|
| Status |
Public on Oct 06, 2020 |
| Title |
CT40-DE_S11 |
| Sample type |
SRA |
| |
|
| Source name |
Primary adult intestinal FBs
|
| Organism |
Homo sapiens |
| Characteristics |
tissue origin: Reprogrammed FBs cultivated from patient-derived colitic colon mucosa
passages: Passage 0
tissue: Definitive Endoderm (DE)
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Generating human intestinal tissue from pluripotent stem cells in vitro, Nat Protoc. 2011 Nov 10; 6(12): 1920–1928.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iPSCs, DE, Spheroids and iHIOs (NL n=3 CT n=3) were isolated/propagated and harvested prior to RNA extraction and standard sequencing/processing
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
UC3 DE RNA-Seq
|
| Data processing |
RNA-seq data was sequenced using Illumina HiSeq 2500
FastQC (version 0.9.5) was used to check the quality of reads (*.FASTQ) --> no need of trimming
STAR (version 2.5.3a) was used for alignment. HG19 reference genome and Gencode V19 annotation were used.
FeatureCounts of Subread package (version 1.5.2) was used for counting mapping reads for genes.
DESeq2 was used for differentially expressed genes analysis
Genome_build: HG19, gencode V19 annotation
Supplementary_files_format_and_content: Read count table compressed by gzip
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Emina Huang |
| E-mail(s) |
huange2@ccf.org
|
| Phone |
2163863265
|
| Organization name |
Lerner Research Institute/Cleveland Clinic
|
| Department |
Stem Cell
|
| Lab |
Huang Lab
|
| Street address |
9500 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE117345 |
Inhibition of CXCR1/2 in human colitis-derived pluripotent stem cell intestinal organoids attenuates the inflammatory phenotype |
|
| Relations |
| BioSample |
SAMN09690505 |
| SRA |
SRX4405705 |
