title: HAP1_WT_H3K27me3_rep1_ChIPSeq

description:
CHH48004
processed data file: HAP1_WT_H3K27me3_peaks.broadPeak

value: H3K27me3  (C36B11, Cell Signaling Technologies)


title: HAP1_WT_H3K27me3_rep2_ChIPSeq

status: Public on Dec 01 2020

type: SRA

city: Singapore

first: Melissa

last: Fullwood

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description:
CHH48008
processed data file: HAP1_WT_H3K27me3_peaks.broadPeak

library_source: genomic

data_processing:
ChIP-seq reads of H3K27me3, H3K27ac and H3K4me3 from HAP1 WT and EZH2  KO cells were mapped by BOWTIE2(v2.2.5) using default parameters in  paired-end mode. We filtered out alignments with mapq scores smaller than 30. The  two replicates were combined and peaks and bigWig files were generated  by MACS2(2.1.0.20150731) using option '-q 0.01' for H3K27ac and  H3K4me3 and '--broad --broad-cutoff 0.1 -q 0.05' for H3K27me3.
For the RNA-seq reads of HAP1 EZH2KO/WT and K562 GSK343/DMSO, we first trimmed off adaptors by trimmomatic (0.38) using option ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Only those paired-end reads that remained properly paired would be then mapped to the hg19 reference GTF file using kallisto(0.44.0) with option '-b 100'. Differentially expressed genes were called using sleuth(0.29.0) with gene-level aggregation and wald test.
For 4C reads, we trimmed off the HINDIII digestion site using tagdust(2.33). The remaining read 1s were mapped by BOWTIE2(v2.2.5) with option '--end-to-end' in single-end mode. r3Cseq(1.24.0) was used to call interactions against the HINDIII digested genome background in hg19.
Genome_build: hg19
Supplementary_files_format_and_content:
*.narrowPeak: ENCODE narrowPeak format generated by MACS2.
*.broadPeak: ENCODE broadPeak format generated by MACS2.
*_abundance.tsv: *_abundances.tsv is a plaintext file of the abundance estimates generated by Kallisto. Fields contained: 1. target_id. Transcript ID; 2. length. Transcript length; 3. eff_length. Effective length of the transcript; 4. est_counts. Estimated read counts given by the bootstrapping process of Kallisto; 5. tpm. Esmated transcript per million (TPM).
*interaction.txt: *.interaction.txt is the output generated by R3Cseq package. Field contained: 1. chromosome. Chromosome name; 2. start. Start of the fragment; 3. end. End of the fragment; 4. nReads. Number of reads mapped to this fragment; 5. RPMs. Reads per million per restriction fragment (RPM) as normalized interaction frequency values; 6. p.value. P value of this fragment interact with the 4C bait; 7. q.value. Q value of this fragment interact with the 4C bait.

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 wildtype cells

growth_protocol: Cell cultures were maintained at 37 °C, 5% CO2 humidified incubator.

extract_protocol:
5 million cells per ChIP was harvested, washed twice and resuspended in PBS. The cells were crosslinked with 1% methanol-free formaldehyde (Thermo Scientific) at room temperature for 10 minutes, followed by quenching with glycine for 5 minutes at room temperature. The cell pellet was washed with twice with PBS supplemented with 1mM PMSF (Sigma). The fixed cell pellet was lysed in 1% SDS lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 1% SDS) supplemented with protease inhibitor cocktail tablet (Roche), and sonicated using Bioruptor (Diagenode) and 200-500bp DNA fragments were achieved. The cell lysate was cleared through centrifugation at 13,200rpm for 35 minutes at 4°C. 9 volumes of dilution buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate) was added to the lysate to achieve 0.1% SDS lysis buffer, and the precleared through incubation with Protein G Dynabeads (Invitrogen) overnight at 4°C, with rotation. Antibody-conjugated beads were prepared by incubating 3.5ug antibody in 15uL Protein G Dynabeads in 50uL wash buffer (PBS, 0.1% Triton X-100) overnight at 4°C, with rotation. The precleared lysate was added into the prepared antibody-conjugated beads, and was incubated overnight at 4°C, with rotation. The beads were washed thrice in 0.1% SDS lysis buffer (50 mM HEPES pH7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once in high salt wash buffer (50 mM HEPES pH 7.5, 350 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS), once in lithium chloride wash buffer (10 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Igepal- CA-630, 0.5% Sodium Deoxycholate), and once in TE buffer. The beads were then eluted in elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS), treated with RNase A (Qiagen) with 55°C for 30 minutes, and decrosslinked with Proteinase K (Ambion) at 37°C overnight. ChIP DNA was cleaned up with QIAquick PCR purification kit (Qiagen), and quantitated using Qubit High Sensitivity dsDNA Assay (Invitrogen).
1ng of ChIP DNA was used for the construction of DNA library for Illumina HiSeq 4000 NGS sequencing using ThruPLEX DNA-seq 48D Kit (Rubicon) as per protocol. Final libraries were quantitated and pooled at the same molarity using Agilent High Sensitivity DNA Kit (Agilent).

tag: cell line background

tag: cell type

value: haploid human cell line that was derived from KBM7 cells (purchased from Horizon)

tag: chip antibody


title: Lung_403_Low_Day30_rep4

type: RNA

city: Vandoeuvre les Nancy

first: Carole

last: Seidel

address: Rue du Morvan

country: France

institute: INRS

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, Low, Day 30, replicate 4

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4853A SurePrint G3 Rat v2 GE 8*60K microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing:
Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were normalized using the GeneSpring software (v 14.9)
Data were normalized by shift to 75.0 percentile and filtered by flags and by expression based on the signal intensity values (to remove very low signal values and those that have reached saturation)

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat, Lung, NM-403, Low, Day 30

label_protocol: For each of the 72 samples (6 control, 6 exposed rats to low dose and 6 exposed rats to high dose per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: Accessory lobe of rat lungs were stored in RNA later at -20°C before use

extract_protocol: Total RNA were disrupted using gentleMACS™ Dissociator (Miltenyi Biotech) and extracted from accessory lobe of lungs with Nucleospin® RNA midi kit (Macherey-Nagel) according to the manufacturer’s instructions. RNA quality was determined by spectrophotometry (A260nm/A280nm > 1.8) and by capillary electrophoresis using Agilent 2100 Bioanalyser (RIN > 7, Agilent RNA 6000 NanoRNA 6000 Nano® Kit, Santa Clara, CA, USA).

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation  6 hours/day, 5 days/week for 4 weeks to two doses of NM-403 carbon nanotube.

tag: strain

value: Sprague Dawley

tag: tissue

value: accessory lobe of lung

tag: gender

value: female

tag: age

value: 13 weeks-old (at the onset of inhalation)

tag: treatment

tag: dose

value: Low

tag: time

value: Day 30


title: Vehicle1

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

country: USA

institute: Cedars-Sinai Medical Center

description: Controls that did not treat anything on microglia

library_source: transcriptomic

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
We trimmed the adapter sequences (TruSeq™ index adapter with option “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC”, and the reverse complementary sequence of TruSeq™ universal adapter with the option “-a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT”) by applying the cutadapter software
The remained reads were then aligned to the Mus musclus genome (GRCm38.89) with STAR (2.5.3a) by with default option. The aligned reads were assembled into genes by calculating read count with HTSeq (0.6.1). Then, TMM normalization method was conducted using EdgeR (3.12.1).
Genome_build: Mus musclus genome (GRCm38.89)
Supplementary_files_format_and_content: tab-delimited text files including TMM normalized count for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Primary microglia cell

growth_protocol: Streptococcus pneumoniae were cultured in sterilized Todd-Hewitt media containing 30 g of Todd Hewitt Broth, 0.5% Yeast extract, and 1.5% Agar per liter. Subsequently, the pneumococcus grown on THY agar plate was transferred into THY broth. The transferred pneumococci were cultured at 37°C incubator for 24~48 hours until OD550 = 0.3 to a concentration of 108 CFU/ml and used to infect cells at MOI=100 for 2 hours. Seperation of the pellets and supernatants is done by centrifugation at 4,000 ×  g at 4°C for 10 min.

extract_protocol:
Total RNA was extracted from primary microglia with Trizol reagent (Invitrogen) and contaminating DNA was depleted with clearance procedure according to the manufacturer's protocol with Riboclear™  plus (GeneAll).
Full length cDNA was generated following manufacturers recommended protocols of the SMARTer-Seq v4 Ultra Low input RNA Kit for sequencing (Clontech, 634888). First-strand cDNA synthesis was initiated by adding 1 μl of 3’ SMART CDS primer II A at 72℃ for 3 min from 10 ng of total RNA. The second strands were synthesis by adding SMARTer-seq v4 oligo and SMARTScribe reverse transcriptase, and the reaction was incubated at 42℃ for 90 min, followed by inactivation at 70℃ for 10 min. Double-strand cDNA was amplified by PCR for 8 cycles and purified using Agencourt AMPure beads(Beckman, A63881).   mRNA-seq library is was generated following manufacturers recommended protocols of the Nextera XT DNA library preparation kit (illumina, FC-131-1024). The cDNA was subjected to tagmentation (simultaneous fragmentation and tagging with sequencing adapters) and amplified by PCR using Index Primers from the Nextera XT DNA Index Kit (Illumina, FC-131-1001). After PCR, the DNA library was purified using AMPure beads and the quality was assessed using an Agilent 2100 Bioanalyzer.  The DNA libraries from individual samples were quantified using KAPA Library Quantification kit (KAPA biosystems, KK4854) followed by pooling. All libraries were sequenced on an illumina Hiseq2500 instrument to generate dual indexed 100 bp paired reads, generating an average 58 million reads for each sample.

treatment_protocol: In each sample condition, microglia was treated with condition specific molecules for 2 hours.

