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| Status |
Public on Oct 20, 2021 |
| Title |
C12 KO control 3 |
| Sample type |
SRA |
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| Source name |
C12 KO control
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| Organism |
Mus musculus |
| Characteristics |
cell type: intestinal epithelial
cell line: IEC4.1
genotype: IEC4.1-Ifnar1-/- KO
agent: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| 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.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample
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| Submission date |
Mar 30, 2020 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Xianming Chen |
| Organization name |
creighton university
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| Street address |
2500 california plaza
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| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68178 |
| Country |
USA |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE147720 |
Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptome profile in IEC 4.1-WT and IEC4.1-Ifnar1-/- KO cells (C12 KO) in response to Cryptosporidium parvum |
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| Relations |
| BioSample |
SAMN14485272 |
| SRA |
SRX8026190 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4443804_E3.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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