title: MSA101_H14_Primidone 10_uM 6_hours 1275-B-3

value: Primidone


title: HBOC-189

status: Public on Oct 31 2018

type: genomic

city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: According to manufracturers recommodations: Agilent Oligonucleotide Array-Based CGH for Genomic DNA analysis. Enzymatic labeling for blood, cells, or tissues (with a high throughput option) protocol Version (7.5, June 2016)

data_processing:
The raw data was processed by feature extraction version 11.0.1.1 (Agilent Technologies)
Aberrations were detected with the ADM-2 algorithm and thresholds of 6 and 2log02 (Cy3/Cy5) in Genomic Workbench (version 7.0.4.0, Agilent Technologies)

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Genomic DNA was extracted from EDTA blood samples by QIAamp DNA Blood Midi Kit (Qiagen, Hilden, Germany)

tag: subject status

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient

tag: tissue

value: blood

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)

tag: sample type

value: reference DNA


title: MSA101_H15_prenylamine 9.6_uM 6_hours 3113-6-3

type: RNA

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

country: USA

institute: ASU-Banner Neurodegenerative Disease Research Center

description: 24 hiPSC-derived NPCs and 8 CCLs were used (total: 32 cell lines). Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: a) phase 1 had 6/79 drugs from pilot, and 73/79 phase 1 test compounds, b) phase 2 had 6 pilot drugs re-tested, 6/73 phase 1 drugs re-tested, and 67/79 phase 2 compounds. 135 unique compounds were tested.

hyb_protocol: PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.

scan_protocol: Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead

data_processing: Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.

label: biotin

molecule: total RNA

label_protocol: mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.

extract_protocol: Cells were lysed with cell lysis buffer (110 µL per well), and stored at -80⁰C

tag: perturbagen

value: prenylamine

tag: cell id

tag: dosage

tag: batch

tag: duration

tag: perturbation type

value: test

tag: well id

tag: plate id


title: MSA101_H13_Primidone 10_uM 6_hours 3113-6-3


title: HBOC-187

scan_protocol: According to manufracturers recommodations: Agilent Oligonucleotide Array-Based CGH for Genomic DNA analysis. Enzymatic labeling for blood, cells, or tissues (with a high throughput option) protocol Version (7.5, June 2016)


title: HBOC-192

label_protocol: According to manufracturers recommodations: Agilent Oligonucleotide Array-Based CGH for Genomic DNA analysis. Enzymatic labeling for blood, cells, or tissues (with a high throughput option) protocol Version (7.5, June 2016)


title: MSA101_H12_4-hydroxyphenazone 10_uM 6_hours 1275-B-3


title: HBOC-190


title: HBOC-197


title: HBOC-186


title: HBOC-188


title: HBOC-184


title: Control 8

type: SRA

city: Karise

first: Rune

middle: Nørgaard

last: Rasmussen

address: Vesterled 4

department: Drug transporters in ADME

country: Denmark

institute: Southern University of Denmark

description:
Single read RNA-sequencing
Poly A RNA
processed data file: Count.table.original.featurecounts.txt

library_source: transcriptomic

data_processing:
Basecallling by CASAVA.
Alignment was performed with Hisat 2.0.5.
Read count was performed using featureCounts v1.5.1.
Genome_build: CFA 3.1
Supplementary_files_format_and_content: Count.table.original.featurecounts.txt: Tab-delimited text file includes counts.

organism: Canis lupus familiaris

source_name: Madin-Darby Canine Kidney (MDCK) I cells

growth_protocol: MDCK I cells were cultured using DMEM/F-12 containing 1% penicillin-streptomycin, 2 mM L-glutamine and 10% FBS in an atmosphere of 5% CO2- 95% O2 at 37 °C at a density of 7.6 x 10.000 in non-coated 24 well plates for a total of 144 h. The cells were treated with different compounds in the last 24 h of the cultivation.

extract_protocol:
RNA was isolated using Nucleospin® RNA/Protein following the protocol of the manufacturer.
The cDNA library was constructed with TruSeq RNA Library Preparation Kit v2 from Illumina following the protocol of the manufacturer.

treatment_protocol: MDCK I cells were treated for 24 h with medium supplemented with 200 mOsm raffinose, NaCl or urea (total of 500 mOsm). The control was regular medium (300 mOsm).

tag: cell line

value: MDCK I

tag: cell passage

tag: treatment

value: Control (300 mOsm)


title: Control 5


title: Control 4


title: HBOC-183


title: Control 1


title: HBOC-193


title: MSA101_H11_4-hydroxyphenazone 10_uM 6_hours 3113-6-3


title: Control 7


title: MSA101_H10_trichostatin NA 6_hours 1275-B-3

value: trichostatin

value: poscon


title: MSA101_H08_emetine 7.2_uM 6_hours 1275-B-3

value: emetine


title: MSA101_H07_emetine 7.2_uM 6_hours 3113-6-3


title: HBOC-182


title: MSA101_H09_trichostatin NA 6_hours 3113-6-3


title: HBOC-211


title: MSA101_H06_melatonin 1_uM 6_hours 1275-B-3

value: melatonin


title: HBOC-178


title: HBOC-177


title: HBOC-180


title: HBOC-181


title: whole_larva_cypermethrin_1ug/L_rep11

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

description: Whole body gene expression after exposure of fathead larvae to 1 ug/L of cypermethrin

hyb_protocol: Individual samples were hybridized onto separate Agilent microarrays, where eight arrays were printed onto a single glass slide. Placement of each treatment within and between slides was balanced as much as possible, given the number of arrays per slide and replicates per treatment. Samples were fragmented and mixed with a blocking agent per recommended protocols, then quickly added onto the microarrays. Microarrays were hybridized at 65° C for 17 hours with constant rotation, disassembled in Wash Buffer 1, washed in Wash Buffer 1 for one minute, then transferred to Wash Buffer 2 at 65° C for 1 minute, 100% acetonitrile for 10 s, followed by drying and stabilization solution for 30 s.

scan_protocol: Slides were covered with an ozone-barrier slide and scanned in an Agilent C scanner with the following settings: Dye channel: G; scan resolution: 5 µm; TIFF file dynamic range: 20 bit; green PMI gain: 100%. TIFF images were uploaded to the Agilent Feature Extraction program and extracted data were used in downstream analysis.

data_processing: Probe intensity (median spot foreground without background subtraction) from each hybridization were quantile normalized, and probeset intensity for individual hybridizations were calculated as the median (within an array) intensity of the replicated probes constituting that probeset. Probeset intensities were then log-base2 transformed.

organism: Pimephales promelas

source_name: whole larva, cypermethrin, 1 ug/L, replicate 11

label_protocol: Samples were processed according to the Agilent One-color Microarray-Based Gene Expression Analysis protocols (Agilent Technologies, Santa Clara, CA). Isolated total RNA was diluted to 100 ng/µL for labeling. , combined with RNA Spike-in controls and converted to cDNA using Affinity Script Reverse Transcriptase.  cDNA was then converted to cRNA with the inclusion of Cyanine-3 (Cy-3) labeled-CTP.  Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and cRNA was eluted twice in a total of 70 µL warm water. Yield and specific activity of purified labeled cRNA were evaluated using the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop, Wilmington, DE) using the microarray measurement package. Samples with yields <0.825 µg or specific activity <6 pmol Cy3 per µg cRNA were excluded from further analysis. In these cases, an alternative sample was selected for analysis; however, when none were available, failed samples were re-labeled.

growth_protocol: Fathead minnow were raised indoors in labline water. Labline water was produced by passing tempered tap water through a set of activated carbon filters, for the removal of chlorine and organics, and then adding liquid calcium chloride to supplement the hardness. Fish were maintained at 20-25 degC, pH 7.0 to 8.0. dissolved oxygen between 6 and 9 mg/L, and conductivity of 510-660 uS. Fish were fed a mixture of high-protein fin-fish starter food (0.6-0.85 um crumb size) and brine shrimp nauplii. At the start of exposures, adults were about 6 months old and larvae were 48 hours post-hatch.

extract_protocol: Following  48-hour exposure, surviving adults were anesthetized with ice and sacrificed by severing the spinal cord. Brains were removed, placed in separate cryotubes and immediately frozen in liquid nitrogen until processed. Two surviving larvae from each exposure vessel were placed in a single cryotube and frozen. RNA was isolated separately from 10 adult brains and 10 pairs of whole larval fish exposed to each of (nominally) two bifenthrin concentrations, two cypermethrin concentrations (Table 1), DMSO carrier added to water, and water only. RNA was isolated using the RiboPure kit (Ambion, Austin, TX) according to the manufacturer’s protocol. RNA was eluted in 100 µL for adult brain and 60 µL for larval homogenates. Following RNA isolation, DNA contamination was removed using Turbo DNA-free (Ambion) according to the manufacturer’s protocol. RNA was concentrated through ethanol precipitation, and integrity was assessed using denaturing gel electrophoresis.

treatment_protocol: 48-hour flow-through exposures were conducted in 10 L tanks, each renewed with exposure media (from continuous mixing of lab water and concentrated pyrethroid stock solution) at a rate of 40 mL/min. The system was pre-equilibrated under flow-through conditions with their respective chemicals nominally at their target concentrations for 24 hours prior to introducing test organisms. Five adult (ranging from six to ten months old) male fathead minnows (FHM; Pimephales promelas) were placed in each tank, as were an exposure vessel containing 10 larval (48 hours post hatch) FHM. The exposure vessels consisted of a three-inch section of 1.5 inch diameter PVC pipe covered on both ends with 400 µm Nitrex mesh. Four exposure experiments were conducted at least one week apart. Each experiment included eight nominal concentrations of a single pyrethroid, and a carrier solvent control (0.002% DMSO; used for the carrier control and as a carrier for pyrethroids, which have very low water solubility). Successive nominal concentrations, targeted to be half the next highest concentration, were achieved by serial dilution. Three replicate tanks were used for each concentration, and chemical concentrations of each tank were measured daily. Tank location in the diluter apparatus was balanced with respect to concentration to minimize location effects. Test organisms were randomly assigned to tanks. Between experiments, water supply lines were replaced, tanks were rinsed with 0.01% DMSO solution overnight, followed by 100% methanol and 24-hour water rinses. Tanks were subsequently scrubbed and rinsed with DMSO and tap water.

value: whole larva

tag: age

value: 48 hrs post-hatch

tag: chemical

value: cypermethrin

value: larva


title: MSA101_H05_melatonin 1_uM 6_hours 3113-6-3


title: MSA101_H04_Loxapine 1_uM 6_hours 1275-B-3

value: Loxapine


title: MSA101_H03_Loxapine 1_uM 6_hours 3113-6-3


title: HBOC-179


title: MSA101_H02_diflorasone 8_uM 6_hours 1275-B-3

value: diflorasone


title: MSA101_H01_diflorasone 8_uM 6_hours 3113-6-3


title: whole_larva_cypermethrin_1ug/L_rep9

source_name: whole larva, cypermethrin, 1 ug/L, replicate 9


title: HBOC-175

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: HBOC-174

value: blood


title: HBOC-176

value: reference DNA


title: MSA101_G24_DMSO NA 6_hours 2484-2-A

value: DMSO

value: vehicle


title: whole_larva_cypermethrin_1ug/L_rep10

source_name: whole larva, cypermethrin, 1 ug/L, replicate 10


title: MSA101_G22_3-acetamidocoumarin 10_uM 6_hours 2484-2-A

value: test


title: whole_larva_cypermethrin_1ug/L_rep4

source_name: whole larva, cypermethrin, 1 ug/L, replicate 4


title: whole_larva_cypermethrin_1ug/L_rep6

source_name: whole larva, cypermethrin, 1 ug/L, replicate 6


title: whole_larva_cypermethrin_1ug/L_rep5

source_name: whole larva, cypermethrin, 1 ug/L, replicate 5


title: MSA101_G23_DMSO NA 6_hours BJ-2-A


title: HBOC-172


title: HBOC-171


title: HBOC-173


title: whole_larva_cypermethrin_1ug/L_rep8

source_name: whole larva, cypermethrin, 1 ug/L, replicate 8


title: HBOC-170


title: HBOC-185


title: whole_larva_cypermethrin_1ug/L_rep7

source_name: whole larva, cypermethrin, 1 ug/L, replicate 7


title: VISp_Vipr2-IRES2-Cre/wt;Slc32a1-T2A-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

description:
processed data file:
cells_exon_counts.csv.gz
cells_intron_counts.csv.gz

