title: WT-R1-mESC_Input

description:
Sample 22
Input chromatin used for ICeChIP-seq in Sample 21.

growth_protocol: WT R1 mESCs were cultured as previously described (Dorighi et al. 2017).

extract_protocol:
WT R1 mouse embryonic cell pellets were washed twice with 5 mL of PBS, then washed twice with 5 mL of Buffer N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized), with each wash consisting of complete resuspension of the pellet, centrifugation at 500 g for 5 minutes at 4°C, and removal of supernatant. The washed pellet was then resuspended in at least 2 packed cell volumes (PCV) of Buffer N and mixed with 1 volume of Lysis Buffer (Buffer N supplemented with 0.6% NP-40 Substitute) and incubated on ice for 10 minutes to lyse cells. The crude nuclei were spun down at 500 g for 5 minutes at 4°C before being resuspended in at least 6 packed nuclear volumes (PNV) of Buffer N and applied to the top of 7.5 mL of Sucrose Cushion N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 30% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized) in a 15 mL centrifuge tube, then spun down at 500 g for 12 minutes at 4°C in a swinging-bucket rotor. The supernatant was discarded after centrifugation, and the pellet was resuspended in approximately 2 PNV of Buffer N. The nuclei were then quantified by diluting 2 uL of nuclei suspension into 48 uL of 2 M NaCl, water-bath sonicating to solubilize DNA, and spectroscopically measuring DNA concentration by Nanodrop measurement, where 1 A280nm¬ = 50 ng/uL chromatin in the measurement sample. After accounting for the 25-fold dilution of the measurement sample, the concentration of the nuclei was adjusted down to 1ug/uL of chromatin. Nuclei were aliquoted into 100 uL aliquots, flash frozen, and stored at -80°C until use. When nuclei aliquots were used, they were first thawed and spiked approximately 1 uL of each barcoded nucleosome standard per 50 ug of chromatin to be used. The nuclei suspension with spiked calibrants was then mixed with a pipette and transferred to a new tube, then warmed to 37°C for 2 minutes. After warming, 1 unit of micrococcal nuclease (MNase) per 4.375 ug of chromatin was added to the nuclei suspension and incubated at 37°C while shaking at 900 rpm for 12 minutes. After incubation, the digestion was stopped by adding 1/9 volume of 10x MNase Stop Buffer (100 mM EDTA, 100 mM EGTA, Filter Sterilized) while slowly vortexing, and nuclei were lysed by adding 5 M NaCl to a final concentration of 600 mM NaCl while slowly vortexing. 66 mg of HAP resin (BioRad, CHTTM Ceramic Hydroxyapatite, Type I, 20 um) per 100 ug of chromatin digested was rehydrated with 200 uL of HAP Buffer 1 (5 mM Sodium Phosphate pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) per 100 ug of chromatin digested. The lysed nuclei were then spun down at 18,000 g for 1 minute to pellet insoluble nuclear debris, and the soluble fraction was added to the rehydrated HAP resin and incubated for 10 minutes on a rotator at 4°C. After incubation, the HAP resin slurry was added to a centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 um) and spun at 1000 g for 30 seconds at 4°C. The HAP resin left on the filter unit was then washed 4 times with 200 uL HAP Buffer 1 and 4 times with 200 uL HAP Buffer 2 (5 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) by spinning at 1000 g for 30 seconds at 4°C. Into a clean tube, the HAP resin was eluted with three elutions of 100 uL HAP Elution Buffer (500 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized). The DNA content of the elution was then quantified spectroscopically with a Nanodrop, and the chromatin concentration was adjusted to 20 ng/uL with ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) with 100 ug/mL of BSA. With the exception of the Koide Lab 304M3B antibody, every ICeChIP was conducted with 12.5 uL of Protein A Dynabeads (Invitrogen) and 3 ug of antibody. The Protein A Dynabeads for each ICeChIP were washed with 50 uL of ChIP Buffer 1 by use of a magnetic rack, then resuspended in 50 uL of ChIP Buffer 1. In a separate set of tubes, 3 ug of each antibody was diluted to 100 uL with ChIP Buffer 1. The antibody suspension and the Protein A Dynabeads suspension were combined and incubated on a rotator at 4°C for at least 1 hour, then washed with 200 uL of ChIP Buffer 1 by use of a magnetic rack and resuspended in 50 uL of ChIP Buffer 1. After antibody washing, 150 uL of the diluted chromatin elution was added to each antibody-bead conjugate and incubated for 15 minutes on a rotator at 4°C. After this incubation, the beads were washed twice with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) and once with ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium Deoxycholate, 0.5% v/v NP-40 Substitute, Filter Sterilized), with a wash consisting of removal of the existing supernatant by use of a magnetic rack, resuspension into 150 uL of buffer, transfer to a new siliconized tube, and incubation on the rotator for 10 minutes at 4°C. After these washes, the supernatant was removed, and the beads were resuspended in ChIP Buffer 1, transferred to a new siliconized tube, then rinsed once with 200 uL of TE before being resuspended in 50 uL of ChIP Elution Buffer and incubated at 55°C for 5 minutes. After incubation, the supernatant was transferred to a new set of siliconized tubes, and the beads were discarded. To each supernatant was then added 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. 15 uL of Input DNA was also diluted to 50 uL with 35 uL of ChIP Elution Buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% w/v SDS, Filter Sterilized) and was supplemented with 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. The IP elutions and diluted input were then incubated at 55°C for 2 hours for a Proteinase K digestion. After digestion, the DNA was purified by adding 1.5 volumes of Serapure HD (1:50 dilution of Sera-Mag SpeedBeads [Fisher], 20% PEG-8000, 2.5 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20, Filter Sterilized prior to addition of SpeedBeads), incubating at room temperature for 15 minutes, then collecting the beads on a magnetic rack, washing twice with 150 uL of 70% ethanol, and eluting into 50 uL of water, which was then recovered and stored at -20°C.
DNA purified with Serapure was quantified using Quant-iT TM PicoGreen (Thermo Fisher) per manufacturer instructions. Up to 10 ng of each DNA sample for which libraries were to be prepared were then carried forward. Libraries were then generated from the NEBNext Ultra II DNA Library Prep kit (New England Biolabs) per manufacturer instructions. The DNA content of the library was then quantified and pooled for Illumina sequencing.

value: WT R1 mESC


title: RC_03: ASML_CD151 Kd

status: Public on Sep 20 2018

type: RNA

city: Heidelberg

first: Jan

last: Provaznik

state: Baden-Wuerttemberg

address: Meyerhofstr. 1

department: Genomics Core Facility

country: Germany

institute: EMBL Heidelberg

hyb_protocol: Hybridization was done as described in miRNA Microarray System protocol v 1.7 from Agilent Technologies

scan_protocol: Scanning was done on Agilent Microarray Scanner G2565BA, Agilent Scan Control Software,

data_processing:
IPA was used for miRNA analysis and for correlating miRNA with protein expression after predicted targets were selected by miRNA databases (http://www.microrna.org, http://www.targetscan.org). For pathway analysis PANTHER (http://pantherdb.org), KEGG (http://www.kegg.jp), Reactome (https://reactome.org), and STRING (http://string-db.org) databases were used
after normalization, data were compared between identical non-transfected versus transfected cells and exosomes, respectively. In most instances, 2-fold differences were considered significant. In exosome preparations, 1.5-fold differences were occassionally included. For processed data, the programm suggestions were followed.

molecule: total RNA

organism: Rattus norvegicus

source_name: exosome

label_protocol: Labeling was done as described in miRNA Microarray System protocol v 1.7 from Agilent Technologies

growth_protocol:
The rat pancreatic adenocarcinoma lines ASML and AS spontaneously arisen in the BDX rat strain are maintained in RPMI1640/10%FCS/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
ASML-EpC kd,ASML-cld7 kd, ASML-CD151 kd, ASML-Tspan8 kd, ASML-CD44v6 kd and AS-CD9 kd lines were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning. (EpC: EpCAM, cld7: claudin7)
ASML-EpCAM mutAG and ASML-cld7mutPalm were derived from ASML-EpC kd, respectively ASML-cld7 kd cells by transfection with mutated EpCAM (exchange of AG in the binding site of EpC to cld7) or mutation in the palmitoylation site of cld7 shRNA (Qiagen, Hilden, Germany). Cells were maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418, 120µg hygromycin. Single cell kd clones were derived by 2 rounds of single cell cloning.

extract_protocol: Cell and exosome mRNA/microRNA was extracted using the miRNeasyMinikit following the supplier's suggestion (Qiagen, Hildesheim, Germany). Exosomes were pretreated with RNAse to avoid contamination by attached free mRNA.

treatment_protocol: Cells have not undergone any special treatment. All exosome preparation were derived from culture supernatant after cells have been cultured in serum-free medium for 48h-72h. Culture supernatant was collected and cleared (2x10min, 500g, 1x20min, 2000g, 1x30min, 10000g), filter sterizied (0.2µm) and were centrifuged (120min, 100000g). The pellet was washed (PBS, 120min, 100000g), resuspended in 40% sucrose overlaid by a discontinuous sucrose gradient (30%-5%) and centrifuged (16h, 100000g). Exosomes were collected from the 10%-5% sucrose interface (light density fractions, d: 1.15-1.56g/ml).

tag: tissue

value: rat pancreatic adenocarcinoma

tag: cell line

value: ASML

tag: condition

value: CD151 Kd


title: JZH

city: Shanghai

first: Xiao-yan

last: dong

state: Shanghai

address: NO 24, Alley 1400, West Beijing Road

department: Department of respiration

country: China

institute: Shanghai Children's Hospital

hyb_protocol: The total 25 μl mixture from Hy3TM-labeled samples with 25 μl hybridization buffer were denatured at 95°C for 2 min, incubated in ice for 2 min, and then hybridized to the microarray at 56°C for 16–20 h with a 12-Bay Hybridization System (Nimblegen, Madison, WI, USA).

scan_protocol: After hybridization, the slides were prepared, washed with a wash buffer kit (Exiqon, Vedbaek, Denmark) and dried by centrifugation at 400 rpm for 5 min. The slides were then scanned by the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA).

data_processing: After low intensity miRNAs filtering, raw signal intensities are normalized in Median method. (miRNAs that intensities>=30 in all samples are chosen for calculating normalization factor)

organism: Homo sapiens

source_name: dust mite_peripheral blood

label_protocol: After RNA was isolated from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guidelines for miRNA labeling. Briefly, 1g of each sample was 3'-end-labeled with Hy3TM fluorescent dye using T4 RNA ligase by the following procedure: RNA in 2.0 μl of water was combined with 1.0 μl of CIP buffer and CIP (Exiqon, Vedbaek, Denmark). The mixture was incubated for 30 min at 37°C and was terminated at 95°C for 5 min. Then, 3.0 μl of labeling buffer, 1.5 μl of fluorescent label (Hy3TM), 2.0 μl of DMSO and 2.0 μl of labeling enzyme were added to the mixture. The labeling reaction was incubated for 1 h at 16°C and was terminated by incubation at 65°C for 15 min. After termination, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) according to the array manual.

