|
Status |
Public on Jan 12, 2021 |
Title |
Linc NR_033736 + C. parvum_W3 |
Sample type |
SRA |
|
|
Source name |
Linc NR_033736 + C. parvum
|
Organism |
Mus musculus |
Characteristics |
cell type: intestinal epithelial cell line: IEC4.1 knockdown: siRNA to lincRNA-NR_033736 infection status: infected with C. parvum
|
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
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|
|
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 |
SAMN14125122 |
SRA |
SRX7739943 |