stranded=yes --format=bam
Differential expression analysis and counts per million (CPM) calculations done using edgeR
genome build: BDGP6
processed data files format and content: Comma separated value (CSV) file of raw and filtered gene counts, and normalized filtered counts (cpm) for each sample.

source_name: WT day 40

value: WT

value: 40 day old post eclosion


title: WT day 40 rep3

description: htseq_weake_aging.csv column: 40_2

value: photoreceptor neurons


title: WT day 30 rep1

description: htseq_weake_aging.csv column: 30_0

source_name: WT day 30

value: adult retina


title: WT day 30 rep2

description: htseq_weake_aging.csv column: 30_1

value: 30 day old post eclosion


title: WT day 25 rep3

description: htseq_weake_aging.csv column: 25_2

source_name: WT day 25

value: 25 day old post eclosion

value: male


title: U-2 OS Stress Granule RNA replicate 3

description:
SG3R1; SG3R2
RNA was extracted from purified stress granules after arsenite stress

value: osteosarcoma (OS) cells

tag: genotype/variation

value: arsenite stress

value: Stress granule RNA purification


title: Mouse 2_control ear

value: Mouse 2


title: Mouse 3_muzzle

source_name: warts

value: Muzzle


title: Mouse 3_tail

value: Tail


title: WT day 25 rep2

description: htseq_weake_aging.csv column: 25_1


title: WT 1

value: wildtype

value: adipose

value: Adipocyte precursor cells

value: Primary


title: cDNA reads, Gal4-ACF1, repl 1

description:
4453_1_pAS05_Gal4Acf1_r1_cDNA_ATCACG_S2_L003
cDNA_Gal4Acf1_r1
processed data: TRIP_ACF1.csv
cDNA reads  of Kc167 TRIP pool with 5xGal4UAS-pMT-GFP reporter integrations transfected with Gal4DBD-ACF1, sorted for transfected cells and collected by two days after transfection. 2.5 % RNA spike-in of independent pool was added based on cell counts. Replicate 1 of 2

value: drosophila melanogaster dorsal closure stage embryonal cell line


title: Mouse 3_ear

value: Ear

value: Mouse 3


title: WT day 25 rep1

description: htseq_weake_aging.csv column: 25_0

value: WT

value: photoreceptor neurons

value: adult retina


title: Mouse 2_muzzle


title: Mouse 2_tail


title: HP_M_2

first: Hongwei

last: ZHAO

address: No.17 Tsinghua East Road, Haidian District

department: Food Science and Nutritional Engineering

institute: China Agricultural University

data_processing:
Illumina Hiseq 2000 platform for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  S288C whole genome using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: yeast strain S288C
Supplementary_files_format_and_content: readcount.txt: total gene reacounts for each sample
Supplementary_files_format_and_content: rpkm.stat.txt: gene numbers at different expression abundance
Supplementary_files_format_and_content: rpkm.txt: gene expression abundance for each sample

source_name: S. cerevisiae BY4741 mutation

growth_protocol: the two strains were grown in SC-Ura medium with or without H2O2 and harvested at mid-exponential phase

extract_protocol:
Total RNA were isolated using RNA extraction kit. RNA quantification and qualification were also detected.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: media

value: without H2O2

tag: phenotype

value: improved oxidation stress tolerance

tag: growth phase

value: mid-exponential phase

value: mutation strain


title: HP_C_2

source_name: S. cerevisiae BY4741

value: with H2O2

value: control

value: control strain


title: HP_M_1


title: nHP_C_2


title: HP_C_1


title: Mouse 2_ear

tag: tissue

value: Mouse 2


title: Mouse 1_control ear

value: Ear (Control)

value: Mouse 1


title: nHP_C_1


title: WT day 20 rep3

description: htseq_weake_aging.csv column: 20_2

source_name: WT day 20

value: 20 day old post eclosion

value: male


title: WT day 10 rep3

description: htseq_weake_aging.csv column: 10_2

source_name: WT day 10

value: 10 day old post eclosion


title: Mouse 1_muzzle

value: Muzzle


title: nHP_M_2


title: WT day 10 rep2

description: htseq_weake_aging.csv column: 10_1

value: WT


title: WT day 20 rep1

description: htseq_weake_aging.csv column: 20_0

value: photoreceptor neurons


title: WT day 10 rep1

description: htseq_weake_aging.csv column: 10_0

value: adult retina


title: Mouse 1_ear

value: Ear


title: WT day 40 rep1

description: htseq_weake_aging.csv column: 40_0

value: 40 day old post eclosion


title: nHP_M_1

value: without H2O2

value: improved oxidation stress tolerance

value: mid-exponential phase


title: Mouse 1_tail

value: Tail


title: WT_2_NET_Seq_IP

status: Public on Nov 09 2017

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
NET_Seq_pombe.txt
library strategy: NET-seq
nascent RNA

data_processing:
After trimming of the 5’-adapter, reads were uniquely mapped to the reference genome (ASM294v2.30) using version 0.12.8 of Bowtie (Langmead et al. 2009), with a tolerance of 2 mismatches.
Bioinformatics analyses used reads uniquely mapped on the reference genome.
Data were normalized on the total number of uniquely mapped reads.
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUTs) in each sample.

organism: Schizosaccharomyces pombe

source_name: Yeast cells

extract_protocol:
NET-Seq analysis was performed from two biological replicates of strain YAM2492 (rpb3-flag). Libraries were constructed as previously described (Churchman and Weissman 2011; Churchman and Weissman 2012; Marquardt et al. 2014), starting from 1L of exponentially growing (OD595 0.7-0.8) cells. RNAPII was immunoprecipitated using anti-FLAG M2 affinity gel (Sigma), then recovered upon two successive elution steps using FLAG peptide (Sigma). Ligation of DNA 3’-linker was performed from 2-3 µg of purified nascent RNA (ie co-immunoprecipitated with RNAPII; IP samples) and total RNA (input samples). Ligated RNAs were then submitted to alkaline fragmentation for 20 minutes at 95°C. Single-end sequencing (50 nt) of the libraries was performed on a HiSeq 2500 sequencer.
NET-Seq is a sequencing of 3' end of nascent transcript produced by RNA Polymerase II. In this protocol, transcribing RNA Pol II is isolated, then nascent transcripts are purified and used to construct libraries, using a non-standard protocol described by Weismann's lab. These samples are called "IP" (as for ChIP). "Input" are control libraries constructed from the same biological samples, using the very same control but without purification of RNA Pol II. So they are similar to "total" RNA libraries, but constructed using the same protocol as IP, for comparison.

