title: POC.D_P36

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: ddt.poc.csv.gz

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 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure 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 10-5 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: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®TMSD®TM obtained from Harlan/Envigo (Indianapolis, IN) at about 70 to 100 days of age were maintained in ventilated (up to 50 air exchanges/hour) isolator cages (cages with dimensions of 10 3⁄4′′ W×19 1⁄4′′ D×10 3⁄4′′ H, 143 square inch floor space, fitted in Micro- vent 36-cage rat racks; Allentown Inc., Allentown, NJ) containing Aspen Sani chips (pinewood shavings from Harlan) as bedding, and a 14 h light: 10 h dark regimen, at a temperature of 70 F and humidity of 25% to 35%. The mean light intensity in the animal rooms ranged from 22 to 26 ft-candles. Rats were fed ad lib with standard rat diet (8640 Teklad 22/5 Rodent Diet; Harlan) and ad lib tap water for drinking. To obtain time- pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (i.e. sperm plug present) (day 0) rats were monitored for diestrus and body weight.The treated gestating female rats were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from the F1 generation of control or DDT or vinclozolin lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring.

extract_protocol:
The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 5 ml of 1X PBS solution for up to 2 hours at 4°C. The epididymal tissue was minced and the released sperm was centrifuged at 6,000 x g, then the supernatant removed, and the pellet resuspended in NIM buffer, to be stored at -80°C until further use. One hundred μl of sperm suspension was sonicated to destroy somatic cells and tissue, spun down at 6,000 x g, the sperm pellet washed with 1X PBS once, and then combined with 820 μl DNA extraction buffer and 80 μl 0.1M DTT. The sample was incubated at 65oC for 15 minutes. Following this incubation 80 μl proteinase K (20 mg/ml) was added and the sample incubated at 55oC for at least 2 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega, A7953) was added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 12,500 x g for 30 minutes at 4oC. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20oC freezer for at least one hour. After precipitation the sample was centrifuged at 12,500 x g for 20 min at 4oC. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500 μl of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4oC at 12,500 x g and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 μl of nuclease free water. Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: rat sperm DNA pools were generated using the appropriate amount of genomic DNA from each individual for 6 pools each of paternal and maternal outcross control, paternal and maternal outcross DDT, and paternal and maternal outcross vinclozolin lineage animals. Genomic DNA pools were sonicated using the Covaris M220 the following way: the pooled genomic DNA was diluted to 130 μl with TE buffer into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube and the volume measured. The sonicated DNA was then diluted with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) to 400 μl, heat-denatured for 10 min at 95 ̊C, then immediately cooled on ice for 10 min. Then 100 μl of 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4 ̊C.  The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; 11201D) were pre-washed as follows: The beads were resuspended in the vial, then the appropriate volume (50 μl per sample) was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 mL PBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. Tube was then placed into a magnetic rack for 1-2 minutes and the supernatant discarded. The tube was removed from the magnetic rack and the beads washed once. The washed beads were resuspended in the same volume of IP buffer (50 mM sodium phosphate ph7.0, 700 mM NaCl, 0.25% TritonX-100) as the initial volume of beads. 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4 ̊C.  After the incubation the bead-antibody-DNA complex was washed three times with IP buffer as follows: The tube was placed into magnetic rack for 1-2 minutes and the supernatant discarded, then washed with IP buffer 3 times. The washed bead-DNA solution is then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was then incubated for 2-3 hours on a rotator at 55 ̊C and then 250 μl of buffered Phenol-Chloroform-Isoamylalcohol solution was added to the supe and the tube vortexed for 30 sec then centrifuged at 12,500 x g for 5 min at room temperature. The aqueous supernatant was carefully removed and transferred to a fresh microfuge tube. Then 250 μl chloroform were added to the supernatant from the previous step, vortexed for 30 sec and centrifuged at 12,500 x g for 5 min at room temperature. The aqueous supernatant was removed and transferred to a fresh microfuge tube. To the supernatant 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol were added and mixed well, then precipitated in -20 ̊C freezer for 1 hour to overnight.  The precipitate was centrifuged at 12,500 x g for 20min at 4 ̊C and the supernatant removed, while not disturbing the pellet. The pellet was washed with 500μl cold 70% ethanol in -20 ̊C freezer for 15 min. then centrifuged again at 12,500 x g for 5min at 4 ̊C and the supernatant discarded. The tube was spun again briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP pools were used to create libraries for next generation sequencing (NGS) using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. NGS was performed at WSU Spokane Genomics Core using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50 bp and approximately 30 million reads per pool. Five to six libraries were run in one lane.

treatment_protocol: On days 8 through 14 of gestation, the females received daily intraperitoneal injections of DDT (25 mg/kg body weight/day) or vinclozolin (100mg/kg body weight/day Chem Services, Westchester PA, USA) or dimethyl sulfoxide (DMSO). The DDT (dichlorodiphenyltrichloroethane) was obtained from Chem Service Inc. (West Chester, PA) and reported to have a purity of 98.2%. DDT and vinclozolin were dissolved and injected in DMSO vehicle. Treatment lineages are designated ‘control’, ‘DDT’ or 'vinclozolin' lineages.

tag: outcross type

value: paternal

tag: treatment

value: DDT


title: N2 mixed population on NA22 bacteria replicate 2-sRNAseq

status: Public on Jul 23 2019

type: SRA

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 North Wolfe Street, PCTB 706

department: Molecular Biology and Genetics

country: USA

institute: JHU School of Medicine

description:
smRNA-Seq
N2_meg34_strain1_mixed_NA22_smRNA_ID.txt

library_source: transcriptomic

data_processing:
Adapters were trimmed with Cutadapt for sRNAseq. This step was omitted for mRNAseq.
Reads were aligned with Bowtie2 for sRNAseq and HiSat2 for mRNAseq.
Read alignments were counted with HTSeq-count for both sRNAseq and mRNAseq.
Normalized read counts were obtained with DEseq2 for both sRNAseq and mRNAseq.
Genome browser views were obtained with IGV.
Genome_build: ce10
Supplementary_files_format_and_content: Tab delimited .txt files with log2FCs, q-values, RPMs, etc.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Whole worm, mixed population on NA22

growth_protocol: Starvation synchronized or mixed population. Grown on either NA22 or HT115 bacteria with L4440 vector at 20 C.

extract_protocol:
TRIzol and Zymo RNA purification kit. TRIzol and Zymo RNA Concentrator
TruSeq Small RNA Library Preparation Kit/TruSeq RNA Library Preparation Kit.

treatment_protocol: RNA for sRNAseq libraries was treated with 5’ polyphosphatase. RNA for mRNAseq libraries was treated with the RiboZero Gold Epedemiology Kit and supplemented with the ERCC Spike-in.

tag: strain/genotype

tag: growth

value: on NA22

tag: tissue

value: whole worm

tag: group

value: mixed population


title: POC.D_P32

description: ddt.poc.csv.gz

library_source: genomic

molecule: genomic DNA


title: EA1448_08: Priming day 3 after injury, biological replicate 2

type: RNA

city: Tochigi

first: Ken-ichi

last: INOUE

address: 880 Kitakobayashi, Mibu-machi, Shimotsuga-gun

country: Japan

institute: Dokkyo Medical University

description: Gene expression of stromal vascular fraction from subcutaneous fat during wound healing: Day 3 after injury

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ̊C on GeneChip Human Genome U133 Plus 2.0 Array.Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Mus musculus

source_name: Stromal vascular fraction from subcutaneous fat during wound healing: Day 3 after injury

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT PLUS Reagent Kit(Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Mice were maintained in standard conditions.

extract_protocol: Total RNA was isolated by RNA iso plus (similar to TRIzol).

treatment_protocol: Inguinal fat was surgically injured and stromal vascular fraction was purified from the tissue during each time point.

value: inguinal fat, stromal vascular fraction

tag: genotype

value: wild type

tag: strain

value: Balb/c

tag: age

value: 10 weeks


title: EA1448_09: Priming day 3 after injury, biological replicate 3


title: POC.D_P31

description: ddt.poc.csv.gz


title: EA1448_07: Priming day 3 after injury, biological replicate 1


title: POC.D_P33

description: ddt.poc.csv.gz


title: EA1448_04: Priming day 1 after injury, biological replicate 1

description: Gene expression of stromal vascular fraction from subcutaneous fat during wound healing: Day 1 after injury

source_name: Stromal vascular fraction from subcutaneous fat during wound healing: Day 1 after injury


title: EA1448_03: Priming day 0 after injury, biological replicate 3

description: Gene expression of stromal vascular fraction from subcutaneous fat during wound healing: Day 0 after injury

source_name: Stromal vascular fraction from subcutaneous fat during wound healing: Day 0 after injury


title: EA1448_06: Priming day 1 after injury, biological replicate 3


title: EA1448_05: Priming day 1 after injury, biological replicate 2


title: POC.D_P34

description: ddt.poc.csv.gz


title: POC.V_P10

description: vin.poc.csv.gz

value: vinclozolin


title: POC.V_P11

description: vin.poc.csv.gz


title: POC.D_P35

description: ddt.poc.csv.gz


title: N2 fed HT115-L4440 young mother replicate 2-sRNAseq

description:
smRNA-Seq
N2_rde11_young_mother_HT115_L4440_smRNA_ID.txt

source_name: Whole worm, young mother on HT115-L4440

value: young mother


title: N2 fed HT115-L4440 young mother replicate 1-sRNAseq


title: POC.V_P12

description: vin.poc.csv.gz


title: P2-E1-028

city: Grand Rapids

first: Alison

middle: I

last: Bernstein

state: MI

address: 400 Monroe Ave NW

department: Translational Neuroscience

institute: Michigan State University

data_processing:
Adapter trimming: Read adapters were trimmed using the trim_galore tool (version 0.4.5). In trim_galore, we used the default minimum quality score and added a stringency value of 6, thereby requiring a minimum overlap of 6 bp. For the RRBS data, reads were trimmed in “RRBS mode” using the --rrbs parameter; this parameter was not included for RNA-seq data trimming.
Read alignment (RRBS): Reads were aligned to the mm10 genome using bismark (version 0.19.1) and bowtie2 (version 2.3.2) with default parameters.
Coverage file generation (RRBS): Methylation data was extracted from the aligned reads in bismark (version 0.19.1) using a minimum threshold of 5 reads to include a CpG site in analysis.
Read count quantification (RNA-seq): Reads were quantified and quasi-mapped to a self-generated mm10 index using the salmon tool (version 0.11.3). During read quantification in salmon, the --numBootstraps parameter was used to generate 100 bootstraps for each sample.
Read abundance generation (RNA-seq): Quantified RNA-seq reads were processed for downstream analyses using the prepare_fish_for_sleuth function in the wasabi R package (version 0.3).
Genome_build: mm10
Supplementary_files_format_and_content: RRBS: bismark coverage files (.cov.gz) contain % methylation beta values for CpG sites with sequencing coverage.
Supplementary_files_format_and_content: RNA-seq: quant.sf and abundance.h5 files contain bootstraps along with the estimates of transcript abundances.