extract_protocol: Twelve pairs of gender- and age-matched Group D dust mite-induced asthma children and Group N normal control children were included in the initial microarray-based discovery analysis. Five ml of EDTA-anticoagulant peripheral blood was collected from each child. Total RNA was isolated by using the TRIzol (Invitrogen, Grand Island, NY, USA) and the miRNeasy mini kits (Qiagen, Chatsworth, CA, USA) according to the manufacturer’s instructions. This protocol efficiently recovered all RNA species, including miRNAs. The quality and quantity of RNAs collected from all participants were measured with a nanodrop spectrophotometer ND-1000 (Nanodrop Technologies, Wilmington, DE, USA), and RNA integrity was determined by gel electrophoresis.

tag: subject status

value: dust mite-induced asthma child

tag: gender

value: male

tag: age(year)

value: peripheral blood


title: dCD-R1-mESC_CST5326_H3K4me1

type: SRA

city: Chicago

first: Rohan

middle: Nishant

last: Shah

state: IL

address: CLSC 856, 920 E. 58th Street

country: USA

institute: University of Chicago

description:
Sample 23
ICeChIP-seq conducted on dCD MLL3/4 R1 mESCs against H3K4me1 using the antibody  Cell Signaling Technologies 5326, Lot 1, anti-H3K4me1.

library_source: genomic

data_processing:
To align reads, a reference genome was first created, consisting of the mouse genome (mm9) appended by the sequences of each of the nucleosome standard barcodes. Reads were then mapped to this reference genome using Bowtie2 using the sensitive preset and end-to-end alignment options.
Using SAMTools, any reads which were not paired, not mapped in a proper pair, or mapped with a map quality below 20 were then discarded to prevent low-quality mapping or sequencing reads from impacting downstream analyses. Reads were then flattened to create a single mapping from each matched pair of reads, and any mappings with lengths greater than 200bp were also discarded to ensure only mononucleosomes were being analyzed.
Bedgraphs of genome coverage were then generated using BEDTools, and IP and input genome coverage bedgraphs were merged using BEDTools7. The sum of reads across ladder members for each nucleosomal standard was computed for each sample and HMD bedgraphs were then generated from the merged bedgraphs using awk to apply the following formula: HMD (%) = 100% * (IPlocus/INlocus) / (IPbarcode/INbarcode). Error and 95% confidence intervals were computed with Poisson statistics and error propagation from the merged bedgraphs using awk to apply the following formula: 95CI Error (%) = 1.96 * HMD (%) * sqrt(1/IPlocus + 1/INlocus). Bigwig files were generated for visualization using the bedGraphToBigWig tool.
To compute average HMD across a series of intervals, a “double mapping” procedure was used. First, the HMD bedgraph was mapped onto 1bp windows made for each interval using BEDTools. Then, the mapped windows were mapped onto the original intervals using BEDTools. This procedure ensured that the degree of overlap of the interval with each value of the HMD bedgraph was accounted for in the mapping procedure.
Genome_build: mm9_bar_Ca1-17 (mm9 appended by synthetic DNA barcodes used with semisynthetic nucleosome standards)
Supplementary_files_format_and_content: Bedgraph files all have the form <chromosome> <start> <end> <value>, where the fourth field represents the value of the measurement. Bigwig files are bedgraph files in binary format, appropriate for viewing on a genome browser. Fasta file (with extension .fa) represents the reference genome used in this study, with the mouse genome (mm9) appended by the DNA barcode sequences used for the semisynthetic nucleosome standards.

molecule: genomic DNA

organism: Mus musculus

source_name: Cell Culture

growth_protocol: dCD R1 mESCs were cultured as previously described (Dorighi et al. 2017).

extract_protocol:
dCD MLL3/4 R1 mouse embryonic cell pellets were washed twice with 5 mL of PBS, then washed twice with 5 mL of Buffer N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 8.5% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized), with each wash consisting of complete resuspension of the pellet, centrifugation at 500 g for 5 minutes at 4°C, and removal of supernatant. The washed pellet was then resuspended in at least 2 packed cell volumes (PCV) of Buffer N and mixed with 1 volume of Lysis Buffer (Buffer N supplemented with 0.6% NP-40 Substitute) and incubated on ice for 10 minutes to lyse cells. The crude nuclei were spun down at 500 g for 5 minutes at 4°C before being resuspended in at least 6 packed nuclear volumes (PNV) of Buffer N and applied to the top of 7.5 mL of Sucrose Cushion N (15 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, 30% w/v Sucrose, 5 mM MgCl2, 1 mM CaCl2, 1 mM DTT, 200 uM PMSF, 50 ug/mL BSA, 1x Roche Protease Inhibitor Cocktail, Filter Sterilized) in a 15 mL centrifuge tube, then spun down at 500 g for 12 minutes at 4°C in a swinging-bucket rotor. The supernatant was discarded after centrifugation, and the pellet was resuspended in approximately 2 PNV of Buffer N. The nuclei were then quantified by diluting 2 uL of nuclei suspension into 48 uL of 2 M NaCl, water-bath sonicating to solubilize DNA, and spectroscopically measuring DNA concentration by Nanodrop measurement, where 1 A280nm¬ = 50 ng/uL chromatin in the measurement sample. After accounting for the 25-fold dilution of the measurement sample, the concentration of the nuclei was adjusted down to 1ug/uL of chromatin. Nuclei were aliquoted into 100 uL aliquots, flash frozen, and stored at -80°C until use. When nuclei aliquots were used, they were first thawed and spiked approximately 1 uL of each barcoded nucleosome standard per 50 ug of chromatin to be used. The nuclei suspension with spiked calibrants was then mixed with a pipette and transferred to a new tube, then warmed to 37°C for 2 minutes. After warming, 1 unit of micrococcal nuclease (MNase) per 4.375 ug of chromatin was added to the nuclei suspension and incubated at 37°C while shaking at 900 rpm for 12 minutes. After incubation, the digestion was stopped by adding 1/9 volume of 10x MNase Stop Buffer (100 mM EDTA, 100 mM EGTA, Filter Sterilized) while slowly vortexing, and nuclei were lysed by adding 5 M NaCl to a final concentration of 600 mM NaCl while slowly vortexing. 66 mg of HAP resin (BioRad, CHTTM Ceramic Hydroxyapatite, Type I, 20 um) per 100 ug of chromatin digested was rehydrated with 200 uL of HAP Buffer 1 (5 mM Sodium Phosphate pH 7.2, 600 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) per 100 ug of chromatin digested. The lysed nuclei were then spun down at 18,000 g for 1 minute to pellet insoluble nuclear debris, and the soluble fraction was added to the rehydrated HAP resin and incubated for 10 minutes on a rotator at 4°C. After incubation, the HAP resin slurry was added to a centrifugal filter unit (Millipore Ultrafree MC–HV Centrifugal Filter 0.45 um) and spun at 1000 g for 30 seconds at 4°C. The HAP resin left on the filter unit was then washed 4 times with 200 uL HAP Buffer 1 and 4 times with 200 uL HAP Buffer 2 (5 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized) by spinning at 1000 g for 30 seconds at 4°C. Into a clean tube, the HAP resin was eluted with three elutions of 100 uL HAP Elution Buffer (500 mM Sodium Phosphate pH 7.2, 100 mM NaCl, 1 mM EDTA, 200 uM PMSF, Filter Sterilized). The DNA content of the elution was then quantified spectroscopically with a Nanodrop, and the chromatin concentration was adjusted to 20 ng/uL with ChIP Buffer 1 (25 mM Tris pH 7.5, 5 mM MgCl2, 100 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) with 100 ug/mL of BSA. With the exception of the Koide Lab 304M3B antibody, every ICeChIP was conducted with 12.5 uL of Protein A Dynabeads (Invitrogen) and 3 ug of antibody. The Protein A Dynabeads for each ICeChIP were washed with 50 uL of ChIP Buffer 1 by use of a magnetic rack, then resuspended in 50 uL of ChIP Buffer 1. In a separate set of tubes, 3 ug of each antibody was diluted to 100 uL with ChIP Buffer 1. The antibody suspension and the Protein A Dynabeads suspension were combined and incubated on a rotator at 4°C for at least 1 hour, then washed with 200 uL of ChIP Buffer 1 by use of a magnetic rack and resuspended in 50 uL of ChIP Buffer 1. After antibody washing, 150 uL of the diluted chromatin elution was added to each antibody-bead conjugate and incubated for 15 minutes on a rotator at 4°C. After this incubation, the beads were washed twice with ChIP Buffer 2 (25 mM Tris pH 7.5, 5 mM MgCl2, 300 mM KCl, 10% v/v glycerol, 0.1% v/v NP-40 Substitute, Filter Sterilized) and once with ChIP Buffer 3 (10 mM Tris pH 7.5, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium Deoxycholate, 0.5% v/v NP-40 Substitute, Filter Sterilized), with a wash consisting of removal of the existing supernatant by use of a magnetic rack, resuspension into 150 uL of buffer, transfer to a new siliconized tube, and incubation on the rotator for 10 minutes at 4°C. After these washes, the supernatant was removed, and the beads were resuspended in ChIP Buffer 1, transferred to a new siliconized tube, then rinsed once with 200 uL of TE before being resuspended in 50 uL of ChIP Elution Buffer and incubated at 55°C for 5 minutes. After incubation, the supernatant was transferred to a new set of siliconized tubes, and the beads were discarded. To each supernatant was then added 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. 15 uL of Input DNA was also diluted to 50 uL with 35 uL of ChIP Elution Buffer (50 mM Tris pH 7.5, 1 mM EDTA, 1% w/v SDS, Filter Sterilized) and was supplemented with 2 uL of 5 M NaCl, 1 uL of 500 mM EDTA, and 1 uL of 10 mg/mL Proteinase K. The IP elutions and diluted input were then incubated at 55°C for 2 hours for a Proteinase K digestion. After digestion, the DNA was purified by adding 1.5 volumes of Serapure HD (1:50 dilution of Sera-Mag SpeedBeads [Fisher], 20% PEG-8000, 2.5 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20, Filter Sterilized prior to addition of SpeedBeads), incubating at room temperature for 15 minutes, then collecting the beads on a magnetic rack, washing twice with 150 uL of 70% ethanol, and eluting into 50 uL of water, which was then recovered and stored at -20°C.
DNA purified with Serapure was quantified using Quant-iT TM PicoGreen (Thermo Fisher) per manufacturer instructions. Up to 10 ng of each DNA sample for which libraries were to be prepared were then carried forward. Libraries were then generated from the NEBNext Ultra II DNA Library Prep kit (New England Biolabs) per manufacturer instructions. The DNA content of the library was then quantified and pooled for Illumina sequencing.

value: dCD MLL3/4 R1 mESC

tag: chip antibody

tag: amplification cycles


title: I_1hr_185

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

library_source: transcriptomic

data_processing:
Bowtie version 1.1.2 was used to map reads to the WS210 version of the genome.
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
edgeR was used on count tables for differential expression analysis. The count tables for the two batches were combined for filtering. The  count table was first filtered to contain those annotated as genes, reducing the number of genes to 22581.
Genes were further filtered by including only genes with counts per million (CPM) > 1 across 4 libraries. This resulted in 18190 genes. These were used for pairwise comparisons using the exact test in edgeR
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries). An excel file of differential expression analyses is included.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: LRB269 maintained at 20C was chunked, then bleached three days later to obtain embryos. Embryos were resuspended in 10 mL S-basal at a density of 1 embryo/uL. For ivermectin samples, ivermectin was added at a concentration of 5 ng/mL. These were then placed on the carousel at 22C. After 24 hours, HB101 was added at a concentration of 25 mg/mL to the food samples

