title: mets participant 7, adipose tissue, pre meal 0 hours, dairy meal intervention


title: mets participant 8, adipose tissue, post meal 4 hours, dairy meal intervention

status: Public on Dec 01 2020

type: RNA

city: Notting Hill

first: Aimee

last: Dordevic

state: VIC

address: Level 1, 264 Ferntree Gully Rd

department: Nutrition, Dietetics & Food

country: Australia

institute: Monash University

hyb_protocol: Labelled cRNA samples were hybridized to Illumina Human WG-6 v3 arrays overnight

scan_protocol: Washed and acanned on the Illumina iScan, then the resulting image files were analysed using Illumina Beadstudio software to annotate the genes and generate quantitative expression scores with mean, standard deviation and statistical evaluation of detection reliability averaged across the 30-50 built in technical replicates for each transcript.

data_processing: Analysed using Illumina Beadstudio software; Data were pre-processed using the functions of the R/Bioconductor packages lumi and limma in ArrayAnalysis (http://arrayanalysis.org/), background was subtracted and data were quantile normalised.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: According to Illumina protocol; RNA was reverse transcribed using a T7-promoter-oligo (dT) primer, followed by an in vitro transcription reaction with biotin-labeled nucleotides

extract_protocol: RNA was extracted using miRNeasy Mini Kit following the manufactures protocol, and on-column DNase treatment (Qiagen) was performed.

treatment_protocol: A randomised, crossover, single meal study. Participants were provided with a standarised evening meal, fasted overnight, then presented at the laboratory between 7-8am. The participants rested for 30 minutes then an adipose tissue sample was collected from the lateral periumbilical region of the subcutaneous abdominal area. Adipose tissue from each biopsy was washed in ice-cold phosphate-buffered saline (PBS) to eliminate blood and immediately frozen and stored in liquid nitrogen. Participants consumed either a dairy-based or a soy-based, high-fat breakfast within 15 minutes. Postprandial adipose tissue biopsies were collected at  4 hours.

tag: disease

value: metabolic syndrome

tag: tissue

value: adipose

tag: Sex

value: male


title: mets participant 6, adipose tissue, pre meal 0 hours, soy meal intervention


title: mets participant 5, adipose tissue, post meal 4 hours, soy meal intervention


title: mets participant 7, adipose tissue, post meal 4 hours, dairy meal intervention


title: mets participant 6, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B2_ad007

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

value: brain

tag: source

value: SSp

tag: target

value: MY

tag: gender

value: female


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B4_ad008


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B2_ad002

value: MOp


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B2_ad001


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B2_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B1_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B1_ad010


title: mets participant 5, adipose tissue, pre meal 0 hours, soy meal intervention


title: mets participant 5, adipose tissue, pre meal 0 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B2_ad008


title: mets participant 4, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B1_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B1_ad002


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B12_ad010


title: mets participant 5, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B12_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_C3_ad006


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B12_ad008


title: mets participant 3, adipose tissue, pre meal 0 hours, soy meal intervention


title: mets participant 3, adipose tissue, post meal 4 hours, soy meal intervention


title: mets participant 4, adipose tissue, pre meal 0 hours, dairy meal intervention


title: mets participant 4, adipose tissue, post meal 4 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B12_ad002


title: mets participant 3, adipose tissue, pre meal 0 hours, dairy meal intervention


title: mets participant 4, adipose tissue, pre meal 0 hours, soy meal intervention


title: mets participant 2, adipose tissue, post meal 4 hours, soy meal intervention


title: mets participant 8, adipose tissue, pre meal 0 hours, dairy meal intervention


title: mets participant 2, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B11_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B11_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B11_ad008


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B12_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B11_ad002


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B10_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B10_ad008


title: mets participant 3, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B10_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B12_ad001


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B10_ad006


title: mets participant 2, adipose tissue, pre meal 0 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_B10_ad004


title: mets participant 1, adipose tissue, post meal 4 hours, dairy meal intervention


title: mets participant 2, adipose tissue, pre meal 0 hours, dairy meal intervention


title: mets participant 1, adipose tissue, post meal 4 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A9_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_C2_ad008


title: ctrl participant 10, adipose tissue, post meal 4 hours, soy meal intervention

value: control


title: ctrl participant 10, adipose tissue, pre meal 0 hours, soy meal intervention


title: mets participant 1, adipose tissue, pre meal 0 hours, soy meal intervention


title: mets participant 1, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 10, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 9, adipose tissue, post meal 4 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A9_ad002


title: ctrl participant 9, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 9, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A8_ad008


title: ctrl participant 8, adipose tissue, pre meal 0 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A8_ad006


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A8_ad002


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A7_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A7_ad008


title: ctrl participant 9, adipose tissue, pre meal 0 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A7_ad010


title: ctrl participant 10, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A8_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A6_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A7_ad001


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A6_ad002


title: ctrl participant 8, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 7, adipose tissue, post meal 4 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A6_ad010


title: ctrl participant 7, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 6, adipose tissue, pre meal 0 hours, soy meal intervention


title: ctrl participant 6, adipose tissue, post meal 4 hours, dairy meal intervention


title: ctrl participant 8, adipose tissue, post meal 4 hours, soy meal intervention


title: ctrl participant 6, adipose tissue, post meal 4 hours, soy meal intervention


title: ctrl participant 5, adipose tissue, post meal 4 hours, dairy meal intervention


title: ctrl participant 7, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A5_ad012


title: ctrl participant 5, adipose tissue, pre meal 0 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A6_ad012


title: ctrl participant 6, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 7, adipose tissue, pre meal 0 hours, soy meal intervention


title: ctrl participant 8, adipose tissue, post meal 4 hours, dairy meal intervention


title: ctrl participant 5, adipose tissue, post meal 4 hours, soy meal intervention


title: ctrl participant 5, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 4, adipose tissue, post meal 4 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A5_ad008


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A6_ad008


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A4_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A4_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A5_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A4_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A3_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A3_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A4_ad001


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A3_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A3_ad002


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A2_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A2_ad010


title: ctrl participant 4, adipose tissue, pre meal 0 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A2_ad006


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A2_ad007


title: ctrl participant 4, adipose tissue, post meal 4 hours, dairy meal intervention


title: ctrl participant 3, adipose tissue, post meal 4 hours, soy meal intervention


title: ctrl participant 3, adipose tissue, pre meal 0 hours, soy meal intervention


title: ctrl participant 4, adipose tissue, pre meal 0 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A5_ad001


title: ctrl participant 2, adipose tissue, post meal 4 hours, soy meal intervention


title: ctrl participant 3, adipose tissue, post meal 4 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A4_ad006


title: ctrl participant 2, adipose tissue, pre meal 0 hours, soy meal intervention


title: ctrl participant 1, adipose tissue, post meal 4 hours, dairy meal intervention


title: ctrl participant 3, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ctrl participant 1, adipose tissue, pre meal 0 hours, soy meal intervention


title: ctrl participant 2, adipose tissue, pre meal 0 hours, dairy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A2_ad001


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A1_ad012


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A1_ad008


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A1_ad007


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A1_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A12_ad001


title: ctrl participant 1, adipose tissue, post meal 4 hours, soy meal intervention


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A11_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A11_ad012


title: ctrl participant 2, adipose tissue, post meal 4 hours, dairy meal intervention


title: Huh7_SMARCB1_11-3

city: seoul

first: Seong Hwi

last: Hong

address: 120 Neungdong-ro

department: School of Medicine

country: South Korea

institute: Konkuk University

description: Replicate 4

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: liver cancer cell line

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol reagent, digested with DNase I and reverse transcribed using a High Capacity cDNA Reverse Transcription Kit

treatment_protocol: shRNA were selected in the presence of 1.25 μg/mL puromycin.

tag: cell line

tag: genotype/variation

value: SMARCB1 knockdown


title: Huh7_SMARCB1_11-4

description: Replicate 4


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A12_ad010


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A10_ad012


title: Huh7_GFP_Con-2

description: Replicate 3


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A11_ad001


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A11_ad006


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A10_ad008


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A10_ad006


title: SKHep1_shcon_2

description: Replicate 1


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A10_ad004


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A10_ad002


title: SKHep1_shSMARCB1_11

description: Replicate 2


title: Huh7_GFP_Con-1

description: Replicate 3


title: SKHep1_shcon_1

description: Replicate 1


title: SKHep1_shSMARCB1_12

description: Replicate 2


title: ctrl participant 1, adipose tissue, pre meal 0 hours, dairy meal intervention


title: ahp4_dehydrated 5h_replicate 1

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

institute: texas tech university

description:
Gene expression data from dehydrated ahp4
ahp4-D5_1

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX12.6.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: ahp4, dehydrated 5h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  µg RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and ahp4 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 5h.