source_name: Midbrain tissue

growth_protocol: Male and female C57BL/6 mice were purchased from Jackson Laboratory (Bar Harbor, ME, USA). Mice were maintained on a 12:12 reverse light/dark cycle. Food and water were available ad libitum. Mice were maintained on standard LabDiet 5021 chow (LabDiet, St. Louis, MO). F0 females were individually housed during dieldrin dosing, except during the mating phase. F1 pups were group housed by sex; no more than four animals were housed per cage. All procedures were conducted in accordance with the National Institutes of Health Guide for Care and Use of Laboratory Animals and approved by the Institutional Animal Care and Use Committee at Michigan State University.

extract_protocol:
DNA: DNA isolation was performed on frozen mouse midbrain samples using the phenol:chloroform:isoamyl alcohol method.
RNA: RNA isolation from frozen mouse midbrain samples was performed using a modified RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany). Several changes were made to the standard RNeasy Lipid Tissue Mini kit to improve RNA yield from midbrain samples. First, tissue was homogenized in 200 µL cold Qiazol lysis reagent using a Kimble Kontes pellet pestle (Kimble Chase, Rockwood, TN) for microcentrifuge tubes. Second, after physical homogenization, an additional 800 µL of Qiazol lysis reagent was added to each tissue sample. Third, after initial centrifugation, supernatant was transferred to an Invitrogen Phasemaker tube (ThermoFisher, Waltham, MA) to facilitate transfer of the RNA-containing aqueous layer. As a result of using the Phasemaker tubes, the second centrifugation step was reduced from 15 minutes to 5 minutes. In addition to these changes, the optional DNase digestion step (RNeasy Lipid Tissue Appendix C) was included to improve purity of isolated RNA.
DNA (RRBS): RRBS library preparation was performed at the University of Michigan Epigenomics Core. Briefly, 200 ng of genomic DNA was digested for 16-18 hours using MspI, a restriction enzyme that preferentially cuts DNA at CCGG nucleotide sequences. Restriction enzyme-digested DNA was purified using phenol:chloroform extraction and ethanol precipitation in the presence of glycogen and sodium acetate. Precipitated DNA was resuspended in 10 mM Tris-Cl pH 8.5 and processed for end-repair, A-tailing, and ligation of adapters with methylated cytosines. The ligated DNA was further cleaned according to the NuGEN TrueMethyl oxBS module (NuGEN, Redwood City, CA; Cat # 0414-32) instructions with 80% acetonitrile and magnetic beads. Ligated DNA was then eluted in UltraPure water and split into two tubes, one processed for bisulfite conversion only and the other processed for oxidative-bisulfite treatment, according to the TrueMethyl kit’s instructions. After bisulfite conversion and cleanup, the samples were amplified using the Roche High Fidelity FastStart system ((Sigma-Aldrich, St. Louis, MO) and TruSeq PCR primers (Illumina Inc., San Diego, CA), according to the following protocol: 94˚C for 5 minutes; 18 cycles of 94˚C for 20 seconds, 65˚C for 30 seconds, and 72˚C for 1 min; 72˚C for 3 minutes. Final library cleanup was done with 1:1 volume of Agencourt AMPure XP SPRI beads (Beckman Coulter, Brea, CA).
RNA (RNA-seq): RNA-seq library preparation was performed at the Van Andel Genomics Core. Libraries were prepared from 100 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems, Wilmington, MA USA). As part of the library prep, RNA was sheared to 300-400 bp. After cDNA synthesis, but prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA).

treatment_protocol: For both adult and developmental exposure, mice were administered 0.3 mg/kg dieldrin dissolved in corn oil vehicle and mixed with peanut butter pellets every 3 days.

value: Mouse midbrain

value: 12 weeks old

tag: Sex

value: Male

tag: exposure type

value: Adult exposure

value: Dieldrin


title: N2 mixed population on NA22 bacteria replicate 1-sRNAseq


title: POC.V_P9

description: vin.poc.csv.gz


title: rde-11(hj37) fed HT115-L4440 young mother replicate 2-sRNAseq


title: EA1448_02: Priming day 0 after injury, biological replicate 2


title: MC38 tumor, IR, rep 1

city: Chicago

first: Ainhoa

last: Arina

state: Illinois

department: Radiation and Cellular Oncology

institute: The University of Chicago

hyb_protocol: Performed following the Affymetrix standard protocol

data_processing: RMA

source_name: MC38 tumor

growth_protocol: 1 × 10^6 MC38 tumor cells were subcutaneously injected into the flank of 6-8 week old C57BL/6 female mice

extract_protocol: Established MC38 tumor cell suspensions obtained by enzymatic digestion with Liberase TM/DNAse I were spun down in 35% Percoll. LN were mechanically disrupted through a sterile 70-μm nylon mesh filter. Tumor and LN cell suspensions were then enriched for CD8+ T cells using EasySep CD8+ positive selection kit before staining with appropriate antibodies and FACS-sorting.

treatment_protocol: Some mice received 5 Gy whole body irradiation (WBI) 5 h before sacrifice and extraction of organs

value: irradiated

tag: cell type

value: CD3+CD8+CD44+CD62L- T cells

tag: gender

value: female

value: 6-8 weeks


title: rde-11(hj37) fed HT115-L4440 young mother replicate 1-sRNAseq

value: whole worm


title: POC.V_P7

description: vin.poc.csv.gz

value: paternal


title: LN, IR, rep 1

scan_protocol: Performed following the Affymetrix standard protocol

source_name: lymph nodes


title: POC.C_P24

description: vin.poc.csv.gz

value: control


title: MC38 tumor, IR, rep 2

label_protocol: Performed following the Affymetrix standard protocol


title: LN, Non IR, rep 1

value: non-irradiated


title: rde-11(hj37) fed HT115-pos-1(400nt) young mother NO PHOSPHATASE replicate 2-sRNAseq

data_processing:
Adapters were trimmed with Cutadapt.
Reads were aligned with Bowtie2
Read alignments were counted with HTseq-count
Normalized read counts were obtained with DEseq2
Genome browser views were obtained with IGV
Genome_build: ce10
Supplementary_files_format_and_content: Tab delimited .txt files with log2FCs, q-values, RPMs, etc.

source_name: Whole worm, young mother

growth_protocol: Starvation synchronized. Grown on HT115 bacteria expressing pos-1 dsRNA at 20 C.

extract_protocol:
TRIzol and Zymo RNA purification kit. TRIzol and Zymo RNA Concentrator
TruSeq Small RNA Library Preparation Kit.

treatment_protocol: RNA was either treated or not treated with 5’ polyphosphatase.

tag: rna treatment

value: Untreated


title: LN, Non IR, rep 2


title: P2-E1-014


title: P2-E1-002


title: POC.C_P23

description: vin.poc.csv.gz


title: POC.C_P22

description: vin.poc.csv.gz


title: P2-E1-017


title: POC.V_P8

description: vin.poc.csv.gz


title: MC38 tumor, Non IR, rep 1


title: EA1448_01: Priming day 0 after injury, biological replicate 1

value: inguinal fat, stromal vascular fraction

value: wild type

value: Balb/c

value: 10 weeks


title: LN, IR, rep 2


title: P2-E1-015

value: Mouse midbrain

value: 12 weeks old


title: meg-3(ax3055) meg-4(ax3052) JH3745 fed HT115-pos-1(400nt) young mother NO PHOSPHATASE replicate 2-sRNAseq

value: young mother


title: POC.C_P21

description: vin.poc.csv.gz


title: P2-E1-013

value: Male

value: Adult exposure

value: Control


title: P2-E1-010


title: rde-11(hj37) fed HT115-pos-1(400nt) young mother NO PHOSPHATASE replicate 1-sRNAseq


title: LN_WIV+CD8a ALN-1, replicate 2

city: Gent

first: Bram

last: Van Den Eeckhout

address: Albert Baertsoenkaai 3

country: Belgium

institute: VIB-UGent

description:
sample name in processed data file:
BVDE@23@LN@S22

data_processing:
Base-calling: Illumina Casava1.7 software and ShortRead 1.36.1
Quality trimming to trim low-quality end (< Q20): FastX 0.0.14
Adapter trimming: cutadapt 1.15
Quality filtering: FastX 0.0.14 and ShortRead 1.36.1
Removal of contaminants: bowtie 2.3.3.1
Aligment of reads to reference genome: read mapping, quality filtering, sorting and indexing: STAR 2.5.2b and samtools 1.5
Computing expression levels: counting/gene, merging with gene annotation, filtering genes, within-sample normalization, between-sample normalization and FPKM value calculation: featureCounts 1.5.3 (parameters: -Q 0 -s 0 -t exon -g gene id) and EDASeq
Genome_build: Ref. genome: Mus musculus.Ensembl.GRCm38.82
Supplementary_files_format_and_content: Excel files with gene ids, gene names, raw counts, FPKM values and additional information

source_name: Lung-draining mediastinal lymph node

growth_protocol: All mice were housed under pathogen-free conditions in individually ventilated cages, placed in a temperature-controlled environment with a 12h day/12h night cycle. Mice received food and water ad libitum.

extract_protocol:
CD8+ T cells were sorted out (4°C) of the mixed cell populations and captured in 350 mL of RLT+ lysis buffer, supplemented with b-mercaptoethanol (4°C) (RNeasy Plus Micro Kit, 74034, Qiagen). The concentration, quality and integrity of RNA was addressed using an Agilent 2100 Bioanalyzer (Agilent) and only samples with an RNA integrity number (RIN) >=  8, 280/260- and 260/230-values > 1.8 were sent for sequencing.
The VIB Nucleomics Core performed the library preparation and library pooling using standard Illumina protocols (TruSeq kit).

treatment_protocol: BALB/c mice were primed by an i.m. injection of whole-inactivated X47 virus (WIV), followed by an i.v. injection with WT IL-1b or CD8a ALN-1 24h post-WIV delivery. AddaVax adjuvant was i.m. co-administered with WIV. An identical boost treatment was administered two weeks after priming. Two weeks post-boost, mice were challenged i.n. with 2xLD50 of the pH1N1. One week post-inoculum, mice were euthanized, lungs and lung-draining mediastinal LNs were isolated and processed and  CD8+ T cells were isolated using FACS.