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit.

treatment_protocol: 1 hour after HB101 is added (25 hours post bleach), the 1hr samples are collected. 24 hours after HB101 is added, the 24hr samples are collected (48 hours post bleach). Fed samples were washed quickly 3-4X with S-basal to remove bacteria prior to collection. Collected samples were flash frozen in liquid nitrogen and stored at -80C until RNA isolation

tag: food or no food

value: no food

tag: 1hr or 24 hr

tag: ivermectin or no ivermectin

value: ivermectin

tag: strain


title: CC

value: female


title: RC_02: ASML_Tspan8 Kd

value: Tspan8 Kd


title: I_1hr_183


title: WT-R1-mESC_CST5326_H3K4me1

description:
Sample 21
ICeChIP-seq conducted on WT R1 mESCs against H3K4me1 using the antibody  Cell Signaling Technologies 5326, Lot 1, anti-H3K4me1.


title: CWX


title: RC_01: ASML_wt

value: wt


title: I_1hr_181


title: NoIver_NoFood_4

value: no ivermectin


title: 630Δerm with pDccA, replicate D

city: Chapel Hill

first: Rita

last: Tamayo

state: NC

address: 125 Mason Farm Rd, CB# 7290

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalling and demultiplexing of the data was done using Illumina bcl2fastq v.2.17.0
Riboswitch annotations were added to the reference genome AM_180355.1 using the predicted riboswitch sequences from Sudarsan et al. Science 2008 and Lee et al. Science 2010.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. difficile 630 whole genome (AM 180355 with riboswitch annotations added) in CLC Genomics Workbench 9. Default settings for RNA-seq were used (allows 1 mismatch per read)
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench
Fold-change between mean RPKM values from pDccA vs. vector samples
Genome_build: AM_180355.1
Supplementary_files_format_and_content: Excel spreadsheet containing RPKM values for all individual samples, means, and highlights of genes >2-fold changed between pDccA and vector samples

organism: Clostridioides difficile

source_name: Clostridium difficile 630-delta-erm

growth_protocol: All steps anaerobic, 37 degrees C. Grown from freezer stocks on BHIS-agar-Tm10 (10 ug/ml thiamphenicol), overnight. Single colonies grown overnight (14-16h) in TY-Tm10 broth. Diluted 1:50 in BHIS-Tm10 broth with 1 ug/ml nisin.

extract_protocol:
Cell pellets collected by centrifugation. RNA extraction with TriSure and chloroform, beadbeating, and isopropanol/ethanol precipitation. Quality verified with Bioanalyzer Assay
Illumina TruSeq RiboZero Gold Kit, manufacturer's protocols

tag: sample type

value: C. difficile with elevated c-di-GMP


title: NoIver_NoFood_3


title: WZC


title: RX_07: AS_wt

source_name: cell line

value: AS


title: 630Δerm with pDccA, replicate A


title: NoIver_Food_4

value: food


title: 630Δerm with pDccA, replicate B


title: NoIver_NoFood_2


title: RX_06: ASML_Cld7 palm

value: Cld7 palm


title: RX_08: AS_CD9 Kd

value: rat pancreatic adenocarcinoma

value: CD9 Kd


title: RX_04: ASML_Tspan8 Kd

value: ASML


title: NoIver_Food_3


title: RX_05: ASML_Cld7 Kd

value: Cld7 Kd


title: 630Δerm with pDccA, replicate C


title: 630Δerm with vector, replicate D

value: C. difficile with basal c-di-GMP


title: ZWH

value: dust mite-induced asthma child

value: male

value: peripheral blood


title: NoIver_Food_2


title: RX_03: ASML_CD151 Kd

value: CD151 Kd


title: 3T3-L1 pre-adipocytes, CD24 siRNA +6 h IBMX/Dex rep3

city: St. John's

first: Sherri

middle: L

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: cDNA (25 ng/ul) was hybridized following the manufacturer's protocol for 16 h at 45˚C. Chip lot # 4226893.

scan_protocol: Scanning was performed by Microarray Facility, The Centre for Applied Genomics, The Hospital for Sick Children using the Affymetrix GeneChip Scanner 3000.

data_processing: Data was processed in R using RMA normalization in the oligo package.

label: Biotin Allonamide Triphosphate

label_protocol: RNA (250 ng) was processed and labeled by Microarray Facility, The Centre for Applied Genomics, The Hospital for Sick Children following the manufacturer's protocol using the Ambion WT kit.

growth_protocol: 3T3-L1 cells, in 12-well plates, were transfected with 100 nmol of siRNA for CD24 (MMC.RNAI.N009846.12.1, IDT, Coralville, Iowa) or 100 nmol of control scrambled siRNA (51-01-19-08, IDT) using a combination of Jetprime (4μl) and Interferin (2μl) (PolyPlus Transfection) according to the manufacturer’s protocol for Jetprime. The cells were grown in high glucose DMEM supplemented with glutamine and pyruvate until confluent. Cells were growth arrested by growing an additional 48 h.

extract_protocol: Cells were lysed and RNA extracted with TRIzol.

treatment_protocol: Media containing 0.5 mM IBMX  and 1 μM Dex (Millipore) in high-glucose DMEM supplemented with 10% FBS and 1% antibiotic/antimycotic (DMEM/FBS) was added to the cells for 6 hours.

value: 3T3-L1 preadipocyte


title: 3T3-L1 pre-adipocytes, CD24 siRNA +6 h IBMX/Dex rep2


title: 3T3-L1 pre-adipocytes, vehicle-control treated rep3


title: 3T3-L1 pre-adipocytes, vehicle-control treated rep1


title: 630Δerm with vector, replicate C


title: 3T3-L1 pre-adipocytes, CD24 siRNA +6 h IBMX/Dex rep1


title: NoIver_NoFood_1

value: no food


title: RX_02: ASML_EpC Kd

value: EpC Kd


title: 630Δerm with vector, replicate A


title: 630Δerm with vector, replicate B


title: 3T3-L1 pre-adipocytes, Scrambled siRNA +6 h IBMX/Dex rep3


title: 3T3-L1 pre-adipocytes, vehicle-control treated rep2


title: TDF AGO2-IP seq IgG control replicate 2

status: Public on Sep 19 2018

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

description:
Small RNA sequencing
TDF_IP_IgG_2_coverage_neg.bedgraph
TDF_IP_IgG_2_coverage_pos.bedgraph

data_processing:
Reads were demuliplexed by using codes in the id of each reads by using the ShortRead package in BioConductor. Identical sequences were collapsed using the occurrenceFilter function in the ShortRead package.
3' adapter sequences were trimmed using the trimLRPatterns function in the ShortRead package. The 3' adapter sequences trimmed were sequences containing CCTGTGGTCGTAGCATCAGCTA.
The trimmed sequences were collapsed and converted to reverse complementary sequences.
CLIP-seq reads were sequentially mapped to rRNA, snRNA, snoRNA, tRNA and microRNA precursors sequences using Bowtie verions 1.12.7  with the following configurations -q –m 70 -n 2 -l 44 -5 1 -3 5 -a --best --strata -p 11 --sam --norc for noncoding RNAs. The remaining reads were aligned with the hg19 human genome  with the configuration -q –m 1 -n 0 -l 70 -5 1 -3 5 -a --best --strata -p 11 --sam  unique genomic sequences to generate bedGraph files.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph. Scores stand for CLIP-seq read coverage

source_name: teratoma-derived fibroblasts (knock-in cells containing a Flag tag at the N-terminus of AGO2)

growth_protocol:
The H1 hESC cells were maintained on a mitotically inactivated mouse feeder (MEF) layer as follows. As a culture medium, DMEM/F12 supplemented with 20% Knockout Serum Replacement, 1% MEM non-essential amino acids, 1mM L-glutamine, 0.1mM β-mercaptoethanol and 4ng/ml basic FGF (Invitrogen) was used. Before analyses, hESCs were passaged three times without the feeder cells. For feeder-free culture, hESCs were dissociated with collagenase IV and plated on a Geltrex-coated plate with MEF-conditioned media supplemented with 50ng/ml basic FGF.
Generation of teratoma-derived fibroblasts (TDFs) was described as follows. Briefly, about 2 million hESC cells dissociated with TrypLE were resuspended in 30% Matrigel and injected into SCID mice subcutaneously. After six weeks, aseptically removed tumor was chopped with scissors to less than 1 cubic millimeters and plated in medium consisting of 10% FBS, nonessential amino acids, 2mM glutamine, 1% penicillin/streptomycin and 0.55μM β-mercaptoethanol. Outgrowing cells were passaged by trypsinization. For the IP analysis, TDFs at passage 10 were used.
To induce neural differentiation, hESCs maintained in feeder-free conditions were plated on a Geltrex-coated plate. After two days, hESC medium was replaced with DMEM/F12 supplemented with 2% B27, 100ng/ml FGF, 100ng/ml EGF and 5ng/ml heparin. Partially differentiated NPCs were dissociated with Accutase and incubated on a plate coated with diluted Geltrex as recommended by the manufacturer for the culture of NPCs. A homogenous population of NPCs was obtained after 3 or 4 subsequent passaging. NPCs at passage 7 were used for the CLIP analysis. Matrigel was purchased from BD Biosciences. All other reagents were purchased from Invitrogen.

extract_protocol:
Two million cells were resuspended in 250 μl lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing EDTA-free protease inhibitor cocktail (Roche) and RNase inhibitor (Ambion) and briefly sonicated by using the Bioruptor.
The lysates were treated with 5 μl of Turbo DNase (Ambion) and 10 μl of 10 U/μl or 1 U/μl RNase I (Ambion) at 37°C for 3 min. Cellular debris was removed by centrifugation at 13,000 rpm for 15 min. Protein-RNA complexes were immunopurified with anti-AGO2 (ProteinTech) or IgG antibody (Bethyl laboratories) bound to Protein A/G Dynabeads. Beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS) followed by two washes with PNK buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20). For dephosphorylation of 3’ ends, 1U of FastAP alkaline phosphatase (Fermentas) was added to the beads and incubated at 37°C for 20 min. After washing the beads twice with PNK buffer, protein-bound RNAs were ligated to a pre-adenylylated 3’ adaptor overnight at 16°C. Beads were washed twice with PNK buffer again and labeled with [γ- 32P] ATP for visualization. The labeled RNAs were separated by 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane, and excised from the membrane. The protein was degraded by proteinase K treatment, and RNA was recovered by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Protein-associated RNAs purified by IP or CLIP were ligated to a pre-adenylylated 3’ adaptor that contains a 2-nt adapter code for de-multiplexing and a 3-nt random sequence to minimize the loss of information after collapsing identical sequences. The RNA-adapter hybrids were converted into cDNAs with RT primer and SuperScript III reverse transcriptase (Invitrogen). The cDNAs were size-fractionated by electrophoresis on a 12% denaturing polyacrylamide gel and circularized by single-stranded DNA ligase (Epicentre). Circularized cDNAs were amplified with PCR primers, in which one of them contained a 6-nt primer code for de-multiplexing. PCR products were purified by agarose gel elution and subjected to next-generation sequencing.