tag: developmental stage

value: Mouse cortex

value: Primary microglia cell

value: no treatment


title: CH041C

city: Cheras

first: Elena

middle: AB

last: Azizan

state: Wilayah Persekutuan Kuala Lumpur

address: PPUKM, Jalan Yaacob Latif, Bandar Tun Razak

department: Department of Medicine

country: Malaysia

institute: The National University of Malaysia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were visualized and extracted with the GenomeStudio data analysis software (version 2009.2; Illumina) with Illumina’s default analysis settings.

label: biotin

source_name: Hyperplastic Adrenal

label_protocol: Each RNA sample (total RNA, 1  g) was converted to cDNAby reverse transcription and subjected to labeling and hybridization using the whole-genome cDNA mediated annealing, selection, extension, and ligation (DASL) assay (Illumina HumanRef-8 version 3 Expression BeadChip; Illumina, San Diego, CA).

extract_protocol: Approximately 0.125 cm3 of tissue was used for RNA extraction.  Total RNA was isolated from AAG and APA using  Trizol with a PureLink kit (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. On-column deoxyribonuclease treatment was performed on all RNA samples.

value: Adrenal

tag: sentrix position

value: A

tag: chip no


title: r2.BS.8

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: combined.testplus.results.csv.gz

data_processing:
The samples were processed and sequenced independently several times. The main analysis only considered the first sequencing of samples IVI1-IVI26.
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 GRCh38 human genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with less than 200 total mapped reads across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
In addition to the main analysis, a second analysis was performed to classify test samples into treatment groups. For this analysis, two additional sets of replicate analysis samples were processed and sequenced with independent MeDIP procedures. The two additional replicate sample sets were combined with the original samples to obtain a set of combined samples containing equal numbers of reads from each replicate set. Seven of the combined case samples showed high levels of correlation with each other, yet diverged considerably with the remaining samples. This appears most likely due to batch effects related to the MeDIP procedure. In this case, the batch effects were largely due to the third replicate analysis of these samples. These seven samples were removed from the analysis. DMR were then identified between the eight remaining combined case samples and the 13 combined control samples using identical methods to those used in the main DMR analysis presented previously. The sites identified as DMR in this analysis were then used to classify ten test samples into sample groups.
The test samples were processed and sequenced in four separate MeDIP-seq procedures. Equal reads from each of the four replicates for each sample were merged into a single combined sample. An additional eight technical replicates were also processed a single time. These technical replicates were selected from the original 26 samples and were used as an additional blinded test set.
Genome_build: GRCh38
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 if applicable.

source_name: Sperm

growth_protocol: A single center (IVIRMA Valencia) performed the prospective and open clinical study. The IRB approval code protocol number is #1311-VLC-136-FC. The men included caucasians between 26 and 54 years of age with a total sperm concentration (concentration in millions/mL x volume in mL). Sperm samples were frozen with liquid nitrogen and stored (-20 C) for the subsequent epigenetic analysis.

extract_protocol:
Frozen human sperm samples were stored at -20 C and thawed for analysis. Genomic DNA from sperm was prepared as follows: A 400 μl of sperm suspension was used and centrifuged for 10 minutes at low speed to concentrate sperm. The supernatant was discarded, and the pellet resuspended in 100 ul PBS. Then 820 μl DNA extraction buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) and 80 μl 0.1 M Dithiothreitol (DTT) were added and the sample incubated at 65 C for 15 min. Proteinase K (20 mg/ml) (80 μl) was added, and the sample was incubated on a rotator at 55 C for at least 2 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A, Madison, WI) was added, the sample was mixed and incubated on ice for 15-30 min, then spun at 4 C at 13,000 rpm for 30 min. The supernatant was transferred to a fresh tube, then precipitated over night at -20 C with the same volume. 100% isopropanol and 2 μl glycoblue. The sample was then centrifuged, and the pellet was washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). The freeze-thaw will destroy any contaminating somatic cells in the sperm collection.Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: individual sperm DNA samples (2-4 ug of total DNA) were diluted to 130 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with the Covaris M220 using the 300 bp setting. Fragment size was verified on a 2% E-gel agarose gel. The sonicated DNA was transferred from the Covaris tube to a 1.7 ml microfuge tube, and the volume was 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 1XPBS with 0.1% BSA and 2mM EDTA) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1-2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of 1xIP 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 2 hours on a rotator at 4 C. After the incubation, the bead-antibody-DNA complex was washed three times with 1X IP buffer as follows: The tube was placed into a magnetic rack for 1-2 min and the supernatant was discarded, then the magnetic bead antibody pellet was washed with 1xIP buffer 3 times. The washed bead antibody DNA pellet was then resuspended in 250 μl digestion buffer with 3.5 μl Proteinase K (20mg/ml). The sample was incubated for 2-3 hours on a rotator at 55 C, then 250 μl of buffered Phenol-Chloroform- Isoamylalcohol solution was added to the sample, and the tube was vortexed for 30 sec and then centrifuged at 14,000rpm 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 14,000rpm 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 14,000rpm for 20 min at 4 C and the supernatant was 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 14,000rpm for 5 min at 4 C and the supernatant was discarded. The tube was spun again briefly to collect residual ethanol to the bottom of the tube and as much liquid as possible was removed with gel loading tip. The pellet was air-dried at RT until it looked dry (about 5 min) then resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA samples (50 ng of each) were used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (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 sample 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 50bp and approximately 20-50 million reads per sample, and 6-7 sample libraries each were run in one lane.

treatment_protocol: We included two groups (sperm from father with offspring with autism (case) or without (control)).

tag: sample

tag: combined sample id

tag: sequencing batch

value: E


title: Lung_403_Low_Day30_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, Low, Day 30, replicate 1


title: CH042C

source_name: APA

value: B


title: Lung_403_High_Day30_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 6

source_name: Rat, Lung, NM-403, High, Day 30

value: High


title: S.pneu1

description: Microglia was treated with MOI 100 S.pneumoniae (S.pneu) culture supernatant for 2 hours


title: r2.BS.7

description: combined.testplus.results.csv.gz


title: Lung_403_Low_Day30_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, Low, Day 30, replicate 2


title: FRABA3: FR & ABA, biological rep3

city: Albany

first: ByungHoon

middle: Brian

state: GA

address: 504 College Dr.

institute: Albany State University

description: 24 hr treatment

hyb_protocol: The labeled cRNA was fragmented to between 35nt and 200nt segments by metal induced hydrolysis at 94°C for 30 min.  The fragments were hybridized to the arrays in standard hybridization buffer by first heating to 95°C for 5min then placed immediately at 45°C for 5 min prior to loading into the arrays.  Hybridization was done using the Affymetrix rotating Hyb oven 640 at 60rpm for 16 hrs. Following hybridization the arrays were transferred to the Affymetrix Fluidics Station 450 for processing.  The arrays were washed using the EukGE-WS2v4_450 program.  The arrays were stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned using the Affymetrix 3000 7G scanner as described by the manufacturer.

data_processing: The data were RMA normalized with Affy package of Bioconductor. In addition, expression calls were identified by MAS5.

organism: Arabidopsis thaliana

source_name: Treated with supplemental far-red light & ABA

label_protocol: RNA was converted to cRNA with an intermediate cDNA step as per the manufacturer’s instructions.  Briefly, one microgram of total RNA was reverse transcribed with an oligo-dT-T7 primer by first heating the total RNA and primer mixture to 65°C for 5min followed by incubation at 25°C for 5min.  Following primer annealing reverse transcription buffer, dNTPs, DTT and Reverse Transcriptase (SuperScript III, Invitrogen, Carlsbad CA) were incubated at 48°C for 90 min.  The cDNA second strand was synthesized using second strand reaction buffer, dNTPs, E. coli polymerase, E. coli ligase and RNAse H with incubation at 16°C for 2hrs immediately followed by addition of T4 DNA Polymerase and incubation for an additional 10min at 16°C.  Double stranded cDNA was purified using column purification by standard techniques.  To produce the labeled cRNA required for hybridization the cDNA was incubated with in vitro transcription (IVT) components including the biotin labeled uracil and T7 RNA polymerase for 16hrs at 37°C.  The cRNA was then cleaned using standard column purification as per the manufacturer’s instructions (Qiagen).

growth_protocol: Plants were grown under standard condition for 9 days: 24 hr continuous white light (cool fluorescent light, 80 mmol/m2sec) at 22°C

extract_protocol: Total RNAs were extracted using TRIreagent (SIGMA). Samples were DNase treated and further purified through RNeasy spin column (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Nine-day old plants were treated with one of the four different conditions for 24 hr: combinations of light (white light alone or white light w/ supplemental far-red light, 6 mmol/m2sec) and ABA (0 mM or 1 mM).

