|
| Status |
Public on Feb 01, 2020 |
| Title |
Injected with PBS as control-24hr [PB24c] |
| Sample type |
SRA |
| |
|
| Source name |
organoid_injected with PBS as control-24hr
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1 (WA01) NIH Registration#0043
cell type source: Human Intestinal Organoid
cell type: induced plueropotent embryonic stem cell
treatment: PBS
time post injection: 24 hours post injection
|
| Treatment protocol |
Organoids were microinjected with 30 ng Shiga toxin and sterile PBS in 100 nL volume.
|
| Growth protocol |
Organoids were grown in Gut Media for 24 days before being microinjected. Medium was changed every 2 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were snap frozen in liquid nitrogen and Total RNA was extracted 4 hour post injection following the Qiagen RNeasy plus mini kit protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns
|
| |
|
| Submission date |
Jan 31, 2020 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Alison A Weiss |
| E-mail(s) |
weissaa@ucmail.uc.edu
|
| Phone |
5135582820
|
| Organization name |
University of Cincinnati
|
| Department |
COM Molecular Genetics
|
| Lab |
Weiss lab
|
| Street address |
231 Albert Sabin Way
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45267 |
| Country |
USA |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE144633 |
Tissue responses to Shiga toxin in human intestinal organoids |
|
| Relations |
| BioSample |
SAMN13958509 |
| SRA |
SRX7657035 |
