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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 08, 2014 |
| Title |
High throughput quantitative whole transcriptome analysis of distal mouse lung epithelial cells from various developmental stages (E14.5, E16.5, E18.5 and adult) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used microfluidic single cell RNA-seq on 198 individual mouse lung epithelial cells at 4 different stages throughout development to measure the transcriptional states which define the developmental and cellular hierarchy of the distal mouse lung epithelium. We classified 80 cells comprising the distal lung epithelium at E18.5 into distinct populations using an unbiased genome-wide approach that did not require a priori knowledge of the underlying cell types or prior purification of cell types. This “reverse tissue engineering” approach confirmed the basic outlines of the conventional model of cell type diversity in the distal lung and led to the discovery of a large number of novel transcriptional regulators and cell type markers that discriminate between the different populations. Moreover, we reconstructed the steps during maturation of bipotential progenitors into both alveolar lineages based on the presence of undifferentiated, differentiated as well as differentiation intermediate cells at the single time point E18.5. Finally, we followed Sftpc-positive cells throughout their lifecycle (E14.5, E16.5, E18.5, adult) and identified 7 gene sets that differentiate between the multipotential, bipotential, mature, as well as intermediate states of the AT2 lineage.
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| Overall design |
198 single-cell transcriptomes from mouse lung epithelium were analyzed in total, two 200-cell bulk control samples as well as one no-cell control; All single cell and control samples contain 92 external RNA spike-ins; For time point E18.5, three individual experiments were performed using 3 different pregnant mice (3 biological replicates): Replicate 1 (pooled sibling lungs) yielded 20 single cell transcriptomes, replicate 2 (one single embryonic lung) yielded 34 single cell transcriptomes and replicate 3 (pooled siibling lungs) yielded 26 single cell transcriptomes; In addition, a 200-cell bulk control sample was prepared for E18.5 replicate 1 and E18.5 replicate 3 experiments; A no-cell control sample was generated for the E18.5 replicate 1 experiment; For time point E14.5, one experiment (one pregnant mouse, pooled sibling lungs) was performed yielding 45 single cell transcriptomes; For time point E16.5, one experiment (one pregnant mouse, pooled sibling lungs) was performed yielding 27 single cell transcriptomes; For the adult time point, one 107 day old mouse was used and transcriptomes of 46 single cells were obtained; All single cell samples were processed on the microfluidic platform, 200-cell-bulk and no-cell control samples were processed in microliter volumes in PCR tubes.
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| Contributor(s) |
Treutlein B, Quake SR |
| Citation(s) |
24739965 |
| Submission date |
Nov 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Treutlein |
| E-mail(s) |
baerbel.treutlein@gmail.com
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| Organization name |
Stanford University
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| Department |
Bioengineering
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| Lab |
Quake
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| Street address |
318 Campus Drive
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| City |
Stanford CA |
| State/province |
CA |
| ZIP/Postal code |
94305-5432 |
| Country |
USA |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
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| Samples (201)
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| GSM1271862 |
E18.5, biological replicate 1, single cells, transcriptome 1 |
| GSM1271863 |
E18.5, biological replicate 1, single cells, transcriptome 2 |
