|
| Status |
Public on Apr 06, 2020 |
| Title |
Gfi1-R412X-HMZ_GMP_Cell42 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Gfi1-R412X/R412X
cell type: Bone marrow derived GMP
cdna synthesis: Fluidigm C1 protocol
library prep: Nextera XT DNA Library Preparation Kit (Illumina)
sequencing parameters: 150bp Paired-End, 150 million reads/96 cell library
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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, then 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 |
Gfi1-R412X-HMZ GMP
Mar27_x_x_308_Cell_42
|
| 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.
Genome_build: mm9
Supplementary_files_format_and_content: [exp.R412X-HMZ.txt] Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: [groups.R412X-HMZ.txt] Group annotations assigned by cellHarmony
|
| |
|
| Submission date |
Sep 25, 2018 |
| Last update date |
Apr 06, 2020 |
| 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 (2) |
| GSE120404 |
A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [Gfi1-R412X-HMZ] |
| GSE120409 |
A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment |
|
| Relations |
| BioSample |
SAMN10120234 |
| SRA |
SRX4735901 |
