|
| Status |
Public on Feb 18, 2022 |
| Title |
s6_CD38_neg |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Mus musculus |
| Characteristics |
population: CD38 neg
strain: C57BL/6
cell type: Haematopoietic Stem Cells
age: 8-16 weeks
|
| Treatment protocol |
Untreated mice C57/BL6 were used
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HSCs (Lin- Kit+ Sca-1+ CD48- CD150+ CD34- CD201+ CD38hi vs CD38lo) were sorted directly to the lysis buffer from RNAeasy Micro Kit (Qiagen), RNA was isolated base on the protocol from the Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENCODE) was used for the alignment.
HTSeq-0.6.1p1 was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read quantification was downloaded from Gencode ().
Genome_build: mm10
Supplementary_files_format_and_content: Raw Counts
|
| |
|
| Submission date |
Feb 15, 2022 |
| Last update date |
Feb 18, 2022 |
| Contact name |
Ben Wielockx |
| E-mail(s) |
[email protected]
|
| Organization name |
IKL, Carl Gustav Carus Universitätklinikum Dresden
|
| Street address |
Fetscherstrasse 74
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE196758 |
CD38 enzymatic activity promotes hematopoietic stem cell dormancy [bulk RNA-Seq] |
| GSE196760 |
CD38 enzymatic activity promotes hematopoietic stem cell dormancy |
|
| Relations |
| BioSample |
SAMN25964979 |
| SRA |
SRX14187406 |