| GSM1271864 |
E18.5, biological replicate 1, single cells, transcriptome 3 |
| GSM1271865 |
E18.5, biological replicate 1, single cells, transcriptome 4 |
| GSM1271866 |
E18.5, biological replicate 1, single cells, transcriptome 5 |
| GSM1271867 |
E18.5, biological replicate 1, single cells, transcriptome 6 |
| GSM1271868 |
E18.5, biological replicate 1, single cells, transcriptome 7 |
| GSM1271869 |
E18.5, biological replicate 1, single cells, transcriptome 8 |
| GSM1271870 |
E18.5, biological replicate 1, single cells, transcriptome 9 |
| GSM1271871 |
E18.5, biological replicate 1, single cells, transcriptome 10 |
| GSM1271872 |
E18.5, biological replicate 1, single cells, transcriptome 11 |
| GSM1271873 |
E18.5, biological replicate 1, single cells, transcriptome 12 |
| GSM1271874 |
E18.5, biological replicate 1, single cells, transcriptome 13 |
| GSM1271875 |
E18.5, biological replicate 1, single cells, transcriptome 14 |
| GSM1271876 |
E18.5, biological replicate 1, single cells, transcriptome 15 |
| GSM1271877 |
E18.5, biological replicate 1, single cells, transcriptome 16 |
| GSM1271878 |
E18.5, biological replicate 1, single cells, transcriptome 17 |
| GSM1271879 |
E18.5, biological replicate 1, single cells, transcriptome 18 |
| GSM1271880 |
E18.5, biological replicate 1, single cells, transcriptome 19 |
| GSM1271881 |
E18.5, biological replicate 1, single cells, transcriptome 20 |
| GSM1271882 |
E18.5, biological replicate 1, 200 cell bulk control, transcriptome 1 |
| GSM1271883 |
E18.5, biological replicate 1, no cell control, transcriptome 1 |
| GSM1271884 |
E18.5, biological replicate 2, single cells, transcriptome 1 |
| GSM1271885 |
E18.5, biological replicate 2, single cells, transcriptome 2 |
| GSM1271886 |
E18.5, biological replicate 2, single cells, transcriptome 3 |
| GSM1271887 |
E18.5, biological replicate 2, single cells, transcriptome 4 |
| GSM1271888 |
E18.5, biological replicate 2, single cells, transcriptome 5 |
| GSM1271889 |
E18.5, biological replicate 2, single cells, transcriptome 6 |
| GSM1271890 |
E18.5, biological replicate 2, single cells, transcriptome 7 |
| GSM1271891 |
E18.5, biological replicate 2, single cells, transcriptome 8 |
| GSM1271892 |
E18.5, biological replicate 2, single cells, transcriptome 9 |
| GSM1271893 |
E18.5, biological replicate 2, single cells, transcriptome 10 |
| GSM1271894 |
E18.5, biological replicate 2, single cells, transcriptome 11 |
| GSM1271895 |
E18.5, biological replicate 2, single cells, transcriptome 12 |
| GSM1271896 |
E18.5, biological replicate 2, single cells, transcriptome 13 |
| GSM1271897 |
E18.5, biological replicate 2, single cells, transcriptome 14 |
| GSM1271898 |
E18.5, biological replicate 2, single cells, transcriptome 15 |
| GSM1271899 |
E18.5, biological replicate 2, single cells, transcriptome 16 |
| GSM1271900 |
E18.5, biological replicate 2, single cells, transcriptome 17 |
| GSM1271901 |
E18.5, biological replicate 2, single cells, transcriptome 18 |
| GSM1271902 |
E18.5, biological replicate 2, single cells, transcriptome 19 |
| GSM1271903 |
E18.5, biological replicate 2, single cells, transcriptome 20 |
| GSM1271904 |
E18.5, biological replicate 2, single cells, transcriptome 21 |
| GSM1271905 |
E18.5, biological replicate 2, single cells, transcriptome 22 |
| GSM1271906 |
E18.5, biological replicate 2, single cells, transcriptome 23 |
| GSM1271907 |
E18.5, biological replicate 2, single cells, transcriptome 24 |
| GSM1271908 |
E18.5, biological replicate 2, single cells, transcriptome 25 |
| GSM1271909 |
E18.5, biological replicate 2, single cells, transcriptome 26 |
| GSM1271910 |
E18.5, biological replicate 2, single cells, transcriptome 27 |
| GSM1271911 |
E18.5, biological replicate 2, single cells, transcriptome 28 |
| GSM1271912 |
E18.5, biological replicate 2, single cells, transcriptome 29 |
| GSM1271913 |
E18.5, biological replicate 2, single cells, transcriptome 30 |
| GSM1271914 |
E18.5, biological replicate 2, single cells, transcriptome 31 |
| GSM1271915 |
