title: HBEC_Clean_Air [TC00504136_N12]


title: HBEC_Clean_Air [TC00504136_N13]

status: Public on Apr 17 2022

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

library_source: transcriptomic

data_processing:
Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

molecule: total RNA

organism: Homo sapiens

source_name: HBEC

growth_protocol: The BEAS-2B cells used are a non-diseased, viral transformed human bronchial epithelial cell line acquired from ATCC (Manassas, VA, CRL-9609). Prior to cell culture, T75 flasks (Corning, One Riverfront Plaza, NY, 430641) and 6.5 mm Transwell® Inserts (Costar, Corning, NY, 3470) were coated with 100 µg/mL bovine collagen (PureCol Collagen [Advanced Biomatrix, San Diego, CA, 5005] diluted in Ultrapure Molecular (nuclease free) Water [Invitrogen, ThermoFisher Scientific, Rockford, IL, 10977023]) for 2 h at room temperature, followed by a water rinse. To prepare the cells for exposure at ALI, cells were thawed from pre-passaged frozen vials, grown on a T75 flask at 37 C 5% CO2 incubator conditions. The cells proliferated while submerged in Keratinocyte Growth Medium (KGM) (Keratinocyte Basal Medium (KBM) [Lonza, Walkersville, MD] plus KGM Gold Bullet Kit [Lonza, Walkersville, MD, 00192151]) with 25 mM HEPES Buffer (Sigma-Aldrich, St. Louis, MO) or Bronchial Epithelial Growth Medium (BEGM) (Bronchial Epithelial Basal Medium (BEBM) [Lonza, Walkersville, MD, CC-3171] plus BEGM Bullet Kit [Lonza, Walkersville, MD, CC-3170]. The utilized media type was switched to the latter (BEGM) for the experiments with dichloromethane, trichloroethylene, carbon tetrachloride, and 1-bromopropane due to vendor formulation changes and availability. BEAS2B Cells were grown for a minimum of two subsequent passages after thawing. Cells were passaged when approximately 75% confluent and new flasks seeded at 1 x 106 cells. The 6.5 mm inserts were seeded at 2-5 x 105 cells/insert and were maintained for 48-72 h before being used for exposure as a fully confluent monolayer. All apical media was removed at least 5 days before using BEAS-2B cells for exposure to the test agent. No FBS was used in the culture of BEAS-2B cells which were observed to have normal basal respiratory cell morphology at ALI. Primary human bronchial epithelial cells (pHBEC) were obtained via bronchial brushing from healthy, non-smoking donors aged 21–40 years. Donors gave their consent after being informed of procedures and associated risks. This study utilized cells from 12 healthy non-smoking donors, 10 male and 2 female donors between age 26-41. The consent and collection protocol were approved by the University of North Carolina School of Medicine Committee on the Protection of the Rights of Human Subjects and by the US Environmental Protection Agency. After collection, pHBECs were seeded at approximately 1 x 106 cells and cultured in BEGM (BEGM Bullet Kit, Lonza, Walkersville, MD CC-3170) on plastic T75 tissue culture flasks and expanded until the third passage. For all exposures, cells were lifted using trypsin-EDTA (Gibco 25300062) and plated on uncoated 6.5 mm diameter (24-well format) Transwell™ inserts (Costar, Corning, NY, 3470) at a density of 1 x 105 cells/insert depending on the donor. Each insert of cells was initially grown submerged with 1:1 DMEM-H (Gibco, 11995-065) and BEGM with complete bullet kit of growth supplements, 50 µg/mL of bovine pituitary extract (Lonza) and 1.5 µg/mL Bovine Serum Albumin (Sigma, A9418) on both the basolateral and apical compartments. The pHBECs were then expanded and grown for 2-4 days until they reached confluency. The cells were then placed at ALI by removing all apical medium and replacing the basolateral medium with the base media described above, supplemented with 100 nM retinol. The pHBECs continue to differentiate for at least 21 days before being used in an exposure. Previous research categorizing the pHBECs we use show a columnar pseudostratified cell layer with both cilia and mucin producing cells present after day 21 of ALI culture.

extract_protocol:
An optimized whole cell lysis procedure was used to preserve the RNA of both BEAS-2B and pHBEC samples. After a 4 h recovery post 2 h test agent exposure, the two technical replicate inserts from each exposure condition were placed on a new 24-well plate (Corning, NY). A single replicate insert of the incubator control cells was also preserved for whole cell lysis. Prior to adding the lysis buffer, the cells were thoroughly washed twice with DPBS to remove any remaining apical mucus or surfactant which may interfere with complete lysis. When transferring the BEAS-2B cells or pHBECs, the BioSpyder lysis buffer (Carlsbad, CA) was added to each of the samples and allowed to incubate for 15 minutes at room temperature. Each sample was mixed and pipetted into an individual well in the 384-well optical imaging plate (Corning, NY). After placing each of the samples into the 384-well plate, it was sealed with ThermalSeal RT 2mil Film (Sigma-Aldrich, MO) and stored in a -80°C freezer until shipment to BioSpyder for analysis.
384-well plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. BEAS-2B and pHBEC lysates were then analyzed by BioSpyder using the TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. Lysates were processed as described in. In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The target depth for each test sample was 6 x 10^6 total sequenced reads.

treatment_protocol: Beginning 2 h prior to test agent exposure, designated cells were prepped for exposure by performing an apical wash with Dulbecco’s Phosphate-Buffered Saline (DPBS) and replacing the basolateral compartment with 0.5 mL of fresh media with 25 mM HEPES Buffer. Cells remained in the incubator (37oC, 5% CO2) to recover for 2 h before being placed in the Cell Culture Exposure System (CCES) to undergo test agent exposures. The CCES was developed at EPA’s Inhalation Toxicology Facility and is comprised of a base module that accommodates a 24-well tissue culture plate with 6.5 mm diameter Transwell® inserts. It supplies air under positive pressure and exhausts air under negative pressure to provide a known concentration of test article over a specific time.  Two CCES modules are used simultaneously. One CCES module receives the test agent at six different concentrations while the other CCES module received filtered humidified dilution air and evaluated as a sham exposure control. A uniform air flow distribution was maintained through each nozzle so the cells in each Transwell® insert was exposed to either humidified air or diluted test agent at a flow rate of 12.5 mL/min/well. Optimal exposure temperature (37oC), relative humidity (85%) and air flow rates were tested and validated for the CCES in previous studies designed to optimize low variability in delivered material to the replicate wells. Cells were exposed to the test agent at ALI for 2 h before being transported back to the incubator (37oC, 5% CO2) for 4 h prior to sample collection and analysis. All sample collection and assays were run 4 h post-exposure to complete a 6 h timepoint to reflect both standard in vivo inhalation exposure regimes of 4 to 6 h of exposure and high-throughput screening studies. A sham exposure control cell culture plate which received only humidified air and an incubator control plate were tested in parallel with the plate which received the test agent.

tag: cell line

value: HBEC

tag: treatment

value: 0 ppm NA

tag: chemical name

tag: chemical id

tag: chemical concentration

value: 0 ppm

tag: dose level

tag: assay plate

tag: assay plate well


title: HBEC_Untrtd [TC00504136_O03]

value: NA NA NA

value: NA NA


title: HBEC_Clean_Air [TC00504136_N11]


title: BEAS-2B_DTXSID8020250_6_50ppm [TC00504137_A04]

value: 50 ppm Carbon Tetrachloride

value: Carbon Tetrachloride

value: 50 ppm


title: HBEC_Clean_Air [TC00504136_N10]


title: HBEC_Clean_Air [TC00504136_N09]


title: HBEC_Clean_Air [TC00504136_N08]


title: HBEC_Clean_Air [TC00504136_N05]


title: HBEC_Clean_Air [TC00504136_N04]


title: HBEC_Clean_Air [TC00504136_M12]


title: HBEC_Clean_Air [TC00504136_M13]


title: HBEC_Clean_Air [TC00504136_N06]


title: HBEC_Clean_Air [TC00504136_N02]


title: HBEC_Clean_Air [TC00504136_M07]


title: HBEC_Clean_Air [TC00504136_M08]


title: HBEC_Clean_Air [TC00504136_N03]


title: HBEC_Clean_Air [TC00504136_M09]


title: HBEC_Clean_Air [TC00504136_M05]


title: HBEC_Clean_Air [TC00504136_M10]


title: HBEC_Clean_Air [TC00504136_M04]


title: HBEC_Clean_Air [TC00504136_M02]


title: HBEC_DTXSID0020868_1_1.59ppm [TC00504136_L13]

value: 1.59 ppm Dichloromethane

value: Dichloromethane


title: HBEC_DTXSID0020868_1_1.59ppm [TC00504136_L12]


title: HBEC_DTXSID0020868_1_1.59ppm [TC00504136_L11]


title: HBEC_DTXSID6021874_1_0.031ppm [TC00504136_L10]

value: 0.031 ppm 1-Bromopropane


title: HBEC_DTXSID0021383_1_0.32ppm [TC00504136_L07]

value: 0.32 ppm Trichloroethylene

value: Trichloroethylene


title: HBEC_DTXSID0021383_1_0.32ppm [TC00504136_L06]


title: HBEC_DTXSID6021874_1_0.031ppm [TC00504136_L09]


title: HBEC_DTXSID6021874_1_0.031ppm [TC00504136_L08]


title: HBEC_Clean_Air [TC00504136_N07]


title: HBEC_DTXSID8020250_1_0.16ppm [TC00504136_L03]

value: 0.16 ppm Carbon Tetrachloride


title: HBEC_DTXSID8020250_1_0.16ppm [TC00504136_L04]


title: HBEC_DTXSID0021383_1_0.32ppm [TC00504136_L05]


title: HBEC_Clean_Air [TC00504136_M11]


title: HBEC_Clean_Air [TC00504136_M06]


title: HBEC_DTXSID8020250_1_0.16ppm [TC00504136_L02]


title: HBEC_DTXSID6021874_1_0.031ppm [TC00504136_K08]


title: HBEC_Clean_Air [TC00504136_M03]


title: HBEC_DTXSID0021383_1_0.32ppm [TC00504136_K05]


title: HBEC_DTXSID0020868_1_1.59ppm [TC00504136_K13]


title: HBEC_DTXSID6021874_1_0.031ppm [TC00504136_K10]


title: HBEC_DTXSID0020868_2_5.01ppm [TC00504136_J13]

value: 5.01 ppm Dichloromethane


title: HBEC_DTXSID8020250_1_0.16ppm [TC00504136_K02]


title: HBEC_DTXSID8020250_1_0.16ppm [TC00504136_K03]


title: HBEC_DTXSID8020250_1_0.16ppm [TC00504136_K04]


title: HBEC_DTXSID0021383_1_0.32ppm [TC00504136_K06]


title: HBEC_DTXSID0020868_1_1.59ppm [TC00504136_K12]


title: HBEC_DTXSID0020868_2_5.01ppm [TC00504136_J12]


title: HBEC_DTXSID0020868_2_5.01ppm [TC00504136_J11]


title: HBEC_DTXSID6021874_2_0.1ppm [TC00504136_J09]

value: 0.1 ppm 1-Bromopropane

value: 0.1 ppm


title: HBEC_DTXSID6021874_2_0.1ppm [TC00504136_J10]

value: HBEC


title: HBEC_DTXSID6021874_1_0.031ppm [TC00504136_K09]


title: HBEC_DTXSID0021383_1_0.32ppm [TC00504136_K07]


title: HBEC_DTXSID0021383_2_1ppm [TC00504136_J07]

value: 1 ppm Trichloroethylene

value: 1 ppm


title: HBEC_DTXSID6021874_2_0.1ppm [TC00504136_J08]


title: HBEC_DTXSID0021383_2_1ppm [TC00504136_J05]


title: HBEC_DTXSID0021383_2_1ppm [TC00504136_J06]


title: HBEC_DTXSID0020868_1_1.59ppm [TC00504136_K11]


title: HBEC_DTXSID8020250_2_0.5ppm [TC00504136_J03]

value: 0.5 ppm Carbon Tetrachloride

value: 0.5 ppm


title: HBEC_DTXSID0020868_2_5.01ppm [TC00504136_I13]


title: HBEC_DTXSID0020868_2_5.01ppm [TC00504136_I12]


title: HBEC_DTXSID8020250_2_0.5ppm [TC00504136_J04]


title: HBEC_DTXSID8020250_2_0.5ppm [TC00504136_J02]


title: HBEC_DTXSID0020868_2_5.01ppm [TC00504136_I11]


title: HBEC_DTXSID6021874_2_0.1ppm [TC00504136_I10]


title: HBEC_DTXSID6021874_2_0.1ppm [TC00504136_I09]


title: HBEC_DTXSID6021874_2_0.1ppm [TC00504136_I08]


title: HBEC_DTXSID0021383_2_1ppm [TC00504136_I07]


title: HBEC_DTXSID0021383_2_1ppm [TC00504136_I05]


title: HBEC_DTXSID8020250_2_0.5ppm [TC00504136_I02]


title: HBEC_DTXSID0020868_3_15.85ppm [TC00504136_H13]

value: 15.85 ppm Dichloromethane


title: HBEC_DTXSID8020250_2_0.5ppm [TC00504136_I03]

value: Carbon Tetrachloride


title: HBEC_DTXSID0020868_3_15.85ppm [TC00504136_H12]


title: HBEC_DTXSID0020868_3_15.85ppm [TC00504136_H11]


title: HBEC_DTXSID6021874_3_0.31ppm [TC00504136_H10]

