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Sample GSM3400071 Query DataSets for GSM3400071
Status Public on Apr 06, 2020
Title Gfi1-R412X-HMZ_GMP-P-CD11b+_Cell57
Sample type SRA
 
Source name Bone marrow
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Gfi1-R412X/R412X
cell type: Bone marrow derived CD11b+ GMP-P
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 CD11b+ GMP-P
Mar12_x_x_309_Cell_57
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 SAMN10120207
SRA SRX4735968

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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