|
| Status |
Public on Apr 13, 2022 |
| Title |
lncRNA Pre_1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marow B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Bone marrow
development stage: Pre-B cells
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from sorted populations of cells by using Trizol Reagent kit and Spin Column & Collection Tube.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
lncRNA.expression.xls
mRNA.expression.xls
circRNA.expression.xls
GHR191286_order_2
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...
|
| |
|
| Submission date |
Feb 03, 2021 |
| Last update date |
Apr 13, 2022 |
| Contact name |
Saineng Hu |
| E-mail(s) |
saineng_hu@pku.edu.cn
|
| Phone |
+86-181-7315-6861
|
| Organization name |
Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center
|
| Department |
Biomedical Research Institute
|
| Street address |
Lianhua Road Futian District
|
| City |
Shenzhen |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE166124 |
Dynamic circRNAs expression profiles and circRNA-associated-ceRNA networks during B-cell development and differentiation in mouse bone marrow |
|
| Relations |
| BioSample |
SAMN17772148 |
| SRA |
SRX10015217 |