value: 0.31 ppm 1-Bromopropane


title: HBEC_DTXSID6021874_3_0.31ppm [TC00504136_H09]


title: HBEC_DTXSID0021383_3_3.16ppm [TC00504136_H07]

value: 3.16 ppm Trichloroethylene


title: HBEC_DTXSID8020250_3_1.6ppm [TC00504136_H03]

value: 1.6 ppm Carbon Tetrachloride

value: 1.6 ppm


title: HBEC_DTXSID0020868_3_15.85ppm [TC00504136_G12]

value: Dichloromethane


title: HBEC_DTXSID8020250_3_1.6ppm [TC00504136_H02]


title: HBEC_DTXSID6021874_3_0.31ppm [TC00504136_G09]


title: HBEC_DTXSID0021383_3_3.16ppm [TC00504136_G06]

value: Trichloroethylene


title: HBEC_DTXSID0020868_3_15.85ppm [TC00504136_G11]


title: HBEC_DTXSID0021383_3_3.16ppm [TC00504136_G05]


title: HBEC_DTXSID0021383_3_3.16ppm [TC00504136_G07]


title: HBEC_DTXSID0021383_3_3.16ppm [TC00504136_H06]


title: HBEC_DTXSID6021874_3_0.31ppm [TC00504136_H08]


title: HBEC_DTXSID6021874_3_0.31ppm [TC00504136_G08]


title: HBEC_DTXSID0020868_3_15.85ppm [TC00504136_G13]


title: HBEC_DTXSID8020250_3_1.6ppm [TC00504136_G03]


title: HBEC_DTXSID0021383_3_3.16ppm [TC00504136_H05]


title: HBEC_DTXSID0020868_4_50.1ppm [TC00504136_F13]

value: 50.1 ppm Dichloromethane


title: HBEC_DTXSID8020250_3_1.6ppm [TC00504136_G02]


title: HBEC_DTXSID8020250_3_1.6ppm [TC00504136_G04]


title: HBEC_DTXSID6021874_3_0.31ppm [TC00504136_G10]


title: HBEC_DTXSID8020250_3_1.6ppm [TC00504136_H04]


title: HBEC_DTXSID6021874_4_1ppm [TC00504136_F10]

value: 1 ppm 1-Bromopropane


title: HBEC_DTXSID0020868_4_50.1ppm [TC00504136_F12]


title: HBEC_DTXSID0020868_4_50.1ppm [TC00504136_F11]


title: HBEC_DTXSID6021874_4_1ppm [TC00504136_F08]


title: HBEC_DTXSID0021383_4_10ppm [TC00504136_F06]

value: 10 ppm Trichloroethylene

value: 10 ppm


title: HBEC_DTXSID0021383_2_1ppm [TC00504136_I06]

value: HBEC


title: HBEC_DTXSID0021383_4_10ppm [TC00504136_F05]


title: HBEC_DTXSID0021383_4_10ppm [TC00504136_F07]


title: HBEC_DTXSID6021874_4_1ppm [TC00504136_F09]


title: HBEC_DTXSID8020250_2_0.5ppm [TC00504136_I04]


title: HBEC_DTXSID8020250_4_5ppm [TC00504136_F04]

value: 5 ppm Carbon Tetrachloride

value: 5 ppm


title: HBEC_DTXSID8020250_4_5ppm [TC00504136_F02]


title: HBEC_DTXSID6021874_4_1ppm [TC00504136_E08]

value: 1 ppm


title: HBEC_DTXSID0020868_4_50.1ppm [TC00504136_E11]


title: HBEC_DTXSID6021874_4_1ppm [TC00504136_E09]


title: HBEC_DTXSID0020868_4_50.1ppm [TC00504136_E13]


title: HBEC_DTXSID0021383_4_10ppm [TC00504136_E06]


title: HBEC_DTXSID0021383_4_10ppm [TC00504136_E07]


title: HBEC_DTXSID0020868_5_158.2ppm [TC00504136_D13]

value: 158.2 ppm Dichloromethane


title: HBEC_DTXSID8020250_4_5ppm [TC00504136_E02]


title: HBEC_DTXSID0020868_5_158.2ppm [TC00504136_D11]


title: HBEC_DTXSID8020250_4_5ppm [TC00504136_F03]


title: HBEC_DTXSID0021383_5_31.6ppm [TC00504136_D07]

value: 31.6 ppm Trichloroethylene


title: HBEC_DTXSID0021383_4_10ppm [TC00504136_E05]


title: HBEC_DTXSID6021874_4_1ppm [TC00504136_E10]


title: HBEC_DTXSID8020250_4_5ppm [TC00504136_E03]

value: Carbon Tetrachloride


title: HBEC_DTXSID6021874_5_3.1ppm [TC00504136_D08]

value: 3.1 ppm 1-Bromopropane

value: 3.1 ppm


title: HBEC_DTXSID0020868_4_50.1ppm [TC00504136_E12]


title: HBEC_DTXSID6021874_5_3.1ppm [TC00504136_D10]


title: HBEC_DTXSID0020868_5_158.2ppm [TC00504136_D12]


title: HBEC_DTXSID8020250_5_15.9ppm [TC00504136_D03]

value: 15.9 ppm Carbon Tetrachloride


title: HBEC_DTXSID0021383_5_31.6ppm [TC00504136_D05]


title: HBEC_DTXSID8020250_5_15.9ppm [TC00504136_D02]


title: HBEC_DTXSID0020868_5_158.2ppm [TC00504136_C13]


title: HBEC_DTXSID0020868_5_158.2ppm [TC00504136_C12]


title: HBEC_DTXSID0020868_5_158.2ppm [TC00504136_C11]


title: HBEC_DTXSID8020250_4_5ppm [TC00504136_E04]


title: HBEC_DTXSID6021874_5_3.1ppm [TC00504136_C09]


title: HBEC_DTXSID0021383_5_31.6ppm [TC00504136_D06]


title: HBEC_DTXSID6021874_5_3.1ppm [TC00504136_C10]


title: HBEC_DTXSID8020250_5_15.9ppm [TC00504136_D04]


title: HBEC_DTXSID6021874_5_3.1ppm [TC00504136_C08]


title: HBEC_DTXSID0021383_5_31.6ppm [TC00504136_C07]


title: HBEC_DTXSID6021874_5_3.1ppm [TC00504136_D09]


title: HBEC_DTXSID0021383_5_31.6ppm [TC00504136_C05]


title: HBEC_DTXSID0020868_6_500ppm [TC00504136_B12]

value: 500 ppm Dichloromethane

value: 500 ppm


title: HBEC_DTXSID8020250_5_15.9ppm [TC00504136_C03]


title: HBEC_DTXSID8020250_5_15.9ppm [TC00504136_C04]


title: HBEC_DTXSID0021383_5_31.6ppm [TC00504136_C06]

value: Trichloroethylene


title: HBEC_DTXSID0020868_6_500ppm [TC00504136_B11]

value: Dichloromethane


title: HBEC_DTXSID8020250_5_15.9ppm [TC00504136_C02]


title: HBEC_DTXSID6021874_6_10ppm [TC00504136_B09]

value: 10 ppm 1-Bromopropane


title: HBEC_DTXSID6021874_6_10ppm [TC00504136_B08]


title: HBEC_DTXSID0021383_6_100ppm [TC00504136_B05]

value: 100 ppm Trichloroethylene

value: 100 ppm


title: HBEC_DTXSID6021874_6_10ppm [TC00504136_B10]

value: HBEC

value: 10 ppm


title: HBEC_DTXSID8020250_6_50ppm [TC00504136_B03]

value: 50 ppm Carbon Tetrachloride

value: 50 ppm


title: HBEC_DTXSID0021383_6_100ppm [TC00504136_B06]


title: HBEC_DTXSID0020868_6_500ppm [TC00504136_B13]


title: HBEC_DTXSID8020250_6_50ppm [TC00504136_B04]


title: HBEC_DTXSID0021383_6_100ppm [TC00504136_B07]


title: HBEC_DTXSID8020250_6_50ppm [TC00504136_B02]


title: HBEC_DTXSID0020868_6_500ppm [TC00504136_A11]


title: HBEC_DTXSID6021874_6_10ppm [TC00504136_A10]


title: HBEC_DTXSID6021874_6_10ppm [TC00504136_A09]


title: HBEC_DTXSID0021383_6_100ppm [TC00504136_A07]


title: HBEC_DTXSID6021874_6_10ppm [TC00504136_A08]


title: HBEC_DTXSID0021383_6_100ppm [TC00504136_A06]


title: HBEC_DTXSID8020250_6_50ppm [TC00504136_A04]


title: HBEC_DTXSID8020250_6_50ppm [TC00504136_A03]


title: HBEC_DTXSID8020250_6_50ppm [TC00504136_A02]


title: BEAS-2B_Untrtd [TC00284742_O14]

value: NA NA NA

value: NA NA


title: BEAS-2B_Untrtd [TC00284742_O12]


title: BEAS-2B_Untrtd [TC00284742_O11]


title: BEAS-2B_Untrtd [TC00284742_O13]


title: HBEC_DTXSID0020868_6_500ppm [TC00504136_A13]


title: BEAS-2B_Untrtd [TC00284742_O06]


title: BEAS-2B_Untrtd [TC00284742_O09]


title: BEAS-2B_Untrtd [TC00284742_O07]


title: BEAS-2B_Untrtd [TC00284742_O05]


title: BEAS-2B_Untrtd [TC00284742_O08]


title: HBEC_DTXSID0020868_6_500ppm [TC00504136_A12]


title: BEAS-2B_Untrtd [TC00284742_O04]


title: BEAS-2B_Untrtd [TC00284742_O03]


title: BEAS-2B_Clean_Air [TC00284742_N12]

value: 0 ppm NA

value: 0 ppm


title: BEAS-2B_Clean_Air [TC00284742_N13]


title: BEAS-2B_Clean_Air [TC00284742_N14]


title: BEAS-2B_Clean_Air [TC00284742_N10]


title: HBEC_DTXSID0021383_6_100ppm [TC00504136_A05]


title: BEAS-2B_Clean_Air [TC00284742_N07]


title: BEAS-2B_Clean_Air [TC00284742_N04]


title: BEAS-2B_Clean_Air [TC00284742_N03]


title: BEAS-2B_Untrtd [TC00284742_O10]


title: BEAS-2B_Clean_Air [TC00284742_N05]


title: BEAS-2B_Untrtd [TC00284742_O02]


title: BEAS-2B_Clean_Air [TC00284742_M13]


title: BEAS-2B_Clean_Air [TC00284742_N11]


title: BEAS-2B_Clean_Air [TC00284742_M10]


title: BEAS-2B_Clean_Air [TC00284742_M06]


title: BEAS-2B_Clean_Air [TC00284742_M11]


title: BEAS-2B_Clean_Air [TC00284742_M12]


title: BEAS-2B_Clean_Air [TC00284742_M08]


title: BEAS-2B_Clean_Air [TC00284742_M04]


title: BEAS-2B_Clean_Air [TC00284742_M09]


title: BEAS-2B_Clean_Air [TC00284742_N09]


title: BEAS-2B_Clean_Air [TC00284742_M07]


title: BEAS-2B_DTXSID7020637_1_0.013ppm [TC00284742_L13]

value: 0.013 ppm Formaldehyde

value: Formaldehyde


title: BEAS-2B_DTXSID7020637_1_0.013ppm [TC00284742_L12]


title: BEAS-2B_Clean_Air [TC00284742_M05]


title: BEAS-2B_Clean_Air [TC00284742_N08]


title: BEAS-2B_Clean_Air [TC00284742_M03]


title: BEAS-2B_Clean_Air [TC00284742_M02]


title: BEAS-2B_DTXSID5039224_1_1.11ppm [TC00284742_L11]

value: 1.11 ppm Acetaldehyde

value: Acetaldehyde


title: BEAS-2B_DTXSID5039224_1_1.11ppm [TC00284742_L10]


title: BEAS-2B_Clean_Air [TC00284742_N06]


title: BEAS-2B_Clean_Air [TC00284742_M14]


title: BEAS-2B_DTXSID3020203_1_0.16ppm [TC00284742_L08]

value: 0.16 ppm 1,3-Butadiene


title: BEAS-2B_DTXSID3020203_1_0.16ppm [TC00284742_L06]


title: BEAS-2B_DTXSID5039224_1_1.11ppm [TC00284742_L09]


title: BEAS-2B_DTXSID3020203_1_0.16ppm [TC00284742_L07]


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_L05]

value: 0.031 ppm Acrolein

value: Acrolein


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_L04]


title: BEAS-2B_Clean_Air [TC00284742_N02]


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_L03]


title: BEAS-2B_DTXSID7020637_1_0.013ppm [TC00284742_K14]


title: BEAS-2B_DTXSID7020637_1_0.013ppm [TC00284742_L14]


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_L02]


title: BEAS-2B_DTXSID5039224_1_1.11ppm [TC00284742_K09]


title: BEAS-2B_DTXSID5039224_1_1.11ppm [TC00284742_K10]


title: BEAS-2B_DTXSID5039224_1_1.11ppm [TC00284742_K11]


title: BEAS-2B_DTXSID7020637_1_0.013ppm [TC00284742_K12]


title: BEAS-2B_DTXSID7020637_1_0.013ppm [TC00284742_K13]


title: BEAS-2B_DTXSID3020203_1_0.16ppm [TC00284742_K08]


title: BEAS-2B_DTXSID3020203_1_0.16ppm [TC00284742_K06]


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_K04]


