title: CNS4KO_Treg2

first: Stanislav

last: Dikiy

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

data_processing:
Trim adapter sequences, removed unpaired reads; Trimmomatic v0.36; options: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Align reads to genome; STAR v2.5.4b; options: --runThreadN 6 --runMode alignReads --genomeLoad NoSharedMemory --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outBAMcompression 6 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.06 --outFilterMatchNminOverLread 0.55 --outFilterMatchNmin 30 --alignIntronMax 1 --alignEndsType Local
Sort by name; samtools v1.10; options: sort -@ 4 -n
Fix mate information; samtools v1.10; options: fixmate -rm
Sort by coordinate; samtools v1.10; options: sort -@ 4
Remove duplicate reads; samtools v1.10; options: markdup -l 1500 -r -d 100
Sort by name; samtools v1.10; options: sort -@ 4 -n
Convert bam to bedgraph and scale for library size; bedtools v2.26.0; options bedtools genomecov -bg -scale -g mm10.genome
Convert bedgraph to bigWig; wigToBigWig; options: wigToBigWig -clip mm10.genome
Genome_build: mm10
Supplementary_files_format_and_content: bigWig format: continuous graph of aligned read density across genome (indexed)

source_name: lymph node and spleen

extract_protocol:
Combined protocol for extraction and library preparation, see below
cells were pelleted in a fixed rotor benchtop centrifuge at 500g for 5 minutes at 4°C. Cells were then washed in 1ml cold 1x PBS and pelleted again. Supernatant was aspirated and cells were resuspended in 50µl ice-cold cell lysis buffer (10mM Tris-Cl pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% NP-40) to disrupt plasma membranes. Nuclei were pelleted at 1000g for 10 minutes. Supernatant was aspirated and nuclei were resuspended in 50µl transposition reaction mixture (25µl TD buffer; 2.5µl TDE1; 22.5µl ddH2O; llumina, 20034197). Samples were incubated in a ThermoMixer at 1100rpm for 45 minutes at 42°C. DNA was then purified using a MinElute PCR Purification Kit (QIAGEN, 28004), per manufacturer instructions. DNA was eluted in 10µl buffer EB. Libraries were then barcoded and amplified with NEBNext High-Fidelity Master Mix and primers from (Buenrostro et al., 2013) (50µl reaction with 10µl DNA and 2.5µl of 25µM primers – 1 cycle of 5min at 72°C, 30sec at 98°C; 5 cycles of 10sec at 98°C, 20sec at 63°C, 1min at 72°C). A qPCR on the product determined that an additional 7 cycles (10sec at 98°C, 20sec at 63°C, 1min at 72°C) were required. Library was purified and size selected with AMPure beads (Beckman Coulter, A63881): 45µl of PCR product was incubated with 18µl beads and supernatant was collected (beads bound larger >2000bp fragments). Supernatant (63µl) was then incubated with an additional 63µl of beads for 5 minutes, supernatant was removed, beads were washed 2x with 75% ethanol, and DNA was eluted into 50µl H2O by incubating for 2 minutes.

value: Regulatory T cell

value: lymph node and spleen


title: CNS4KO_Treg1

status: Public on Mar 16 2021

type: SRA

city: La Jolla

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: genotype

tag: cell type

tag: tissue


title: CNS4fl_Treg1


title: RNASeq_WT_1

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

description: RNA-Seq in stomach gland of a wild type mouse

library_source: transcriptomic

data_processing:
The trimmed pair-end reads were aligned to mouse reference genome (GRCm38) with STAR (version 2.4.2a), and gene expression was then quantified using the reads per kilobase per million mapped reads (RPKM) method.
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing the gene expression matrix

molecule: polyA RNA

source_name: stomach gland of a wild type mouse

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

extract_protocol:
The corpus regions of the stomach that have tumors (or analogous region in normal stomachs) were dissected and incubated in 20 mM EDTA for 30 minutes. The glands were then extracted by gently scraping the surface using a glass slide. The glands were washed thoroughly in PBS before downstream application. Isolated epithelial cells were immediately frozen and RNA isolation was conducted using an RNA isolation kit (Qiagen, Cat No. 74104).
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.

value: stomach gland

value: wild type


title: SY10R2

city: Irapuato

first: Octavio

last: Martinez de la Vega

state: Guanajuato

address: km 9.6 Libramiento Norte

department: Unidad de Genómica Avanzada (Langebio)

country: Mexico

institute: Cinvestav

description: Whole fruits of accession Piquin Sonora Yellow at 10 Days After Anthesis. Biological replicate R2.

data_processing:
Total RNA Sample QC. All samples need to pass through the following four steps before library construction: (1) Nanodrop: tests RNA purity (OD260/OD280). (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination. (3) Agilent 2100: checks RNA integrity.
Library Construction. After the QC procedures, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
Library QC and sequencing. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were fed into Illumina NovaSeq 6000 machines for sequencing.
Raw data and quality control. The original raw data from Illumina were transformed to Sequenced Reads by base calling. Raw data were recorded in a FASTQ files. GC content distribution was evaluated. Raw reads were filtered to remove reads containing adapters or reads of low quality.
Mapping to the Capsicum annuum reference genome. For mapping TopHat (v2.0.12) was employed with mismatch parameter set to 2 and other parameters set to defaults. Only filtered reads were used to analyze the mapping status of RNA-seq data to the reference genome. RAW FILES  were created in the binary alignment/map format (".bam").
Genome_build: Capsicum_annuum.Annuum.v.2.0.genome.fa
Supplementary_files_format_and_content: Processed data files are in the cvs format with three columns, 1 - "id" (a unique numeric identifier of each feature), 2 - "Gene.id" (the identifier of the gene or gene feature) and 3 - A column with the same name than the sample which contains the read count for the corresponding feature.

molecule: total RNA

organism: Capsicum annuum

source_name: Piquin Sonora Yellow

growth_protocol: Seeds of 10 Capsicum annuum accessions were surface sterilized with a 70% ethanol solution for 10 s before treatment with a 10% hypochlorite solution for 10 s and six rinses with distilled water. Wild accession seeds were similarly treated, after an initial treatment with 50% sulfuric acid solution to break seed dormancy. All accession seeds were germinated in plastic trays containing a mixture of three parts peat moss, one part perlite, one part vermiculite, one part sludge and two parts forest soil in a growth chamber, with 16 h light (photon flux of 70 μmol m-2 s-1) at 28 °C and 66% relative humidity. Three-week-old chili pepper plants were transplanted individually into plastic 5 L pots containing the same soil mixture described above. During transplantation, 15 g of a mycorrhizae fungal and beneficial bacteria mixture were added to optimize root growth and development. Plants were fertilized with Long Ashton solution every two weeks. Flowers and fruits at 0, 10, 20, 30, 40, 50 and 60 DAA were collected and immediately frozen in liquid nitrogen, and stored at -80 °C.

extract_protocol:
Total RNA was extracted from flowers and whole chili pepper fruits at different developmental stages using a NucleoSpin™ RNA Plant kit (MACHEREY-NAGEL) according to the manufacturer’s instructions. RNA was extracted from two biological samples comprising either flowers (time 0 DAA) fruits or seedlings from 2-6 different plants. RNA quality was verified by determining the RNA Integrity Number (RIN) for each sample.
Samples of total RNA were shipped to Novogene (https://en.novogene.com/) for library construction, sequencing and mapping to a reference genome. At Novogene, libraries were prepared and sequenced using the Illumina NovaSeq platform to obtain at least 20 million raw paired-end reads of 150 bp per sample.

treatment_protocol: No treatments were employed. Samples of fruits and seedlings were collected at the times indicated in the "characteristics: collection time" of the "SAMPLES" section.

tag: sample type

value: Wild accession (C. a. var. glabriusculum)

value: Whole fruit

tag: collection time

value: 10 Days After Anthesis (DAA)


title: RNASeq_Arid1a_Het_1

description: RNA-Seq in stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/+ mouse

value: Atp4bCre; Rosa26NICD; Arid1aflox/+


title: RNASeq_Ctrl_2

description: RNA-Seq in stomach gland of a Atp4bCre; Rosa26NICD mouse

value: Atp4bCre; Rosa26NICD


title: ChIP-Seq_H3K4me3_WT_1

description: H3K4me3 ChIP-Seq in stomach gland of a wild type mouse

data_processing:
For ChIP-Seq, the filtered single-end reads were aligned to mouse reference genome (GRCm38) using Bowtie2 with default parameters. ChIP-Seq peaks were then called by MACS2 -callpeak with parameters “--keep-dup=1” and “--SPMR”. ENCODE mm10 blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were excluded from the called peaks for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files containing ChIP-Seq peak regions generated by MACS2.

extract_protocol:
Fresh epithelial pellets were fixed in 1% PFA for 10 minutes at room temperature, quenched with 1/20th volume of 2.5 M glycine for 5 minutes, washed twice with cold 1x PBS and flash frozen. When enough sample was acquired (approximately 0.1g of tissue per region), fixed pellets were pooled, dounced in cold PBS with protease inhibitor, and filtered through a 70 µm mesh. Samples were then incubated in cold cell membrane and nuclear lysis buffers containing non-denaturating detergents for 30 mins each on a shaker at 4˚C. Washed samples were pelleted and resuspend in 300µl of sonication buffer containing 0.1% SDS. Sonication was conducted using the Diagenode bioruptor (Diagenode, B01020001) at high power for 30 cycles, 30 seconds ON/OFF. Sonicated samples were cleared with 1:10 dilution of 30% Triton-X and added to antibody bound beads (rabbit anti-H3K27ac: abcam, ab4729). The next day, beads were washed with high and low salt buffers and treated with Proteinase K overnight at 65˚C. DNA was isolated using phenol/chloroform extraction and 10ng of immunoprecipitated DNA was used for cDNA library construction using the Rubicon DNA-seq Thruplex 48S kit. Libraries were size selected and submitted to be sequenced at 50 base pair read length, single end reads with 15-20 million reads per library.
ThruPLEX DNA-Seq kit

tag: antibody


title: Mtl_2

type: RNA

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with Affymetrix RJpGene-1_1-st-v1 (Affymetrix) and scanned at GreenGene biotech.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We extracted a probeset as present with default options  apt-probeset-summarize with options: -p RJpGene-1_1-st.pgf -b RJpGene-1_1-st.bgp --qc-probesets RJpGene-1_1-st.qcc -m RJpGene-1_1-st.mps -a rma-sketch

label: biotin

organism: Oryza sativa

source_name: rice embryo

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Rice embryos were harvested from whole rice seeds (Oryza sativa L. cv. Dongjin),

extract_protocol: Rice embryos were ground to a fine powder with liquid nitrogen using a mortar and pestle, and extracted with TLE (0.2 M Tris, 0.1 M LiCl, and 5 mM EDTA; pH 8.2) and phenol-chloroform-isoamylalcohol solution. Total RNA was extracted with TRIZOL® reagent (Invitrogen, UK) and RNeasy plant mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. The quantity and purity of the extracted RNA were assessed by measuring the OD260/280 using a NanoDrop spectrophotometer. For microarray experiments, total RNA was re-purified using low-elution Qiagen RNeasy columns (Qiagen), according to the manufacturer’s instructions. Total RNA was also used for the synthesis of the first strand cDNA for real-time quantitative reverse transcriptase PCR (qRT-PCR).