value: YAM2492 (Rpb3-flag) strain

tag: biological replicate

tag: sample type

value: IP


title: WT day 20 rep2

description: htseq_weake_aging.csv column: 20_1

tag: Sex


title: X63/0_cell_non-treated

city: Sendai

first: Mitsuyo

last: Matsumoto

address: 2-1 Seiryo-machi Aoba-ku

department: Biochemistry

country: Japan

institute: Tohoku university school of medicine

description: none - IonXpressRNA_015_ME--26-RNAseq.v3.OT2 (single) (GE) - RPKM

data_processing:
Obtained fastq file data was analyzed by using  the CLC Workbench software (ver. 7.5.1). As parameter, mapping type was used ‘Map to gene region only (fast)’ and the setting was used default setting (nucleotide mismatch cost = 2; insertion cost = 3; deletion cost = 3; similarity fraction = 0.8; Length fraction = 0.8).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix data containing RPKM: Out put file from "data processing step"

growth_protocol: Cells were maintained in Iscov's modified Dulbecco's medium (IMDM, Gibco-BRL) supplemented with 10% fetal bovine serum, penicillin (100 U/ml), streptomycin (0.1 mg/ml) and 2-mercaptoethanol (50 µM).

extract_protocol:
The cells were harvested by centrifugation, and the total RNA was isolated using a RNeasy Plus Mini kit (QIAGEN) following the instruction manual. Five microgram of total RNA was treated using a GeneRead rRNA Depletion kit (Qiagen) for remove Ribosomal RNA (rRNA) and an RNeasy MiniElute kit (Qiagen) for cleanup. One hundred ng of rRNA-depleted RNA was incubated at 95 ºC for 10 min for fragmentation and was purified by Magnetic Beads Cleanup Module (Life Technologies).
The library was constructed with an RNA-seq library kit ver. 2 (Life Technologies) on ABI library builder (Life Technologies) and were barcoded with Ion Xpress RNA-seq BC primer (Life Technologies, 16 PCR cycles). Barcoded library fragment with the size range of 100-200 bp was selected with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). The emulsion PCR was performed on the OneTouch system using an Ion P1 OT2 200 kit (Life Technologies) to amplify single library fragments onto microbeads and sequencing was performed on an Ion Proton system using the P1 v3 chip (Life Technologies).

treatment_protocol: A 0.2 M stock solution of cycloleucine (Sigma-Aldrich) dissolved in the culture medium was added to the X63/0 cell culture at the final concentration of 30 mM. Three hours later, the cells were harvested for RNA isolation.

value: plasmacytoma line

tag: treated with

value: none (untreated)


title: WT_1_NET_Seq_IP


title: X63/0_cell_cycloleucine-treated

description: cyclo. - IonXpressRNA_016_ME--26-RNAseq.v3.OT2 (single) (GE) - RPKM

value: 30 mM cycloleucine


title: H3K27ac_F2_Chipseq_6D122 [re-analysis]

city: Saint Lucia, Brisbane

first: Tony

last: Vuocolo

state: Queensland

address: 306 Carmody Road

country: Australia

institute: CSIRO

description:
processed data file:
H3K27ac_fdr10_two_replicates.bed

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then each sample individually mapped to  the unmasked OARv3.1.74  sheep genome using the NGS core tool mapping application in CLCBIO (mapping parameters: length fraction =0.7; similarity fraction =0.8; penalties, mismatch =2, insertion =3, deletion =3). H3K27ac samples that had multiple runs on the sequencer were independently merged for each sample and these merged data for each sample were mapped to the genome. Data for each independent sequence run (i.e. not merged) is provided.
Peak calling comparing the H3K4me3 or H3K27ac ChiP-Seq versus the input control was performed using MACS (Zhang et al. 2008). Only peaks found in both replicates per chromatin mark, either H3K4me3 or H3K27ac, were further considered. For H3K4me3 there were 16098 peaks with a FDR 0.1%, whereas for H3K27ac there were 35622 peaks with 1% FDR
Genome_build: OARv3.1
Supplementary_files_format_and_content: 1) xls out of MACS peak calling presenting peak location chr, start, end, length, summit, tags, 10 log(pvalue),fold enrichment, FDR(%) ; 2) bed format showing H3K27ac and H3K4me3 peaks found in both replicates and used in the analysis

organism: Ovis aries

source_name: perirenal adipose_H3K27ac

growth_protocol: Tissues for this study were provided by Janna L Morrison and Isabella C McMillen from Sansom Institute for Health Research, The University of South Australia, Adelaide, 5001, SA, Australia.  All procedures involving animals were carried out with approval from the University of Adelaide Animal Ethics Committee.  Animals were maintained on 100% maintenance energy requirement diets and  cared for humanely as a research flock according to strict animal ethics guidelines. The  ewes for the fetal samples were housed from 110 dpc (days post conception (dpc); term, 150 d) in pens for two weeks before sampling. The pregnant ewes were maintained on a diet that provided 100% of their maintenance energy requirements. Three pregnant ewes were humanely euthanased with an intravenous overdose of sodium pentobarbitone (8.2 g Lethobarb, Virbac Pty ltd, Peakhurst, NSW, Australia) and the uterus removed and fetuses tissue collected at 132±1 dpc.