value: Aerial part, 10-day-old


title: RRBS of STAT5ab-KO mouse liver_female6_G132_M21-B

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: RRBS libraries

data_processing:
Raw FASTQ files were first processed by Trim Galore (version 0.4.3) using options: (--rrbs --paired).  The trimmed paired end read1 and paired end read2 files were mapped by Bismark (Krueger and Andrews, 2011) using default parameters.  PileOMeth  was used to extract and quantify all CpG dinucleotides in the bam files, outputting the location, total coverage, number of thymines and number of cytosines of each CpG in methylKit compatible format (parameter: --methylKit), while avoiding double counting reads where paired end reads overlap.
The pileometh results were directly inputted into methylKit, two sample groups at a time, for pair-wise differential analysis.  MethylKit (Akalin et al., 2012) differential analysis was performed at the level of both 100 bp tiles and individual CpGs levels using default parameters with the following: context="CpG", filterByCoverage count=10, destrand=T.
The significantly changing tiles and individual CpGs are defined as fold difference of 15% and qvalue < 0.05, and were combined such that individual CpGs not captured at the tile level were also included.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file showing differentially methylated regions identified in 4 pair-wise comparisons

source_name: STAT5ab-KO mouse liver_female

extract_protocol:
Reduced representation bisulfite sequencing (RRBS) libraries were prepared from frozen liver tissues as previously described with modifications (Gu et al., 2011).  Briefly, small sample frozen liver tissue (~50 mg)  was homogenized by vigorous pipeting in 370 μl TE buffer (10mM Tris, 1mM EDTA, pH 8) containing 10 ul of proteinase K solution (10mg/ml), and 20 μl of 10% (v/v) SDS was quickly.  The homogenate was incubated at 50 °C for 2 hr,  and purified by 400ul phenol chloroform extraction with the addition 32 ul of 5M NaCl, using large-bore pipet tips and gentle inversions (no vortexing). Intact genomic DNA was spooled from the aqueous phase with the addition of equal volume 100% ethanol. The spooled gDNA was subjected to RNase treatment in PBS buffer (298 ul 1X PBS, 2 μl of 10 mg/ml RNase A) for 1 hr at room temperature. The RNA free gDNA was washed in ethanol and thoroughly resuspended in TE buffer for Qubit quantification of DNA, taking care to sample a large volume (10 μl) first and shearing it by vigorous pipeting to ensure that the subsequent 2 μl input for Qubit is as homogenous as possible.
500 ng of intact gDNA was digested with 2.5 μl of MspI (20,000 units/ml; NEB Cat. no. R0106S) in supplied digestion buffer (40 μl total volume) at 37°C (with lid at 40°C) overnight, directly subjected to end-repair in the same reaction and purified by phenol chloroform.  450 ng of MpsI digested, end-repaired material quantified nanodrop measurement was ligated to Illumina adaptors supplied in NEB DNA-seq kit (NEB cat. E7370S, using 1/20 diluted adaptor) and NEB Quick DNA ligase kit (NEB cat. E6056S) , incubating at 16°C overnight without heated lid.   After USER enzyme digestion and cleanup with Zymo's DNA clean and concentrator -5 (Zymo Cat. D4003T), the adaptor-ligated MspI fragments were bisulfite treated for two consecutive rounds using Zymo's EZ Gold bisultfit kit (Zymo Cat. D5005) per manufacturer's instructions.  From the 12 μl bisulfite treated DNA, 5 μl was amplified using KAPA hifi HS Uracil+ polymerase system (Kapa Cat. KM2800) for 12-15 PCR cycles, the optimal cycle determined empirically to attain the lowest number of cycles that yield sufficient material without over-amplification.  Finally, size selection for 160-340 bp was accomplished by performing a double SPRI purification of 0.65X and 0.55X (To 50 μl reaction volume, 32.5ul of SPRI beads were added.  The supernatant was saved. Then 27.5 μl of SPRI was added to supernatant.  Beads were washed and eluted in 0.1X TE).  The final libraries were analyzed on a 1% agarose SYBR green gel, quantified by Qubit and sequenced on Illumina HiSeq (paired-end, 50bp reads) with no more than 1/3 of a lane being RRBS material to avoid problems caused by non-degenerate bases.

treatment_protocol: Hepatocyte-specific STAT5ab-deficient mice were generated by mating C57BL/6 x 129J mice having a floxed Stat5a-Stat5b locus with albumin promoter-driven Cre transgenic mice (FVB/N).  Livers from 8 to 12-wk old hepatocyte STAT5ab-deficient males and females, and floxed controls, were excised, snap frozen in liquid nitrogen and stored at -80C until use. STAT5ab knockout mouse liver samples are those described in MG Holloway et al.,Molecular Endocrinology 2007).

tag: strain background

value: mixed; C57BL/6 x 129J

tag: genotype/variation

value: Alb-Cre-LoxP STAT5ab KO

tag: Sex

value: Female

value: 8-12 weeks

value: liver

tag: molecule subtype

value: Genomic DNA, MspI digested, 40-220 bp


title: Lung_403_Low_Day90_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, Low, Day 90, replicate 6

source_name: Rat, Lung, NM-403, Low, Day 90

tag: strain

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Low

value: Day 90


title: RRBS of STAT5ab-KO mouse liver_female4_G132_M19-B

description: RRBS libraries

tag: tissue


title: r2.BS.6

description: combined.testplus.results.csv.gz


title: RRBS of STAT5ab-KO mouse liver_female5_G132_M20-B

description: RRBS libraries


title: CH049C

value: Adrenal

value: D


title: Lung_403_Low_Day30_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, Low, Day 30, replicate 3

tag: gender

value: Day 30


title: RRBS of STAT5ab-KO mouse liver_female3_G132_M18-B

description: RRBS libraries

tag: age


title: Lung_403_High_Day30_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 5

tag: treatment

value: High


title: r2.BS.4

description: combined.testplus.results.csv.gz

value: E


title: FRABA2: FR & ABA, biological rep2

description: 24 hr treatment

value: Aerial part, 10-day-old


title: CH042N

source_name: AAG

value: C


title: Lung_403_High_Day30_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 4

tag: dose


title: RRBS of STAT5ab-KO mouse liver_female1_G131_M20-B

description: RRBS libraries

value: mixed; C57BL/6 x 129J

value: Alb-Cre-LoxP STAT5ab KO

value: Female


title: RRBS of STAT5ab-KO mouse liver_female2_G132_M17-B

description: RRBS libraries

value: 8-12 weeks

value: liver

value: Genomic DNA, MspI digested, 40-220 bp


title: r2.BS.3

description: combined.testplus.results.csv.gz


title: r2.BS.2

description: combined.testplus.results.csv.gz


title: r2.BS.1

description: combined.testplus.results.csv.gz


title: r2.BS.5

description: combined.testplus.results.csv.gz


title: Lung_403_High_Day30_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 3

value: Sprague Dawley

value: accessory lobe of lung

value: female

tag: time


title: RRBS of STAT5ab-KO mouse liver_male6_G131_M19-B

description: RRBS libraries

source_name: STAT5ab-KO mouse liver_male

value: Male


title: RRBS of STAT5ab-KO mouse liver_male5_G131_M18-B

description: RRBS libraries


title: r2.test.O

description: combined.testplus.results.csv.gz

value: case

value: IVIO


title: FRABA1: FR & ABA, biological rep1

description: 24 hr treatment


title: RRBS of STAT5ab-KO mouse liver_male4_G131_M17-B

description: RRBS libraries


title: r2.test.I

description: combined.testplus.results.csv.gz

value: IVII


title: Lung_403_High_Day30_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 1

value: 13 weeks-old (at the onset of inhalation)

value: High

value: Day 30


title: RRBS of STAT5ab-KO mouse liver_male3_G131_M16

description: RRBS libraries


title: FR3: FR only, biological rep3

description: 24 hr treatment

source_name: Treated with supplemental far-red light

value: Aerial part, 10-day-old


title: Lung_403_Control_Day30_rep4

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-403, Control, Day 30, replicate 4

source_name: Rat, Lung, NM-403, Control, Day 30

value: control

value: Control


title: FR1: FR only, biological rep1

description: 24 hr treatment


title: Lung_403_High_Day30_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-403, High, Day 30, replicate 2


title: Lung_403_Control_Day30_rep6

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-403, Control, Day 30, replicate 6


title: FR2: FR only, biological rep2

description: 24 hr treatment


title: Lung_403_Control_Day30_rep5

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-403, Control, Day 30, replicate 5


title: WLABA3: ABA only, biological rep3

description: 24 hr treatment

source_name: Treated with white light & ABA


title: r2.test.A

description: combined.testplus.results.csv.gz

value: IVIA

value: E


title: 493_German Shepherd Dog_Acute_GDV_Female

type: genomic

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

description:
493
Canis familiaris

hyb_protocol: SNP array genotyping was performed on samples using the Illumina CanineHD Whole-Genome Genotyping BeadChip arrays including 173,662 SNPs located on autosomes and sex chromosomes.

scan_protocol: Arrays were scanned.

data_processing: Genotype calling of SNPs as well as data visualization were performed with GenomeStudio v2.0 and exported to PLINK format using the CanFam3.1.75 genome assembly to retrieve chromosomal coordinates. SNP array data imputation was conducted using a phased genotype reference dataset of 365 dogs from multiple breeds genotyped by whole-genome sequencing. The reference dataset was filtered excluding sex chromosomes, removing insertion/deletions, non-PASS variants, and variants with more than two alleles. The SNP array dataset of all 241 dogs on our study (target dataset) was filtered excluding sex chromosomes and duplicate variants, including variants with: minor allele frequency (MAF) ≥ 0.005, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. The resulting dataset was subjected to principal component analysis (PCA) in PLINK v1.9 to identify outliers and dogs whose PCA clustering would differ from the owner-identified breed information. We computed the relatedness PIHAT metric using PLINK v1.9 for each pair of samples aiming to identify duplicated samples (PIHAT=1.0). Outliers, duplicated and misclassified samples were removed from the dataset. Reference and target datasets were compared using the Conform-gt software, keeping only variants shared between the target and the reference dataset. Finally, the genotypes were imputed with the software Beagle v5, using the recombination rate map reference, default settings and effective population size = 200. After imputation, variants were filtered with dosage R2 (DR2)< 0.4, ultimately including only with MAF ≥ 0.05, genotyping rate ≥ 95%, Hardy-Weinberg p-value in unaffected: > 1.0x10-7, and samples with genotyping rate ≥ 90%. Gene annotation of SNPs was performed with R-BiomartTv2.40.4 using the dog genome reference CanFam3.1.

label: biotin/dinitrophenyl

organism: Canis lupus familiaris

source_name: Peripheral blood

label_protocol: Extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labeled nucleotide. C and G nucleotides are biotin-labeled; A and T nucleotides are dinitrophenyl-labeled. Signal amplification of the incorporated label further improves the overall signal-to-noise ratio of the assay.