value: Lung-draining mediastinal lymph node

value: CD8+ T cells

value: BALB/c

tag: age at vaccination

value: 7 weeks

tag: vaccinated with

value: WIV+CD8a ALN-1

tag: infection with

value: 2xLD50 H1N1 influenza A intranasal


title: LN_WIV+CD8a ALN-1, replicate 3

description:
sample name in processed data file:
BVDE@24@LN@S23


title: LN_WIV+CD8a ALN-1, replicate 1

description:
sample name in processed data file:
BVDE@22@LN@S21


title: POC.C_P20

description: vin.poc.csv.gz

tag: outcross type

value: paternal

value: control


title: MC38 tumor, Non IR, rep 2

tag: treatment

value: non-irradiated

value: CD3+CD8+CD44+CD62L- T cells

value: female

value: 6-8 weeks


title: N2 fed HT115-pos-1(400nt) young mother NO PHOSPHATASE replicate 2-sRNAseq

tag: strain/genotype

value: whole worm

value: Untreated


title: P2-E1-007

value: Mouse midbrain

value: 12 weeks old

value: Male


title: N2 fed HT115-pos-1(400nt) young mother NO PHOSPHATASE replicate 1-sRNAseq

value: young mother


title: LN_WIV+IL-1b, replicate 2

description:
sample name in processed data file:
BVDE@20@LN@S19

value: Lung-draining mediastinal lymph node

value: CD8+ T cells


title: P2-E1-005

value: Adult exposure

value: Control


title: LN_WIV+IL-1b, replicate 3

description:
sample name in processed data file:
BVDE@21@LN@S20

value: BALB/c

value: 7 weeks

value: 2xLD50 H1N1 influenza A intranasal


title: MOC.D_P30

description: ddt.moc.csv.gz

value: maternal

value: DDT


title: P3-E1-195

value: Female

value: Developmental exposure

value: Dieldrin


title: POC.C_P19

description: vin.poc.csv.gz

value: paternal

value: control


title: MOC.D_P29

description: ddt.moc.csv.gz


title: rde-11(hj37) fed HT115-pos-1(400nt) young mother replicate 2-sRNAseq

value: whole worm

value: 5’ Polyphosphatase treated


title: P2-E1-009

value: Mouse midbrain

value: 12 weeks old

value: Male


title: LN_WIV+IL-1b, replicate 1

description:
sample name in processed data file:
BVDE@19@LN@S18

value: Lung-draining mediastinal lymph node

value: CD8+ T cells


title: rde-11(hj37) fed HT115-pos-1(400nt) young mother replicate 1-sRNAseq

value: young mother


title: meg-3(ax3055) meg-4(ax3052) JH3745 fed HT115-pos-1(400nt) young mother replicate 2-sRNAseq


title: P3-E1-179


title: meg-3(ax3055) meg-4(ax3052) JH3475 fed HT115-pos-1(400nt) young mother NO PHOSPHATASE replicate 1-sRNAseq

value: Untreated


title: MOC.D_P28

description: ddt.moc.csv.gz


title: LN_WIV+AddaVax, replicate 3

description:
sample name in processed data file:
BVDE@18@LN@S17

value: BALB/c

value: 7 weeks

value: WIV+AddaVax

value: 2xLD50 H1N1 influenza A intranasal


title: P3-E1-172

value: Female

value: Developmental exposure


title: P3-E1-164

value: Dieldrin


title: MOC.D_P26

description: ddt.moc.csv.gz

value: maternal

value: DDT


title: MOC.D_P27

description: ddt.moc.csv.gz


title: LN_WIV+AddaVax, replicate 2

description:
sample name in processed data file:
BVDE@17@LN@S16


title: LN_WIV+AddaVax, replicate 1

description:
sample name in processed data file:
BVDE@16@LN@S15


title: N2 fed HT115-pos-1(400nt) young mother replicate 2-sRNAseq

value: whole worm

value: 5’ Polyphosphatase treated


title: P3-E1-140

value: Mouse midbrain

value: 12 weeks old


title: LN_WIV alone, replicate 3

description:
sample name in processed data file:
BVDE@15@LN@S14

value: Lung-draining mediastinal lymph node

value: WIV alone


title: P3-E1-132


title: N2 fed HT115-pos-1(400nt) young mother replicate 1-sRNAseq

value: young mother


title: MOC.V_P6

description: vin.moc.csv.gz

value: vinclozolin


title: P3-E1-121

value: Control


title: LN_WIV alone, replicate 1

description:
sample name in processed data file:
BVDE@13@LN@S13

value: CD8+ T cells

value: BALB/c

value: 7 weeks


title: meg-3(ax3055) meg-4(ax3052) JH3475 fed HT115-pos-1(400nt) young mother replicate 1-sRNAseq


title: Lung_WIV+CD8a ALN-1, replicate 3

description:
sample name in processed data file:
BVDE@12@LUNG@S12

source_name: Lung

value: Lung

value: WIV+CD8a ALN-1

value: 2xLD50 H1N1 influenza A intranasal


title: MOC.V_P4

description: vin.moc.csv.gz

value: maternal


title: Lung_WIV+CD8a ALN-1, replicate 1

description:
sample name in processed data file:
BVDE@10@LUNG@S10


title: MOC.V_P3

description: vin.moc.csv.gz


title: Transformed_EZH2_rep3

city: London

first: Paola

last: Scaffidi

state: Choose a state

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Reads were adapter-trimmed using cutadapt. BWA (version 0.6.2) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the human hg19 genome. Read pairs that were duplicated, mapped to DAC Blacklisted Regions from the ENCODE/DAC, were discordant, mapped to different chromosomes, ambiguously mapped, or had a mismatch > 4 in any read were removed. A third replicate of EZH2 ChIP-seq generated and processed as indicated above was used to validate differential regions identified using the first two replicates.
Genome_build: Hg19
Supplementary_files_format_and_content: Tiled data format (tdf) files for viewing ChIP-seq enrichment in IGV viewer

organism: Homo sapiens

source_name: Dermal Fibroblasts

growth_protocol: All cell lines were cultured at 37⁰C in 5% CO2 in Modified Eagle Media (Gibco) + 15% tetracycline free fetal bovine serum (Gibco) + 100mM L-glutamine + Penicillin/streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde in cell culture media for 10 minutes at room temperature. Cells were lysed in 1:1 SDS-containing buffer (100mM NaCl, 50mM Tris-HCl pH 8.0, 5mM EDTA pH 8.0, 0.2% NaN3, 0.5% SDS): triton-containing dilution buffer (100mM NaCl, 500mM Tris-HCl pH 8.6, 5mM EDTA pH 8.0, 0.2% NaN3, 5% Triton X-100) plus protease inhibitors (Cell Signalling). Chromatin was then sheared to 200-400bp using a Biouptor Pico Sonicator (Diagenode). Co-immunoprecipitation was performed by combining 1mg of clarified chromatin lysate and EZH2 (Cell Signalling - 5246S, 1:40) or H3K27me3 (Upstate - 07-449, 1:100) antibodies, which were then rotated at 4⁰C o/n. The following day, protein-G magnetic beads (ThermoFisher) were added to the immunoprecipitations and rotated at 4⁰C for 4 hours. The bead-antibody complexes were washed and chromatin was eluted by shaking at 65⁰C o/n 0.1M NaHCO3 1% SDS solution. Chromatin was isolated by PCR purification (Qiagen).
Library preparation was undertaken with 5-10ng of DNA using the Illumina TruSeq ChIP protocol.

tag: chip antibody

value: EZH2 (Cell Signalling - 5246S, 1:40)

tag: neoplastic stage

value: transformed


title: Untransformed_EZH2_rep3

value: untransformed


title: Lung_WIV+CD8a ALN-1, replicate 2

description:
sample name in processed data file:
BVDE@11@LUNG@S11

tag: tissue


title: P3-E1-098

value: Mouse midbrain

value: Female

value: Developmental exposure


title: P3-E1-073

value: 12 weeks old


title: Transformed_H3K27me3_rep2


title: MOC.D_P25

description: ddt.moc.csv.gz

value: DDT


title: Lung_WIV+IL-1b, replicate 3

description:
sample name in processed data file:
BVDE@09@LUNG@S9


title: Preneoplastic_EZH2_rep3

value: preneoplastic


title: Transformed_input


title: MOC.V_P1

description: vin.moc.csv.gz

value: vinclozolin


title: P3-E1-063

value: Control


title: MOC.V_P2

description: vin.moc.csv.gz


title: P3-E1-053


title: Transformed_H3K27me3_rep1


title: Lung_WIV+IL-1b, replicate 1

description:
sample name in processed data file:
BVDE@07@LUNG@S7

value: CD8+ T cells

value: BALB/c


title: MOC.V_P5

description: vin.moc.csv.gz


title: P3-E1-135

value: Male

value: Dieldrin


title: MOC.C_P18

description: vin.moc.csv.gz

value: control


title: P3-E1-104


title: MOC.C_P17

description: vin.moc.csv.gz

value: maternal


title: P3-E1-127


title: Transformed_EZH2_rep2

value: EZH2 (Cell Signalling - 5246S, 1:40)


title: Transformed_EZH2_rep1

value: transformed


title: Lung_WIV+IL-1b, replicate 2

description:
sample name in processed data file:
BVDE@08@LUNG@S8

value: Lung

value: 7 weeks

value: 2xLD50 H1N1 influenza A intranasal


title: Lung_WIV+AddaVax, replicate 3

description:
sample name in processed data file:
BVDE@06@LUNG@S6

value: WIV+AddaVax


title: Lung_WIV+AddaVax, replicate 2

description:
sample name in processed data file:
BVDE@05@LUNG@S5


title: MOC.C_P16

description: vin.moc.csv.gz


title: P3-E1-175

value: Mouse midbrain

value: 12 weeks old

value: Developmental exposure


title: Lung_WIV+AddaVax, replicate 1

description:
sample name in processed data file:
BVDE@04@LUNG@S4


title: P3-E1-192


title: Preneoplastic_input

value: preneoplastic


title: Preneoplastic_H3K27me3_rep2


title: Lung_WIV alone, replicate 3

description:
sample name in processed data file:
BVDE@03@LUNG@S3

value: WIV alone


title: MOC.C_P14

description: vin.moc.csv.gz


title: MOC.C_P15

description: vin.moc.csv.gz


title: Preneoplastic_EZH2_rep2


title: P3-E1-159


title: Preneoplastic_H3K27me3_rep1


title: P3-E1-094

value: Control


title: P3-E1-167


title: Lung_WIV alone, replicate 1

description:
sample name in processed data file:
BVDE@01@LUNG@S1

value: CD8+ T cells

value: BALB/c


title: P3-E1-196-SN-R

value: Female

value: Dieldrin


title: P3-E1-065

value: Male


title: Untransformed_input

value: untransformed


title: P3-E1-058


title: MOC.C_P13

description: vin.moc.csv.gz

value: maternal

value: control


title: Untransformed_H3K27me3_rep2


title: P3-E1-180-SN-R


title: P3-E1-173-SN-R


title: P3-E1-100


title: Lung_WIV alone, replicate 2

description:
sample name in processed data file:
BVDE@02@LUNG@S2

value: Lung

value: 7 weeks


title: P3-E1-116


title: P3-E1-165-SN-R


title: Untransformed_EZH2_rep2

value: EZH2 (Cell Signalling - 5246S, 1:40)


title: P3-E1-051

value: Mouse midbrain


title: Untransformed_H3K27me3_rep1


title: Untransformed_EZH2_rep1


title: Preneoplastic_EZH2_rep1


title: WGBS_RGCs

city: Miami

first: Dmitry

last: Ivanov

state: FL

address: 1638 NW 10th Avenue

department: Ophthalmology

institute: University of Miami Miller School of Medicine

data_processing:
Quality control of sequencing reads was performed using FastQC.
To obtain the qualified clean data, the raw reads were trimmed using Trimmomatic, a trimming tool for Illumina NGS data, to filter out the contaminated adapter sequence and low-quality reads.
The cleaned reads were then aligned to the Mus musculus reference genome (Genome Reference Consortium 37, mm10) using bismark.
The cytosine2coverage and bismark_methylation_extractor modules of bismark were used to infer the methylation state of all cytosines in a CpG, CHH, or CHG context (for every single mappable read) and to compute the percentage of methylation for each CpG site.
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig files were generated.