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
Cells with fewer than 2,000 detected genes (count > 0) and less than 30% of reads mapped to the transcriptome were removed. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. For each class, we selected highly specific genes that are only present in this class against all other classes, and computed the eigengene (the first principle component based on the given gene set). Eigengenes for all classes were normalized in the range of 0 and 1, and we removed any cells that scored > 0.2 in more than one class.
We mapped all non-genome-mapped reads to sequences in Extended Data Table 6 (Tasic et al., 2018). To avoid ambiguous counting due to stretches of sequence identity, we designated unique regions within these sequences to count mRNAs of interest. We counted only reads for which at least one of the paired ends had an overlap with the unique regions of at least 10 bp.
Genome_build: mm10
Supplementary_files_format_and_content:
cells_*_counts.csv.gz: matrix file of exon or intron counts of non-control samples
controls_*_counts.csv.gz: matrix file of exon or intron counts of control samples

organism: Mus musculus

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols 1508, 1510, and 1511 at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 12-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background, and newly received or generated transgenic lines were backcrossed to C57BL/6J. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Tamoxifen treatment for Nkx2.1-CreERT2;Ai14 was performed at embryonic day (E)17 (oral gavage of the dam at 1 mg per 10 g of body weight), pups were delivered by cesarean section at E19 and then fostered. Cux2-CreERT2;Ai14 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. Trimethoprim was administered to animals containing Ctgf-2A-dgCre by oral gavage at P40 ± 5 for three consecutive days (0.015 ml per g of body weight using 20 mg ml−1 trimethoprim solution). Ndnf-IRES2-dgCre animals did not receive trimethoprim induction, since the baseline dgCre activity (without trimethoprim) was sufficient to label the cells with the Ai14 reporter (Tasic et al., 2016). We excluded any animals with anophthalmia or microphthalmia.

extract_protocol:
We isolated single cells as previously described (Hempel et al., 2007; Sugino et al., 2006; Tasic et al., 2016) with modifications. We mostly employed layer-enriching dissections, with focus on a single layer. Broader dissections (no layer enrichment or multiple layers combined) were employed for lines which label small numbers of cells, in order to facilitate isolation of sufficient number of cells. We updated our ACSF formulation to consist of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), thiourea (2 mM), and bubbled with carbogen gas (95% O2 and 5% CO2). For samples collected after 12/16/2016, the ACSF formulation also included trehalose (13.2 mM). Mice were anesthetized with isoflurane and perfused with cold carbogen-bubbled ACSF. The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-µm coronal sections on a compresstome (Precisionary). Enzymatic digestion, trituration into single cell suspension, and fluorescence-activated cell sorting (FACS) of single cells were carried out as previously described (Tasic et al., 2016). Cells were sorted into 8-well strips containing lysis buffer from SMART-Seq v4 kit with RNase inhibitor (0.17 U/µl), immediately frozen on dry ice, and stored at -80°C.
We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat#634894) to reverse transcribe poly(A) RNA and amplify cDNA according to the manufacturer’s instructions. We performed reverse transcription and cDNA amplification for 18 PCR cycles in 8-well strips, in sets of 12-24 strips at a time. At least 1 control strip was used per amplification set, which contained 4 wells without cells and 4 wells with 10 pg control RNA. Control RNA was either Mouse Whole Brain Total RNA (Zyagen, MR-201) or control RNA provided in the SMART-Seq v4 kit. All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT DNA Library prep was performed according to manufactorer’s instructions except that the volumes of all reagents including cDNA input were decreased to 0.4× or 0.5× by volume. Details are available in Documentation on the Allen Institute data portal at: http://celltypes.brain-map.org/.

treatment_protocol: For retrogradely-labeled samples, we injected AAV2-retro-EF1a-Cre (Tervo et al., 2016), SADB-rabies-dGdL-Cre, or CAV-Cre (gift of Miguel Chillon Rodrigues, Universitat Autònoma de Barcelona) (Hnasko et al., 2006) into brains of heterozygous or homozygous Ai14 mice as previously described (Tasic et al., 2016). For ALM experiments, we also injected AAV2-retro-CAG-GFP or AAV2-retro-CAG-tdTomato (Tervo et al., 2016) into wild-type mice. For two VISp experiments, we injected into SCs by inserting the needle through the cerebellum at a 45°-angle in the posterior to anterior direction. TdT+ or GFP+ single cells were isolated from VISp or ALM, depending on the injection area.

value: No Injection

value: Primary Visual Cortex (VISp)


title: MSA101_G21_3-acetamidocoumarin 10_uM 6_hours BJ-2-A


title: MSA101_G20_DL-thiorphan 1_uM 6_hours 2484-2-A

value: DL-thiorphan


title: whole_larva_cypermethrin_0.25ug/L_rep8

description: Whole body gene expression after exposure of fathead larvae to 0.25 ug/L of cypermethrin

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 8


title: MSA101_G16_prenylamine 9.6_uM 6_hours 2484-2-A

value: prenylamine


title: MSA101_G17_Prestwick-675 10_uM 6_hours BJ-2-A


title: whole_larva_cypermethrin_1ug/L_rep3

source_name: whole larva, cypermethrin, 1 ug/L, replicate 3


title: whole_larva_cypermethrin_1ug/L_rep1

source_name: whole larva, cypermethrin, 1 ug/L, replicate 1


title: whole_larva_cypermethrin_0.25ug/L_rep11

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 11


title: MSA101_G13_Primidone 10_uM 6_hours BJ-2-A

value: Primidone


title: MSA101_G14_Primidone 10_uM 6_hours 2484-2-A


title: whole_larva_cypermethrin_0.25ug/L_rep9

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 9

value: whole larva


title: HBOC-169


title: whole_larva_cypermethrin_0.25ug/L_rep12

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 12

value: 48 hrs post-hatch


title: MSA101_G18_Prestwick-675 10_uM 6_hours 2484-2-A


title: MSA101_G19_DL-thiorphan 1_uM 6_hours BJ-2-A


title: whole_larva_cypermethrin_1ug/L_rep2

source_name: whole larva, cypermethrin, 1 ug/L, replicate 2

value: cypermethrin


title: whole_larva_cypermethrin_0.25ug/L_rep7

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 7

value: larva


title: HBOC-161

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: whole_larva_cypermethrin_0.25ug/L_rep13

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 13


title: HBOC-162


title: HBOC-167


title: HBOC-165


title: MSA101_G15_prenylamine 9.6_uM 6_hours BJ-2-A


title: HBOC-168


title: HBOC-166


title: MSA101_G12_4-hydroxyphenazone 10_uM 6_hours 2484-2-A


title: whole_larva_cypermethrin_0.25ug/L_rep10

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 10


title: HBOC-163


title: HBOC-164


title: VISp_Vipr2-IRES2-Cre/wt;PhiC31-neo/Ai14(RCL-tdT)_No Injection_1


title: MSA101_G10_trichostatin NA 6_hours 2484-2-A

value: trichostatin

value: poscon


title: MSA101_G11_4-hydroxyphenazone 10_uM 6_hours BJ-2-A


title: MSA101_G06_melatonin 1_uM 6_hours 2484-2-A

value: melatonin


title: VISp_Th-Cre_FI172/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: HBOC-157

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient

value: blood


title: HBOC-159

value: reference DNA


title: whole_larva_cypermethrin_0.25ug/L_rep6

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 6


title: whole_larva_cypermethrin_0ug/L_rep10

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of cypermethrin

source_name: whole larva, cypermethrin, 0 ug/L, replicate 10


title: MSA101_G05_melatonin 1_uM 6_hours BJ-2-A


title: whole_larva_cypermethrin_0.25ug/L_rep5

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 5


title: whole_larva_cypermethrin_0ug/L_rep11

source_name: whole larva, cypermethrin, 0 ug/L, replicate 11


title: MSA101_G08_emetine 7.2_uM 6_hours 2484-2-A

value: emetine


title: whole_larva_cypermethrin_0ug/L_rep9

source_name: whole larva, cypermethrin, 0 ug/L, replicate 9


title: HBOC-160


title: whole_larva_cypermethrin_0.25ug/L_rep1

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 1


title: HBOC-152


title: HBOC-158


title: MSA101_G04_Loxapine 1_uM 6_hours 2484-2-A

value: Loxapine

value: test


title: whole_larva_cypermethrin_0.25ug/L_rep3

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 3


title: MSA101_G07_emetine 7.2_uM 6_hours BJ-2-A


title: whole_larva_cypermethrin_0.25ug/L_rep2

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 2


title: MSA101_G02_diflorasone 8_uM 6_hours 2484-2-A

value: diflorasone


title: HBOC-150


title: VISp_Tac1-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: No Injection

value: Primary Visual Cortex (VISp)


title: MSA101_G01_diflorasone 8_uM 6_hours BJ-2-A


title: MSA101_F24_LY379268 0.1_uM 6_hours 1275-B-3


title: whole_larva_cypermethrin_0ug/L_rep6

source_name: whole larva, cypermethrin, 0 ug/L, replicate 6


title: MSA101_G03_Loxapine 1_uM 6_hours BJ-2-A


title: whole_larva_cypermethrin_0ug/L_rep8

source_name: whole larva, cypermethrin, 0 ug/L, replicate 8


title: VISp_Vipr2-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_F22_methylbenzethonium chloride 8.6_uM 6_hours 1275-B-3

value: methylbenzethonium chloride


title: HBOC-147


title: HBOC-148


title: whole_larva_cypermethrin_0ug/L_rep3

source_name: whole larva, cypermethrin, 0 ug/L, replicate 3

value: whole larva


title: HBOC-151


title: VISp_Tac1-IRES2-Cre/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: HBOC-145


title: whole_larva_cypermethrin_0ug/L_rep5

source_name: whole larva, cypermethrin, 0 ug/L, replicate 5

value: 48 hrs post-hatch


title: whole_larva_cypermethrin_0ug/L_rep7

source_name: whole larva, cypermethrin, 0 ug/L, replicate 7

value: cypermethrin


title: MSA101_F20_anisomycin 10_uM 6_hours 1275-B-3

value: anisomycin


title: HBOC-154


title: HBOC-146


title: whole_larva_cypermethrin_0ug/L_rep2

source_name: whole larva, cypermethrin, 0 ug/L, replicate 2

value: larva


title: whole_larva_cypermethrin_0ug/L_rep4

source_name: whole larva, cypermethrin, 0 ug/L, replicate 4


title: MSA101_F21_methylbenzethonium chloride 8.6_uM 6_hours 3113-6-3


title: MSA101_F23_LY379268 0.1_uM 6_hours 3113-6-3


title: VISp_Slc17a8-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: whole_larva_bifenthrin_0.593ug/L_rep11

description: Whole body gene expression after exposure of fathead larvae to 0.593 ug/L of bifenthrin