extract_protocol: Peripheral blood samples were collected from all animals with DNA extracted by Qiagen DNeasy Blood and Tissue kit or Qiagen Genomic DNA Midi Kit (Qiagen Inc., Hilden, Germany # 69504, # 51183). DNA was quantified by Qubit with the Qubit Broad Range dsDNA assay kit (Life Technologies, Carlsbad, CA, USA #Q32853). DNA quality was determined by DNA Integrity Number on an Agilent 4400 Tapestation (Agilent, Santa Clara, CA, USA #G2991AA).

tag: breed

value: German Shepherd Dog

tag: status (hc = healthy control, gdv

value: gastric dilatation-volvulus:Acute_GDV

value: Female

value: Peripheral blood


title: RRBS of STAT5ab-KO mouse liver_male1_G130_M20

description: RRBS libraries

value: mixed; C57BL/6 x 129J

value: Alb-Cre-LoxP STAT5ab KO

value: 8-12 weeks

value: liver

value: Genomic DNA, MspI digested, 40-220 bp


title: 491_German Shepherd Dog_Acute_GDV_Female

description:
491
Canis familiaris


title: r2.IVI.32

description: combined.testplus.results.csv.gz


title: Lung_403_Control_Day30_rep3

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-403, Control, Day 30, replicate 3

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)


title: RRBS of control mouse liver_female5_G130_M19

description: RRBS libraries

source_name: control mouse liver_female

value: Control, Floxed STAT5ab locus


title: WLABA1: ABA only, biological rep1

description: 24 hr treatment

value: Aerial part, 10-day-old


title: r2.test.E

description: combined.testplus.results.csv.gz

value: case

value: IVIE


title: WLABA2: ABA only, biological rep2

description: 24 hr treatment


title: RRBS of control mouse liver_female4_G130_M18

description: RRBS libraries


title: RRBS of STAT5ab-KO mouse liver_male2_G130_M21

description: RRBS libraries

value: Male


title: WL3: Control, biological rep3

description: 24 hr mock treatment

source_name: Treated with white light


title: 488_German Shepherd Dog_Acute_GDV_Female

description:
488
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV


title: 487_Poodle Standard_Acute_GDV_Female

description:
487
Canis familiaris

value: Poodle Standard

value: Female

value: Peripheral blood


title: RRBS of control mouse liver_female3_G130_M17

description: RRBS libraries

value: mixed; C57BL/6 x 129J

value: 8-12 weeks


title: r2.IVI.30

description: combined.testplus.results.csv.gz

value: control

value: E


title: RRBS of control mouse liver_female2_G129_M19

description: RRBS libraries

value: liver

value: Genomic DNA, MspI digested, 40-220 bp


title: 483_Doberman Pinscher_Acute_GDV_Male

description:
483
Canis familiaris

value: Doberman Pinscher


title: Lung_403_Control_Day30_rep2

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-403, Control, Day 30, replicate 2

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Control

value: Day 30


title: 477_Labrador Retriever_Acute_GDV_Female

description:
477
Canis familiaris

value: Labrador Retriever

value: gastric dilatation-volvulus:Acute_GDV


title: Lung_403_Low_Day3_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, Low, Day 3, replicate 5

source_name: Rat, Lung, NM-403, Low, Day 3

value: Low

value: Day 3


title: r2.IVI.28

description: combined.testplus.results.csv.gz

value: case


title: WL1: Control, biological rep1

description: 24 hr mock treatment

value: Aerial part, 10-day-old


title: WL2: Control, biological rep2

description: 24 hr mock treatment


title: Lung_403_Control_Day30_rep1

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-403, Control, Day 30, replicate 1

value: control


title: RRBS of control mouse liver_female1_G129_M18

description: RRBS libraries

value: mixed; C57BL/6 x 129J

value: Control, Floxed STAT5ab locus

value: Female

value: 8-12 weeks


title: r2.IVI.27

description: combined.testplus.results.csv.gz

value: E


title: 471_German Shepherd Dog_Acute_GDV_Male

description:
471
Canis familiaris

value: German Shepherd Dog

value: Male

value: Peripheral blood


title: Lung_403_Low_Day3_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, Low, Day 3, replicate 4

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)


title: Lung_403_Low_Day3_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, Low, Day 3, replicate 6

value: Low


title: r2.IVI.31

description: combined.testplus.results.csv.gz


title: 470_German Shepherd Dog_Acute_GDV_Male

description:
470
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: RRBS of control mouse liver_male5_G129_M16

description: RRBS libraries

source_name: control mouse liver_male

value: liver

value: Genomic DNA, MspI digested, 40-220 bp


title: r2.IVI.29

description: combined.testplus.results.csv.gz

value: control


title: RRBS of control mouse liver_male6_G129_M17

description: RRBS libraries

value: mixed; C57BL/6 x 129J


title: Lung_403_Low_Day3_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, Low, Day 3, replicate 3

value: Day 3


title: r2.IVI.26

description: combined.analysis.results.csv.gz


title: Lung_403_Low_Day3_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, Low, Day 3, replicate 2


title: r2.IVI.25

description: combined.analysis.results.csv.gz


title: RRBS of control mouse liver_male4_G128_M18-B

description: RRBS libraries

value: Control, Floxed STAT5ab locus


title: Lung_403_High_Day90_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-403, High, Day 90, replicate 3

source_name: Rat, Lung, NM-403, High, Day 90

value: High

value: Day 90


title: Lung_403_Low_Day3_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, Low, Day 3, replicate 1


title: r2.IVI.24

description: combined.analysis.results.csv.gz

source_name: Sperm

value: E


title: 469_Poodle Standard_Acute_GDV_Male

description:
469
Canis familiaris

value: Poodle Standard

value: Male


title: 467_Poodle Standard_Acute_GDV_Male

description:
467
Canis familiaris

value: Peripheral blood


title: RRBS of control mouse liver_male3_G128_M17-B

description: RRBS libraries

value: 8-12 weeks


title: RRBS of control mouse liver_male2_G128_M16-B

description: RRBS libraries


title: 465_German Shepherd Dog_Acute_GDV_Female

description:
465
Canis familiaris

value: German Shepherd Dog

value: Female


title: Lung_403_High_Day3_rep5

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, High, Day 3, replicate 5

source_name: Rat, Lung, NM-403, High, Day 3

value: Sprague Dawley

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)


title: Lung_403_High_Day3_rep6

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, High, Day 3, replicate 6


title: Lung_403_High_Day3_rep4

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, High, Day 3, replicate 4


title: 464_Doberman Pinscher_Acute_GDV_Male

description:
464
Canis familiaris

value: Doberman Pinscher

value: gastric dilatation-volvulus:Acute_GDV


title: r2.IVI.23

description: combined.analysis.results.csv.gz

value: control


title: 458_Borzoi_Acute_GDV_Male

description:
458
Canis familiaris

value: Borzoi


title: r2.IVI.22

description: combined.analysis.results.csv.gz


title: r2.IVI.21

description: combined.analysis.results.csv.gz


title: RNA-seq of control mouse liver_male-pool2_G140_M13

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene, Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results.

source_name: RNA-seq of control mouse liver_male

extract_protocol:
RNA was extracted from flash frozen mouse liver using Trizol per the manufacturer's instructions.
; Stranded RNA-seq libraryRNA was depleted of rRNA using the NEB rRNA depletion kit (NEB, Ipswich, MA, Cat# E6310). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

treatment_protocol: Hepatocyte-specific STAT5ab-deficient mice were generated by mating C57BL/6 x 129J mice having a floxed Stat5a-Stat5b locus with albumin promoter-driven Cre transgenic mice (FVB/N). Livers from 8 to 12-wk old hepatocyte STAT5ab-deficient males and females, and floxed controls, were excised, snap frozen in liquid nitrogen and stored at -80C until use.  STAT5 knockout mouse liver samples were those described in MG Holloway et al., Molecular Endocrinology, 2007.

value: mixed:C57BL/6 x 129J

value: Control, Floxed STAT5ab locus

value: Total RNA_Ribo-minus


title: 457_German Shepherd Dog_Acute_GDV_Male

description:
457
Canis familiaris


title: 450_Great Dane_Acute_GDV_Female

description:
450
Canis familiaris

value: Great Dane


title: RNA-seq of control mouse liver_male-pool1_G140_M12

value: Male


title: RRBS of control mouse liver_male1_G128_M15-B

description: RRBS libraries

value: mixed; C57BL/6 x 129J

value: liver

value: Genomic DNA, MspI digested, 40-220 bp


title: r2.IVI.20

description: combined.analysis.results.csv.gz

value: E


title: Lung_403_High_Day3_rep3

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, High, Day 3, replicate 3

value: Sprague Dawley

value: High

value: Day 3


title: 449_German Shepherd Dog_Acute_GDV_Male

description:
449
Canis familiaris

value: German Shepherd Dog

value: Peripheral blood


title: RNA-seq of STAT5ab-KO mouse liver_male-pool2_G140_M11

source_name: RNA-seq of STAT5ab-KO mouse liver_male

value: Alb-Cre-LoxP STAT5ab KO

value: 8-12 weeks


title: 448_Great Dane_Acute_GDV_Female

description:
448
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV

value: Female


title: RNA-seq of STAT5ab-KO mouse liver_male-pool1_G138_M9

value: mixed:C57BL/6 x 129J


title: r2.IVI.18

description: combined.analysis.results.csv.gz

value: control


title: r2.IVI.17

description: combined.analysis.results.csv.gz


title: 446_German Shepherd Dog_Acute_GDV_Male

description:
446
Canis familiaris


title: Lung_403_High_Day3_rep2

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, High, Day 3, replicate 2

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)


title: 444_Borzoi_Acute_GDV_Female

description:
444
Canis familiaris

value: Borzoi


title: r2.IVI.16

description: combined.analysis.results.csv.gz


title: Lung_403_Control_Day3_rep4

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-403, Control, Day 3, replicate 4