tag: genotype/variatino

value: ahp4 mutant

value: rosette leaves

value: 24 day-old

tag: stress

value: dehydrated

tag: time


title: ahp4_dehydrated 5h_replicate 3

description:
Gene expression data from dehydrated ahp4
ahp4-D5_3


title: ahp4_dehydrated 2h_replicate 3

description:
Gene expression data from dehydrated ahp4
ahp4-D2_3

source_name: ahp4, dehydrated 2h


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad010

value: RSP

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad008


title: ahp4_dehydrated 2h_replicate 2

description:
Gene expression data from dehydrated ahp4
ahp4-D2_2


title: Rpd3-V5_Input

city: Salt Lake City

first: David

middle: J

last: Stillman

state: Utah

address: 15 N Medical Drive East, EEJMRB

department: Pathology

institute: University of Utah

data_processing:
Fastq files were aligned to sacCer3 using Novocraft Novoalign (v3.8.2) with options to trim Illumina adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) and allow for one random multi-alignment. Files were converted to Bam format with samtools (v1.5).
Replicate ChIP and corresponding Input Bam files were processed with Multi-Replicate Macs2 ChIPSeq Pipeline (version 8, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq), with options to sub-sample replicate fragments to 20%, exclude chrM and 2-micron chromosome, exclude custom high-copy intervals (telomeres and rDNA), depth-normalize to 1 million reads and average replicates, and call peaks using Macs2 (v. 2.1.0) with q-value cutoff of 2, peak size of 200 bp, peak gap of 100 bp, and depth normalized to 5 million reads. Normalized paired-end fragment coverage files were saved as bigWig files.
Genome_build: sacCer3
Supplementary_files_format_and_content: Paired-end fragment coverage files in bigWig format after duplicate sub-sampling, high-copy region exclusion, replicate averaging, and depth normalization to 1 million reads.

organism: Saccharomyces cerevisiae

source_name: log phase yeast cells

growth_protocol: Yeast cells were grown at 30°C in YPA medium (1% yeast extract, 2% bactopeptone, 0.002% adenine) supplemented with 2% dextrose to an OD660 of 0.7 to 0.9. Cells were cross-linked in 1% formaldehyde for 20 minutes at 25°C (Ash1-V5) or overnight at 4°C (Tup1-V5, Rpd3-V5) and quenched with the addition of 2.5M glycine to a final concentration of 125mM. Cells were harvested by centrifugation and washed twice in Tris-buffered saline and stored at -80°C.

extract_protocol:
Cells were resuspended in Lysis Buffer (0.1% deoxycholic acid, 1 mM EDTA, 50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton X-100, protease inhibitors) and lysed with ten 2-min rounds of bead beating with zirconia beads. Lysed cells were collected by centrifugation, washed once with Lysis Buffer and sonicated in fresh Lysis Buffer for 9 rounds of 30 seconds each with a Misonix sonicator, power level 3.5. Sonicated material was centrifuged, and supernatants were used for chromatin immunoprecipitations. Anti-mouse magnetic Dyna beads (Invitrogen) were prepared for immunoprecipitation by blocking with 1 mg/mL BSA overnight, followed by several hours of incubation with mouse anti-V5 antibody (Abcam). Normalized chromatin amounts were added to prepared Dyna beads and incubated overnight at 4°C with rotation. Beads were washed twice with Lysis Buffer, twice with Lysis Buffer supplemented up to 500 mM NaCl, twice with LiCl Wash Buffer (0.5% deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris pH 8.0) and once with TE. Protein-DNA complexes were eluted from the beads with Elution Buffer (50 mM Tris pH 8.0, 1% SDS, 10 mM EDTA) and incubated at 65°C overnight to reverse cross-links. Multiple identical ChIPs from each cell sample replicate were combined and purified using the MinElute PCR purification kit (QIAGEN), per manufacturer’s instructions.
NEB Next ChIP-Seq with dual index primers

treatment_protocol: Not applicable

value: DY17577 - MATa  RPD3-V5::HIS3MX

tag: strain background

tag: chip antibody


title: ahp4_well-watered (0h)_replicate 2

description:
Gene expression data from well-watered ahp4
ahp4-C_2

source_name: ahp4, well-watered

value: well-watered


title: ahp4_well-watered (0h)_replicate 3

description:
Gene expression data from well-watered ahp4
ahp4-C_3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad007


title: Tup1-V5_Input

value: DY17937 - MATa  TUP1-V5::HIS3MX


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad006

value: PTLp


title: ahp4_dehydrated 2h_replicate 1

description:
Gene expression data from dehydrated ahp4
ahp4-D2_1


title: Rpd3-V5_rep3

value: anti-V5 (SV5-Pk1; Abcam)


title: ahp4_dehydrated 5h_replicate 2

description:
Gene expression data from dehydrated ahp4
ahp4-D5_2


title: Rpd3-V5_rep2


title: Ash1-V5_Input

value: DY18407 - MATa  ASH1-V5::HIS3MX


title: ahp4_well-watered (0h)_replicate 1

description:
Gene expression data from well-watered ahp4
ahp4-C_1


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A8_ad004

value: brain

value: MY

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad001


title: WT_dehydrated 5h_replicate 3

description:
Gene expression data from dehydrated WT
WT-D5_3

source_name: WT, dehydrated 5h

value: WT


title: Ash1-V5_rep3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad012

value: female


title: Tup1-V5_rep3


title: Tup1-V5_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad002


title: WT_dehydrated 5h_replicate 1

description:
Gene expression data from dehydrated WT
WT-D5_1


title: Tup1-V5_rep2


title: Ash1-V5_rep2


title: Rpd3-V5_rep1


title: WT_dehydrated 2h_replicate 3

description:
Gene expression data from dehydrated WT
WT-D2_3

source_name: WT, dehydrated 2h


title: WT_dehydrated 5h_replicate 2

description:
Gene expression data from dehydrated WT
WT-D5_2


title: WT_dehydrated 2h_replicate 1

description:
Gene expression data from dehydrated WT
WT-D2_1


title: N1

city: shanghai

first: heming

last: huang

address: 1665 Kongjiang Road

country: China

institute: Xinhua Hospital, School of Medicine, Shanghai Jiaotong University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: treatment


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H9_ad004


title: N2


title: Ash1-V5_rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad008


title: M2


title: Input AthDNAb

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description:
Sample 11
Input DNA for samples 7-10

data_processing:
Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4

source_name: 10 days-old seedlings

growth_protocol: 10 days-old seedlings grown in MS medium

extract_protocol:
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.

tag: protein

value: Input DNA for samples 7-10

tag: gene id

tag: protein expression

value: Input DNA


title: DAP-bHLH17_rep1

description:
Sample 9
Protein-DNA interaction

value: E.coli expressed


title: M1

tag: tissue


title: input_wildtype_vehicle [chipseq_from_saha_treatment]

city: Goettingen

first: Md Rezaul

last: Islam

address: von siebold str. 3a

country: Germany

institute: DZNE

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
Raw data were mapped to mouse genome (mm10) using bowtie2 (v 2.0.2). Generated sam files were converted to bam files using samtools view (samtools v. 1.3.1). Bam files were sorted using samtools sort.
Sorted Bam files were filtered based on quality (-q 5) prior to removal of duplicates using samtools rmdup. Correlation patterns of the replicates were investigated using DEEPTOOLS (v. 3.0.1)
Highly correlatied replicate bam files from corresponding conditions were merged using samtools merge
merged bam files were used to investigate genome wide distribution of H3K4me3 using ngsplot(Shen et al, 2014). Distribution pattern in Input bam files from corresponding conditions were also visualized
Genome_build: mm10
Supplementary_files_format_and_content: processed data files contain macs2 peaks after removing the blacklisted peaks

source_name: hippocampal CA1

extract_protocol:
CA1 region of hippocapus was surgically dissected under microscope, snap frozen in liquid nitrogen and stored at -80c until further use. NeuN+ neuronal nuclei were FACS sorted and used to perform chromatin immunoprecipitation (ChIP) for H3K4me3
Chromatin immunoprecipitation was performed according to (Halder et al., 2016) with 0.2 µg chromatin and 1µg H3K4me3 (ab8580) antibody. ChIPseq library preparation was performed using NEBNext Ultra II DNA library preparation according to manufacturer’s protocol.
2nM libraries were pooled and sequenced in Illumina Hiseq 2000 with 50-bp single end reads.

treatment_protocol: transgenic mice were randomly distributed into two groups. While one group got access to Vorinostat in drinking water, the other drank vehicle containing drinking water. As control, littermate controls were used and vehicle was administered in drinking water. The experiment started when mice were 2 months old and continued for 4 weeks. Male mice were investigated for the experiment.

tag: genotype

value: wildtype

tag: agent

value: vehicle

tag: antibody

value: IgG


title: DAP-MYC4_rep2

description:
Sample 8
Protein-DNA interaction


title: wildtype_vehicle_3 [chipseq_from_saha_treatment]


title: M3

tag: age

tag: strain


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad006

tag: source

tag: target

value: VISp

tag: gender


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad004


title: WT_well-watered (0h)_replicate 2

description:
Gene expression data from well-watered WT
WT-C_2

source_name: WT, well-watered

tag: genotype/variatino

value: rosette leaves

value: 24 day-old

tag: stress

value: well-watered


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad002

value: PTLp


title: wildtype_vehicle_2 [chipseq_from_saha_treatment]

value: brain


title: anti-Myc IP of Myc-EhAgo2-3, total lysate [IPAgo3_TAP]