extract_protocol:
Perirenal adipose tissue was removed from the animals within 10 minutes of euthanasia, flash frozen in liquid nitrogen, stored on dry ice and then stored at -80 o Celcius.  ChIP DNA was isolated briefly as follows:  Frozen tissue was gently pulverised under liquid nitrogen and homogenised in a hand held glass homogeniser in nuclei extraction buffer and nuclei isolated by centrifugation. The isolated chromatin was subsequently treated with micrococcal nuclease and soluble chromatin isolated by mild sonication and centrifugation yielding a relatively homogeneous DNA fragment size of ~ 150bp.  A portion of this isolated soluble chromatin was stored away for each sample and pooled according to its respective group and used as the Input DNA for the INPUT DNA Fetal control libraries.  The remainder of the isolated soluble chromatin  was pre-cleared with Protein A-Sepharose / salmon sperm DNA (Millipore, USA) and then subjected to immunoprecipitation using 10ug of  antibodies specific to, H3K27me3 or H3K27ac or H3K4me3.  Immune complexes were recovered by incubation with Protein A-Sepharose, buffer washes and the DNA- histone protein complexes released  using 1% SDS, 0.1 M NaHCO3, treated with proteinase K, extracted with TE-saturated phenol/chloroform (1:1) and the DNA purified using Minielute DNA columns (Qiagen). The purified DNA (20-100 ng) was quantified using Quant-IT PicoGreen and  validated for purity and size using a High Sensitivity DNA chip run on an Agilent 2100 Bioanalyser (Agilent Technologies).
Illumina TruSeq ChIP-Seq Sample Prep Kit  was used according to Illumina recommendations with 10ng  of isolated  immuno-purified nucleosomes to generate single end read libraries for sequencing.
ChIP-Seq  50 bp single end read libraries for the samples were run on either an Illumina GA11X or HiSeq20000 sequencing platform.  Input DNA libraries was  run independently on a single flow cell per library on an Illumina GA11X sequencer . H3K27ac and H3K4me3  were run randomly 2 or 4/flowcell on 5 flowcells of an Illumina HiSEQ2000 sequencer.

treatment_protocol: No treatment was applied to the  animals.

tag: breed

value: pure bred merino

tag: genotype

value: wild type

tag: developmental stage

value: 132 day old fetus

value: perirenal adipose tissue

tag: chip antibody

value: H3K27ac (Abcam ab4729)

tag: molecule subtype

value: chromatin immunoprecipitated nucleosomal DNA


title: H3K4me3_F2_Chipseq_6D122 [re-analysis]

description:
processed data file:
H3K4me3_fdr1_two_replicates.bed

source_name: perirenal adipose_H3K4me3

value: H3K4me3 (Abcam ab8580)


title: H3K27ac_F1_ChIPseq_6D1159 [re-analysis]


title: H3K4me3_F1_ChIPseq_6D1159 [re-analysis]


title: WT_1_NET_Seq_IN

value: Input


title: WT_2_H3K14ac_ChIP_IP

description: processed data file: ChIP_pombe.txt

data_processing:
Reads were uniquely mapped to the S. pombe reference genome (ASM294v2.30) using version 2.1.0 of Bowtie2, with a tolerance of 1 mismatch in seed alignment.
Bioinformatics analyses used reads uniquely mapped on the reference genome.
Tags densities were normalized on the total number of uniquely mapped reads.
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUTs) in each sample.

extract_protocol:
ChIP-Seq analysis was performed from two biological replicates of the YAM2394 (wild-type) strain. Exponentially growing cells were fixed for 10 minutes at room temperature using formaldehyde (1% final concentration). Cross-link was stopped by addition of glycine to 0.4 M final concentration. Antibodies used were ab1791 (Abcam) for histone H3, 05-1355 (Millipore) for acetyl-H4 (Lys5/8/12/16) and 07-353 (Millipore) for acetyl-H3 (Lys14).
Libraries were prepared from 5 ng of “input” or “IP” DNA using the TruSeq ChIP Sample Preparation Kit (Illumina). Single-end sequencing (50 nt) was performed on a HiSeq 2500 sequencer.

value: YAM2394 wild-type

tag: antibody

value: H3K14ac (07-353 Millipore)


title: WT_1_H3_ChIP_IP

description: processed data file: ChIP_pombe.txt

value: H3 (ab1791 Abcam)


title: WT_1_ChIP_IN

description: processed data file: ChIP_pombe.txt


title: WT_2_H4ac_ChIP_IP

description: processed data file: ChIP_pombe.txt

value: H4ac (05-1355 Millipore)


title: WT_1_H3K14ac_ChIP_IP

description: processed data file: ChIP_pombe.txt


title: WT_2_ChIP_IN

description: processed data file: ChIP_pombe.txt


title: WT_1_H4ac_ChIP_IP

description: processed data file: ChIP_pombe.txt


title: WT_2_H3_ChIP_IP

description: processed data file: ChIP_pombe.txt


title: exo2_1_Total_RNA

description: Biological replicate 1

data_processing:
Reads were mapped to the S. pombe reference genome (ASM294v2.30) using version 2.0.6 of TopHat, with a tolerance of 3 mismatches and a maximum size for introns 2 Kb.
All bioinformatics analyses used reads uniquely mapped on the reference genome.
Tags densities were normalized on snoRNAs, that are insensitive to Exo2.
Supplementary_files_format_and_content: a single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUTs) in each sample.

extract_protocol:
Total RNA was extracted using standard hot phenol procedure. rRNAs were depleted from total RNA using the RiboMinus Eukaryote System v2 (Life Technologies).
Strand-specific total RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina), starting from 125 ng of rRNA-depleted RNA, and paired-end sequenced (2x50 nt) on a HiSeq 2500 sequencer.

