|
| Status |
Public on Jun 23, 2021 |
| Title |
75C-FliC-RD1-D3 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
region: ascending colon
Sex: male
age: 58
rounds of damage: 1
flic treatment: Yes
|
| Treatment protocol |
Cells were damaged with the addition of apical media, and flagellin was added basolaterally to some wells for 3 hours. Cells were recovered by growth back into ALI and this was repeated five times.
|
| Growth protocol |
Cells were grown until fully confluent ( 10 days) on a Transwell insert. Media was removed from the apical side and the cells were differentiated for 7 days (air liquid interface ALI). Following differentiation, media is added to the apical side for 4 hours to induce submergence damage, and flagellin was either added or not, to the basolateral side for 3 hours. Following submergence damage, the apical media was removed and the cells were grown back into ALI to recover from damage. This constitutes one round of damage and was repeated five total times.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using miRNeasy mini kit (Qiagen)
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq2000 with Paired End 61bp × 61bp reads. Sequencing data was demultiplexed using Illumina's bcl2fastq2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
1 round of ALI damage + FliC
|
| Data processing |
The RNA-seq Alignment app v1.1.1 on Basespace Illumina was used to align raw reads using STAR to the hg19 reference genome (abundant reads were filtered out before running STAR)
RnaReadCounter on Basespace Illumina was used to generate the count matrix
DESeq2 v1.1.0 via Basespace Illumina was used for differential expression analysis with the apried-end reads parameter
Differentially expressed genes at a log2FC of =>1 and a BH adjusted p-value of <=0.05 were considered for further analyses
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 22, 2021 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Theodore S Steiner |
| E-mail(s) |
tsteiner@mail.ubc.ca
|
| Organization name |
University of British Columbia
|
| Department |
Medicine/Infectious Diseases
|
| Street address |
Rm. C328 HP East, VGH
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 3J5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE178698 |
RNA sequencing of chronically damage human colon organoids via Air-liquid interface submergence |
|
| Relations |
| BioSample |
SAMN19814415 |
| SRA |
SRX11199839 |
