|
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.
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|
|
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
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|
|
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 |