treatment_protocol: Approximately 150~200 surface-sterilized embryos were placed on a single layer of 3 mm Whatman paper soaked in 10 mM calcium chloride (CaCl2) solution containing 60 mM of either glucose or mannitol and incubated for 24 h at 28°C in the dark for aerobic germination. For anaerobic germination, 150~200 surface-sterilized rice embryos were submerged in orange conical tubes containing 50 mL of the aforementioned incubation media and flushed with N2 gas and incubated under the same conditions as aerobic germination. To induce energy starvation in cells, rice embryos were germinated aerobically as described above, except that 0.08 mM of the uncoupler 2,4-dinitrophenol (DNP; Sigma Aldrich, St. Louis, MO, USA) was added to the incubation media.

value: embryo

tag: condition

value: Mtl


title: ChIP-Seq_H3K4me3_Ctrl_1

description: H3K4me3 ChIP-Seq in stomach gland of a Atp4bCre; Rosa26NICD mouse


title: SY00R2

description: Whole fruits of accession Piquin Sonora Yellow at 0 Days After Anthesis. Biological replicate R2.

value: 0 Days After Anthesis (DAA)


title: FMThyTregFL2

data_processing:
Basecalls performed using CASAVA
Paired-end reads were mapped by STAR(v2.5.2b) using parameters "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --twopassMode Basic --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 " and counted reads by HTSEQ(0.6.1p1) on GENCODE annotation(vM14).
Samples were processed early using STAR(2.3.0e_r291) with default parameters and also counted by HTSEQ based on GENCODE(vM6).
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: gene-based raw counts csv file

source_name: Female mice

growth_protocol: Regulatory T cells were immediately lysed with TRIzol after FACS sorting for downstream processing.

extract_protocol:
Cells were lysed with the TRIzol reagent (Thermo Fisher Scientific) and stored at -80°C. Total RNA extraction according the manufacturer’s protocols.
Libraries were constructed by using SMARTer Stranded RNA-Seq Kits according the manufacturer’s protocols (Takara).

treatment_protocol: Cells were not treated after sorting.

tag: background strain

value: CNS4 floxed heterozygotes

value: FACS sorted CD4+Foxp3+ regulatory T cells

tag: Sex

value: female


title: FMThyTregKO3

value: CNS4 knockout heterozygotes


title: MThyTregKO2

source_name: Male mice

value: CNS4 knockout

value: male


title: SY10R1

description: Whole fruits of accession Piquin Sonora Yellow at 10 Days After Anthesis. Biological replicate R1.


title: SY00R1

description: Whole fruits of accession Piquin Sonora Yellow at 0 Days After Anthesis. Biological replicate R1.


title: SR60R2

description: Whole fruits of accession Piquin Sonora Red at 60 Days After Anthesis. Biological replicate R2.

source_name: Piquin Sonora Red

value: 60 Days After Anthesis (DAA)


title: FMThyTregKO2


title: FMThyTregFL3


title: FMThyTregKO1


title: SR60R1

description: Whole fruits of accession Piquin Sonora Red at 60 Days After Anthesis. Biological replicate R1.


title: MThyTregKO3


title: FMThyTregFL1


title: SR50R2

description: Whole fruits of accession Piquin Sonora Red at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: MThyTregKO1


title: MThyTregFL4

value: CNS4 floxed (wild type)


title: CNS4fl_Treg2

value: Regulatory T cell

value: lymph node and spleen


title: ChIP-Seq_H3K4me3_Arid1a_Het_1

description: H3K4me3 ChIP-Seq in stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/flox mouse

value: stomach gland

value: Atp4bCre; Rosa26NICD; Arid1aflox/flox


title: ChIP-Seq_H3K27ac_Ctrl_2

description: H3K27ac ChIP-Seq in stomach gland of a Atp4bCre; Rosa26NICD mouse

value: Atp4bCre; Rosa26NICD


title: SR50R1

description: Whole fruits of accession Piquin Sonora Red at 50 Days After Anthesis. Biological replicate R1.

value: Wild accession (C. a. var. glabriusculum)

value: Whole fruit


title: Nsc_TBL_1XR1_F_F_GFP2_S3

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Fastq files were mapped to the mm10 mouse reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
Statistical and downstream bioinformatics analyses were performed within the R environment.
Gene expression heatmaps were produced with GENE-E (Broad Institute).
Genome_build: mm10

source_name: Embryonic cortex

growth_protocol: Neural Stem Cells (NSCs) were derived from telencephalic cortex of embryos at E14.5. Embryonic  cortices were dissociated, frag- mented in Hank’s Balanced Salt Solution (HBSS, Life Technologies)  with 1% Penicillin/Streptomycin (Sigma- Aldrich) and digested with papain (10 U/ml, Worthington  Biochemical) and cysteine (1mM, Sigma-Aldrich) in HBSS with 0.5mM EDTA at 37° C. The  obtained NSCs were routinely cultured in suspension as neurospheres.  Cells were cultured in neural inducing medium (NIM) composed of: DMEM/F12 (Sigma-Aldrich)  supplemented with Hormon Mix (DMEM/F12, 0.6% Glucose (Sigma-Aldrich) (30% in phosphate  buffer (PBS) (Euroclone)), Insulin (Sigma-Aldrich) 250 g/ml, putrescine powder (Sigma-Aldrich)  97 g/ml, apotransferrin powder (Sigma Aldrich), sodium selenite 0,3 M, progesterone 0,2 M),  1mg/ml penicillin/streptomycin (Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich), 0.66% Glucose  (30% in phosphate buffer salt (PBS) (Euroclone)), Heparin 4 g/ml, 10 ng/ml basic fibroblast growth  factor (bFGF) (ThermoFisher Scientific) and 10 ng/ml epithelial growth factor (EGF) (ThermoFisher  Scientific). To assess multipotent differentiation capacity of NSCs, cells were seeded on matrigel  (Corning) coated glass coverslips at a density of 3-4x10^5 cells per well in a 24 multiwell plate. The  first day after plating media was changed adding normal NIM without EGF for two days. Media was  then changed again adding NIM without both EGF and FGF, supplemented with 2% fetal bovine  serum (FBS) (Sigma-Aldrich) for 6 days.  To measure the NSCs proliferation rate 6x10^5 cells were seeded in adherent condition in a 6 multi-  wells plate. Every 2-3 day cells were detached and counted, after this passage, 6x10^5 cells were  seeded again. This was repeated for 6 time points. The experiment was repeated 3 times for each time  point.

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

treatment_protocol: Tbl1xr1 flox/flox NSCs infected with either Cre or GFP

value: Embryonic cortex

tag: genotype/variation

value: Tbl1xr1 flox/flox NSCs infected with GFP


title: SR40R2

description: Whole fruits of accession Piquin Sonora Red at 40 Days After Anthesis. Biological replicate R2.

value: 40 Days After Anthesis (DAA)


title: Nsc_TBL_1XR1_F_F_GFP1_S5


title: ChIP-Seq_H3K27ac_WT_1

description: H3K27ac ChIP-Seq in stomach gland of a wild type mouse

value: wild type


title: ChIP-Seq_H3K27ac_Ctrl_1

source_name: stomach gland of a Atp4bCre; Rosa26NICD mouse


title: ChIP-Seq_H3K27ac_WT_2


title: Nsc_TBL_1XR1_F_F_GFP1_1_S1


title: MThyTregFL2

value: FACS sorted CD4+Foxp3+ regulatory T cells


title: ChIP-Seq_H3K27ac_Arid1a_Het_1

description: H3K27ac ChIP-Seq in stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/+ mouse

value: Atp4bCre; Rosa26NICD; Arid1aflox/+


title: Nsc_TBL_1XR1_F_F_CRE2_2_S6

value: Tbl1xr1 flox/flox NSCs infected with Cre


title: pMek_Unsorted_R3

city: Berlin

first: Oriana

last: Genolet

address: Ihnestrasse 63

department: OWL Schulz

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Replicate 3.
mpimg_L10982_Sample_10_S32
processed data file: pMek_Screen_counts.txt

data_processing:
Tab delimited text files with normalized counts were generated on the public Galaxy server usegalaxy.eu (Afgan et al., 2016) with the MAGeCK CRISPR screen analysis tools (Li et al., 2014, 2015)
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: normalized counts for each sample
Supplementary_files_format_and_content: GeCKOx/GeCKOxs sgRNA library; sgRNA name, sgRNA sequence and Gene for read alignment

growth_protocol: All mESC lines were grown without feeder cells on gelatin-coated flasks (Millipore, 0.1%) in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (PanBiotech), 0.1 mM ß-Mercaptoethanol (Sigma), 1000 U/ml leukemia inhibitory factor (LIF, Merck)). mESCs were passaged every second day at a density of 4*104 cells/cm2 and medium was changed daily. For stable expression of the Cas9 endonuclease, cells were transduced with virus carrying Cas9 and selected for cells with stable integration. Cells were then transduced with the respective sgRNA library with a MOI (multiplicity of infection) of 0.3 and selected for stable sgRNA cassette integration. Cells were then grown for seven days prior to sorting.

extract_protocol:
For the primary screen, genomic DNA was isolated from the frozen cell pellets by using the DNeasy Blood and Tissue kit (Qiagen) following the manufacturer's instructions. For the secondary screens, genomic DNA from frozen cell pellets was isolated via Phenol/Chloroform extraction due to higher yields. Briefly, cell pellets were thawed and resuspended in 250µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2M NaCl and 5mM DTT (Roth) in TE Buffer) and incubated over night at 65°C. 200µg of RNAse A (Thermo Fisher Scientific) was added to the sample and incubated at 37°C for 1h. 100µg of Proteinase K (Sigma) were subsequently added followed by a 1h incubation at 50°C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at RT for 1 min and subsequently centrifuged at 16000 xg for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 hr. DNA was pelleted by centrifugation for 13000 rpm for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50µl H2O.
The PCR amplification of the sgRNA cassette was performed in two PCR steps as described previously with minor modifications (Shalem et al. 2014).

treatment_protocol: No treatment was carried out.

tag: strain/cell line background

value: mouse embryonic stem cells (mESCs)

tag: gdna isolation

value: Phenol/Chloroform


title: gen_4_35

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: rpkm.txt

data_processing:
Following sequencing, Illumina Primary Analysis version RTA v1.18.61 and Secondary Analysis version CASAVA-1.8.2 were run to demultiplex reads for all libraries and generate FASTQ files.
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt contains tab-delimited RPKM vales for each sample.