source_name: Rat, Lung, NM-403, Control, Day 3

value: Control


title: RNA-seq of control mouse liver_female-pool2_G138_M8

source_name: RNA-seq of control mouse liver_female

value: Control, Floxed STAT5ab locus

value: Total RNA_Ribo-minus


title: Lung_403_High_Day3_rep1

description:
Gene expression  in lung of rat exposed to NM-403 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-403, High, Day 3, replicate 1

value: Sprague Dawley

value: High


title: Lung_403_Control_Day3_rep6

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-403, Control, Day 3, replicate 6

value: Day 3


title: Lung_403_Control_Day3_rep3

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-403, Control, Day 3, replicate 3


title: RNA-seq of control mouse liver_female-pool1_G138_M7


title: Lung_403_Control_Day3_rep5

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-403, Control, Day 3, replicate 5


title: RNA-seq of STAT5ab-KO mouse liver_female-pool2_G137_M9


title: r2.IVI.19

description: combined.analysis.results.csv.gz

value: E


title: Lung_403_Control_Day3_rep2

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-403, Control, Day 3, replicate 2


title: Lung_403_Control_Day3_rep1

description:
Gene expression  in lung of control rat (filterd air) 3 days post exposure
Rat, Lung, NM-403, Control, Day 3, replicate 1


title: 442_German Shepherd Dog_Acute_GDV_Female

description:
442
Canis familiaris

value: German Shepherd Dog

value: Peripheral blood


title: RNA-seq of STAT5ab-KO mouse liver_female-pool1_G137_M8

value: Alb-Cre-LoxP STAT5ab KO

value: 8-12 weeks


title: r2.IVI.14

description: combined.analysis.results.csv.gz


title: 440_Great Dane_Acute_GDV_Male

description:
440
Canis familiaris

value: Great Dane

value: gastric dilatation-volvulus:Acute_GDV

value: Male


title: 441_Labrador Retriever_Acute_GDV_Male

description:
441
Canis familiaris

value: Labrador Retriever


title: r2.IVI.12

description: combined.analysis.results.csv.gz

value: case


title: 22-unmanip-total-micro

city: La Jolla,

first: Inge

last: Holtman

state: California

address: 9500 Gilman Drive

department: CMM

institute: UCSD

data_processing:
Star Aligner 2.3.11 allowing for 2 mismatches to map reads to genome
SAM tools 0.1.19 to sort aligned reads
HT-seq 0.5.4 for quantification, mode=union, stranded=no, Ensembl version 71
EdgeR 3.12.0 for data exploration and differential expression
WGCNA 1.49 for co-expression network analysis and detection of modules
Genome_build: GRCm38
Supplementary_files_format_and_content: HT-seq count .txt files

source_name: Pure microglia

extract_protocol:
Ex vivo microglia isolation using CD11C and CD11B and CD45
Illumina TruSeq RNA-preparation kit standard protocol

tag: microglia population

value: Control mouse CD11C negative


title: r2.IVI.15

description: combined.analysis.results.csv.gz

value: control

tag: sample


title: r2.IVI.11

description: combined.analysis.results.csv.gz

tag: combined sample id


title: Lung_401_Low_Day180_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 180, replicate 4

treatment_protocol: 13 week old female Sprague Dawley rats were exposed by nose-only inhalation  6 hours/day, 5 days/week for 4 weeks to two doses of NM-401 carbon nanotube.

value: accessory lobe of lung

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Low

value: Day 180


title: Lung_401_Low_Day180_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 180, replicate 6

value: Sprague Dawley


title: 438_German Shepherd Dog_Acute_GDV_Male

description:
438
Canis familiaris

value: German Shepherd Dog


title: 21-unmanip-total-micro


title: Lung_401_Low_Day180_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 180, replicate 5


title: r2.IVI.13

description: combined.analysis.results.csv.gz

tag: sequencing batch

value: E


title: 437_Poodle Standard_Acute_GDV_Female

description:
437
Canis familiaris

value: Poodle Standard

value: Female

value: Peripheral blood


title: 12-NMO-micro

tag: strain background

value: NMO mouse CD11C negative


title: 431_German Shepherd Pointer_HC_Female

description:
431
Canis familiaris

value: German Shepherd Pointer

value: gastric dilatation-volvulus:HC


title: 433_German Shepherd Pointer_HC_Female

description:
433
Canis familiaris


title: r2.IVI.9

description: combined.analysis.results.csv.gz

value: case


title: r2.IVI.10

description: combined.analysis.results.csv.gz


title: 11-NMO-micro


title: r2.IVI.7

description: combined.testplus.results.csv.gz


title: 10-NMO-micro


title: r2.IVI.8

description: combined.analysis.results.csv.gz


title: 7-NMO-CD11c-microglia

value: NMO mouse CD11c positive


title: 428_German Shepherd Pointer_HC_Female

description:
428
Canis familiaris


title: 429_German Shepherd Pointer_HC_Male

description:
429
Canis familiaris

value: Male


title: 8-NMO-CD11c-microglia


title: r2.IVI.6

description: combined.testplus.results.csv.gz


title: Lung_401_High_Day180_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 180, replicate 5

value: accessory lobe of lung

value: High


title: r2.IVI.5

description: combined.testplus.results.csv.gz


title: Lung_401_Low_Day180_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 180, replicate 2

value: female

value: 13 weeks-old (at the onset of inhalation)


title: 427_German Shepherd Pointer_HC_Male

description:
427
Canis familiaris


title: 426_German Shepherd Pointer_HC_Male

description:
426
Canis familiaris


title: 23-unmanip-total-micro

value: Control mouse CD11C negative


title: r2.IVI.4

description: combined.testplus.results.csv.gz


title: Lung_401_High_Day180_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 180, replicate 6

value: Sprague Dawley

value: Day 180


title: 423_German Shepherd Pointer_HC_Male

description:
423
Canis familiaris


title: Lung_401_High_Day180_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 180, replicate 4


title: r2.IVI.3

description: combined.testplus.results.csv.gz

value: E


title: r2.IVI.2

description: combined.testplus.results.csv.gz


title: Lung_401_Low_Day180_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 180, replicate 3

value: Low


title: 422_German Shepherd Dog_Acute_GDV_Female

description:
422
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV

value: Female


title: r2.IVI.1

description: combined.testplus.results.csv.gz


title: 421_Golden Retriever_Acute_GDV_Male

description:
421
Canis familiaris

value: Golden Retriever

value: Peripheral blood


title: Lung_401_High_Day180_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 180, replicate 3


title: Lung_401_Low_Day180_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 180, replicate 1


title: 418_Poodle Standard_Acute_GDV_Female

description:
418
Canis familiaris

value: Poodle Standard


title: test3.O

description: combined.testplus.results.csv.gz

value: case

value: IVIO

value: D


title: Lung_401_High_Day180_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 180, replicate 2

value: accessory lobe of lung

value: High


title: test3.E

description: combined.testplus.results.csv.gz

value: IVIE


title: hTCEpi_R2

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

description: ATAC-seq

data_processing:
Libraries were sequenced on Illumina Hi-seq platform in paired-end mode for 75 cycles. Sequencing reads were assessed for quality using  FastQC v0.11.4 and adaptor sequences were trimmed using cutadapt in paired-end mode. Reads were aligned to UCSC hg19 using bowtie2 ( default parameters with -X 2000  --very-sensitive --no-discordant  --no-mixed --no-unal). PCR duplicates were removed using PICARD and reads mapping to mitochondrial genome and ENCODE blacklisted regions were removed using samtools. Finally, we converted alignments to BED format and extracted fragment lengths using bedtools suite
Bigwig files were generated with HOMER’s makeUCSCfile and bedGraphToBigWig from  UCSC tools
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for ATAC-seq signal mapped to Hg19 (UCSC) genome assembly

source_name: cell line from primary human corneal ketratocytes

growth_protocol: hTCEpi and hTK  cells were cultured respectively in KGMTM-2 basal medium with KGMTM-2 Single-QuotsTM supplements (Lonza) and Dulbecco’s Modified Eagle  Medium ( DMEM)  supplemented with 10% fetal bovine serum, with addition of 1% penicillin and streptavidin in both media. Two replicates of hTCEpi and hTK cell batches were harvested at 70-90% confluence for ATAC-seq

extract_protocol:
50,000 cells of each cell line were collected by spinning at 500rcf for 5min at 4°C. Cells were washed by adding 100uL of cold PBS, mixing and spinning at 500rcf for 5min at 4°C. Cells were lysed by resuspension in 100uL ice-cold ATAC-seq lysis buffer (10mM Tris-Cl ph7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40), followed by incubation on ice for 30 minutes with occasional mixing. A nuclear pellet was isolated by spinning at 1000rcf for 5 minutes at 4°C and resuspended in 50uL transposition mix (2.5uL Tn5 transposase in 10mM Tris ph8, 5mM   MgCl2, 10% Dimethylformamide). Tagmentation reaction was incubated at 37C for 35min in a thermomixer at 800rpm. Tagmentation was stopped by immediate purification using MinElute Reaction Cleanup Kit (Qiagen Cat No:28204). Tagmented DNA was eluted in 11uL of water.
Libraries were prepared as described by Buenrostro et. al. (2015) with a universal forward primer and a reverse primer with a different index for each experiment. A 32ul reaction was prepared containing: the tagmented DNA (10ul), NEBNext High-Fidelity 2X PCR Master Mix (M0541S, NEB), 50X SYBR green for PCR (163795-75-3, Sigma-Aldrich) and 10uM each of forward and reverse nextera adaptor. The cycling conditions were: 1 cycle of 72°C for 5 minutes, 98°C for 30 seconds followed by 11-13 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute.  PCR reactions were stopped before reaching a plateau, recovered and supplemented with water to a final volume of 50ul. PCR reactions were then purified using 50ul (ratio 1:1) of the SPRI beads (Beckman) to remove excess adaptors using manufacturer’s protocol. DNA concentration was checked on Qbit followed by estimation of digestion profiles using double-stranded DNA high sensitivity assay on Bioanalyzer (Agilent) to make sure that Tn5 produced a nucleosomal ladder pattern.
Nextera