tag: strain


title: WT_1_Total_RNA

description: Biological replicate 1

value: wild-type


title: WT_2_Total_RNA

description: Biological replicate 2


title: B10.2

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were mapped to mm9/rn5  whole genome using tophat v2.0.11 with parameters -p 8 -r 100.
Gene Based read counts were obtained with HTSeq counts module v0.5.3p9
Genome_build: mm9,rn5
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Bridge Day 10 single nerve M2

extract_protocol:
RNA was isolated by using RNAeasy Plus Micro Kit (Qiagen) and Schwann cells sorted based on tdTomato epxression
RNA sequencing libraries were prepared according to the Smart-seq2 protocol (Picelli et al., 2013)

tag: cell type

value: Schwann cells

value: tdTomato+

tag: biological repeat/animal id


title: B10.3

source_name: Bridge Day 10 single nerve M3


title: B8.2

source_name: Bridge Day 8 single nerve M2


title: B8.0

source_name: Bridge Day 8 single nerve M0


title: B10.1

source_name: Bridge Day 10 single nerve M0


title: B6.3

source_name: Bridge Day 6 single nerve M3


title: B8.1

source_name: Bridge Day 8 single nerve M1


title: WT_2_NET_Seq_IN

tag: genotype/variation

value: YAM2492 (Rpb3-flag) strain


title: B6.1

source_name: Bridge Day 6 single nerve M1


title: B6.0

source_name: Bridge Day 6 single nerve M0


title: T8

organism: Rattus norvegicus

source_name: cultured rat SC+tgfb R3


title: T2

source_name: cultured rat SC+tgfb R1


title: exo2_Small_RNA

description: Small RNA

data_processing:
After removal of adapter sequences using cutadapt, reads were uniquely mapped to the reference genome (ASM294v2.30) using the version 0.12.8 of Bowtie, with a tolerance of 3 mismatches.
Bioinformatics analyses used reads uniquely mapped on the reference genome.
Tags densities were normalized on the total number of uniquely mapped reads.
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUTs) in each sample

extract_protocol:
Total RNA was extracted from exponentially growing YAM2394 (wild-type) and YAM2397 (exo2-delta) cells of S. pombe using standard hot phenol procedure.
Libraries were constructed according to the Small RNA Sample Preparation Guide (Illumina) using 10-40 nt small RNAs purified from total RNA on 15% TBE-urea PAGE. Single-end sequencing (40 nt) of libraries was performed on a Genome Analyzer IIx (Illumina).

value: YAM2397 exo2-delta


title: WT_Small_RNA

description: Small RNA


title: T5

source_name: cultured rat SC+tgfb R2


title: C7

source_name: cultured rat SC R3


title: exo2_2_Total_RNA

description: Biological replicate 2


title: C1

source_name: cultured rat SC R1


title: WT-H3K36me3-ChIP

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Peaks were called using MACS2 v2.1.0, with the input library as background.
All reads were mapped to the mouse genome (mm10) using BOWTIE (v2.2.9) to yield unique alignments and only uniquely matching reads were retained. Redundant reads were also filtered out to minimize potential PCR bias.
Quality control checks on raw sequence data by FastQC.
Peaks were called using MACS2 with the following setting: FDR=10%,  p-value <= 10-5.Fold changes for H3K36me3 peaks were obtained from MACS2 output.
Each high confidence peak was annotated to genetic regions using the BedTools package and fold enrichment was calculated from the ratio between observed peaks per region and expected number of peaks normalized by average region size.
Genome_build: mm10
Supplementary_files_format_and_content: To extract signal from background noise, we determined ChIP enriched regions using the Model-based Analysis of ChIP-Seq (MACS) which was developed by X. Shirley Liu from Harvard University. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. It also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS was run using the recommend settings for transcription factor (TF) like binding. False Discovery Rate (FDR) cut off was set at an initial value of 0.1(10%) for all peaks. The tag density was normalized to 1x10^7 tags and further displayed and interrogated using the UCSC genome browser. Peak overlaps were processed with ChIPseek.

source_name: brain

growth_protocol: E13 forebrain was used to ChIP

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Briefly, E13 neural progenitor cells were crosslinked with 1% formaldehyde solution (50 mM, HEPES-KOH, pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1% formaldehyde) for 10 minutes at room temperature, and the reaction was quenched with glycine. After washing two times with ice-cold PBS, cells were resuspending the cells in lysis buffer 1(50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x protease inhibitors) for 10 minutes at 4℃. Nuclei were isolated at at 4000rpm for 5 minutes at 4°C and resuspended in lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x protease inhibitors), and then rocked gently at room temperature for 10 minutes. Nuclei was sonicated in lysis buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, 1x Protease Inhibitor) using a Scientz-IID sonicator. Chromatin was immunoprecipitated overnight at 4℃with 50 μl Protein A bead (Dynabeads, Invitrogen) pre-coupled with 10 μg appropriate antibodies. Beads were washed three times with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, Tris-HCl, pH 8.1) and three times with high-salt buffer buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, Tris-HCl, pH 8.1). After reverse crosslinking was performed, DNA was eluted and purified using a DNA purification kit (Tiangen).

tag: strain background

value: brain

value: neural progenitor cells


title: B4.1

source_name: Bridge Day 4 single nerve M1


title: H2A.z1cKO-H3K36me3-ChIP


title: WT-input

description: WT-input DNA

value: wild type


title: H2A.z1cKO-input

description: H2A.z1cKO-input DNA


title: D10.3

source_name: Distal Day 10 single nerve M3


title: D10.1

source_name: Distal Day 10 single nerve M1


title: D10.0

source_name: Distal Day 10 single nerve M0


title: Fetal_Input_Control [re-analysis]

source_name: Fetal Input Sample

value: pure bred merino

value: 132 day old fetus

value: perirenal adipose tissue

value: nucleosomal DNA


title: B4.2

source_name: Bridge Day 4 single nerve M2


title: D8.1

source_name: Distal Day 8 single nerve M1


title: Ezh2 deficient activated CD8 T cells

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Tophat2
Cuffdiff v2.2.1: cuffdiff -u
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: T cells

growth_protocol: Mouse CD8 T cells were cultured in suspension in IMDM medium supplemented with 10% fetal bovine serum and antibiotics in 5% CO2 at 37°C.