organism: Schmidtea mediterranea

source_name: asexual CIW4 adult

extract_protocol:
RNA was isolated using TRIZOL.
mRNAseq libraries were generated from 500 ng of high quality total RNA, as assessed using the Bioanalyzer 2100 (Agilent). Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA LT– set A and B (Illumina, San Diego, CA; Cat. No. RS-122-2101 and RS-122-2102) and using NEXTflex DNA Barcodes (BiooScientific, Austin, TX; Cat. No. 514104). Resulting short fragment libraries were checked for quality and quantity using a LabChip GX (Perkin Elmer) and Qubit Fluorometer (Life Technologies, Carlsbad, CA).

treatment_protocol: 4 biological replicates of 4 worms were collected at the specified times after the transition from recirculation to static culture in the presence or absence of 50 μg/ml gentamycin.

value: whole body

tag: age

value: adult

tag: day

tag: drug

value: gentamycin

tag: replicate


title: pMek_Unsorted_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Replicate 2.
mpimg_L10978_Sample_6_S28
processed data file: pMek_Screen_counts.txt


title: ChIP-Seq_H3K27ac_Arid1a_Het_2

source_name: stomach gland of a Atp4bCre; Rosa26NICD; Arid1aflox/+ mouse

value: stomach gland


title: gen_4_36

description: rpkm.txt

tag: strain


title: SR20R1

description: Whole fruits of accession Piquin Sonora Red at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: nt_4_32

description: rpkm.txt

value: no treatment


title: SR30R1

description: Whole fruits of accession Piquin Sonora Red at 30 Days After Anthesis. Biological replicate R1.

value: Wild accession (C. a. var. glabriusculum)

value: 30 Days After Anthesis (DAA)


title: MThyTregFL1

tag: genotype

value: CNS4 floxed (wild type)

value: male


title: SR40R1

description: Whole fruits of accession Piquin Sonora Red at 40 Days After Anthesis. Biological replicate R1.

value: Whole fruit

value: 40 Days After Anthesis (DAA)


title: pMek_Unsorted_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOxs sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Replicate 1.
mpimg_L10974_Sample_2_S24
processed data file: pMek_Screen_counts.txt

tag: cell type


title: Nsc_TBL_1XR1_F_F_CRE2_S2

tag: tissue

value: Embryonic cortex


title: SR30R2

description: Whole fruits of accession Piquin Sonora Red at 30 Days After Anthesis. Biological replicate R2.

tag: sample type


title: gen_4_33

description: rpkm.txt


title: nt_4_31

description: rpkm.txt


title: nt_4_29

description: rpkm.txt


title: gen_3_28

description: rpkm.txt


title: SR10R2

description: Whole fruits of accession Piquin Sonora Red at 10 Days After Anthesis. Biological replicate R2.

tag: collection time

value: 10 Days After Anthesis (DAA)


title: SRE-Elk_DoubleSorted_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the highest reporter activity (based on GFP levels whose expression was driven by a MAPK sensitive promoter) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the highest fluorescence. Replicate 3.
mpimg_L9431-1_Sample12_S40
processed data file: SRE-Elk_Screen_counts.txt

value: DNeasy Blood and Tissue kit (Qiagen)


title: gen_3_27

description: rpkm.txt


title: Nsc_TBL_1XR1_F_F_CRE3_S4

value: Tbl1xr1 flox/flox NSCs infected with Cre


title: gen_4_34

description: rpkm.txt


title: SR20R2

description: Whole fruits of accession Piquin Sonora Red at 20 Days After Anthesis. Biological replicate R2.


title: nt_4_30

description: rpkm.txt


title: gen_3_26

description: rpkm.txt


title: SR10R1

description: Whole fruits of accession Piquin Sonora Red at 10 Days After Anthesis. Biological replicate R1.


title: SR00R2

description: Whole fruits of accession Piquin Sonora Red at 0 Days After Anthesis. Biological replicate R2.

value: 0 Days After Anthesis (DAA)


title: nt_3_21

description: rpkm.txt

value: whole body


title: nt_3_22

description: rpkm.txt

value: adult


title: gen_2_19

description: rpkm.txt

value: gentamycin


title: SRE-Elk_DoubleSorted_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the highest reporter activity (based on GFP levels whose expression was driven by a MAPK sensitive promoter) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the highest fluorescence. Replicate 1.
mpimg_L9427-1_Sample8_S36
processed data file: SRE-Elk_Screen_counts.txt

value: mouse embryonic stem cells (mESCs)


title: nt_3_23

description: rpkm.txt


title: gen_3_25

description: rpkm.txt


title: PLSTR2

description: Whole 30 days seedlings of accession Serrano Tampiqueno 74. Biological replicate R2.

source_name: Serrano Tampiqueno 74

value: Domesticated variety

value: Whole 30 days seedlings

value: 30 days after germination


title: SRE-Elk_Unsorted_R3

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOx sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells are carrying a randomly integrated MAPK fluorescent reporter. Replicate 3.
mpimg_L9424-1_Sample5_S33
processed data file: SRE-Elk_Screen_counts.txt
processed data file: SRE-Elk_Screen_counts.txt


title: nt_3_24

description: rpkm.txt

value: no treatment


title: gen_2_20

description: rpkm.txt


title: SRE-Elk_Unsorted_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOx sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells are carrying a randomly integrated MAPK fluorescent reporter. Replicate 2.
mpimg_L9422-1_Sample3_S31
processed data file: SRE-Elk_Screen_counts.txt


title: SR00R1

description: Whole fruits of accession Piquin Sonora Red at 0 Days After Anthesis. Biological replicate R1.

value: Wild accession (C. a. var. glabriusculum)


title: SRE-Elk_Unsorted_R1

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
Unsorted population of cells 7 days after transduction with GeCKOx sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells are carrying a randomly integrated MAPK fluorescent reporter. Replicate 1.
mpimg_L9420-1_Sample1_S29
processed data file: SRE-Elk_Screen_counts.txt


title: PLQUR2

description: Whole 30 days seedlings of accession Piquin Queretaro. Biological replicate R2.

source_name: Piquin Queretaro


title: gen_2_17

description: rpkm.txt


title: gen_2_18

description: rpkm.txt


title: nt_2_15

description: rpkm.txt


title: XO_R2

data_processing:
The tab delimited text files containing raw counts for each sample were generated by mapping reads with the STAR aligner allowing for maximally 2 mismatches to the mm10 mouse reference genome (GRCm38) and quantified using the ENSEMBL gene annotation (Dobin et al. 2013). Rpkm normalized counts were generated using the EdgeR package.
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: raw counts or rpkm normalized counts for each sample

growth_protocol: All mESC lines were grown without feeder cells on gelatin-coated flasks (Millipore, 0.1%) in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (PanBiotech), 0.1 mM ß-Mercaptoethanol (Sigma), 1000 U/ml leukemia inhibitory factor (LIF, Merck)). mESCs were passaged every second day at a density of 4*104 cells/cm2 and medium was changed daily.

extract_protocol:
For gene expression profiling, ~ 2*106 cells were washed with ice-cold PBS and lysed by directly adding 500µl of Trizol (Invitrogen). RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions.
Libraries were generated using the  Tru-Seq Stranded Total RNA library preparation kit (Illumina) with 1µg starting material and amplified with 15 Cycles of PCR

value: XO subclone


title: nt_2_14

description: rpkm.txt


title: nt_2_16

description: rpkm.txt


title: PLQUR1

description: Whole 30 days seedlings of accession Piquin Queretaro. Biological replicate R1.


title: XO_R3


title: JE70R2

description: Whole fruits of accession Jalapeno Espinalteco at 70 Days After Anthesis. Biological replicate R2.

source_name: Jalapeno Espinalteco

value: Whole fruit

value: 70 Days After Anthesis (DAA)


title: nt_2_13

description: rpkm.txt


title: SRE-Elk_DoubleSorted_R2

description:
PCR amplicon of sgRNAs integrated into the gDNA of the target population via lentiviral transduction
25% of cells with the highest reporter activity (based on GFP levels whose expression was driven by a MAPK sensitive promoter) were FACS-sorted, put into culture again for two days, to then sort again the 25% cells with the highest fluorescence. Replicate 2.
mpimg_L9429-1_Sample10_S38
processed data file: SRE-Elk_Screen_counts.txt


title: gen_1_12

description: rpkm.txt


title: XO_R1


title: gen_1_11

description: rpkm.txt


title: PLSTR1

description: Whole 30 days seedlings of accession Serrano Tampiqueno 74. Biological replicate R1.


title: JE70R1

description: Whole fruits of accession Jalapeno Espinalteco at 70 Days After Anthesis. Biological replicate R1.


title: XX_R3

value: Female wildtype


title: gen_1_9

description: rpkm.txt


title: JE60R2

description: Whole fruits of accession Jalapeno Espinalteco at 60 Days After Anthesis. Biological replicate R2.

value: 60 Days After Anthesis (DAA)


title: nt_1_8

description: rpkm.txt


title: XX_R2


title: nt_1_7

description: rpkm.txt


title: nt_1_5

description: rpkm.txt


title: nt_0_4

description: rpkm.txt


title: JE50R2

description: Whole fruits of accession Jalapeno Espinalteco at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: nt_1_6

description: rpkm.txt


title: XX_R1


title: JE40R2

description: Whole fruits of accession Jalapeno Espinalteco at 40 Days After Anthesis. Biological replicate R2.

value: 40 Days After Anthesis (DAA)


title: nt_0_2

description: rpkm.txt


title: RNA differentiating D3lKO rep1 [Mut_D_0]

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial biology

country: Taiwan

institute: Academia Sinica

data_processing:
RNA-seq alignment using Tophat 2.1.0 with default parameters
Calculate RPKM of genes by using cuffdiff (cufflinks-2.2.1) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values for WT and Dnmt3L KO samples

source_name: RNA differentiating D3lKO_MSCs

growth_protocol: MSCs were cultured in alphaMEM (Gibco, Grand Island, NY, US) supplemented with 20% of fetal bovine serum (FBS; Hyclone, Logan, UT, US) and antibiotics (100 U/mL of penicillin and 100 μg/mL of streptomycin; Gibco) on 100 mm dish (TPP, Trasadingen, CH)

extract_protocol:
Total RNA was extracted by Trizol reagent (Invitrogen, Carlsbad, CA, US) following RNeasy mini kit (Qiagen, Hilden, DE) by manufacturer’s instruction.
Ribosomal RNA (rRNA) was removed from 2.5 ug total RNA using illumina Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat). Then Libraries were constructed by illumina TruSeq Stranded Total RNA Sample Prep kit.

treatment_protocol: Osteogenic induction medium was comprised of 10% FBS-αMEM with 0.1 μM dexamethasone (Sigma-Aldrich), 10 mM β-Glycerophosphate (Sigma-Aldrich) and 50 μM L-ascorbic acid 2-phosphate (Sigma-Aldrich)

tag: strain background

value: Dnmt3l KO

value: mesenchymal stem cells (MSCs)

tag: cell subtype

value: after 3 days of osteogenic induction of  MSCs

tag: passage


title: RNA differentiating D3lKO rep2 [Mut_D_1]


title: RNA undifferentiated D3lKO rep2 [Mut_Un_1]

source_name: RNA undifferentiated D3lKO_MSCs

value: undifferentiated


title: JE40R1

description: Whole fruits of accession Jalapeno Espinalteco at 40 Days After Anthesis. Biological replicate R1.