treatment_protocol: Human ESCs were transfected with miRNA inhibitors or mimics as follows. Briefly, hESCs maintained in the feeder-free condition were treated with 10μM Y-27632 for 2h before dissociation with TrypLE. About three million hESCs were washed once with Opti-MEM, resuspended in 600μl of Lipofectamine 2000/RNA complex in Opti-MEM, and incubated for 15min. 30μl of Lipofectamine 2000 and 100nM of antagomirs/mimics were used. The transfected cells were cultured with Y-27632 for another 24h before UV-crosslinking. For CLIP analysis of let-7a- or miR-125a-transfected cells, hESCs were transfected with hsa-miR-302a/b/c inhibitors (50nM each), cultured for 24h, and transfected again with the mimics or control. miRNA hairpin inhibitors, mimics and controls were purchased from Dharmacon (hairpin negative control#1, IN-001005-01; negative control#2, IN-002005-01; hsa-miR-302a/b/c inhibitors, IH-300753-07/IH-300669-07/IH-300671-07; hsa-miR-367 inhibitor, IH-300673-07; mimic negative control #1, CN-001000-01; negative control #2, CN-002000-01; hsa-let-7a mimic, C-300473-05; hsa-miR-125a mimic, C-300624-05). For CLIP experiments cells were irradiated with 300 mJ/cm2 of UVC light (254 nm) by using the CL-1000 ultraviolet crosslinker (UVP).

tag: cell type

tag: rip antibody

value: rabbit IgG (Bethyl laboratories, P120-101)


title: 3T3-L1 pre-adipocytes, Scrambled siRNA +6 h IBMX/Dex rep1


title: Bulk RNA-seq DT replicate 3

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
bulk RNA-seq
normalised_bulk_counts.txt

data_processing:
Samples 1 - 313: Raw reads were trimmed using TrimGalore and Cutadapt. Alignment of the reads to the GRCm38 genome was performed using TopHat. Reads per gene were counted using htseq-count (single-cell RNA-seq) or Seqmonk (bulk RNA-seq). Reads were normalised using DESeq2 (bulk RNA-seq) or the scran Bioconductor R package (sinlge-cell RNA-seq) using the computeSumFactors function.
Samples 314 - 317: Raw sequencing data were processed through the 10X genomics Cellranger pipeline (v2). Cellranger demultiplexed the raw sequencing data, produced the fastq files, aligned the reads to the mouse genome (mm10, STAR aligner) performed unique molecular identifier (UMI) counting.
Genome_build: mm10
Supplementary_files_format_and_content: Samples 1 - 313: Tab separated text files contain normalised read counts with genes in rows and cells/samples in columns. Samples 314 - 317: Filtered gene barcode matrices output by the 10X genomics Cellranger pipeline in the h5 format (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)

source_name: Medial layer of mouse aorta

extract_protocol:
Aortas from healthy male mice (8-14 weeks) were dissected free of fat and connective tissue. Dissected aortas were immediately transferred to RNAlater solution (Ambion) followed by isolation of AA and DT segments before manual removal of the adventitial and endothelial cell layers. The cleaned medial layer from 3-5 animals was then lysed in Trizol (Thermo-Fisher) and total RNA isolated. The extracted RNA was cleaned on a RNeasy column (Qiagen) and quality-assessed on a Bioanalyzer (Agilent, RNA integrity number [RIN] 7.8-9)
Sequencing libraries were made from 550 ng total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: region

value: Descending thoracic aorta

tag: genotype

value: wild type

value: Vascular smooth muscle cells

tag: background


title: Bulk RNA-seq DT replicate 1

description:
bulk RNA-seq
normalised_bulk_counts.txt


title: Bulk RNA-seq AA replicate 1

description:
bulk RNA-seq
normalised_bulk_counts.txt

value: Aortic arch


title: Bulk RNA-seq AA replicate 2

description:
bulk RNA-seq
normalised_bulk_counts.txt


title: Bulk RNA-seq DT replicate 2

description:
bulk RNA-seq
normalised_bulk_counts.txt


title: Bulk RNA-seq AA replicate 3

description:
bulk RNA-seq
normalised_bulk_counts.txt


title: 3T3-L1 pre-adipocytes, Scrambled siRNA +6 h IBMX/Dex rep2

tag: cell line


title: TDF AGO2-IP seq replicate 2

description:
Small RNA sequencing
TDF_IP_2_coverage_neg.bedgraph
TDF_IP_2_coverage_pos.bedgraph

value: teratoma-derived fibroblasts (knock-in cells containing a Flag tag at the N-terminus of AGO2)

value: anti-FLAG M1 (Waco)


title: TDF AGO2-IP seq IgG control replicate 1

description:
Small RNA sequencing
TDF_IP_IgG_1_coverage_neg.bedgraph
TDF_IP_IgG_1_coverage_pos.bedgraph


title: TDF AGO2-IP seq replicate1

description:
Small RNA sequencing
TDF_IP_1_coverage_neg.bedgraph
TDF_IP_1_coverage_pos.bedgraph


title: Muscle_Control 4

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

description: gender: male, condition: Control, tissue: skeletal muscle

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

label: Biotin

source_name: Muscle Control

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: The animal experiment was approved by the local Animal Care and Use Committee (Regierungspräsidium Giessen; permission no: JLU 462_M). All experimental procedures described followed established guidelines for the care and handling of laboratory animals. The animal experiment included a total of 60 male, 3 wk-old NMRI mice (Harlan Winkelmann, Borchen, Germany). Mice were housed in groups of 5 mice each under controlled conditions (Macrolon cages, lighting from 07.00 to 19.00 h, 22 ± 1°C ambient temperature, 50-60 % relative humidity). After one wk of acclimatization, the mice were randomly assigned to two groups (control and carnitine) of 30 mice per group with similar body weights (control group: 12.0 ± 0.2, carnitine group: 12.0 ± 0.3; n = 30). Mice of the two groups were fed the same basal natural ingredient diet containing all nutrients in accordance with National Research Council recommendations of laboratory rodents (1995). The basal natural ingredient diet consisted of (g/kg diet): wheat, 429.5; maize, 252; soybean extraction meal (44% crude protein), 200; wheat bran, 40; soybean oil, 28; oat, 20; vitamin-mineral mix, 6; DL-methionine, 4.5; L-lysine-HCl, 1.5; calcium carbonate, 6; choline chloride, 1.5; calcium hydrogen phosphate dihdyrate, 11. Soybean extraction meal was used instead of casein due to its low native carnitine concentration.

extract_protocol: Total RNA from 30 mg frozen skeletal muscle aliquots was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. Afterwards, total RNA concentration and purity were estimated from the optical density at 260 and 280 nm respectively, using an Infinite 200M microplate reader equipped with a NanoQuant plate (both from Tecan, Mainz, Germany). The average optical density A260/A280 ratio of skeletal muscle total RNA samples was 1.87 ± 0.02 and 1.87 ± 0.02 (mean ± SD, n = 10) for the control group and the carnitine group, respectively.

treatment_protocol: In the control group, the basal natural ingredient diet, which had a low carnitine concentration of < 5 mg/kg diet as determined by tandem mass spectrometry, was fed unsupplemented. In the L-carnitine group, the basal natural ingredient diet was supplemented with 1,000 mg L-carnitine (Carnifeed; Lonza, Basel, Switzerland) per kg diet. The mice had free access to the diets and food intake was recorded weekly. Water was available ad libitum from nipple drinkers during the whole experiment. At an age of 9, 15 and 18 mo, 10 mice of each group were decapitated under CO2 anesthesia. Blood was collected into ethylenediaminetetraacetic acid (EDTA) polyethylene tubes (Sarstedt, Nürnbrecht, Germany), and plasma was separated from blood by centrifugation (1,100 x g; 10 min) at 4°C. The liver and an aliquot of skeletal muscle (M. gastrocnemius) were excised and immediately snap-frozen in liquid nitrogen. Afterwards, all samples were stored at -80°C pending analysis.

tag: condition

value: control

tag: tissue

value: skeletal muscle


title: NoIver_Food_1

value: food

value: no ivermectin


title: Muscle_Control 3

tag: gender

value: male


title: RX_01: ASML_wt

value: rat pancreatic adenocarcinoma

value: ASML

value: wt


title: Muscle_Control 5


title: Muscle_Carnitine 5

description: gender: male, condition: Carnitine, tissue: skeletal muscle

source_name: Muscle Carnitine

value: carnitine


title: Muscle_Carnitine 2


title: Muscle_Carnitine 1


title: NP AGO2-IP seq IgG control replicate 2

description:
Small RNA sequencing
NP_IP_IgG_2_coverage_neg.bedgraph
NP_IP_IgG_2_coverage_pos.bedgraph

source_name: Neural progenitor derived from H1

value: Neural progenitor derived from H1


title: Muscle_Carnitine 3


title: NP AGO2-IP seq IgG control replicate 1

description:
Small RNA sequencing
NP_IP_IgG_1_coverage_neg.bedgraph
NP_IP_IgG_1_coverage_pos.bedgraph

value: rabbit IgG (Bethyl laboratories, P120-101)


title: NP AGO2-IP seq replicate1

description:
Small RNA sequencing
NP_IP_1_coverage_neg.bedgraph
NP_IP_1_coverage_pos.bedgraph


title: NP AGO2-CLIP-seq replicate 2 high RNase I

description:
CLIP-seq for AGO2
NP_AGO2_coverage_neg.bedgraph
NP_AGO2_coverage_pos.bedgraph

value: anti-AGO2 (Proteintech, 10686-1)


title: Muscle_Control 2


title: NP AGO2-IP seq replicate 2

description:
Small RNA sequencing
NP_IP_2_coverage_neg.bedgraph
NP_IP_2_coverage_pos.bedgraph


title: Muscle_Control 1


title: Muscle_Carnitine 4


title: NP AGO2-CLIP-seq replicate 2 low RNase I


title: NP AGO2-CLIP-seq IgG control

description:
CLIP-seq for AGO2 IgG control
NP_AGO2_IgG_coverage_neg.bedgraph
NP_AGO2_IgG_coverage_pos.bedgraph


title: ESC FLAG-AGO2-CLIP-seq replicate 1 high RNase I

description:
CLIP-seq for FLAG-AGO2
ES_FLAG_AGO2_coverage_neg.bedgraph
ES_FLAG_AGO2_coverage_pos.bedgraph

source_name: Human embryonic stem cell H1

value: Human embryonic stem cell H1


title: ESC AGO2-CLIP-seq replicate 2 low RNase I

description:
CLIP-seq for AGO2
ES_AGO2_coverage_neg.bedgraph
ES_AGO2_coverage_pos.bedgraph


title: ESC FLAG-AGO2-CLIP-seq replicate 2 low RNase I


title: ESC AGO2-CLIP-seq IgG control

description:
CLIP-seq for AGO2 IgG control
ES_AGO2_IgG_coverage_neg.bedgraph
ES_AGO2_IgG_coverage_pos.bedgraph