E18.5, biological replicate 2, single cells, transcriptome 32 |
| GSM1271916 |
E18.5, biological replicate 2, single cells, transcriptome 33 |
| GSM1271917 |
E18.5, biological replicate 2, single cells, transcriptome 34 |
| GSM1271918 |
E18.5, biological replicate 3, single cells, transcriptome 1 |
| GSM1271919 |
E18.5, biological replicate 3, single cells, transcriptome 2 |
| GSM1271920 |
E18.5, biological replicate 3, single cells, transcriptome 3 |
| GSM1271921 |
E18.5, biological replicate 3, single cells, transcriptome 4 |
| GSM1271922 |
E18.5, biological replicate 3, single cells, transcriptome 5 |
| GSM1271923 |
E18.5, biological replicate 3, single cells, transcriptome 6 |
| GSM1271924 |
E18.5, biological replicate 3, single cells, transcriptome 7 |
| GSM1271925 |
E18.5, biological replicate 3, single cells, transcriptome 8 |
| GSM1271926 |
E18.5, biological replicate 3, single cells, transcriptome 9 |
| GSM1271927 |
E18.5, biological replicate 3, single cells, transcriptome 10 |
| GSM1271928 |
E18.5, biological replicate 3, single cells, transcriptome 11 |
| GSM1271929 |
E18.5, biological replicate 3, single cells, transcriptome 12 |
| GSM1271930 |
E18.5, biological replicate 3, single cells, transcriptome 13 |
| GSM1271931 |
E18.5, biological replicate 3, single cells, transcriptome 14 |
| GSM1271932 |
E18.5, biological replicate 3, single cells, transcriptome 15 |
| GSM1271933 |
E18.5, biological replicate 3, single cells, transcriptome 16 |
| GSM1271934 |
E18.5, biological replicate 3, single cells, transcriptome 17 |
| GSM1271935 |
E18.5, biological replicate 3, single cells, transcriptome 18 |
| GSM1271936 |
E18.5, biological replicate 3, single cells, transcriptome 19 |
| GSM1271937 |
E18.5, biological replicate 3, single cells, transcriptome 20 |
| GSM1271938 |
E18.5, biological replicate 3, single cells, transcriptome 21 |
| GSM1271939 |
E18.5, biological replicate 3, single cells, transcriptome 22 |
| GSM1271940 |
E18.5, biological replicate 3, single cells, transcriptome 23 |
| GSM1271941 |
E18.5, biological replicate 3, single cells, transcriptome 24 |
| GSM1271942 |
E18.5, biological replicate 3, single cells, transcriptome 25 |
| GSM1271943 |
E18.5, biological replicate 3, single cells, transcriptome 26 |
| GSM1271944 |
E18.5, biological replicate 3, 200 cell bulk control, transcriptome 1 |
| GSM1271945 |
E14.5, biological replicate 1, single cells, transcriptome 1 |
| GSM1271946 |
E14.5, biological replicate 1, single cells, transcriptome 2 |
| GSM1271947 |
E14.5, biological replicate 1, single cells, transcriptome 3 |
| GSM1271948 |
E14.5, biological replicate 1, single cells, transcriptome 4 |
| GSM1271949 |
E14.5, biological replicate 1, single cells, transcriptome 5 |
| GSM1271950 |
E14.5, biological replicate 1, single cells, transcriptome 6 |
| GSM1271951 |
E14.5, biological replicate 1, single cells, transcriptome 7 |
| GSM1271952 |
E14.5, biological replicate 1, single cells, transcriptome 8 |
| GSM1271953 |
E14.5, biological replicate 1, single cells, transcriptome 9 |
| GSM1271954 |
E14.5, biological replicate 1, single cells, transcriptome 10 |
| GSM1271955 |
E14.5, biological replicate 1, single cells, transcriptome 11 |
| GSM1271956 |
E14.5, biological replicate 1, single cells, transcriptome 12 |
| GSM1271957 |
E14.5, biological replicate 1, single cells, transcriptome 13 |
| GSM1271958 |
E14.5, biological replicate 1, single cells, transcriptome 14 |
| GSM1271959 |
E14.5, biological replicate 1, single cells, transcriptome 15 |
| GSM1271960 |
E14.5, biological replicate 1, single cells, transcriptome 16 |
| GSM1271961 |
E14.5, biological replicate 1, single cells, transcriptome 17 |
| GSM1271962 |
E14.5, biological replicate 1, single cells, transcriptome 18 |
| GSM1271963 |
E14.5, biological replicate 1, single cells, transcriptome 19 |
| GSM1271964 |
E14.5, biological replicate 1, single cells, transcriptome 20 |
| GSM1271965 |
E14.5, biological replicate 1, single cells, transcriptome 21 |
| GSM1271966 |
E14.5, biological replicate 1, single cells, transcriptome 22 |