source_name: RGCs isolated from P14 retinas

extract_protocol:
Genomic DNA was purified from the samples using the DNeasy Blood & Tissue Kit (QIAGEN #69504). DNA concentration was measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). The DNA quality of the samples was assessed with the Fragment AnalyzerTM and the DNF-487 Standard Sensitivity genomic DNA Analysis Kit (Advanced Analytical).
Approximately 5 μg of genomic DNA per sample spiked with lambda DNA was fragmented by sonication to 200–400 bp using Covaris S220 followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA, and then these fragments were treated with bisulfite (EZ DNA Methylation-GoldTM Kit, Zymo Research). The resulting single-stranded DNA fragments were amplified by PCR using KAPA HiFi HotStart Uracil + ReadyMix (2×). DNA concentration of the libraries was measured using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific). The library profiles were checked using the High Sensitivity DNA chip for the 2100 Bioanalyzer (Agilent). WGBS libraries were sequenced on a HiSeq X-10 platform using 150 bp paired-end sequencing.

value: retina

tag: developmental stage

value: Postnatal Day 14 (P14)


title: P3-E1-122-SN-R

tag: strain

value: 12 weeks old

value: Developmental exposure


title: P3-E1-133-SN-R

tag: age


title: P3-E1-099-SN-R

tag: Sex

value: Control


title: GSC1123-R

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: Glioma stem cells

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

treatment_protocol: Radiation treatment

value: glioma tumor cells

tag: protocol

value: Treated with four rounds of fractionated radiation of 6 Gy every four days (total 24 Gy)


title: GSC1123-C

tag: cell type

value: Non radiation treatment


title: WGBS_retina_E12.5

source_name: whole retinal cell populations

value: Embryonic Day 12.5 (E12.5)


title: FNY01_3_3_RNASeq

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
primary cultured cells
all files with 3_3 in their name come from this sample

data_processing:
Base called using CASAVA
read aligned using Salmon
Genome_build: hg19
Supplementary_files_format_and_content: Files *.maternal.coverage.bgr contain the number of reads containing maternal or paternal SNPs genome-wide. When reads contained multiple SNPs, only the first SNP was taken into consideration. Files  *.collapsed_gene_expression.txt contains expression scores for collapsed Gencode V22 isoforms. CAGE profiles from FANTOM in the context of CAGEr analysis and high-resolution promoterome mining for integrative analyses42 was used to determine unambiguously expressed isoforms. Promoter regions were defined for each isoform as the union of all the -400 to +100 intervals for all of the overlapping isoforms and a CAGE score equal to the sum of the CAGE scores of the individual overlapping promoters was then assigned to these promoter regions. Each promoter region was also assigned an associated gene body equal to the longest transcript with Salmon Transcript Per Million (TPM) score >1, and a Salmon expression score defined as the sum of TPM of all its associated isoforms. Genes were considered not expressed when the Salmon TPM of the collapsed isoforms was <1, when there was no CAGE signal associated with the collapsed promoter, and when the gene was not overlapping an expressed gene. For each cell line this expression analysis yielded about 35,000 active or inactive promoter regions and about 4,000 ambiguous promoter regions that exhibited an RNA-seq signal and no CAGE signal. These ambiguous promoter regions were excluded from further analysis. The total number of promoter regions in each cell type differed slightly because the CAGE and RNA-seq data is cell type-specific.

source_name: basophilic erythroblasts

growth_protocol: Mononuclear cells were isolated from peripheral blood by density gradient centrifugation on Histopaque and were expanded and differentiated into basophilic erythroblasts in culture for two weeks in serum-free condition as described in    PMID 18024790

extract_protocol:
10 million BasoE were generated using the protocol described in the cell culture section and total RNA were extracted using a Qiagen RNA extraction kit.
PolyA+ libraries were then constructed using the Illumina Stranded mRNA LT Sample Prep Kit using the recommended protocols
stranded, polyA+

treatment_protocol: the cells were treated

tag: type

value: Healthy control


title: P3-E1-105-SN-R

value: Female

tag: exposure type


title: FNY01_3_2_RNASeq

description:
primary cultured cells
all files with 3_2 in their name come from this sample


title: WGBS_retina_E11.5

value: Embryonic Day 11.5 (E11.5)


title: WGBS_RPCs_P3

source_name: Notch1+ cells (RPCs) isolated from developing retinas

value: Postnatal Day 3 (P3)


title: P3-E1-064-SN-R


title: FNY01_3_3_MethylSeq

description:
all files with 3_3 in their name come from this sample
primary cultured cells

data_processing:
CASAVA
BSMAP
BisSNP
MethylPhase
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited contains number of methylated and unmethylated C or methylated fraction

extract_protocol:
Genomic DNA was extracted according to standard protcol
Genomic DNA was extracted from about 50 million basophilic erythroblasts and libraries were produced using a protocol developed at the Einstein epigenomic facility. Extracted genomic DNA was fragmented (400-500 bp) with Covaris, end-repaired, dA tailed and then premethylated adapters (Illumina TruSeq adapters) were ligated at the ends of the fragmented DNA. The adapter ligated DNA samples were purified with AMPure XP beads (1:1 dilution) to eliminate adapter dimers and products with short insert, and then treated with sodium bisulphite using EZ DNA Methylation lightning kit (Zymo Research). The bisulphite treated products were used as a template for PCR amplification using following condition: 25 µl of 2x KAPA HiFi HotStart Uracil+ ReadyMix, 1.5 µl of 10 µM of primer P5, 1.5 µl of 10 µM of primer P7 and bisulphite treated library in a final volume of 50 µl; 98oC for 2 minutes, then 10 cycles of 98 oC for 30 seconds, 60 oC for 30 seconds and 72 oC for 4 minutes followed by 10 minutes at 72 oC for final extension. Amplified libraries were purified with MinElute PCR purification kit, and then we performed size selection with MinElute Gel Extraction kit (the insert size was 250 bp to 850 bp). For each of the two individuals analyzed, paired-end 2x100bp reads were then generated on six lanes of an Illumina HiSeq 2500.
Methyl Seq library

treatment_protocol: cells were not treated after the culture


title: P3-E1-069-SN-R


title: WGBS_RPCs_P0

value: Postnatal Day 0 (P0)


title: FNY01_3_2_MethylSeq

description:
all files with 3_2 in their name come from this sample
primary cultured cells


title: Liver, chlorpyrifos-methyl containing diet (High), Fish36

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

country: Norway

institute: University of Bergen

data_processing:
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform and paired-end reads were generated. Clean reads (49,654,219±5,149,769, n=36, mean±st.dev.) were obtained by removing reads containing adapter, reads containing poly-N and low-quality reads from raw data.
Alignment and mapping were conducted by using TopHat2 and the Atlantic cod reference genome (deposited at ENSEMBL, about 70% of clean reads mapped to the genome). RSEM software was used to estimate gene expression levels for each sample (Li et al., 2012). Clean data were mapped back onto the assembled transcriptome, and a read-count for each gene was acquired from the mapping results.
Genome_build: ftp://ftp.ensembl.org/pub/release-81/fasta/gadus_morhua/cds/Gadus_morhua.gadMor1.cds.all.fa.gz
Supplementary_files_format_and_content: Excel file with each line consisting of Atlantic cod ENSEMBL  sequence name, and raw counts for all 36 samples

organism: Gadus morhua

source_name: Liver

extract_protocol:
Liver specimen were thoroughly homogenized on dry ice before RNA extraction using the RNeasy Plus mini kit (Qiagen, Oslo, Norway). RNA quantity and quality were determined by using the NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto-CA, USA). The RNA integrity number (RIN value) was 9.3±0.1 (mean±SEM, n=36).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First-Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation, NEBNext Adaptor were ligated to prepare for hybridization. Library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA before PCR. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Dietary exposure to chlorpyrifos-methyl containing diet for 30 days

tag: nominal chlorpyrifos-methyl dose (mg/kg)

tag: measured chlorpyrifos-methyl dose (mg/kg)

tag: body weight end (g)

tag: length end (cm)

value: liver


title: P3-E1-141-SN-R

tag: treatment

value: Dieldrin


title: Liver, chlorpyrifos-methyl containing diet (High), Fish35


title: NEMOIEC-KO Il23a-/-_5

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

country: Germany

institute: University of Cologne

description:
K002000080_52735
Sample 25_52735

data_processing:
RNA-Seq data were processed through the QuickNGS analysis pipeline (Wagle et al., 2015), version 1.2.7, based on Ensembl release 87.
Reads were mapped to the GRCm38 assembly of the mouse genome using Tophat2, version 2.0.10, and reassembled with Cufflinks, version 2.1.1.
Differential gene expression was analyzed using the DESeq2 package, version 1.10.1.
The results were uploaded into the QuickNGS database and combined with multiple annotations using the biomaRt package.
Biological processes enriched among the differentially expressed genes were identified by the QuickNGS platform using Fisher's exact test on GO term associations.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel files include fold changes of experimental samples with respect to control (=NemoFL samples) and expression RPKM values for each Sample.

source_name: NEMOIEC-KO Il23a-/-_colon

growth_protocol: Mice were in the C57Bl/6 genetic background and were kept at an SPF animal facility under a 12 hr light cycle and were given a regular chow diet ad libitum. They were sacrificed at the age of 6 weeks.

extract_protocol:
Total RNA was extracted with Trizol Reagent (Life Technologies) and RNeasy columns (Qiagen)
RNA-seq libraries were prepared using the Illumina® TruSeq stranded® RNA sample preparation Kit. Library preparation started with 1µg total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (15 PCR cycles, 20ul template) to create the final cDNA libraries. After library validation and quantification (Agilent tapestation), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The pool was sequenced by using an Illumina HiSeq 4000 sequencer with a paired-end (76x7x76 cycles) protocol.

tag: strain background

tag: genotype/variation

value: NEMOIEC-KO Il23a-/-

value: 6 weeks

value: distal colon


title: P3-E1-193-SN-R

value: Mouse midbrain

value: 12 weeks old

value: Male


title: Liver, chlorpyrifos-methyl containing diet (High), Fish33


title: NEMOIEC-KO Il23a-/-_3

description:
K002000079_52731
Sample 23_52731


title: P3-E1-168-SN-R

value: Developmental exposure


title: P3-E1-176-SN-R


title: Liver, chlorpyrifos-methyl containing diet (High), Fish32


title: NEMOIEC-KO Il23a-/-_4

description:
K002000079_52733
Sample 24_52733


title: NEMOIEC-KO Il23a-/-_2

description:
K002000079_52709
Sample 22_52709


title: P3-E1-160-SN-R


title: Liver, chlorpyrifos-methyl containing diet (High), Fish31


title: NEMOIEC-KO Il12a-/-_5

description:
K002000079_52719
Sample 20_52719

source_name: NEMOIEC-KO Il12a-/-_colon

value: NEMOIEC-KO Il12a-/-


title: P3-E1-136-SN-R


title: P3-E1-128-SN-R


title: NEMOIEC-KO Il23a-/-_1

description:
K002000079_52707
Sample 21_52707


title: NEMOIEC-KO Il12a-/-_4

description:
K002000079_52717
Sample 19_52717


title: Liver, chlorpyrifos-methyl containing diet (High), Fish28


title: WGBS_Müller glia Exp2

data_processing:
Quality control of sequencing reads was performed using FastQC.
Adapter removal was performed using Trim Galore! version 0.4.5.
The cleaned reads were then aligned to the Mus musculus reference genome (Genome Reference Consortium 37, mm10) using bismark v0.16.1.
The cytosine2coverage and bismark_methylation_extractor modules of bismark were used to infer the methylation state of all cytosines in a CpG, CHH or CHG context (for every single mappable read) and to compute the percentage methylation for each CpG site.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files were generated using bismark_methylation_extractor module of bismark.