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

data_processing:
Basecalling was performed using Illumina Sequencing Data Analysis software
Adaptor sequences were removed from each read
Duplicate sequences were removed
Unique reads were filtered by removing all reads that mapped to genomic  tRNA, rDNA, LINES and SINES
Filtered reads were mapped to the genome using bowtie with the parameters: -v 1 --all
Genome_build: E. histoyiitca HM-1:IMSS  version 1.3 (http://amoebadb.org);E. invadens IP-1 version 1.3 (http://amoebadb.org)
Supplementary_files_format_and_content: txt files are bowtie output

organism: Entamoeba histolytica

source_name: E. histolytica trophozoites

growth_protocol: E. histolytica trohozoites were grown in TYI at 37°C; E. invadens was grown in standard axenic culture conditions (LYI @ 25°C); E. histolytica overexpressing cell lines are kept at 6μg/ml G418.

extract_protocol:
Parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS. RNA was isolated using Trizol (Invitrogen) following the manufacturer's protocol.
We used the NEBNext multiplex small RNA library prep set for Illumina (NEB#E7300S) and followed the manufacturer’s protocol with the following modifications: total RNA (25-50 µg) was first fractioned for the size 15-30nt RNA or 30-45nt RNA using 12% polyacrylamide urea gel. The size-selected RNA was then treated with tobacco acid pyrophosphatase [TAP] to convert 5’ poly-P to 5’ single-P (Epicentre) or RppH (NEB). The RNA sample was then fed into the pipeline as described in the manufacturer's protocol. Once the cDNA was made, the barcode primers were incorporated into each sample using PCR with kit’s provided barcoded primer; typically we used 8-12 PCR cycles to get a clear final PCR product band. The final PCR product was quantified using Nanodrop, and samples were pooled and shipped to the collaborator for Illumina sequencing. The platform MiSeq (Illumina) was used, the number
Sequencing of E. histolytica small RNAs for size-selected (30-45nt)  total RNA of E. histolytica trophozoites; from size-selected (30-45nt)  total RNAs of development of E. invadens; from IP-ed RNAs of EhAgo proteins and mutant.

treatment_protocol: The cell lysates for transfected cells: parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS and lysed by lysis buffer contains 20 mM Tris-HCl (pH 7.5), 1 mM MgCl2, 10% (v/v) glycerol and 50 mM NaCl, IGEPAL CA-630 (equivalent of NP-40) at 0.5% (v/v) plus 1mM NaF, 1mM DTT, 1mM PMSF and HALT EDTA free protease inhibitors (100x stock diluted to 2x)(Thermo Scientific) and RNase inhibitor (1 unit/ml).

tag: strain/genotype

tag: development stages

value: trophozoites

value: IP-ed RNA, cloned use TAP

tag: isolation method

value: IP-ed RNA  isolated by Trizol

tag: molecule subtype

value: small RNA


title: WT_well-watered (0h)_replicate 1

description:
Gene expression data from well-watered WT
WT-C_1

value: WT

tag: time


title: WT_dehydrated 2h_replicate 2

description:
Gene expression data from dehydrated WT
WT-D2_2

value: dehydrated


title: anti-Myc IP of Myc-EhAgo2-2, total lysate [IPAgo2_TAP]

tag: treatment


title: HSC-3-M3 rep3

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

country: Japan

institute: Fujita Health University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA was hybridized to the Agilent expression microarray according to the manufacturer's instruction.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Data processig was performed using Agilent Feature Extraction v11.0.1.1.

label_protocol: Labeled cRNA was prepared from total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: HSC-3 and HSC-3-M3 cells were maintained in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum.

extract_protocol: Total RNA was isolated using TRIzol reagent according to the manufacturer's instruction.

tag: cell type

value: tongue cancer cell

tag: cell line


title: HSC-3-M3 rep2


title: HSC-3 rep3


title: HSC-3-M3 rep4


title: HSC-3-M3 rep1


title: HSC-3 rep1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad012

tag: tissue

value: RSP

value: female


title: HSC-3 rep2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H8_ad001

value: male


title: DAP-bHLH17_rep2

description:
Sample 10
Protein-DNA interaction

tag: protein

tag: gene id

tag: protein expression

value: E.coli expressed


title: WT_well-watered (0h)_replicate 3

description:
Gene expression data from well-watered WT
WT-C_3

tag: age


title: wildtype_vehicle_1 [chipseq_from_saha_treatment]

tag: genotype

value: wildtype

tag: agent

value: vehicle

tag: antibody


title: anti-Myc IP of Myc-EhAgo2-2, nuclear lysate [IPAgo2_nuc_RppH]

value: IP-ed RNA, cloned use RppH


title: anti-Myc IP of Myc-EhAgo2-2, cytosolic lysate [IPAgo2_cyto_RppH]


title: input_transgenic_vehicle [chipseq_from_saha_treatment]

value: CamkdeltaC transgenic

value: IgG


title: transgenic_vehicle_4 [chipseq_from_saha_treatment]

value: brain


title: anti-Myc IP of Myc-EhAgo2-3, total lysate [IPAgo3_RppH]

value: trophozoites


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad008

tag: strain

tag: source

tag: target

value: VISp

tag: gender


title: HSC-3 rep4


title: anti-Myc IP of Myc-EhAgo2-2, total lysate [IPAgo2_RppH]

tag: strain/genotype

tag: development stages

tag: isolation method

value: IP-ed RNA  isolated by Trizol

tag: molecule subtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad007


title: transgenic_vehicle_3 [chipseq_from_saha_treatment]


title: anti-Myc IP of Myc-EhAgo2-1, total lysate [IPAgo1_RppH]

value: HM-1:IMSS, Myc-EhAgo2-1

tag: treatment

value: small RNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad006

tag: tissue

value: PTLp


title: anti-Myc IP of Myc-EhAgo2-1, total lysate [IPAgo1_TAP]

value: IP-ed RNA, cloned use TAP


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad004


title: CM_NoStress_MitoQ_rep1

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

description: PNM_v_PNS.counts; PNM_v_PSM.counts; PNM_v_PSS.counts

hyb_protocol: Samples were hybridised using the NanoString nCounter rat miRNA v1.5 Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

scan_protocol: Samples were analysed using the NanoString nCounter Analysis System (Gen2). See Gen2 Prep Station User Manual.

data_processing:
Raw output files were converted into lists of counts. To compare two groups, the respective raw counts were passed into RUVSeq for normalisation and removal of unwanted variation. Adjusted counts were then analysed for differential expression analysis using edgeR.
Normalised counts can be found in linked text files, instead of in the matrix table, as specified in the 'Description' column under the 'Samples' heading. Values are Reporter Probe signal intensities captured with the nCounter Analysis System and normalised using RUVSeq.

organism: Rattus norvegicus

source_name: placenta conditioned medium at E20, no stress, maternal MitoQ injection

label_protocol: Samples were labelled using the NanoString nCounter rat miRNA v1.5 Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

growth_protocol: Female Sprague-Dawley rats (initial body weight: 240–250g; Charles River, Margate, Kent, UK) were maintained on ad libitum standard rat chow and filtered tap water under a 12:12-h light-dark cycle (lights on at 07:00h). Rats were group housed (4-6/cage) in individually ventilated cages until gestational day (GD) 16 and individually thereafter.

extract_protocol: Foetal blood was collected into EDTA-containing tubes, pooled per litter, and plasma was extracted. Placentae were isolated, placed into cell culture medium and incubated for 24 h. Total RNA was extracted from 100 μl foetal plasma using the Qiagen miRNeasy Serum/Plasma Kit or from 200 μl filtered conditioned media using the Qiagen miRNeasy Mini Kit.

treatment_protocol: On GD16, pregnant rats were weighed and 4% (w/w) lidocaine cream was applied topically to the tail prior to administration of either 0.9% sterile saline (vehicle; 0.34 ml/kg) or 125 µM nanoparticle-bound mitoquinone (MitoQ-NP; 0.34 ml/kg) i.v. into the tail vein. Approximately 1 h later, half of the vehicle and MitoQ-NP-treated rats were exposed to 10 min social stress, while the remainder served as non-stressed controls and remained undisturbed in their home cage. Social stress was induced using a modified resident-intruder paradigm.