| GSM1271967 |
E14.5, biological replicate 1, single cells, transcriptome 23 |
| GSM1271968 |
E14.5, biological replicate 1, single cells, transcriptome 24 |
| GSM1271969 |
E14.5, biological replicate 1, single cells, transcriptome 25 |
| GSM1271970 |
E14.5, biological replicate 1, single cells, transcriptome 26 |
| GSM1271971 |
E14.5, biological replicate 1, single cells, transcriptome 27 |
| GSM1271972 |
E14.5, biological replicate 1, single cells, transcriptome 28 |
| GSM1271973 |
E14.5, biological replicate 1, single cells, transcriptome 29 |
| GSM1271974 |
E14.5, biological replicate 1, single cells, transcriptome 30 |
| GSM1271975 |
E14.5, biological replicate 1, single cells, transcriptome 31 |
| GSM1271976 |
E14.5, biological replicate 1, single cells, transcriptome 32 |
| GSM1271977 |
E14.5, biological replicate 1, single cells, transcriptome 33 |
| GSM1271978 |
E14.5, biological replicate 1, single cells, transcriptome 34 |
| GSM1271979 |
E14.5, biological replicate 1, single cells, transcriptome 35 |
| GSM1271980 |
E14.5, biological replicate 1, single cells, transcriptome 36 |
| GSM1271981 |
E14.5, biological replicate 1, single cells, transcriptome 37 |
| GSM1271982 |
E14.5, biological replicate 1, single cells, transcriptome 38 |
| GSM1271983 |
E14.5, biological replicate 1, single cells, transcriptome 39 |
| GSM1271984 |
E14.5, biological replicate 1, single cells, transcriptome 40 |
| GSM1271985 |
E14.5, biological replicate 1, single cells, transcriptome 41 |
| GSM1271986 |
E14.5, biological replicate 1, single cells, transcriptome 42 |
| GSM1271987 |
E14.5, biological replicate 1, single cells, transcriptome 43 |
| GSM1271988 |
E14.5, biological replicate 1, single cells, transcriptome 44 |
| GSM1271989 |
E14.5, biological replicate 1, single cells, transcriptome 45 |
| GSM1271990 |
adult AT2, biological replicate 1, single cells, transcriptome 1 |
| GSM1271991 |
adult AT2, biological replicate 1, single cells, transcriptome 2 |
| GSM1271992 |
adult AT2, biological replicate 1, single cells, transcriptome 3 |
| GSM1271993 |
adult AT2, biological replicate 1, single cells, transcriptome 4 |
| GSM1271994 |
adult AT2, biological replicate 1, single cells, transcriptome 5 |
| GSM1271995 |
adult AT2, biological replicate 1, single cells, transcriptome 6 |
| GSM1271996 |
adult AT2, biological replicate 1, single cells, transcriptome 7 |
| GSM1271997 |
adult AT2, biological replicate 1, single cells, transcriptome 8 |
| GSM1271998 |
adult AT2, biological replicate 1, single cells, transcriptome 9 |
| GSM1271999 |
adult AT2, biological replicate 1, single cells, transcriptome 10 |
| GSM1272000 |
adult AT2, biological replicate 1, single cells, transcriptome 11 |
| GSM1272001 |
adult AT2, biological replicate 1, single cells, transcriptome 12 |
| GSM1272002 |
adult AT2, biological replicate 1, single cells, transcriptome 13 |
| GSM1272003 |
adult AT2, biological replicate 1, single cells, transcriptome 14 |
| GSM1272004 |
adult AT2, biological replicate 1, single cells, transcriptome 15 |
| GSM1272005 |
adult AT2, biological replicate 1, single cells, transcriptome 16 |
| GSM1272006 |
adult AT2, biological replicate 1, single cells, transcriptome 17 |
| GSM1272007 |
adult AT2, biological replicate 1, single cells, transcriptome 18 |
| GSM1272008 |
adult AT2, biological replicate 1, single cells, transcriptome 19 |
| GSM1272009 |
adult AT2, biological replicate 1, single cells, transcriptome 20 |
| GSM1272010 |
adult AT2, biological replicate 1, single cells, transcriptome 21 |
| GSM1272011 |
adult AT2, biological replicate 1, single cells, transcriptome 22 |
| GSM1272012 |
adult AT2, biological replicate 1, single cells, transcriptome 23 |
| GSM1272013 |
adult AT2, biological replicate 1, single cells, transcriptome 24 |
| GSM1272014 |
adult AT2, biological replicate 1, single cells, transcriptome 25 |
| GSM1272015 |
adult AT2, biological replicate 1, single cells, transcriptome 26 |
| GSM1272016 |
adult AT2, biological replicate 1, single cells, transcriptome 27 |
