|
| Status |
Public on Apr 20, 2021 |
| Title |
RNA-seq_Gut rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Gut
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Gut
processed sample name: Gut2
raw name: 6AG2
strain: mixed genetic background
genotype: Krt8YFP
cell sorting: Cells have been sorted on YFP expression
|
| 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 |
SAMN14614745 |
| SRA |
SRX8133392 |