value: Sprague-Dawley

value: Female

tag: foetal age

value: Placenta

tag: maternal exposure

value: No stress

tag: maternal injections

value: MitoQ-NP


title: CM_NoStress_MitoQ_rep3


title: CM_NoStress_MitoQ_rep2


title: HM1 Basal growth [HM1_35]

value: size-selected at 30-45nt, cloned use TAP

value: RNA isolated by mirVana kit


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad010

tag: age

value: RSP

value: male


title: transgenic_vehicle_1 [chipseq_from_saha_treatment]

value: brain

tag: genotype

value: CamkdeltaC transgenic

value: vehicle


title: transgenic_vehicle_2 [chipseq_from_saha_treatment]

tag: agent


title: input_transgenic_vorinostat [chipseq_from_saha_treatment]

value: Vorinostat

tag: antibody

value: IgG


title: CM_NoStress_Saline_rep3

description: PNM_v_PNS.counts; PNS_v_PSM.counts; PNS_v_PSS.counts

source_name: placenta conditioned medium at E20, no stress, maternal saline injection

tag: strain

value: Saline


title: CM_NoStress_Saline_rep2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H7_ad001

tag: source

value: PTLp

value: VISp


title: anti-Myc IP of Myc-EhAgo2-2△NLS-DR, total lysate [IPAgo2_mut_RppH]

value: trophozoites

value: IP-ed RNA, cloned use RppH

value: IP-ed RNA  isolated by Trizol

value: small RNA


title: transgenic_vorinostat_4 [chipseq_from_saha_treatment]


title: CM_NoStress_Saline_rep1

value: Sprague-Dawley

value: Female

value: Placenta

value: No stress


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H6_ad012

value: RSP

tag: target

value: female


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H6_ad010

value: brain

tag: gender

value: male


title: transgenic_vorinostat_3 [chipseq_from_saha_treatment]

value: CamkdeltaC transgenic

value: Vorinostat


title: CM_Stress_MitoQ_rep2

description: PNM_v_PSM.counts; PNS_v_PSM.counts; PSM_v_PSS.counts

source_name: placenta conditioned medium at E20, maternal stress, maternal MitoQ injection

value: Stress

value: MitoQ-NP


title: CM_Stress_Saline_rep2

description: PNM_v_PSS.counts; PNS_v_PSS.counts; PSM_v_PSS.counts

source_name: placenta conditioned medium at E20, maternal stress, maternal saline injection

value: Saline


title: CM_Stress_MitoQ_rep3


title: CM_Stress_MitoQ_rep1


title: transgenic_vorinostat_2 [chipseq_from_saha_treatment]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H6_ad006

source_name: C57BL/6J P56 Mouse Brain

value: PTLp

value: VISp


title: Plasma_NoStress_MitoQ_rep3

description: FNM_v_FNS.counts; FNM_v_FSM.counts; FNM_v_FSS.counts

source_name: foetal plasma at E20, no stress, maternal MitoQ injection

value: Plasma


title: CM_Stress_Saline_rep1


title: Plasma_NoStress_Saline_rep3

description: FNM_v_FNS.counts; FNS_v_FSM.counts; FNS_v_FSS.counts

source_name: foetal plasma at E20, no stress, maternal saline injection


title: Plasma_NoStress_MitoQ_rep2


title: CM_Stress_Saline_rep3


title: 190425_CEMBA_mm_P53_P63_RS2_190425_P1_190425_P2_A11_ad007

value: SSp

value: MY


title: transgenic Vorinostat/SAHA [C_9]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
samples were mapped to mouse genome (mm10) and microRNA counts were generated using miRDeep2
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv file contains unprocessed raw microRNA counts. normalized_all_conditions_Mxe.csv contains log2 normalized counts after regressing the effects due to library size, gender, sample batches (birth, sequencing lane, preparation), RNA quality, body weight, heart weight, lung weight, left ventricle weight, tibia length, sequencing lane and other latent covariates as determined by Sva package in R
Supplementary_files_format_and_content: Columns in module_memberships_mirnaseq.csv contains information about different RNA cluster modules, Their correlation and p values.

extract_protocol:
CA1 region of hippocapus was surgically dissected under microscope, snap frozen in liquid nitrogen and stored at -80c until further use. RNA was prepared used RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq Small RNA Library Preparation Kit
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: transgenic mice were randomly distributed into two groups. While one group got access to Vorinostat in drinking water, the other drank vehicle containing drinking water. As control, littermate controls were used and vehicle was administered in drinking water. The experiment started when mice were 2 months old and continued for 4 weeks. Both male and female mice were included for the experiment.

value: transgenic

value: Vorinostat/SAHA


title: Plasma_Stress_Saline_rep3

description: FNM_v_FSS.counts; FNS_v_FSS.counts; FSM_v_FSS.counts

source_name: foetal plasma at E20, maternal stress, maternal saline injection

value: Sprague-Dawley

value: Female


title: transgenic Vorinostat/SAHA [C_7]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H6_ad004

value: female


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H6_ad001

value: brain


title: transgenic_vorinostat_1 [chipseq_from_saha_treatment]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H5_ad012

value: RSP


title: Plasma_NoStress_Saline_rep1

value: No stress


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H5_ad010

value: male


title: Plasma_Stress_Saline_rep2

value: Stress


title: transgenic Vorinostat/SAHA [C_6]


title: Plasma_Stress_MitoQ_rep1

description: FNM_v_FSM.counts; FNS_v_FSM.counts; FSM_v_FSS.counts

source_name: foetal plasma at E20, maternal stress, maternal MitoQ injection

value: MitoQ-NP


title: DAP-MYC4_rep1

description:
Sample 7
Protein-DNA interaction

tag: protein

tag: gene id

tag: protein expression

value: E.coli expressed


title: Plasma_Stress_MitoQ_rep2


title: transgenic Vorinostat/SAHA [C_5]


title: Plasma_Stress_Saline_rep1

value: Saline


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H6_ad008

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H5_ad007


title: transgenic Vorinostat/SAHA [C_4]


title: Plasma_NoStress_Saline_rep2

value: Plasma


title: transgenic Vorinostat/SAHA [C_8]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad012


title: Plasma_NoStress_MitoQ_rep1


title: transgenic Vorinostat/SAHA [C_3]


title: transgenic Vorinostat/SAHA [C_2]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H5_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad007


title: transgenic Vorinostat/SAHA [C_10]


title: transgenic Vorinostat/SAHA [C_1]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad006

value: PTLp


title: transgenic vehicle [B_9]

value: vehicle


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad004


title: transgenic vehicle [B_8]

value: transgenic


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H4_ad001


title: transgenic vehicle [B_6]


title: Plasma_Stress_MitoQ_rep3


title: ND3_24_2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: Labeled samples were randomly hybridized to Agilent SurePrint G3Human GE 8x60K DNA microarrays, according to the manufacturer’s protocol (Agilent).

scan_protocol: Hybridized slides were scanned using the Agilent microarray scanner (Model G2505C) and raw data were extracted using Agilent feature extraction software (version 12.0.1.1).

data_processing: mRNA expression raw intensity values were quality checked and exported from Agilent Feature Extraction software. The raw median foreground intensitites were imported into R software and a quantile-based strategy was used to filter out low quality probes based on the value of negative control probes. Data was analysed with Bioconductor package Limma. Experiment was two-colour, but the data were analysed as a single-channel arrays.

label_protocol: RNA samples were labeled with Cy3 or Cy5 (Quick Amp Gene Expression Labelling kit, Agilent).

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 2 mM glutamine, 100 U/mL penicillin, 100 μg/mL streptomycin, and 0.05mM β-mercaptoethanol. The cell density was strictly maintained at 0.1-2.0 x 10^6 cells/mL. 10^6 cells per well were seeded in a 12-well plate one day prior to exposure.

extract_protocol: After exposure, the cells were washed twice with ice-cold PBS by centrifugation at 300 g, 5 min at 4°C. RNA extraction was performed using the AllPrep DNA/RNA/miRNA Universal Kit, according to the manufacturer’s instruction.

treatment_protocol: Cells were exposed for 24 h to the respective EC10 doses of freshly resuspended ENMs and to a fixed concentration for the non-cytotoxic ENMs.

tag: cell type

value: monocytic cell line

tag: cell line

tag: exposure time

value: 24 hours

tag: slide #

tag: functionalization

value: carboxyl/carboxylate

tag: nanomaterial

value: Nanodiamond


title: ND4_24_3

value: polyethylene glycol (PEG)


title: transgenic vehicle [B_5]

tag: tissue

value: brain


title: ND4_24_1


title: Au54_24_3


title: Au202_24_2

value: amino/ammonium


title: ND2_24_1


title: Au204_24_2


title: transgenic vehicle [B_3]

tag: genotype


title: Au52_24_3


title: Au52_24_1


title: Ag4_24_2

value: Silver


title: Au203_24_3


title: Au203_24_1


title: ND2_24_3


title: Au53_24_2


title: transgenic vehicle [B_2]

tag: agent


title: Ag3_24_3_a

description: raw file is: US11263921_257236314240_S01_GE2_1200_Jun14_2_4.txt; available on GSM4476923


title: Au54_24_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad010

tag: age

value: RSP

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad012

tag: strain

value: female


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad007

tag: source


title: transgenic vehicle [B_10]


title: Ag3_24_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad008

tag: target


title: wild type vehicle [A_9]

value: wild type


title: QD4_24_3

value: QuantumDot


title: QD3_24_2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad004

value: VISp

tag: gender


title: Ag2_24_2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad001

value: PTLp


title: wild type vehicle [A_8]

value: vehicle


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad012


title: wild type vehicle [A_7]


title: wild type vehicle [A_6]


title: wild type vehicle [A_5]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H3_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad010


title: wild type vehicle [A_4]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad007


title: wild type vehicle [A_2]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad004


title: wild type vehicle [A_3]


title: Tunica6h_mm_rna_sr_islamr_B_6

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Differential expression analysis was performed in DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Significantly differentially (adjusted p value < 0.05) regulated genes are summarized in supplementary files.

