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| Status |
Public on Apr 17, 2024 |
| Title |
7-wk control scmultiome GE |
| Sample type |
SRA |
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| Source name |
lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: epithelial cells
genotype: CebpaCKO/+; SftpcCreER;SUN1GFP
age: 7-wk
treatment: 2 doses of Tamoxifen each 3mg at 5-wk
Sex: pooled male and female
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
FACS-purified lung epithelial, were processed through the CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_Revf.
scRNA-seq 28 cycles read1, 90 cycles read2, 10 cycles Index1, and 10 cycles Index2
scATAC-seq 50 cycles for read 1, 49 cycles for read2, 8 cycles for index1, and 24 cycles for index2
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Deletion of cebpa in mature AT2 cells
Aggregate7-wk_filtered_feature_bc_matrix.h5
Aggregate7-wk_raw_feature_bc_matrix.h5
Aggregate7-wk_cloupe.cloupe
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| Data processing |
Raw sequencing data (fastq file) was demultiplexed and analyzed using 10X Genomics Cell Ranger ARC software
Further analysis can be achieved using the Cell Ranger ARC-derived analysis files in 10X Genomics Loupe Browser software.
Assembly: mm10
Supplementary files format and content: Rds, tsv and mtx files can be opened with Seurat&Signac (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.
Supplementary files format and content: filtered_feature_bc_matrix.h5 can be opened with Seurat (R package)
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| Submission date |
Nov 06, 2023 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Dalia Hassan |
| E-mail(s) |
dhassan@mdanderson.org
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| Phone |
3467146254
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| Organization name |
MD Anderson Cancer Center
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| Department |
Pulmonary Medicine
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| Lab |
Jichao Chen
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| Street address |
6565 MD Anderson Blvd, Z9.4040, Z9.4040
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE247130 |
CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair [1] |
| GSE247272 |
CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair |
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| Relations |
| BioSample |
SAMN38144879 |
| SRA |
SRX22384756 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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