title: nt_0_1

description: rpkm.txt

value: whole body

value: adult


title: ESC-3

city: Yangzhou City

first: Xia

last: Yuan

state: Jiangsu Province

address: 88 South University Ave

country: China

institute: Yangzhou university, Yangzhou, China

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic
the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the galgal6
FPKM of each gene was calculated using Cufflinks , and the read counts of each gene were obtained by HTSeq-count
Genome_build: galgal6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and counts for each Sample

organism: Gallus gallus

source_name: embryonic stem cells

growth_protocol: cDNA library of chicken ESCs was constructed according to the instruction of HiScript® 1st Strand cDNA Synthesis Kit (TIANGEN, Beijing, China, KR118). The CDS sequences of Oct4, Sox2, Nanog, and Lin28A (OSNL) genes were cloned into the pCDH-CMV-MCS-GFP vector (Save in own laboratory). The constructed vector was then performed double-enzyme digestion with EcoRI (NEB, Beijing, China, R3101) and BamHI (NEB, Beijing, China, R3136). The products were identified by 1% agarose (TSINGKE, Beijing, China, TSJ001) gel electrophoresis and sequenced. After lentivirus encapsulation, 1.5×105/well CEF were seeded into a 24-well plate. When cell density became 60%, the OSNL four-factor lentiviral vector (1: 1: 1: 1) was used to infect CEF under 10 multiplicity of infection and 5ng/ml polybrene (Santa Cruz, California, USA, SC-134220). After 24 hours, culture medium was replaced by DMEM containing 10% FBS and cultured for 72 hours. The medium was then replaced by ESCs medium. Cells were cultured until the 5th day and transferred to CEF feeder layer treated with mitomycin C (MCE, New Jersey, USA, HY-13316). On the 7th day, cells were picked for single-cell clones under a stereomicroscope (Olympus, Tokyo, Japan, DP72). Single-cell clones were digested with accutase for 10 minutes, and then seeded on 96-well plates with feeder cells for amplification. The entire iPS reprogram process lasted 21d. For compounds treatment, the cells were cultured in chicken ESCs medium and were treated with 2i(3 µM SB431542 , MCE, USA, HY-10431; 1 µM PD0325901, MCE, USA, HY-10254)，1 µg/mL Vc(sigma, USA,  A4544-25G) and 1 mM VPA (sigma, USA, P4543-10G). The media were changed every 2 days depending on the cell density.

extract_protocol:
RNA Isolation and Library Preparation  Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: After the CEF culture is finished, remove the culture medium and wash once with PBS buffer. Add 1 ml TRIzol per 10cm2 cells to the separation solution. Pipette repeatedly with a 1ml pipette tip until no clumps of cells are visible, forming a clear and non-viscous liquid; transfer all the TRNzol liquid to RNase-free cryopreservation tubes; store in the refrigerator at -80°C and transport on dry ice. After the ESCs iPS culture is finished, centrifuge (4°C, 1500g, 10min) to remove the culture solution, wash it quickly with PBS buffer once; add 1ml TRNzol to every 5x105-107 cells in the lysis solution. Pipette repeatedly with a 1ml pipette tip until no clumps of cells are visible, forming a clear and non-sticky liquid; store in a refrigerator at -80°C, and transport on dry ice.

tag: breed

value: Rugao yellow chicken

value: Primary chicken embryonic stem cells


title: ESC-2


title: LP52: no disease

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

source_name: no disease

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. F1- F3 generation plastics lineages were housed in the same room and racks with lighting, food and water. All experimental protocols for the procedures with rats were pre-approved by the Washington State University Animal Care and Use Committee (protocol IACUC # 6252).

extract_protocol: See attached Word document (Extraction_Library_Construction_Protocol.docx)

treatment_protocol: Outbred Sprague Dawley gestating female rats (F0 generation) were administered an intraperitoneal dose of the plastic compound mixture (BPA 25 mg/kg BW/day, DEHP 375 mg/kg BW /day, and DBP 33mg/kg BW/day). These doses were administered at 90 days of age, during embryonic days 8-14 (E8-E14) of fetal gonadal sex determination. The F1 generation offspring was directly exposed as a fetus and F2 generation grand-offspring exposed as the germline in the F1 generation. These were each bred at 90 days of age within the lineage. The F3 generation great-grand-offspring is required to establish the transgenerational inheritance generation of ancestral exposure.

value: Sprague Dawley

tag: Sex

value: male

value: Sperm

tag: measurement

value: MeDIP

tag: disease

value: no disease

tag: lineage

value: plastics


title: ESC-1


title: CEF-3

source_name: chicken embryo fibroblasts

value: Black Langshan Chicken

value: Primary chicken embryo fibroblasts


title: RNA undifferentiated D3lKO rep1 [Mut_Un_0]

tag: genotype/variation


title: LP51: no disease


title: RNA differentiating WT rep1 [WT_D_0]

source_name: RNA differentiating WT_MSCs

value: wild type


title: RNA undifferentiated WT rep2 [WT_Un_1]

source_name: RNA undifferentiated WT_MSCs


title: CEF-2


title: JE20R1

description: Whole fruits of accession Jalapeno Espinalteco at 20 Days After Anthesis. Biological replicate R1.

value: Domesticated variety

value: Whole fruit

value: 20 Days After Anthesis (DAA)


title: JE30R2

description: Whole fruits of accession Jalapeno Espinalteco at 30 Days After Anthesis. Biological replicate R2.

value: 30 Days After Anthesis (DAA)


title: LP50: obesity

source_name: obesity

value: obesity


title: gen_1_10

description: rpkm.txt

value: whole body

tag: age

value: adult

tag: day

tag: drug

value: gentamycin


title: CEF-1


title: JE20R2

description: Whole fruits of accession Jalapeno Espinalteco at 20 Days After Anthesis. Biological replicate R2.


title: JE50R1

description: Whole fruits of accession Jalapeno Espinalteco at 50 Days After Anthesis. Biological replicate R1.

value: 50 Days After Anthesis (DAA)


title: RNA undifferentiated WT rep1 [WT_Un_0]

value: mesenchymal stem cells (MSCs)

value: undifferentiated


title: iPS (OSNL+2i+Vc+VPA)-3

source_name: induced pluripotent stem cells

tag: induction system

value: CEF-derived induced pluripotent stem cells


title: JE10R2

description: Whole fruits of accession Jalapeno Espinalteco at 10 Days After Anthesis. Biological replicate R2.

value: 10 Days After Anthesis (DAA)


title: phase-sfifted cow mammary, 26PS

city: West Lafayette

first: Theresa

last: Casey

state: Indiana

address: 270 S. Russell Street

department: Animal Sciences

institute: Purdue University

data_processing:
Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Bos_taurus reference genome (ARS-UCD1.2) available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used for differential gene expression analysis and the Wald test was used to generate p-values and log2 fold changes
Genome_build: Bos_taurus reference genome (ARS-UCD1.2)
Supplementary_files_format_and_content: DESeq2 - normalized counts
Supplementary_files_format_and_content: DESeq2 - raw counts
Supplementary_files_format_and_content: DESeq2 - rLog trasnformed counts

organism: Bos taurus

source_name: mammary biopsy

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit
total RNA samples were depleted for ribosomes using QIAseq FastSelect –rRNA HMR kits
RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA)
The sequencing libraries were multiplexed and clustered on two lanes of a flowcell and loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150 paired end configuration.

value: mammary

tag: physiological state

value: gestation

value: Holstein

tag: time point

value: three weeks prepartum

tag: treatment

value: circadian disruption


title: JE10R1

description: Whole fruits of accession Jalapeno Espinalteco at 10 Days After Anthesis. Biological replicate R1.

tag: sample type

value: Domesticated variety

tag: tissue

value: Whole fruit

tag: collection time


title: LP47: testis disease

source_name: testis disease

tag: strain

value: Sprague Dawley

value: male

value: Sperm

value: MeDIP

value: testis disease

value: plastics


title: control cow mammary, 26C

value: control


title: LP46: testis disease


title: JE00R2

description: Whole fruits of accession Jalapeno Espinalteco at 0 Days After Anthesis. Biological replicate R2.

value: 0 Days After Anthesis (DAA)


title: RNA differentiating WT rep2 [WT_D_1]

tag: strain background

value: wild type

tag: cell type

value: mesenchymal stem cells (MSCs)

tag: cell subtype

value: after 3 days of osteogenic induction of  MSCs

tag: passage


title: iPS (OSNL+2i+Vc+VPA)-1

tag: breed

value: Black Langshan Chicken

value: CEF-derived induced pluripotent stem cells


title: LP49: no disease

tag: Sex

tag: measurement

tag: disease

value: no disease

tag: lineage


title: iPS (OSNL+Vc+VPA)-3

tag: induction system

value: OSNL+Vc+VPA


title: LP45: no disease


title: JE00R1

description: Whole fruits of accession Jalapeno Espinalteco at 0 Days After Anthesis. Biological replicate R1.

value: Domesticated variety


title: control cow mammary, 25C

value: mammary

tag: physiological state

value: gestation

value: Holstein

value: three weeks prepartum


title: iPS (OSNL+2i+Vc+VPA)-2


title: iPS (OSNL+Vc+VPA)-2


title: LP48: multiple disease

source_name: multiple disease

value: Sprague Dawley

value: male

value: Sperm

value: MeDIP

value: multiple disease


title: iPS (OSNL+Vc+VPA)-1


title: iPS (OSNL+2i)-3


title: control cow mammary,24C

tag: time point

value: control


title: LP43: no disease

value: plastics


title: AS80R1

description: Whole fruits of accession Ancho San Luis at 80 Days After Anthesis. Biological replicate R1.

source_name: Ancho San Luis

value: Whole fruit

value: 80 Days After Anthesis (DAA)


title: AS80R2

description: Whole fruits of accession Ancho San Luis at 80 Days After Anthesis. Biological replicate R2.


title: LP42: no disease


title: phase-sfifted cow mammary, 23PS

tag: treatment

value: circadian disruption


title: iPS (OSNL+2i)-2

value: Black Langshan Chicken

value: CEF-derived induced pluripotent stem cells


title: AS70R2

description: Whole fruits of accession Ancho San Luis at 70 Days After Anthesis. Biological replicate R2.

tag: sample type

value: Domesticated variety

value: 70 Days After Anthesis (DAA)


title: control cow mammary, 23C

tag: tissue

value: mammary

value: gestation


title: AS70R1

description: Whole fruits of accession Ancho San Luis at 70 Days After Anthesis. Biological replicate R1.

tag: collection time


title: iPS (OSNL+2i)-1


title: LP41: obesity

tag: strain

value: obesity


title: AS60R2

description: Whole fruits of accession Ancho San Luis at 60 Days After Anthesis. Biological replicate R2.

value: 60 Days After Anthesis (DAA)


title: phase-sfifted cow mammary, 22PS

value: Holstein

value: three weeks prepartum


title: phase shifted cow mammary, 24PS


title: iPS (OSNL)-3

value: OSNL


title: AS60R1

description: Whole fruits of accession Ancho San Luis at 60 Days After Anthesis. Biological replicate R1.