title: ESC FLAG-AGO2-CLIP-seq replicate 2 high RNase I


title: NP AGO2-CLIP-seq replicate 1 high RNase I


title: NP AGO2-CLIP-seq replicate 1 low RNase I


title: ESC AGO2-CLIP-seq (let-7a mimic) IgG control

description:
CLIP-seq for AGO2 IgG control (let-7a transfection)
ES_AGO2_IgG_let7_coverage_neg.bedgraph
ES_AGO2_IgG_let7_coverage_pos.bedgraph

tag: treatment

value: let-7a transfection


title: ESC AGO2-CLIP-seq (let-7a mimic) low Rnase I

description:
CLIP-seq for AGO2 (let-7a transfection)
ES_AGO2_let7_coverage_neg.bedgraph
ES_AGO2_let7_coverage_pos.bedgraph


title: ESC AGO2-CLIP-seq replicate 1 low RNase I


title: ESC AGO2-CLIP-seq (miR-125a mimic) IgG control

description:
CLIP-seq for IgG (miR-125a transfection)
ES_AGO2_IgG_miR125_coverage_neg.bedgraph
ES_AGO2_IgG_miR125_coverage_pos.bedgraph

value: miR-125a transfection


title: ESC AGO2-CLIP-seq (let-7a mimic) high Rnase I


title: ESC AGO2-CLIP-seq (miR-125a mimic) high Rnase I

description:
CLIP-seq for AGO2 (miR-125a transfection)
ES_AGO2_miR125_coverage_neg.bedgraph
ES_AGO2_miR125_coverage_pos.bedgraph


title: ESC AGO2-CLIP-seq (miR-125a mimic) low Rnase I


title: ESC FLAG-AGO2-CLIP-seq replicate 1 low RNase I


title: ESC AGO2-CLIP-seq (miRNA control) high Rnase I

description:
CLIP-seq for AGO2 (miRNA transfection control)
ES_AGO2_miR_control_coverage_neg.bedgraph
ES_AGO2_miR_control_coverage_pos.bedgraph

value: miRNA-mock treatment


title: ESC FLAG-AGO2-CLIP-seq IgG control

description:
CLIP-seq for FLAG-AGO2 IgG control
ES_FLAG_AGO2_IgG_coverage_neg.bedgraph
ES_FLAG_AGO2_IgG_coverage_pos.bedgraph


title: ESC AGO2-CLIP-seq (antagomir-367) replicate 2 low RNase I

description:
CLIP-seq for AGO2 (miR-367 depleted cells)
ES_AGO2_i367_coverage_neg.bedgraph
ES_AGO2_i367_coverage_pos.bedgraph

value: antagomir-367 treatment


title: ESC AGO2-CLIP-seq (antagomir-367) IgG control

description:
CLIP-seq for AGO2 IgG control (miR-367 depleted cells)
ES_AGO2_IgG_i367_coverage_neg.bedgraph
ES_AGO2_IgG_i367_coverage_pos.bedgraph


title: ESC AGO2-CLIP-seq (antagomir-367) replicate 2 high RNase I


title: ESC AGO2-CLIP-seq replicate 2 high RNase I


title: ESC AGO2-CLIP-seq (antagomir-367) replicate 1 high RNase I


title: ESC AGO2-CLIP-seq (antagomir-367) replicate 1 low RNase I


title: ESC AGO2-CLIP-seq (antagomir control) IgG control

description:
CLIP-seq for AGO2 IgG control (miR-367 depletion control cells)
ES_AGO2_IgG_i367c_coverage_neg.bedgraph
ES_AGO2_IgG_i367c_coverage_pos.bedgraph

value: rabbit IgG (Bethyl)

value: antagomir-mock treatment


title: ESC AGO2-CLIP-seq (antagomir control) replicate 2 low RNase I

description:
CLIP-seq for AGO2 (miR-367 depletion control cells)
ES_AGO2_i367c_coverage_neg.bedgraph
ES_AGO2_i367c_coverage_pos.bedgraph


title: ESC AGO2-CLIP-seq (antagomir control) replicate 2 high RNase I


title: ESC AGO2-CLIP-seq (antagomir control) replicate 1 low RNase I


title: ESC AGO2-CLIP-seq (antagomir control) replicate 1 high RNase I


title: ESC AGO2-CLIP-seq replicate 1 high RNase I


title: ESC AGO2-CLIP-seq (miRNA control) low Rnase I


title: DEL_Input

city: New York

first: Richard

last: Koche

state: NY

address: 417 East 68th St

department: Center for Epigenetic research

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Peak calls was performed using MACS2 using the command macs2 callpeak with --nomodel --pvalue 0.001 over input. Matched input DNA was used as background for the peak calling.
Reads were trimmed using trimgalore
Trimmed reads were aligned to mm9 using bowtie2
FeatureCount was used to count the reads to the combined peak atlas
DESeq2 was used to normalise samples to the peak atlas
bedtools genomeCoverageBed was used to create normalised bw files using the DESeq2 normfactors. Input bigWig files were kept at depth normalisation to 10M reads.
Genome_build: mm9
Supplementary_files_format_and_content: normalised bigWig files

growth_protocol: RPMI 1640 + 10% h.i. FBS + 10 ng/ml mouse IL-3 or 10%

extract_protocol:
Lysates were cross-linked in 1% formaldehyde and lysed
Librairires were prepared using NEB ChIP-seq Library Preparation Kit

value: murine pro B cell line

tag: genotype/variation

value: expressing DEL Calreticuline (CALR)

tag: chip antibody

value: none (input)


title: WT_ChIP

description: Chr3852_WT_si_FLI1_282_2000_TS2_A12_IGO_08887_2_S44

value: expressing WT Calreticuline (CALR)

value: Fli1 antibody (Abcam, #ab15289, GR3183316-1)


title: INS_ChIP

description: Chr3854_INS_si_FLI1_282_2000_TS4_A12_IGO_08887_4_S46

value: expressing INS Calreticuline (CALR)


title: WT_Input


title: ESC AGO2-CLIP-seq (miRNA control) IgG control

description:
CLIP-seq for AGO2 IgG control (miRNA transfection control)
ES_AGO2_IgG_miR_control_coverage_neg.bedgraph
ES_AGO2_IgG_miR_control_coverage_pos.bedgraph


title: DEL_ChIP

description: Chr3853_DEL_si_FLI1_282_2000_TS3_A12_IGO_08887_3_S45


title: INS_Input


title: EV_ChIP

description: Chr3851_EV_si_FLI1_282_2000_TS1_A12_IGO_08887_1_S43

value: expressing Empty vector


title: Dermal CCR6+ innate lymphoid cells rep2; [RNA-Seq]

city: Bethesda

first: Tetsuro

last: Kobayashi

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm12N256

institute: NIAMS/NIH

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sample reads were trimmed adapters and low quality bases using Trimmomatic software. The trimmed reads were aligned with reference mouse genome mm10 and Gencode M9 annotation using STAR software
The gene expression quantification analysis was performed for all sample using STAR/RSEM
Genome_build: mm10

source_name: skin

extract_protocol:
RNA easy plus mini for RNA isolation
samples were prepared using SMRT-seq Ultra Low Input RNA kit with Nextera XT library prep protocol.

value: Dermal innate lymphoid cells

value: skin

tag: developmental stage

value: adult


title: Dermal Sca1+ innate lymphoid cells rep2; [RNA-Seq]


title: Epidermal innate lymphoid cells rep1; [RNA-Seq]

value: Epidermal innate lymphoid cells


title: Subcutaneous innate lymphoid cells rep3; [RNA-Seq]

value: Subcutaneous innate lymphoid cells


title: Dermal CCR6+ innate lymphoid cells rep1; [RNA-Seq]

value: Dermal CCR6+ innate lymphoid cells


title: Subcutaneous innate lymphoid cells rep1; [RNA-Seq]


title: Dermal Sca1+ innate lymphoid cells rep1; [RNA-Seq]

value: Dermal Sca1+ innate lymphoid cells


title: Subcutaneous innate lymphoid cells rep2

data_processing:
Basecalls performed using CASAVA version 1.8.4
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 alignment (Bowtie2.2.10)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.


title: Epidermal innate lymphoid cells rep2; [RNA-Seq]


title: Epidermal innate lymphoid cells rep2


title: Dermal innate lymphoid cells rep2


title: Subcutaneous innate lymphoid cells rep1


title: Dermal innate lymphoid cells rep1


title: EV_Input


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_H7_t

description:
Single-cell RNA seq, Smart-Seq2
normalised_counts_smartseq2_sca1.txt

extract_protocol:
Myh11-CreERt2/Rosa26-Confetti males received intraperitoneal injections of tamoxifen in corn oil, at 6-8 weeks of age (10 injections of 1 mg/ml each) for lineage labelling. Aortas of healthy male mice were dissected free of fat and connective tissue. To generate single-cell suspensions, endothelial cells were removed manually from dissected aortas using a cotton bud and vessels incubated for 10 minutes in Collagenase Type IV (1 mg/ml, Life Technologies) and porcine pancreatic elastase (1 U/ml, Worthington BioChem) to allow for separation of the adventitia and medial cell layers. Tissue isolated from 5-11 animals was pooled and further digested for 1-2 hours to achieve a single-cell suspension, which was filtered through a 40 μm cell strainer. Individual Sca1-positive (S+) and Sca1-negative (S-) cells expressing a single VSMC-lineage marker (L+) or no VSMC-lineage marker (L-) were FACS-sorted on an Aria-Fusion flow cytometer (BD Bioscience) into separate wells of a 96-well plate. Sca1+ and Sca1- cells were included on the same plate and processed together to generate amplified cDNA using the Smart-seq2 protocol carried out as described previously (Picelli et al, Nature protocols 2014), with the following minor modifications: Primescript (Clontech) was used for reverse transcription, 24 PCR cycles were used for amplification of cDNA, and ERCC control RNA (Invitrogen) was added (1:40,000,000 or 1:80,000,000 dilution in RT-mix).
After quality assessment by Bioanalyzer (Agilent) and Quant-iT PicoGreen (Thermo Fisher) quantification, sequencing libraries were prepared from amplified cDNA (approximately 1-6 ng per sample) using the Nextera XT library prep kit (Illumina).

value: Aorta

value: Vascular cell


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_H6_t


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_H4_t


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_H5_t


title: Epidermal innate lymphoid cells rep1


title: Epidermal innate lymphoid cells rep3; [RNA-Seq]


title: Subcutaneous innate lymphoid cells rep2; [RNA-Seq]


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_H3_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_H12_t


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_G6_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_G9_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_H11_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_H10_t


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_G5_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_G8_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_G10_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_F2_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_F1_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_E9_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_F3_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_F9_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_F8_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_E2_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_E8_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_E1_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_E10_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_D9_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_E12_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_D8_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_D6_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_D2_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_D12_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_D10_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_D1_t


title: Lineage negative Sca1 positive  cell CnSp.w01b1.sca1_G7_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_C3_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_G11_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_C9_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_C2_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_C8_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_F11_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_C11_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_F10_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_C1_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_B9_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_C10_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_B8_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_B3_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_B11_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_B2_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_B12_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_A9_t


