|
| Status |
Public on Aug 08, 2016 |
| Title |
Sample SC EMP preMac Mac e10.25 |
| Sample type |
SRA |
| |
|
| Source name |
whole_embryo EMPs_preMac_Mac, E10.25
|
| Organism |
Mus musculus |
| Characteristics |
cell type: EMPs preMac Mac
tissue: whole embryo
tissue group: whole embryo
time: E10.25
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
MARS-seq
MARS-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Single-cells mouse EMPs preMac Macs from whole embryo at day E10.25
|
| Data processing |
After de-multiplexing, Cell barcode and RMT were extracted from Read 2 and stored in Read 1. Reads with a Phred<27 for any RMT base were removed from further analysis. Next, we removed contamination, by alignment against the e.coli genome and de-multiplexed the unmapped reads by pool barcode and cell barcode. Reads were aligned using Bowtie v 1.1.1 (parameters:“-m 1 -t --best --chunkmbs 64 –strata) to the Ensembl mouse mm10 + ERCC pseudo genome assembly. We used HTSeq-count (v 0.6.0) to quantify gene count levels based on the ensembl exon-model for mm10. Following UMI sequencing errors were filtered nad a gene expression matrix was generated.
Raw molecule counts were loaded into R and all cells with a mito-to-endogenous gene molecule count of 0.15, with less than 320 unique molecule counts or 150 unique genes were removed from further analysis. In addition we filtered for mitichondrial, ribosomal and predicted genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE81760 |
Differentiation and specification of resident tissue macrophages [MARS-seq] |
| GSE81774 |
Differentiation and specification of resident tissue macrophages |
|
| Relations |
| BioSample |
SAMN05163655 |
| SRA |
SRX1793048 |
