|
| Status |
Public on Nov 28, 2018 |
| Title |
Ski-WT SLAM Cell5 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Fetal liver derived HSC - transplanted for 6 months
genotype/variation: Ski-WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA Synthesis: Fluidigm C1 protocol
Nextera XT DNA Library Preparation Kit (Illumina)
150bp Paired-End, 150 million reads/96 cell library
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The single cell suspension was enriched using CD117 Microbeads on an AutoMACS Pro (Mitenyi) and stained with fluorchome-conjugated antibodies for FACS-sorting of Cd45.2+ Lineage- c-Kit+ Sca-1+ Cd48- Cd150+ bone marrow cells. Single cells were separated using the Fluidigm C1 system and lysed on chip for subsequent reverse transcription.
cDNA was made with the SMARTer mRNA-Seq Kit (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
061016_Cell53-E1
Ski-WT SLAM
|
| Data processing |
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell RNA-Seq data were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
|
| |
|
| Submission date |
Jun 17, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
H. Leighton Grimes |
| E-mail(s) |
Lee.Grimes@cchmc.org
|
| Phone |
513-636-6089
|
| Organization name |
Cincinnati Childrens Hospital Medical Center
|
| Department |
Immunobiology
|
| Lab |
Grimes
|
| Street address |
3333 Burnet Ave. MLC 7038
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE115903 |
Understanding Early Stage Myelodysplastic Syndrome Pathobiology |
|
| Relations |
| BioSample |
SAMN09434587 |
| SRA |
SRX4224320 |