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_A8_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_A12_t


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_A3_t


title: Lineage positive Sca1 negative  cell CpSn.sca1_H9_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_H6_s


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_A10_t


title: Lineage positive Sca1 negative  cell CpSn.sca1_H8_s


title: Lineage positive Sca1 positive  cell CpSp.w13b1.sca1_A11_t


title: Lineage positive Sca1 negative  cell CpSn.sca1_H3_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_H5_s


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_A1_t


title: Lineage positive Sca1 positive  cell CpSp.w13b2.sca1_C12_t


title: Lineage positive Sca1 negative  cell CpSn.sca1_H12_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_H10_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G7_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G8_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G6_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G3_s


title: Lineage positive Sca1 positive  cell CpSp.w01b1.sca1_B1_t


title: Lineage positive Sca1 negative  cell CpSn.sca1_F8_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G5_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F4_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F5_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G4_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F7_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_E7_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_G10_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F6_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F2_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F11_s


title: Lineage positive Sca1 negative  cell CpSn.sca1_F1_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_E12_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_E6_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_E10_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_E11_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_E5_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_D11_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_C11_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_C2_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_B8_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_D8_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_D7_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_D2_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_B12_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_C6_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_C1_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_A7_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_B7_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_B6_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_B11_s


title: Lineage negative Sca1 positive  cell CnSp.sca1_93_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_94_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_A10_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_B1_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_C7_s


title: Lineage negative Sca1 positive  cell CnSp.sca1_83_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_82_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_A12_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_86_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_85_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_91_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_78_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_C4_s


title: Lineage positive Sca1 positive  cell CpSp.sca1_76_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_70_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_74_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_71_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_95_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_67_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_79_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_65_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_66_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_81_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_62_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_49_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_47_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_89_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_45_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_46_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_43_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_39_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_42_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_35_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_34_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_37_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_27_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_24_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_33_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_22_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_31_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_19_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_23_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_18_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_57_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_10_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_7_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_21_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_6_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_4_f


title: Lineage negative Sca1 positive  cell CnSp.sca1_12_f


title: Lineage positive Sca1 negative  cell CpSn.sca1_9_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_5_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_1_f


title: Lineage positive Sca1 positive  cell CpSp.sca1_40_f


title: AA ex vivo cell AA_B11_93

description:
Single-cell RNA seq, Fluidigm C1
normalised_aadt_counts.txt

extract_protocol:
Aortas from healthy male mice (8-14 weeks) were dissected free of fat and connective tissue. To generate single-cell suspensions, endothelial cells were removed manually from dissected aortas using a cotton bud, AA and DT segments isolated and incubated for 10 minutes in Collagenase Type IV (1 mg/ml, Life Technologies) and porcine pancreatic elastase (1 U/ml, Worthington BioChem) to allow for separation of the adventitia and medial cell layers. The medial layer from 5-8 animals was pooled and further digested for 1-2 hours to achieve a single-cell suspension, which was filtered through a 40 μm cell strainer. The AA and DT samples were processed using a Fluidigm C1 system. Cell suspensions (100 cells/μl) were loaded onto medium-sized (17-25 μm) Auto Prep Arrays (Fluidigm) and processed according to the manufacturer’s instructions. The loaded arrays were visually assessed under an inverted microscope to select capture sites containing a single cell, yielding a 40-70% capture efficiency.
Cells were processed using the SMARTer® Ultra™ Low RNA Kit (Clontech) and amplified cDNA was isolated from the arrays. Sequencing libraries were made from 0.125-0.375 ng amplified cDNA using the Nextera XT library preparation kit (Illumina).

value: Aortic arch

value: wild type

value: Vascular smooth muscle cell


title: AA ex vivo cell AA_C10_89


title: AA ex vivo cell AA_F10_91


title: AA ex vivo cell AA_E10_90


title: AA ex vivo cell AA_A11_92


title: AA ex vivo cell AA_F11_96


title: AA ex vivo cell AA_C11_94


title: AA ex vivo cell AA_E11_95


title: AA ex vivo cell AA_B6_65


title: AA ex vivo cell AA_A7_69


title: AA ex vivo cell AA_B8_72


title: AA ex vivo cell AA_D3_37


title: Lineage positive Sca1 positive  cell CpSp.sca1_16_f


title: AA ex vivo cell AA_E7_70


title: AA ex vivo cell AA_C6_66


title: AA ex vivo cell AA_F2_33


title: AA ex vivo cell AA_F3_38


title: AA ex vivo cell AA_A3_34


title: AA ex vivo cell AA_A9_73


title: AA ex vivo cell AA_A4_40


title: AA ex vivo cell AA_B3_35


title: AA ex vivo cell AA_B10_80


title: Lineage positive Sca1 positive  cell CpSp.sca1_2_f


title: AA ex vivo cell AA_G3_39


title: AA ex vivo cell AA_C5_45


title: AA ex vivo cell AA_D9_76


title: AA ex vivo cell AA_D4_42


title: AA ex vivo cell AA_B4_41


title: AA ex vivo cell AA_A6_48


title: AA ex vivo cell AA_B5_44


title: AA ex vivo cell AA_D5_46


title: AA ex vivo cell AA_F9_77


title: AA ex vivo cell AA_E5_47


title: DT ex vivo cell DT_H5_25

value: Descending thoracic aorta


title: DT ex vivo cell DT_B6_27


title: DT ex vivo cell DT_D6_28


title: DT ex vivo cell DT_A7_32


title: AA ex vivo cell AA_C3_36


title: DT ex vivo cell DT_E4_19


title: DT ex vivo cell DT_H6_31


title: DT ex vivo cell DT_B5_21


title: AA ex vivo cell AA_H9_79


title: DT ex vivo cell DT_H3_17


title: DT ex vivo cell DT_G5_24


title: DT ex vivo cell DT_C4_18


title: DT ex vivo cell DT_D7_51


title: 10X Whole aorta

description:
Single-cell RNA seq, 10X Chromium
10X_whole_aorta_filtered_gene_bc_matrices_h5.h5

source_name: Mouse aorta

extract_protocol:
Aortas from three male animals were dissected free of fat and connective tissue and subjected to enzymatic digestion. Single cell suspensions were pooled, filtered through a 40 um filter and 20,000 singlet cells isolated by FACS-sorting on an Aria-Fusion flow cytometer (BD Bioscience).
Libraries were prepared using the 10X Chromium platform.


title: 10X Lineage positive medial cells

description:
Single-cell RNA seq, 10X Chromium
10X_lineage_positive_filtered_gene_bc_matrices_h5.h5

extract_protocol:
Aortas from three tamoxifen-labelled Myh11-CreERt2/Confetti males were dissected free of fat and connective tissue and subjected to enzymatic digestion. Single cell suspensions were pooled, filtered through a 40 um filter and FACS sorted on an Aria-Fusion flow cytometer (BD Bioscience) for expression of a single confetti colour only.
Libraries were prepared using the 10X Chromium platform.


title: DT ex vivo cell DT_B7_49


title: 10X Lineage positive plaque cells 18w

description:
Single-cell RNA seq, 10X Chromium
10X_plaque_18w_filtered_gene_bc_matrices_h5.h5

extract_protocol:
Plaques were manually isolated by dissection from Myh11-CreERt2/Rosa26-Confetti/ApoE-/- animals that had been tamoxifen labelled and then fed a high fat diet for 18 weeks (as described in Chappell et al  2016). Plaques were digested as described (Butcher et al 2011) and plaque cells from two-three animals per time point were pooled and processed in parallel, filtered through a 40 um filter and 20,000 singlet cells expressing a single confetti protein isolated by FACS-sorting on an Aria-Fusion flow cytometer (BD Bioscience). Sorted cells were pelleted and resuspended in 35 ul PBS with 0.1% BSA.
Libraries were prepared using the 10X Chromium platform.


title: DT ex vivo cell DT_G7_53


title: 10X Lineage positive plaque cells 14w

description:
Single-cell RNA seq, 10X Chromium
10X_plaque_14w_filtered_gene_bc_matrices_h5.h5

extract_protocol:
Plaques were manually isolated by dissection from Myh11-CreERt2/Rosa26-Confetti/ApoE-/- animals that had been tamoxifen labelled and then fed a high fat diet for 14 weeks (as described in Chappell et al  2016). Plaques were digested as described (Butcher et al 2011) and plaque cells from two-three animals per time point were pooled and processed in parallel, filtered through a 40 um filter and 20,000 singlet cells expressing a single confetti protein isolated by FACS-sorting on an Aria-Fusion flow cytometer (BD Bioscience). Sorted cells were pelleted and resuspended in 35 ul PBS with 0.1% BSA.
Libraries were prepared using the 10X Chromium platform.


title: DT ex vivo cell DT_E5_23


title: DT ex vivo cell DT_C7_50


title: AA ex vivo cell AA_G11_88


title: PTHrP-mCherry_CE

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of mCherry to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 500 genes per cell and with more than 20% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and t-SNE), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv (celluar barcodes), genes.tsv (gene identifiers), matrix.mtx (UMI counts)

source_name: FACS-sorted at P6

extract_protocol:
Mandibular molars were extracted, dental follicle cells were enzymatically dissociated and mCherry+ cells were FACS-isolated. ~8,000 cells were loaded onto 10X Genomic Chromium platform
10X Genomic Chromium Single Cell 3' v2 Libraries

value: PTHrP(mCherry/+)

value: Postnatal day 6

value: Dental follile (mandibular molars)

value: PTHrP+ dental follicle cells (mCherry+)


title: DT ex vivo cell DT_B8_55


title: DT ex vivo cell DT_G6_30


title: DT ex vivo cell DT_C10_61


title: DT ex vivo cell DT_A9_58


title: DT ex vivo cell DT_H10_64


title: DT ex vivo cell DT_A10_60


title: DT ex vivo cell DT_E10_62


title: DT ex vivo cell DT_E7_52


title: DT ex vivo cell DT_D11_82


title: DT ex vivo cell DT_A11_81


title: DT ex vivo cell DT_C12_84


title: DT ex vivo cell DT_E12_86


title: DT ex vivo cell DT_D9_59


title: DT ex vivo cell DT_D8_56


title: DT ex vivo cell DT_C1_100


title: DT ex vivo cell DT_D1_101


title: 5mm_B6

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

hyb_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY

data_processing: Gene-level probeset summary of microarray data were obtained using RMA background correction and quantile normalization provided in Expression Console Software, version 1.4.1 (Affymetrix).  Control probesets and probesets lacking mRNA accession tags were removed from further analysis.  Statistical analysis was performed using the limma R package with paired sample comparison.

