characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-08-18T13:52:55Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-08-18T13:52:55Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113565864
characteristics.characteristic: External Id
characteristics.text: IRB Barcelona, BIST
characteristics.characteristic: INSDC center name
characteristics.text: 2023-08-18T13:52:55Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-08-18T13:52:55Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15562012
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13032:Iron_day2
characteristics.characteristic: Submitter Id
characteristics.text: 8 to 10
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: To induce pulmonary fibrosis 8-10-week-old C57BL/6 wild-type mice were anesthetized by intraperitoneal injection of a mix containing ketamine (75 mg/kg) and medetomidine (1 mg/kg). Animals were placed on a Tilting WorkStand for rodents (EMC Hallowell) and intubated intratracheally with a 24GA catheter (BD Biosciences), and delivered 30 ul aqueous iron solution containing a concentration of 8,3 mM Fe(II)Sulfate and 8,3 mM Fe(III)Nitrate (in total 16,5 mM iron), control animals received 30 μl phosphate buffered saline (PBS). Iron solution was sterile filtered with a 0.22 µm pore size syringe filter. Mice receiving intratracheal iron developed within a day sepsis-like symptoms, with severe weight-loss, from which day recovered on the fourth day post-iron. We found that treatment with a daily dose of subcutaneous buprenorphine (0.1 mg/kg) considerably mitigated these symptoms, and the overall mortality in this model remained very low (<10%). Mice were sacrificed in CO2 chambers, and lungs were removed, separated into lobes, frozen on dry ice, and stored at -80 °C until the day of nuclei isolation. Nuclei were isolated from the lung lobes using the Chromium 10X nuclei isolation kit following the manufacturer´s instructions. Three single nuclei suspensions were used for transcriptome analysis at IRB Barcelona Functional Genomics Core Facility. Briefly, nuclei isolated using the 10x genomics Chromium Nuclei Isolation with RNase Inhibitor Kit (10x Genomics), were filtered using a 40 μm flowmi cell strainer (SP Bel-Art), and quality controlled on a LUNA-FL automated fluorescence cell counter (Logos biosystems). The suspensions were used to target between 10,000 and 12,000 nuclei per sample. Partition into GEMs was performed using Chip G and the 3’ v3.1 chemistry (10X Genomics). Barcoded cDNA was amplified for 13 cycles, quantified, and quality controlled on the Bioanalyzer 2100 using a high sensitivity DNA assay (Agilent). The generated illumina-compatible libraries were quantified using the Qubit dsDNA HS assay (Invitrogen), quality controlled with the Bioanalyzer 2100 DNA HS assay (Agilent) and used to generate an equimolar pool.
characteristics.characteristic: description
characteristics.text: juvenile stage
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: lung
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: aqueous iron solution
characteristics.characteristic: stimulus
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: Iron_day2
characteristics.characteristic: title