source_name: Glast+ cells from P28 retinas

extract_protocol:
Genomic DNA was purified from samples using the DNeasy Blood & Tissue Kit (QIAGEN #69504). DNA concentration of the samples was measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific). DNA quality of the samples was assessed with the Fragment AnalyzerTM and the DNF-487 Standard Sensitivity genomic DNA Analysis Kit (Advanced Analytical).  Genomic DNA was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001). 1μl of this sample was used to assess the size of the DNA fragments obtained by High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). DNA concentration of the sample was measured after shearing using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific).
WGBS libraries were prepared using the Whole Genome Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030034) following the kit manual. 1μg of sheared genomic DNA was used to start library preparation for each sample. Following library preparation, samples were bisulfite converted and amplified by PCR using 9 amplification cycles. Final PCR clean-up was performed twice using a 1.1x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). DNA concentration of the libraries was measured using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific). The library profiles were checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). WGBS libraries were sequenced on a HiSeq3000 (Illumina) using 150 bp single-end sequencing.

value: retina

value: Postnatal Day 28 (P28)

value: Glast+ cells


title: Liver, chlorpyrifos-methyl containing diet (High), Fish29


title: P3-E1-054-SN-R

value: Female

value: Control


title: WGBS_Müller glia Exp1


title: P3-E1-117-SN-R


title: NEMOIEC-KO Il12a-/-_3

description:
K002000079_52715
Sample 18_52715


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish27


title: NEMOIEC-KO Il12a-/-_2

description:
K002000079_52713
Sample 17_52713


title: Liver, chlorpyrifos-methyl containing diet (High), Fish34


title: P3-E1-101-SN-R


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish26


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish25


title: Liver, chlorpyrifos-methyl containing diet (High), Fish30


title: NEMOIEC-KO Il12a-/-_1

description:
K002000079_52711
Sample 16_52711


title: P3-E1-095-SN-R


title: P3-E1-066-SN-R


title: NEMOIEC-KO Il12b-/-_5

description:
K002000079_52729
Sample 15_52729

source_name: NEMOIEC-KO Il12b-/-_colon

value: NEMOIEC-KO Il12b-/-


title: P3-E1-059-SN-R

source_name: Midbrain tissue


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish23


title: 8367_CP6406907: Glast+ cells P21.2

description: We processed individual samples that each contained 200,000-500,000 cells.

hyb_protocol: Biotinylated complementary RNA samples were fragmented, diluted in a formamide-containing hybridization buffer, and loaded on to the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) microarray slides enclosed in custom hybridization chambers (for more information on the MEEBO oligonucleotide set please refer to http://alizadehlab.stanford.edu/). The slides were hybridized for 16-18 hours in a Model 400 hybridization oven (Scigene, Sunnyvale, CA).

scan_protocol: After hybridization, the microarray slides were washed under stringent conditions, stained with Streptavidin-Alexa-647 (Invitrogen, Carlsbad, CA), and scanned using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA).

data_processing: Spot intensities for each probe were calculated by subtracting median local background from median local foreground for each spot. The spot intensities were then normalized. After removing data for low quality spots, the mouse probes’ intensities were filtered to identify all probes with an intensity above a normalized threshold. For statistical analysis, microarray data were examined for differences by One-way ANOVA. Values of F > Fcrit. = 2.83 were designated as statistically significant.

source_name: Glast (Slc1a3) positive cells isolated from developing retinas

label_protocol: Biotin-labeled complementary RNA was made from the total RNA according to Van Gelder’s protocol (Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, et al. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87: 1663-1667.)

extract_protocol: To isolate Notch1+ cells and Glast+ cells, we employed an immunomagnetic cell separation approach using monoclonal biotin-conjugated anti-Notch1 and anti-Glast mouse antibodies and anti-biotin magnetic microbeads. RNA was extracted from cells using the Absolutely RNA Nanoprep kit (Agilent Technologies, Santa Clara, CA).

value: Postnatal Day 21 (P21)

value: Glast (Slc1a3) positive cells


title: NEMOIEC-KO Il12b-/-_4

description:
K002000079_52727
Sample 14_52727


title: NEMOIEC-KO Il12b-/-_2

description:
K002000079_52723
Sample 12_52723


title: P3-E1-052-SN-R


title: NEMOIEC-KO Il12b-/-_3

description:
K002000079_52725
Sample 13_52725


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish21

value: liver


title: 8366_CP6406906: Glast+ cells P21.1


title: KO- NPC-13

city: Pasadena

first: Brittany

middle: Megan

last: Edens

state: CA

address: 1200 E California Blvd

institute: Caltech

data_processing:
Reads were trimmed using cutadapt version 1.14 and default parameters
Trimmed were aligned to mm10 reference genome using STAR version 020201 and default parameters
Read counts were determined with htseq-count version 0.7.2
Differential expression was determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample

source_name: Neural precursor cells (NPCs)

growth_protocol: The dorsal hem of the forebrain was harvested from timed-pregnant E13.5 mice and digested with Accutase (Fisher) to yield dissociated cortical neural precursor cells (NPCs) for culture.  NPCs were carried on Matrigel-coated plates (Corning) (~90ug/ml) and maintained in DMEM-F12 medium (Gibco) supplemented with B27 (Gibco), N2 (Gibco), and Glutamax (Gibco).  A growth factor cocktail containing EGF (PeproTech) (20ng/ml) and basic FGF (PeproTech) (20ng/ml) in Heparin (5ug/ml) was added to the medium fresh.  Cells were carried at densities not exceeding 80%, and all experiments were performed on density- and passage-matched NPC cultures.  Cells were incubated in standard conditions: 37C with 5% CO2.

extract_protocol:
NPCs were harvested at ~80% confluency with Accutase (Fisher), and nuclear fractions were prepared as described in the NE-PER Nuclear and Cytoplasmic Extraction Kit (Thermo/Fisher) manufacturer’s protocol, with minor modifications.  0.5U/ul of RNAse inhibitor (Ambon/Fisher) was added to the CERI reagent to prevent degradation.  After separation from the cytoplasmic fraction, the nuclear pellet was washed twice with PBS (prepared in DEPC water), and resuspended in an appropriate volume of TRIzol reagent (Invitrogen).  The nuclear pellet was homogenized with a Polytron PT 1200E (Kinematica).  RNA was purified using the TRIzol reagent manufacturer’s protocol, and quantified using the Quant-iT RNA HS Assay Kit (Invitrogen).  The efficiency of separation was determined by subjecting both nuclear and cytoplasmic RNA fractions to RT-qPCR and measuring the relative quantities of both nuclear (U1) and cytoplasmic (beta-actin) control genes.  Only nuclear RNA preparations with high U1 expression and low beta-actin expression were utilized
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NPCs derived from E13.5 forebrain

tag: passage

tag: genotype

value: Fmr1 KO


title: KO- NPC-16


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish20

tag: tissue


title: KO- NPC-3


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish24


title: 8364_CP6406904: Glast+ cells P14.2

tag: strain

tag: developmental stage

value: Postnatal Day 14 (P14)


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish19


title: WT- NPC-8

value: Fmr1 WT


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish18


title: Liver, chlorpyrifos-methyl containing diet (Medium), Fish22


title: 8361_CP6406901: Glast+ cells P7.1

value: Postnatal Day 7 (P7)


title: 8362_CP6406902: Glast+ cells P7.2


title: 8363_CP6406903: Glast+ cells P14.1


title: 8365_CP6406905: Glast+ cells P14.3


title: 8359_CP6105712: Notch1+ cells P14.3

source_name: Notch1 positive cells isolated from developing retinas

value: Notch1 positive cells


title: NEMOIEC-KO_3

description:
K002000081_52697
Sample 8_52697

value: NEMOIEC-KO

tag: age

value: 6 weeks

value: distal colon


title: 8355_CP6105710: Notch1+ cells P14.1

value: retina


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish16


title: WT- NPC-3


title: NEMOIEC-KO_1

description:
K002000079_52703
Sample 6_52703


title: 8354_CP6105709: Notch1+ cells P7.3


title: NEMOIEC-KO_4

description:
K002000081_52699
Sample 9_52699


title: Intermittent donor 3

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and Trimmomatic.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Intermittent donor

extract_protocol:
After treatment, total RNA was isolated using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Periodontal ligament cells

tag: treated with

value: intermittent compressive forces


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish17


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish15


title: NEMOIEC-KO Il12b-/-_1

description:
K002000079_52721
Sample 11_52721


title: Nemofl/fl_5

description:
K002000081_52695
Sample 5_52695

value: Nemofl/fl


title: 8353_CP6105707: Notch1+ cells P7.1

tag: cell type


title: NEMOIEC-KO_5

description:
K002000081_52701
Sample 10_52701


title: Intermittent donor 2


title: WT- NPC-19


title: 8352_CP6105706: Notch1+ cells P3.3

value: Postnatal Day 3 (P3)


title: 8351_CP6105705: Notch1+ cells P3.2


title: Intermittent donor 1


title: Nemofl/fl_4

description:
K002000081_52693
Sample 4_52693


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish14


title: NEMOIEC-KO_2

description:
K002000079_52705
Sample 7_52705


title: Control-Intermittent donor 2

source_name: Control-Intermittent donor

value: none (control for intermittent)


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish13


title: Nemofl/fl_2

description:
K002000081_52689
Sample 2_52689


title: Nemofl/fl_3

description:
K002000081_52691
Sample 3_52691


title: Control-Intermittent donor 3


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish12


title: Control-Intermittent donor 1


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish11


title: Static donor 3

source_name: Static donor

value: static compressive force stimuli


title: 8350_CP6105702: Notch1+ cells P0.2

value: Postnatal Day 0 (P0)


title: input Müller glia DNA Exp2

data_processing:
Quality control of sequencing reads was performed using FastQC.
Reads were then aligned to the reference genome (mm10) obtained from the UCSC genome browser using BWA software v.0.7.5a.
Samples were filtered for regions blacklisted by the ENCODE project. Subsequently samples were deduplicated using SAMtools version 1.3.1.
Alignment coordinates were converted to BED format using BEDTools v.2.17 and peak calling was performed using SICER with customized parameters for each histone mark.
Genome_build: mm10
Supplementary_files_format_and_content: BED files were generated using SICER with customized parameters for each histone mark. The first column is the name of the chromosome; second - the starting position of the peak; third - the ending position of the peak; fourth - the name of the peak; fifth - the p-value of the peak

extract_protocol:
Freshly isolated cells were cross-linked in 1% formaldehyde with 1X PBS. To stop the cross linking reaction, glycine was added to a final concentration of 0.125M. The chromatin was prepared using the True MicroChIP Kit (Diagenode Cat# C01010130). Chromatin was sheared using the Bioruptor® Pico sonication device (Diagenode Cat# B01060001). ChIP was performed using IP-Star® Compact Automated System (Diagenode Cat# B03000002) following the protocol of the aforementioned kit. Chromatin corresponding to 25,000 cells was immunoprecipitated using the antibodies.
Libraries were prepared from input and ChIP’d DNA (500 pg) using the MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010013). Library amplification is assessed using the High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). Libraries were then purified using Agencourt® AMPure® XP (Beckman Coulter) and quantified using Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Finally their fragment size was analyzed by High Sensitivity NGS Fragment Analysis Kit (DNF-474) on a Fragment Analyzer™ (Advanced Analytical Technologies, Inc.). When the proportion of fragments >500bp was too high, libraries were subjected to a double size selection using Agencourt® AMPure® XP (Beckman Coulter). Libraries were pooled and sequenced on an Illumina HiSeq 4000 with single-end reads of 50bp lengths, running HiSeq Control Software HD version 3.4.0.38.