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_K05]


title: BEAS-2B_DTXSID3020203_1_0.16ppm [TC00284742_K07]


title: BEAS-2B_DTXSID7020637_2_0.04ppm [TC00284742_J14]

value: 0.04 ppm Formaldehyde


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_K02]


title: BEAS-2B_DTXSID7020637_2_0.04ppm [TC00284742_J12]


title: BEAS-2B_DTXSID5039224_2_3.51ppm [TC00284742_J09]

value: 3.51 ppm Acetaldehyde


title: BEAS-2B_DTXSID7020637_2_0.04ppm [TC00284742_J13]


title: BEAS-2B_DTXSID3020203_2_0.5ppm [TC00284742_J08]

value: 0.5 ppm 1,3-Butadiene

value: 0.5 ppm


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_J05]

value: 0.1 ppm Acrolein

value: 0.1 ppm


title: BEAS-2B_DTXSID3020203_2_0.5ppm [TC00284742_J07]


title: BEAS-2B_DTXSID3020203_2_0.5ppm [TC00284742_J06]


title: BEAS-2B_DTXSID5039224_2_3.51ppm [TC00284742_J10]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_J04]


title: BEAS-2B_DTXSID5020023_1_0.031ppm [TC00284742_K03]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_J03]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_J02]


title: BEAS-2B_DTXSID7020637_2_0.04ppm [TC00284742_I14]


title: BEAS-2B_DTXSID7020637_2_0.04ppm [TC00284742_I13]


title: BEAS-2B_DTXSID5039224_2_3.51ppm [TC00284742_I11]


title: BEAS-2B_DTXSID7020637_2_0.04ppm [TC00284742_I12]


title: BEAS-2B_DTXSID3020203_2_0.5ppm [TC00284742_I08]


title: BEAS-2B_DTXSID5039224_2_3.51ppm [TC00284742_I10]


title: BEAS-2B_DTXSID5039224_2_3.51ppm [TC00284742_I09]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_I05]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_I03]


title: BEAS-2B_DTXSID5039224_2_3.51ppm [TC00284742_J11]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_I04]


title: BEAS-2B_DTXSID7020637_3_0.13ppm [TC00284742_H14]

value: 0.13 ppm Formaldehyde


title: BEAS-2B_DTXSID3020203_2_0.5ppm [TC00284742_I06]


title: BEAS-2B_DTXSID5020023_2_0.1ppm [TC00284742_I02]


title: BEAS-2B_DTXSID7020637_3_0.13ppm [TC00284742_H13]


title: BEAS-2B_DTXSID3020203_2_0.5ppm [TC00284742_I07]


title: BEAS-2B_DTXSID5039224_3_11.1ppm [TC00284742_H11]

value: 11.1 ppm Acetaldehyde


title: BEAS-2B_DTXSID3020203_3_1.7ppm [TC00284742_H08]

value: 1.7 ppm 1,3-Butadiene

value: 1.7 ppm


title: BEAS-2B_DTXSID7020637_3_0.13ppm [TC00284742_H12]


title: BEAS-2B_DTXSID5039224_3_11.1ppm [TC00284742_H09]


title: BEAS-2B_DTXSID3020203_3_1.7ppm [TC00284742_H07]


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_H04]

value: 0.31 ppm Acrolein


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_H05]


title: BEAS-2B_DTXSID3020203_3_1.7ppm [TC00284742_H06]


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_H03]


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_H02]


title: BEAS-2B_DTXSID7020637_3_0.13ppm [TC00284742_G14]

value: Formaldehyde


title: BEAS-2B_DTXSID7020637_3_0.13ppm [TC00284742_G13]


title: BEAS-2B_DTXSID7020637_3_0.13ppm [TC00284742_G12]


title: BEAS-2B_DTXSID5039224_3_11.1ppm [TC00284742_G09]


title: BEAS-2B_DTXSID5039224_3_11.1ppm [TC00284742_G10]


title: BEAS-2B_DTXSID3020203_3_1.7ppm [TC00284742_G08]


title: BEAS-2B_DTXSID5039224_3_11.1ppm [TC00284742_H10]


title: BEAS-2B_DTXSID3020203_3_1.7ppm [TC00284742_G06]


title: BEAS-2B_DTXSID5039224_3_11.1ppm [TC00284742_G11]


title: BEAS-2B_DTXSID3020203_3_1.7ppm [TC00284742_G07]


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_G05]


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_G02]


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_G03]


title: BEAS-2B_DTXSID7020637_4_0.4ppm [TC00284742_F13]

value: 0.4 ppm Formaldehyde

value: 0.4 ppm


title: BEAS-2B_DTXSID5020023_3_0.31ppm [TC00284742_G04]


title: BEAS-2B_DTXSID3020203_4_5ppm [TC00284742_F07]

value: 5 ppm 1,3-Butadiene

value: 5 ppm


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_F04]

value: 1 ppm Acrolein

value: Acrolein

value: 1 ppm


title: BEAS-2B_DTXSID5039224_4_35.1ppm [TC00284742_F10]

value: 35.1 ppm Acetaldehyde

value: Acetaldehyde


title: BEAS-2B_DTXSID5039224_4_35.1ppm [TC00284742_F11]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_F05]


title: BEAS-2B_DTXSID5039224_4_35.1ppm [TC00284742_F09]


title: BEAS-2B_DTXSID7020637_4_0.4ppm [TC00284742_E14]


title: BEAS-2B_DTXSID7020637_4_0.4ppm [TC00284742_E12]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_F03]


title: BEAS-2B_DTXSID3020203_4_5ppm [TC00284742_F06]


title: BEAS-2B_DTXSID7020637_4_0.4ppm [TC00284742_F12]


title: BEAS-2B_DTXSID3020203_4_5ppm [TC00284742_F08]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_F02]


title: BEAS-2B_DTXSID5039224_4_35.1ppm [TC00284742_E11]


title: BEAS-2B_DTXSID7020637_4_0.4ppm [TC00284742_E13]


title: BEAS-2B_DTXSID7020637_4_0.4ppm [TC00284742_F14]


title: BEAS-2B_DTXSID3020203_4_5ppm [TC00284742_E08]


title: BEAS-2B_DTXSID5039224_4_35.1ppm [TC00284742_E10]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_E05]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_E02]


title: BEAS-2B_DTXSID7020637_5_1.3ppm [TC00284742_D13]

value: 1.3 ppm Formaldehyde

value: 1.3 ppm


title: BEAS-2B_DTXSID5039224_4_35.1ppm [TC00284742_E09]


title: BEAS-2B_DTXSID3020203_4_5ppm [TC00284742_E06]


title: BEAS-2B_DTXSID3020203_4_5ppm [TC00284742_E07]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_E03]


title: BEAS-2B_DTXSID5020023_4_1ppm [TC00284742_E04]


title: BEAS-2B_DTXSID7020637_5_1.3ppm [TC00284742_D12]


title: BEAS-2B_DTXSID5039224_5_110.8ppm [TC00284742_D11]

value: 110.8 ppm Acetaldehyde


title: BEAS-2B_DTXSID3020203_5_16ppm [TC00284742_D07]

value: 16 ppm 1,3-Butadiene

value: 16 ppm


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_D02]

value: 3.1 ppm Acrolein

value: 3.1 ppm


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_D05]


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_D03]


title: BEAS-2B_DTXSID5039224_5_110.8ppm [TC00284742_C11]


title: BEAS-2B_DTXSID3020203_5_16ppm [TC00284742_D08]


title: BEAS-2B_DTXSID7020637_5_1.3ppm [TC00284742_C14]

value: Formaldehyde


title: BEAS-2B_DTXSID5039224_5_110.8ppm [TC00284742_D09]


title: BEAS-2B_DTXSID3020203_5_16ppm [TC00284742_C08]


title: BEAS-2B_DTXSID7020637_5_1.3ppm [TC00284742_C13]


title: BEAS-2B_DTXSID3020203_5_16ppm [TC00284742_C07]


title: BEAS-2B_DTXSID3020203_5_16ppm [TC00284742_D06]


title: BEAS-2B_DTXSID7020637_5_1.3ppm [TC00284742_C12]


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_C05]


title: BEAS-2B_DTXSID7020637_5_1.3ppm [TC00284742_D14]


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_C04]


title: BEAS-2B_DTXSID5039224_5_110.8ppm [TC00284742_C09]


title: BEAS-2B_DTXSID5039224_5_110.8ppm [TC00284742_C10]


title: BEAS-2B_DTXSID5039224_5_110.8ppm [TC00284742_D10]


title: BEAS-2B_DTXSID3020203_5_16ppm [TC00284742_C06]


title: BEAS-2B_DTXSID7020637_6_4ppm [TC00284742_B14]

value: 4 ppm Formaldehyde

value: 4 ppm


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_C02]


title: BEAS-2B_DTXSID7020637_6_4ppm [TC00284742_B12]


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_D04]


title: BEAS-2B_DTXSID7020637_6_4ppm [TC00284742_B13]


title: P19-input-rep2

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

country: China

institute: Shandong University of Technology

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with default parameters. MACS (v.2.2.7.1) was used to call peaks (-q 0.01) relative to the input sample.
Assembly: GRCm38
Supplementary files format and content: bigWig
Supplementary files format and content: TXT

molecule: genomic DNA

organism: Mus musculus

growth_protocol: P19 embryonal carcinoma (EC) cells were routinely grown in proliferation medium [MEM α (Gibco) contained 10% fetal bovine serum (Gibco)].

extract_protocol:
Standard Native Chromatin Immunoprecipitation (N-ChIP) was employed to extract chromatin and perform immunoprecipitation, the IPed DNA was extracted by the phenol-chloroform method.
ChIP’s DNA was subjected to end-repair and then was 3’adenylated. Adaptors were ligated to the ends of these 3’adenylated fragments. Next, polymerase chain reaction amplification was to amplify those fragments with adaptors from previous step.

tag: cell type

value: Embryonal carcinoma cell

tag: chip antibody


title: BEAS-2B_DTXSID5039224_6_350ppm [TC00284742_B11]

value: 350 ppm Acetaldehyde

value: 350 ppm


title: BEAS-2B_DTXSID5039224_6_350ppm [TC00284742_B10]


title: P19-input-rep1


title: P19-H3K9cr-rep2

tag: antibody vendor

value: PTM Biolab, Hangzhou, China

tag: antibody catalog#

tag: antibody lot#


title: BEAS-2B_DTXSID5039224_6_350ppm [TC00284742_B09]


title: BEAS-2B_DTXSID3020203_6_50ppm [TC00284742_B08]

value: 50 ppm 1,3-Butadiene

value: 50 ppm


title: P19-H3K9ac-rep1


title: P19-H3K9cr-rep1


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_B03]

value: 10 ppm Acrolein

value: Acrolein

value: 10 ppm


title: BEAS-2B_DTXSID3020203_6_50ppm [TC00284742_B06]


title: BEAS-2B_DTXSID3020203_6_50ppm [TC00284742_B07]


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_B04]


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_B05]


title: BEAS-2B_DTXSID5020023_5_3.1ppm [TC00284742_C03]


title: BEAS-2B_DTXSID7020637_6_4ppm [TC00284742_A13]


title: RAD21_8H

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: 8h LPS (10ng/ml) stimulated Rad21-/- bone marrow-derived macrophages

data_processing:
Quality check of the generated reads was performed with the FastQC quality control suite. Samples that reached the quality standards were then processed to deconvolute the reads to single-cell level by de-multiplexing according to the cell and pool barcodes. Reads were filtered to remove polyT sequences.
Sequencing reads from human, mouse, or canine cells were mapped with the RNA pipeline of the GEMTools 1.7.0 suite (Marco-Sola et al. 2012)  using default parameters (6% of mismatches, minimum of 80% matched bases, and minimum quality threshold of 26) and the genome references for human (Gencode release 24, assembly GRCh38.p5), mouse (Gencode release M8, assembly GRCm38.p4), and dog (Ensembl v84, assembly CanFam3.1).
The analysis of spike-in control RNA content allowed us to identify empty wells and barcodes with more than 15% of reads mapping to spike-in artificial transcripts were discarded.
Cells with less than 60% of reads mapping on the reference genome or more than 2x10^6 total reads were discarded.
Gene quantification was performed using UMI corrected transcript information to correct for amplification biases, collapsing read counts for reads mapping on a gene with the same UMI (allowing an edit distance up to two nucleotides in UMI comparisons). Only unambiguously mapped reads were considered.
Genes not expressed in at least 5% of the cells were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix_Annotated.csv