title: LP44: testis disease

value: Sprague Dawley

value: male

value: Sperm

value: MeDIP

value: testis disease


title: LP40: kidney disease

source_name: kidney disease

value: kidney disease

value: plastics


title: iPS (OSNL)-2

value: Black Langshan Chicken

value: CEF-derived induced pluripotent stem cells


title: phase-sfifted cow mammary, 21PS

value: circadian disruption


title: iPS (OSNL)-1


title: JE30R1

description: Whole fruits of accession Jalapeno Espinalteco at 30 Days After Anthesis. Biological replicate R1.

value: Domesticated variety

value: Whole fruit

value: 30 Days After Anthesis (DAA)


title: LP37: multiple disease

value: multiple disease


title: LP38: no disease

value: no disease


title: phase-sfifted cow mammary, 19PS

value: mammary

value: gestation

value: Holstein

value: three weeks prepartum


title: JE60R1

description: Whole fruits of accession Jalapeno Espinalteco at 60 Days After Anthesis. Biological replicate R1.

value: 60 Days After Anthesis (DAA)


title: LP36: no disease

value: Sprague Dawley

value: male

value: Sperm

value: MeDIP


title: LP39: testis disease

value: testis disease

value: plastics


title: AS50R2

description: Whole fruits of accession Ancho San Luis at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: PGC-3

source_name: primordial germ cells

growth_protocol: The collected iPS were seeded in a 100 mm petri dish and adhered differentially for 45 minutes. The supernatant of cells was harvested after removing the feeder cells in the iPS. 5×104/well iPS were seeded into a 24-well plate, and added with 40ng/mL BMP4 (ProSpec, Rehovot, Israel, CYT-361), 40ng/mL BMP8b (R&D, Minneapolis, USA, 9316-BP) and 50ng/mL EGF (Thermo Scientific, Shanghai, China, PHG0314). Medium was changed every other day and cell morphology change was observed. The entire process lasted for 6 days. For compounds treatment, the cells were cultured in chicken ESCs medium and were treated with 1 mM VPA (sigma, USA, P4543-10G), 20 µM VK3(Macklin, China, M813096) and 10 µM 5Aza (MCE, USA, HY-10586 ). The media were changed every 2 days depending on the cell density.

treatment_protocol: After the iPGC and primary PGCs culture is finished, centrifuge (4°C, 1500g, 10min) to remove the culture solution, wash it quickly with PBS buffer once; add 1ml TRNzol to every 5x105-107 cells in the lysis solution. Pipette repeatedly with a 1ml pipette tip until no clumps of cells are visible, forming a clear and non-sticky liquid; store in a refrigerator at -80°C, and transport on dry ice.

value: Rugao yellow chicken

value: primordial germ cells


title: PGC-2


title: control cow mammary, 21C

value: control


title: control cow mammary, 19C


title: phase-sfifted cow liver, 26PS

source_name: liver biopsy

value: liver

value: circadian disruption


title: PGC-1


title: control cow liver, 26C


title: iPGC (iPS-derived)-3

source_name: primordial germ-like cells

value: Langshan Chicken

value: iPS-derived primordial germ-like cells


title: AS50R1

description: Whole fruits of accession Ancho San Luis at 50 Days After Anthesis. Biological replicate R1.

value: Domesticated variety

value: Whole fruit


title: LP35: prostate

source_name: prostate

value: prostate


title: LP34: prostate

value: Sprague Dawley


title: phase-sfifted cow liver, 25PS

value: gestation

value: Holstein

value: three weeks prepartum


title: AS40R1

description: Whole fruits of accession Ancho San Luis at 40 Days After Anthesis. Biological replicate R1.

value: 40 Days After Anthesis (DAA)


title: control cow liver, 25C


title: LP33: no disease

value: male

value: Sperm

value: MeDIP

value: no disease

value: plastics


title: AS30R1

description: Whole fruits of accession Ancho San Luis at 30 Days After Anthesis. Biological replicate R1.

value: 30 Days After Anthesis (DAA)


title: AS20R2

description: Whole fruits of accession Ancho San Luis at 20 Days After Anthesis. Biological replicate R2.

value: 20 Days After Anthesis (DAA)


title: LP32: no disease


title: AS40R2

description: Whole fruits of accession Ancho San Luis at 40 Days After Anthesis. Biological replicate R2.


title: LP31: no disease


title: AS20R1

description: Whole fruits of accession Ancho San Luis at 20 Days After Anthesis. Biological replicate R1.


title: LP30: testis disease

value: testis disease


title: iPGC (iPS-derived)-1

value: Langshan Chicken

value: iPS-derived primordial germ-like cells


title: phase-sfifted cow liver, 24PS

value: liver

value: circadian disruption


title: AS10R2

description: Whole fruits of accession Ancho San Luis at 10 Days After Anthesis. Biological replicate R2.

value: Domesticated variety

value: Whole fruit

value: 10 Days After Anthesis (DAA)


title: iPGC (iPS-derived)-2


title: LP29: multiple disease

value: Sprague Dawley

value: multiple disease


title: phase-sfifted cow liver, 23PS

value: gestation

value: Holstein

value: three weeks prepartum


title: iPGC (5Aza)-2

value: Rugao yellow chicken

value: ESC-derived primordial germ-like cells


title: AS10R1

description: Whole fruits of accession Ancho San Luis at 10 Days After Anthesis. Biological replicate R1.


title: iPGC (5Aza)-1


title: control cow liver, 23C

value: control


title: LP28: multiple disease

value: male

value: Sperm

value: MeDIP

value: plastics


title: iPGC (VK3)-3


title: AS00R2

description: Whole fruits of accession Ancho San Luis at 0 Days After Anthesis. Biological replicate R2.

value: 0 Days After Anthesis (DAA)


title: phase-sfifted cow liver, 22PS

value: liver

value: circadian disruption


title: AS00R1

description: Whole fruits of accession Ancho San Luis at 0 Days After Anthesis. Biological replicate R1.

value: Domesticated variety

value: Whole fruit


title: LP27: multiple disease

value: Sprague Dawley


title: iPGC (VK3)-2


title: iPGC (VK3)-1


title: control cow liver, 24C


title: AS30R2

description: Whole fruits of accession Ancho San Luis at 30 Days After Anthesis. Biological replicate R2.

value: 30 Days After Anthesis (DAA)


title: ZU60R2

description: Whole fruits of accession Zunla-1 at 60 Days After Anthesis. Biological replicate R2.

value: 60 Days After Anthesis (DAA)


title: iPGC (5Aza)-3


title: phase-sfifted cow liver, 19PS

value: gestation

value: Holstein


title: control cow liver, 21C

value: three weeks prepartum


title: LP25: kidney disease

value: kidney disease


title: iPGC (VPA)-2

value: Rugao yellow chicken

value: ESC-derived primordial germ-like cells


title: nt_0_3

description: rpkm.txt

source_name: asexual CIW4 adult

value: whole body

tag: age

value: adult

tag: day

tag: drug

value: no treatment

tag: replicate


title: iPGC (VPA)-3

tag: breed

tag: cell type


title: ZU50R2

description: Whole fruits of accession Zunla-1 at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: LP24: kidney disease

tag: Sex

value: male

value: Sperm

tag: measurement

value: MeDIP

value: plastics


title: ZU60R1

description: Whole fruits of accession Zunla-1 at 60 Days After Anthesis. Biological replicate R1.

value: Domesticated variety

value: Whole fruit


title: iPGC (VPA)-1


title: ZU50R1

description: Whole fruits of accession Zunla-1 at 50 Days After Anthesis. Biological replicate R1.


title: LP23: no disease

value: Sprague Dawley

tag: disease

value: no disease

tag: lineage


title: ZU40R2

description: Whole fruits of accession Zunla-1 at 40 Days After Anthesis. Biological replicate R2.

value: 40 Days After Anthesis (DAA)


title: iPGC (BMP4+BMP8b+EGF)-3

tag: induction system


title: LP21: no disease


title: LP26: testis disease

value: testis disease


title: LP22


title: ZU40R1

description: Whole fruits of accession Zunla-1 at 40 Days After Anthesis. Biological replicate R1.


title: iPGC (BMP4+BMP8b+EGF)-1


title: ZU30R1

description: Whole fruits of accession Zunla-1 at 30 Days After Anthesis. Biological replicate R1.

value: 30 Days After Anthesis (DAA)


title: iPGC (BMP4)-1

value: Rugao yellow chicken


title: ZU20R2

description: Whole fruits of accession Zunla-1 at 20 Days After Anthesis. Biological replicate R2.

value: 20 Days After Anthesis (DAA)


title: control cow liver, 19C

value: liver

tag: physiological state

value: gestation

value: Holstein

tag: time point

value: three weeks prepartum

value: control


title: iPGC (BMP4)-2

value: ESC-derived primordial germ-like cells


title: WY-7_trachea_CF_pig id 13034

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

data_processing:
Illumina software HCS HD version 3.4.0 was used for basecalling.
Alignment of raw fastq files to pig genome assembly Sscrofa11.1, filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Genome_build: susScr11
Supplementary_files_format_and_content: HDF5 format file containing counts for each gene (row) and cell barcode (column)

organism: Sus scrofa

extract_protocol:
Trachea and small airways from neonatal WT and CF pigs were dissected and kept in cold 1 x DPBS. Tracheal tissues were scraped off and small airways were chopped into short segments. Tissues were washed with 1xDPBS with dithiothreitol (2 mM), incubated with red blood cell lysis buffer for 5 minutes, and dissociated in DMEM medium with Pronase (1.4 mg/ml) and DNase (50 U/ml) for 2 hours. Dissociation mix was terminated by adding 1 volume of cold 1 x DPBS with 10% fetal bovine serum and filtered with 40-µm tissue strainers to collect single cells.
10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system

tag: animal id

tag: genotype

value: CFTR-/-

value: lung

tag: region

value: trachea


title: Pooled Pancreatic RNA from KK/HIJ Male mice_rep3

city: Riyadh

first: Katharine

middle: Sara

last: Collison

state: Central

address: Riyadh, Saudi Arabia

department: Cell Biology

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Center

hyb_protocol: The labeled and fragmented DNA was hybridized to Mouse Gene 2.0 ST Array for 17 hours at 45°C and 60rpm. Arrays were washed and stained on the Affymetrix fluidics station 450.

scan_protocol: Genechip were scanned using Genechip 7G scanner.

data_processing: The data were analyzed with Partek Genomics Suite using RMA (Robust Multi-Array Average) settings and quantile normalization method was applied. Intensities less than log value of 6 were filtered. Fold change cut-off was ±1.4Significant DEGs were based on criteria of p-value <0.05 and False Discovery Rate<0.05.

label: Biotin

source_name: Pancreas

label_protocol: 5.5ug of fragmented cDNA was end labeled according to standard Affymerix protocol using Affymetrix Genechip WT terminal labeling kit.