extract_protocol:
T cells were collected before and after culture. The RNA was extracted using the miRNeasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T cells were activated with CD3 Ab (2ug/ml) and CD28 Ab (2ug/ml)

tag: condition

value: CD3/CD28 Ab activated d3 T


title: Ezh2 deficient naive CD8 T cells

value: CD44lo naïve T


title: Wild type naïve CD8 T cells


title: Wild type activated CD8 T cells


title: D8.0

source_name: Distal Day 8 single nerve M0


title: Primary T cells - Donor 266 - AKTi

city: Charleston

first: Chrystal

middle: M

last: Paulos

address: 173 Ashley Avenue

institute: Medical University of South Carolina

description: Paired-end RNASeq data

data_processing:
Acquired gzipp'ed FASTQ files from the sequencing provider
B37 transcripts (http://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.75.cdna.all.fa.gz) were indexed according to the user manual: "kallisto index -i transcripts.idx transcripts.fasta.gz"
Kallisto (v0.42.3) was ran on each FASTQ pair as recommended by the user manual: "kallisto quant -i transcripts.idx -o output -b 100 <(gzcat reads_1.fastq.gz) <(gzcat reads_2.fastq.gz)"
Genome_build: B37 (GChr37)
Supplementary_files_format_and_content: Tab-delimeted values corrresponding to estimated transcript-level quantification per transcript per sample (default kallisto output: abundance.tsv)

source_name: Human peripheral blood

growth_protocol: CD3+ T cells derived from normal donor peripheral blood were grown ex vivo for seven days under vehicle (DMSO and IL-2) or drug (1uM AKTi and 10uM CAL-101) before processing for mRNA (2-4e6 cells/donor)

extract_protocol:
mRNA extracted and libraries prepared using Illumina TruSeq RNA V2 kit
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. cDNA libraries were denatured and diluted to get clonally clustered onto the sequencing flow cell using the c-BOT (Illumina) Cluster Generation Station and Hiseq Rapid Paired-End Cluster Kit v2 (Illumina). The clustered flow cell then sequenced on the Illumina HiSeq2500 Sequencing System using the Hiseq Rapid SBS Kit V2 (Illumina).

tag: tissue

value: Peripheral blood

value: CD3+ Lymphocytes

tag: source

value: Primary cells

tag: treatment

value: AKTi

tag: donor


title: Primary T cells - Donor 265 - CAL101

description: Paired-end RNASeq data


title: Primary T cells - Donor 265 - Vehicle

description: Paired-end RNASeq data

value: Vehicle


title: Primary T cells - Donor 265 - AKTi

description: Paired-end RNASeq data


title: Primary T cells - Donor 266 - CAL101

description: Paired-end RNASeq data


title: C4

source_name: cultured rat SC R2

value: Schwann cells


title: D8.2

source_name: Distal Day 8 single nerve M2

value: tdTomato+


title: Primary T cells - Donor 266 - Vehicle

description: Paired-end RNASeq data


title: D6.3

source_name: Distal Day 6 single nerve M3


title: B4.0

source_name: Bridge Day 4 single nerve M0


title: Primary T cells - Donor 264 - Vehicle

description: Paired-end RNASeq data


title: Primary T cells - Donor 264 - CAL101

description: Paired-end RNASeq data


title: D6.1

source_name: Distal Day 6 single nerve M1


title: Primary T cells - Donor 264 - AKTi

description: Paired-end RNASeq data


title: EWS/FLI rep4

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description: Processed data file: FLI_peaks.xls

data_processing:
Basecalls performed using CASAVA.
ChIP-seq reads were aligned to the hg19 genome assembly using Novoalign.
Reads aligned to multiple locations were filtered.
Peaks were called using MACS2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FLI_peaks.xls: Excel file contains peaks location, length, height, p-value and fold-enrichment calculated using MACS2 with FDR cut-off of 5%.

source_name: Ewing sarcoma cells, FLI ChIP

growth_protocol: A673 Ewing sarcoma cells were grown to 95% confluence in 15cm culture dishes in DMEM medium supplemented with FBS and Na-Pyruvate.

extract_protocol:
A673 cells were fixed with 1% Formaldehyde in PBS for 8 minutes and nuclear extract was fragmented to a size range of 200-700 bases with a Misonix Sonicator. Solubilized chromatin was immunoprecipitated with antibodies against FLI (Santa Cruz, sc-356X Santa Cruz Biotechnology, Inc.). Antibody-chromatin complexes were pulled down with M-280 sheep anti-rabbit IgG Dynabeads (Thermo Scientific), washed and then eluted. After crosslink reversal, RNase A and Proteinase K treatment, immunoprecipitated DNA was extracted with the Mini-Elute PCR purification kit (Qiagen).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Qiagen). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 platform following the manufacturer's protocols.

tag: cell line

value: patient-derived Ewing sarcoma cells

tag: passage

value: anti-FLI (sc-356X Santa Cruz Biotechnology, Inc)


title: EWS/FLI rep2

description: Processed data file: FLI_peaks.xls


title: D6.0

source_name: Distal Day 6 single nerve M0

tag: genotype


title: EWS/FLI rep3

description: Processed data file: FLI_peaks.xls


title: Input DNA rep4

description: Processed data file: FLI_peaks.xls

source_name: Ewing sarcoma cells, input


title: D4.2

source_name: Distal Day 4 single nerve M2


title: D4.1

source_name: Distal Day 4 single nerve M1


title: Input DNA rep2

description: Processed data file: FLI_peaks.xls


title: D2.4

source_name: Distal Day 2 single nerve M4


title: D4.0

source_name: Distal Day 4 single nerve M0


title: D2.0

source_name: Distal Day 2 single nerve M0


title: Healthy_NOTNV75LH2E

city: Tartu

first: Viktorija

last: Kukushkina

address: Riia 23b

country: Estonia

institute: Estonian Genome Center, University of Tartu

data_processing:
Data quality was checked with fastQC v.0.11.3 before and after preprocessing step.
Adapter removal and trimming with Trimmomatic tool v. 0.32. Parameters:  PE, -phred33,ILLUMINACLIP:/gpfs/depoofs/a73038/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa:2:30:10:8:'true', LEADING:3, TRAILING:3, HEADCROP:11, SLIDINGWINDOW:4:30, MINLEN:36.
Low quality reads removal was made with fastq_quality_filter from Fastx toolkit v. 0.0.13. Parameters: -Q33, -q 30, -p 50
Good quality reads were mapped using TopHat v. 2.0.11. Parameters: --bowtie1, -p 12, --mate-inner-dist 300, --mate-std-dev 100, --library-type fr-firststrand. Bam files name sorted with picard-tools-1.102 SortSam script. Parameters: SO=queryname.
Raw read counts were counted with HTSeq-count v.0.6.1. Parameters: --format=bam, --stranded=reverse, --type=exon, --idattr=gene_id. Annotation GTF version: Ensembl v.75
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count tab delimited matrix, edgeR CountsPerMillion comma delimited matrix.