tag: cell type

value: corneal epithelial cell


title: 412_Labrador Retriever_Acute_GDV_Female

description:
412
Canis familiaris

value: Labrador Retriever

tag: Sex


title: Lung_401_Control_Day180_rep3

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-401, Control, Day 180, replicate 3

source_name: Rat, Lung, NM-401, Control, Day 180

value: Sprague Dawley

value: female

value: 13 weeks-old (at the onset of inhalation)

value: control

value: Control

value: Day 180


title: 410_Doberman Pinscher_Acute_GDV_Male

description:
410
Canis familiaris

value: Doberman Pinscher

value: gastric dilatation-volvulus:Acute_GDV

value: Male


title: Lung_401_Control_Day180_rep4

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-401, Control, Day 180, replicate 4


title: test3.A

description: combined.testplus.results.csv.gz

value: case

value: IVIA


title: Lung_401_Control_Day180_rep5

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-401, Control, Day 180, replicate 5


title: Lung_401_Control_Day180_rep6

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-401, Control, Day 180, replicate 6


title: JJ101 fed MDX mouse muscle rep2

description: Gene expression after 10 months of bioceramic water fed MDX mouse

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028279 SurePrint G3 Rat GE Microarray 8x60K for 17 hours at 65°C in a rotating SureHyb chamber.  After hybridization, microarrays were washed 1minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: gastrocnemius muscle, bioceramic water fed MDX mouse, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Samples were lysed and RNA isolation was carried out using the RNA-spin total RNA extraction kit (iNtRON Biotechnology, Sungnam, Kyungki-Do, South Korea) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: MDX mice were fed ceramic water for 10 months. Freshly collected gastronemius muscles were used.

value: MDX

value: gastrocnemius muscle


title: Tap water fed B10 mouse muscle rep1

description: Gene expression after 10 months of tap water fed C57BL/10 mouse

source_name: gastrocnemius muscle, tap water fed C57BL/10 mouse, replicate 1


title: 407_German Shepherd Pointer_Acute_GDV_Male

description:
407
Canis familiaris

source_name: Peripheral blood

value: German Shepherd Pointer

value: Peripheral blood


title: Lung_401_Control_Day180_rep2

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-401, Control, Day 180, replicate 2

value: accessory lobe of lung


title: Lung_401_High_Day180_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 180 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 180, replicate 1

value: High


title: Tap water fed B10 mouse muscle rep2

source_name: gastrocnemius muscle, tap water fed C57BL/10 mouse, replicate 2


title: test3.6

description: combined.testplus.results.csv.gz

value: D


title: Tap water fed MDX mouse muscle rep2

description: Gene expression after 10 months of tap water fed MDX mouse

source_name: gastrocnemius muscle, tap water fed MDX mouse, replicate 2


title: hTK_R1

description: ATAC-seq

source_name: cell line from primary human corneal epithelium

value: corneal keratocyte


title: 405_Poodle Standard_Acute_GDV_

description:
405
Canis familiaris

value: Poodle Standard


title: 408_Great Dane_Acute_GDV_Female

description:
408
Canis familiaris

value: Great Dane

value: Female


title: Tap water fed MDX mouse muscle rep1

source_name: gastrocnemius muscle, tap water fed MDX mouse, replicate 1


title: JJ101 fed MDX mouse muscle rep1

source_name: gastrocnemius muscle, bioceramic water fed MDX mouse, replicate 1


title: hTK_R2

description: ATAC-seq


title: test3.5

description: combined.testplus.results.csv.gz

source_name: Sperm

value: control


title: hTCEpi_R1

description: ATAC-seq

value: corneal epithelial cell


title: 10dTGFB_24dwithdrawn_Rep2

city: Waco

first: Joe

last: Taube

state: Texas

address: One Bear Place #97388

institute: Baylor University

description: 10d +TGFB, 24d -TGFB MCF10A mRNA

data_processing:
Adapter sequences and bases with lower quality than three removed using Trimmomatic (Galaxy Version 0.38.0).
Bases of reads less than window size 4, mean quality 15 were trimmed using Trimmomatic (Galaxy Version 0.38.0).
Reads trimmed to 36 bp using Trimmomatic (Galaxy Version 0.38.0).
Aligned to reference genome UCSC hg19 with HISAT2 (Galaxy Version 2.1.0+galaxy5)
Known genes assembled via StringTie (Galaxy Version 1.3.6)
Genome_build: hg19

source_name: MCF10A cells

growth_protocol: Cells were plated at 10,000 cells/mm^2 and treated with TGFB.  Cell density was maintained every other day and media was removed and replenished with TGFB

extract_protocol:
Cells lysed in TriZol reagent and phenol/chloroform extracted
Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: 5 ng/mL TGFB in 4 mM HCL with 0.01% BSA

value: 10d +TGFB, 24d -TGFB MCF10A mRNA


title: test3.I

description: combined.testplus.results.csv.gz

value: IVII


title: Lung_401_Low_Day90_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 90, replicate 5

value: Sprague Dawley

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Low

value: Day 90


title: test3.4

description: combined.testplus.results.csv.gz


title: Lung_401_Control_Day180_rep1

description:
Gene expression  in lung of control rat (filterd air) 180 days post exposure
Rat, Lung, NM-401, Control, Day 180, replicate 1

value: Control

value: Day 180


title: 4TGFB_10dwithdrawn_Rep2

description: 4d +TGFB, 10d -TGFB MCF10A mRNA

value: 4d +TGFB, 10d -TGFB MCF10A mRNA


title: 400_Poodle Standard_Acute_GDV_Female

description:
400
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV

value: Peripheral blood


title: Lung_401_Low_Day90_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 90, replicate 6

value: accessory lobe of lung


title: 4TGFB_6dwithdrawn_Rep2

description: 4d +TGFB, 6d -TGFB MCF10A mRNA

value: 4d +TGFB, 6d -TGFB MCF10A mRNA


title: test3.3

description: combined.testplus.results.csv.gz

value: D


title: 10dTGFB_10dwithdrawn_Rep2

description: 10d +TGFB, 10d -TGFB MCF10A mRNA

value: 10d +TGFB, 10d -TGFB MCF10A mRNA


title: test3.2

description: combined.testplus.results.csv.gz

value: case


title: test3.1

description: combined.testplus.results.csv.gz

value: control


title: 396_Great Dane_Acute_GDV_Female

description:
396
Canis familiaris

value: Great Dane

value: Female


title: Lung_401_Low_Day90_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 90, replicate 4

value: Sprague Dawley

value: female


title: rIVI26

description: combined.analysis.results.csv.gz


title: 4TGFB_4dwithdrawn_Rep2

description: 4d +TGFB, 4d -TGFB MCF10A mRNA

value: 4d +TGFB, 4d -TGFB MCF10A mRNA


title: 10dTGFB_6dwithdrawn_Rep2

description: 10d +TGFB, 6d -TGFB MCF10A mRNA

value: 10d +TGFB, 6d -TGFB MCF10A mRNA


title: rIVI25

description: combined.analysis.results.csv.gz


title: Lung_401_Low_Day90_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 90, replicate 3

value: 13 weeks-old (at the onset of inhalation)

value: Low

value: Day 90


title: rIVI24

description: combined.analysis.results.csv.gz


title: 394_Labrador Retriever_Acute_GDV_Male

description:
394
Canis familiaris

value: Labrador Retriever

value: gastric dilatation-volvulus:Acute_GDV

value: Male


title: 392_German Shepherd Dog_Acute_GDV_Male

description:
392
Canis familiaris

value: German Shepherd Dog

value: Peripheral blood


title: Lung_401_Low_Day90_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 90, replicate 2

value: accessory lobe of lung


title: 401_Poodle Standard_Acute_GDV_Female

description:
401
Canis familiaris

value: Poodle Standard


title: 391_Great Dane_Acute_GDV_Female

description:
391
Canis familiaris


title: Lung_401_Low_Day90_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 90, replicate 1


title: 10dTGFB_4dwithdrawn_Rep2

description: 10d +TGFB, 4d -TGFB MCF10A mRNA

value: 10d +TGFB, 4d -TGFB MCF10A mRNA


title: Lung_401_High_Day90_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 90, replicate 4

value: High


title: 10dTGFB_2dwithdrawn_Rep2

description: 10d +TGFB, 2d -TGFB MCF10A mRNA

value: 10d +TGFB, 2d -TGFB MCF10A mRNA


title: rIVI22

description: combined.analysis.results.csv.gz

value: control

value: D


title: 390_Great Dane_HC_Female

description:
390
Canis familiaris

value: Great Dane

value: gastric dilatation-volvulus:HC

value: Female


title: rIVI23

description: combined.analysis.results.csv.gz


title: Lung_401_High_Day90_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 90, replicate 5

value: Sprague Dawley

value: female

value: 13 weeks-old (at the onset of inhalation)


title: 393_Poodle Standard_Acute_GDV_Female

description:
393
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: 4TGFB_2dwithdrawn_Rep2

description: 4d +TGFB, 2d -TGFB MCF10A mRNA

value: 4d +TGFB, 2d -TGFB MCF10A mRNA


title: 10dTGFB_Rep2

description: 10d +TGFB MCF10A mRNA

value: 10d +TGFB MCF10A mRNA


title: rIVI21

description: combined.analysis.results.csv.gz


title: Lung_401_High_Day90_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 90, replicate 2

value: Day 90


title: Lung_401_High_Day90_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 90, replicate 6

