|
| Status |
Public on Oct 01, 2019 |
| Title |
E28_S11_L005_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
tissue sample from patient with endometriosis
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: patient with endometriosis
tissue: endometrial samples and lesions
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue specimens were immediately stabilized in RNAlater (Qiagen, Germany) and then stored at -70 °C. RNA extraction was performed immediately before the preparation of sequencing libraries using Direct-zol™ RNA MiniPrep (Zymo Research) with TRI Reagent (MRC) following the manufacturer’s protocol.
KAPA RNA Hyper with RiboErase (KAPA Biosystem) Kit was used for depletion of ribosomal RNA and library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA sequencing FASTQ files were processed with STAR aligner30 in ‘GeneCounts’ mode with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89).
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts table generated by merging of STAR output. Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset (https://www.genenames.org, database version of July 13, 2017). In total, read counts values were established for 37233 annotated genes with corresponding HGNC identifiers.
|
| |
|
| Submission date |
Aug 07, 2019 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Daniil Nikitin |
| E-mail(s) |
danya.nikitin.orel@gmail.com
|
| Phone |
89295743391
|
| Organization name |
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
|
| Street address |
Miklucho-Maklaya
|
| City |
Moscow |
| ZIP/Postal code |
117198 |
| Country |
Russia |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE135485 |
Gene expression signature of endometrial samples from women with and without endometriosis. |
|
| Relations |
| BioSample |
SAMN12513046 |
| SRA |
SRX6664938 |