source_name: Endometrium

extract_protocol:
Tissue samples were extracted with Pipelle® catheters under sterile conditions from 23-36-year-old  healthy and IVF women in with BMI of 19-29 Kg/m2, rinsed with PBS and processed immediately or frozen at -80 °C.
Up to 30 mg of the tissue was homogenized in the presence of QIAzol reagent (Qiagen) and processed using miRNeasy Mini kit (Qiagen), following manufacturer's protocol. miRNA content was decreased using Qiagen's MinElute protocol. Purified RNA quality was assigned with Bioanalyzer (Agilent Technologies).cDNA libraries were generated from ~1 μg of endometrial total RNA using Illumina TruSeq Stranded technology (Illumina), followed by cDNA quality control with Bioanalyzer

tag: gender

value: Female

value: Endometrium

tag: receptivity time-point

tag: country of origin

value: Estonia

tag: tissue state

value: Healthy

tag: sequencing batch


title: Input DNA rep3

description: Processed data file: FLI_peaks.xls

tag: cell type

tag: chip antibody


title: Healthy_ERTK11LH2E


title: Input DNA rep1

description: Processed data file: FLI_peaks.xls


title: D2.3

source_name: Distal Day 2 single nerve M3

tag: biological repeat/animal id


title: Healthy_NOTNV48LH8E


title: Healthy_NOTNV47LH8E


title: panCBFB_total

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: Pan-Cbfb ChIP-seq of total thymocytes

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumlated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file format of mapped reads per kilobase

source_name: Adult total thymocyte

growth_protocol: Lineage negative liver cells were derived from E12.5 fetus and total thymocytes were derived from 4-6 wk old mice.

extract_protocol: Libraries were prepared according to NEB's instructions accompanying the NEBNext ChIP-seq Library prep Kit (E6240). The purified library was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were subjected to crosslinking and nuclei were lysed. Nuclei sample was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON). Sonicated chromatin was incubated overnight at 4 °C with magnetic beads-attached anti-Cbfb1, anti-Cbfb2, or pan-Cbfb polyclonal antibodies that were generated in our laboratory. Immunoprecipitated DNA was then purified.

value: Adult total thymocyte

tag: antibody

value: pan-Cbfb


title: Healthy_NOTNV48LH2E


title: CBFB1_total

description: Cbfb1 ChIP-seq of total thymocytes


title: CLs treated-1

city: Shanghai

first: Li

last: Ying

address: Changhai Road No. 225

department: Department of Pharmacy

institute: Eastern Hepatobiliary Surgery Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
Count counting were calculated and adjusted using HTseq Version 0.6.1
Genome_build: hg19_GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: HepG2 cells

growth_protocol: HepG2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) containing 10% Fetal bovine Serum (FBS, Hyclone), 100U/ml penicillin and 100μg/ml streptomycin and maintained at 37oC in a humidified 5% carbon dioxide (CO2) atmosphere.

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen). The RNA quality was checked by Bioanalyzer 2200
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: HepG2 cells were seeded in 6-well plates at a density of 1.25×105 cells/well and incubated for 24 h. In CLs treated group, cells were then exposed to 120μM CLs for another 24h.

value: HepG2 liver hepatocellular cells

tag: agent

value: CLs


title: D1.1

source_name: Distal Day 1 single nerve M1


title: CLs treated-3


title: panCBFB_Lin_negative

description: Pan-Cbfb ChIP-seq of Lin- FL

source_name: E12.5 lin negative fetal liver cells

value: E12.5 lin negative fetal liver cells


title: Healthy_ERTK11LH8E

tag: tissue


title: CBFB2_total

description: Cbfb2 ChIP-seq of total thymocytes


title: Healthy_NOTNV75LH8E


title: I.5

source_name: Intact single nerve M5


title: D1.0

source_name: Distal Day 1 single nerve M0


title: Control-2

value: control


title: EWS/FLI rep1

description: Processed data file: FLI_peaks.xls


title: Healthy_NOTNV47LH2E


title: Healthy_NOTNV40LH8E


title: Control-3


title: D1.2

source_name: Distal Day 1 single nerve M2


title: CLs treated-2


title: Healthy_NOTNV40LH2E


title: Control-1


title: Healthy_NOTNV25LH8E


title: I.4

source_name: Intact single nerve M4


title: CBFB2_Lin_negative

description: Cbfb2 ChIP-seq of Lin- FL


title: I.1

source_name: Intact single nerve M1


title: Ani6_D6

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

description: Cynomolgus macaque

data_processing:
Base calls generated on a HiSeq 2500 using paired end 2x100bp dual-index format.
Trimmed with FASTX-Toolkit v0.0.14.
Alignment: Tophat v2.1.0 with Bowtie2 v2.2.6.
Count Tables generated with HTSeq v0.5.4.
Genome_build: Macaca_fascicularis_5.0 (GCF_000364345.1)
Supplementary_files_format_and_content: *txt: Tab-delimited text file contains unnormalized count data from HTSeq output.

organism: Macaca fascicularis

source_name: Whole blood, intramuscular 1000PFU, day 6

extract_protocol:
Previously flash-frozen whole blood (250ul) treated with 750ul of Trizol.
PureLink RNA Mini Kit.
TruSeq Stranded Total RNA Library Prep Kit (Illumina) on Silicone G3 Liquid Handling Robot (PerkinElmer).