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
Neurons were treated with trizol and RNA was prepared  using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: Endoplasmic reticulum stress was induced in primary hippocampal neurons using Tunicamycin (Sigma Aldrich). 2ug/mL of Tunicamycin was added to primary neuronal culture and incubated for 6 hours and compared to those treated with DMSO for same time

value: primary hippocampal neurons

tag: div

value: tunicamycin


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad002


title: QD4_24_1

value: monocytic cell line

value: 24 hours


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad006


title: TiO2r3_24_1

value: carboxyl/carboxylate


title: TiO2r4_24_2

value: polyethylene glycol (PEG)


title: QD2_24_3


title: TiO2s1_24_3

value: core


title: QD2_24_1

value: amino/ammonium


title: TiO2r3_24_3


title: wild type vehicle [A_1]

value: brain


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H2_ad001


title: TiO2r1_24_3


title: TiO2s2_24_2


title: TiO2r1_24_1


title: CNT4_24_2

value: CarbonNanotube


title: TiO2s4_24_2


title: CNT3_24_1


title: TiO2s3_24_3


title: CNT3_24_3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad012

value: RSP


title: TiO2r2_24_2


title: TiO2s3_24_1


title: CNT2_24_2


title: Tunica6h_mm_rna_sr_islamr_B_4


title: Tunica6h_mm_rna_sr_islamr_B_5


title: TiO2s1_24_1


title: Tunica6h_mm_rna_sr_islamr_B_3


title: Tunica6h_mm_rna_sr_islamr_B_2


title: CNT1_24_3


title: Tunica6h_mm_rna_sr_islamr_B_1


title: CuO3_24_3

value: CopperOxide


title: DMSO6h_mm_rna_sr_islamr_A_4

value: DMSO


title: CuO4_24_2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad006

value: female


title: CNT1_24_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad007

value: VISp

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad008


title: DMSO6h_mm_rna_sr_islamr_A_3


title: DMSO6h_mm_rna_sr_islamr_A_2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad004

value: PTLp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H1_ad001


title: CuO1_24_3


title: CuO3_24_1


title: DMSO6h_mm_rna_sr_islamr_A_1

value: primary hippocampal neurons


title: media_24_0_2

source_name: control

value: control

value: media


title: CuO2_24_2

value: monocytic cell line

value: 24 hours


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad012


title: control_5 [rnaseq_tg_vs_wt_3m]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Expression counts were adjusted for gender effect.
Genome_build: mm10
Supplementary_files_format_and_content: adjusted normalized counts were used for further analysis. Comma separated files containing Upregulated and downregulated genes and normalized reads.

extract_protocol:
CA1 region of hippocapus was surgically dissected under microscope, snap frozen in liquid nitrogen and stored at -80c until further use.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: camkdelta C transgenic mice were investigated at age of 3 months. As control, littermate controls were used. Both male and female mice were included for the experiment.

value: 3 months


title: control_4 [rnaseq_tg_vs_wt_3m]


title: ND3_24_3

value: carboxyl/carboxylate

value: Nanodiamond


title: ND4_24_2

value: polyethylene glycol (PEG)


title: ND3_24_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad010

value: brain


title: Au202_24_3

value: amino/ammonium


title: Au53_24_3


title: Au204_24_1


title: Au204_24_3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad008

value: RSP


title: Au202_24_1


title: Au203_24_2


title: Au54_24_2


title: Au52_24_2


title: control_3 [rnaseq_tg_vs_wt_3m]


title: Ag4_24_1

value: Silver


title: ND2_24_2_a

description: Raw data file for this sample is the same raw file for GSM4476970.


title: Ag2_24_3


title: Ag4_24_3


title: control_2 [rnaseq_tg_vs_wt_3m]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad006

value: female


title: control_1 [rnaseq_tg_vs_wt_3m]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad004

value: VISp


title: Au53_24_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H12_ad002

value: male


title: transgenic_5 [rnaseq_tg_vs_wt_3m]

value: CamkdeltaC transgenic


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad012


title: transgenic_4 [rnaseq_tg_vs_wt_3m]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad010


title: Ag3_24_2


title: transgenic_3 [rnaseq_tg_vs_wt_3m]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad008


title: transgenic_6 [rnaseq_tg_vs_wt_3m]


title: transgenic_2 [rnaseq_tg_vs_wt_3m]


title: Ag2_24_1


title: transgenic_1 [rnaseq_tg_vs_wt_3m]


title: TiO2r4_24_1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad006

value: PTLp


title: QD2_24_2

value: QuantumDot


title: TiO2r4_24_3


title: QD3_24_3


title: QD4_24_2


title: hypoxia_5  [rnaseq_hypoxia_4h]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Differential expression analysis is performed in DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Significantly differentially (adjusted p value < 0.05) regulated genes are summarized in supplementary files.
Supplementary_files_format_and_content: genecounts

treatment_protocol: To model hypoxia, primary hippocampal neuronal cultures were incubated in normoxia (20% O2) in a standard cell culture incubator for 10 days before they were used in an experiment. For hypoxic conditions cells were incubated at 1% O2 for 4 hours using the in invivo2 400 hypoxia workstation (Baker Ruskin). Cells from the same isolation were kept in normoxia at 20% O2 as a control.

value: primary hippocampal neurons

tag: protocol

value: hypoxia


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad004


title: TiO2r2_24_3

value: monocytic cell line

value: 24 hours


title: QD3_24_1

value: carboxyl/carboxylate


title: TiO2r3_24_2


title: hypoxia_4  [rnaseq_hypoxia_4h]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad007


title: TiO2s2_24_3


title: TiO2r1_24_2

value: core


title: TiO2s4_24_1

value: polyethylene glycol (PEG)


title: TiO2s4_24_3


title: TiO2s3_24_2


title: TiO2s1_24_2


title: CNT4_24_1

value: CarbonNanotube


title: TiO2r2_24_1

value: amino/ammonium


title: TiO2s2_24_1


title: CNT3_24_2


title: CNT4_24_3


title: CNT2_24_1


title: CNT2_24_3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad002

value: brain


title: hypoxia_2  [rnaseq_hypoxia_4h]


title: hypoxia_3 [rnaseq_hypoxia_4h]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad010

value: RSP


title: hypoxia_1  [rnaseq_hypoxia_4h]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad008

value: female


title: control_6 [rnaseq_hypoxia_4h]

value: control


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H11_ad001

value: VISp

value: male


title: control_5 [rnaseq_hypoxia_4h]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad007


title: CNT1_24_2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad006

value: PTLp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad004


title: CuO4_24_1

value: CopperOxide


title: CuO4_24_3


title: control_3 [rnaseq_hypoxia_4h]

value: primary hippocampal neurons


title: WT-rep3-Inp

city: Philadelphia

first: Lan

last: Lin

state: PA

address: 3501 Civic Center Boulevard, Office 9052

department: Pathology and Laboratory Medicine

institute: The Children’s Hospital of Philadelphia

description: no IP (input RNA) replicate 3

data_processing:
mapping with STAR (version 2.5.3a)
gene expression estimation with Kallisto (v0.43.0)
peak calling with CLAM (version 1.2.0)
Genome_build: the mouse genome (GRCm38) with GENCODE annotation  (release M13)
Supplementary_files_format_and_content: MeRIP-seq: m6A peak bed files

source_name: embryonic stem cells

growth_protocol: The stem cells were grown in DMEM medium supplemented with 15% fetal calf serum (FBS), 1000 U/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 100 U/mL penicillin and 100 ug/mL streptomycin on 0.1% Gelatin coated plates.

