|
| 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 |
