|
| Status |
Public on Mar 07, 2016 |
| Title |
HSPC_44 |
| Sample type |
SRA |
| |
|
| Source name |
E12_HSPC
|
| Organism |
Mus musculus |
| Characteristics |
strain: c57bl6
age: embryonic day E12.5
genotype/variation: wild type
tissue: placenta
sorted cell population: hematopoeitic stem/progenitor cells CD45+CD34+cKit+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted by FACS. Single cells isolated, RNA extracted and cDNA prepared using Fluidigm C1 System.
Single cell RNAseq libraries prepared with Nextera XT DNA Library Preparation Kit according to manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: E10_E12_HSPC_SingleCell_FPKM.txt.gz
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite
Alignment to mm9 using Tophat release v2.0.12 and Bowtie2 release v2.2.3
Differential expression performed with Cufflinks release v2.2.1 and Mus musculus mm9 reference annotation
Genome_build: mm9
Supplementary_files_format_and_content: FPKM tables derived from Cufflinks cuffdiff output E10_E12_HSPC_SingleCell_FPKM.txt.gz output tab-delimited file. See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.
|
| |
|
| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Betty Chang |
| E-mail(s) |
[email protected]
|
| Organization name |
Mount Sinai School of Medicine
|
| Street address |
1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE54574 |
Direct Conversion from Mouse Fibroblasts Informs the Identification of Hemogenic Precursor Cells In Vivo |
|
| Relations |
| BioSample |
SAMN04100311 |
| SRA |
SRX1271751 |
