|
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)
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|
|
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
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|
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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 |