{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Aiyu Gong"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13448"],"description":["This study is to investigate the potential impact of an lncRNA NR_126553 (Nostril) in murine intestinal epithelial cells (IEC4.1 cells) in response to Cryptosporidium parvum (C. parvum)  infection.  NR_126553 (Nostril) was knocked down by using a pool of gene specific siRNAs (SiNostril). Cells treated with a scramble non-specific siRNA were used as the control (siNegative control). After siRNA transfection 24h, cells were exposed to C. parvum infection for 24h. Then total RNA was collected for sequencing via BGISEQ-500 platform to obtain a comprehensive view of the transcriptome."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - IEC 4.1 cells were harvested, and RNAs were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104) according to the manufacturerM-bM-^@M-^Ys instructions.  Agilent 2100 or Fragment Analyzer was used to detect the quality of RNA. 2 ug of total RNA for the construction of sequencing libraries.","Sequencing - The samples were sent to the company BGI as RNA for sequencing. They performed the nucleic acid sequencing protocol.","Sample Collection - IEC cells were plated and transfected with siRNA for 16 hours before being infected with Cryptosporidium oocytes. After 4 hours infection, the media was changed to fresh complete media and samples were incubated for 24 hours.","Library Construction - The samples were sent to the company BGI as RNA for sequencing. They performed the nucleic acid library construction.The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo^Battached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational ProbeAnchor Synthesis Sequencing Method"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - This shows the raw FPKM values. The data were downloaded from the BGO website and stored in an excel file."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["BGISEQ-500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Aiyu Gong"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic profile of IEC4.1 cells treated with an siRNA to lncRNA NR_126553 (Nostril)  in response to  Cryptosporidium parvum","description":"This study is to investigate the potential impact of an lncRNA NR_126553 (Nostril) in murine intestinal epithelial cells (IEC4.1 cells) in response to Cryptosporidium parvum (C. parvum)  infection.  NR_126553 (Nostril) was knocked down by using a pool of gene specific siRNAs (SiNostril). Cells treated with a scramble non-specific siRNA were used as the control (siNegative control). After siRNA transfection 24h, cells were exposed to C. parvum infection for 24h. Then total RNA was collected for sequencing via BGISEQ-500 platform to obtain a comprehensive view of the transcriptome.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2025-12-31T02:02:06.856Z","creation":"2023-10-16T14:14:29.413Z"},"accession":"E-MTAB-13448","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}