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were isolated from WT or Rad21-/- mice and plated in 10 cm dishes containing 10 ml medium (DMEM containing 10% FCS, 20% L929-conditioned media, 0.05 mM β-mercaptoethanol, PenStrep 1% and Sodium Pyruvate 1mM). 96 hours later media was replaced by fresh media containing 200nM 4-hydroxy-tamoxifen to induce nuclear translocation of ERt2-Cre. Experiments were done at day 7

extract_protocol:
Single macrophages were sorted by flow cytometry into 384 well plates containing lysis buffer and the plates were frozen
Libraries were prepared using the MARS-Seq protocol (Jaitin et al., 2014)

treatment_protocol: When indicated, macrophages were stimulated with 10ng/ml LPS

value: Bone marrow-derived macrophages

tag: genotype

tag: rosa26 locus

tag: stimulation

value: 8h LPS


title: WT_8H

description: 8h LPS (10ng/ml) stimulated wild-type bone marrow-derived macrophages

value: wild-type


title: BEAS-2B_DTXSID5039224_6_350ppm [TC00284742_A11]

value: Acetaldehyde


title: BEAS-2B_DTXSID5039224_6_350ppm [TC00284742_A10]


title: BEAS-2B_DTXSID7020637_6_4ppm [TC00284742_A12]


title: RAD21_2H

description: 2h LPS (10ng/ml) stimulated Rad21-/- bone marrow-derived macrophages

value: 2h LPS


title: P19-H3K9ac-rep2


title: BEAS-2B_DTXSID5039224_6_350ppm [TC00284742_A09]


title: WT_2H

description: 2h LPS (10ng/ml) stimulated wild-type bone marrow-derived macrophages


title: BEAS-2B_DTXSID3020203_6_50ppm [TC00284742_A08]


title: BEAS-2B_DTXSID3020203_6_50ppm [TC00284742_A07]


title: BEAS-2B_DTXSID3020203_6_50ppm [TC00284742_A06]


title: RAD21_UT

description: Unstimulated Rad21 -/- bone marrow-derived macrophages

value: Untreated


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_A05]


title: WT_UT

description: Unstimulated wild-type bone marrow-derived macrophages


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_A03]


title: BEAS-2B_DTXSID7020637_6_4ppm [TC00284742_A14]

value: 4 ppm Formaldehyde

value: Formaldehyde


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_B02]


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_A04]


title: BEAS-2B_DTXSID5020023_6_10ppm [TC00284742_A02]


title: 21-002-B_2 | 050 | Segment 1

status: Public on Apr 16 2022

type: RNA

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

institute: NYU Langone Health Ambulatory Care Center

description: 20210326_P1001660004391A_P1001660004391A_02.RCC

hyb_protocol: They are mixed with 7ul of the corresponding DSP aspirate, plates are sealed and incubated overnight at 67 deg C for 16-24 hrs. After the incubation, using the downloaded worksheet, appropriate volume of hyb products from each column are pooled into wells of a 12-well strip tube.

scan_protocol: After mixing and spinning down, the strip tubes are loaded on to the nCounter MAX/FLEX system to run.

data_processing: After the run, the save zipped RCC files are transferred back to the DSP instrument for data analysis.

label: not provided

label_protocol: Working pools of hybridization codes (Probe R and Probe U) are made following the instructions from protocol and then combined with hybridization buffer to make Probe/Buffer mix. Aliquots of the above was then added to each GeoMx Hyb code pack, mixed and added to all 12 wells of the appropriate row.

extract_protocol: Once dried, the wells of the collection plate are rehydrated with 7ul of DEPC water, mixed and spun.

treatment_protocol:
Once the data collection is complete, the collection plate is sealed and stored at -20 deg Celsius.
After thawing, the plates are sealed with AeraSeal film (Excel Scientific, CA) and the aspirates are dried at 65 deg C in a thermal cycler with an open top.