growth_protocol: C57Bl/6J and KKHIJ mice were housed 3/cage in a controlled environment (pathogen-free conditions of 12 h light/dark cycle, 22 ± 2°C) with standard chow and water available ad libitum. The breeding and care of the animals were in accordance with the protocols approved by the Animal Care and Use Committee of the King Faisal Specialist Hospital & Research Centre

extract_protocol: Total RNA was extracted from snap frozen Pancreas using RNeasy Lipid mini kit (Qiagen UK)

treatment_protocol: Commencing from 6 weeks of age both strains and sexes had body weights, fasting glucose and Insulin tolerance test performed at set timepoints . During weeks 14-16 all animals performed a series of behavioral tests. At 21 weeks mice were euthanized and the Adrenals were snap-frozen for RNA extraction.

value: Male

tag: strain

value: KK/HIJ


title: LP16: kidney disease

value: Sprague Dawley

value: male

tag: tissue

value: Sperm

value: MeDIP

value: kidney disease

value: plastics


title: ZU30R2

description: Whole fruits of accession Zunla-1 at 30 Days After Anthesis. Biological replicate R2.

tag: sample type

value: Domesticated variety

value: Whole fruit

tag: collection time

value: 30 Days After Anthesis (DAA)


title: LP18


title: LP19: no disease

source_name: no disease

value: no disease


title: Pooled Pancreatic RNA from KK/HIJ Female mice_rep3

value: Female


title: Pooled Pancreatic RNA from KK/HIJ Female mice_rep1


title: WY-5_trachea_non-CF_pig id 13036

value: CFTR+/+


title: ZU10R1

description: Whole fruits of accession Zunla-1 at 10 Days After Anthesis. Biological replicate R1.

value: 10 Days After Anthesis (DAA)


title: ZU20R1

description: Whole fruits of accession Zunla-1 at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: LP17: testis disease

value: testis disease


title: Pooled Pancreatic RNA from KK/HIJ Male mice_rep2

value: Male


title: LP14: no disease


title: LP15: no disease


title: LP20: kidney disease


title: WY-4_distal airway_CF_pig id 13003

source_name: distal airway_CF

value: CFTR-/-

value: lung

value: distal airway


title: WY-6_trachea_non-CF_pig id 13031

value: trachea


title: LP13: no disease

value: Sprague Dawley

value: male

value: Sperm

value: MeDIP


title: Pooled Pancreatic RNA from C57BL/6J Female mice_rep1


title: Pooled Pancreatic RNA from C57BL/6J Female mice_rep2


title: ZU00R2

description: Whole fruits of accession Zunla-1 at 0 Days After Anthesis. Biological replicate R2.

value: Domesticated variety

value: Whole fruit

value: 0 Days After Anthesis (DAA)


title: Pooled Pancreatic RNA from C57BL/6J Female mice_rep3

value: Female


title: ZU10R2

description: Whole fruits of accession Zunla-1 at 10 Days After Anthesis. Biological replicate R2.


title: Pooled Pancreatic RNA from KK/HIJ Male mice_rep1

value: KK/HIJ


title: WY-3_distal airway_non-CF_pig id 13004

source_name: distal airway_non-CF

value: CFTR+/+


title: ST60R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 60 Days After Anthesis. Biological replicate R1.

source_name: Serrano Tampiqueno 74

value: 60 Days After Anthesis (DAA)


title: ST60R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 60 Days After Anthesis. Biological replicate R2.


title: ZU00R1

description: Whole fruits of accession Zunla-1 at 0 Days After Anthesis. Biological replicate R1.


title: WY-2_trachea_CF_pig id 13003


title: LP11: no disease

value: no disease

value: plastics


title: Pooled Pancreatic RNA from C57BL/6J Male mice_rep3

value: Male


title: Pooled Pancreatic RNA from C57BL/6J Male mice_rep1


title: Pooled Pancreatic RNA from C57BL/6J Male mice_rep2


title: WY-1_trachea_non-CF_pig id 13004

value: lung


title: ST50R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: LP10: no disease


title: Pooled Adrenal RNA from KK/HIJ Female mice_rep3

data_processing: The data were analyzed with Partek Genomics Suite using RMA (Robust Multi-Array Average) settings and quantile normalization method was applied. Intensities less than log value of 7 were filtered. Fold change cut-off was ±1.4Significant DEGs were based on criteria of p-value <0.05 and False Discovery Rate<0.05.

source_name: Adrenal tissue

growth_protocol: C57Bl/6J and KK/HIJ mice were housed 3/cage in a controlled environment (pathogen-free conditions of 12 h light/dark cycle, 22 ± 2°C) with standard chow and water available ad libitum. The breeding and care of the animals were in accordance with the protocols approved by the Animal Care and Use Committee of the King Faisal Specialist Hospital & Research Centre

extract_protocol: Total RNA was extracted from snap frozen Adrenals using RNeasy Lipid mini kit (Qiagen UK)


title: Pooled Pancreatic RNA from KK/HIJ Female mice_rep2


title: S6_distal airway_non-CF_pig id 3894

value: distal airway


title: ST50R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 50 Days After Anthesis. Biological replicate R1.


title: LP12: multiple disease

value: Sprague Dawley

value: multiple disease


title: S4_distal airway_CF_pig id 3885

value: CFTR-/-


title: LP9: no disease

value: male

value: Sperm

value: MeDIP


title: S5_distal airway_CF_pig id 3887


title: LP8: no disease


title: ST40R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 40 Days After Anthesis. Biological replicate R2.

value: Domesticated variety

value: Whole fruit

value: 40 Days After Anthesis (DAA)


title: LP7: kidney disease

value: kidney disease


title: ST40R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 40 Days After Anthesis. Biological replicate R1.


title: LP6: testis disease

value: testis disease


title: S2_distal airway_CF_pig id 3882


title: Pooled Adrenal RNA from KK/HIJ Female mice_rep1

value: Female

value: KK/HIJ


title: ST30R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 30 Days After Anthesis. Biological replicate R2.

value: 30 Days After Anthesis (DAA)


title: S1_distal airway_non-CF_pig id 3788

value: CFTR+/+

value: lung


title: Pooled Adrenal RNA from KK/HIJ Female mice_rep2


title: Pooled Adrenal RNA from KK/HIJ Male mice_rep3

value: Male


title: LP5: no disease

value: Sprague Dawley

value: no disease

value: plastics


title: Pooled Adrenal RNA from KK/HIJ Male mice_rep2


title: ST30R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 30 Days After Anthesis. Biological replicate R1.


title: LP4: testis disease

value: male


title: ST20R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 20 Days After Anthesis. Biological replicate R2.

value: 20 Days After Anthesis (DAA)


title: Pooled Adrenal RNA from KK/HIJ Male mice_rep1


title: L5_trachea_CF_pig id 3887

value: CFTR-/-

value: trachea


title: LP3: multiple disease

value: Sperm

value: MeDIP

value: multiple disease


title: Pooled Adrenal RNA from C57BL/6J Female mice_rep3


title: ST10R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 10 Days After Anthesis. Biological replicate R2.

value: Domesticated variety

value: Whole fruit

value: 10 Days After Anthesis (DAA)


title: LP2: multiple disease


title: L4_trachea_CF_pig id 3885


title: S3_distal airway_non-CF_pig id 3884

value: distal airway


title: L3_trachea_non-CF_pig id 3884

value: CFTR+/+


title: LP1: multiple disease


title: Pooled Adrenal RNA from C57BL/6J Female mice_rep2

value: Female


title: pas-319a-2

city: Beijing

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

institute: Chinese Academy of Sciences

description: high-throughput profiling of polyadenylation in Y319A mutated CPSF30-L complementary line of cpsf30-2

data_processing:
Library strategy: PAS-seq
Tags less than 20 nt after removal of the 3’ linker and 4 nt random sequences were discarded. All tags were reverse-complemented because the tags were sequenced from 3'-end of transcripts (Fu et al., 2011). Trimmed tags were then mapped to the Arabidopsis genome (TAIR10) using Bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only uniquely mapped tags were kept for downstream analyses. Uniquely located tags with six or more continuous adenines downstream from the poly(A) junction in a 10-nt window were identified as internal priming tags and discarded (Shepard et al., 2011).
For MeRIP-seq data, low-quality reads were discarded and the adaptor sequences were trimmed using Trimmomatic(0.36). Clean Reads were further treated with in-house scripts to eliminate duplication bias. The de-duplicated consensus sequences were further aligned the Arabidopsis thaliana genome (TAIR10) using STAR (2.5.3a).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using bedtools and bedGraphToBigWig program

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background.The seedlings were grown in 1/2 MS medium (aseptic hydroponics) for 12 d.

extract_protocol:
The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).
PAS-seq libraries generated from Col and cpsf30-2 mutants were constructed following the published method in Arabidopsis (Zhang et al., 2015).

tag: developmental stage

value: 12-day-old seedlings


title: ST10R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 10 Days After Anthesis. Biological replicate R1.


title: Pooled Adrenal RNA from C57BL/6J Male mice_rep3

value: Male


title: L2_trachea_CF_pig id 3882

value: lung


title: t821_9_rl

city: Ulm

first: Susanne

last: Lux

address: Albert-Einstein-Allee 23

institute: University Hospital Ulm

data_processing:
alignment with STAR 2.4.2
normalization with DEseq2
Genome_build: hg19
Supplementary_files_format_and_content: txt with normalized read counts

organism: Homo sapiens

source_name: AML leukemic blasts

extract_protocol:
QIAGEN AllPrep
TruSeq Stranded Total RNA Ribominus Gold
100 bp paired-end sequencing on HiSeq2000

tag: mutation

value: relapse


title: pas-310a-2

description: high-throughput profiling of polyadenylation in W310A mutated CPSF30-L complementary line of cpsf30-2


title: Pooled Adrenal RNA from C57BL/6J Female mice_rep1


title: L6_trachea_non-CF_pig id 3894


title: ST00R2

description: Whole fruits of accession Serrano Tampiqueno 74 at 0 Days After Anthesis. Biological replicate R2.

data_processing:
Total RNA Sample QC. All samples need to pass through the following four steps before library construction: (1) Nanodrop: tests RNA purity (OD260/OD280). (2) Agarose Gel Electrophoresis: tests RNA degradation and potential contamination. (3) Agilent 2100: checks RNA integrity.
Library Construction. After the QC procedures, mRNA was enriched using oligo(dT) beads. The mRNA was then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.
Library QC and sequencing. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/µl before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). Libraries were fed into Illumina NovaSeq 6000 machines for sequencing.
Raw data and quality control. The original raw data from Illumina were transformed to Sequenced Reads by base calling. Raw data were recorded in a FASTQ files. GC content distribution was evaluated. Raw reads were filtered to remove reads containing adapters or reads of low quality.
Mapping to the Capsicum annuum reference genome. For mapping TopHat (v2.0.12) was employed with mismatch parameter set to 2 and other parameters set to defaults. Only filtered reads were used to analyze the mapping status of RNA-seq data to the reference genome. RAW FILES  were created in the binary alignment/map format (".bam").
Genome_build: Capsicum_annuum.Annuum.v.2.0.genome.fa
Supplementary_files_format_and_content: Processed data files are in the cvs format with three columns, 1 - "id" (a unique numeric identifier of each feature), 2 - "Gene.id" (the identifier of the gene or gene feature) and 3 - A column with the same name than the sample which contains the read count for the corresponding feature.

