|
| Status |
Public on Mar 14, 2017 |
| Title |
primary HSCs infected with lncRNA-shRNA1, biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
primary HSCs infected with lncRNA-shRNA1
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
tissue: liver
cell type: primary HSCs
Stage: day 6
infection: lncRNA-shRNA1
|
| Treatment protocol |
primary HSCs infected with shRNA-control (n=2), lncRNA-shRNA1 (n=2) and lncRNA-shRNA3 (n=2)
|
| Growth protocol |
primary HSCs were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
lncRNA-shRNA1 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 mm8 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: mm8
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts for each Sample
|
| |
|
| Submission date |
Mar 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Zhang |
| E-mail(s) |
zhangkun@tmu.edu.cn
|
| Phone |
022-83336819
|
| Organization name |
Tianjin medical university
|
| Department |
Department of Histology and Embryology
|
| Street address |
Qixiangtai Road NO.22
|
| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE96526 |
Expression data that were specifically regulated by lncRNA-LFAR1 in mouse primary HSCs |
|
| Relations |
| BioSample |
SAMN06563710 |
| SRA |
SRX2635295 |