tag: segment

value: Segment 1

tag: aoi


title: 21-002-B_2 | 051 | Segment 1

description: 20210326_P1001660004391A_P1001660004391A_04.RCC


title: 21-002-B_2 | 050 | Segment 2

description: 20210326_P1001660004391A_P1001660004391A_03.RCC

value: Segment 2


title: 21-002-B_2 | 049 | Segment 1

description: 20210326_P1001660004391A_P1001660004391A_12.RCC


title: 21-002-B_2 | 049 | Segment 2

description: 20210326_P1001660004391A_P1001660004391A_01.RCC


title: 21-002-B_2 | 048 | Segment 2

description: 20210326_P1001660004391A_P1001660004391A_11.RCC


title: 21-002-B_2 | 046 | Segment 2

description: 20210326_P1001660004391A_P1001660004391A_07.RCC


title: 21-002-B_2 | 048 | Segment 1

description: 20210326_P1001660004391A_P1001660004391A_10.RCC


title: 21-002-B_2 | 047 | Segment 1

description: 20210326_P1001660004391A_P1001660004391A_08.RCC


title: 21-002-B_2 | 045 | Segment 1


title: 21-002-B_2 | 045 | Segment 2

description: 20210326_P1001660004391A_P1001660004391A_05.RCC


title: 21-002-B_2 | 046 | Segment 1

description: 20210326_P1001660004391A_P1001660004391A_06.RCC


title: 21-002-B_2 | 044 | Segment 2


title: 21-002-B_2 | 047 | Segment 2

description: 20210326_P1001660004391A_P1001660004391A_09.RCC


title: 21-002-B_2 | 044 | Segment 1


title: 21-002-B_2 | 043 | Segment 1


title: 21-002-B_2 | 043 | Segment 2


title: 21-002-B_2 | 042 | Segment 2


title: 21-002-B_2 | 041 | Segment 1


title: 21-002-B_2 | 042 | Segment 1


title: 21-002-B_2 | 041 | Segment 2


title: 21-002-B_2 | 040 | Segment 2


title: 21-002-B_2 | 051 | Segment 2


title: 21-002-B_2 | 040 | Segment 1


title: 21-002-B_2 | 037 | Segment 1


title: 21-002-B_2 | 039 | Segment 2


title: 21-002-B_2 | 038 | Segment 2


title: 21-002-B_2 | 037 | Segment 2


title: 21-002-B_2 | 036 | Segment 2


title: 21-002-B_2 | 039 | Segment 1


title: 21-002-B_2 | 038 | Segment 1


title: 21-002-B_2 | 036 | Segment 1


title: 21-002-B_2 | 035 | Geometric Segment

value: Geometric Segment


title: 21-002-B_2 | 033 | Geometric Segment


title: 21-002-B_2 | 032 | Segment 2


title: 21-002-B_2 | 032 | Segment 1


title: 21-002-B_2 | 034 | Geometric Segment


title: 21-002-B_2 | 030 | Segment 2


title: 21-002-B_2 | 030 | Segment 1


title: 21-002-B_2 | 029 | Segment 1


title: 21-002-B_2 | 031 | Segment 1


title: 21-002-B_2 | 028 | Segment 2


title: 21-002-B_2 | 027 | Segment 2


title: 21-002-B_2 | 027 | Segment 1


title: 21-002-B_2 | 026 | Segment 2


title: 21-002-B_2 | 028 | Segment 1


title: 21-002-B_2 | 026 | Segment 1


title: 21-002-B_2 | 025 | Segment 2


title: 21-002-B_2 | 025 | Segment 1


title: 21-002-B_2 | 024 | Segment 1


title: 21-002-B_2 | 024 | Segment 2


title: 21-002-B_2 | 023 | Geometric Segment

description: 20210326_P1001660004390A_P1001660004390A_12.RCC


title: 21-002-B_2 | 020 | Segment 2

description: 20210326_P1001660004390A_P1001660004390A_09.RCC


title: 21-002-B_2 | 022 | Geometric Segment

description: 20210326_P1001660004390A_P1001660004390A_11.RCC


title: 21-002-B_2 | 029 | Segment 2


title: 21-002-B_2 | 031 | Segment 2


title: 21-002-B_2 | 021 | Geometric Segment

description: 20210326_P1001660004390A_P1001660004390A_10.RCC


title: 21-002-B_2 | 020 | Segment 1

description: 20210326_P1001660004390A_P1001660004390A_08.RCC


title: 21-002-B_2 | 019 | Segment 2

description: 20210326_P1001660004390A_P1001660004390A_07.RCC


title: 21-002-B_2 | 019 | Segment 1

description: 20210326_P1001660004390A_P1001660004390A_06.RCC


title: 21-002-B_2 | 018 | Segment 2

description: 20210326_P1001660004390A_P1001660004390A_05.RCC


title: 21-002-B_2 | 017 | Segment 1

description: 20210326_P1001660004390A_P1001660004390A_02.RCC


title: 21-002-B_2 | 016 | Segment 2

description: 20210326_P1001660004390A_P1001660004390A_01.RCC


title: 21-002-B_2 | 017 | Segment 2

description: 20210326_P1001660004390A_P1001660004390A_03.RCC


title: 21-002-B_2 | 015 | Segment 1


title: 21-002-B_2 | 013 | Segment 1


title: 21-002-B_2 | 016 | Segment 1


title: 21-002-B_2 | 013 | Segment 2


title: 21-002-B_2 | 014 | Segment 2


title: 21-002-B_2 | 012 | Segment 2


title: 21-002-B_2 | 012 | Segment 1

description: 20210326_P1001660004390A_P1001660004390A_04.RCC


title: 21-002-B_2 | 011 | Segment 2


title: 21-002-B_2 | 014 | Segment 1


title: 21-002-B_2 | 010 | Segment 2


title: 21-002-B_2 | 010 | Segment 1


title: 21-002-B_2 | 018 | Segment 1


title: 21-002-B_2 | 008 | Segment 2


title: 21-002-B_2 | 008 | Segment 1


title: 21-002-B_2 | 009 | Segment 1


title: 21-002-B_2 | 007 | Segment 2


title: 21-002-B_2 | 007 | Segment 1


title: 21-002-B_2 | 009 | Segment 2


title: 21-002-B_2 | 006 | Segment 1


title: 21-002-B_2 | 015 | Segment 2


title: 21-002-B_2 | 006 | Segment 2


title: 21-002-B_2 | 005 | Segment 2


title: 21-002-B_2 | 011 | Segment 1


title: 21-002-B_2 | 003 | Segment 1


title: 21-002-B_2 | 005 | Segment 1


title: 21-002-B_2 | 004 | Segment 2


title: 21-002-B_2 | 002 | Segment 2


title: 21-002-B_2 | 001 | Segment 2


title: 21-002-B_2 | 002 | Segment 1


title: 21-002-B_2 | 001 | Segment 1


title: 21-002-B_1 | 043 | Segment 1


title: 21-002-B_1 | 042 | Segment 2


title: 21-002-B_1 | 040 | Segment 1


title: 21-002-B_1 | 040 | Segment 2


title: 21-002-B_1 | 041 | Segment 2


title: 21-002-B_1 | 041 | Segment 1


title: 21-002-B_1 | 042 | Segment 1


title: 21-002-B_1 | 043 | Segment 2


title: 21-002-B_1 | 039 | Segment 2


title: 21-002-B_2 | 003 | Segment 2


title: 21-002-B_1 | 036 | Geometric Segment


title: 21-002-B_1 | 039 | Segment 1


title: 21-002-B_1 | 038 | Geometric Segment


title: 21-002-B_1 | 035 | Segment 2


title: 21-002-B_1 | 037 | Geometric Segment


title: 21-002-B_1 | 034 | Segment 2


title: 21-002-B_1 | 035 | Segment 1


title: 21-002-B_1 | 028 | Segment 1


title: 21-002-B_1 | 034 | Segment 1


title: 21-002-B_1 | 033 | Segment 2


title: 21-002-B_1 | 033 | Segment 1


title: 21-002-B_1 | 032 | Segment 2


title: 21-002-B_1 | 031 | Segment 1


title: 21-002-B_1 | 030 | Geometric Segment


title: 21-002-B_1 | 029 | Segment 1


title: 21-002-B_1 | 032 | Segment 1


title: 21-002-B_1 | 027 | Segment 1


title: 21-002-B_1 | 027 | Segment 2


title: 21-002-B_1 | 029 | Segment 2


title: 21-002-B_1 | 024 | Segment 1


title: 21-002-B_1 | 028 | Segment 2


title: 21-002-B_1 | 026 | Segment 2


title: 21-002-B_1 | 024 | Segment 2


title: 21-002-B_1 | 025 | Segment 1


title: 21-002-B_1 | 023 | Segment 2


title: 21-002-B_1 | 021 | Segment 1


title: 21-002-B_1 | 025 | Segment 2


title: 21-002-B_1 | 023 | Segment 1


title: 21-002-B_1 | 022 | Segment 1


title: 21-002-B_1 | 018 | Segment 2


title: 21-002-B_1 | 020 | Segment 2


title: 21-002-B_1 | 022 | Segment 2


title: 21-002-B_1 | 020 | Segment 1


title: 21-002-B_1 | 021 | Segment 2


title: 21-002-B_1 | 014 | Segment 2


title: 21-002-B_1 | 017 | Segment 1


title: 21-002-B_1 | 019 | Segment 2


title: 21-002-B_1 | 026 | Segment 1


title: 21-002-B_1 | 017 | Segment 2


title: 21-002-B_1 | 016 | Segment 2


title: 21-002-B_1 | 016 | Segment 1


title: 21-002-B_1 | 011 | Segment 1

description: 20210326_P1001660004389A_P1001660004389A_06.RCC


title: 21-002-B_1 | 019 | Segment 1


title: 21-002-B_1 | 018 | Segment 1


title: 21-002-B_1 | 015 | Segment 2


title: 21-002-B_1 | 015 | Segment 1


title: 21-002-B_1 | 014 | Segment 1

description: 20210326_P1001660004389A_P1001660004389A_12.RCC


title: 21-002-B_1 | 013 | Segment 2

description: 20210326_P1001660004389A_P1001660004389A_11.RCC


title: 21-002-B_1 | 012 | Segment 2

description: 20210326_P1001660004389A_P1001660004389A_09.RCC


title: 21-002-B_1 | 013 | Segment 1

description: 20210326_P1001660004389A_P1001660004389A_10.RCC


title: 21-002-B_1 | 005 | Segment 1


title: 21-002-B_1 | 004 | Segment 1

description: 20210326_P1001660004389A_P1001660004389A_07.RCC


title: 21-002-B_1 | 011 | Segment 2


title: 21-002-B_1 | 010 | Segment 2

description: 20210326_P1001660004389A_P1001660004389A_05.RCC


title: 21-002-B_1 | 012 | Segment 1

description: 20210326_P1001660004389A_P1001660004389A_08.RCC


title: 21-002-B_1 | 008 | Geometric Segment

description: 20210326_P1001660004389A_P1001660004389A_02.RCC


title: 21-002-B_1 | 010 | Segment 1

description: 20210326_P1001660004389A_P1001660004389A_04.RCC


title: 21-002-B_1 | 009 | Geometric Segment

description: 20210326_P1001660004389A_P1001660004389A_03.RCC


title: 21-002-B_1 | 007 | Geometric Segment

description: 20210326_P1001660004389A_P1001660004389A_01.RCC


title: 21-002-B_1 | 006 | Segment 2


title: 21-002-B_1 | 006 | Segment 1


title: 21-002-B_1 | 005 | Segment 2


title: 21-002-A_5 | 070 | Segment 2


title: 21-002-B_1 | 004 | Segment 2


title: 21-002-B_1 | 002 | Segment 2


title: 21-002-B_1 | 003 | Segment 2


title: 21-002-B_1 | 003 | Segment 1


title: 21-002-A_5 | 068 | Segment 1


title: 21-002-A_5 | 068 | Segment 2


title: 21-002-A_5 | 067 | Segment 2


title: 21-002-B_1 | 001 | Segment 2


title: 21-002-B_1 | 002 | Segment 1


title: 21-002-A_5 | 070 | Segment 1


title: 21-002-A_5 | 071 | Segment 1


title: 21-002-A_5 | 071 | Segment 2


title: 21-002-A_5 | 069 | Segment 1


title: 21-002-A_5 | 067 | Segment 1


title: 21-002-A_5 | 069 | Segment 2


title: 21-002-A_5 | 061 | Segment 2


title: 21-002-A_5 | 066 | Geometric Segment


title: 21-002-A_5 | 062 | Geometric Segment


title: 21-002-B_1 | 001 | Segment 1


title: 21-002-A_5 | 065 | Geometric Segment


title: 21-002-A_5 | 060 | Segment 2


title: 21-002-A_5 | 064 | Geometric Segment


title: 21-002-A_5 | 059 | Segment 2


title: 21-002-A_5 | 063 | Geometric Segment


title: 21-002-A_5 | 055 | Segment 2


title: 21-002-A_5 | 056 | Segment 2


title: 21-002-A_5 | 059 | Segment 1


title: 21-002-A_5 | 058 | Segment 1


title: 21-002-A_5 | 058 | Segment 2


title: 21-002-A_5 | 057 | Segment 2


title: 21-002-A_5 | 056 | Segment 1


title: 21-002-A_5 | 061 | Segment 1


title: 21-002-A_5 | 054 | Segment 2


title: 21-002-A_5 | 054 | Segment 1


title: 21-002-A_5 | 053 | Geometric Segment


title: 21-002-A_5 | 052 | Geometric Segment


title: 21-002-A_5 | 057 | Segment 1


title: 21-002-A_5 | 055 | Segment 1


title: 21-002-A_5 | 050 | Geometric Segment


title: 21-002-A_5 | 051 | Geometric Segment


title: 21-002-A_5 | 049 | Geometric Segment


title: 21-002-A_5 | 048 | Geometric Segment


title: 21-002-A_5 | 060 | Segment 1


title: 21-002-A_5 | 047 | Segment 2


title: 21-002-A_5 | 047 | Segment 1


title: 21-002-A_5 | 042 | Segment 1


title: 21-002-A_5 | 043 | Geometric Segment


title: 21-002-A_5 | 044 | Geometric Segment


title: 21-002-A_5 | 046 | Segment 1


title: 21-002-A_5 | 046 | Segment 2


title: 21-002-A_5 | 042 | Segment 2


title: 21-002-A_5 | 045 | Geometric Segment


title: 21-002-A_5 | 041 | Segment 1


title: 21-002-A_5 | 038 | Segment 1


title: 21-002-A_5 | 040 | Segment 1


title: 21-002-A_5 | 039 | Segment 2


title: 21-002-A_5 | 038 | Segment 2


title: 21-002-A_5 | 037 | Segment 2


title: 21-002-A_5 | 039 | Segment 1


title: 21-002-A_5 | 036 | Segment 1


title: 21-002-A_5 | 036 | Segment 2


title: 21-002-A_5 | 035 | Segment 1


title: 21-002-A_5 | 034 | Segment 2


title: 21-002-A_5 | 034 | Segment 1


title: 21-002-A_5 | 035 | Segment 2


title: 21-002-A_5 | 037 | Segment 1


title: 21-002-A_5 | 040 | Segment 2


title: 21-002-A_5 | 031 | Segment 2


title: 21-002-A_5 | 033 | Segment 2


title: 21-002-A_5 | 033 | Segment 1


title: 21-002-A_5 | 032 | Segment 2


title: 21-002-A_5 | 030 | Segment 2


title: 21-002-A_5 | 031 | Segment 1


title: 21-002-A_5 | 041 | Segment 2


title: 21-002-A_5 | 032 | Segment 1


title: 21-002-A_5 | 029 | Segment 2


title: 21-002-A_5 | 028 | Segment 2

description: 20210326_P1001660004388A_P1001660004388A_12.RCC


title: 21-002-A_5 | 029 | Segment 1


title: 21-002-A_5 | 030 | Segment 1


title: 21-002-A_5 | 028 | Segment 1

description: 20210326_P1001660004388A_P1001660004388A_11.RCC


title: 21-002-A_5 | 027 | Segment 2

description: 20210326_P1001660004388A_P1001660004388A_10.RCC


title: 21-002-A_5 | 026 | Segment 2

description: 20210326_P1001660004388A_P1001660004388A_08.RCC


title: 21-002-A_5 | 027 | Segment 1

description: 20210326_P1001660004388A_P1001660004388A_09.RCC


title: 21-002-A_5 | 025 | Segment 1

description: 20210326_P1001660004388A_P1001660004388A_05.RCC


title: 21-002-A_5 | 025 | Segment 2

description: 20210326_P1001660004388A_P1001660004388A_06.RCC


title: 21-002-A_5 | 023 | Segment 2

description: 20210326_P1001660004388A_P1001660004388A_02.RCC


title: 21-002-A_5 | 024 | Segment 1

description: 20210326_P1001660004388A_P1001660004388A_03.RCC


title: 21-002-A_5 | 024 | Segment 2

description: 20210326_P1001660004388A_P1001660004388A_04.RCC


title: 21-002-A_5 | 022 | Segment 1


title: 21-002-A_5 | 022 | Segment 2


title: 21-002-A_5 | 021 | Segment 2


title: 21-002-A_5 | 021 | Segment 1


title: 21-002-A_5 | 019 | Segment 2


title: 21-002-A_5 | 020 | Segment 1

description: 20210326_P1001660004388A_P1001660004388A_07.RCC


title: 21-002-A_5 | 026 | Segment 1


title: 21-002-A_5 | 017 | Segment 2


title: 21-002-A_5 | 017 | Segment 1

description: 20210326_P1001660004388A_P1001660004388A_01.RCC


title: 21-002-A_5 | 020 | Segment 2


title: 21-002-A_5 | 018 | Segment 1


title: 21-002-A_5 | 016 | Segment 2


title: 21-002-A_5 | 016 | Segment 1


title: 21-002-A_5 | 018 | Segment 2


title: 21-002-A_5 | 019 | Segment 1


title: 21-002-A_5 | 015 | Segment 2


title: 21-002-A_5 | 023 | Segment 1


title: 21-002-A_5 | 012 | Segment 2


title: 21-002-A_5 | 015 | Segment 1


title: 21-002-A_5 | 009 | Segment 2


title: 21-002-A_5 | 010 | Segment 2


title: 21-002-A_5 | 009 | Segment 1


title: 21-002-A_5 | 008 | Segment 2


title: 21-002-A_5 | 014 | Segment 1


title: 21-002-A_5 | 014 | Segment 2


title: 21-002-A_5 | 013 | Segment 2


title: 21-002-A_5 | 011 | Segment 2


title: 21-002-A_5 | 005 | Segment 2


title: 21-002-A_5 | 006 | Segment 2


title: 21-002-A_5 | 008 | Segment 1


title: 21-002-A_5 | 007 | Segment 1


title: 21-002-A_5 | 006 | Segment 1


title: 21-002-A_5 | 005 | Segment 1


title: 21-002-A_5 | 004 | Segment 2


title: 21-002-A_5 | 003 | Segment 2


title: 21-002-A_5 | 004 | Segment 1


title: 21-002-A_5 | 003 | Segment 1


title: 21-002-A_4 | 022 | Segment 2


title: 21-002-A_5 | 002 | Segment 1


title: 21-002-A_5 | 012 | Segment 1


title: 21-002-A_4 | 023 | Segment 2


title: 21-002-A_5 | 001 | Segment 2


title: 21-002-A_5 | 001 | Segment 1


title: 21-002-A_5 | 002 | Segment 2


title: 21-002-A_4 | 023 | Segment 1


title: 21-002-A_4 | 020 | Geometric Segment


title: 21-002-A_4 | 022 | Segment 1


title: 21-002-A_4 | 021 | Segment 2


title: 21-002-A_4 | 019 | Segment 1


title: 21-002-A_4 | 018 | Segment 2


title: 21-002-A_4 | 015 | Segment 1


title: 21-002-A_4 | 016 | Segment 2


title: 21-002-A_4 | 017 | Segment 1


title: 21-002-A_4 | 016 | Segment 1


title: 21-002-A_4 | 015 | Segment 2


title: 21-002-A_4 | 014 | Segment 2


title: 21-002-A_4 | 012 | Segment 2


title: 21-002-A_4 | 012 | Segment 1


title: 21-002-A_4 | 014 | Segment 1


title: 21-002-A_4 | 021 | Segment 1


title: 21-002-A_4 | 011 | Segment 1


title: 21-002-A_4 | 013 | Segment 2


title: 21-002-A_4 | 011 | Segment 2


title: 21-002-A_4 | 009 | Segment 2


title: 21-002-A_4 | 010 | Segment 2


title: 21-002-A_4 | 019 | Segment 2


title: 21-002-A_4 | 008 | Segment 2


title: 21-002-A_4 | 010 | Segment 1


title: 21-002-A_4 | 018 | Segment 1


title: 21-002-A_4 | 009 | Segment 1


title: 21-002-A_4 | 007 | Segment 1


title: 21-002-A_4 | 008 | Segment 1


title: 21-002-A_4 | 007 | Segment 2


title: 21-002-A_4 | 006 | Segment 2


title: 21-002-A_4 | 004 | Segment 2


title: 21-002-A_4 | 005 | Segment 2


title: 21-002-A_4 | 013 | Segment 1


title: 21-002-A_4 | 006 | Segment 1


title: 21-002-A_4 | 003 | Segment 2


title: 21-002-A_4 | 003 | Segment 1


title: 21-002-A_4 | 005 | Segment 1


title: iBAT ZT_21 rep4

city: Leiden

first: Robin

last: van Eenige

address: Albinusdreef 2

department: Division of Endocrinology, Department of Medicine

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Sequencing quality was assessed with MultiQC
Reads were mapped to the Mus Musculus reference genome mm10 (Ensembl build 38.88) using GSNAP (version 2017-09-11) and reads per gene were counted using HTSeq-count (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iBAT ZT_21

extract_protocol:
Total RNA of snap-frozen iBAT (approx. 10-20 mg) was isolated using the nucleospin kit (Macherey-Nagel, Düren, Germany; 740955.50) after homogenization by a FastPrep-24™ 5G bead beating grinder and lysis system (4.0 m · s-1, 10 s; MP Biomedicals™, Santa Ana, California, USA) in a mixture of 400 µL RA1 (Macherey-Nagel, Düren, Germany; 740955.50) with 4 µL β-mercaptoethanol in Lysing Matrix D tubes (MP Biomedicals™, Santa Ana, California, USA; 116913500). RNA was quality-controlled on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).
A stranded library was constructed for 100bp paired-end sequencing on BGI's platform.

tag: strain

tag: developmental stage

value: 10 weeks old

tag: tissue

value: Interscapular brown adipose tissue

tag: condition

value: Zeitgeber time 21


title: iBAT ZT_18 rep2

source_name: iBAT ZT_18

value: Zeitgeber time 18


title: iBAT ZT_18 rep4


title: iBAT ZT_18 rep3


title: iBAT ZT_21 rep2


title: 21-002-A_4 | 002 | Segment 2


title: iBAT ZT_21 rep3


title: 21-002-A_4 | 004 | Segment 1


title: iBAT ZT_21 rep1


title: iBAT ZT_18 rep1


title: iBAT ZT_15 rep4

source_name: iBAT ZT_15

value: Zeitgeber time 15


title: 21-002-A_4 | 001 | Segment 2


title: 21-002-A_4 | 001 | Segment 1


title: 21-002-A_4 | 002 | Segment 1


title: iBAT ZT_15 rep3


title: iBAT ZT_15 rep2


title: iBAT ZT_09 rep3

source_name: iBAT ZT_09

value: Zeitgeber time 9


title: iBAT ZT_12 rep4

source_name: iBAT ZT_12

value: Zeitgeber time 12


title: iBAT ZT_12 rep3


title: iBAT ZT_06 rep4

source_name: iBAT ZT_06

value: Zeitgeber time 6


title: iBAT ZT_09 rep2


title: iBAT ZT_12 rep2


title: iBAT ZT_09 rep1


title: iBAT ZT_15 rep1


title: iBAT ZT_06 rep3


title: iBAT ZT_09 rep4


title: iBAT ZT_06 rep1


title: iBAT ZT_03 rep3

source_name: iBAT ZT_03

value: Zeitgeber time 3


title: iBAT ZT_12 rep1


title: iBAT ZT_06 rep2


title: iBAT ZT_03 rep4


title: TOV-21G_cell_line

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database without allowing any mismatch.
The data was normalized using reads per million mapped reads.
Assembly: miRbase 21
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

growth_protocol: The cell lines were maintained in RPMI (Nacalai Tesque, Kyoto, Japan) containing 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO), penicillin, and streptomycin (Meiji Seika Pharma, Tokyo, Japan).