treatment_protocol: Cynomolgus macaques were infected with Ebola variant Makona at three different doses and three different routes of infection.

value: Whole blood

tag: status

value: Infected

tag: virus

value: EBOV Makona

tag: virus dose

tag: infection route

value: Intramuscular

tag: dpi

tag: animal id


title: Healthy_NOTNV24LH8E

tag: gender


title: primary mouse beta cells_3

city: Pittsburgh

first: Xiangwei

last: Xiao

state: PA

address: 4401 Penn Ave

department: Surgery

institute: Children's Hospital of Pittsburgh

description:
Sample name in processed data: B
Sample 2-3
green cells

data_processing:
Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and Trimmomatic. Reads with a remaining length of fewer than 20bp after trimming were discarded.
Single reads were mapped to the mouse genome (m10) using STAR in a strand specific manner.
Cufflinks was used to determine FPKM levels for each gene from the STAR alignment and was used as input for Cuffdiff.
Pairwise differential expression was quantified using Cuffdiff. Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05.
Genome_build: m10
Supplementary_files_format_and_content: FPKM tracking file contains mean FPKM for cell type. CuffDiff output files contains all differentially expressed genes, P value and adjusted P value.

source_name: primary mouse beta cells

extract_protocol:
Total RNA was extracted from FAC sorted primary mouse cells using Rneasy kit (Qiagen)
Total RNA libraries were generated using Illumina TruSeq Stranded mRNA sample preparation kit.

treatment_protocol: Alpha-cell-derived INS+ cells (yellow cells) were isolated 1 month after AAV-PM infusion from ALX-treated GCG-Cre; R26RTomato; MIP-GFP mice, based on expression of tomato red (alpha-cell lineage) and GFP by flow cytometry. Sorted normal GFP+ beta cells and normal TOM+ alpha cells from GCG-Cre; R26RTomato; MIP-GFP mice without any treatment were used as controls.

value: pancreas

value: primary mouse beta cells

tag: genotype

value: GCG-Cre+/-; R26RTomato+/-; MIP-GFP+/- mice

tag: strain

value: GCG-Cre; R26RTomato; MIP-GFP mice

tag: age

value: 14 week-old


title: CBFB1_Lin_negative

description: Cbfb1 ChIP-seq of Lin- FL


title: primary mouse beta cells_2

description:
Sample name in processed data: B
Sample 2-2
green cells


title: Ani6_D10

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 1000PFU, day 10


title: Ani6_D0

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 1000PFU, day 0

value: Control


title: Healthy_NOTNV25LH2E

value: Female

value: Endometrium

tag: receptivity time-point

tag: country of origin

value: Estonia

tag: tissue state

value: Healthy

tag: sequencing batch


title: reprogrammed mouse beta cells_2

description:
Sample name in processed data: C
Sample 3-2
yellow cells

source_name: reprogrammed mouse beta cells

tag: cell type

value: reprogrammed mouse beta cells


title: Ani6_D3

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 1000PFU, day 3


title: I.0

source_name: Intact single nerve M0

value: Schwann cells

value: tdTomato+

tag: biological repeat/animal id


title: Healthy_NOTNV24LH2E

source_name: Endometrium

tag: tissue


title: D5

source_name: Distal Day 6 pooled nerves M5


title: Ani5_D10

description: Cynomolgus macaque

source_name: Whole blood, ophthalmic 100PFU, day 10

value: Whole blood

tag: status

value: 100 PFU

value: ophthalmic


title: reprogrammed mouse beta cells_1

description:
Sample name in processed data: C
Sample 3-1
yellow cells


title: primary mouse beta cells_1

description:
Sample name in processed data: B
Sample 2-1
green cells


title: Healthy_NOTNV18LH2E


title: I.3

source_name: Intact single nerve M3


title: primary mouse alpha cells_3

description:
Sample name in processed data: A
Sample 1-3
red cells

source_name: primary mouse alpha cells

value: primary mouse alpha cells


title: Ani5_D6

description: Cynomolgus macaque

source_name: Whole blood, ophthalmic 100PFU, day 6

value: Infected

tag: virus

value: EBOV Makona


title: reprogrammed mouse beta cells_3

description:
Sample name in processed data: C
Sample 3-3
yellow cells

value: pancreas

value: GCG-Cre+/-; R26RTomato+/-; MIP-GFP+/- mice


title: D1

source_name: Distal Day 6 pooled nerves M1


title: Healthy_NOTNV16LH8E


title: Healthy_NOTNV16LH2E


title: B5

source_name: Bridge Day 6 pooled nerves M5


title: primary mouse alpha cells_2

description:
Sample name in processed data: A
Sample 1-2
red cells

value: GCG-Cre; R26RTomato; MIP-GFP mice

value: 14 week-old


title: D3

source_name: Distal Day 6 pooled nerves M3


title: Ani5_D0

description: Cynomolgus macaque

source_name: Whole blood, ophthalmic 100PFU, day 0

value: Control

tag: virus dose


title: Ani5_D3

description: Cynomolgus macaque

source_name: Whole blood, ophthalmic 100PFU, day 3

tag: infection route


title: GPRshRNA

city: coralville

first: Wenjie

last: Yu

state: Iowa

address: 512 7th Ave apt 2

institute: The University of Iowa

data_processing:
Raw data were processed and analyzed by Huada Gene (Shenzhen, China) with the typical Illumina analysis software
Sequenced reads were trimmed: 3' adaptor sequence, empty reads, low quality tags and tags with a copy number of 1 were removed. Clean tags were generate for further processing.
Following the protocols published in  't Hoen et al., 2008 and Morrissy et al., 2009, all clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).
Genome_build: NCBI human genome build 36
Supplementary_files_format_and_content: Microsoft Excel 97-2003 Worksheet including raw intensity of gene reads and ratio of GPRshRNA V.S.  NC