| GSM1272017 |
adult AT2, biological replicate 1, single cells, transcriptome 28 |
| GSM1272018 |
adult AT2, biological replicate 1, single cells, transcriptome 29 |
| GSM1272019 |
adult AT2, biological replicate 1, single cells, transcriptome 30 |
| GSM1272020 |
adult AT2, biological replicate 1, single cells, transcriptome 31 |
| GSM1272021 |
adult AT2, biological replicate 1, single cells, transcriptome 32 |
| GSM1272022 |
adult AT2, biological replicate 1, single cells, transcriptome 33 |
| GSM1272023 |
adult AT2, biological replicate 1, single cells, transcriptome 34 |
| GSM1272024 |
adult AT2, biological replicate 1, single cells, transcriptome 35 |
| GSM1272025 |
adult AT2, biological replicate 1, single cells, transcriptome 36 |
| GSM1272026 |
adult AT2, biological replicate 1, single cells, transcriptome 37 |
| GSM1272027 |
adult AT2, biological replicate 1, single cells, transcriptome 38 |
| GSM1272028 |
adult AT2, biological replicate 1, single cells, transcriptome 39 |
| GSM1272029 |
adult AT2, biological replicate 1, single cells, transcriptome 40 |
| GSM1272030 |
adult AT2, biological replicate 1, single cells, transcriptome 41 |
| GSM1272031 |
adult AT2, biological replicate 1, single cells, transcriptome 42 |
| GSM1272032 |
adult AT2, biological replicate 1, single cells, transcriptome 43 |
| GSM1272033 |
adult AT2, biological replicate 1, single cells, transcriptome 44 |
| GSM1272034 |
adult AT2, biological replicate 1, single cells, transcriptome 45 |
| GSM1272035 |
adult AT2, biological replicate 1, single cells, transcriptome 46 |
| GSM1272036 |
E16.5, biological replicate 1, single cells, transcriptome 1 |
| GSM1272037 |
E16.5, biological replicate 1, single cells, transcriptome 2 |
| GSM1272038 |
E16.5, biological replicate 1, single cells, transcriptome 3 |
| GSM1272039 |
E16.5, biological replicate 1, single cells, transcriptome 4 |
| GSM1272040 |
E16.5, biological replicate 1, single cells, transcriptome 5 |
| GSM1272041 |
E16.5, biological replicate 1, single cells, transcriptome 6 |
| GSM1272042 |
E16.5, biological replicate 1, single cells, transcriptome 7 |
| GSM1272043 |
E16.5, biological replicate 1, single cells, transcriptome 8 |
| GSM1272044 |
E16.5, biological replicate 1, single cells, transcriptome 9 |
| GSM1272045 |
E16.5, biological replicate 1, single cells, transcriptome 10 |
| GSM1272046 |
E16.5, biological replicate 1, single cells, transcriptome 11 |
| GSM1272047 |
E16.5, biological replicate 1, single cells, transcriptome 12 |
| GSM1272048 |
E16.5, biological replicate 1, single cells, transcriptome 13 |
| GSM1272049 |
E16.5, biological replicate 1, single cells, transcriptome 14 |
| GSM1272050 |
E16.5, biological replicate 1, single cells, transcriptome 15 |
| GSM1272051 |
E16.5, biological replicate 1, single cells, transcriptome 16 |
| GSM1272052 |
E16.5, biological replicate 1, single cells, transcriptome 17 |
| GSM1272053 |
E16.5, biological replicate 1, single cells, transcriptome 18 |
| GSM1272054 |
E16.5, biological replicate 1, single cells, transcriptome 19 |
| GSM1272055 |
E16.5, biological replicate 1, single cells, transcriptome 20 |
| GSM1272056 |
E16.5, biological replicate 1, single cells, transcriptome 21 |
| GSM1272057 |
E16.5, biological replicate 1, single cells, transcriptome 22 |
| GSM1272058 |
E16.5, biological replicate 1, single cells, transcriptome 23 |
| GSM1272059 |
E16.5, biological replicate 1, single cells, transcriptome 24 |
| GSM1272060 |
E16.5, biological replicate 1, single cells, transcriptome 25 |
| GSM1272061 |
E16.5, biological replicate 1, single cells, transcriptome 26 |
| GSM1272062 |
E16.5, biological replicate 1, single cells, transcriptome 27 |
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| Relations |
| BioProject |
PRJNA229411 |
| SRA |
SRP033209 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52583_RAW.tar |
117.6 Mb |
(http)(custom) |
TAR (of FPKM_TRACKING) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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