|
| Status |
Public on Mar 14, 2016 |
| Title |
Cell 16 |
| Sample type |
SRA |
| |
|
| Source name |
Placenta
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary placental cells
develpomental stage: E9.5
strain: C57BL/6J;CD-1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were digested from dissected E9.5 placenta using Liberase TM and cells of interest enriched by FACS. Single cells were picked by mouth pipette and cDNA prepared exactly as in Tang et al., Nature Protocols 5, - 516 - 535 (2010).
Sequencing libraries were prepared using the Illumina ChIP-seq DNA Sample Prep Kit. Libraries were size selected at ~200bp, multiplexed and sequenced using a HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were mapped to mm9 using Stampy with default parameters.
Read pairs with the same outer coordinates were filtered out using samtools rmdup.
Reads were assigned to Ensembl transcripts using htseq-count.
TMM normalization was performed using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file containing Ensembl gene IDs and gene names in the first two columns, followed by normalized gene expression values (tags per million) for each individual sample in the subsequent 78 columns.
|
| |
|
| Submission date |
Oct 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Christopher Nelson |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Warwick
|
| Department |
School of Life Sciences
|
| Street address |
Gibbet Hill Campus
|
| City |
Coventry |
| ZIP/Postal code |
CV4 7AL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE74406 |
Single-cell RNA-seq transcriptome profiling of Prdm1+ lineages in E9.5 mouse placenta |
| GSE74410 |
Prdm1 |
|
| Relations |
| BioSample |
SAMN04218459 |
| SRA |
SRX1388870 |