extract_protocol:
Total RNA was extracted using the miRNeasy FFPE Kit or miRNeasy Mini Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

tag: sample type

value: cell line

tag: cell line


title: SKOV3_cell_line


title: iBAT ZT_00 rep4

source_name: iBAT ZT_00

value: Zeitgeber time 0


title: Case21_PDX

source_name: Ovary

value: Ovary

value: fresh frozen

tag: Sex

value: female


title: A2780_cell_line


title: iBAT ZT_03 rep1


title: iBAT ZT_00 rep3


title: iBAT ZT_03 rep2


title: ES2_cell_line


title: A2780cis_cell_line


title: iBAT ZT_00 rep2


title: Case22_PDX


title: Case25_omental_metastatic_cancer

tag: disease stage

value: IIIC


title: Case25_primary_cancer


title: Case25_peritoneal_metastatic_cancer


title: Case24_primary_cancer(right)


title: Case23_PDX


title: Case24_primary_cancer(left)


title: Case24_omental_metastatic_cancer


title: MIDAS_Stage9_rep_3

city: Irapuato

first: Alfredo

middle: Heriberto

last: Herrera

state: Guanajuato

address: Libr.  Norte Carr. Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

data_processing:
fastq files were aligned to the genome Phaseolus vulgaris V2.1 donwloaded from phytozome. Reads were aligned to the genome using the pseudoaligner Kallisto
tsv files resulting from the aligments were summarized to a table of counts with in house script in R.
Expression data was normalized using the Limma package in R
Differentially expressed genes (log2 |FC| > 1 and FDR < 0.05) were identified by pairwise comparison using the edgeR package in R
Genome_build: Phaseolus vulgaris V2.1
Supplementary_files_format_and_content: kallisto abundance measurements

organism: Phaseolus vulgaris

source_name: pod R9 Phaseolus vulgaris MIDAS

growth_protocol: plants of each accessiion were cultivated until the first pod emerged, then the stage R7 was collected. Pods filling (R8) was collected as well as the final mature pod (R9) stage of all the P. Vulgaris accessions.

extract_protocol:
Total RNA was isolated using the TRIAZol Reagent and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq sample preparation kit 1 x75, according to the manufacturer’s instructions.

treatment_protocol: Untreated

tag: accessions

value: Phaseolus vulgaris MIDAS

tag: phenotype

value: Indehiscent

value: domesticated

tag: treatment

value: untreated


title: MIDAS_Stage8_rep_2

source_name: pod R8 Phaseolus vulgaris MIDAS


title: Expo.phase_P.aeruginosa.PAO1_sequence

city: Quebec

first: Patrick

last: PROVOST

state: QUEBEC

address: 2705 , Boulevard Laurier, Bloc T

department: Centre Hospitalier de l'Université Laval (CHUL) - Microbiology, Infectious diseases, Immunology

country: Canada

institute: CRCHU of Québec City - Université LAVAL

description:
RNA 8-30nt library
Bacterial sRNA-Seq analysis

data_processing:
Raw sequences were generated as clean reads from Illumina NextSeq by real-time base calling and quality filtering.
Subsequently, the 3’ adapter sequence was trimmed from the clean reads and the reads with lengths shorter than 8 nt were discarded. As the 5’ adapter was also used as the sequencing primer site, the 5’ adapter sequence is not present in the sequencing reads.
The trimmed reads (length ≥8 nt) were aligned to the corresponding genome database using novoalign software (http://www.novocraft.com). sRNA read counts were normalized as tag counts per million.
Sequences known to be contaminant confounders from RNA isolation procedures were discarded before analysis. Finally, a second dataset was generated for the E. coli and OMV samples by excluding the reads that are also present in the LB culture medium sample.
Assembly: See Supplementary_file_Genome_Database_GEO_PROVOST_LAB.pdf.
Supplementary files format and content: *.trimmed_tags.fa: Trimmed Reads Data contains trimmed reads (FASTA format). Defline: Unique identifier/name_Rank (from most to least abundant)_Quantitative information = copy number = Tags per million reads (TPM).

organism: Pseudomonas aeruginosa PAO1

growth_protocol: The growth protocols used for each sample are mentioned in the characteristics field.

extract_protocol:
Total RNA from bacterial strains was extracted using the hot phenol procedure or the RiboPure™ Bacteria Kit (Invitrogen, ON, Canada, Cat. No. AM1925) following the manufacturer's recommendations. OMV-derived RNAs were isolated with RiboPure™ Bacteria Kit or RNAzol RT (Sigma, MO, USA, Cat. No. R4533) reagents following the manufacturer’s recommendations. RNAzol RT kit allowed selective isolation (enrichment) of small RNAs (<200 nt). All RNA samples were subjected to treatment with DNase-I when applicable, quantified with the NanoDrop™ 2000 Spectrophotometer (Thermo Scientific™, Cat. No. ND-2000) and saved at -80°C before downstream applications.
For each biological condition, an RNA sample was prepared by pooling equivalent amounts of total RNA isolated from 2 or 3 biological replicate samples. Total RNA was shipped on dry ice to the sequencing platform of Arraystar Inc. (Rockville, MD, USA). Total RNA of each sample was used to prepare the sRNA sequencing library which included the following steps: 1) 3’ adapter ligation with T4 RNA ligase 2 (truncated); 2) 5’ adapter ligation with T4 RNA ligase; 3) cDNA synthesis with RT primer; 4) PCR amplification; 5) extraction and purification of ~130-150 bp PCR amplified fragments from the PAGE gel. After the completed libraries were quantified with Agilent 2100 Bioanalyzer, the DNA fragments in the libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ and finally sequenced for 51 cycles on Illumina NextSeq according to the manufacturer’s instruction.

treatment_protocol: The treatments used for each sample are mentioned in the characteristics field.

value: WT (T3SS+; exlA-)

tag: stress

value: Untreated _ exponential growth _ 37C

tag: media

value: LB


title: MIDAS_Stage9_rep_2

tag: genotype


title: Case23_primary_cancer

value: IA


title: Case13_normal_ovary

value: FFPE


title: iBAT ZT_00 rep1

value: 10 weeks old

value: Interscapular brown adipose tissue


title: Case22_primary_cancer


title: Case12_normal_ovary


title: Case10_normal_ovary


title: MIDAS_Stage8_rep_3


title: Case21_primary_cancer


title: SXB_405_Stage9_rep_1

source_name: pod R9 Phaseolus vulgaris SXB 405

value: Phaseolus vulgaris SXB 405

value: middle Dehiscent


title: Case7_normal_ovary

value: Ovary


title: MIDAS_Stage8_rep_1


title: SXB_405_Stage9_rep_3


title: SXB_405_Stage8_rep_3

source_name: pod R8 Phaseolus vulgaris SXB 405


title: MIDAS_Stage7_rep_1

source_name: pod R7 Phaseolus vulgaris MIDAS


title: MIDAS_Stage7_rep_2


title: Case2_normal_ovary


title: Case19_normal_ovary


title: MIDAS_Stage7_rep_3


title: Case4_normal_ovary


title: SXB_405_Stage8_rep_1


title: Case1_normal_ovary


title: Case11_normal_ovary


title: SXB_405_Stage9_rep_2


title: Case8_recurrent_cancer


title: SXB_405_Stage7_rep_2

source_name: pod R7 Phaseolus vulgaris SXB 405


title: SXB_405_Stage7_rep_1


title: MIDAS_Stage9_rep_1


title: SXB_405_Stage8_rep_2


title: Case18_normal_ovary


title: SXB_405_Stage7_rep_3


title: Case4_recurrent_cancer


title: ICA_BUNSI_Stage8_rep_3

source_name: pod R8 Phaseolus vulgaris ICA Bunsi

value: Phaseolus vulgaris ICA Bunsi


title: Case3_recurrent_cancer

value: female


title: Case1_recurrent_cancer


title: ICA_BUNSI_Stage9_rep_3

source_name: pod R9 Phaseolus vulgaris ICA Bunsi


title: LB_Sterile.culture.medium_sequence

description:
RNA 8-30nt library
Bacterial sRNA-Seq analysis
Sterile medium

organism: synthetic construct

value: Untreated _ Control


title: ICA_BUNSI_Stage9_rep_2


title: Case19_primary_cancer


title: Case20_primary_cancer


title: VA-008-Placebo-AA

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
Placebo
randominzed control or treatment
AfricanAm_vs_Caucasian_deseq_13010_115.txt
VitD_vs_Placebo_AA_deseq_12736_116.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: Prostate

extract_protocol:
Around 100–200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, CA, USA), following the protocol described by the manufacturer. High-throughput sequencing (HTS) was performed using an Illumina HiSeq2500 with each sample sequenced to a minimum depth of ∼ 50 million reads.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.
mRNA libraries were prepared using Illumina's TruSeq™ RNA Sample Prep Kit v2 as described by the manufacturer

value: Prostate

value: adult

tag: concentration

value: 0 IU of vitamin D3 per day


title: VA-003-Placebo-AA 729


title: AA 728__VA002-VitD

description:
VitD
randominzed control or treatment
AfricanAm_vs_Caucasian_deseq_13010_115.txt
VitD_vs_Placebo_AA_deseq_12736_116.txt

value: 4000 IU of vitamin D3 per day


title: VA-007-Placebo-AA


title: ICA_BUNSI_Stage8_rep_2

value: domesticated

value: untreated


title: Case18_primary_cancer


title: ICA_BUNSI_Stage7_rep_3

source_name: pod R7 Phaseolus vulgaris ICA Bunsi


title: Case17_primary_cancer


title: Case5_recurrent_cancer


title: ICA_BUNSI_Stage7_rep_2


title: AA 722__39-VitD


title: AA 724__42 Placebo


title: ICA_BUNSI_Stage9_rep_1


title: Case16_primary_cancer


title: AA 723__40-VitD


title: Case15_primary_cancer


title: ICA_BUNSI_Stage7_rep_1


title: AA 720__37-Placebo


title: Case14_primary_cancer


title: Case13_primary_cancer


title: AA 727__E000-VitD


title: EA 952__04 VitD

description:
VitD
randominzed control or treatment
AfricanAm_vs_Caucasian_deseq_13010_115.txt
Placebo_vs_VitD_EA_32448_340.txt


title: EA 950__35 VitD


title: ICA_BUNSI_Stage8_rep_1


title: EA 951__36 VitD


title: Case12_primary_cancer


title: EA 949__34 Placebo

description:
Placebo
randominzed control or treatment
AfricanAm_vs_Caucasian_deseq_13010_115.txt
Placebo_vs_VitD_EA_32448_340.txt


title: G12873_Stage9_rep_1

source_name: pod R9 Phaseolus vulgaris G12873

value: Phaseolus vulgaris G12873

value: full Dehiscent

value: wild-type


title: EA 946__31 Placebo


title: AA 721__38-VitD


title: Case10_primary_cancer

value: FFPE


title: EA 947__32 VitD


title: EA 945__30 VitD


title: EA 943__26 VitD


title: G12873_Stage8_rep_2

source_name: pod R8 Phaseolus vulgaris G12873


title: G12873_Stage8_rep_1


title: EA 942__25 Placebo

value: 0 or 4000 U of vitamin D3 per day


title: EA 953__05 VitD


title: G12873_Stage9_rep_3


title: EA 941__24 Placebo

value: 0 or 4000 IU  of vitamin D3 per day


title: G12873_Stage9_rep_2


title: G12873_Stage7_rep_3

source_name: pod R7 Phaseolus vulgaris G12873


title: EA 940__23 Placebo


title: Case8_primary_cancer


title: EA 948__33 Placebo


title: EA 937__18 VitD


title: G12873_Stage8_rep_3


title: Case6_primary_cancer


title: EA 938__20 VitD


title: Case11_primary_cancer


title: G12873_Stage7_rep_2


title: Case7_primary_cancer


title: Case5_primary_cancer


title: OMVs_E.coli(R)_sequence

description:
RNA 8-30nt library
Bacterial sRNA-Seq analysis
WT K-12 MG1655
Outer membrane vesicles (OMVs)

organism: Escherichia coli str. K-12 substr. MG1655

value: WT

value: Untreated _ exponential growth _ 37C (Reference, R)

value: LB


title: EA 944__27 Placebo


title: Case4_primary_cancer

value: Ovary

value: female

value: IA


title: RNaseE-.E.coli_sequence

description:
RNA 8-30nt library
Bacterial sRNA-Seq analysis
Mut. K-12 MG1655 rne-3071 ts (EM1277)

value: Heat shock (30C to 44C) _ RNase E inhibition


title: Case9_primary_cancer


title: (+)rifampicin_E.coli(R)_sequence

description:
RNA 8-30nt library
Bacterial sRNA-Seq analysis
WT K-12 MG1655

value: Treated with rifampicin (R) _ 37C


title: Expo.phase_P.aeruginosa.PA7_sequence

organism: Pseudomonas paraeruginosa PA7

value: WT (T3SS-; exlA+)