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 11

value: bifenthrin


title: MSA101_F16_tyloxapol 4_uM 6_hours 1275-B-3

value: tyloxapol


title: MSA101_F17_DMSO NA 6_hours 3113-6-3

value: DMSO

value: vehicle


title: whole_larva_cypermethrin_0ug/L_rep1

source_name: whole larva, cypermethrin, 0 ug/L, replicate 1


title: whole_larva_bifenthrin_0.593ug/L_rep9

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 9


title: whole_larva_bifenthrin_0.593ug/L_rep10

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 10


title: MSA101_F14_diphemanil metilsulfate 10_uM 6_hours 1275-B-3

value: diphemanil metilsulfate


title: HBOC-142

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient

value: blood

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)

value: reference DNA


title: VISp_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: HBOC-144


title: whole_larva_cypermethrin_0.25ug/L_rep4

source_name: whole larva, cypermethrin, 0.25 ug/L, replicate 4


title: MSA101_F13_diphemanil metilsulfate 10_uM 6_hours 3113-6-3

value: test


title: MSA101_G09_trichostatin NA 6_hours BJ-2-A

value: trichostatin

value: poscon


title: MSA101_F18_DMSO NA 6_hours 1275-B-3


title: HBOC-153


title: HBOC-140


title: HBOC-138


title: whole_larva_bifenthrin_0.593ug/L_rep6

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 6


title: HBOC-141


title: VISp_Tlx3-Cre_PL56/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: No Injection

value: Primary Visual Cortex (VISp)


title: MSA101_F15_tyloxapol 4_uM 6_hours 3113-6-3


title: HBOC-143


title: HBOC-156


title: HBOC-155


title: whole_larva_bifenthrin_0.593ug/L_rep5

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 5

value: whole larva

value: 48 hrs post-hatch


title: MSA101_F10_nordihydroguaiaretic acid 1_uM 6_hours 1275-B-3

value: nordihydroguaiaretic acid


title: HBOC-137


title: HBOC-134


title: HBOC-135


title: VISp_Slc17a7-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: HBOC-132


title: whole_larva_bifenthrin_0.593ug/L_rep7

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 7

value: larva


title: MSA101_F12_DMSO NA 6_hours 1275-B-3


title: MSA101_F11_DMSO NA 6_hours 3113-6-3


title: whole_larva_bifenthrin_0.593ug/L_rep4

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 4

value: bifenthrin


title: HBOC-136


title: MSA101_F05_furosemide 10_uM 6_hours 3113-6-3

value: furosemide


title: MSA101_F06_furosemide 10_uM 6_hours 1275-B-3


title: MSA101_F08_bumetanide 10_uM 6_hours 1275-B-3

value: bumetanide


title: whole_larva_bifenthrin_0.148ug/L_rep14

description: Whole body gene expression after exposure of fathead larvae to 0.148 ug/L of bifenthrin

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 14


title: whole_larva_bifenthrin_0.593ug/L_rep1

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 1


title: whole_larva_bifenthrin_0.593ug/L_rep2

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 2


title: HBOC-133


title: whole_larva_bifenthrin_0.148ug/L_rep13

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 13


title: whole_larva_bifenthrin_0.593ug/L_rep3

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 3


title: VISp_Scnn1a-Tg2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_F09_nordihydroguaiaretic acid 1_uM 6_hours 3113-6-3


title: MSA101_F07_bumetanide 10_uM 6_hours 3113-6-3


title: VISp_Rorb-P2A-FlpO/wt;Ai65F/wt_No Injection_1


title: HBOC-130


title: whole_larva_bifenthrin_0.148ug/L_rep12

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 12


title: HBOC-139


title: MSA101_F04_nefopam 1.38_uM 6_hours 1275-B-3

value: nefopam


title: whole_larva_bifenthrin_0.593ug/L_rep8

source_name: whole larva, bifenthrin, 0.593 ug/L, replicate 8


title: MSA101_F03_nefopam 1.38_uM 6_hours 3113-6-3


title: whole_larva_bifenthrin_0.148ug/L_rep11

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 11


title: HBOC-129


title: HBOC-131


title: VISp_Rasgrf2-T2A-dgFlpO/wt;Ai65F/wt_No Injection_1


title: MSA101_F01_phenazone 1_uM 6_hours 3113-6-3

value: phenazone


title: VISp_Rorb-IRES2-Cre-neo/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_E23_LY379268 0.1_uM 6_hours BJ-2-A


title: whole_larva_bifenthrin_0.148ug/L_rep10

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 10


title: HBOC-125

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: HBOC-127

value: blood


title: HBOC-128

value: reference DNA


title: MSA101_E20_anisomycin 10_uM 6_hours 2484-2-A

value: anisomycin

value: test


title: HBOC-126


title: VISp_Pdyn-T2A-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Penk-IRES2-Cre-neo/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: whole_larva_bifenthrin_0.148ug/L_rep9

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 9


title: whole_larva_bifenthrin_0.148ug/L_rep7

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 7


title: whole_larva_bifenthrin_0.148ug/L_rep4

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 4


title: MSA101_E18_DMSO NA 6_hours 2484-2-A

value: DMSO

value: vehicle


title: VISp_Oxtr-T2A-Cre/wt;Pvalb-T2A-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1

value: No Injection

value: Primary Visual Cortex (VISp)


title: VISp_Oxtr-T2A-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_E22_methylbenzethonium chloride 8.6_uM 6_hours 2484-2-A

value: methylbenzethonium chloride


title: HBOC-124

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: MSA101_F02_phenazone 1_uM 6_hours 1275-B-3


title: whole_larva_bifenthrin_0.148ug/L_rep8

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 8

value: whole larva

value: 48 hrs post-hatch


title: MSA101_E21_methylbenzethonium chloride 8.6_uM 6_hours BJ-2-A


title: HBOC-122


title: MSA101_E17_DMSO NA 6_hours BJ-2-A


title: HBOC-123


title: whole_larva_bifenthrin_0.148ug/L_rep5

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 5

value: bifenthrin

value: larva


title: whole_larva_bifenthrin_0.148ug/L_rep3

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 3


title: MSA101_E16_tyloxapol 4_uM 6_hours 2484-2-A

value: tyloxapol


title: HBOC-149


title: whole_larva_bifenthrin_0.148ug/L_rep1

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 1


title: whole_larva_bifenthrin_0.148ug/L_rep6

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 6


title: whole_larva_bifenthrin_0.148ug/L_rep2

source_name: whole larva, bifenthrin, 0.148 ug/L, replicate 2


title: HBOC-121


title: HBOC-120


title: HBOC-119


title: HBOC-118


title: VISp_Oxtr-T2A-Cre/wt;Ai11(RCL-FnGF-nT)/wt_No Injection_1


title: whole_larva_bifenthrin_0ug/L_rep11

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of bifenthrin

source_name: whole larva, bifenthrin, 0 ug/L, replicate 11


title: VISp_Ntsr1-Cre_GN22/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_E15_tyloxapol 4_uM 6_hours BJ-2-A


title: HBOC-117


title: MSA101_E14_diphemanil metilsulfate 10_uM 6_hours 2484-2-A

value: diphemanil metilsulfate


title: whole_larva_bifenthrin_0ug/L_rep7

source_name: whole larva, bifenthrin, 0 ug/L, replicate 7


title: HBOC-116


title: MSA101_E12_DMSO NA 6_hours 2484-2-A


title: MSA101_E11_DMSO NA 6_hours BJ-2-A


title: MSA101_E13_diphemanil metilsulfate 10_uM 6_hours BJ-2-A


title: whole_larva_bifenthrin_0ug/L_rep8

source_name: whole larva, bifenthrin, 0 ug/L, replicate 8


title: VISp_Nos1-CreERT2/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: HBOC-115


title: HBOC-114


title: VISp_Npy-IRES2-FlpO/wt;Ai65F/wt_No Injection_1


title: VISp_Ndnf-IRES2-dgCre/wt;Slc32a1-IRES2-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: MSA101_E10_nordihydroguaiaretic acid 1_uM 6_hours 2484-2-A

value: nordihydroguaiaretic acid


title: HBOC-113

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: whole_larva_bifenthrin_0ug/L_rep9

source_name: whole larva, bifenthrin, 0 ug/L, replicate 9


title: VISp_Ndnf-IRES2-dgCre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_E24_LY379268 0.1_uM 6_hours 2484-2-A


title: whole_larva_bifenthrin_0ug/L_rep10

source_name: whole larva, bifenthrin, 0 ug/L, replicate 10


title: MSA101_E08_bumetanide 10_uM 6_hours 2484-2-A

value: bumetanide


title: HBOC-110

value: blood

value: reference DNA


title: MSA101_E07_bumetanide 10_uM 6_hours BJ-2-A

value: test


title: whole_larva_bifenthrin_0ug/L_rep4

source_name: whole larva, bifenthrin, 0 ug/L, replicate 4


title: MSA101_E09_nordihydroguaiaretic acid 1_uM 6_hours BJ-2-A


title: HBOC-111


title: VISp_Htr3a-Cre_NO152/wt;Pvalb-T2A-Dre/wt;Ai66(RCRL-tdT)/wt_No Injection_1


title: VISp_Htr3a-Cre_NO152/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: whole_larva_bifenthrin_0ug/L_rep6

source_name: whole larva, bifenthrin, 0 ug/L, replicate 6


title: HBOC-109


title: whole_larva_bifenthrin_0ug/L_rep3

source_name: whole larva, bifenthrin, 0 ug/L, replicate 3


title: VISp_Htr3a-Cre_NO152/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Gng7-Cre_KH71/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: whole_larva_bifenthrin_0ug/L_rep5

source_name: whole larva, bifenthrin, 0 ug/L, replicate 5


title: MSA101_E06_furosemide 10_uM 6_hours 2484-2-A

value: furosemide


title: VISp_Glt25d2-Cre_NF17/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Gad67-GFP_X98/wt_No Injection_1

source_name: VISp_Gad67-GFP_X98/wt_No Injection


title: adult_brain_cypermethrin_1ug/L_rep12

description: Gene expression in brain after exposure of fathead adults to 1 ug/L of cypermethrin

source_name: adult brain, cypermethrin, 1 ug/L, replicate 12

value: brain

value: 6 months

value: cypermethrin

value: adult


title: whole_larva_bifenthrin_0ug/L_rep2

source_name: whole larva, bifenthrin, 0 ug/L, replicate 2

value: whole larva


title: MSA101_E04_nefopam 1.38_uM 6_hours 2484-2-A

value: nefopam


title: MSA101_E05_furosemide 10_uM 6_hours BJ-2-A


title: HBOC-108

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: whole_larva_bifenthrin_0ug/L_rep1

source_name: whole larva, bifenthrin, 0 ug/L, replicate 1

value: 48 hrs post-hatch

value: bifenthrin


title: adult_brain_cypermethrin_1ug/L_rep13

source_name: adult brain, cypermethrin, 1 ug/L, replicate 13


title: HBOC-105


title: HBOC-106


title: HBOC-107


title: VISp_Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3

value: No Injection

value: Primary Visual Cortex (VISp)


title: MSA101_E02_phenazone 1_uM 6_hours 2484-2-A

value: phenazone


title: HBOC-104

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: MSA101_E03_nefopam 1.38_uM 6_hours BJ-2-A


title: MSA101_D24_quinpirole 0.1_uM 6_hours 1275-B-3

value: quinpirole


title: adult_brain_cypermethrin_1ug/L_rep9

source_name: adult brain, cypermethrin, 1 ug/L, replicate 9


title: MSA101_D22_hydroquinine 1_uM 6_hours 1275-B-3

value: hydroquinine


title: MSA101_E01_phenazone 1_uM 6_hours BJ-2-A


title: adult_brain_cypermethrin_1ug/L_rep11

source_name: adult brain, cypermethrin, 1 ug/L, replicate 11


title: adult_brain_cypermethrin_1ug/L_rep8

source_name: adult brain, cypermethrin, 1 ug/L, replicate 8


title: HBOC-103

value: blood

value: reference DNA


title: MSA101_D23_quinpirole 0.1_uM 6_hours 3113-6-3

value: test


title: adult_brain_cypermethrin_1ug/L_rep10

source_name: adult brain, cypermethrin, 1 ug/L, replicate 10

value: brain


title: VISp_Etv1-CreERT2/wt;Pvalb-T2A-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: VISp_Esr2-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Ctgf-T2A-dgCre/wt;Snap25-LSL-F2A-GFP/wt_Retrograde_1