extract_protocol:
Total RNA was extracted from the mESCs using TRIzol  reagent. Enrichment of mRNA from total RNA was performed using a Dynabeads mRNA  Purification Kit (Invitrogen), according to the manufacturer’s instructions.
mRNA samples were  chemically fragmented into ~100-nucleotide-long fragments by incubation with 10X RNA  Fragmentation Reagent (Invitrogen) at 90°C for 90 seconds. The fragmentation reaction was  stopped by adding 0.5 M EDTA, followed by standard ethanol precipitation. The fragmented RNA  samples were resuspended in 10 mM Tris-HCl (pH 7.4). 20 ng of fragmented RNA to be used as  input control was stored in -80°C in a final volume of 8.5 μl in FPF (Fragment, Prime, Finish) mix  from the TruSeq Stranded Total RNA Kit (Illumina). The remaining RNA was subjected to m6Aseq.  Specifically, 2 μg of fragmented mRNA was incubated for 2 h at 4°C with 4 μg of affinitypurified  anti-m6A polyclonal antibody (Synaptic Systems) in m6A-IP buffer (150 mM NaCl, 0.1%  NP-40, 10 mM Tris-HCl, [pH 7.4], and 0.2 U/μl of RNasin). The RNA–antibody mixture was  immunoprecipitated by incubation with protein A beads (Millipore) at 4°C for another 2 h. The  beads were extensively washed with m6A-IP buffer. The bound RNA was eluted with m6A elution  buffer (150 mM NaCl, 6.7 mM m6A nucleotides, 0.1% NP-40, 10 mM Tris-HCl, [pH 7.4], and 0.2  U/μl of RNasin) and elution wash buffer (150 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, [pH 7.4],  0.2 U/μl of RNasin). The m6A eluate was purified using Agencourt AMPure XP beads (Beckman  Coulter). The immunopurified RNA and non-IP input control samples were used for library  generation using the TruSeq Stranded Total RNA Kit (Illumina).
library strategy: MeRIP-seq

tag: genotype/variation

value: Wild-type embryonic stem cell

value: embryonic stem cells

tag: condition

value: no IP (input RNA)


title: CuO3_24_2

tag: cell type

value: monocytic cell line

tag: cell line

value: 24 hours

value: carboxyl/carboxylate


title: CuO1_24_2

tag: exposure time

tag: slide #

value: core


title: WT-rep3-IP

description: RNA IP against m6A replicate 3

value: RNA IP against m6A


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad002

value: brain


title: CuO2_24_3

tag: functionalization

value: amino/ammonium

tag: nanomaterial


title: CuO2_24_1_b


title: media_24_0_3

value: media


title: media_24_0_1

value: control


title: control_2 [rnaseq_hypoxia_4h]


title: WT-rep2-Inp

description: no IP (input RNA) replicate 2


title: WT-rep2-IP

description: RNA IP against m6A replicate 2


title: control_1 [rnaseq_hypoxia_4h]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_H10_ad001

tag: tissue

value: VISp


title: CuO1_24_1


title: WT-rep1-Inp

description: no IP (input RNA) replicate 1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad012

value: RSP

value: female


title: WT-rep1-IP

description: RNA IP against m6A replicate 1


title: control_4 [rnaseq_hypoxia_4h]


title: Sham_6 [rnaseq_from_MI_experiment]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Using a mixed linear model, expression counts were adjusted for effects due to library size, gender, sequencing lane, body weight, heart weight and other latent covariates as determined by Sva package in R
Genome_build: mm10
Supplementary_files_format_and_content: adjusted log2 normalized counts were used for further analysis.

extract_protocol:
CA1 region of hippocapus was surgically dissected under microscope, snap frozen in liquid nitrogen and stored at -80c until further use. RNA was extracted using RNA clean and concentrator kit.
Libraries were generated according to the instructions of TruSeq RNA Library Prep Kit v2.
Libraries were multiplexed and sequenced on Illumina HiSeq2000 to generate 50bp single end reads.

treatment_protocol: Myocardial infarction was introduced via an established protocol in our laboratory through coronary artery ligation Sham-operated mice (similar surgery, but no artery ligation) was used as controls (Mohamed et al, 2018).

value: Sham


title: KO_13RK-rep3-Inp

description: no IP (input RNA) replicate 3

value: METTL14 KO rescued with arginine methylation-deficient (13RK) METTL14 embryonic stem cell


title: Sham_5 [rnaseq_from_MI_experiment]


title: KO_13RK-rep3-IP

description: RNA IP against m6A replicate 3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad010

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

value: male


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad008


title: KO_13RK-rep2-Inp

description: no IP (input RNA) replicate 2

value: embryonic stem cells


title: KO_13RK-rep2-IP

description: RNA IP against m6A replicate 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad007


title: Sham_4 [rnaseq_from_MI_experiment]


title: KO_13RK-rep1-Inp

description: no IP (input RNA) replicate 1

value: no IP (input RNA)


title: KO_13RK-rep1-IP

description: RNA IP against m6A replicate 1


title: KO_5RK-rep3-Inp

description: no IP (input RNA) replicate 3

value: METTL14 KO rescued with arginine methylation-deficient (5RK) METTL14 embryonic stem cell


title: Sham_3 [rnaseq_from_MI_experiment]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad006

value: PTLp


title: Sham_2 [rnaseq_from_MI_experiment]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad004


title: KO_5RK-rep2-IP

description: RNA IP against m6A replicate 2


title: KO_5RK-rep2-Inp

description: no IP (input RNA) replicate 2


title: Sham_1 [rnaseq_from_MI_experiment]


title: MI_6 [rnaseq_from_MI_experiment]

value: Myocardial infarction


title: KO_5RK-rep1-Inp

description: no IP (input RNA) replicate 1


title: KO_5RK-rep1-IP

description: RNA IP against m6A replicate 1


title: KO_WT-rep3-IP

description: RNA IP against m6A replicate 3

value: METTL14 KO rescued with METTL14 embryonic stem cell


title: KO_WT-rep2-Inp

description: no IP (input RNA) replicate 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G8_ad012


title: KO_WT-rep2-IP

description: RNA IP against m6A replicate 2

value: RNA IP against m6A


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad002

value: brain


title: KO_WT-rep1-IP

description: RNA IP against m6A replicate 1


title: MI_5 [rnaseq_from_MI_experiment]


title: KO-rep3-Inp

description: no IP (input RNA) replicate 3

value: METTL14 KO embryonic stem cell


title: KO_5RK-rep3-IP

description: RNA IP against m6A replicate 3


title: MI_2 [rnaseq_from_MI_experiment]


title: MI_3 [rnaseq_from_MI_experiment]


title: KO-rep3-IP

description: RNA IP against m6A replicate 3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G8_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G8_ad007


title: KO-rep2-Inp

description: no IP (input RNA) replicate 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G8_ad008


title: KO_WT-rep1-Inp

description: no IP (input RNA) replicate 1


title: KO-rep1-Inp

description: no IP (input RNA) replicate 1


title: MI_1 [rnaseq_from_MI_experiment]


title: KO-rep2-IP

description: RNA IP against m6A replicate 2


title: KO_WT-rep3-Inp

description: no IP (input RNA) replicate 3


title: KO-rep1-IP

description: RNA IP against m6A replicate 1


title: transgenic_vorinostat_9 [rnaseq_after_saha]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
were mapped to mouse genome (mm10) using STAR (v 2.5.2b)
Expression counts were enumerated using featureCounts of subread (v 1.5.1) package.
Using a mixed linear model, expression counts were adjusted for library size, gender, sample batches (birth, sequencing lane, preparation), RNA quality, body weight, heart weight, lung weight, left ventricle weight, tibia length, sequencing lane and other latent covariates as determined by Sva package in R
Genome_build: mm10
Supplementary_files_format_and_content: adjusted normalized counts were used for further analysis. mixed_linear_model_normalized_counts_RNAseq_camk.csv contains log2 normalized counts after adjustments.

tag: genotype

value: CamkdeltaC transgenic

tag: agent

value: vorinostat

value: 3 months old


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G9_ad001

tag: strain

tag: age

value: VISp


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G8_ad001

tag: source

tag: target


title: transgenic_vorinostat_8 [rnaseq_after_saha]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad012

value: RSP

tag: gender

value: female


title: CDH11 Heterozygous Gemcitabine 3

city: Washington

first: Sonia

last: de Assis

state: DC

address: 3970 Reservoir Rd. NW, New Research Building E408

department: Oncology

institute: Georgetown University

data_processing:
Basecalling done using GenerateFASTQ: 1.1.0.64 via the Illumina BaseSpace platform
Reads were trimmed using Fqtrim 0.9.5 and mapped to the GRCm38 build of the Mus Musculus genome using RSEM (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323. Published 2011 Aug 4. doi:10.1186/1471-2105-12-323)
Genome_build: GRCm38
Supplementary_files_format_and_content: Expected Counts provided as tab-delimited text files

source_name: CDH11 Heterozygous Gemcitabine_PDAC

extract_protocol:
Total RNA was extracted from snap frozen pancreatic cancer tissues using Direct-zol RNA Miniprep Kit (Cat# R2053, Zymo Research). RNA concentration and purity was measured by NanoDrop (Thermo Scientific), and integrity and quality by Bioanalyzer 2100 (Agilent Technologies) and Qubit (Thermo Fisher Scientific).
Indexed, single-index sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded Total RNA Library Preparation Kit (human/mouse/rat) with rRNA depletion and random-primed cDNA synthesis (Cat# 20020596, Illumina).

tag: strain background

tag: treatment

value: gemcitabine

value: pancreatic ductal adenocarcinoma (PDAC)


title: CDH11 Heterozygous Gemcitabine 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad010