extract_protocol:
Total RNA was extracted from flowers and whole chili pepper fruits at different developmental stages using a NucleoSpin™ RNA Plant kit (MACHEREY-NAGEL) according to the manufacturer’s instructions. RNA was extracted from two biological samples comprising either flowers (time 0 DAA) fruits or seedlings from 2-6 different plants. RNA quality was verified by determining the RNA Integrity Number (RIN) for each sample.
Samples of total RNA were shipped to Novogene (https://en.novogene.com/) for library construction, sequencing and mapping to a reference genome. At Novogene, libraries were prepared and sequenced using the Illumina NovaSeq platform to obtain at least 20 million raw paired-end reads of 150 bp per sample.

value: 0 Days After Anthesis (DAA)


title: Pooled Adrenal RNA from C57BL/6J Male mice_rep2


title: t821_9

value: diagnosis


title: ST00R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 0 Days After Anthesis. Biological replicate R1.


title: pas-259a-2

description: high-throughput profiling of polyadenylation in W259A mutated CPSF30-L complementary line of cpsf30-2


title: ST20R1

description: Whole fruits of accession Serrano Tampiqueno 74 at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: QU60R2

description: Whole fruits of accession Piquin Queretaro at 60 Days After Anthesis. Biological replicate R2.

source_name: Piquin Queretaro

value: Wild accession (C. a. var. glabriusculum)

value: 60 Days After Anthesis (DAA)


title: t821_8


title: QU60R1

description: Whole fruits of accession Piquin Queretaro at 60 Days After Anthesis. Biological replicate R1.


title: t821_7_rl


title: pas-30L-2

description: high-throughput profiling of polyadenylation in CPSF30-L complementary line of cpsf30-2

value: CPSF30-L complementary line of cpsf30-2


title: Pooled Adrenal RNA from C57BL/6J Male mice_rep1


title: QU50R2

description: Whole fruits of accession Piquin Queretaro at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: t821_7


title: L1_trachea_non-CF_pig id 3788

value: trachea


title: QU50R1

description: Whole fruits of accession Piquin Queretaro at 50 Days After Anthesis. Biological replicate R1.

value: Whole fruit


title: Rheumatic valvular heart disease (RVHD) plasma sample circRNA 3

city: Ningbo

first: Linwen

last: Zhu

address: 57 Xingning Road, Yinzhou District

institute: Ningbo Medical Treatment Center Lihuili Hospital

description: circRNA expression data from rheumatic valvular heart disease (RVHD) plasma

hyb_protocol: standard Agilent protocol

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 8 samples have flags in P or M (“All Targets Value”) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: RVHD and healthy controls plasma samples

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

treatment_protocol: Plasma samples from RVHD patients and healthy controls were centrifugal from whole blood

tag: plasma sample

value: RVHD plasma sample

tag: gender

value: female


title: t821_6


title: pas-319a-1

value: Y319A mutated CPSF30-L complementary line of cpsf30-2


title: t821_5


title: HFD_PBS3d triplicate 3

city: Toronto

first: Tianru

last: Jin

address: 101 college street

institute: University Health Network

data_processing:
The RNA-seq reads were aligned to the mm10 genome assembly with corresponding RefSeq annotation using STAR2 version 2.4.2a.
The reads per gene were counted with --quantMode GeneCounts option of STAR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

growth_protocol: Mice were fed on high-fat diet for 4 weeks.

extract_protocol:
Liver were removed, flash frozen on dry ice, and total RNA was harvested using Rneasy Mini Kit (Cat#74104, QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were subcutaneously injected with liraglutide for 3 days after 4 weeks of high-fat diet.

value: Liver

tag: age

value: 8 weeks

tag: treatment

value: PBS


title: pas-310a-1

value: 12-day-old seedlings

value: W310A mutated CPSF30-L complementary line of cpsf30-2


title: pas-259a-1

value: W259A mutated CPSF30-L complementary line of cpsf30-2


title: QU40R2

description: Whole fruits of accession Piquin Queretaro at 40 Days After Anthesis. Biological replicate R2.

value: 40 Days After Anthesis (DAA)


title: QU40R1

description: Whole fruits of accession Piquin Queretaro at 40 Days After Anthesis. Biological replicate R1.


title: t821_4

value: diagnosis


title: t821_3


title: Healthy control plasma sample circRNA 3

description: circRNA expression data from healthy control plasma

source_name: Healthy control plasma sample

value: Healthy control plasma sample

value: male


title: QU30R2

description: Whole fruits of accession Piquin Queretaro at 30 Days After Anthesis. Biological replicate R2.

value: Wild accession (C. a. var. glabriusculum)

value: 30 Days After Anthesis (DAA)


title: pas-30L-1

value: CPSF30-L complementary line of cpsf30-2


title: Healthy control plasma sample circRNA 2


title: pas-cpsf30-2

description: high-throughput profiling of polyadenylation in cpsf30-2 (mutant)

value: cpsf30-2 (mutant)


title: Healthy control plasma sample circRNA 1


title: t821_2


title: Rheumatic valvular heart disease (RVHD) plasma sample circRNA 2

value: RVHD plasma sample


title: HFD_Lira3d triplicate 3

value: liraglutide at 300 ug/kg


title: pas-wt-2

description: high-throughput profiling of polyadenylation in Col (wild type)

value: Col (wild type)


title: t821_1


title: Rheumatic valvular heart disease (RVHD) plasma sample circRNA 1


title: pas-cpsf30-1


title: QU30R1

description: Whole fruits of accession Piquin Queretaro at 30 Days After Anthesis. Biological replicate R1.

value: Whole fruit


title: pas-wt-1


title: HFD_Lira3d triplicate 2

value: Liver

value: 8 weeks


title: QU20R1

description: Whole fruits of accession Piquin Queretaro at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: HFD_PBS3d triplicate 2

value: PBS


title: t821_14


title: cpsf30-2-rep3

data_processing:
Tags less than 20 nt after removal of the 3’ linker and 4 nt random sequences were discarded. All tags were reverse-complemented because the tags were sequenced from 3'-end of transcripts (Fu et al., 2011). Trimmed tags were then mapped to the Arabidopsis genome (TAIR10) using Bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only uniquely mapped tags were kept for downstream analyses. Uniquely located tags with six or more continuous adenines downstream from the poly(A) junction in a 10-nt window were identified as internal priming tags and discarded (Shepard et al., 2011).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated using bedtools and bedGraphToBigWig program

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background.The seedlings were grown in 1/2 MS medium (aseptic hydroponics) for 7 d.

extract_protocol:
The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).
PAS-seq libraries generated from Col and cpsf30-2 mutants were constructed following the published method in Arabidopsis (Zhang et al., 2015).
PAS-seq

treatment_protocol: No treatment

value: 12-day-old seedlings


title: t821_13


title: HFD_Lira3d triplicate 1


title: QU10R2

description: Whole fruits of accession Piquin Queretaro at 10 Days After Anthesis. Biological replicate R2.

value: 10 Days After Anthesis (DAA)


title: QU10R1

description: Whole fruits of accession Piquin Queretaro at 10 Days After Anthesis. Biological replicate R1.


title: cpsf30-2-rep2


title: t821_12_rl

value: relapse


title: cpsf30-2-rep1


title: HFD_PBS3d triplicate 1


title: QU20R2

description: Whole fruits of accession Piquin Queretaro at 20 Days After Anthesis. Biological replicate R2.


title: UTX CUT&Tag Utx-/- CD8+ T cells D15 Rep 2

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling was done using Genome Analyzer Pipeline Software
FASTQ files were trimmed with the TruSeq adapter and an additional 3bp on each end.
CUT&RUN or CUT&Tag aligment to the mm9 or ecoli genome was performed using Bowtie2, CUT&Tag with options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 1500
CUT&Tag bigwig files generated from merged bam files with deepTools options: bamCoverage --ignoreDuplicates
CUT&RUN peaks called with MACS2 and hiddenDomains CUT&Tag peaks called with MACS2 on merged bamfiles with options: --broad --broad-cutoff 0.1
CUT&Tag UTX peaks were merged from D0 and D15 timepoints, and filtered for blacklisted regions and RPKM > 1
CUT&Tag UTX peak readcounts for individual bam files were counted with deepTools: multiBamSummary --outRawCounts --ignoreDuplicates
EdgeR identified significant UTX peaks between D15 WT vs. D0 WT or D15 WT vs. D15 KO with mapped reads per ecoli reads normalization factors
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files with reads per gene (RNA-seq) or peak (CUT&RUN or CUT&Tag)

source_name: Utx-/- CD8+ T cells

extract_protocol:
RNA was extracted using TRIZOL reagent, followed by mRNA purification
Libraries were generated using KAPA mRNA HyperPrep Kit (KK8580) for RNA-seq, KAPA HyperPrep Kit (KK8504) for CUT&RUN, or PCR amplification for CUT&Tag

treatment_protocol: WT or Utx-/- P14+CD8+ T cells were transferred to C57BL/6 recipient mice, CD4+ T cells were depleted prior to LCMV-A22 infection, and donor P14+CD8+ T cells were sorted from spleens at day 21 post-infection (RNA-Seq) or 15 days post-infection (CUT&RUN or CUT&Tag).

tag: timepoint

value: 15 days post infection

value: Utx-/- knock-out


title: UTX CUT&Tag Utx-/- CD8+ T cells D15 Rep 1


title: QU00R2

description: Whole fruits of accession Piquin Queretaro at 0 Days After Anthesis. Biological replicate R2.

value: Wild accession (C. a. var. glabriusculum)

value: 0 Days After Anthesis (DAA)


title: QU00R1

description: Whole fruits of accession Piquin Queretaro at 0 Days After Anthesis. Biological replicate R1.


title: t821_12

value: diagnosis


title: t821_11


title: Col-rep1


title: QC60R2

description: Whole fruits of accession F1 of cross QU x CM at 60 Days After Anthesis. Biological replicate R2.

