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Sample GSM6051753 Query DataSets for GSM6051753
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
BioSample SAMN27672008
SRA SRX14936143

Supplementary file Size Download File type/resource
GSM6051753_112415_11PT1_podo_low_ecadh_high_NL.xlsx 1.9 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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