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: male


title: MI_4 [rnaseq_from_MI_experiment]

tag: protocol


title: transgenic_vorinostat_7 [rnaseq_after_saha]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad008


title: CDH11 Heterozygous Gemcitabine 1


title: transgenic_vorinostat_6 [rnaseq_after_saha]


title: transgenic_vorinostat_5 [rnaseq_after_saha]


title: Wildtype Gemcitabine 2

source_name: Wildtype Gemcitabine_PDAC


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad007


title: transgenic_vorinostat_4 [rnaseq_after_saha]

source_name: hippocampal CA1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad006


title: Wildtype Gemcitabine 1


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad004


title: CDH11 Heterozygous Control 2

source_name: CDH11 Heterozygous control_PDAC

value: untreated


title: transgenic_vorinostat_1 [rnaseq_after_saha]


title: CDH11 Heterozygous Control 1


title: Wildtype Control 3

source_name: Wildtype control_PDAC


title: transgenic_vorinostat_2 [rnaseq_after_saha]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad002


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G6_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G6_ad010


title: transgenic_vehicle_8 [rnaseq_after_saha]

value: vehicle


title: Wildtype Control 2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G6_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G6_ad007


title: Wildtype Gemcitabine 3


title: transgenic_vehicle_7 [rnaseq_after_saha]


title: Wildtype Control 1


title: transgenic_vehicle_6 [rnaseq_after_saha]


title: transgenic_vehicle_5 [rnaseq_after_saha]


title: transgenic_vorinostat_3 [rnaseq_after_saha]


title: CDH11 Heterozygous Control 3


title: Liver sample from male offpring exposed to Corn oil (control) in utero; sample ID 7

city: Los Angeles

first: Xia

last: Yang

address: 610 Charles E. Young Drive East

institute: University of California, Los Angeles

data_processing:
HiSeq Control Software (HCS) was used and initial analysis of data was analyzed in BaseSpace.
Pooled libraries of the samples were ran on two lanes (L007 and L008) and sequences were merged for each sample. The read quality was assessed using FastQC. After quality control, sequence alignment and transcript assembly was done using the HISAT-StringTie pipeline (Pertea et al., 2016). Reads were mapped to the GRCm38/mm10 reference genome.
Raw data was normalized and identification of differentially expressed genes (DEGs) were conducted using DEseq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table contains raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Livers were extracted and flash frozen in liquid nitrogen then stored at -80C until analysis. RNA was extracted using the MiRNeasy Mini Kit purchased from Qiagen following manufracturer's instructions.
Libraries were prepared using the Total RNA Library Prep kit with Ribo-Zero Gold at the UCLA Neuroscience Genomics Core.

treatment_protocol: Samples are from mice offspring only exposed to bisphenol A in utero.

value: Liver

value: Control

tag: Sex

value: Male


title: Liver sample from male offpring exposed to Corn oil (control) in utero; sample ID 3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G5_ad012


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G5_ad010


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G7_ad001

value: PTLp


title: Liver sample from male offpring exposed to Corn oil (control) in utero; sample ID 2


title: 21T

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description: Methamphetamine-treated SIV-infected rhesus monkey with encephalitis, enriched microglia/brain macrophages

data_processing:
Cellranger pipeline (version 3.1.0) was used here. Cellranger mkfastq was used for demultiplexing and generate fastq files and cellranger count was used to align the reads to Mmul10 and M33262.1 reference genomes.
M33262.1 was split and annotated into 5 regions as described in the manuscript.
Genome_build: Mmul10
Genome_build: M33262.1
Supplementary_files_format_and_content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

organism: Macaca mulatta

source_name: Methamphetamine before and after SIVmac251 infection

extract_protocol:
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the brain and cryopreserved. Isolates were immunomagnetically enriched for CD11b+ cells, and then flow cytometry sorted for CD11b positive, live events, and processed for scRNA.
scRNA10x Genomics Chromium GEM Chip and placed into Chromium Controller for library preparation. The prepared libraries  were sequenced using Illumina Nextseq550 sequencer.

treatment_protocol: Animals were infected with SIV and treated with either saline or methamphetamine injections.

value: CD11b enriched brain microgla and macrophages

value: SIVmac251, SIVE, Meth


title: transgenic_vehicle_9 [rnaseq_after_saha]

value: brain

value: CamkdeltaC transgenic


title: transgenic_vehicle_3 [rnaseq_after_saha]

value: 3 months old


title: 34T

description: Saline-treated SIV-infected rhesus monkey with encephalitis, enriched microglia/brain macrophages

source_name: Saline before and after SIVmac251 infection

value: SIVmac251, SIVE, saline


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G5_ad008

value: RSP

value: VISp


title: transgenic_vehicle_4 [rnaseq_after_saha]


title: Liver sample from male offpring exposed to Corn oil (control) in utero; sample ID 10


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G5_ad007


title: transgenic_vehicle_2 [rnaseq_after_saha]


title: 17T


title: Liver sample from male offpring exposed to BPA in utero; sample ID 4

value: BPA


title: M3_NL_5d

city: Uppsala

first: Kristian

middle: Erik

last: Persson Hodén

address: Almas allé 5

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

data_processing:
fastqc, version 0.11.5
trimmomatic, version  0.36, "PE ILLUMINACLIP:adapters.fasta:2:30:10 HEADCROP:13 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"
hisat2, version 2.0.4,
kallisto, version 0.43, 10000 bootstraps
Genome_build: Potato DM 4.04 (http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml), P. infestans ASM14294v1 (https://protists.ensembl.org/Phytophthora_infestans/Info/Index)
Supplementary_files_format_and_content: tsv, kallisto count

organism:
Solanum tuberosum
Phytophthora infestans

source_name: Solanum tuberosum leaves inoculated with Phytophthora infestans (Strain NL11388)

growth_protocol: Potato plants cv. Sarpo Mira were grown in-vitro at 22°C with a 16-h photoperiod on Murashige-Skoog (MS) medium (Duchefa Biochemie B.V., Amsterdam, Netherlands), supplemented with 2% (w/v) sucrose and 0.3% (w/v) gelrite (Duchefa). After 3 weeks plants were transferred to pots with soil in a growth chamber with the same light and temperature regime. Plants were grown for 4 weeks post transfer to soil from in-vitro conditions before inoculation. Mycelia was grown for 7 days in liquid pea broth.

extract_protocol:
RNeasy plant mini kit (Qiagen; Limburg, Netherlands)
Illumina TruSeq stranded Total RNA Library preparation kit. Libraries were prepared by the SciLife sequencing platform (Stockholm, Sweden) under their in-house conditions and sequenced by using Illumina HiSeq 2500

treatment_protocol: 5x104 spores/ml water of each P. infestans strain was used for potato leaf inoculations.

value: Leaves (infected)

tag: inoculum

tag: days past inoculation

tag: potato cultivar

value: Sarpo Mira


title: transgenic_vehicle_1 [rnaseq_after_saha]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G4_ad012

source_name: C57BL/6J P56 Mouse Brain

value: female


title: Liver sample from male offpring exposed to BPA in utero; sample ID 3


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad010

value: male


title: wildtype_vehicle_10 [rnaseq_after_saha]

value: wildtype

value: vehicle


title: M3_88069_5d

source_name: Solanum tuberosum inoculated with Phytophthora infestans (Strain NL88069)


title: Liver sample from male offpring exposed to BPA in utero; sample ID 15

value: Liver

value: Male


title: 32T

value: CD11b enriched brain microgla and macrophages


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad008


title: wildtype_vehicle_9 [rnaseq_after_saha]


title: Liver sample from male offpring exposed to BPA in utero; sample ID 12


title: M2_88069_5d


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad007


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad006

value: PTLp


title: Liver sample from female offpring exposed to Corn oil (control) in utero; sample ID 1

value: Control

value: Female


title: wildtype_vehicle_7 [rnaseq_after_saha]

value: brain

value: 3 months old


title: M1_NL_5d


title: M1_88069_5d


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad004


title: Liver sample from female offpring exposed to Corn oil (control) in utero; sample ID 18


title: wildtype_vehicle_6 [rnaseq_after_saha]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad002


title: wildtype_vehicle_5 [rnaseq_after_saha]


title: Liver sample from female offpring exposed to Corn oil (control) in utero; sample ID 17


title: E95_R_MeRIP-ip_3

city: shenzhen

first: Xin

middle: xin

last: Zhang

state: china/guangdong

address: No.7 pengfei road Dapend

department: agricultural genomics institute at shenzhen

institute: chinese academy of agricultural science

description: m6A immunoprecipitate rRNA_depleted RNA

data_processing:
Trimmomatic was used for trimming adapters and filtering on length and quality of the raw sequencing reads with default settings
Clean reads were mapped to respective reference genome using hisat2 with default settings.
reference genome:Sscrofa11.1 (GCA_000003025.6)

organism: Sus scrofa

source_name: longissimus dorsi

extract_protocol:
Total RNA (PK15 and skeletal muscle) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.
MeRIP-seq/R-MeRIP-seq

