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| Status |
Public on Apr 14, 2017 |
| Title |
Olfactory stem cell differentiation: horizontal basal cell (HBC) lineage |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The lineage of the horizontal basal cells (HBC) stem cells and other Sox2eGFP-positive cells from the olfactory epithelium were profiled by single-cell RNA-Seq to identify differentiated cells types, intermediate stages, transition states, and to infer the lineage trajectories.
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| Overall design |
Horizontal basal cell (HBC) stem cells from the olfactory epithelium that were either wild-type or mutant for the transcription factor Trp63/p63 were lineage traced, collected by FACS, and profiled by single-cell RNA-seq. Additionally, Sox2eGFP transgenic cells from the olfactory epithelium were combined with this data into one data set that was processed together. A minimum of two biological replicates were collected for each time-point/experimental condition. A total of 680 YFP-positive lineage traced cells plus 169 Sox2eGFP-positive cells were used in this analysis.
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| Contributor(s) |
Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J |
| Citation(s) |
28506465 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DC007235 |
Programs of Gene Expression in Olfactory Neurogenesis |
UNIVERSITY OF CALIFORNIA BERKELEY |
JOHN J. NGAI |
| S10 RR029668 |
Genome Sequencer FLX |
UNIVERSITY OF CALIFORNIA BERKELEY |
JOHN J. NGAI |
| U01 MH105979 |
Classification of Cortical Neurons by Single Cell Transcriptomics |
UNIVERSITY OF CALIFORNIA BERKELEY |
JOHN J. NGAI |
| K01 AG045344 |
Age-related changes in the neural stem cells of the olfactory epithelium |
UNIVERSITY OF CALIFORNIA BERKELEY |
RUSSELL B FLETCHER |
| T32 HG000047 |
Genomics |
UNIVERSITY OF CALIFORNIA BERKELEY |
Daniel Soleyman Rokhsar |
| S10 RR027303 |
Illumina Sequencer to Facilitate Functional Genomics at Berkeley |
UNIVERSITY OF CALIFORNIA BERKELEY |
JOHN W. TAYLOR |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Diya Das |
| E-mail(s) |
diyadas@berkeley.edu
|
| Organization name |
University of California, Berkeley
|
| Department |
Molecular & Cell Biology
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| Lab |
Ngai Lab
|
| Street address |
265 Life Sciences Addition #3200
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| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (849)
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| Relations |
| BioProject |
PRJNA377622 |
| SRA |
SRP100980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95601_oeHBCdiff_Cufflinks_eSet.Rda.gz |
197.0 Mb |
(ftp)(http) |
RDA |
| GSE95601_oeHBCdiff_Cufflinks_eSet_counts_table.txt.gz |
7.1 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_Cufflinks_eSet_featureData.txt.gz |
335.9 Kb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_Cufflinks_eSet_fpkm_table.txt.gz |
29.8 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_Cufflinks_eSet_protocolData.txt.gz |
50.0 Kb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_Cufflinks_eSet_tpm_table.txt.gz |
64.0 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_RSEM_eSet.Rda.gz |
98.4 Mb |
(ftp)(http) |
RDA |
| GSE95601_oeHBCdiff_RSEM_eSet_expectedCounts_table.txt.gz |
8.8 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_RSEM_eSet_fpkm_table.txt.gz |
11.9 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_RSEM_eSet_protocolData.txt.gz |
44.9 Kb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_RSEM_eSet_tpm_table.txt.gz |
11.8 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_kallisto_eSet.Rda.gz |
164.1 Mb |
(ftp)(http) |
RDA |
| GSE95601_oeHBCdiff_kallisto_eSet_estimatedCounts_table.txt.gz |
26.4 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_kallisto_eSet_tpm_table.txt.gz |
32.7 Mb |
(ftp)(http) |
TXT |
| GSE95601_oeHBCdiff_phenoData.txt.gz |
16.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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