|
| Status |
Public on Dec 04, 2018 |
| Title |
Extracted RNA from Ki67-RFP+ cells of hearts of Ki67TagRFP mice 3 days post-MI surgery, replicate 2_bulk RNA |
| Sample type |
SRA |
| |
|
| Source name |
Ki67-RFP+ cells of hearts of Ki67TagRFP mice 3 days post-MI surgery
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Ki67TagRFP
time point: 3 days post-MI surgery
tissue: Heart
cell type: proliferative cardiac cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5 ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ki67_3dpMI_1910-M02
Murine hearts 3 days after myocardial infarction
|
| Data processing |
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: coutb files contain UMI barcode normalised abundance counts
|
| |
|
| Submission date |
Jul 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kai Kretzschmar |
| E-mail(s) |
kai.kretzschmar@uni-wuerzburg.de
|
| Organization name |
University Hospital Würzburg
|
| Street address |
Josef-Schneider-Str. 2
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE102048 |
Profiling proliferative cells and their progeny in damaged murine hearts |
|
| Relations |
| BioSample |
SAMN07427089 |
| SRA |
SRX3049482 |