value: accessory lobe of lung


title: 4dTGFB_Rep2

description: 4d +TGFB MCF10A mRNA

value: 4d +TGFB MCF10A mRNA


title: rIVI19

description: combined.analysis.results.csv.gz


title: 389_Great Dane_Acute_GDV_Male

description:
389
Canis familiaris

value: Male

value: Peripheral blood


title: rIVI18

description: combined.analysis.results.csv.gz


title: 8dTGFB_Rep2

description: 8d +TGFB MCF10A mRNA

value: 8d +TGFB MCF10A mRNA


title: 385_Golden Retriever_Acute_GDV_Male

description:
385
Canis familiaris

value: Golden Retriever


title: 383_German Shepherd Dog_HC_Male

description:
383
Canis familiaris

value: German Shepherd Dog


title: rIVI20

description: combined.analysis.results.csv.gz

value: control

value: D


title: Lung_401_High_Day90_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 90, replicate 1

value: High


title: 6dTGFB_Rep2

description: 6d +TGFB MCF10A mRNA

value: 6d +TGFB MCF10A mRNA


title: Lung_401_Control_Day90_rep4

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-401, Control, Day 90, replicate 4

source_name: Rat, Lung, NM-401, Control, Day 90

value: Sprague Dawley

value: female

value: Control


title: rIVI17

description: combined.analysis.results.csv.gz


title: Untreated_D2_Rep2

description: Untreated MCF10A mRNA

value: Untreated MCF10A mRNA


title: Lung_401_Control_Day90_rep6

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-401, Control, Day 90, replicate 6

value: 13 weeks-old (at the onset of inhalation)


title: Untreated_D20_Rep2

description: Untreated MCF10A mRNA


title: 376_German Shepherd Dog_Acute_GDV_Female

description:
376
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV

value: Female


title: 381_Poodle Standard_Acute_GDV_Male

description:
381
Canis familiaris

value: Poodle Standard


title: 375_Golden Retriever_Acute_GDV_Male

description:
375
Canis familiaris

value: Male


title: 2dTGFB_Rep2

description: 2d +TGFB MCF10A mRNA

value: 2d +TGFB MCF10A mRNA


title: 382_German Shepherd Dog_Acute_GDV_Male

description:
382
Canis familiaris

value: Peripheral blood


title: rIVI15

description: combined.analysis.results.csv.gz


title: RWPE 3

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina base calling
BWA and STAR mapping
HTSEQ counting
Genome_build: hg19
Supplementary_files_format_and_content: transcript level raw read count

source_name: cell line

growth_protocol: Culture medium: RPMI-1640 supplemented with 5% (v/v) FBS, 1% (v/v) antibiotic/antimycotic, 1% (v/v) glutamine, 1x puromycin for selecting transfected gene of interest

extract_protocol:
Total RNA was extracted using an RNeasy Plus Mini Kit (Qiagen)
total stranded RNA protocol

treatment_protocol: Culture condition: Cell lines were maintained at 37  C with 5% CO2 and passaged ~ 70-90% confluency

tag: cell line

value: Benign human prostate stromal cells (BHPrS1)

tag: genotype/variation

value: RWPE


title: 378_Doberman Pinscher_Acute_GDV_Female

description:
378
Canis familiaris

value: Doberman Pinscher

tag: tissue


title: 374_Poodle Standard_Acute_GDV_Female

description:
374
Canis familiaris


title: rIVI14

description: combined.analysis.results.csv.gz

value: control

value: D


title: Lung_401_High_Day90_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 90 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 90, replicate 3

tag: strain

value: accessory lobe of lung

tag: gender

value: High

value: Day 90


title: 373_Labrador Retriever_Acute_GDV_Male

description:
373
Canis familiaris

value: Labrador Retriever


title: Lung_401_Control_Day90_rep5

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-401, Control, Day 90, replicate 5

value: Sprague Dawley

value: female

tag: age

tag: treatment

value: Control


title: RWPE 1


title: Mutant NPF P4 2

value: Mutant NPF P4


title: rIVI16

description: combined.analysis.results.csv.gz


title: rIVI12

description: combined.analysis.results.csv.gz

value: case


title: 371_German Shepherd Dog_HC_Male

description:
371
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:HC

value: Male


title: Mutant NPF P4 1

value: Benign human prostate stromal cells (BHPrS1)


title: rIVI10

description: combined.analysis.results.csv.gz


title: Mutant NPF P4 3


title: rIVI9

description: combined.analysis.results.csv.gz


title: rIVI13

description: combined.analysis.results.csv.gz


title: 366_Briard_Acute_GDV_Male

description:
366
Canis familiaris

value: Briard

value: gastric dilatation-volvulus:Acute_GDV

value: Peripheral blood


title: rIVI8

description: combined.analysis.results.csv.gz

value: D


title: Lung_401_Low_Day30_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 30, replicate 6

value: accessory lobe of lung

value: 13 weeks-old (at the onset of inhalation)

tag: dose

value: Low

tag: time

value: Day 30


title: Lung_401_Control_Day90_rep1

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-401, Control, Day 90, replicate 1

value: Sprague Dawley

value: control

value: Day 90


title: Lung_401_Control_Day90_rep2

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-401, Control, Day 90, replicate 2

value: female

value: Control


title: Lung_401_Control_Day90_rep3

description:
Gene expression  in lung of control rat (filterd air) 90 days post exposure
Rat, Lung, NM-401, Control, Day 90, replicate 3


title: 370_German Shepherd Dog_HC_Female

description:
370
Canis familiaris

tag: breed

value: German Shepherd Dog

tag: status (hc = healthy control, gdv

value: Female


title: Lung_401_Low_Day30_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 30, replicate 5


title: Lung_401_Low_Day30_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 30, replicate 4


title: 369_German Shepherd Dog_HC_Female

description:
369
Canis familiaris

value: gastric dilatation-volvulus:HC


title: Lung_401_Low_Day30_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 30, replicate 3


title: rIVI11

description: combined.analysis.results.csv.gz

value: case

tag: sample


title: RWPE 2

value: Benign human prostate stromal cells (BHPrS1)

value: RWPE


title: Lung_401_Low_Day30_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 30, replicate 2


title: 365_Doberman Pinscher_Acute_GDV_Male

description:
365
Canis familiaris

value: Doberman Pinscher

value: gastric dilatation-volvulus:Acute_GDV

value: Male

value: Peripheral blood


title: Lung_401_High_Day30_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 30, replicate 6

value: accessory lobe of lung

value: 13 weeks-old (at the onset of inhalation)

value: High


title: Lung_401_Low_Day30_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to Low dose, Day 30, replicate 1

value: Sprague Dawley

value: Low

value: Day 30


title: HMLE_LACZ_RNAseq

city: Detroit

first: Allison

middle: V

last: Mitchell

state: MI

address: 4100 John R Rd

department: Oncology

institute: Wayne State University

description: vector control

data_processing:
Read aligment using Bowtie2 (Galaxy Version 2.3.2.2).
Enriched ChIP peaks were called using MACS2 (Galaxy Version 2.1.1.20160309.0)vwith the mapped input DNA reads as the background control. FDR (q-value) was set to 0.001. Peaks that were detected in both the replicate ChIP samples were utilized for downstream analysis.
RNA seq: The count abundance was estimated using RSEM and the differential expression analysis was done using EdgeR v3.12.1 in the Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files include all differentially expressed genes identfied by RNA-seq of HMLE/FOXQ1 and HMLE/LACZ cells. Alignment of the differentially expressed gene promoter regions (+/- 10kb of TSS) as bed files with the FOXQ1 and RbBP5 ChIP-seq binidng peaks (bed) revealed gene targets under direct transcriptional regulation. Direct gene targets with FOXQ1 bound within the promoter are included (FOXQ1_DEGtargets.csv) with the differential expression p-value and fold change from EdgeR.  Direct gene targets that were bound by both FOXQ1 and RbBP5 within the promoter are included (FOXQ1_RbBP5_DEGtargets.csv) with the differential expression p-value and fold change from EdgeR.

source_name: HMLE/LACZ cells

growth_protocol: Human mammary epithelial (HMLE) cells were obtain from Dr. Robert Weinbergs lab at MIT and cultured in 50:50 DMEM/F12 media (HyClone) containing 10% FBS, 1% pen/strep, EGF (10µg/L), insulin (10µg/L) and hydrocotrisol (500ng/L). HMLE cells were subject to lentiviral transduction of human FOXQ1 gene or LACZ vector control and maintained under 10µg/mL blasticidin.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (QIAGEN, 74134) according to manufacturer's protocol.
Library preparation and sequencing were perfomred at LC Sciences (Houston, TX). Briefly, RNA library was prepared (including Poly (A) selection, fragmentation, Adapter attachment, reverse transcription, PCR amplification , and Library size selection) using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's protocol. Library was sequences in Illumina HiSeq2000 platform, 100 bp paired-end reads.

value: human mammary luminal epithelial cells

tag: stable expression

tag: chip antibody


title: 358_Great Dane_Acute_GDV_Female

description:
358
Canis familiaris

value: Great Dane


title: rIVI7

description: combined.testplus.results.csv.gz

tag: combined sample id

tag: sequencing batch

value: D


title: 368_German Shepherd Dog_Acute_GDV_Female

description:
368
Canis familiaris

value: German Shepherd Dog

tag: Sex

value: Female


title: rIVI6

description: combined.testplus.results.csv.gz

value: case


title: WT 1

tag: cell line

value: Benign human prostate stromal cells (BHPrS1)

value: wild type


title: WT 3

tag: genotype/variation


title: 357_German Shepherd Dog_Acute_GDV_Male

description:
357
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV

tag: tissue


title: Lung_401_High_Day30_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 30, replicate 5

tag: strain

value: female


title: rIVI4

description: combined.testplus.results.csv.gz


title: SUDHL6 DMSO D4 R2

city: Cambridge

first: Barbara

middle: M

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
Sequencing was performed on the HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold.  Samples with fewer than 10 reads FPKM are replaced with  the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19

source_name: Diffuse large B cell lymphoma

growth_protocol: HT and SUDHL6 cell lines were grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol: RNA-seq

treatment_protocol: 96 hours of treatment with iEZH

value: DMSO


title: rIVI3

description: combined.testplus.results.csv.gz


title: rIVI1

description: combined.testplus.results.csv.gz


title: 356_Great Dane_Acute_GDV_Male

description:
356
Canis familiaris

value: Male

value: Peripheral blood


title: 351_German Shepherd Dog_Acute_GDV_Male

description:
351
Canis familiaris


title: rIVI2

description: combined.testplus.results.csv.gz


title: HT iEZH D4 R2

value: HT

value: iEZH


title: HT DMSO D4 R2


title: 353_German Shepherd Dog_Acute_GDV_Male

description:
353
Canis familiaris


title: Lung_401_High_Day30_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 30, replicate 2