value: Retrograde


title: adult_brain_cypermethrin_1ug/L_rep7

source_name: adult brain, cypermethrin, 1 ug/L, replicate 7

value: 6 months

value: cypermethrin


title: adult_brain_cypermethrin_1ug/L_rep6

source_name: adult brain, cypermethrin, 1 ug/L, replicate 6

value: adult


title: adult_brain_cypermethrin_1ug/L_rep5

source_name: adult brain, cypermethrin, 1 ug/L, replicate 5


title: MSA101_D21_hydroquinine 1_uM 6_hours 3113-6-3


title: MSA101_D20_haloperidol 0.1_uM 6_hours 1275-B-3

value: haloperidol


title: MSA101_D19_haloperidol 0.1_uM 6_hours 3113-6-3


title: HBOC-102


title: MSA101_D18_ethionamide 10_uM 6_hours 1275-B-3

value: ethionamide


title: adult_brain_cypermethrin_1ug/L_rep3

source_name: adult brain, cypermethrin, 1 ug/L, replicate 3


title: HBOC-101


title: HBOC-99


title: HBOC-97


title: HBOC-100


title: HBOC-98


title: adult_brain_cypermethrin_1ug/L_rep4

source_name: adult brain, cypermethrin, 1 ug/L, replicate 4


title: MSA101_D17_ethionamide 10_uM 6_hours 3113-6-3


title: HBOC-112


title: HBOC-95


title: VISp_Chrnb3-Cre_SM93/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: VISp_Ctgf-T2A-dgCre/wt;Snap25-LSL-F2A-GFP/wt_No Injection_1


title: VISp_Crh-IRES-Cre_ZJH/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: VISp_Ctgf-T2A-dgCre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_D15_zardaverine 10_uM 6_hours 3113-6-3

value: zardaverine


title: HBOC-96


title: adult_brain_cypermethrin_0.25ug/L_rep8

description: Gene expression in brain after exposure of fathead adults to 0.25 ug/L of cypermethrin

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 8


title: adult_brain_cypermethrin_0.25ug/L_rep10

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 10


title: HBOC-94


title: adult_brain_cypermethrin_1ug/L_rep1

source_name: adult brain, cypermethrin, 1 ug/L, replicate 1


title: adult_brain_cypermethrin_0.25ug/L_rep11

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 11


title: MSA101_D11_BAS-012416453 10_uM 6_hours 3113-6-3


title: HBOC-93


title: MSA101_D12_BAS-012416453 10_uM 6_hours 1275-B-3


title: VISp_Chat-IRES-Cre-neo/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: No Injection


title: adult_brain_cypermethrin_1ug/L_rep2

source_name: adult brain, cypermethrin, 1 ug/L, replicate 2


title: adult_brain_cypermethrin_0.25ug/L_rep9

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 9


title: HBOC-92

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: MSA101_D13_tanespimycin NA 6_hours 3113-6-3

value: tanespimycin

value: poscon


title: HBOC-91

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: adult_brain_cypermethrin_0.25ug/L_rep6

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 6


title: MSA101_D14_tanespimycin NA 6_hours 1275-B-3


title: adult_brain_cypermethrin_0.25ug/L_rep7

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 7


title: HBOC-90


title: VISp_Calb1-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: Primary Visual Cortex (VISp)


title: VISp_Ai14(RCL-tdT)/wt_Retrograde_3


title: VISp_Ai14(RCL-tdT)/wt;Ai148(TIT2L-GC6f-ICL-tTA2)/wt_Retrograde_1


title: MSA101_D10_DMSO NA 6_hours 1275-B-3

value: DMSO

value: vehicle


title: MSA101_D09_DMSO NA 6_hours 3113-6-3


title: MSA101_D07_Vorinostat 1_uM 6_hours 3113-6-3

value: Vorinostat


title: Control: No Template Control_1

description:
processed data file:
controls_exon_counts.csv.gz
controls_intron_counts.csv.gz

source_name: Control: No Template Control

value: Control:No Template Control


title: adult_brain_cypermethrin_0.25ug/L_rep5

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 5

value: brain


title: Control: No Template Control_2


title: MSA101_D08_Vorinostat 1_uM 6_hours 1275-B-3

value: test


title: MSA101_D06_DMSO NA 6_hours 1275-B-3


title: adult_brain_cypermethrin_0.25ug/L_rep2

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 2

value: 6 months


title: MSA101_D04_alpha-ergocryptine 7_uM 6_hours 1275-B-3

value: alpha-ergocryptine


title: MSA101_D05_DMSO NA 6_hours 3113-6-3


title: adult_brain_cypermethrin_0.25ug/L_rep1

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 1

value: cypermethrin

value: adult


title: MSA101_D03_alpha-ergocryptine 7_uM 6_hours 3113-6-3


title: adult_brain_cypermethrin_0.25ug/L_rep3

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 3


title: HBOC-88

value: blood

value: reference DNA


title: HBOC-87


title: HBOC-85


title: HBOC-84


title: HBOC-82


title: MSA101_D02_moxonidine 1_uM 6_hours 1275-B-3

value: moxonidine


title: HBOC-86


title: adult_brain_cypermethrin_0ug/L_rep12

description: Gene expression in brain after exposure of fathead adults to 0 ug/L of cypermethrin

source_name: adult brain, cypermethrin, 0 ug/L, replicate 12


title: adult_brain_cypermethrin_0ug/L_rep11

source_name: adult brain, cypermethrin, 0 ug/L, replicate 11


title: adult_brain_cypermethrin_0.25ug/L_rep4

source_name: adult brain, cypermethrin, 0.25 ug/L, replicate 4


title: HBOC-89


title: HBOC-81


title: HBOC-80


title: HBOC-83


title: Control: 1E-8 ERCC MIX1_2

source_name: Control: 1E-8 ERCC MIX1

value: Control:1E-8 ERCC MIX1


title: Control: 1E-8 ERCC MIX1_1


title: Control: 10pg Zyagen Mouse Whole Brain Total RNA_2

value: Control:10pg Zyagen Mouse Whole Brain Total RNA


title: adult_brain_cypermethrin_0ug/L_rep13

source_name: adult brain, cypermethrin, 0 ug/L, replicate 13


title: Control: 10pg Zyagen Mouse Whole Brain Total RNA_1


title: adult_brain_cypermethrin_0ug/L_rep10

source_name: adult brain, cypermethrin, 0 ug/L, replicate 10


title: MSA101_C23_quinpirole 0.1_uM 6_hours BJ-2-A

value: quinpirole


title: MSA101_C21_hydroquinine 1_uM 6_hours BJ-2-A

value: hydroquinine


title: MSA101_C22_hydroquinine 1_uM 6_hours 2484-2-A


title: ALM_wt/wt_Retrograde_1

value: wt/wt

value: Retrograde

value: Anterior Lateral Motor Cortex (ALM)


title: MSA101_C24_quinpirole 0.1_uM 6_hours 2484-2-A


title: HBOC-76

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: MSA101_C20_haloperidol 0.1_uM 6_hours 2484-2-A

value: haloperidol


title: adult_brain_cypermethrin_0ug/L_rep6

source_name: adult brain, cypermethrin, 0 ug/L, replicate 6

value: brain


title: HBOC-78


title: ALM_Vipr2-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: No Injection


title: HBOC-79


title: Control: 10pg Takara Control Total RNA_2

source_name: Control: 10pg Takara Control Total RNA

value: Control:10pg Takara Control Total RNA


title: adult_brain_cypermethrin_0ug/L_rep8

source_name: adult brain, cypermethrin, 0 ug/L, replicate 8

value: 6 months

value: cypermethrin


title: ALM_Vip-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: adult_brain_cypermethrin_0ug/L_rep7

source_name: adult brain, cypermethrin, 0 ug/L, replicate 7

value: adult


title: MSA101_C18_ethionamide 10_uM 6_hours 2484-2-A

value: ethionamide

value: test


title: adult_brain_cypermethrin_0ug/L_rep4

source_name: adult brain, cypermethrin, 0 ug/L, replicate 4


title: HBOC-74

value: blood

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)

value: reference DNA


title: adult_brain_cypermethrin_0ug/L_rep5

source_name: adult brain, cypermethrin, 0 ug/L, replicate 5


title: MSA101_C17_ethionamide 10_uM 6_hours BJ-2-A


title: adult_brain_cypermethrin_0ug/L_rep3

source_name: adult brain, cypermethrin, 0 ug/L, replicate 3


title: HBOC-77


title: ALM_Trib2-F2A-CreERT2/wt;Snap25-LSL-F2A-GFP/wt_No Injection_1


title: MSA101_D16_zardaverine 10_uM 6_hours 1275-B-3

value: zardaverine


title: MSA101_C13_tanespimycin NA 6_hours BJ-2-A

value: tanespimycin

value: poscon


title: HBOC-73


title: ALM_Th-Cre_FI172/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: adult_brain_cypermethrin_0ug/L_rep9

source_name: adult brain, cypermethrin, 0 ug/L, replicate 9


title: HBOC-75


title: ALM_Sst-IRES-Cre/wt;Pvalb-T2A-Dre/wt;Ai66/wt_No Injection_1


title: MSA101_C14_tanespimycin NA 6_hours 2484-2-A


title: HBOC-69


title: ALM_Tlx3-Cre_PL56/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Tac1-IRES2-Cre/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: adult_brain_bifenthrin_0.593ug/L_rep10

description: Gene expression in brain after exposure of fathead adults to 0.593 ug/L of bifenthrin

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 10

value: bifenthrin


title: adult_brain_cypermethrin_0ug/L_rep1

source_name: adult brain, cypermethrin, 0 ug/L, replicate 1


title: HBOC-71


title: adult_brain_bifenthrin_0.593ug/L_rep12

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 12


title: adult_brain_bifenthrin_0.593ug/L_rep11

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 11


title: ALM_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_4

value: Anterior Lateral Motor Cortex (ALM)


title: MSA101_C19_haloperidol 0.1_uM 6_hours BJ-2-A


title: HBOC-68

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: MSA101_C15_zardaverine 10_uM 6_hours BJ-2-A


title: ALM_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3


title: MSA101_C12_BAS-012416453 10_uM 6_hours 2484-2-A


title: ALM_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: ALM_Snap25-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: HBOC-70


title: MSA101_C07_Vorinostat 1_uM 6_hours BJ-2-A

value: Vorinostat


title: HBOC-67


title: MSA101_C11_BAS-012416453 10_uM 6_hours BJ-2-A


title: ALM_Sst-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: adult_brain_bifenthrin_0.593ug/L_rep9

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 9

value: brain


title: ALM_Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3

value: No Injection


title: adult_brain_bifenthrin_0.593ug/L_rep8

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 8


title: MSA101_C08_Vorinostat 1_uM 6_hours 2484-2-A


title: adult_brain_bifenthrin_0.593ug/L_rep7

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 7


title: HBOC-66


title: HBOC-65


title: ALM_Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: HBOC-61


title: HBOC-64


title: adult_brain_bifenthrin_0.593ug/L_rep6

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 6


title: HBOC-63


title: HBOC-62


title: adult_brain_bifenthrin_0.593ug/L_rep5

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 5


title: adult_brain_bifenthrin_0.593ug/L_rep4

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 4


title: MSA101_C06_DMSO NA 6_hours 2484-2-A

value: DMSO

value: vehicle


title: MSA101_C04_alpha-ergocryptine 7_uM 6_hours 2484-2-A

value: alpha-ergocryptine


title: MSA101_C05_DMSO NA 6_hours BJ-2-A


title: adult_brain_bifenthrin_0.593ug/L_rep2

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 2

value: 6 months

value: adult


title: ALM_Slc17a8-iCre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_C03_alpha-ergocryptine 7_uM 6_hours BJ-2-A

value: test


title: adult_brain_bifenthrin_0.593ug/L_rep3

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 3


title: HBOC-60

value: blood


title: HBOC-58

value: reference DNA


title: ALM_Slc32a1-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_C09_DMSO NA 6_hours BJ-2-A


title: adult_brain_bifenthrin_0.148ug/L_rep11

description: Gene expression in brain after exposure of fathead adults to 0.148 ug/L of bifenthrin