label: biotin

source_name: distance from tumor, patient id

growth_protocol: 108 samples taken from patients at tumor, 5mm, 10mm, 15mm, 20mm from tumor were subjected to microarray analysis using HG-U133 Plus 2 affymetrix arrays

extract_protocol: RNA was isolated QIAGEN RNeasy MinElute Cleanup Kit. RNA quantity and quality for all samples were determined by bioanalysis (Agilent Technologies), and samples stored in nuclease-free water at −80°C. 10 μg of pooled RNA was used for microarray analysis using HG-U133 Plus 2 (Affymetrix), according to the manufacturer instructions

tag: distance from tumor

tag: patient id


title: 5mm_B8

scan_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity,  located at NYU Health NY, NY


title: DT ex vivo cell DT_G10_63


title: 5mm_B1

label_protocol: label, hybridization, and scanning protocols were performed by the NYUMC genomics core facitlity, located at NYU Health NY, NY


title: DT ex vivo cell DT_B3_107


title: 5mm_5


title: 5mm_B5


title: 5mm_7


title: DT ex vivo cell DT_F1_103


title: DT ex vivo cell DT_D2_105


title: 5mm_6


title: DT ex vivo cell DT_F12_87


title: 5mm_4


title: 5mm_1141


title: 5mm_1140


title: 5mm_8


title: 5mm_147


title: DT ex vivo cell DT_A3_106


title: 5mm_1136


title: 5mm_2


title: AA ex vivo cell AA_run5_H5


title: 5mm_1132


title: AA ex vivo cell AA_run5_H6


title: 5mm_1131


title: AA ex vivo cell AA_run5_H4


title: 5mm_12


title: AA ex vivo cell AA_run5_H3


title: AA ex vivo cell AA_run5_H2


title: 5mm_1122


title: AA ex vivo cell AA_run5_H1


title: 5mm_1127


title: 5mm_1124


title: 5mm_1121


title: 5mm_1108


title: AA ex vivo cell AA_run5_G6


title: AA ex vivo cell AA_run5_G4


title: AA ex vivo cell AA_run5_G3


title: AA ex vivo cell AA_run5_G2


title: AA ex vivo cell AA_run5_G1


title: AA ex vivo cell AA_run5_F6


title: AA ex vivo cell AA_run5_F5


title: AA ex vivo cell AA_run5_F3


title: AA ex vivo cell AA_run5_F2


title: AA ex vivo cell AA_run5_G5


title: 20mm_B7


title: AA ex vivo cell AA_run5_F1


title: 20mm_B8


title: 5mm_1105


title: AA ex vivo cell AA_run5_E5


title: 5mm_1


title: 20mm_B6


title: 5mm_1100


title: AA ex vivo cell AA_run5_E4


title: AA ex vivo cell AA_run5_F4


title: 20mm_B1


title: 20mm_B5


title: 20mm_3


title: 20mm_147


title: AA ex vivo cell AA_run5_E3


title: 20mm_6


title: 20mm_4


title: 20mm_5


title: AA ex vivo cell AA_run5_E2


title: 20mm_8


title: AA ex vivo cell AA_run5_E6


title: 20mm_1136


title: 20mm_1132


title: 20mm_1141


title: AA ex vivo cell AA_run5_E1


title: 20mm_1130


title: 20mm_1127


title: AA ex vivo cell AA_run5_D4


title: AA ex vivo cell AA_run5_D3


title: 20mm_1


title: AA ex vivo cell AA_run5_D2


title: AA ex vivo cell AA_run5_D5


title: 20mm_1124


title: AA ex vivo cell AA_run5_D1


title: AA ex vivo cell AA_run5_C6


title: AA ex vivo cell AA_run5_C5


title: AA ex vivo cell AA_run5_C4


title: AA ex vivo cell AA_run5_C2


title: AA ex vivo cell AA_run5_B6


title: AA ex vivo cell AA_run5_B7


title: AA ex vivo cell AA_run5_B5


title: 20mm_1108


title: AA ex vivo cell AA_run5_B4


title: 15mm_6


title: 20mm_1120


title: 15mm_3


title: AA ex vivo cell AA_run5_B2


title: 15mm_1124


title: 15mm_1


title: 15mm_8


title: AA ex vivo cell AA_run5_B1


title: 15mm_1123


title: AA ex vivo cell AA_run5_A6


title: AA ex vivo cell AA_run5_A7


title: 15mm_4


title: AA ex vivo cell AA_run5_A4


title: 15mm_1106


title: AA ex vivo cell AA_run5_A5


title: 15mm_1108


title: 15mm_1121


title: AA ex vivo cell AA_run5_B3


title: DT ex vivo cell DT_run3_H5


title: DT ex vivo cell DT_run3_H4


title: DT ex vivo cell DT_run3_H1


title: DT ex vivo cell DT_run3_G9


title: DT ex vivo cell DT_run3_G6


title: 10mm_B6


title: 10mm_B5


title: DT ex vivo cell DT_run3_G5


title: 10mm_B8


title: AA ex vivo cell AA_run5_A2


title: DT ex vivo cell DT_run3_G1


title: 4 ppm R3

city: Barcelona

first: Rubén

middle: Francisco

last: Martínez López

state: Cataluña

address: Carrer Jordi Girona, 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

data_processing:
Real Time Analysis (RTA 1.13.48) software was used for basecalling and the quality scoring of the run.
Generation of FASTQ sequence files was carried out with CASAVA software.
RNA-seq reads were aligned to the GRCz10 genome reference using STAR version 2.5.1b
Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters
Differential expression analysis between all BPA conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option (Li and Dewey, 2011; Love et al., 2014)
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include absolute reads values (counts) for each sample.

organism: Danio rerio

source_name: Whole larvae

growth_protocol: Zebrafish (Danio rerio) embryos were obtained by natural mating following standard procedures. At 2 hours post fertilization (hpf), eggs were collected, rinsed and fertilized viable eggs were transferred to embryo water (90 µg/ml of Instant Ocean -Aquarium Systems, Sarrebourg, France-, 0.58 mM CaSO4·2H2O, dissolved in reverse osmosis purified water) and kept under standard conditions (28.5 ºC and 12L:12D photoperiod).

extract_protocol:
ZF embryos were taken in an Eppendorf (10 larvae per replicate) and flash frozen on dry ice. Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA). Then, total RNA was assayed for quantity and quality using Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent Technologies).
Libraries for RNA-Seq were prepared from total RNA using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems) with minor modifications. Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads and 500 ng of total RNA as the input material, the mRNA was fragmented (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters (Illumina) were added by ligation. The ligation product was enriched through 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired-end mode with a read length of 2x76bp. We generated on average 40 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina) following the manufacturer’s protocol.

treatment_protocol: The exposure of the larvae was driven through the water: Bisphenol A (BPA, Sigma-Aldrich, St. Louis, MO, USA) stock solutions (50, 500 and 2000 mg·L-1) were prepared in DMSO and stored at -20 °C. During the exposure period, fresh working solutions were prepared everyday by dissolving the stock solutions in fish water, with a final concentration of DMSO of 0.2% (v/v). The final BPA working concentrations were: 0 (control), 0.1, 1 and 4 mg·L-1.

tag: age

value: 5 days post fertilization

tag: Stage

value: eleutheroembryo

tag: agent

value: BPA

value: 4 ppm

tag: exposure time

value: from 2 to 5 dpf

tag: number of larvae/replicate


title: 10mm_B1


title: 10mm_3


title: 15mm_1120


title: 4 ppm R1

tag: genotype


title: DT ex vivo cell DT_run3_F7

tag: region

tag: cell type

tag: background


title: 10mm_5


title: 4 ppm R2

tag: condition


title: 10mm_1136


title: 10mm_7


title: 10mm_1131


title: 10mm_1471


title: 10mm_1140


title: 10mm_1141


title: 10mm_1127


title: 10mm_1132


title: 10mm_1475


title: 10mm_8


title: DT ex vivo cell DT_run3_F3


title: 1 ppm R2

value: 1 ppm


title: 10mm_1121


title: 1 ppm R1


title: 0.1 ppm R3

value: 0.1 ppm


title: DT ex vivo cell DT_run3_F1


title: 1 ppm R3


title: 10mm_1120


title: 0.1 ppm R2


title: 0.1 ppm R1


title: DT ex vivo cell DT_run3_E1


title: 10mm_1123


title: 10mm_1108


title: DT ex vivo cell DT_run3_E8


title: Ctrl R2

value: Control


title: Ctrl R1


title: DT ex vivo cell DT_run3_D7


title: DT ex vivo cell DT_run3_D3


title: 10mm_1106


title: 10mm_1


title: 0mm_B8


title: Ctrl R3


title: DT ex vivo cell DT_run3_C8


title: DT ex vivo cell DT_run3_D1


title: DT ex vivo cell DT_run3_C12


title: Ao-sided DA_IP_rep2

city: Tokyo

first: Toru

last: Akaike

address: 3-25-8 Nishi-Shimbashi, Minato-ku

department: Cell Physiology

country: Japan

institute: The Jikei University

description: Gene expression data from chicken aorta-sided ductus arteriosus at IP

hyb_protocol: Following fragmentation, 50ng of cRNA were hybridized for 17 hr at 45C on Affymetrix GeneChip® Chicken Gene 1.0 ST-v1 Array. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using  Affymetrix GeneChip® Scanner.

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® Software version 2.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Gallus gallus

source_name: chicken aorta-sided ductus arteriosus, IP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Sepasol®-RNA I Super G extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: chicken aorta-sided ductus arteriosus

value: internal pipping (IP)


title: PA-sided DA_IP_rep1

description: Gene expression data from chicken pulmonary-sided ductus arteriosus at IP

source_name: chicken pulmonary-sided ductus arteriosus, IP


title: Ao_IP_rep2

description: Gene expression data from chicken aorta at IP

source_name: chicken aorta, IP

value: chicken aorta


title: Ao_IP_rep1


title: PA-sided DA_IP_rep2

value: chicken pulmonary-sided ductus arteriosus


title: Ao-sided DA_IP_rep1


title: 0mm_B7


title: 0mm_B2T


title: DT ex vivo cell DT_run3_C3

value: Descending thoracic aorta

value: wild type

value: Vascular smooth muscle cell


title: 0mm_B6


title: DT ex vivo cell DT_run3_B7


title: DT ex vivo cell DT_run3_B6


title: 0mm_B1


title: 0mm_8


title: DT ex vivo cell DT_run3_B4


title: 0mm_5


title: MYC, tumor, replicate 1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.40.2).

source_name: tumor liver tissue sample, obtained from liver-specific MYC-overexpressing mouse

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Diethylnitrosamine (DEN) driven liver tumors [PMID: 15329734], Lymphotoxin-α/b-(LTa/b) driven tumors [PMID: 15661974] and Myc-driven liver tumors [PMID: 17589519] were generated as described previously. In brief, for generation of DEN-driven tumors, mice were given intraperitoneal injections of DEN (Sigma) at a dose of 10 mg per kg body weight at 15 d of age [PMID: 26502405]. Mice were observed for development of tumors at 9 months of age. For LTα/β driven tumors, tg1223 mice expressing LTα and -β in a liver-specific manner at high level were followed for 12 months for tumor development [PMID: 19800575]. Finally, for Myc-driven liver tumors, TRE-MYC mice were crossed to LAP-tTA (liver-specific promoter) mice. Animals were maintained on doxycycline (200 mg/kg doxy chow) to suppress MYC expression until 8 weeks of age. Doxycycline was then removed, and mice were followed for evidence of tumor formation [PMID: 19061838].