value: Glast+ cells

tag: chip antibody

value: none (input)


title: Static donor 2


title: Liver, chlorpyrifos-methyl containing diet (Low), Fish10

value: liver


title: Liver, Control, Fish9

value: Control


title: 8349_CP6105701: Notch1+ cells P0.1


title: Liver, Control, Fish8


title: 8347_CP6105708: Notch1+ cells P7.2

value: Postnatal Day 7 (P7)


title: 8345_CP6105703: Notch1+ cells P0.3

value: Notch1 positive cells


title: Control-static donor 3

source_name: Control-static donor

value: none (control for static)


title: Liver, Control, Fish7


title: H3K9me3_ChIPSeq_Müller glia Exp2

value: H3K9me3 (Diagenode Cat# C15410193)


title: Control-static donor 2


title: Nemofl/fl_1

description:
K002000081_52687
Sample 1_52687

value: 6 weeks

value: distal colon


title: H3K4me3_ChIPSeq_Müller glia Exp2

value: retina

value: H3K4me3 (Diagenode Cat# C15410003-50)


title: Liver, Control, Fish6


title: H3K4me1_ChIPSeq_Müller glia Exp2

value: H3K4me1 (Diagenode Cat# C15410194)


title: Liver, Control, Fish5


title: H3K27me3_ChIPSeq_Müller glia Exp2

value: H3K27me3 (Diagenode Cat# C15410195)


title: Liver, Control, Fish4


title: 8339_CP6406908: Glast+ cells P28.2

value: Postnatal Day 28 (P28)

value: Glast (Slc1a3) positive cells


title: H3K27me3_ChIPSeq_Müller glia Exp1


title: Liver, Control, Fish3


title: Control-static donor 1

value: Periodontal ligament cells


title: Static donor 1

value: static compressive force stimuli


title: H3K9me3_ChIPSeq_Müller glia Exp1

value: Glast+ cells


title: H3K4me3_ChIPSeq_Müller glia Exp1


title: Liver, Control, Fish2

value: liver


title: 8346_CP6105704: Notch1+ cells P3.1

value: Postnatal Day 3 (P3)


title: Liver, Control, Fish1

value: Control


title: Commensal biofilm exposed RHG

city: Amsterdam

first: Susan

last: Gibbs

address: Gustav Mahlerlaan 3004

department: Oral Cell Biology

country: Netherlands

institute: Academic Centre for Dentistry Amsterdam

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://dataanalysis.qiagen.com/pcr/arrayanalysis
For the normalization it uses the average of two housekeeping genes: B2M and GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
fold_change.txt reports test/control (i.e., commensal biofilm exposure/unexposed) ratios.

label: SYBR Green

source_name: Immortalized human gingiva keratinocyte

label_protocol: PCR assays were performed using the RT² Profiler PCR Array Human Toll-like Receptor Signaling Pathway (Qiagen) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT² First Strand Kit (Qiagen). Quantitative real-time PCR was performed (Bio-Rad iCycler) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted using AllPrep RNA/Protein Kit (Qiagen) and cDNA was prepared using RT² First Strand Kit (Qiagen).

value: Immortalized gingiva keratinocyte

tag: expose to microbial biofilm

value: Commensal

tag: time

value: 24 hours


title: Unexposed RHG

description: Control


title: Gingivitis biofilm exposed RHG

description: Test

value: Gingivitis


title: H3K4me1_ChIPSeq_Müller glia Exp1


title: Cariogenic biofilm exposed RHG

description: Test

value: Cariogenic


title: Z-4: Salt_Input2

status: Public on Jul 22 2019

city: Beijing

first: guoweijun

last: guoweijun

address: No. 12, Zhongguancun South Street

department: Biotechnology Research  Institute

institute: Chinese Academy of Agricultural Sciences

data_processing:
ChIP DNA samples described above were prepared for high throughput Illumina sequencing (one hundred and fifty pair-end read sequencing).
The ChIP-seq data was analyzed as described previously (Wang et al., 2016; Xu et al., 2018). The first 30 base pairs from the 5' end containing primer or adapter sequences were trimmed. The 3' end of the sequencing reads were trimmed based on base-call quality using the BWA quality trim algorithm (Li and Durbin, 2009).
The sequencing reads were aligned Glycine max reference genome (Glycine max Wm82.a2.v1). Only uniquely mapped reads that mapped to one location of the genome only (as opposed to those that mapped to multiple reads) were retained for peak calling.
Three biological replicates were performed for each sample. Each input was used as a control for peak calling for each sample using MACS 1.4 (Zhang et al., 2008). The statistical identification of peaks was performed for each sample using MACS with the default 10-5 p-value cutoff.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: The three replicates results were overlapped using BedTools (Quinlan and Hall, 2010). The resulting BED format files that contain the peak location were visualized with the Integrated Genome Viewer (Robinson et al., 2011; Thorvaldsdottir et al., 2013).

organism: Glycine max

source_name: Soybean root cells

growth_protocol: The Glycine line, Glycine max Williams 82, was used in this study. Seeds were sterilized with 75% ethanol and then germinated in pots filled with coconut fiber. Soybean seedlings were grown in soil in an incubator with 25℃/20℃ (light/dark) and 16h/8h (light/dark) cycles until the second trifoliate leaves started expand.  As a control, the untreated seedlings (0 mM/L) were planted and harvested at the same time with the stress-treated plants. The 100 mM/L salt treated seedlings were used for RNA-seq and ChIP-seq analysis since the phenotypic differences were clear at this concentration which is also commonly used for salinity test on soybean.

extract_protocol:
ChIP assay was performed from approximately 2 g of soybean roots as previously described (Kim et al., 2012b; Xu et al., 2018).
Library construction and deep sequencing were performed as described previously (Wang et al., 2016; Xu et al., 2018).

treatment_protocol: For the salt stress treatment, the uniformly growing plants were kept in 0 mM/L, 50 mM/L, 75 mM/L, 100 mM/L, 150 mM/L and 200 mM/L of NaCl solutions for 30 hours.

value: Soybean root cells


title: Z-4: Salt_IP_rep1

value: Anti-H3K27me3 (Millipore, #07-449)


title: Z-4: Salt_IP_rep3


title: Z-4: Salt rep3

data_processing:
Paired-end reads were generated with the Illumina HiSeq 2500 system.
The RNA sequencing reads were aligned to the Glycine max reference genome (Glycine max Wm82.a2.v1) using TopHat2 (Kim et al., 2013). Genes that met the criterion of a detectable expression signal in control or salt plants were further analyzed.
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: The fold change (FC) was calculated by comparing the expression level of the salt samples to control (salt/control). Briefly, the ‘‘|Log2FC|>1 and p-adj < 0.05’’ was used as the threshold to judge the significance of gene expression difference. Genes that display a greater than 2-FC in the salt-treated were designated as up- or down-regulated if the salt RNA level was higher or lower than that of control plants, respectively.

source_name: salt-treated

extract_protocol:
Total RNA was extracted from the root of soybeans with TRIzol reagent (Invitrogen) according to the manufacturer's instructions.
Library making, RNA-seq and data analysis were performed as described previously (Xu et al., 2018).


title: Z-1: WT rep2

source_name: wild type


title: Z-1: WT rep1


title: Z-4: Salt rep2


title: Z-4: Salt_IP_rep2


title: Z-4: Salt rep1


title: Z-4: Salt_Input1


title: Z-1: WT rep3


title: Z-1: Control_Input2


title: Z-1: Control_Input1


title: Z-1: Control_IP_rep3


title: Z-1: Control_IP_rep2


title: 8348_CP6105711: Notch1+ cells P14.2

value: retina

value: Postnatal Day 14 (P14)

value: Notch1 positive cells


title: 8338_CP6406908: Glast+ cells P28.1

value: Postnatal Day 28 (P28)

value: Glast (Slc1a3) positive cells


title: Z-1: Control_IP_rep1


title: Low pod shattering force soybean 072

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

description: paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with trim-galore (v0.4.4, --stringency 6); Clean reads were aligned to reference genomes (Gmax_275_Wm82.a2.v1) using tophat2  with following parameters: -N 5 --read-edit-dist 5.
Raw counts of refrence genes were calculated with "featureCounts" in subread package (v1.6.2) with following parameters: -p -t exon -g gene_id; "edgeR" was used to do differential expression (DE) analysis.
Genome_build: Gmax_275_Wm82.a2.v1
Supplementary_files_format_and_content: Text file including raw read count table for reference genes

source_name: total RNAs, pod

growth_protocol: For growing soybean plants, seeds were grown on fields.

extract_protocol:
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq RNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.

tag: sample id

value: pods

value: Pods after 18 days flowering

tag: phenotype

value: Low pod shattering force


title: Low pod shattering force soybean 092

description: paired-end RNA-seq


title: Low pod shattering force soybean 109

description: paired-end RNA-seq


title: Low pod shattering force soybean 038

description: paired-end RNA-seq


title: High pod shattering force soybean 071

description: paired-end RNA-seq

value: High pod shattering force


title: High pod shattering force soybean 060

description: paired-end RNA-seq


title: High pod shattering force soybean 044

description: paired-end RNA-seq


title: High pod shattering force soybean 018

description: paired-end RNA-seq


title: High pod shattering force soybean 015

description: paired-end RNA-seq


title: OS4F7

city: Gainesville

first: Tom

last: Foster

address: 1149 Newell Drive

institute: University of Florida

data_processing:
Data was analyzed using Partek Flow (Partek Inc.). Reads were trimmed based on the size such that reads below 5 bp and reads above 250 bp were discarded. Following trimming, reads were aligned using STAR against the mouse genome reference (mm10). All parameters were kept default.
Gene annotation was completed with the mm10-Ensembl Transcripts release 92. Normalization was performed on total counts in Partek Flow based on the TMM method. Gene annotation was also done using mm10-Ensembl Transcripts release 92.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated values files which contain the normalized counts for each sample.

source_name: Hippocampus

extract_protocol:
Animals were sacrificed either 24 hours or 4 days following sepsis. Age and sex-matched control groups were sacrificed directly from the home cage, without receiving surgery or anesthesia. Mice were anesthetized with isoflurane and swiftly decapitated and mixed arteriovenous blood was collected in a heparinized vacutainer tube. The brains were rapidly removed and the hippocampi were dissected. All brain samples were flash frozen in liquid nitrogen and were stored at -80 C. One whole hippocampus was used for next-generation sequencing.
Sequencing libraries were constructed using the library preparation kit Ion Total RNA-Seq kit v2 (Thermo Fisher, Cat# 4475936). Ion Xpress barcodes (Thermo Fisher, catalog number4475485) were added for multiplex sequencing.