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 11


title: adult_brain_bifenthrin_0.148ug/L_rep9

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 9


title: adult_brain_bifenthrin_0.593ug/L_rep1

source_name: adult brain, bifenthrin, 0.593 ug/L, replicate 1


title: HBOC-59

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: ALM_Slc17a7-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_3


title: ALM_Slc17a6-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: adult_brain_bifenthrin_0.148ug/L_rep8

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 8


title: ALM_Sim1-Cre_KJ18/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Slc17a7-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: adult_brain_bifenthrin_0.148ug/L_rep10

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 10


title: ALM_Slc17a7-IRES2-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: HBOC-72


title: MSA101_C02_moxonidine 1_uM 6_hours 2484-2-A

value: moxonidine


title: MSA101_C01_moxonidine 1_uM 6_hours BJ-2-A


title: adult_brain_bifenthrin_0.148ug/L_rep7

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 7


title: adult_brain_bifenthrin_0.148ug/L_rep6

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 6


title: HBOC-57


title: MSA101_B24_trimethadione 10_uM 6_hours 1275-B-3

value: trimethadione


title: HBOC-55


title: HBOC-56


title: ALM_Scnn1a-Tg3-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_B21_DMSO NA 6_hours 3113-6-3


title: ALM_Rorb-P2A-FlpO/wt;Ai65F/wt_No Injection_1


title: HBOC-51


title: ALM_Rorb-IRES2-Cre-neo/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_B19_phenelzine 10_uM 6_hours 3113-6-3

value: phenelzine


title: ALM_Rbp4-Cre_KL1/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: HBOC-53


title: HBOC-54


title: MSA101_B18_naringenin 10_uM 6_hours 1275-B-3

value: naringenin


title: HBOC-52


title: adult_brain_bifenthrin_0.148ug/L_rep4

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 4

value: bifenthrin


title: MSA101_B23_trimethadione 10_uM 6_hours 3113-6-3


title: MSA101_B20_phenelzine 10_uM 6_hours 1275-B-3


title: adult_brain_bifenthrin_0.148ug/L_rep3

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 3


title: adult_brain_cypermethrin_0ug/L_rep2

source_name: adult brain, cypermethrin, 0 ug/L, replicate 2

value: cypermethrin


title: MSA101_B16_Aripiprazole 1_uM 6_hours 1275-B-3

value: Aripiprazole


title: MSA101_B22_DMSO NA 6_hours 1275-B-3


title: MSA101_B15_Aripiprazole 1_uM 6_hours 3113-6-3


title: MSA101_C16_zardaverine 10_uM 6_hours 2484-2-A

value: zardaverine


title: MSA101_B17_naringenin 10_uM 6_hours 3113-6-3


title: MSA101_B14_chenodeoxycholic acid 10_uM 6_hours 1275-B-3

value: chenodeoxycholic acid


title: HBOC-48

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: adult_brain_bifenthrin_0.148ug/L_rep5

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 5

value: brain


title: HBOC-49


title: ALM_Oxtr-T2A-Cre/wt;Pvalb-T2A-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1

value: No Injection

value: Anterior Lateral Motor Cortex (ALM)


title: adult_brain_bifenthrin_0.148ug/L_rep1

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 1

value: 6 months

value: adult


title: HBOC-50

value: blood


title: adult_brain_bifenthrin_0ug/L_rep13

description: Gene expression in brain after exposure of fathead adults to 0 ug/L of bifenthrin

source_name: adult brain, bifenthrin, 0 ug/L, replicate 13


title: ALM_Pvalb-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Rbp4-Cre_KL1/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Ntsr1-Cre_GN22/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Pdyn-T2A-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_B13_chenodeoxycholic acid 10_uM 6_hours 3113-6-3

value: test


title: adult_brain_bifenthrin_0ug/L_rep11

source_name: adult brain, bifenthrin, 0 ug/L, replicate 11


title: ALM_Rasgrf2-T2A-dgFlpO/wt;Ai65F/wt_No Injection_1


title: adult_brain_bifenthrin_0ug/L_rep12

source_name: adult brain, bifenthrin, 0 ug/L, replicate 12


title: adult_brain_bifenthrin_0ug/L_rep8

source_name: adult brain, bifenthrin, 0 ug/L, replicate 8


title: HBOC-45

value: reference DNA


title: HBOC-46


title: HBOC-44


title: MSA101_C10_DMSO NA 6_hours 2484-2-A

value: DMSO

value: vehicle


title: ALM_Htr3a-Cre_NO152/wt;Pvalb-T2A-Dre/wt;Ai66(RCRL-tdT)/wt_No Injection_1


title: adult_brain_bifenthrin_0ug/L_rep9

source_name: adult brain, bifenthrin, 0 ug/L, replicate 9


title: ALM_Nkx2-1-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Ndnf-IRES2-dgCre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: HBOC-47


title: HBOC-43


title: MSA101_B12_fendiline 10_uM 6_hours 1275-B-3

value: fendiline


title: ALM_Nos1-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: adult_brain_bifenthrin_0ug/L_rep10

source_name: adult brain, bifenthrin, 0 ug/L, replicate 10

value: bifenthrin


title: MSA101_B08_arachidonyltrifluoromethane 10_uM 6_hours 1275-B-3

value: arachidonyltrifluoromethane


title: MSA101_B11_fendiline 10_uM 6_hours 3113-6-3


title: adult_brain_bifenthrin_0.148ug/L_rep2

source_name: adult brain, bifenthrin, 0.148 ug/L, replicate 2


title: HBOC-42

source_name: Megapool Reference DNA (female) EA-100F (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: MSA101_B10_diclofenamide 10_uM 6_hours 1275-B-3

value: diclofenamide


title: MSA101_B09_diclofenamide 10_uM 6_hours 3113-6-3


title: ALM_Htr3a-Cre_NO152/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_B07_arachidonyltrifluoromethane 10_uM 6_hours 3113-6-3


title: MSA101_B06_Chlorpromazine 0.1_uM 6_hours 1275-B-3

value: Chlorpromazine


title: adult_brain_bifenthrin_0ug/L_rep5

source_name: adult brain, bifenthrin, 0 ug/L, replicate 5


title: adult_brain_bifenthrin_0ug/L_rep6

source_name: adult brain, bifenthrin, 0 ug/L, replicate 6


title: HBOC-41


title: ALM_Nos1-CreERT2/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: HBOC-39


title: HBOC-37


title: adult_brain_bifenthrin_0ug/L_rep4

source_name: adult brain, bifenthrin, 0 ug/L, replicate 4


title: ALM_Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_2


title: adult_brain_bifenthrin_0ug/L_rep7

source_name: adult brain, bifenthrin, 0 ug/L, replicate 7


title: ALM_Gad2-IRES-Cre/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: MSA101_B05_Chlorpromazine 0.1_uM 6_hours 3113-6-3


title: HBOC-38


title: ALM_Gng7-Cre_KH71/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: ALM_Etv1-CreERT2/wt;Pvalb-T2A-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: 110

city: Ames

first: Laura

last: Miller

state: Iowa

address: 1920 Dayton Ave

department: Virus and Prion Research Unit

institute: USDA-ARS-National Animal Disease Center

data_processing:
Quality assessment and control were performed using FastQC and TrimGalore [15] to remove adaptors and barcodes from multiplexing. Reads with a quality score below 38 and length less than 18 or longer than 72 nucleotides were discarded. A total of 24 sequences were generated for downstream analysis.
The sequenced reads were mapped to the S.scrofa 10.2 reference genome  using the Hisat2 [16] package with default settings. Annotation of gene counts was performed using FeatureCounts software package [17] coupled with an in-house created sncRNA GTF file. The in-house GTF file was based on annotations from release 21 of miRbase, GtRNAdb using tRNAscan-SE 2.0, Ensembl 84 ncRNA database, and the RTH S.scrofa 10.2 ncRNA database
differential gene expression was calculated using the DeSeq2 package with the dispersion model set as local with all other parameters set at their default values.
Genome_build: ssc10.2
Supplementary_files_format_and_content: excel workbook with tRNA and miRNA log2fc values by dpi

organism: Sus scrofa

source_name: whole blood

extract_protocol:
whole blood samples (~2.5 ml/pig) collected from 9-week old anesthetized pigs by jugular venipuncture. Total RNA was extracted from 2.5 ml cryopreserved whole blood samples using the protocol from Fleming et al.,2018 [10] and a modified miRNA extraction kit protocol optimized according to Taxis et al., 2017 [11] for the PAXgene  miRNA and MirVana miRNA isolation kit™ (Thermo Scientific, Wilmington, DE, USA). Optimization of these protocols was done to increase small RNA recovery for downstream library creation. All RNA was globin depleted to account for high levels of globin transcripts
Globin reduced total RNA for sncRNA and globin and ribo-depleted mRNA library prep

value: HP-PRRSV

tag: dpi


title: adult_brain_bifenthrin_0ug/L_rep2

source_name: adult brain, bifenthrin, 0 ug/L, replicate 2


title: adult_brain_bifenthrin_0ug/L_rep3

source_name: adult brain, bifenthrin, 0 ug/L, replicate 3


title: 109


title: 111


title: HBOC-36

tag: subject status

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: MSA101_B03_dihydroergocristine 1_uM 6_hours 3113-6-3

value: dihydroergocristine


title: MSA101_B04_dihydroergocristine 1_uM 6_hours 1275-B-3


title: HBOC-34

tag: tissue


title: 108


title: MSA101_A24_trimethadione 10_uM 6_hours 2484-2-A

value: trimethadione


title: ALM_Ctgf-T2A-dgCre/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: No Injection

value: Anterior Lateral Motor Cortex (ALM)


title: ALM_Cux2-CreERT2/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: 96

value: Control


title: ALM_Crh-IRES-Cre_ZJH/wt;Sst-IRES-FlpO/wt;Ai65(RCFL-tdT)/wt_No Injection_1


title: ALM_Chrnb3-Cre_SM93/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: 95


title: 94


title: 93


title: 107


title: 106


title: MSA101_A21_DMSO NA 6_hours BJ-2-A


title: MSA101_A20_phenelzine 10_uM 6_hours 2484-2-A

value: phenelzine


title: HBOC-35

value: blood

tag: sample type


title: adult_brain_bifenthrin_0ug/L_rep1

source_name: adult brain, bifenthrin, 0 ug/L, replicate 1

value: brain

value: 6 months

value: adult


title: MSA101_A18_naringenin 10_uM 6_hours 2484-2-A

tag: perturbagen

value: naringenin

value: test


title: HBOC-27

value: reference DNA


title: HBOC-33


title: HBOC-31


title: MSA101_A22_DMSO NA 6_hours 2484-2-A

value: DMSO

tag: cell id

value: vehicle


title: MSA101_A19_phenelzine 10_uM 6_hours BJ-2-A

tag: dosage


title: MSA101_A23_trimethadione 10_uM 6_hours BJ-2-A

tag: batch


title: HBOC-29


title: 105

value: HP-PRRSV


title: 104


title: HBOC-25

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: 92


title: HBOC-32


title: HBOC-26


title: HBOC-28


title: 90


title: MSA101_A16_Aripiprazole 1_uM 6_hours 2484-2-A

value: Aripiprazole

tag: duration


title: ALM_Chrna2-Cre_OE25/wt;Pvalb-T2A-Dre/wt;Ai66(RCRL-tdT)/wt_No Injection_1


title: 89


title: ALM_Ai14(RCL-tdT)/wt_Retrograde_1

value: Retrograde


title: ALM_Chat-IRES-Cre-neo/wt;Ai14(RCL-tdT)/wt_No Injection_1

value: No Injection


title: ALM_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_1

value: Anterior Lateral Motor Cortex (ALM)