value: Untreated _ exponential growth _ 37C


title: (+)chloramphenicol_E.coli(R)_sequence

value: Treated with chloramphenicol (R) _ 37C


title: Stat.phase_E.coli_sequence

value: Untreated _ stationary growth _ 37C


title: Case2_primary_cancer


title: Case3_primary_cancer


title: Expo.phase_L.pneumophila_sequence

organism: Legionella pneumophila

value: WT JR32 Philadelphia-1 (LPDL5)

value: AYE


title: EA 939__22 Placebo

value: Prostate

value: adult

value: 0 IU of vitamin D3 per day


title: Expo.phase.reference(R)_E.coli_sequence

value: WT


title: G12873_Stage7_rep_1

value: Phaseolus vulgaris G12873

value: full Dehiscent

value: wild-type

value: untreated


title: Case1_primary_cancer

value: Ovary

value: FFPE

value: female

value: IA


title: iBAT ZT_12 input

data_processing:
Sequencing quality was assessed with MultiQC
Reads were mapped to the Mus Musculus reference genome mm10 (Ensembl build 38.88) using BWA-MEM (version 0.7.17) and peaks were called using Macs2 (version 2.1.2).
Reads per peak were counted using HTSeq-count (version 1.99.2) and peak annotation was performed using HOMER (version 4.11).
Peaks were selected on significance (FDR<0.05) in at least six out of eight samples.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every peak and every sample

source_name: Interscapular brown adipose tissue

extract_protocol:
ChIP was performed as previously described (Mir AA et al., Methods Mol Biol. 2019). Briefly, iBAT samples pooled from eight mice (approx. 250-350 mg combined; experiment 1) were homogenized in lysis buffer (10 mM HEPES-KOH, pH 7.3, 10 mM KCl, 5 mM MgCl2, 0.5 mM DTT, 1× cOmplete™ Protease Inhibitor (Roche Diagnostics, Almere, The Netherlands)), filtered through a Falcon® 70 µm cell strainer (Life Sciences, Corning, New York, USA), cross-linked in 10 mL 1% formaldehyde in PBS for 15 minutes and quenched with 1.5 mL 1 M glycine for 5 minutes. After washing, pelleted nuclei were further lysed twice by resuspension in 1 mL cold fast IP buffer (50 mM NaCl, 50 mM Tris–HCl (pH 7.5), 5 mM EDTA, 0.5% v/v NP40, 1% v/v Triton X-100, 1× cOmplete™ Protease Inhibitor) and passing through a 24G syringe. Chromatin was subsequently sheared (Bioruptor® plus, Diagenode, Liège, Belgium) in 1 mL shearing buffer (1% v/v SDS, 10 mM EDTA, 50 mM Tris–HCl (pH 8), 1× cOmplete™ Protease Inhibitor). Sheared chromatin was then centrifuged, and 10% of each sample was stored at -20°C to be used as input. The chromatin was diluted in 7.2 mL dilution buffer (0.01% v/v SDS, 1.1% v/v Triton X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl (pH 8.0), 0.167 M NaCl, 1× cOmplete™ Protease Inhibitor) and incubated overnight at 4°C with 8 µg of PPARγ antibody (2443, Cell Signaling Technology, Danvers, Massachusetts, USA). IP was cleared by centrifugation, and the top 90% was incubated with 100 µL bovine serum albumin-blocked DynaBeads™ (11203D; Thermo Fisher Scientific, Waltham, USA) for 6 hours at 4°C. Unbound complexes were removed by washing with fast IP buffer. Beads were collected and washed in Tris-EDTA buffer (10 mM Tris-HCl, 1 mM disodium EDTA, pH 8.0), and ChIP’ed chromatin was collected by elution with 100 µL beads elution buffer (0.105 M NaHCO3, 1% SDS) for 15 minutes at room temperature two times. Both the input sample and the ChIP’ed chromatin were de-cross-linked by addition of 4 µL and 8 µL 5 M NaCl, respectively, followed by overnight incubation at 65°C. Samples were subsequently treated with RNAse A and Proteinase K, and DNA was purified using MinElute® columns from the PCR Purification Kit (QIAGEN, Hilden, Germany) using the manufacturer’s protocol.
A stranded library (fragment selection 100-500bp) was constructed for 100bp paired-end sequencing on BGI's platform.

value: 10 weeks old

value: Interscapular brown adipose tissue

value: Zeitgeber time 12


title: dus1Δ dus2Δ dus3Δ dus4Δ rep3 RNA-seq

city: NEW HAVEN

first: Wendy

middle: V

last: Gilbert

state: CT

address: 333 Cedar St

department: MB&B

institute: Yale University

data_processing:
adapter trimming using bbduk.shk trim=r k=23 mink=11 hdist=1 tpe tbo
PCR duplicate/UMI collapsing using dedupe.sh
UMI trimming using bbduk.sh ftl=10
alignment using bbmap.sh  maxindel=25 intronlen=5000
Assembly: sacCer3
Supplementary files format and content: tsv files

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: BY 4741 and DUS KO cells were grown to mid-log phase, harvested by centrifugation, and flash frozen

extract_protocol:
Total RNA was extracted using hot phenol
Briefly, polyA+ mRNA was treated with sodium borohydride to reduce D residues. mRNA was then fragmented, and end-repaired using a combination of T4 PNK and CIP. RNA fragments were then size selected on 8% UREA-PAGE gels. A preadenylated 3' adapter was ligated to the RNA fragments with T4 RNA Ligase I, and RT was performed using SSIII RT at 50C for 1h. Truncated cDNAs were then size selected on 8% UREA-PAGE gels. A 5' adapter was then ligated to the truncated cDNAs using T4 RNA Ligase I. After adapter ligation DNA was PCR amplified with barcoded primers for 13-18 cycles with phusion DNA polymerase. Bands corresponding to adapters + insert were then size selected using an 8% TBE-PAGE gel. Libraries were run on an Agilent Bioanalyzer and quantified using a qubit. They were then pooled and sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. RNAseq libraries were generated in paralell to the D-seq libraries, except  NaBH4 treatment and truncated cDNA selection were omitted.

value: dus1[delta] dus2[delta] dus3[delta] dus4[delta]


title: dus1Δ dus2Δ dus3Δ dus4Δ rep1 RNA-seq


title: dus1Δ dus2Δ dus3Δ dus4Δ rep2 RNA-seq


title: Wide type-1, IRI,24h

city: Shanghai

first: Sijia

last: Yan

address: Huashan Road

department: Institute for Personalized Medicine

institute: Shanghai Jiaotong University

data_processing:
Filtering of Clean Reads
Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads will be removed.
The rRNA removed reads of each sample were then mapped to reference genome(Ensembl release 90 GRCm38.p5) by TopHat2(version 2.0.3.12)
The reconstruction of transcripts was carried out with software Cufflinks together with TopHat2
Gene abundances were quantified by software RSEM.The gene expression level was normalized by using FPKM (Fragments Per Kilobase of transcript per Million   mapped reads) method
Assembly: Ensembl release 90 GRCm38.p5
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

growth_protocol: A mouse renal IRI model was established with three 7-week-old Ptpn6+/mev mice and three wild-type littermates

extract_protocol:
Kidneys were removed, flash frozen on dry ice. RNA was harvested using Rneasy mini plus kit (Qiagen).
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR.

treatment_protocol: An abdominal midline incision was made, and then the right kidney of the mice was resected. The pedicle of the left kidney was clamped for 34 min with a nontraumatic vascular clamp.At 24 hours post-IRI, the mice were sacrificed, and the left kidneys were removed for  RNA analyses.

value: kidney

value: wide type

value: 24h after renal ischemia-reperfusion injury


title: Wide type-2, IRI,24h


title: Wide type-3, IRI,24h


title: Ptpn6+/mev 2, IRI,24h

value: SHP1 knockdown


title: Ptpn6+/mev 3, IRI,24h


title: iBAT ZT_15

value: Zeitgeber time 15


title: iBAT ZT_12


title: iBAT ZT_18

value: Zeitgeber time 18


title: BY4741 rep3 RNA-seq


title: Caco2+ 1 ug / mL for 2 hours rep 3

city: MADRID

first: Eduardo

last: Martínez-Naves

state: MADRID

address: AVDA COMPLUTENSE S/N

department: Dpt. Immunología, Ophthalmology and ORL

country: Spain

institute: Universidad Complutense de Madrid, Facultad de Medicina

hyb_protocol: Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Microarray sequences and annotations are listed in sheet '039494_hg19_20140813'. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: Raw data files: FeatureExtraction generated Txt files (quantification, annotation and flagging). In two-color experiments, FE Software performs intra-array Lowess global normalization.

source_name: Caco2 cell line

label_protocol:
Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.7 kit by following manufacturer instructions. Agilent manual G4140-90040 of Sep2014. Amplification: by RNA polymerases.
Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.
Labeled samples are purified with silica-based spin columns.

growth_protocol: The human colorectal adenocarcinoma cell lines Caco-2 was grown in DMEM supplemented with 20% heat-inactivated fetal calf serum (FCS) (Lonza) and 5% L-glutamine, 5% antibiotic-antifungal and 5% non-essential amino acids until reaching 70-80% confluence

extract_protocol: RNA was extracted from cell lysates using the NucleoSpinRNA Mini Kit (Macherey-Nagel).

treatment_protocol: Different treatments are represented as C (non-treated cells), Fl (treated with flagellin 1 μg / mL for 2 hours), TG (treated with TG at 1 μM for 5 hours), or X (treated with 1 μM TG for 5 hours, and with 1 μg / mL Fl for additional 2 hours).

value: Caco2+ 1 ug / mL for 2 hours

tag: rin


title: Caco2+ 1 ug / mL for 2 hours rep 1


title: Ptpn6+/mev 1, IRI,24h


title: Caco2+TG at 1 uM for 5 hours+ 1 ug / mL for 2 hours rep 1


title: Caco2+TG at 1 uM for 5 hours+ 1 ug / mL for 2 hours rep 2


title: Caco2+ 1 ug / mL for 2 hours rep 2


title: Caco2+TG at 1 uM for 5 hours+ 1 ug / mL for 2 hours rep 3


title: BY4741 rep2 RNA-seq


title: Caco2+TG at 1 uM for 5 hours rep 3

value: Caco2+TG at 1 uM for 5 hours


title: iBAT ZT_09

value: Zeitgeber time 9


title: iBAT ZT_21

value: Zeitgeber time 21


title: BY4741 rep1 RNA-seq


title: Vav3-/-_leukmeic B-cell progenitors rep3

city: cincinnati

first: Ramesh

middle: C

last: Nayak

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's

description: Vav3-/- p190 BCR-ABL+ B-cell progenitors isolated from leukemic mouse bone marrow, expt#3

data_processing:
Reads were aligned with TopHat software, using  mm10 as the reference genome and Reads Per Kilobase of transcript per Million mapped reads (RPKM) as output.
RPKM were log2-transformed and baselined to the median expression of the average of each class of samples.
Analysis of differential gene expression and gene ontology (GO) pathway analyses using Altanalyze software v2.1 and Topp Gene Suite (https://toppgene.cchmc.org/enrichment.jsp). Both platforms are developed by Cincinnati Children's research foundation)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Bone Marrow

growth_protocol: WT and Vav3-/- leukemic (p190 BCR-ABL+) B-cell progenitors (FSChiEYFP+B220+IgM-CD43+CD19+) were sorted from the BM of transplanted leukmeic WT and Vav3-/- chimeric mice. BM cells were stained with fluorochromo tagged antibodies in 1x PBS containing 1% FBS, and B-cell progenitors were sorted into IMDM media containing 10% FBS. Cells were washed once with 1X PBS and processed for RNA purification.

extract_protocol:
After sorting, total RNA was isolated using RNAeasy mini kit (QIAGEN, Catalog 74104) according to manufacturer's protocols.
Total RNA samples (10ng) from leukemic B-cell progenitors were used for cDNA amplification using Ovation RNA-seq v2 assay kit (Tecan Genomics) to generate 2-4 microgram of double stranded cDNA. The illumina protocol, Nextera XT DNA Library Preparation Kit was used to create DNA libeary templates from double stranded cDNA followed by Next generation paired end sequeining using Illumina Hiseq2500 following manufacturer's protocol.