value: Hippocampus

value: Old (18-22 months)

tag: gender

value: Female

tag: time after sepsis

value: 4 days after sepsis


title: YS4F3

value: Young (3-5 months)


title: YS4F1


title: OS4F2


title: YS4F2


title: OMS4F

value: 24 hours after sepsis


title: YMS4F


title: Low pod shattering force soybean 055

description: paired-end RNA-seq


title: OMC1F

value: Control


title: YMS3F


title: YMS2F


title: OS4F4


title: OMC3F


title: OMS3F


title: YMC2F


title: OMC4F


title: YS4F4


title: OS4M8

value: Male


title: OS4M5


title: YMC4F


title: OS4M3


title: OS4M2


title: YS4M4


title: OMS2F


title: OMS1F


title: OMC2F


title: YMS1F


title: YMC3F


title: OMS2M


title: OMS3M


title: YS4M3


title: YS4M2


title: OMC2M


title: YMS2M


title: YMC1F


title: YMS3M


title: OMS4M


title: YMS1M


title: YMS4M


title: OMC4M


title: OMS1M


title: OMC1M


title: YMC3M


title: YMC2M


title: OMC3M


title: YS4M1


title: YMC1M


title: YMC4M


title: YTK383-1-IP (spike-in control)

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
FastQC-0.11.5 checked the quality of raw sequences. If necessary, FASTX Toolkit-0.0.13 was used filtered out reads with low qualities and mates were properly paired.
Bowtie2-2.2.5 aligned sequences to the S. cerevisiae genome (R61-1-1). QualiMap-2.2.0 checked the quality of the alignment.
Picard-tools-2.6 removed duplicates with parameters VALIDATION_STRINGENCY=silent AS=true.
Genome_build: R64-1-1/sacCer3
Supplementary_files_format_and_content: bigWig files were generated using command genomeCoverageBed -bg -scale SCALE_FACTOR in BEDTools-2.26.0; SCALE_FACTOR is 10^6/(the number of reads originated from S. pombe) . Scores represent RPM.
Supplementary_files_format_and_content: narrowPeak files were generated using macs2-2.1.0 with corresponding controls and a parameter -q 0.05

organism: Saccharomyces cerevisiae

source_name: Yeast cell

growth_protocol: All strains were grown in 200ml of YPD (Yeast extract Peptone Dextrose; 1% Yeast Extract, 2% Peptone, 2% Dextrose (Glucose)) at 30℃ until OD600 was 0.5-0.6

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies. At the same time, S. pombe spike-in controls were added for normalization.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift BioSciences, 21096) following the manufacture’s instruction.

value: Yeast cell

value: Purified anti-c-Myc (BioLegend, 626802)


title: YTK383-2-Input (spike-in control)


title: YTK383-1-Input (spike-in control)


title: YTK376-2-Input (spike-in control)


title: YTK376-2-IP (spike-in control)


title: YTK376-1-Input (spike-in control)


title: YTK376-1-IP (spike-in control)


title: YTK304-2-Input (spike-in control)

value: Untag


title: YTK304-1-Input (spike-in control)


title: YTK304-1-IP (spike-in control)


title: YTK304-2-IP (spike-in control)


title: YTK202-1-H3 (spike-in control)

value: Anti-Histone H3 (Abcam, ab1791)


title: YTK113-1-H3 (spike-in control)


title: YTK113-2-H4ac (spike-in control)

value: Anti-acetyl-Histone H4 (Millipore, 06-598)


title: YTK202-2-H4ac (spike-in control)


title: YSB787-2-H4ac (spike-in control)

value: wild type


title: YSB787-1-H4ac (spike-in control)


title: YTK113-Gal-30-1

data_processing:
FastQC-0.11.5 checked the quality of raw sequences.
HISAT2-2.0.4 aligned sequences to the transcriptome (ENSEMBL 86) of S. cerevisiae (R61-1-1) with a parameter --rna-strandness RF. QualiMap-2.2.0 and NOISeq-2.16.0 checked the quality of the alignment.
Command samtools view -f 128 -F 16 and samtools view -f 80 extracted reads located on the forward strand. Command samtools view -f 144 and samtools view -f 64 -F 16 extracted reads located on the reverse strand.
Reads on known transcript were counted by StringTie-1.3.0 with parameters -e -B.
ballgown-2.4.2 (Frazee et al., 2014) merged expression profiles from individual samples. FPKM was used as a normalized expression level.
Genome_build: R64-1-1/sacCer3
Supplementary_files_format_and_content: bigWig files were generated using command genomeCoverageBed –bg -split -scale SCALE_FACTOR in BEDTools-2.26.0; Scores represent RPM.
Supplementary_files_format_and_content: gtf files were generated using StringTie-1.3.0 with parameters -e -B.

growth_protocol: Cells were initially grown in synthetic complete medium containing raffinose (Ra, 0 min) and subsequently shifted to galactose (Gal 15, 30 and 120 min), glucose (Glu 30 and 120 min) and then back to galactose (Gal, 15 and 30 min).

extract_protocol:
RNA was extracted from cells harvested with hot phenol. Isolated RNA was resuspended in formamide for stability.
Libraries constructed with NEXTflex Rapid Directional mRNA-Seq Kit (Bioo Scientific, NOVA-5138-10) following the manufacture’s instruction.

tag: Stage


title: YTK202-1-H4ac (spike-in control)


title: YTK113-Glu-30


title: YTK202-2-H3 (spike-in control)


title: YTK113-1-H4ac (spike-in control)


title: YTK113-Gal-120


title: YSB787-2-H3 (spike-in control)


title: YTK113-2-H3 (spike-in control)


title: YTK383-2-IP (spike-in control)


title: YTK113-Glu-120


title: YSB787-1-H3 (spike-in control)


title: YTK113-Gal-30


title: YTK113-Ra-0


title: YTK113-Gal-15


title: YSB787-Gal-30-1


title: YSB787-Gal-15-1


title: YSB787-Glu-30


title: YSB787-Glu-120


title: YSB787-Gal-120


title: YTK113-Gal-15-1


title: YSB787-Gal-15


title: YSB787-Gal-30


title: YSB787-Ra-0


title: YTK383-2-IP

data_processing:
FastQC-0.11.5 checked the quality of raw sequences. If necessary, FASTX Toolkit-0.0.13 was used filtered out reads with low qualities and mates were properly paired.
Bowtie2-2.2.5 aligned sequences to the S. cerevisiae genome (R61-1-1). QualiMap-2.2.0 checked the quality of the alignment.
Picard-tools-2.6 removed duplicates with parameters VALIDATION_STRINGENCY=silent AS=true.
Genome_build: R64-1-1/sacCer3
Supplementary_files_format_and_content: bigWig files were generated using command genomeCoverageBed -bg -scale SCALE_FACTOR in BEDTools-2.26.0; Scores represent RPM.
Supplementary_files_format_and_content: narrowPeak files were generated using macs2-2.1.0 with corresponding controls and a parameter -q 0.01

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift BioSciences, 21096) following the manufacture’s instruction.


title: YTK383-2-Input


title: YTK383-1-Input


title: YTK376-1-IP


title: YTK376-1-Input


title: YTK202-1-H3


title: YTK304-1-Input


title: YTK304-2-Input


title: YTK376-2-IP


title: YTK304-1-IP


title: YTK202-2-H4ac


title: YTK202-2-H3ac

value: Anti-acetyl-Histone H3 (Millipore, 06-599)


title: YTK202-1-H4ac


title: YTK113-2-H3


title: YTK202-1-H3ac


title: YTK113-1-H3


title: YTK202-2-H3


title: YTK113-2-H4ac


title: input Müller glia DNA Exp1

source_name: Glast+ cells from P28 retinas

value: retina

value: Glast+ cells

value: none (input)


title: YTK113-1-H4ac


title: YTK113-2-H3ac


title: YTK113-1-H3ac


title: YTK383-1-IP


title: YSB787-2-H3


title: YTK376-2-Input


title: YSB787-1-H3


title: YSB787-2-H4ac


title: YSB787-1-H3ac


title: YSB787-2-H3ac


title: YTK304-2-IP


title: YSB787-1-H4ac


title: Frontal_Cortex control (9031356077_C)

first: Hamel

last: Patel

address: De Crespigny Park

department: Biostatistics and health informatics

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was Maximum Likelihood Estimation (MLE) background corrected using R package “MBCB” (version 1.18.0), log2 transformed, and Robust Spline Normalisation (RSN) using R package “lumi” (version 2.16.0)

label_protocol: Total RNA (25ng) was prepared for array expression profiling using the Ovation Pico WTA system (NuGEN Technologies, Inc., San Carlos, CA), as described by the manufacturer

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen,74804) and according to manufactures protocol.

treatment_protocol: Tissue blocks, approximately 0.5-1cm3, were obtained and stored in RNAlater RNA Stabilization Reagent (Qiagen) before RNA extraction.

value: MALE

tag: individual

value: Subject  111

tag: disease state

value: control


title: Temporal_Cortex control (9031356091_C)

value: FEMALE

value: Subject  110


title: Cerebellum control (9257302083_D)

source_name: Cerebellum

value: Subject  112

value: Cerebellum


title: Entorhinal_Cortex control (9031356094_C)


title: Temporal_Cortex control (9344744052_K)


title: Temporal_Cortex AsymAD (9031356085_L)

value: Subject  106

value: AsymAD


title: Frontal_Cortex AD (9345344027_G)

value: Subject  107

value: AD


title: Cerebellum control (9031356072_C)


title: Entorhinal_Cortex AsymAD (9345725010_A)

value: Subject  108


title: Frontal_Cortex control (9344744014_K)


title: Entorhinal_Cortex control (9216457022_C)


title: Temporal_Cortex control (9031356081_C)


title: Frontal_Cortex control (9031356097_C)


title: Cerebellum AsymAD (9344744014_F)


title: Frontal_Cortex AsymAD (9031356076_L)


title: Temporal_Cortex AD (9371242065_A)


title: Cerebellum control (9344732094_D)


title: Entorhinal_Cortex AsymAD (9216457002_L)


title: Cerebellum control (9031356084_C)


title: Temporal_Cortex AD (9371242082_H)


title: Entorhinal_Cortex AsymAD (9031356088_L)


title: Frontal_Cortex AsymAD (9344744094_D)


title: Entorhinal_Cortex AD (9371242082_A)


title: Cerebellum AsymAD (9031356073_L)


title: Cerebellum AD (9344744089_C)


title: Entorhinal_Cortex control (9216457027_C)


title: Frontal_Cortex control (9344744001_I)

value: Subject  109


title: Temporal_Cortex AsymAD (9345344014_A)


title: Frontal_Cortex AsymAD (9344744089_H)

value: Subject  104


title: Entorhinal_Cortex AsymAD (9216457022_I)

value: Subject  105


title: Entorhinal_Cortex AsymAD (9345344031_C)


title: Temporal_Cortex AsymAD (9031356091_I)


title: Temporal_Cortex control (9344744043_B)

value: Subject  103


title: Cerebellum control (9344732094_I)


title: Frontal_Cortex AsymAD (9031356097_I)


title: Cerebellum control (9257302083_I)


title: Temporal_Cortex AsymAD (9345344002_L)

value: Subject  101


title: Entorhinal_Cortex AsymAD (9345344027_L)

value: MALE


title: Temporal_Cortex AsymAD (9345344009_C)


title: Entorhinal_Cortex AsymAD (9216457027_I)


title: Frontal_Cortex control (9031356052_D)

value: Subject  98


title: Temporal_Cortex AD (9345725025_E)

value: Subject  102


title: Cerebellum AsymAD (9031356084_I)

value: FEMALE


title: Temporal_Cortex AD (9345725010_D)

