|
| Status |
Public on Dec 31, 2018 |
| Title |
WT rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CD34-Flt3- Lin-ScaI+C-Kithigh cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
age: 8 weeks
genotype: WT
|
| Treatment protocol |
CD34-Flt3- LSK cells were sorted with a BD AriaII directly into Trizol reagent
|
| Growth protocol |
CD34-Flt3- LSK were isolated by cell sorting from WT or Lrp5/6 double deficient mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 6K CD34-Flt3- Lin-ScaI+C-Kithigh cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
Libraries are constructed according to the standard protocol for Smart-seq2Â
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
FastQC version 0.11.5 was used to identify features of the raw data that may indicate quality problems
Low quality bases were removed using Trimmomatic
Reads were mapped to the mouse reference genome (mm9) with Tophat2 version 2.1.1. and post-processed with RSEM version 1.2.31. Default parameter settings were used for alignment
The uniquely mapped reads were assigned to genes using Htseq
The fold change and p-value of all the detected genes were estimated by DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: txt format. Read counts for each gene and TPM for each gene
|
| |
|
| Submission date |
Nov 16, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Shuyang Yu |
| E-mail(s) |
ysy@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
College of Biological Sciences
|
| Street address |
2 Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE122635 |
LRP5 and LRP6 are required for maintaining self-renewal and differentiation of hematopoietic stem cells |
|
| Relations |
| BioSample |
SAMN10437008 |
| SRA |
SRX5020222 |