title: ALM_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_3


title: ALM_Ai14(RCL-tdT)/Ai14(RCL-tdT)_Retrograde_2


title: ALM_Chrna2-Cre_OE25/wt;Ai14(RCL-tdT)/wt_No Injection_1


title: HBOC-30


title: MSA101_A17_naringenin 10_uM 6_hours BJ-2-A

tag: perturbation type


title: MSA101_A14_chenodeoxycholic acid 10_uM 6_hours 2484-2-A

value: chenodeoxycholic acid

tag: well id


title: MSA101_A15_Aripiprazole 1_uM 6_hours BJ-2-A

tag: plate id


title: 88

value: Control


title: 103


title: MSA101_A13_chenodeoxycholic acid 10_uM 6_hours BJ-2-A


title: 98


title: MSA101_A11_fendiline 10_uM 6_hours BJ-2-A

value: fendiline


title: 102


title: HBOC-24

value: blood


title: MSA101_A12_fendiline 10_uM 6_hours 2484-2-A


title: 87


title: HBOC-40


title: 86


title: HBOC-21


title: MSA101_A09_diclofenamide 10_uM 6_hours BJ-2-A

value: diclofenamide


title: HBOC-19


title: MSA101_A07_arachidonyltrifluoromethane 10_uM 6_hours BJ-2-A

value: arachidonyltrifluoromethane


title: MSA101_A10_diclofenamide 10_uM 6_hours 2484-2-A


title: 60


title: 84


title: HBOC-22


title: MSA101_A08_arachidonyltrifluoromethane 10_uM 6_hours 2484-2-A


title: 82


title: MSA101_A03_dihydroergocristine 1_uM 6_hours BJ-2-A

value: dihydroergocristine


title: MSA101_A05_Chlorpromazine 0.1_uM 6_hours BJ-2-A

value: Chlorpromazine

value: test


title: HBOC-17

value: reference DNA


title: MSA101_A06_Chlorpromazine 0.1_uM 6_hours 2484-2-A


title: HBOC-12


title: HBOC-14


title: HBOC-15


title: HBOC-10


title: HBOC-13


title: lncapc9r3_prostate_rep3

city: DUBLIN

first: JOHN

last: GREENE

address: ST JAMES'S HOSPITAL

country: Ireland

institute: TRINITY COLLEGE DUBLIN

description: enza resistant - low

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

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed
A list of probe names, circRNA names and circRNA aliases used in this study is available on the series record.

source_name: prostate cancer

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: The isogenic enzalutamide resistance LNCaP model was gifted from Novartis (13). The panel consisted of an aged match control cell line (drug sensitive), and two sub-lines termed clone 1 and clone 9. Clone 1 was most resistance to the drug, with clone 9 displaying moderate resistance. Cells were cultured in RPMI-1640 media (Merck KGaA, Darmstadt, Germany) with 10% FBS (Merck KGaA) and 1% Penicillin Streptomycin (Merck KGaA).

extract_protocol: Total RNA was prepared from cell lines using TRIzol (Life Technologies, CA, USA) according to manufacturer’s instructions. Subsequently, the RNA underwent DNase treatment with Ambion® TURBO™ DNase (Thermo Fisher Scientific, MA, USA) and a further RNA clean-up was performed using standard ethanol precipitation protocol.

tag: cell line

value: LNCaP

tag: drug resistance

value: enzalutamide resistant subline 9 (low)

tag: Sex

value: male


title: lncapc9r2_prostate_rep2

description: enza resistant - low


title: HBOC-9

value: BRCA1/2 negative Hereditary breast and/or ovarian cancer (HBOC) patient


title: lncapc9r1_prostate_rep1

description: enza resistant - low


title: lncapc1r3_prostate_rep3

description: enza resistant - high

value: enzalutamide resistant subline 1 (high)


title: lncapcontrolr5_prostate_rep3

description: control

value: drug sensitive


title: lncapc1r1_prostate_rep1

description: enza resistant - high


title: HBOC-11


title: lncapcontrolr3_prostate_rep2

description: control


title: HBOC-8


title: HBOC-18


title: lncapc1r2_prostate_rep2

description: enza resistant - high


title: HBOC-20


title: HBOC-7


title: HBOC-4


title: HBOC-5

source_name: Megapool Reference DNA (male) EA-100M (Kreatech Biotechnology, Amsterdam, The Netherlands)


title: HBOC-6


title: HBOC-16


title: HBOC-2


title: HBOC-3


title: lncapcontrolr1_prostate_rep1

description: control


title: Pineapple_NAD_4hr_rep3

status: Public on Oct 30 2018

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Gene expression 4 hr after NAD treatment

hyb_protocol: Samples were hybridized with rotation at 45°C for 16 hours to the Affymetrix GeneChip Citrus Genome Array.  The arrays were washed and stained with the reagents supplied in GeneChip® Hybridization Wash and Stain kit (Affymetrix, Inc) on an Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner

data_processing: The data were normalized using RMA approach with affy package.

organism: Citrus sinensis

source_name: Pineapple, NAD, 4hr

label_protocol: All microarray sample preparation used the GeneChip® 3’ IVT Plus Express kit (Affymetrix, Inc.), and reactions were done following the manufacturer’s protocols.  Briefly, cDNA was synthesized from 200 ng of total RNA and template for in vitro transcription during which a biotin-modified nucleotide was incorporated.  The biotin-labeled aRNA was then purified and fragmented.

growth_protocol: Pineapple sweet orange (Citrus sinensis L. Osbeck) seedlings were maintained in standard greenhouses at the Citrus Research and Education Center of the University of Florida.

extract_protocol: Six leaf discs of 6-mm diameter per sample were ground into a fine powder in liquid nitrgen.  RNA was extracted using an RNeasy Mini kit (QIAGEN, Germantown, MD) according to the manufacturer’s instructions.

treatment_protocol: Citrus seedlings were cut back to produce expanding leaves 6 weeks prior to NAD treatments.  Fully expanded young leaves were infiltrated with 1 mM NAD or water by pressing the needleless syringe tip against the abaxial leaf surface to produce water soaked tissues.  The water-soaked areas were marked and leaf discs were collected from these areas at 4 hr after the infiltration.

tag: cultivar

value: Pineapple

tag: agent

value: NAD

tag: time

value: 4 hr

value: leaf


title: Pineapple_water_4hr_rep3

description: Gene expression 4 hr after water treatment

source_name: Pineapple, water, 4hr

value: water


title: HBOC-1

tag: subject status

value: blood


title: Pineapple_NAD_4hr_rep1

tag: tissue


title: EWAT_SCO_rep2

city: Baton Rouge

first: Jacqueline

middle: M

last: Stephens

state: LA

address: 6400 Perkins Road

department: Adipocyte Biology

institute: LSU

hyb_protocol: 750ng labeled RNA was hybridized to MouseRef-8 v2 BeadChip arrays (Illumina) according to manufacturer’s protocol.

scan_protocol: Chips were scanned using Illumina iScan system with default settings

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6. Raw data were background-subtracted and normalized using the quantile normalization method (lumi software package). Normalized data were filtered for genes with significant expression levels compared to negative control beads.  The dataset was log2 transformed.
Limma V3.18.13 processed the data for contrast statistics and quality control.  Gene expression analysis was performed Cyber-T web version 2014, http://cybert.ics.uci.edu/.  Pathway and processes analysis done with GSEA web version 2014, http://software.broadinstitute.org/gsea/index.jsp .  The file non-normalized_data.txt contains  no background subtracted non-normalized data exported from GenomeStudio

source_name: epididymal white adipose tissue

label_protocol: 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system

growth_protocol: high-fat diet (HFD)-induced obese male mice, singly housed, 17 weeks of age at start of experimental diet.

extract_protocol: RNA was extracted with TriReagent (Molecular Research Center), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 4-week ad libitum feeding with HFD +/- supplementation with 1% w/w Artemisia scoparia extract. Sacrificed at 21 weeks of age.

tag: strain

value: epididymal white adipose tissue

value: Male

tag: diet

value: Research Diets D12492, 60% kcal fat supplemented with 1% w/w of ethanolic Artemisia scoparia extract


title: EWAT_SCO_rep1


title: EWAT_SCO_rep3


title: EWAT_CON_rep4

value: Research Diets D12492, 60% kcal fat


title: IWAT_CON_rep4

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue


title: IWAT_SCO_rep3


title: IWAT_SCO_rep2


title: Pineapple_NAD_4hr_rep2


title: IWAT_CON_rep3


title: EWAT_CON_rep1


title: Pineapple_water_4hr_rep1


title: Pineapple_water_4hr_rep2


title: EWAT_CON_rep3


title: EWAT_SCO_rep4


title: IWAT_SCO_rep4


title: EWAT_CON_rep2


title: HBOC-23

tag: sample type

value: reference DNA


title: IWAT_CON_rep1


title: IWAT_SCO_rep1


title: R_9

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Gene expression in livers of six week old mice

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 manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute 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 using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: diet-induced obesity susceptible (DIO responder)

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated according to the manufacturer's instructions using QIAzolTM-Reagent (QIAGEN). RNA integrity was measured on LabChips in an Agilent bioanalyzer, and RNA concentration was determined spectrophotometrically using a Nanodrop spectrophotometer (Thermo Scientific).

treatment_protocol: Male C57BL/6J mice were kept on a high-fat diet (60%kcal from fat) directly after weaning. At the age of 6 wks, livers were collected for transcriptome analysis.

value: liver

tag: gender

tag: age

value: 6 weeks


title: 116-B (RNA-Seq)

city: Leioa

first: Begoña

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Sequence reads were trimmed and filtered with Trimmomatic [v0.36] with the following criteria: (1) palindrome mode allowing up to two mismatches; (2) filter reads with an average Phred quality score within a sliding window of 5 nucleotides of 20; (3) filter reads with a length below 36.
The STAR RNA-seq aligner [v2.5.2b] was used to align clean reads to the Ovis aries reference genome using the 2-pass mode.
For each library, the featureCounts software from the SourceForge Subread package [v1.5.0-p1] was applied to assign uniquely aligned fragments to annotated genes in a strand specific manner.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text file matrix with the raw counts of sequencing reads for annotated genes in the genome annotation for every sample. The genes are identified with the Ensembl ID and the samples are identified by the name of the title column of the SAMPLES section.

organism: Ovis aries

source_name: Blood

growth_protocol: The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the Ethical Committee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.

extract_protocol:
For isolation of ovine peripheral blood mononuclear cells (PBMCs), blood was collected from the jugular vein of 6 Rasa sheep. The blood was collected into heparinised Vacutainer tubes (Becton, Dickinson and Company, Sparks, MD), transferred into 50-ml centrifuge tubes and diluted 1∶2 in HBSS. Twenty-five millilitres of blood:HBSS were layered over 10 ml of Ficoll-Paque (1.084 g/cm3) (GE HealthCare Bio-Sciences, Uppsala, Sweden) in 50-ml centrifuge tubes. Cells were centrifuged at 900×g for 30 min to separate erythrocytes and polymorphonuclear cells from PBMCs. PBMCs were collected from the HBSS-Ficoll-Paque interface, washed with HBSS by centrifugation at 400×g for 10 min, lysed in 1 ml of Trizol and storage at -80 ⁰C until used. Total RNA was extracted from PBMCs using RNA Clean & Concentrator™-5 kit (Zymo Research, Irvine, CA, USA) following manufacturer’s instructions and stored at -80 ⁰C. The TruSeq Stranded Total RNA kit with Ribo-Zero Globin (Illumina, San Diego, CA, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The animals were treated with two different treatments: one group was inoculated with nine different commercial vaccines and the other one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium. Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and April of 2106, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.