extract_protocol: Total RNA, along with miRNA, was isolated  by Directzol RNA Miniprep (Zymo Research, Irvine, CA). RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for analysis only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice had free access to chow and water. At the indicated time points, mice were killed and livers were removed. Livers were macroscopically dissected and tumor material, non-tumorous control liver tissue as well as liver tissue from untreated, sex- and age-matched control mice were immediately snap frozen, followed by histopathological confirmation of the tumor tissue.

tag: experiment

value: LT/MYC

tag: mouse id

value: liver


title: DT ex vivo cell DT_run3_B3


title: MYC, tumor, replicate 5


title: MYC, NTL, replicate 2

source_name: non-tumorous liver (NTL) tissue sample, obtained from liver-specific MYC-overexpressing mouse


title: 0mm_7


title: MYC, tumor, replicate 4


title: DT ex vivo cell DT_run3_B12


title: MYC, tumor, replicate 3


title: MYC, NTL, replicate 3


title: LTα/β, tumor, replicate 3

source_name: tumor liver tissue sample, obtained from liver-specific Lymphotoxin-α/β (LTα/β)-overexpressing mouse


title: LTα/β, tumor, replicate 2


title: 0mm_305


title: MYC, NTL, replicate 1


title: LTα/β, NTL, replicate 4

source_name: non-tumorous liver (NTL) tissue sample, obtained from liver-specific Lymphotoxin-α/β (LTα/β)-overexpressing mouse


title: LTα/β, NTL, replicate 5


title: MYC, tumor, replicate 2


title: 0mm_4


title: LTα/β, NTL, replicate 3


title: LTα/β, tumor, replicate 1


title: miRNA_MYC, tumor, replicate 5

data_processing:
OpenArray Digital PCR Software Software (v1.0, Applied Biosystems) was used to analyze and review the amplification plots and threshold cycle (Ct) values obtained. Default analysis settings were used, except that for baseline estimations data from cycles 2-10 were used, and that for some samples the minimum signal value was set at 100 instead of the default value of 300. Data was then exported, and further analyzed in R using the Bioconductor packages HTqPCR [PMID: 19808880] and limma [PMID: 25605792]. In HTqPCR, the minimum and maximum allowable Ct value were set at 8 and 31, respectively.
The qPCR data was normalized by the ΔCt method, using for each sample as internal reference the mean Ct value of 5 endogenous small non-coding RNA controls (U87, Y1, U6, snoRNA135, snoRNA202).
Next, only those miRNAs that were reliably expressed (i.e. Ct<31) in all samples were included for further analysis. This stringent filtering was applied to limit the screening to a set of robustly expressed miRNAs and to increase statistical power, and resulted in the removal of 620 miRNAs. The remaining 130 miRNAs were included in the statistical analysis.
The non-normalized data file reports the Ct values of 846 miRNAs and controls (non-normalized data). Note that some controls are present multiple times. Ct values of 40 indicates N/A.
The file Feature Category reports the Feature Category (i.e. "OK" and "Undetermined") based on expression (Ct-value) of the target. Features having Ct>31 were considered non-expressed, and were thus labeled "Undetermined".
The file normalized  reports the ΔCt values of 130 robustly expressed miRNAs, obtained after filtering as described above. (ΔCt normalized data).

label: FAMTP

label_protocol: miRNA expression levels were profiled using the TaqMan OpenArray Rodent MicroRNA Panel (Applied Biosystems; cat.no. 4461105). This platform allows the simultaneous profiling of 750 well-characterized miRNAs (miRBase v15) and 6 controls. Samples were processed according to the manufacturer’s instructions. In brief, for each sample 100ng of total RNA (that included the miRNA fraction) was reverse transcribed using Megaplex RT primers in a set of two pre-defined pools (Pool A and Pool B), each pool contained 381 stem-looped RT primers (375 miRNA targets, 5 positive controls, 1 negative control). The recommended RT thermal cycling conditions were used: i.e. [16°C, 2 min; 42°C, 1 min; 50°C, 1 sec for 40 cycles]; 85°C, 5 min; 4°C hold. The cDNA products (2.5µl) then underwent unbiased PCR preamplification using Megaplex PreAmp Primers in a set of two pools (Pool A and Pool B) of gene-specific forward and reverse primers. Thermal cycling conditions were: 95°C 10 min; 55°C, 2 min; 72°C, 2 min; [95°C, 15 sec, 60°C, 4 min for 12 cycles], 99.9°C, 10 min; 4°C hold. The preamplified cDNA products (4µL) were subsequently 40x diluted in 0.1X TE buffer pH 8.0, and subjected to real-time PCR amplification and analysis using the TaqMan OpenArray Rodent MicroRNA Panel in 3072-well microfluidic (33nL) OpenArray plates that contained dried TaqMan primers and probes for miRNAs and controls.


title: genomic DNA from primitive cerebellar tumor 2

type: genomic

city: Paris

first: Julien

last: Masliah-Planchon

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Cerebellar tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: iScan Control Software

label: Cy5 and Cy3

source_name: Cerebellar tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from frozen tumors using phenol-chloroform procedure

tag: gender

value: Female


title: DT ex vivo cell DT_run3_A9

source_name: Medial layer of mouse aorta


title: LTα/β, NTL, replicate 1


title: genomic DNA from primitive cerebellar tumor 1

description: Cerebellar tumor


title: 0mm_2


title: miRNA_MYC, tumor, replicate 4


title: DT ex vivo cell DT_run3_A7


title: miRNA_MYC, tumor, replicate 3


title: DT ex vivo cell DT_run3_A5


title: LTα/β, NTL, replicate 2


title: miRNA_MYC, tumor, replicate 2


title: DT ex vivo cell DT_run3_A1


title: Sca1+ Adventitial pooled rep 2

description:
pooled RNA-seq
normalised_pooled_counts.txt

source_name: Adventitial layer of mouse aorta

extract_protocol:
Pooled samples were prepared from the cell suspension used for Fluidigm C1 analysis of single cells. Total RNA was extracted from 2000-4000 cells using the Qiagen RNeasy Plus Micro Kit.
RNA from 100-200 cells was used to generate amplified cDNA using the SMARTer® Ultra™ Low RNA Kit (Clontech) following the protocol for tube controls. Sequencing libraries were made from 0.125-0.375 ng amplified cDNA using the Nextera XT library preparation kit (Illumina).

value: Aorta

value: Adventitial cells


title: LTα/β - MYC, control, replicate 4

source_name: control liver tissue sample, obtained from sex- and age-matched transgene negative mouse (LT/MYC experiment)


title: 0mm_147


title: miRNA_MYC, NTL, replicate 3


title: Sca1+ Adventitial pooled rep 1


title: miRNA_MYC, NTL, replicate 2


title: miRNA_MYC, NTL, replicate 1


title: Sca1- Adventitial pooled rep 3


title: 0mm_300


title: Sca1- Adventitial pooled rep 2


title: LTα/β - MYC, control, replicate 3


title: 0mm_120T


title: miRNA_MYC, tumor, replicate 1


title: LTα/β - MYC, control, replicate 1


title: DEN, tumor, replicate 5

source_name: tumor liver tissue sample, obtained from diethylnitrosamine (DEN)-treated mouse (DEN experiment)

value: DEN


title: 0mm_1141


title: 0mm_12


title: Sca1+ Adventitial pooled rep 3


title: miRNA_LTα/β, tumor, replicate 2


title: miRNA_LTα/β, tumor, replicate 3


title: DEN, tumor, replicate 2


title: Sca1- Adventitial pooled rep 1


title: LTα/β - MYC, control, replicate 2


title: 0mm_1136


title: DEN, tumor, replicate 4


title: 0mm_1140


title: Sca1- VSMC pooled rep 3

value: Vascular smooth muscle cells


title: DEN, tumor, replicate 3


title: miRNA_LTα/β, tumor, replicate 1


title: 0mm_1132


title: 0mm_1127


title: miRNA_LTα/β, NTL, replicate 5


title: Sca1- VSMC pooled rep 2


title: Sca1- VSMC pooled rep 1


title: DEN, tumor, replicate 1


title: DEN, NTL, replicate 5

source_name: non-tumorous liver (NTL) tissue sample, obtained from diethylnitrosamine (DEN)-treated mouse (DEN experiment)


title: miRNA_LTα/β, NTL, replicate 2


title: miRNA_LTα/β, NTL, replicate 4


title: miRNA_LTα/β, NTL, replicate 3


title: DEN, NTL, replicate 4


title: 0mm_1123


title: 0mm_1131


title: miRNA_LTα/β, NTL, replicate 1


title: set2_invitro_CD8_GFP_Minus

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

description:
Sorted naïve IL-2.eGFP CD8 T cells were stimulated in-vitro. Total RNA was isolated from sorted CD69+ GFP– T cells.
set1_set2_invitro_CD8_GFP_Minus_plus_gene_differential_expression.xlsx

data_processing:
The raw reads were trimmed of the adaptors and aberrant reads were removed by TrimGalore (version 0.4.5). The quality controlled reads were mapped onto the mouse genome build GRCm38 using Tophat2 (version 2.0.12). BAM files were sorted using SAMtools (version 0.1.18) (Li et al., 2009), and reads were counted for each gene using HTSeq (version 0.7.2) (Anders et al., 2015)
Differential expression analysis was performed using DESeq2 (version 1.18.1) (Love et al., 2014) using R (version 3.4.3).
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq count values for each sample

source_name: In-vitro stimulated CD69+ IL-2.eGFP– CD8 T cells

growth_protocol: All mouse strains were bred and maintained at UAB in accordance with IACUC guidelines.

extract_protocol:
Total RNA was isolated with Qiazol and miRNeasy micro kits according to manufacturer’s recommendations (Qiagen 217084 and 79306)
TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: For in vitro experiments, sorted naïve IL2.eGFP CD4 or CD8 T cells were stimulated with 5ug/mL anti-CD3, 0.5ug/mL anti-CD28 and irradiated CD4-depleted feeders for 16-20hrs. For ex vivo experiments, sorted naïve IL2.eGFP CD4 T cells were transferred into ActA-LM infected mice and recovered after 18-24hrs. For both experiments, total RNA was isolated from sorted CD69+ IL-2.eGFP+ and CD69+ IL-2.eGFP– CD4 T cells.

tag: strain

value: Splenic CD8 T cells


title: set2_invitro_CD8_GFP_Plus

description:
Sorted naïve IL-2.eGFP CD8 T cells were stimulated in-vitro. Total RNA was isolated from sorted CD69+ GFP+T cells.
set1_set2_invitro_CD8_GFP_Minus_plus_gene_differential_expression.xlsx

source_name: In-vitro stimulated CD69+ IL-2.eGFP+ CD8 T cells


title: set1_invitro_CD8_GFP_Minus


title: set1_invitro_CD8_GFP_Plus


title: set3_invivo_GFP_Plus

description: Sorted naïve IL-2.eGFP CD4 T cells were transferred into ActA-LM infected recipients. Total RNA was isolated from ex-vivo sorted CD69+ GFP+ CD4 T cells.

source_name: Ex-vivo CD69+ IL-2.eGFP+ CD4 T cells

value: Splenic CD4 T cells


title: miRNA_LTα/β - MYC, control, replicate 3


title: DEN, NTL, replicate 3