value: B-cell progenitors


title: iBAT ZT_06

value: Zeitgeber time 6


title: Vav3-/-_leukmeic B-cell progenitors rep2

description: Vav3-/- p190 BCR-ABL+ B-cell progenitors isolated from leukemic mouse bone marrow, expt#2


title: Caco2+TG at 1 uM for 5 hours rep 2


title: iBAT ZT_03

value: Zeitgeber time 3


title: dus1Δ dus2Δ dus3Δ dus4Δ  rep3

data_processing:
adapter trimming using bbduk.shk trim=r k=23 mink=11 hdist=1 tpe tbo
PCR duplicate/UMI collapsing using dedupe.sh
UMI trimming using bbduk.sh ftl=10
alignment using bbmap.sh  maxindel=25 intronlen=5000
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files

extract_protocol:
Total RNA was extracted using hot phenol
Briefly, polyA+ mRNA was treated with sodium borohydride to reduce D residues. mRNA was then fragmented, and end-repaired using a combination of T4 PNK and CIP. RNA fragments were then size selected on 8% UREA-PAGE gels. A preadenylated 3' adapter was ligated to the RNA fragments with T4 RNA Ligase I, and RT was performed using SSIII RT at 50C for 1h. Truncated cDNAs were then size selected on 8% UREA-PAGE gels. A 5' adapter was then ligated to the truncated cDNAs using T4 RNA Ligase I. After adapter ligation DNA was PCR amplified with barcoded primers for 13-18 cycles with phusion DNA polymerase. Bands corresponding to adapters + insert were then size selected using an 8% TBE-PAGE gel. Libraries were run on an Agilent Bioanalyzer and quantified using a qubit. They were then pooled and sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
D-seq


title: Caco2 nonstimulated rep 3

value: Caco2 nonstimulated


title: dus1Δ dus2Δ dus3Δ dus4Δ  rep2


title: Vav3-/-_leukmeic B-cell progenitors rep1

description: Vav3-/- p190 BCR-ABL+ B-cell progenitors isolated from leukemic mouse bone marrow, expt#1


title: dus1Δ dus2Δ dus3Δ dus4Δ  rep1


title: WT_leukmeic B-cell progenitors rep3

description: WT p190 BCR-ABL+ B-cell progenitors isolated from leukemic mouse bone marrow, expt#3

value: Wild type


title: rd10 mouse retina, MSC-EVs (Exo)-treated, P28, rep2

city: Qingyuan

first: le

last: li

address: B24 Yinquan South Road, Qingyuan 511518, Guang Dong, China

institute: the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (parameter- removing reads containing adapters;removing reads containing more than 10% of unknown nucleotides(N);removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.)
Trimmed sequence reads were mapped to ribosome RNA (rRNA) database using Bowtie2 ,The rRNA mapped reads then will be removed.
The remaining clean reads were mapped to Ensembl_release103 using HISAT2. 2.4  (parameters- -rna-strandness RF and other parameters set as a default)
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release103
Supplementary files format and content: tab-delimited xls files include FPKM values and counts for each Sample

source_name: retina

growth_protocol: MSC-EVs (MSC-Exo) or NS were injected into the vitreous of rd10 mice at postnatal day 14 (P14) and P21

extract_protocol:
RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified

treatment_protocol: 1 μL MSC-EVs (1× 1010 in 1 μL) or NS was intravenously injected into both eyes of the animal

value: retina

value: rd10 mouse

value: MSC-EVs (Exo)-treated


title: rd10 mouse retina, MSC-EVs (Exo)-treated, P28, rep3


title: BY4741 rep3


title: rd10 mouse retina, MSC-EVs (Exo)-treated, P28, rep1


title: WT_leukmeic B-cell progenitors rep1

description: WT p190 BCR-ABL+ B-cell progenitors isolated from leukemic mouse bone marrow, expt#1


title: BY4741 rep2


title: rd10 mouse retina, NS-treated, P28, rep3

value: NS-treated


title: Caco2 nonstimulated rep 1


title: Leukemic B-cell progenitors_Vav3-/-_H2aK119Ub-Rep2

description: CUT&RUN assay for maping  H2aK119Ub

data_processing:
Data analysis was performed in Scientific Data Analyses platform “SciDAP” (https://scidap.com, Datirium, LLC) using “TrimGalore Chip-Seq PE” pipeline. This and other containerized CWL pipelines used in analysis are available at https://github.com/datirium/workflows. Briefly, adapters were trimmed from raw reads  with Trim Galore and the reads were aligned to the mm10 reference genome with BowTie. Maximum 3 mismatches per read were allowed. Only uniquely mapped reads were reported. In the next step, all PCR duplicates were removed by Samtools. For peak calling MACS281 was run with the FDR of 0.05.
Differentially Bmi1, Ring1b and H2AK119Ub bound sites between WT and Vav3-/- leukemic B-cell progenitors (n=2/group) were identified by using Diffbind- Differential Binding Analysis of ChIP-Seq Peak Data - 1.0.082 pipeline attached to SciDAP platform, using “Deseq2” analyses method. Only significant differentially bound sites with p-value ≤ 0.05 and with a minimum of 2 fold change (Log2Fold Change ≥ 1 and ≤ -1)  were reported. Based on this, all differential peaks were divided into two groups: 1) Log2FC ≥ 1, 2) Log2FC ≤ -1. Each peak group was cleaned from duplicates based on the peak start and end coordinates and centered by peak center. Re-centered peaks were used for generating tag-density plots within 20kb radius from peak center with “Homer”. For gene TSS-centered tag density plots, each peak was assigned to the nearest gene within 20kb radius from TSS. The resulted two groups of genes were deduplicated and intersected based on the gene names thus obtaining three groups of genes. Genes from every group were re-centered on the TSS and used for generating tag-density heatmap within 20kb radius from gene TSS with Homer. The tag density maps were generated using https://software.broadinstitute.org/morpheus/. The representative genome browser map of specific loci was obtained from IGV browser in “SciDAP” platform.

source_name: BM marrow

growth_protocol: Leukemic B-cell progenitors (FSChiB220+IgM-CD43+CD19+) were sorted from the the BM of WT and Vav3-/- leuekmic B-cell progenitors derived from bone maarow of WT and Vav3-/- leukmeic chimeric mice.

extract_protocol:
Sorted leukemic B-cell progenitors were washed twice with wash buffer [20 mM HEPES; PH-7.5, 150mM NaCl, 0.5mM spermidine] containing protease inhibitor cocktail (Roche, Catalog. 11873580001). Cells were bound to Concanavalin A magnetic beads (Bangs Laboratories, Inc. Catalog. BP531) followed by permeabilization and antibody binding (Bmi1 Ab, Cell signaling technologies, Catalog-5856; Ring1b Ab, Cell Signaling technolgies, Catalog. 5694; H2aK119Ub Ab, Cell Signaling Technologies, Catalog. 8240) at 1:50 dilution in wash buffer containing 0.025% digitonin. Antibody bound cells were treated with proteinA-MNase (700 ng/mL) for 1h at 40C followed by targeted digestion in presence of CaCl2 at 00C for 30 min. The digestion reaction was stopped by adding STOP buffer containing 20 mM EDTA and 4mM EGTA.  The MNase digested DNA fragments were released at 370C, and extracted using QIAGEN MinElute Reaction Cleanup kits (Catalog. 28204), and used for DNA library preparation.
The CUT&RUNseq libraries were prepared by using NEBNext Ultra II DNA library preparation kit for Illumina (Catalog. E7103S) and NEBNext multiplex Oligoes for Illumina (Catalog. E7335S). The libraries were run on Illumina sequencer NextSeq500 and NovaSeq6000 with paired end sequencing.
CUT&RUNseq

tag: cell type

value: B-cell progenitor


title: rd10 mouse retina, NS-treated, P28, rep2


title: BY4741 rep1

tag: strain


title: Caco2 nonstimulated rep 2


title: rd10 mouse retina, normal saline (NS)-treated, P28, rep1


title: Leukemic B-cell progenitors_WT_H2aK119Ub-Rep2

description: CUT&RUN assay for maping  H2aK119Ub

value: WT


title: C1

city: Hiroshima

first: Kentaro

last: Tokumo

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Molecular and Internal Medicine

institute: Hiroshima University

hyb_protocol: 2.3 µg of single-strand DNA was incubated in GeneChip® Hybridization Oven 645 (Affymeterix) using the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher). Hybridized with Clariom S Array, human (Termo Fisher).

scan_protocol: The arrays were then stained and washed in a GeneChip® Fluidics Station 450 (Affymetrix) and scanned in a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: A CEL file is automatically created after scanning. CELL files were analyzed with Transcriptome Analysis Console (TAC) ver. 4.0 to create a text file of expression levels.

label: biotin

source_name: EGFR mutation-positive lung adenocarcinoma cell line PC-9, after 1 week of osimertinib treatment

label_protocol: Using the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher), 250 ng of total RNA to cRNA was processed into biotin-labeled single-stranded DNA.

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, penicillin, and streptomycin (100 U/mL and 100 µg/mL, respectively) in a humidified 5% CO2 atmosphere at 37°C in an incubator. Cells were seeded at a density of 1 × 105 cells/well in six-well plates

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: After 24 h of incubation, the medium of the plates was replaced with a medium containing 0.5 µM osimertinib. Starting from this time point as day 1, the medium was changed every 3 days (day 4, day 7), and the surviving cells on day 8 were determined to be EGFR-TKI-tolerant cells

value: normal cells


title: Expo.phase_S.thyphimirium_sequence

organism: Salmonella enterica subsp. enterica serovar Typhimurium

value: Untreated _ exponential growth _ 37C

value: LB


title: C2


title: Leukemic B-cell progenitors_Vav3-/-_Ring1b-Rep2

description: CUT&RUN assay for maping  Ring1b


title: Expo.phase_S.aureus_sequence

organism: Staphylococcus aureus

value: WT HG001 (AEs1)

value: BHI


title: C3


title: Caco2+TG at 1 uM for 5 hours rep 1

value: Caco2+TG at 1 uM for 5 hours


title: Leukemic B-cell progenitors_Vav3-/-_Ring1b-Rep1

description: CUT&RUN assay for maping  Ring1b


title: iBAT ZT_00

tag: developmental stage

value: 10 weeks old

value: Interscapular brown adipose tissue

value: Zeitgeber time 0


title: WT_leukmeic B-cell progenitors rep2

description: WT p190 BCR-ABL+ B-cell progenitors isolated from leukemic mouse bone marrow, expt#2

tag: tissue

value: B-cell progenitors


title: A8+LLC_1

city: Sydney

first: Sze Wing

last: Wong

state: NSW

address: PO Box 81 Randwick

country: Australia

institute: Children's Cancer Institute

data_processing: Gene expression was calculated with the web-based software package (SABiosciences). For the normalization it uses the geometric mean of two housekeeping genes: β-actin and β2m.Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)], the cut off value for all Cts was set to 38. The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: lungs

label_protocol: PCR assays were performed using varified in-house qPCR array (98 genes and 2 housekeeping genes) in 384-well plates. Reactions were performed using the LightCycler® 480 system (Roche) under standard cycle conditions. Reactions contained 2´SYBR Green master mixture (4 µl), 2 µl diluted cDNA template or non-amplified controls and 2.5 µM of each primer (1 µl) in a final volume of 7 ul.

growth_protocol: Mice were orthotopically injected with LLC cells or vehicle.

extract_protocol: Total RNA was extracted from the lung by standard procedures using TRIzol® Reagent (Invitrogen), genomic DNA removed with DNase (Turbo DNase, Ambion) before reverse transcription (1.5 µg) using Super Script® VILO™ Master Mix (Invitrogen).

treatment_protocol: S100A8 (10 μg) or HBSS was intranasally administered to mice 3, 6 and 9 days after tumor implantation. Lungs were harvested on day 10.

tag: gender

value: female


title: OR3

value: osimertinib-tolerant cells


title: C57 mouse retina, non-treated, P28, rep2

value: retina

value: C57 BL/6J mouse

value: non-treated


title: OR1


title: OR2


title: LLC_1

value: HBSS+LLC


title: Leukemic B-cell progenitors_Vav3-/-_Bmi1-Rep2

description: CUT&RUN assay for maping Bmi1

value: B-cell progenitor


title: Leukemic B-cell progenitors_WT_Ring1b-Rep1

description: CUT&RUN assay for maping  Ring1b

value: WT


title: Leukemic B-cell progenitors_WT_Ring1b-Rep2

description: CUT&RUN assay for maping  Ring1b


title: A8_1


title: Ctrl_1

value: HBSS+vehicle


title: C-3

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, naive cells cultured for 3 week

value: normal cells


title: C57 mouse retina, non-treated, P28, rep3


title: Leukemic B-cell progenitors_WT_Bmi1-Rep2

description: CUT&RUN assay for maping Bmi1


title: Leukemic B-cell progenitors_Vav3-/-_Bmi1-Rep1

description: CUT&RUN assay for maping Bmi1


title: C-1

source_name: EGFR mutation-positive lung adenocarcinoma cell line H1975, naive cells cultured for 1 week


title: C57Bl/6 mice treated with AngII and AngII + 2HOBA

city: Nashville

first: David

last: Patrick

state: TN

address: 2213 Garland Avenue

institute: Vanderbilt University Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw BCL were demultiplexed and mapped using the Cell Ranger Single Cell v.6.0.0 software (10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files, barcode files, and matrix files

source_name: Spleen

extract_protocol:
10 week old C57Bl/6 mice were implanted with 2-week alzet minipumps containing sham or 490 ug/kg/min of angiotensin II. Mice treted with angiotensin II were treated with placebo or 2hydoxybenzylamine. 7 week old and B6.SLE123 mice were treated with 2HOBA or placebo for 6-weeks. Age Matched C57Bl/6 mice were used as control. Spleens were harvested and T-cells depleted with miltenyi CD3 microbeads. Live single cells were submitted for single cell sequencing.
Cells from 3 mice per condition were combined and single cells from each condition were hashed using TotalSeq-C antibodies (Biolegend). Single cell sequencing was performed using the Chromium Single-Cell v2 5’ Chemistry Library, Gel Bead, Multiplex, and Chip Kits (10x Genomics) according to the manufacturer’s protocol. A total of 12,000 cells were targeted per well. Libraries were then sequenced utilizing the NovaSeq 6000 platform (Illumina).

value: Splenocytes

value: Spleen

value: C57Bl/6 mice

tag: age

value: 12-14 weeks old


title: Male Sham and Female C57Bl/6 mice

description: 10x Genomics


title: B6.SLE123 and B6.SLE123+2HOBA

description: 10x Genomics

value: B6.SLE123 mice