|
| Status |
Public on Feb 07, 2019 |
| Title |
Wild Type Cell 35 |
| Sample type |
SRA |
| |
|
| Source name |
Murine marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: wild type
cell type: erythroblast
normalized ter119: 0.629460585969873
class: WC7
|
| Treatment protocol |
SCP3-WT-H8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
single-cell isolation protocol: Individual cells were isolated for mRNA sequencing using the C1 Single-Cell Auto Prep System (Fluidigm).
imageing protocol: Each cell isolation chamber was imaged at 20X (Leica DMI 6000) with bright-field illumination and fluorescent channels. The Ter119 antibody was labeled with PCP-Cy5.5 and imaged using a 488/705 nm (excitation/emission) fluorescence filter cube.
Cells were lysed, their mRNA reversely transcribed into cDNA, and the cDNA amplifed using the SMART-Seq whole-transcriptome amplification method on the C1 System according to the manufacturer's instructions.
The cDNA libraries were collected from the C1 and prepared for sequencing using a Nextera XT DNA Sample preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SCP3-WT-H8
wild-type cell 35
RefSeq_mm9_expr_rpkm.txt
|
| Data processing |
Illumina BaseSpace Informatics Suite was used for basecalling and demultiplexing.
Raw sequence reads were aligned to the mouse genome (NCBI build 37.2) using TopHat v2.0.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each cell
|
| |
|
| Submission date |
Feb 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shinya Tanaka |
| E-mail(s) |
stanaka@ifrec.osaka-u.ac.jp
|
| Organization name |
Osaka University
|
| Department |
Immunology Frontier Research Center
|
| Street address |
2nd Fl. IFReC Research Building, Osaka University 3-1 Yamadaoka, Suita
|
| City |
Osaka |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE94898 |
Heme and GATA1 coordinately regulate erythroid differentiation [RNA-seq] |
| GSE94917 |
Heme and GATA1 coordinately regulate erythroid differentiation |
|
| Relations |
| BioSample |
SAMN06335033 |
| SRA |
SRX2563531 |
