|
| Status |
Public on Jan 12, 2021 |
| Title |
Linc NR_033736_V3 |
| Sample type |
SRA |
| |
|
| Source name |
Linc NR_033736
|
| Organism |
Mus musculus |
| Characteristics |
cell type: intestinal epithelial
cell line: IEC4.1
knockdown: siRNA to lincRNA-NR_033736
infection status: not infected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104). Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Rmats v3.2.5 with parameters -analysis U -t paired -a 8.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Feb 18, 2020 |
| Last update date |
Jan 13, 2021 |
| Contact name |
Xianming Chen |
| Organization name |
creighton university
|
| Street address |
2500 california plaza
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68178 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE145464 |
Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptome profile in IEC 4.1 cells in response to Cryptosporidium parvum |
|
| Relations |
| BioSample |
SAMN14125113 |
| SRA |
SRX7739940 |
