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Sample GSM3039261 Query DataSets for GSM3039261
Status Public on Mar 14, 2018
Title Akita replicate 1
Sample type SRA
 
Source name Renal cortex
Organism Mus musculus
Characteristics age (days): 116
genotype/variation: C57BL/6-Ins2Akita/J
Growth protocol C57BL/6-Ins2Akita/J mice and their wild-type counterparts were obtained from The Jackson Laboratory, USA. The water and feed (standard lab chow) were provided ad libitum. Mice were housed in specific pathogen-free conditions with exposure to 12:12-h light-dark cycles for 24 weeks (n=8/group). All animal studies were performed in accordance with the guidelines of the AMREP Animal Ethics Committee and the NHMRC of Australia.
Extracted molecule total RNA
Extraction protocol Renal cortex was collected from one harvested kidney and minced with a scalpel then pushed through a 70 micron sieve followed by digestion with collagenase IV for 30 mins at 37 C. Cells were pelleted by centrifugation for 3 mins at 300g, followed by two washes with PBS.
Cell suspensions underwent drop-seq according to the protocol of Macosko et al (PMID: 26000488). Cell barcode is the first 12 nt of read 1. UMI is position 13 to 20 of read 1.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing NextSeq v2 reagents
Genome sequence and annotation were downloaded from Ensembl (Mus_musculus.GRCm38.91.gtf.gz and Mus_musculus.GRCm38.dna.primary_assembly.fa.gz)
UMI-tools version: 0.5.3 (PMID:28100584) was used to whitelist and extract cell barcodes
Skewer v0.2.2 was used to trim low quality bases from the end of read 2 containing the transcript sequence
STAR version 2.5.2b was used to map read2 to the
featureCounts v1.6.0 was used to assign reads to genes using the Ensembl v91 annotation in gtf format.
UMI-tools version: 0.5.3 was used to tabulate the gene counts for each cell barcode
Our custom script is available from Zenodo https://doi.org/10.5281/zenodo.1195057
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene-wise raw read counts of gene expression per cell in tsv format
Supplementary_files_format_and_content: 3 column table gene /cell barcode/count
 
Submission date Mar 13, 2018
Last update date Mar 14, 2018
Contact name Mark D Ziemann
E-mail(s) mark.ziemann@gmail.com
Organization name Burnet Institute
Department Bioinformatics Working Group
Street address 85 Commercial Rd
City Melbourne
State/province VIC
ZIP/Postal code 3004
Country Australia
 
Platform ID GPL19057
Series (1)
GSE111752 Droplet based single cell RNA sequencing profiles of a murine model of type-1 diabetes
Relations
BioSample SAMN08689882
SRA SRX3785034

Supplementary file Size Download File type/resource
GSM3039261_AkitaC57_rep1_counts.tsv.gz 1.7 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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