|
| Status |
Public on Jun 15, 2022 |
| Title |
112415 11PT1 podo low ecadh high NL |
| Sample type |
SRA |
| |
|
| Source name |
esophageal biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: esophageal biopsy
cell type: suprabasal epithelium
treatment: Healthy controls
|
| Growth protocol |
Three biopsies collected from the distal esophagus typically yielded ~2,500–10,000 epithelial cells in each subpopulation, which were subsequently collected into RPMI-1640 media supplemented with 10% FBS and pelleted/centrifuged for immediate RNA isolation procedures
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Micro Kit (Qiagen).
Total RNA was amplified using the Ovation RNA-Seq System v2 assay (Tecan Genomics) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA sequencing analysis was performed by BioWardrobe
Adapter sequences were trimmed from unaligned reads using TrimGalore.
Alignment of trimmed raw sequencing data to Homo sapiens (GRCh37/hg19) reference genome is done by STAR allowing maximum 5 mismatches and reporting only uniquelly mapped reads.
Mapped reads are then being sorted and indexed by Samtools sort and index utilities. Sorted reads are used for RPKM calculation.
Assembly: hg19
Supplementary files format and content: Excel file containing read counts per gene including RefSeq ID, gene symbol, raw read count, and RPKM-normalized read count
|
| |
|
| Submission date |
Apr 20, 2022 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Hee-Woong Lim |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Division of Biomedical Informatics
|
| Street address |
3333 Burnet Ave. MLC 7024
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE201154 |
Bulk RNA Sequencing of Human Esophageal Epithelium in Homeostasis and Allergic Inflammation |
|
| Relations |
| BioSample |
SAMN27672008 |
| SRA |
SRX14936143 |
