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Sample GSM2748296 Query DataSets for GSM2748296
Status Public on Oct 31, 2017
Title Microdissected cTAL, Single-tubule RNA-Seq, transcriptome 05
Sample type SRA
 
Source name Microdissected cTAL_Single-tubule RNA-Seq_transcriptome
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
tissue: Kidney
Growth 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. For single-tubule RNA-Seq, the CCDs and cTALs were manually dissected in ice-cold Burg solution under a Wild M8 dissection stereomicroscope equipped with on-stage cooling. After washes in ice-cold PBS (2 times), the microdissected tubules were transferred to Trizol reagent for RNA extraction and cDNA generation.
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
Genome_build: GRCm38.p5 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
 
Submission date Aug 22, 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 SAMN07532576
SRA SRX3113449

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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