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Sample GSM4484816 Query DataSets for GSM4484816
Status Public on Apr 20, 2021
Title RNA-seq_K5SmoM2 rep6
Sample type SRA
 
Source name Esophagus
Organism Mus musculus
Characteristics tissue: Esophagus
processed sample name: Smo6
raw name: 2AM5
strain: CD1
genotype: Krt5-SmoM2
cell sorting: Cells have been sorted on high expression of EpCam
Extracted molecule total RNA
Extraction protocol Tissues were digested, sorted in TRK lysis buffer and extracted using E.Z.N.A Total RNA Kit. RNA quality was checked before library preparation using a Bioanalyzer 2100.
Libraries were obtained using the Ovation Solo RNA-seq System (NuGen) following manufacturer's recommendations and loaded on a Novaseq 6000 (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software (version 2.5.3a)
Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq
Total raw counts were uploaded on degust 4.1.1 and analyzed using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample and genome annotations
 
Submission date Apr 17, 2020
Last update date Apr 20, 2021
Contact name Alizee Vercauteren Drubbel
E-mail(s) alizeevd@gmail.com
Organization name Université Libre de Bruxelles
Lab Beck lab
Street address 808 route de Lennik
City Anderlecht
ZIP/Postal code 1070
Country Belgium
 
Platform ID GPL24247
Series (2)
GSE148874 mRNA sequencing of esophageal cells and columnar cells from different tissues
GSE148876 RNA-seq and ATAC-sequencing of esophageal cells after HH pathway activation
Relations
BioSample SAMN14614733
SRA SRX8133376

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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