|
| Status |
Public on Sep 21, 2022 |
| Title |
Caco2_WT-1, RNA |
| Sample type |
SRA |
| |
|
| Source name |
Caco2
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: colorectal adenocarcinoma
cell line: Caco2
cell type: colorectal adenocarcinoma cells
genotype: WT
|
| Treatment protocol |
Mice were provided with food and water ad libitum and maintained in conformity to national and international laws and policies and with appropriate permissions,
|
| Growth protocol |
Caco-2 cells were maintained in MEM medium containing 20% (vol/vol) FCS at 37 °C with 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from Caco-2 cells and purified IECs using RNeasy kit (Qiagen) according to manufacturer´s instructions.
RNA samples from Caco-2 cells were sequenced on HiSeq3000 (Illumina, San Diego, United States) (2 X 75 bp) while that from mice IECs were sequenced NovaSeq 6000 (2 X 50 bp) using Illumina total RNA stranded TruSeq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
2 X 75 bp
|
| Data processing |
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) or mouse genome (GRCm38) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Assembly: GRCh38 (gencode version 25) and GRCm38
Supplementary files format and content: tab-delimited text files include feature counts
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Sep 21, 2022 |
| Contact name |
Neha Mishra |
| E-mail(s) |
n.mishra@ikmb.uni-kiel.de
|
| Organization name |
Institute of Clinical Molecular Biology
|
| Lab |
Cell biology Lab
|
| Street address |
Rosalind-Franklin-Str. 12
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE210714 |
DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon [RNA-seq] |
| GSE210763 |
DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon |
|
| Relations |
| BioSample |
SAMN30192015 |
| SRA |
SRX16978109 |