tag: cell type

value: PBMC

tag: group

value: Adjuvant

value: tf

tag: sample source


title: IWAT_CON_rep2


title: R_5

value: male


title: R_10


title: R_8


title: NR_10

source_name: diet-induced obesity resistant (DIO non-responder)


title: NR_7


title: R_6


title: 111-B (RNA-Seq)


title: R_4


title: NR_9


title: NR_8


title: A. thaliana-untreated-smRNA-rep1

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

institute: University of Copenhagen

description:
Small RNA libraries were prepared using “The NEBNext Multiplex Small RNA” kit according to manufactures protocol
arabidopsis_tRNA_out.txt

data_processing:
Sequencing reads were processed with Cutadapt (version 1.14) to remove adapter sequences using the setting -a AGATCGGAAGAGCACACGTCT. For reads generated nextseq platform, the option --nextseq-trim=20” was included.
All samples (except small RNA-Seq experiments): The RNAProbR preprocessing.sh script (http://people.binf.ku.dk/~jvinther/data/rna_probing/) was used to remove the 7 base barcode from the sequencing read using the options “-b NNNNNNN -t 9”
Reads were aligned with bowtie2 (version 2.2.3) using high sensitivity options “--local -N 1 -D 20 -R 3 -L 15”
All samples (except small RNA-Seq experiments): Potential PCR duplicates among the sequencing reads were removed by discarding all but one of the reads having identical barcode and mapping to the same position using the collapse.sh script (available at http://people.binf.ku.dk/jvinther/data/RNA-seq).
The mapped reads for the control and NaBH4 treated samples were processed with the mpileup tool from the samtools package (version 1.7).
Genome_build: E. coli strain bw25113 (ensembl cDNA release 87), S. cerevisiae (ensembl cDNA release 84). rRNA sequences were obtained were obtained from the CRW database (http://www.rna.ccbb.utexas.edu). tRNA sequences were obtained from the genomic tRNA database (http://gtrnadb.ucsc.edu/index.html).
Supplementary_files_format_and_content: The mutation frequency file is the output from the GetFreq function (available at https://github.com/jeppevinther/m7g_map_seq) includes a number of statistics for each position, including coverage,  mutation frequency for the treated and control samples and the mutation rate difference between the treated and control samples. It includes p-values for the observed mutation rates being different in the treated and the control samples and for the replicate samples being different.

organism: Arabidopsis thaliana

source_name: Arabidopsis, Col-0 genotype

extract_protocol:
Hot acid phenol extraction
RNA-seq: Methods in molecular biology, 1038, 213-231 (2013) with RNA fragmentation step included.  Small RNA-seq: NEBNext Multiplex Small RNA Kit.

tag: nabh4 treatment


title: A. thaliana-untreated-smRNA-rep3


title: A. thaliana-NaBH4 treated-smRNA-rep1

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: A. thaliana-NaBH4 treated-smRNA-rep3


title: A. thaliana-NaBH4 treated-smRNA-rep2


title: A. thaliana-untreated-smRNA-rep2


title: NR_1


title: R_7


title: R_2


title: NR_2


title: R_1


title: NR_6


title: NR_4


title: NR_5


title: 125-B* (RNA-Seq)

value: Vaccine


title: NR_3


title: R_3


title: 125-B (RNA-Seq)


title: 124-B (RNA-Seq)


title: 114-A (RNA-Seq)


title: 116-A (RNA-Seq)


title: 125-A (RNA-Seq)


title: 124-A (RNA-Seq)


title: 111-A (RNA-Seq)


title: MNase_YPD30_WT-B_166_80U.sgr.gz

first: Sam

last: Cutler

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch Cancer Research Center

library_source: genomic

data_processing:
Align with tophat: $ tophat2 -p 4 -G ~/GenomeIndex/Saccharomyces_cerevisiae.EF4.65.gtf -I 200 -o tophat_out ~/GenomeIndex/yeast *R1_merged.fastq *R2_merged.fastq
Sort and filter with samtools: $ samtools sort accepted_hits.bam FILENAME_sorted       $ samtools view -b -f 67 -F 256 *sorted.bam -o FILENAME_sorted_filtered.bam $ samtools view *sorted_filtered.bam -o FILENAME_sorted_filtered.sam
Custom Python script that infers the center of each paired end read (which we interpret as the dyad, center of nucleosome-protected DNA fragment), and plots that in an .sgr file.
.sgr coverage file has 3 columns, column 1 = chromosome (chrI, chrVI, etc.), column 2 = basepair, column 3 = signal at that basepair
Custom Python script that calculates the average read depth at each base pair in the genome, and divides the signal at each base pair by that value, thus normalizing each sample for read depth.
Genome_build: Saccharomyces_cerevisiae.EF4.65.gtf
Supplementary_files_format_and_content: sgr

organism: Saccharomyces cerevisiae

source_name: Asynchronous growth in liquid YPD

growth_protocol: Saturated YPD cultures were inoculated into 100 ml fresh YPD, shaken overnight at 180 RPM at 30 degrees C, and then cells were collected at mid-log phase, OD660 ~ 0.5-0.8.

extract_protocol:
Cells were spheroplasted with zymolyase, then digested with MNase and exonuclease, treated with Proteinase K and RNase A, extracted with phenol:chloroform:IAA and ethanol precipitation.
Samples were generally digested with 40 units of MNase, but a few samples also treated with 20U or 80U for control experiments.
In all experiments, digested DNA was run on a low-melt agarose gel, the mononucleosomal band was gel-purified, and this DNA was sequenced.
Libraries prepared with Nugen Ovation Ultralow System V2 (catalog # 0344-32).

treatment_protocol: Collected cells were formaldehyde cross-linked, washed in water.

tag: digest

value: micrococcal nuclease (MNase) and exonuclease I


title: MNase_YPD30_nhp10-B_3333_40U.sgr.gz


title: MNase_YPD30_WT-B_166_40U.sgr.gz


title: MNase_YPD30_WT-B_166_20U.sgr.gz


title: MNase_YPD30_isw2nhp10-D_2109_40U.sgr.gz


title: MNase_YPD30_isw2nhp10-E_3337_40U.sgr.gz


title: E. coli-WT-NaBH4 treated-mRNA-rep2

description:
Libraries were prepared from total RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The DNA was amplified with PCR using primers compatible with Illumina sequencing.
coli_mrna_rrna_out.txt

organism: Escherichia coli

source_name: bacteria


title: MNase_YPD30_isw2-B_3320_40U.sgr.gz


title: MNase_YPD30_isw2nhp10-B_3337_80U.sgr.gz


title: E. coli-WT-NaBH4 treated-mRNA-rep1


title: MNase_YPD30_isw2nhp10-B_3337_20U.sgr.gz


title: MNase_YPD30_isw2nhp10-B_3337_40U.sgr.gz


title: E. coli-WT-NaBH4 treated-mRNA-rep3


title: E. coli-WT-untreated-mRNA-rep3


title: E. coli-WT-untreated-mRNA-rep2


title: 121-A (RNA-Seq)


title: MNase_YPD23_WT-A_166_40U.sgr.gz


title: 121-B (RNA-Seq)


title: E. coli-WT-untreated-mRNA-rep1


title: E. coli-RsmG KO-NaBH4 treated-total RNA

description:
Libraries were prepared from total RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The DNA was amplified with PCR using primers compatible with Illumina sequencing.
srsmg_coli_out.txt

value: BW25113 RsmG KO


title: MNase_YPD23_isw2nhp10-A_3337_40U.sgr.gz


title: MNase_YPD23_isw2nhp10-C_2109_40U.sgr.gz


title: 114-B (RNA-Seq)


title: E. coli-WT-NaBH4 treated-total RNA

description:
Libraries were prepared from total RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The DNA was amplified with PCR using primers compatible with Illumina sequencing.
swt_coli_out.txt


title: MNase_YPD23_isw2-A_3320_40U.sgr.gz


title: Pol2_YPD30_WT-B_6916_IP

data_processing:
Align with bowtie: $ bowtie2 -x <reference-genome> -U <file>.fastq -S <file>-mapped.sam
Filter and sort with samtools: $ samtools view -S -b -o <file>mapped_unique.bam -F 256 <file>mapped.sam       $ samtools sort <file>unique.bam <file>mapped_unique_sorted
Generate coverage file with genomecoveragebed: $ genomeCoverageBed -d -ibam <file>sorted.bam -g <file>.fastq > <file>coverage.sgr    --> .sgr coverage file has 3 columns, column 1 = chromosome (chrI, chrVI, etc.), column 2 = basepair, column 3 = signal at that basepair
Custom Python script that calculates the average read depth at each base pair in the genome, and divides the signal at each base pair by that value, thus normalizing each sample for read depth.
Custom Python script that calculates the ratio between the normalized signal at each base pair in the IP sample relative to the matched input sample.
Genome_build: Saccharomyces_cerevisiae.EF4.65.gtf

growth_protocol: Saturated YPD cultures were inoculated into 70 ml fresh YPD and then shaken overnight at 180 RPM at 30 degrees C, and then cells were collected at mid-log phase, OD660 ~ 0.5-0.8.

extract_protocol:
Cells were broken by bead-beating, chromatin was sonicated, stored in FA buffer.
Libraries prepared with Nugen Ovation Ultralow System V2 (catalog # 0344-32).

treatment_protocol: Collected cells were formaldehyde cross-linked, washed in TBS.

tag: chip antibody

value: Sigma anti-FLAG monoclonal (F3165)


title: Pol2_YPD30_WT-B_6916_input

value: none (input)


title: E. coli-RsmG KO-untreated-total RNA


title: Pol2_YPD30_WT-A_6915_input


title: MNase_YPD23_nhp10-A_3333_40U.sgr.gz


title: E. coli-WT-untreated-total RNA


title: Pol2_YPD30_nhp10-A_6919_input


title: Pol2_YPD30_nhp10-B_6920_input


title: Pol2_YPD30_WT-A_6915_IP


title: Pol2_YPD30_isw2nhp10-B_6922_input


title: Pol2_YPD30_isw2nhp10-A_6921_input


title: Pol2_YPD30_isw2nhp10-B_6922_IP


title: Pol2_YPD30_nhp10-A_6919_IP


title: Pol2_YPD30_isw2nhp10-A_6921_IP


title: Pol2_YPD30_isw2-B_6918_input


title: Pol2_YPD30_isw2-B_6918_IP


title: Pol2_YPD30_isw2-A_6917_IP


title: Pol-III_YPD30_isw2nhp10_6693_input


title: Pol2_YPD30_nhp10-B_6920_IP


title: Pol-III_YPD30_isw2nhp10_6693_IP


title: Pol-III_YPD30_WT_6686_input


title: Pol-I_YPD30_isw2nhp10_6673_input


title: Pol-III_YPD30_WT_6686_IP


title: Pol-I_YPD30_isw2nhp10_6673_IP


title: Pol2_YPD30_isw2-A_6917_input


title: Pol-I_YPD30_WT_6679_IP


title: Serum_AA6

city: San Francisco

first: Heather

middle: H

last: Pua

state: CA

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

data_processing:
data filtering step: Data was demultiplexed and adapters trimmed using FastX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and cutadapt (Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10.)
alignment: Sequence alignment and small RNA read counts were obtained using the exceRpt small RNA-seq Pipeline (v4) (https://www.genboree.org/epigenomeatlas/genboreeWorkbench.rhtml).
expression analysis: Comparative expression analysis was performed with DESeq2 (PMID:25516281)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain raw read counts from the exceRpt small RNA-seq Pipeline. The supplementary file DESeq2norm_AAexRNA_rpm contains DESeq2 normalized rpm counts for each sample.

