|
| Status |
Public on Jan 21, 2022 |
| Title |
19-L-958-13bp-KO-LT-1 |
| Sample type |
SRA |
| |
|
| Source name |
LT-HSCs_KO
|
| Organism |
Mus musculus |
| Characteristics |
stain: C57BL/6
age: 2 months
genotype/variation: Hmces knockout
tissue: bone marrow
cell type: FACS-sorted LT-HSCs
|
| Treatment protocol |
Bone marrow cells stained with fluorochrome-labeled HSC antibodies were sorted on an Influx cell sorter (BD Biosciences).
|
| Growth protocol |
All mice were bred in-house under specific-pathogen-free (SPF) conditions in individually ventilated cages (IVC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 1500 FACS-sorted LT-HSCs was extracted using Quick-RNA Kits (ZYMO) and resuspended in nuclease-free water.
cDNA synthesized and amplified from the total RNA was used the Smart-seq2 method as described previously (Picelli et al., 2014). Sequencing libraries were generated from 500pg cDNA using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer’s protocols. All the samples were sequenced on the Illumina HiSeq X Ten sequencers with 150 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
RNA-seq was performed with three biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the mouse genome (mm9) with TopHat (v2.1.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts guided by reference annotation [University of California at Santa Cruz (UCSC) gene models] with Cufflinks (v2.2.1). The expression level of each gene was quantified as FPKM, and FPKM values of replicates were averaged.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of all RNA-seq samples
|
| |
|
| Submission date |
May 17, 2020 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Li Shen |
| E-mail(s) |
shenlab@zju.edu.cn
|
| Phone |
86-0571-88981751
|
| Organization name |
Life Sciences Institute, Zhejiang University
|
| Lab |
Shenlab
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE150721 |
HMCES safeguards genome integrity and long-term self-renewal of hematopoietic stem cells during stress responses |
|
| Relations |
| BioSample |
SAMN14943209 |
| SRA |
SRX8356094 |