value: Subject  97


title: Cerebellum control (9031356069_D)

value: control


title: Entorhinal_Cortex AD (9371242066_F)


title: Frontal_Cortex AD (9345344009_I)


title: Entorhinal_Cortex AD (9371242073_E)

value: Subject  99


title: Entorhinal_Cortex AD (9371242073_C)


title: Temporal_Cortex control (9031292027_D)


title: Temporal_Cortex control (9216457028_E)


title: Temporal_Cortex AD (9031292037_F)

value: Subject  100


title: Frontal_Cortex AD (9345344009_K)


title: Temporal_Cortex AD (9031356081_F)


title: Frontal_Cortex AsymAD (9344744052_L)

value: AsymAD


title: Temporal_Cortex AD (9345725025_G)


title: Frontal_Cortex AD (9345344002_B)


title: Cerebellum AD (9344744001_E)

value: Cerebellum


title: Cerebellum AD (9031356072_F)

value: AD


title: Frontal_Cortex AsymAD (9344744052_H)

value: Subject  96


title: Cerebellum AsymAD (9257302083_L)


title: Entorhinal_Cortex AsymAD (9216457002_J)

value: Subject  94


title: Temporal_Cortex AsymAD (9345344002_H)


title: Entorhinal_Cortex AD (9371242073_D)

value: Subject  95


title: Temporal_Cortex AD (9345725025_D)


title: Cerebellum AsymAD (9344732094_L)


title: Temporal_Cortex AsymAD (9031356085_J)


title: Cerebellum AD (9344744052_A)


title: Cerebellum control (9031356084_D)

value: Subject  93


title: Frontal_Cortex AsymAD (9031356076_J)


title: Cerebellum AsymAD (9216457020_G)

value: Subject  92


title: Frontal_Cortex AsymAD (9031356052_L)


title: Entorhinal_Cortex AsymAD (9345344027_F)


title: Cerebellum AsymAD (9031356073_J)


title: Entorhinal_Cortex AsymAD (9031356088_J)


title: Frontal_Cortex AD (9345344014_I)


title: Frontal_Cortex control (9031356097_D)


title: Temporal_Cortex control (9031356091_D)


title: Entorhinal_Cortex control (9216457027_D)


title: Temporal_Cortex AD (9031292037_G)

value: Subject  91


title: Entorhinal_Cortex AD (9371242073_H)

value: Subject  90


title: Temporal_Cortex AD (9031356081_G)

value: MALE


title: Temporal_Cortex AsymAD (9031292027_L)


title: Cerebellum AD (9344744052_E)


title: Entorhinal_Cortex control (9216457022_D)


title: Cerebellum control (9216457020_A)

value: Subject  89


title: Frontal_Cortex AD (9031356077_G)


title: Entorhinal_Cortex AsymAD (9031356102_L)


title: Frontal_Cortex AD (9345344014_B)

value: FEMALE


title: Temporal_Cortex control (9216457028_A)


title: Cerebellum AsymAD (9031356069_L)


title: Temporal_Cortex AD (9345725025_I)

value: Subject  88


title: Cerebellum AD (9344744043_A)


title: Temporal_Cortex control (9031356081_B)

value: Subject  87

value: control


title: Frontal_Cortex AD (9345344009_B)


title: Cerebellum AD (9031356072_G)


title: Temporal_Cortex control (9031292037_B)


title: Entorhinal_Cortex control (9031356094_B)


title: Temporal_Cortex AD (9345725025_H)


title: Frontal_Cortex AD (9031356077_H)

value: Subject  86


title: Cerebellum AD (9031356072_H)


title: Entorhinal_Cortex AD (9371242073_G)


title: Cerebellum AsymAD (9344744043_F)

value: Subject  85

value: AsymAD


title: Entorhinal_Cortex control (9031356094_D)


title: Frontal_Cortex AsymAD (9344744102_J)


title: Entorhinal_Cortex AsymAD (9345725025_A)


title: Cerebellum control (9031356072_B)

value: Cerebellum


title: Frontal_Cortex control (9031356077_B)


title: Temporal_Cortex AD (9371242065_G)

value: Subject  84

value: AD


title: Temporal_Cortex AD (9031356081_H)


title: Cerebellum AD (9344744094_A)


title: Frontal_Cortex AD (9345344027_B)


title: Entorhinal_Cortex AD (9371242082_I)


title: Cerebellum AsymAD (9344744001_H)

value: Subject  81


title: Temporal_Cortex AsymAD (9031356085_K)

value: Subject  83


title: Frontal_Cortex AsymAD (9031356076_K)


title: Temporal_Cortex AsymAD (9031356081_I)

value: Subject  82


title: Cerebellum AsymAD (9031356072_I)


title: Cerebellum AsymAD (9031356073_K)


title: Frontal_Cortex AsymAD (9031356077_I)


title: Entorhinal_Cortex AsymAD (9216457002_K)


title: Entorhinal_Cortex AsymAD (9031356094_I)


title: Temporal_Cortex AsymAD (9031292037_I)


title: Cerebellum control (9031356072_D)

value: Subject  80


title: Temporal_Cortex AD (9031356091_F)

value: Subject  78


title: Frontal_Cortex control (9031356077_D)

value: MALE


title: Temporal_Cortex AsymAD (9345344002_C)

value: Subject  79


title: Temporal_Cortex control (9031292037_D)


title: Cerebellum control (9257302083_K)

value: Subject  77


title: Temporal_Cortex control (9031356081_D)


title: Frontal_Cortex AsymAD (9344744043_L)


title: Temporal_Cortex control (9344744043_D)


title: Temporal_Cortex AD (9031356091_G)

value: Subject  76


title: Cerebellum AsymAD (9257302083_H)


title: Entorhinal_Cortex control (9344744094_I)


title: Cerebellum AsymAD (9344732094_H)


title: Cerebellum AD (9031356084_F)


title: Temporal_Cortex AsymAD (9345344009_H)

value: FEMALE


title: Frontal_Cortex AsymAD (9344744089_L)


title: Frontal_Cortex control (9344744001_D)

value: control


title: Frontal_Cortex AD (9345344031_E)

value: Subject  75


title: Cerebellum control (9344732094_K)


title: Temporal_Cortex AD (9371242065_K)


title: Temporal_Cortex AD (9345344031_D)

value: Subject  74


title: Cerebellum AD (9344744094_E)


title: Entorhinal_Cortex AsymAD (9345344031_H)

value: AsymAD


title: Entorhinal_Cortex AD (9371242082_B)


title: Frontal_Cortex AD (9344744102_D)


title: Entorhinal_Cortex AD (9371242066_I)


title: Temporal_Cortex AsymAD (9031292037_J)

value: Subject  73


title: Cerebellum AD (9031356084_G)

value: Cerebellum


title: Entorhinal_Cortex AsymAD (9031356094_J)


title: Frontal_Cortex AsymAD (9031356077_J)


title: Temporal_Cortex AsymAD (9031356081_J)


title: CMT-785-tumor

first: Sangwoo

last: Kim

state: State...

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Biomedical Systems Informatics

institute: Yonsei University College of Medicine

description: processed data file: CMT_222S_FPKM.csv

data_processing:
Base-calling process was performed using FastQC version 0.10.1.
Alignment was conducted using Tophat version 2.0.9 with Ensembl gene annotation of CanFam3.1 and fr-firststrand library type. Canine reference genome sequence CanFam3.1 (Ensembl, Canis lupus familiaris) was used in alignment process through Bowtie2 Index.
FPKM values are calculated by Cufflinks version 2.1.1 using bam files. Parameters including fr-firststrand, CanFam3.1 GTF, CanFam3.1 Bowtie2 Index are used.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CMT_222S_FPKM.csv: Comma-separated text file includes FPKM values for each Sample.

organism: Canis lupus familiaris

source_name: canine mammary tumor tissue

extract_protocol:
Fresh tissue samples were transferred in to RNAlater (Thermo Fisher Scientific), refrigerated overnight at 4°C and then stored at -80°C. Total RNA was extracted from tissues using RNeasy mini kit (Qiagen).
RNA quality was assessed by analysis of rRNA band integrity on an Agilent RNA 6000 Nano kit. Ahead of cDNA library construction, the 1ug of total RNA and magnetic beads with Oligo (dT) were used to enrich poly (A) mRNA from it. Then, the purified mRNAs were disrupted into short fragments, and the double-stranded cDNAs were immediately synthesized. The cDNAs was subjected to end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). The suitable fragments automatically purified by BluePippin 2% agarose gel cassette (Sage Science, MA) were selected as templates for PCR amplification. The final library sizes and qualities were evaluated electrophoretically with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA) and the fragment was found to be between 350–450 bp. Libraries were sequenced on the HiSeq 2500 following the manufacturer's protocols.

tag: dog id

value: mammary tumor tissue

tag: tumor grade

tag: diagnosis

value: Complex carcinoma

tag: Sex

value: Female

tag: neuter status

value: Intact

tag: lymphatic vessel invasion

value: Absent

tag: breed

value: Old English Sheepdog

tag: er allred score

tag: er status

value: Positive

tag: her2 score (hercep test score)

tag: date of surgery

tag: survival status (until 2018-08-01)

value: loss to follow-up

tag: survival (day)


title: Cerebellum AD (9031356069_E)

tag: gender

tag: age

value: Subject  72

tag: tissue

value: AD


title: CMT-785-normal

description: processed data file: CMT_222S_FPKM.csv

source_name: canine mammary normal tissue

value: mammary normal tissue


title: Temporal_Cortex AD (9031292027_E)

value: FEMALE

tag: individual

tag: disease state


title: Frontal_Cortex AD (9344744102_B)

value: Subject  70


title: Entorhinal_Cortex AD (9216457022_G)


title: Cerebellum AsymAD (9257302083_J)

value: Subject  68


title: Frontal_Cortex AD (9031356052_E)


title: Cerebellum AD (9257302083_G)


title: Cerebellum AsymAD (9031356069_J)

value: Subject  69

value: AsymAD


title: Cerebellum AD (9344732094_G)

value: Cerebellum


title: Cerebellum AsymAD (9344732094_J)


title: Temporal_Cortex AsymAD (9345344002_F)


title: Cerebellum AsymAD (9031356072_J)

value: Subject  73


title: Entorhinal_Cortex AsymAD (9031356102_J)


title: CMT-776-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: dog id

value: mammary tumor tissue

tag: tumor grade

value: Benign

value: Simple adenoma

value: Neutered

value: Maltese

value: Y


title: Entorhinal_Cortex AD (9371242066_G)


title: Entorhinal_Cortex AsymAD (9345344027_C)


title: CMT-756-tumor

description: processed data file: CMT_222S_FPKM.csv

tag: diagnosis

value: Carcinoma in benign mixed tumor

tag: Sex

value: Female

value: Intact

value: Absent

value: Positive

value: loss to follow-up


title: Frontal_Cortex AD (9344744102_K)

value: FEMALE

value: Subject  67

value: AD


title: CMT-771-tumor

description: processed data file: CMT_222S_FPKM.csv

value: Simple carcinoma (Tubulopapillary type)

tag: neuter status

tag: lymphatic vessel invasion


title: Temporal_Cortex AD (9345344031_K)


title: Temporal_Cortex AD (9031356074_E)

value: Subject  72


title: Entorhinal_Cortex AD (9216457027_G)