source_name: F1 of cross QU x CM

value: F1 cross between Domesticated and Wild

value: 60 Days After Anthesis (DAA)


title: set1_fmn1 ATAC-seq

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

description: set1_fmn1 ATAC-seq

data_processing:
FASTQ files from biological and technical replicates for each sample were merged. Reads were aligned to the sacCer3 reference genome (release R64-2-1) using Bowtie2 version 2.2.5 in ‘very-sensitive’ mode
Aligned reads were filtered and indexed using SAMtools. Reads were adjusted so that the genome average was set at 1-fold enrichment, then data from immunoprecipitated samples were divided by data from input samples.
Heatmaps were generated using deepTools. Transcription frequency was calculated by a sum of signal in a range TSS to TSS + 200 bp of each yeast gene adapted from the results of NET-seq (Nature 469, 368-373 (2011))
Genome_build: sacCer3 reference genome (release R64-2-1)
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: log phase

growth_protocol: SC medium; yeast cell were cultured to exponetial phase

extract_protocol:
For ChIP experiments: The formaldehyde-crosslinked cell pellets were transferred to to a 2-ml flat-bottom screw-cap tube containing 300 μl glass beads, and disrupt the cells in a mini beadbeater for 5 min or until 90% of cells are disrupted. Sonicate samples in a cold Bioruptor sonicator bath at maximum output, cycling 30 sec on, 30 sec off, for a total of 30 min. Centrifuge samples for 30 min at 16,000 × g, 4°C, and transfer the supernatant to a new 1.5-ml siliconized microcentrifuge tube.After sonication, solubilized chromatin will stay in the supernatant. Libraries were prepared using the Ovation Ultralow v2 kit (NuGEN, catalog #0344).
For ATAC-seq experiements: Spheroplasts were prepared by resuspending 3 OD600 units of cells in 400 ul of sorbitol buffer [1.4 M sorbitol, 40 mM HEPES-KOH (pH 7.5), 0.5 mM MgCl2] containing 0.5 mg/ml Zymolyase®-100T (Nacalai Tesque, Inc.) and 10 mM DTT and incubating at 30°C for 15 min. The spheroplasts were washed twice in sorbitol buffer, resuspended in 300 ul of sorbitol buffer, and then, 10 ul of cell suspension (0.1 OD600 units) was used to incubate with 2.5 ul of Tn5 Transposase (TDE1), reaction buffer (TD) from Nextera™ kit and additional 0.01% digitonin in a final volume of 50 ul at 37°C for 30 min. Transposed DNA was purified using MinElute™ PCR Purification Kit (QIAGEN) and then amplified by PCR with custom primers in Nextera™ DNA CD Indexes kit.

tag: strain background

tag: genotype/variation


title: UTX CUT&Tag WT CD8+ T cells D15 Rep 3

source_name: WT CD8+ T cells

value: wild-type


title: UTX CUT&Tag WT CD8+ T cells D15 Rep 4


title: Col-rep2


title: UTX CUT&Tag WT CD8+ T cells D0 Rep 2


title: QC60R1

first: Octavio

last: Martinez de la Vega

description: Whole fruits of accession F1 of cross QU x CM at 60 Days After Anthesis. Biological replicate R1.

growth_protocol: Seeds of 10 Capsicum annuum accessions were surface sterilized with a 70% ethanol solution for 10 s before treatment with a 10% hypochlorite solution for 10 s and six rinses with distilled water. Wild accession seeds were similarly treated, after an initial treatment with 50% sulfuric acid solution to break seed dormancy. All accession seeds were germinated in plastic trays containing a mixture of three parts peat moss, one part perlite, one part vermiculite, one part sludge and two parts forest soil in a growth chamber, with 16 h light (photon flux of 70 μmol m-2 s-1) at 28 °C and 66% relative humidity. Three-week-old chili pepper plants were transplanted individually into plastic 5 L pots containing the same soil mixture described above. During transplantation, 15 g of a mycorrhizae fungal and beneficial bacteria mixture were added to optimize root growth and development. Plants were fertilized with Long Ashton solution every two weeks. Flowers and fruits at 0, 10, 20, 30, 40, 50 and 60 DAA were collected and immediately frozen in liquid nitrogen, and stored at -80 °C.


title: inv16_9


title: QC50R2

description: Whole fruits of accession F1 of cross QU x CM at 50 Days After Anthesis. Biological replicate R2.

value: 50 Days After Anthesis (DAA)


title: t821_10


title: inv16_8


title: UTX CUT&Tag WT CD8+ T cells D15 Rep 1


title: t821_11_rl


title: QC50R1

description: Whole fruits of accession F1 of cross QU x CM at 50 Days After Anthesis. Biological replicate R1.

value: Whole fruit


title: set1 ATAC-seq

description: set1 ATAC-seq


title: Col-rep3


title: WT ATAC-seq

description: WT ATAC-seq

value: WT


title: fmn1 ATAC-seq

description: fmn1 ATAC-seq


title: UTX CUT&Tag WT CD8+ T cells D0 Rep 1


title: QC40R2

description: Whole fruits of accession F1 of cross QU x CM at 40 Days After Anthesis. Biological replicate R2.

value: 40 Days After Anthesis (DAA)


title: inv16_7


title: QC30R2

description: Whole fruits of accession F1 of cross QU x CM at 30 Days After Anthesis. Biological replicate R2.

value: 30 Days After Anthesis (DAA)


title: inv16_6


title: QC40R1

description: Whole fruits of accession F1 of cross QU x CM at 40 Days After Anthesis. Biological replicate R1.


title: set1_fmn1 Mcm4 ChIP

description: set1_fmn1 Mcm4 ChIP

value: W303a Mcm4-3xFLAG

tag: chip antibody

value: anti-Flag


title: IL-27Day14-2

city: rochester

first: Yugo

last: Morita

state: New York

address: 601 Elmwood Avenue, Box 665, Center for Musculoskeletal Research

institute: University of Rochester Medical Center

data_processing:
The libraries were sequenced with the Illumina NovaSeq6000 platform (Illumina).
Quality filtering and adapter removal were performed by fastp version 0.20.0 (78) using the following parameters: “--in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json”.
The remaining high quality processed reads were then mapped to the Mus musculus genome reference (GRCm38.p6) with STAR version 2.7.0f using the following parameters: “--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical”.
The mapped reads were counted within the GRCm38.p6 gene annotations using featureCounts read quantification program in Subread version 1.6.4.
Data normalization were performed using DESeq2 version 1.22.1 within the R version 3.5.1.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include normarized gene counts for every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tibia

extract_protocol:
Tibia were pulverized at liquid nitrogen temperature and homogenized using Bullet Blender Gold (Next Advance). Collection of Total RNA from homogenized tibia was performed using TRIzol extraction (ThermoFisherScientific) and RNeasy Mini Kits (Qiagen).
The TruSeq Stranded Total RNA Library Prep Gold (Illumina) was utilized for next generation sequencing library preparation per the manufacture’s instructions.

value: tibia

value: expressing murine IL-27 (rAAV-IL-27)

tag: time post-septic surgery

value: day 14


title: UTX CUT&Tag WT CD8+ T cells D15 Rep 2

value: 15 days post infection

tag: genotype


title: IL-27Day14-3


title: set1_fmn1 Mcm4 input

description: set1_fmn1 Mcm4 input


title: fmn1 Mcm4 ChIP

description: fmn1 Mcm4 ChIP


title: inv16_4_rl

value: relapse


title: IL-27Day14-1


title: QC30R1

city: Irapuato

address: km 9.6 Libramiento Norte

institute: Cinvestav

description: Whole fruits of accession F1 of cross QU x CM at 30 Days After Anthesis. Biological replicate R1.


title: inv16_4


title: inv16_3


title: QC20R1

description: Whole fruits of accession F1 of cross QU x CM at 20 Days After Anthesis. Biological replicate R1.

value: 20 Days After Anthesis (DAA)


title: IL-27Day7-2

value: day 7


title: QC10R1

description: Whole fruits of accession F1 of cross QU x CM at 10 Days After Anthesis. Biological replicate R1.

value: F1 cross between Domesticated and Wild

value: 10 Days After Anthesis (DAA)


title: QC20R2

description: Whole fruits of accession F1 of cross QU x CM at 20 Days After Anthesis. Biological replicate R2.


title: WT Mcm4 ChIP

description: WT Mcm4 ChIP


title: QC00R2

description: Whole fruits of accession F1 of cross QU x CM at 0 Days After Anthesis. Biological replicate R2.

value: 0 Days After Anthesis (DAA)


title: set1 Mcm4 ChIP

description: set1 Mcm4 ChIP


title: IL-27Day7-1


title: IL-27Day3-3

value: day 3


title: inv16_1

value: diagnosis


title: set1 Mcm4 input

description: set1 Mcm4 input


title: inv16_2


title: inv16_11


title: QC00R1

description: Whole fruits of accession F1 of cross QU x CM at 0 Days After Anthesis. Biological replicate R1.

value: Whole fruit


title: WT Mcm4 input

description: WT Mcm4 input

value: WT


title: inv16_10_rl


title: IL-27Day3-2


title: IL-27Day3-1


title: set1_fmn1 Rpb3 ChIP

description: set1_fmn1 Rpb3 ChIP

value: anti-Rpb3 Neoclone 1Y26


title: CW70R2

description: Whole fruits of accession California Wonder at 70 Days After Anthesis. Biological replicate R2.

source_name: California Wonder

value: Domesticated variety

value: 70 Days After Anthesis (DAA)


title: inv16_5


title: fmn1 Mcm4 input

description: fmn1 Mcm4 input

value: W303a Mcm4-3xFLAG


title: inv16_10


title: IL-27Day7-3

value: tibia

value: expressing murine IL-27 (rAAV-IL-27)


title: IL-27Day1-3

value: day 1


title: CW70R1

description: Whole fruits of accession California Wonder at 70 Days After Anthesis. Biological replicate R1.


title: CW60R2

description: Whole fruits of accession California Wonder at 60 Days After Anthesis. Biological replicate R2.

value: 60 Days After Anthesis (DAA)


title: IL-27Day1-2


title: set1_fmn1 Rpb3 input

description: set1_fmn1 Rpb3 input


title: fmn1 Rpb3 input

description: fmn1 Rpb3 input


title: set1 Rpb3 ChIP

description: set1 Rpb3 ChIP


title: healthy_CD34_5

source_name: healthy G-CSF mobilized CD34+ cells

value: G-CSF mobilized healthy CD34+


title: GFPDay14-3

value: expressing GFP

value: day 14


title: healthy_CD34_7


title: CW50R1

description: Whole fruits of accession California Wonder at 50 Days After Anthesis. Biological replicate R1.

value: 50 Days After Anthesis (DAA)


title: CW50R2

description: Whole fruits of accession California Wonder at 50 Days After Anthesis. Biological replicate R2.


title: CW60R1

description: Whole fruits of accession California Wonder at 60 Days After Anthesis. Biological replicate R1.


title: WT Rpb3 ChIP

description: WT Rpb3 ChIP


title: set1 Rpb3 input

description: set1 Rpb3 input


title: healthy_CD34_6


title: healthy_CD34_9


title: CW40R1

description: Whole fruits of accession California Wonder at 40 Days After Anthesis. Biological replicate R1.

value: 40 Days After Anthesis (DAA)


title: CW40R2

description: Whole fruits of accession California Wonder at 40 Days After Anthesis. Biological replicate R2.


title: healthy_CD34_2


title: CW30R2

description: Whole fruits of accession California Wonder at 30 Days After Anthesis. Biological replicate R2.

value: 30 Days After Anthesis (DAA)


title: fmn1 Rpb3 ChIP

description: fmn1 Rpb3 ChIP


title: WT Rpb3 input

description: WT Rpb3 input


title: IL-27Day1-1


title: GFPDay14-1


title: GFPDay7-3

value: day 7