extract_protocol:
RNA prep from HT-29 cells
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: genotype/variation

value: GPR126 knockdown


title: NC

value: Scramble


title: Ani4_D11

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 10PFU, day 11

value: 10 PFU

value: Intramuscular

tag: dpi

tag: animal id


title: B3

source_name: Bridge Day 6 pooled nerves M3

value: Schwann cells

tag: genotype


title: Healthy_NOTNV15LH8E

tag: gender

value: Female

value: Endometrium

value: Estonia

value: Healthy


title: D2

source_name: Distal Day 6 pooled nerves M2

value: tdTomato+


title: Healthy_NOTNV09LH8E

tag: receptivity time-point


title: Healthy_NOTNV18LH8E

tag: country of origin


title: Ani4_D10

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 10PFU, day 10

value: Whole blood

value: Infected


title: I5

source_name: Intact pooled nerve M5


title: B2

source_name: Bridge Day 6 pooled nerves M2


title: Healthy_NOTNV09LH2E

source_name: Endometrium

tag: tissue state


title: Ani4_D3

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 10PFU, day 3

value: EBOV Makona


title: primary mouse alpha cells_1

description:
Sample name in processed data: A
Sample 1-1
red cells

value: pancreas

value: primary mouse alpha cells

value: GCG-Cre+/-; R26RTomato+/-; MIP-GFP+/- mice

tag: strain

tag: age


title: Ani4_D6

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 10PFU, day 6


title: B1

source_name: Bridge Day 6 pooled nerves M1

tag: cell type

tag: biological repeat/animal id


title: Healthy_NOTNV15LH2E

tag: tissue

tag: sequencing batch


title: GEK28

city: Porto Alegre

first: Guilherme

last: Cordenonsi da Fonseca

state: RS

address: Av. Bento Gonçalves, 9500

department: Centro de Biotecnologia

country: Brazil

institute: UFRGS

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Oryza sativa

source_name: ASR5 RNAi shoot treated

growth_protocol: Rice seeds were germinated on filter paper for 4 d in the dark at 28°C. The seedlings were grown in hydroponic Baier’s solution (Baier et al., 1995) for 12 d in a growth chamber at 28°C under 12h of light. The hydroponic solution was replaced every 4 d. After 12 d, shoot samples from NT and ASR5-silenced (ASR5_RNAi) rice plants (ssp. Japonica cv. Nipponbare) grown under control conditions or subjected to Al treatment (8h with 450 μM AlCl3 at pH 4.5) were collected and immediately frozen in liquid nitrogen.

extract_protocol: Total RNA was extracted from 100 mg of homogenized shoot tissue from ASR5_RNAi and NT plants using Trizol (Invitrogen, CA, USA) according to the manufacturer’s protocol. The quality of the extracted RNA was evaluated using 1 % agarose gel electrophoresis. Total RNA ([10 lg) was sent to Fasteris SA (Plan-les-Ouates, Switzerland) for processing and shotgun sequencing using an Illumina Hiseq 2000 (Illumina, CO). Four small RNA libraries were constructed: two from shoots of NT seedlings (Al treatment and control)  and another two from shoots of ASR5_RNAi seedlings (Al treatment and control). The libraries were constructed using the following successive steps: acrylamide gel purification of the RNA bands corresponding to 20–30 nt in size; ligation of the 30 and 50 adapters to the RNA in two separate subsequent steps, each followed by acrylamide gel purification; cDNA synthesis followed by acrylamide gel purification; and a final step of polymerase chain reaction (PCR) amplification to generate a cDNA colony template library for Illumina sequencing. All low-quality reads and adapter sequences were removed.

tag: cultivar

value: ssp. Japonica cv. Nipponbare

tag: sample

value: single

value: shoots


title: GEK27

description: small RNA

source_name: ASR5 RNAi shoot control


title: I4

source_name: Intact pooled nerves M4


title: Healthy_NOTNV13LH8E


title: Ani4_D0

description: Cynomolgus macaque

source_name: Whole blood, intramuscular 10PFU, day 0

tag: status

value: Control

tag: virus

tag: virus dose

value: 10 PFU

tag: infection route


title: GEK26

description: small RNA

source_name: shoot treated


title: Healthy_NOTNV13LH2E


title: Healthy_NOTNV12LH8E


title: Ani3_D6

description: Cynomolgus macaque

value: Intramuscular

tag: dpi

tag: animal id


title: I1

source_name: Intact pooled nerves M1

value: Schwann cells

tag: genotype


title: GEK25

description: small RNA

source_name: shoot control


title: I2

source_name: Intact pooled nerves M2


title: E14-LY_rep2

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

description: Otocysts from E14 embryos (treated with LY411575) replicate 2

data_processing:
Alignment: reads were aligned using mm9 assembly as reference genome and Bowtie2 software.
Filtering duplicates: duplicated pairs were removed using Samtools software.
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions.
Visualization: bigWig files were visualized using UCSC Browser
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bigWig format for visualization of nucleosome free signal (fragment lengh < 130 bp)

growth_protocol: Wild-type C57BL/6 mice

extract_protocol:
E10.5 mouse otocysts or E14 mouse cochleae were dissected, tissue was digested with Collagenase (C0130, Sigma, 0.3mg/ml) during 45 minutes at 37ºC and cells were suspended and counted in a Neubauer chamber.
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: LY411575 treatment (University of Dundee, UK, 100nM) was performed overnight on E14 mouse cochlea previous to ATAC-Seq procedure in a DMEM media with 1% FBS with L-glutamine and antibiotics

tag: genotype/variation

value: WT

value: otocysts

tag: developmental stage

tag: treatment


title: E14-LY_rep1

description: Otocysts from E14 embryos (treated with LY411575) replicate 1

tag: strain


title: Ani3_D3

description: Cynomolgus macaque


title: Ani3_D10

description: Cynomolgus macaque


title: E14-WT_rep2

description: Otocysts from E14 embryos (WT) replicate 2

source_name: Otocysts from E14 embryos (WT)

value: control