source_name: Serum

extract_protocol:
Blood was drawn slowly from the inferior vena cava immediately postmortem into a 1 or 3ml syringe using a 23G needle to limit hemolysis and collected into a microtainer serum separator tube. Serum was isolated by centrifugation at 6000 rpm for 3 minutes, followed by centrifugation at 1200 g for 20 minutes to remove residual red blood cells. Serum from one mouse (approximately 200ul) was lysed in Trizol LS.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
20-65ng of total RNA was used to build miRNA librarires as previously described (PMID 23440203) with slight modification. Five random nucleotides were added to the 5’ end of the 3’ oligodeoxynucleotide adapterto reduce ligation bias. A mix of calibrators 1, 2, 3, 4 and 7 from the orginal publication were used at a final combined concentration of 0.025nM in the 3’ ligation reaction.

treatment_protocol: Mice were injected intraperitoneally weekly for 3-4 weeks with 50 ug ovalbumin in 100 ul of PBS plus 100 ul of Imject alum. Starting 7 days after the last injection, mice were challenged daily by oropharyngeal aspiration of 50 ug OVA in 20 ul of PBS for three consecutive days. Specimens were collected on day 4 after the first lung challenge.

value: Blood

tag: tissue biofluid

value: Serum

tag: treatment group

value: intrapertioneal immunization and airway challenge (allergic)


title: Serum_AA7


title: Serum_AA5


title: H3_YPD30_isw2nhp10-B_2109_input

data_processing:
Align with bowtie: $ bowtie2 -x <reference-genome> -U <file>.fastq -S <file>-mapped.sam
Filter and sort with samtools: $ samtools view -S -b -o <file>mapped_unique.bam -F 256 <file>mapped.sam       $ samtools sort <file>unique.bam <file>mapped_unique_sorted
Generate coverage file with genomecoveragebed: $ genomeCoverageBed -d -ibam <file>sorted.bam -g <file>.fastq > <file>coverage.sgr    --> .sgr coverage file has 3 columns, column 1 = chromosome (chrI, chrVI, etc.), column 2 = basepair, column 3 = signal at that basepair
Custom Python script that calculates the average read depth at each base pair in the genome, and divides the signal at each base pair by that value, thus normalizing each sample for read depth.
Custom Python script that calculates the log2 ratio between the normalized signal at each base pair in the IP sample relative to the matched input sample.
Custom Python script that Z-score normalizes based on average read depth at TSSs (approach described in Rodriguez and Tsukiyama, Genes & Development 2012)
Genome_build: Saccharomyces_cerevisiae.EF4.65.gtf


title: Serum_AA4


title: H3_YPD30_isw2nhp10-B_2109_IP

value: Abcam anti-histone H3 C-term (ab1791)


title: Pol-I_YPD30_WT_6679_input


title: Serum_AA3


title: H3_YPD30_isw2nhp10-A_3337_input


title: Serum_AA2


title: Serum_AA1


title: Serum_IMM3

treatment_protocol: Mice were injected intraperitoneally weekly for 3-4 weeks with 50 ug ovalbuminin 100 ul of PBS plus 100 ul of Imject alum. Starting 7 days after the last injection, mice were challenged daily by oropharyngeal aspiration of 20 ul of PBS alone for three consecutive days. Specimens were collected on day 4 after the first lung challenge.

value: intrapertioneal immunization


title: H3_YPD30_isw2nhp10-A_3337_IP


title: Serum_IMM2


title: 454153_A01

city: Philadelphia

first: Jay

middle: S

last: Schneider

state: PA

address: 1020 Locust St

department: Anatomy,Pathology and Cell biology

institute: Thomas Jefferson University

description:
LPN- 150ppm - Methylation
MeDIP_Hippocampus

hyb_protocol: The immunoprecipitated CpG-methylated DNA (test, experimental samples) and the untreated, sonicated DNA (input DNA) were differentially labeled and hybridized to a single array as a two-color experiment (Rat DNA Methylation 3 × 720 K CpG Island Plus RefSeq Promoter Array (GPL 18610) for 20 h at 42°C, followed by washing with the Nimblegen Wash Kit.

scan_protocol: Scanning was performed with 100% gain and double pass for optimal sensitivity and scanning accuracy.

data_processing:
Raw data were extracted as pair files by NimbleScan software.  The intensity ratio of immunoprecipitated to control DNA was plotted versus genomic position to identify regions where increased signal (i.e. DNA fragment enrichment) was present relative to the control sample. The R/Bioconductor package Ringo was utilized to extract the green (Cy3, 532nm, associated to total DNA) and red (Cy5, 635nm, associated to MeDIP fraction) channels from the provided pair files.  Normalization of the probe intensities was carried out by applying the Nimblegen algorithm, following the recommendation of Adriaens et al. for ChIP-on-chip and DNA methylation microarrays (Adriaens et al., 2012).
Signals from the two channels were then summarized by calculating the log2 ratio of the MeDIP and input channels.  Being log2-ratios, a value of 1 corresponds to a two-fold enrichment of the MeDIP signal relative to total DNA, while a value of -1 is interpreted as a MeDIP signal two times smaller than the input channel. The normalized data for the control "RANDOM" probes are available on the series record.

organism: Rattus norvegicus

source_name: MeDIP DNA_LPN- 150ppm - Methylation

label_protocol: Experimental (IP) samples were labeled with Cy5 and control (input) samples with Cy3.

extract_protocol: Genomic DNA was extracted from hippocampus tissue samples using PureGene DNA isolation kits.

tag: Sex

value: Male

value: hippocampus

value: Long-Evans

source_name: Input DNA_LPN- 150ppm - Methylation


title: Serum_IMM1


title: H3_YPD30_nhp10-B_2060_input


title: 454431_A01

description:
LPN - 150ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_LPN - 150ppm - Methylation

value: Female

source_name: Input DNA_LPN - 150ppm - Methylation


title: 454153_A02


title: 454259_A01


title: 454148_A01


title: 454157_A01

description:
LPN - 375ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_LPN - 375ppm - Methylation

source_name: Input DNA_LPN - 375ppm - Methylation


title: 454161_A01


title: 453916_A03


title: 453777_A02


title: 454153_A03


title: 454434_A03


title: Serum_IMM4


title: 454006_A03


title: 454146_A03


title: Serum_CTR3

treatment_protocol: No treatment

value: untreated


title: Serum_CTR2


title: 454159_A03


title: H3_YPD30_nhp10-B_2060_IP


title: 454150_A03


title: Serum_CTR1


title: 454150_A02


title: 454198_A03

description:
LPN - 750ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_LPN - 750ppm - Methylation

source_name: Input DNA_LPN - 750ppm - Methylation


title: 454428_A03


title: Pellet_AA7

source_name: Hematopoeitic cell rich cell pellets from brochoalveolar lavage

extract_protocol:
Bronchoalveolar lavage was performed with 1 ml of cold PBS. BAL fluid was centrifuged at 500 g for 5 minutes and the hematopoeitic cell rich pellet lyzed in Trizol.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
20-65ng of total RNA was used to build miRNA librarires as previously described (PMID 23440203) with slight modification. Five random nucleotides were added to the 5’ end of the 3’ oligodeoxynucleotide adapterto reduce ligation bias. A mix of calibrators 1, 2, 3, 4 and 7 from the orginal publication were used at a final combined concentration of 0.025nM in the 3’ ligation reaction.

value: Lung

value: Bronchoalveolar Lavage


title: Pellet_AA6


title: Pellet_AA4


title: H3_YPD30_nhp10-A_3333_input


title: H3_YPD30_nhp10-A_3333_IP


title: 454120_A01

description:
LPN- 375ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_LPN- 375ppm - Methylation

source_name: Input DNA_LPN- 375ppm - Methylation


title: H3_YPD30_isw2-B_6809_IP


title: Pellet_AA1


title: Pellet_IMM4


title: 454120_A02


title: Pellet_AA3


title: Pellet_AA2


title: 454259_A02


title: Pellet_IMM3


title: 454006_A02


title: 454434_A02


title: 453916_A02


title: H3_YPD30_isw2-A_3320_input


title: Pellet_IMM2


title: Pellet_CTR3


title: Pellet_IMM1


title: 453777_A01


title: H3_YPD30_isw2-A_3320_IP


title: Pellet_CTR2


title: H3_YPD30_WT-B_166_input


title: H3_YPD30_WT-B_166_IP


title: Pellet_CTR1


title: Epith_AA3

source_name: Lung epithelial brushings

extract_protocol:
Lung epithelial brushings were performed as previously described (PMID: 22232213) and cells from 1-3 mice lysed in Trizol.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
20-65ng of total RNA was used to build miRNA librarires as previously described (PMID 23440203) with slight modification. Five random nucleotides were added to the 5’ end of the 3’ oligodeoxynucleotide adapterto reduce ligation bias. A mix of calibrators 1, 2, 3, 4 and 7 from the orginal publication were used at a final combined concentration of 0.025nM in the 3’ ligation reaction.

value: Lung epithelial brushings


title: H3_YPD30_WT-A_166_input


title: Epith_IMM2


title: Epith_AA2


title: 454161_A03


title: Epith_IMM1


title: H3_YPD30_WT-A_166_IP


title: Nhp10_YPD30_Nhp10-B_3427_input


title: Epith_AA1


title: 454256_A02


title: Epith_CTR1


title: BALF_AA7

source_name: Bronchoalveolar Lavage Fluid

extract_protocol:
Bronchoalveolar lavages were performed with 1 ml of cold PBS. BAL fluid was centrifuged at 500 g for 5 minutes to separate cell free BALF supernatant
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
20-65ng of total RNA was used to build miRNA librarires as previously described (PMID 23440203) with slight modification. Five random nucleotides were added to the 5’ end of the 3’ oligodeoxynucleotide adapterto reduce ligation bias. A mix of calibrators 1, 2, 3, 4 and 7 from the orginal publication were used at a final combined concentration of 0.025nM in the 3’ ligation reaction.

value: Bronchoalveolar Lavage Fluid


title: BALF_AA6


title: BALF_AA5


title: BALF_AA4


title: Nhp10_YPD30_Nhp10-B_3427_IP


title: BALF_AA3


title: BALF_AA1


title: H3_YPD30_isw2-B_6809_input


title: BALF_AA2


title: BALF_IMM4


title: BALF_IMM3


title: Isw2_YPD30_Isw2-B_1997_input


title: Nhp10_YPD30_Nhp10-A_3426_IP


title: BALF_IMM1


title: BALF_CTR3


title: Isw2_YPD30_Isw2-A_1996_input


title: BALF_CTR2


title: BALF_CTR1

extract_protocol:
Bronchoalveolar lavage was performed with 1 ml of cold PBS. BAL fluid was centrifuged at 500 g for 5 minutes and 500ul of cell-free BALF supernatant lysed in Trizol LS.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
20-65ng of total RNA was used to build miRNA librarires as previously described (PMID 23440203) with slight modification. Five random nucleotides were added to the 5’ end of the 3’ oligodeoxynucleotide adapterto reduce ligation bias. A mix of calibrators 1, 2, 3, 4 and 7 from the orginal publication were used at a final combined concentration of 0.025nM in the 3’ ligation reaction.


title: 453899_A01


title: Pellet_AA5


title: 453954_A02


title: Isw2_YPD30_Isw2-A_1996_IP