|
| Status |
Public on Jul 07, 2020 |
| Title |
MPP4 control rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lin- bone marrow progenitors
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wt
strain: BALB/c
population: MPP4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
No RNA extraction was performed. Cells were sorted into the lysis and reaction buffer.
Libraries were constructed with the CellSeq2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Sequencing batch B
MPP4.counts.tsv [WT984_P11]
DESeq2.results.MPP4.tsv
|
| Data processing |
Basecalling was performed with Illumina HiSeq Control Software/RTA version 2.7.6.
Raw sequencing reads were processed with the snakePipes version 0.5 scRNAseq-mapcount workflow to produce a count table per sample. Read trimming was enabled, and annotation was filtered to remove entries with keywords “decay” or “pseudogene” in biotype description.
Postprocessing and differential gene expression analysis were performed in R version 3.4.0. Counts were normalized by downscaling to 200.000 transcripts per sample with RaceID3 package and rounded to integer counts. Outlier samples were removed. Differentially expressed genes were called between Dnmt1 mutant and wildtype replicates in each cell population separately, using R packages zingeR and DESeq2. Sequencing batch was not included in the model.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated tables with downsampled integer counts for retained samples per cell population, as well as tables with DESeq2 results of differential gene expression analysis are provided.
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Thomas Boehm |
| E-mail(s) |
boehm@ie-freiburg.mpg.de
|
| Organization name |
MPI-IE Freiburg
|
| Department |
Immunology
|
| Street address |
Stübeweg 51
|
| City |
Freiburg im Breisgau |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE98648 |
Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 |
| GSE142223 |
Structural basis of epigenetic protection of mouse lymphoid progenitor cells by Dnmt1 [Mouse RNA-seq] |
|
| Relations |
| BioSample |
SAMN13615940 |
| SRA |
SRX7398115 |
