|
| Status |
Public on Jan 27, 2021 |
| Title |
983A.epi: VEO-IBD Epithelium from 983A |
| Sample type |
SRA |
| |
|
| Source name |
Epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: inflammatory bowel disease (IBD)
cell type: Epithelium
group: VEO-IBD
|
| Growth protocol |
Colonoids were expanded and passaged once prior to washing with ice-cold DMEM/F12 to remove Matrigel and snap-frozen for subsequent RNA isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using NEBNext Ultra RNA library prep with rRNA depletion
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to GRCh37 human reference genome using the STAR 2-pass method
Read counts were calculated using RSEM
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes raw count values calculated for each sample using RSEM
|
| |
|
| Submission date |
Jul 31, 2019 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Kathryn Elizabeth Hamilton |
| E-mail(s) |
hamiltonk1@email.chop.edu
|
| Phone |
267-426-5266
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE135170 |
RNA-Sequencing of epithelium and colonoids from patients with pediatric inflammatory bowel disease |
|
| Relations |
| BioSample |
SAMN12401847 |
| SRA |
SRX6621312 |
