NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6505776 Query DataSets for GSM6505776
Status Public on Jan 20, 2023
Title CD41neg, KO2
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics tissue: bone marrow
cell type: CD41ned HSC
genotype: MxCre1+/-,RUNX1f/f
treatment: polyIC injection*4
time: 4 weeks post-injection
Extracted molecule total RNA
Extraction protocol HSC cells from poly(I:C)-treated WT control and RUNX1 KO mice were sorted by FACS. RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 18-KO2-CD41-Neg-18803
Data processing RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7,Trm Galore! v0.4.2 and cutadapt v1.9.1
The trimmed reads were aligned to the reference mouse genome version mm10 with the program STAR v2.6.1e .
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database . Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Bigwig files containing trimmed and aligned reads for each sample; matrix_RNAseq.feat contain raw read counts for all samples (tab separated file); matrix_RNAseq.tpm contain Transcripts Per Million(TPM) counts for all samples.
 
Submission date Aug 24, 2022
Last update date Jan 23, 2023
Contact name Chen Wang
E-mail(s) wang2c3@mail.uc.edu
Phone 5135506715
Organization name CCHMC
Department Experimental Hematology/Oncology
Lab Yi Zheng
Street address 3333 Burnet Avenue
City Cincinnati
State/province OH
ZIP/Postal code 45219
Country USA
 
Platform ID GPL24247
Series (2)
GSE211935 A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [RNA-seq]
GSE212002 A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation
Relations
BioSample SAMN30473413
SRA SRX17214064

Supplementary file Size Download File type/resource
GSM6505776_run0643_lane9_read1_indexN703-S507_18-KO2-CD41-Neg-18803_trimmed.bw 202.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap