|
| Status |
Public on Oct 31, 2017 |
| Title |
Type B intercalated cell, single-cell RNA-Seq, transcriptome 09 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Kidney
facs antibody: PNA
|
| Treatment protocol |
Male mice were grown and maintained in the Animal Facility of the NHLBI. 2 month-old mice were used in the experiments.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells at 500-700 cells/ul were loaded to C1 IFC, single cell was captured in each champer. After cell lysis, reverse transcription, and PCR on the C1 system, cDNAs were harvested from each IFC outlet.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequenced reads were mapped to Ensembl mouse gene set (GRCm38.p5) using STAR v2.5.1b
Transcript abundances in TPM were caculated by RSEM/1.2.31
Single-cell RNA-seq data analysis were carried out using Seurat package
GRCm38.p5 (Ensembl)
Genome_build: tab-delimited text files include TPM values for each cell
|
| |
|
| Submission date |
Jun 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihe Chen |
| E-mail(s) |
lihe.chen@nih.gov
|
| Phone |
3015947152
|
| Organization name |
NHLBI
|
| Street address |
10 center drive MSC 1603, Building 10, Room 6N318
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE99701 |
Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-Seq |
|
| Relations |
| BioSample |
SAMN07195468 |
| SRA |
SRX2884825 |