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: 13 weeks-old (at the onset of inhalation)

value: High


title: HMLE_FOXQ1_RNAseq

source_name: HMLE/FOXQ1 cells

value: human mammary luminal epithelial cells


title: WT 2


title: 360_Golden Retriever_Acute_GDV_Male

description:
360
Canis familiaris

value: Golden Retriever


title: Lung_401_High_Day30_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 30, replicate 1

tag: age

value: Day 30


title: SUDHL6 iEZH D4 R1

tag: treatment


title: test2.I

description: combined.testplus.results.csv.gz

value: case

value: IVII

value: C


title: SUDHL6 DMSO D4 R1


title: Lung_401_Control_Day30_rep6

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-401, Control, Day 30, replicate 6

source_name: Rat, Lung, NM-401, Control, Day 30

value: control

tag: dose

value: Control


title: rIVI5

description: combined.testplus.results.csv.gz

value: D


title: 338_Doberman Pinscher_Acute_GDV_Male

description:
338
Canis familiaris

value: Doberman Pinscher

value: gastric dilatation-volvulus:Acute_GDV

value: Male


title: Lung_401_High_Day30_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 30, replicate 4

value: female

tag: time


title: 349_German Shepherd Pointer_Chronic_bloater_Female

description:
349
Canis familiaris

tag: breed

value: German Shepherd Pointer

value: Female

value: Peripheral blood


title: Lung_401_High_Day30_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 30 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 30, replicate 3

value: Sprague Dawley

value: accessory lobe of lung

value: 13 weeks-old (at the onset of inhalation)

value: High


title: test2.O

description: combined.testplus.results.csv.gz

value: case

value: IVIO


title: HT iEZH D4 R1

value: HT

value: iEZH


title: test2.E

description: combined.testplus.results.csv.gz

value: IVIE

value: C


title: 336_Poodle Standard_Acute_GDV_Male

description:
336
Canis familiaris

value: Poodle Standard

tag: status (hc = healthy control, gdv


title: test2.A

description: combined.testplus.results.csv.gz

tag: sample

value: IVIA


title: test2.6

description: combined.testplus.results.csv.gz

value: control


title: Lung_401_Control_Day30_rep3

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-401, Control, Day 30, replicate 3

value: female

value: Control

value: Day 30


title: Lung_401_Control_Day30_rep4

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-401, Control, Day 30, replicate 4


title: 350_Borzoi_Acute_GDV_Male

description:
350
Canis familiaris

value: Borzoi

value: gastric dilatation-volvulus:Acute_GDV

value: Male

value: Peripheral blood


title: HT DMSO D4 R1

value: DMSO


title: Lung_401_Control_Day30_rep5

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-401, Control, Day 30, replicate 5

value: Sprague Dawley

value: accessory lobe of lung

value: 13 weeks-old (at the onset of inhalation)


title: SUDHL6 iEZH H3K36me1

data_processing:
The 50-nt sequence reads from Illumina's Genome Analyzer 2 were mapped to the genome using the BWA algorithm.  Only tags that mapped uniquely, had no more than 2 mismatches, and passed quality control filtering were used in the subsequent analysis.
Mapped reads were extended in silico at their 3' ends to a length of 200 bp, reflecting the average fragment length in the size selected library.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain the output of applying SICER to each sample.  WIG and TDF files were generating using IGVTools' count function on aligned sequence reads, assuming a fragment length of 200, and using a bin size of 25 nt for WIG and 10 nt for TDF files.

growth_protocol: SUDHL6 cells were grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol: baseline measurement of methylation / occupancy without perturbation

treatment_protocol: 1.5 uM iEZH for 96 hours

value: iEZH

tag: chip antibody manufacturer

value: SysBio


title: Lung_401_Control_Day30_rep2

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-401, Control, Day 30, replicate 2


title: test2.5

description: combined.testplus.results.csv.gz

value: C


title: SUDHL6 DMSO H3K36me1

tag: chip antibody


title: 333_Great Dane_Acute_GDV_Female

description:
333
Canis familiaris

value: Great Dane

value: Female


title: test2.4

description: combined.testplus.results.csv.gz

value: control

tag: combined sample id


title: Lung_401_Low_Day3_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to low dose, Day 3, replicate 5

source_name: Rat, Lung, NM-401, Exposed to Low dose, Day 3

value: female

value: Low

value: Day 3


title: Lung_401_Low_Day3_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to low dose, Day 3, replicate 6


title: Lung_401_Control_Day30_rep1

description:
Gene expression  in lung of control rat (filterd air) 30 days post exposure
Rat, Lung, NM-401, Control, Day 30, replicate 1

value: Control

value: Day 30


title: 334_German Shepherd Dog_Acute_GDV_Male

description:
334
Canis familiaris

value: German Shepherd Dog

value: gastric dilatation-volvulus:Acute_GDV

value: Male


title: SUDHL6 iEZH EZH2

tag: chip antibody catalog #

value: Cell Signaling


title: Lung_401_Low_Day3_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to low dose, Day 3, replicate 4

value: Sprague Dawley

value: accessory lobe of lung


title: SUDHL6 DMSO EZH2

value: DMSO


title: 332_Collie Smooth_Acute_GDV_Female

description:
332
Canis familiaris

value: Collie Smooth

tag: Sex

value: Peripheral blood


title: 328_Great Dane_HC_Male

description:
328
Canis familiaris

value: Great Dane

value: gastric dilatation-volvulus:HC


title: 337_Poodle Standard_HC_Male

description:
337
Canis familiaris

value: Poodle Standard


title: test2.2

description: combined.testplus.results.csv.gz

value: case

tag: sequencing batch

value: C


title: SUDHL6 iEZH Input

value: iEZH

tag: cell line


title: test2.1

description: combined.testplus.results.csv.gz

value: control


title: 327_German Shepherd Dog_Acute_GDV_Male

description:
327
Canis familiaris

tag: tissue


title: 326_German Shepherd Dog_HC_Male

description:
326
Canis familiaris


title: Lung_401_Low_Day3_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to low dose, Day 3, replicate 3

tag: strain

value: female

value: 13 weeks-old (at the onset of inhalation)

value: Low

value: Day 3


title: SUDHL6 DMSO Input


title: SUDHL6 iEZH H3K27me3

value: Cell Signaling


title: testO

description: combined.testplus.results.csv.gz

value: IVIO

value: B


title: 325_German Shepherd Dog_HC_Male

description:
325
Canis familiaris

value: German Shepherd Dog

value: Male


title: test2.3

description: combined.testplus.results.csv.gz


title: 324_German Shepherd Dog_HC_Female

description:
324
Canis familiaris

value: Female

value: Peripheral blood


title: testE

description: combined.testplus.results.csv.gz

value: IVIE


title: testI

description: combined.testplus.results.csv.gz

value: IVII


title: SUDHL6 DMSO H3K27me3

value: DMSO


title: testA

description: combined.testplus.results.csv.gz

value: case

value: IVIA


title: Lung_401_High_Day3_rep6

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 3, replicate 6

value: Sprague Dawley

value: accessory lobe of lung

tag: gender

value: High


title: Lung_401_High_Day3_rep5

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 3, replicate 5

value: female

tag: age

value: 13 weeks-old (at the onset of inhalation)


title: Lung_401_Low_Day3_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to low dose, Day 3, replicate 1

tag: treatment

value: Low

value: Day 3


title: 320_Doberman Pinscher_HC_

description:
320
Canis familiaris

value: Doberman Pinscher

value: gastric dilatation-volvulus:HC


title: 319_Doberman Pinscher_Acute_GDV_Female

description:
319
Canis familiaris

value: gastric dilatation-volvulus:Acute_GDV


title: test6

description: combined.testplus.results.csv.gz

value: control

value: B


title: test5

description: combined.testplus.results.csv.gz


title: Lung_401_Low_Day3_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (0.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to low dose, Day 3, replicate 2

tag: dose


title: 318_Doberman Pinscher_HC_Male

description:
318
Canis familiaris

value: Male

value: Peripheral blood


title: test4

description: combined.testplus.results.csv.gz


title: test3

description: combined.testplus.results.csv.gz


title: Lung_401_High_Day3_rep4

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 3, replicate 4

tag: time


title: 314_German Shepherd Dog_Acute_GDV_Male

description:
314
Canis familiaris

tag: breed

value: German Shepherd Dog


title: 313_Labrador Retriever_Acute_GDV_Male

description:
313
Canis familiaris

value: Labrador Retriever

tag: status (hc = healthy control, gdv


title: 310_Great Dane_Acute_GDV_Female

description:
310
Canis familiaris

value: Great Dane

value: Female


title: Lung_401_High_Day3_rep2

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 3, replicate 2

value: Sprague Dawley

value: accessory lobe of lung


title: Lung_401_High_Day3_rep3

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 3, replicate 3

value: female

value: High


title: Lung_401_High_Day3_rep1

description:
Gene expression  in lung of rat exposed to NM-401 (1.5 mg/m3) 3 days post exposure
Rat, Lung, NM-401, Exposed to high dose, Day 3, replicate 1

value: 13 weeks-old (at the onset of inhalation)