|
| Status |
Public on Jan 27, 2021 |
| Title |
EORG-2 rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
EORG-2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue/cell type: endometrial organoids
internal id: 43220
|
| Growth protocol |
Endometrial organoids (EORG) were established by embedding the isolated epithelial cells of decidua in 60% Matrigel and organoid media (advanced DMEM/F12, 10 mM Hepes, 1xB27, 1x N2 and 20mM Glutamine supplemented with 100 ng/ml R-Spondin, 1 µM A83-01, 100 ng/ml recombinant hEGF, 100 ng/ml Noggin, 10mM CH99021).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy kit (Qiagen) with the DNaseI (Qiagen) digest performed on the column according to manufacturer's protocol
mRNA was isolated using the Dyabeads mRNA purification kit (Life Technologies 61006) and prepared into an indexed library using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106) according to the manufacturers' instructions. Indexed libraries were pooled and sequenced with a 100-bp single end protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
EORG-2.1
C9N3PANXX_43220_ACAGTG
|
| Data processing |
Basecalling performed using RTA 1.18.64.0
Raw reads were trimmed with trimgalore (v0.5.0).
The strand specific reads were depleted of abundant sequences (iGenomes, hg38) by aligning with bowtie2 (v2.3.4.1).
Salmon (v0.11.0) was used to derive TPMs by using the transcriptome based on GRCh38 and Ensembl 94.
Genome_build: GRCh38/Ensembl 94
Supplementary_files_format_and_content: Tab-delimited text files containing gene id and Salmon TPMs.
|
| |
|
| Submission date |
Mar 20, 2019 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Paulina Anna Latos |
| E-mail(s) |
paulina.latos@meduniwien.ac.at
|
| Phone |
+43 1 4016037718
|
| Organization name |
Medical University of Vienna
|
| Department |
Center for Anatomy and Cell Biology
|
| Lab |
Latos
|
| Street address |
Schwarzspanierstraße 17
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN11178167 |
| SRA |
SRX5547587 |