value: skeletal muscle

tag: developmental stage

value: 95 days post coitus

tag: m6a antibody

value: Synaptic systems, 202003


title: E95_R_MeRIP-in_3

description:
rRNA_depleted RNA
E95-3-n.TPM

tag: tissue


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G3_ad001

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: VISp


title: Liver sample from female offpring exposed to BPA in utero; sample ID 9

value: BPA


title: E95_R_MeRIP-ip_2

description: m6A immunoprecipitate rRNA_depleted RNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad012

value: RSP

value: female


title: wildtype_vehicle_3 [rnaseq_after_saha]

tag: genotype

value: wildtype


title: Liver sample from female offpring exposed to BPA in utero; sample ID 8


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad008


title: E95_R_MeRIP-in_2

description:
rRNA_depleted RNA
E95-2-n.TPM


title: wildtype_vehicle_2 [rnaseq_after_saha]

tag: agent

value: vehicle


title: Liver sample from female offpring exposed to BPA in utero; sample ID 1

tag: strain

value: Liver


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad007

tag: age

value: male


title: wildtype_vehicle_8 [rnaseq_after_saha]


title: Liver sample from female offpring exposed to Corn oil (control) in utero; sample ID 4


title: E95_R_MeRIP-ip_1

description: m6A immunoprecipitate rRNA_depleted RNA


title: Liver sample from female offpring exposed to BPA in utero; sample ID 14


title: littermate_control_4 [chipseq_tg_wt_3m]

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Quality of sequencing files were determined using FastQC (v 0.11.5).
Raw data were mapped to mouse genome (mm10) using bowtie2 (v 2.0.2). Generated sam files were converted to bam files using samtools view (samtools v. 1.3.1). Bam files were sorted using samtools sort.
Sorted Bam files were filtered based on quality (-q 5) prior to removal of duplicates using samtools rmdup. Correlation patterns of the replicates were investigated using DEEPTOOLS (v. 3.0.1)
Highly correlatied replicate bam files from corresponding conditions were merged using samtools merge
merged bam files were used to investigate genome wide distribution of H3K4me3 using ngsplot(Shen et al, 2014). Distribution pattern in Input bam files from corresponding conditions were also visualized
Genome wide narrow peaks were determined using MACS2 (https://github.com/taoliu/MACS). Regions that have been previously associated with high signals regardless of experimental condition were removed and input normalized peaks were determined using DiffBind. Differential peaks were determined using linear mixed effect model in limma. Peaks with FDR <0.05 were used for further analysis. Peaks were annotated using ChipSeeker13.
Genome_build: mm10
Supplementary_files_format_and_content: processed data files contain MACS2 peaks after removing backlisted peaks and also the differential peaks between conditions.

tag: antibody

value: 3 months


title: M2_NL_5d

value: Leaves (infected)

value: Sarpo Mira


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad004

tag: source

value: PTLp

tag: target


title: littermate_control_3 [chipseq_tg_wt_3m]

value: brain


title: wildtype_vehicle_4 [rnaseq_after_saha]

value: 3 months old


title: littermate_control_2 [chipseq_tg_wt_3m]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad006

tag: gender


title: E95_R_MeRIP-in_1

description:
rRNA_depleted RNA
E95-1-n.TPM

value: skeletal muscle


title: E70_R_MeRIP-in_3

description:
rRNA_depleted RNA
E70-3-n.TPM

value: 70 days post coitus


title: YAP-TFE3 rep 2 (rnaseq_3T3)

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project
Reads from the NIH 3T3 line was aligned against the ensembl reference ‘mm10'
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample ...

source_name: NIH 3T3 murine fibroblast cells ATCC

growth_protocol: NIH3T3 cells were stably transduced and grown to confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)

extract_protocol:
Total RNA was isolated using the PureLink™ RNA mini kit (Invitrogen-ThermoFisher Scientific).  On-column DNase (Invitrogen) treatment was performed according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: NIH 3T3 murine fibroblast cells


title: YAP-TFE3 rep 1 (rnaseq_3T3)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad001

value: VISp


title: littermate_control_1 [chipseq_tg_wt_3m]

extract_protocol:
CA1 region of hippocapus was surgically dissected under microscope, snap frozen in liquid nitrogen and stored at -80c until further use. NeuN+ neuronal nuclei were FACS sorted and used to perform chromatin immunoprecipitation (ChIP) for H3K4me3
Chromatin immunoprecipitation was performed according to (Halder et al., 2016) with 0.2 µg chromatin and 1µg H3K4me3 (ab8580) antibody. ChIPseq library preparation was performed using NEBNext Ultra II DNA library preparation according to manufacturer’s protocol.
2nM libraries were pooled and sequenced in Illumina Hiseq 2000 with 50-bp single end reads.


title: E70_R_MeRIP-in_2

description:
rRNA_depleted RNA
E70-2-n.TPM


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad012


title: transgenic_4 [chipseq_tg_wt_3m]

value: CamkdeltaC transgenic


title: E70_R_MeRIP-ip_2

description: m6A immunoprecipitate rRNA_depleted RNA

value: Synaptic systems, 202003


title: YAP5SA rep 2 (rnaseq_3T3)


title: transgenic_3 [chipseq_tg_wt_3m]


title: wildtype_vehicle_1 [rnaseq_after_saha]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad008

value: RSP

value: female


title: YAP5SA rep 1 (rnaseq_3T3)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad010


title: E70_R_MeRIP-in_1

description:
rRNA_depleted RNA
E70-1-n.TPM


title: E70_R_MeRIP-ip_1

description: m6A immunoprecipitate rRNA_depleted RNA


title: transgenic_2 [chipseq_tg_wt_3m]


title: YAP-TFE3 rep 3 (rnaseq_3T3)


title: E70_R_MeRIP-ip_3

description: m6A immunoprecipitate rRNA_depleted RNA


title: transgenic_1 [chipseq_tg_wt_3m]


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G2_ad002


title: TFE3 rep 2 (rnaseq_3T3)


title: E60_R_MeRIP-ip_3

description: m6A immunoprecipitate rRNA_depleted RNA

value: 60 days post coitus


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad007


title: YAP5SA rep 3 (rnaseq_3T3)


title: E60_R_MeRIP-in_3

description:
rRNA_depleted RNA
E60-3-n.TPM


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad006


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad004


title: TFE3 rep 1 (rnaseq_3T3)


title: E60_R_MeRIP-ip_2

description: m6A immunoprecipitate rRNA_depleted RNA


title: transgenic_input [chipseq_tg_wt_3m]

value: IgG


title: TAZ-CAMTA1 rep 3 (rnaseq_3T3)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad002

value: male


title: TAZ-CAMTA1 rep 2 (rnaseq_3T3)


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G1_ad001


title: MSB_2

city: Durham

first: Terry

last: Lechler

state: NC

institute: Duke University

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
Data filtering:(1) Remove reads containing adaptors;(2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
TopHat2 was used to accomplish the map all the reads to reference genome.mouse genome sequence and annotation from Ensembl project as reference.
Genome_build: mouse genome from Ensembl project
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Keratinocytes

extract_protocol:
K10-rtTA;TRE-H2B-GFP;TRE-Spastin pregnant dams were fed with doxycycline chow at E14.5, then sacrificed at E16.5. Back skins were cut off and treated with dispase to separate the epidermis from the dermis, and digested in 1:1 trypsin with versene and FACS sorted for H2BGFP+ cells. RNA was extracted and DNA digested. Three independent RNA samples from control and K10-Spastin were collected and sent for sequencing and analysis by Novogene.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD1 IGS

value: skin


title: TAZ-CAMTA1 rep 1 (rnaseq_3T3)


title: MSB_1


title: E60_R_MeRIP-ip_1

description: m6A immunoprecipitate rRNA_depleted RNA


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad012


title: TFE3 rep 3 (rnaseq_3T3)


title: E60_R_MeRIP-in_1

description:
rRNA_depleted RNA
E60-1-n.TPM


title: WTSB_3

value: control


title: WTSB_2


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad010


title: E50_R_MeRIP-ip_3

description: m6A immunoprecipitate rRNA_depleted RNA

value: 50 days post coitus


title: TAZ4SA rep 3 (rnaseq_3T3)


title: TAZ4SA rep 2 (rnaseq_3T3)


title: E50_R_MeRIP-in_3

description:
rRNA_depleted RNA
E50-3-n.TPM


title: TAZ4SA rep 1 (rnaseq_3T3)


title: E50_R_MeRIP-ip_2

description: m6A immunoprecipitate rRNA_depleted RNA


title: WTSB_1


title: littermate_control_input [chipseq_tg_wt_3m]

value: brain

value: 3 months

value: wildtype


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad008


title: 190321_CEMBA_mm_P56_P63_RS2_190321_P7_190321_P8_G12_ad007


title: E50_R_MeRIP-in_2

description:
rRNA_depleted RNA
E50-2-n.TPM

value: skeletal muscle


title: E60_R_MeRIP-in_2

description:
rRNA_depleted RNA
E60-2-n.TPM


title: MSB_3