|
Status |
Public on Oct 01, 2019 |
Title |
E70_S2_L002_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.
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|
|
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.
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|
|
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 |
SAMN12513021 |
SRA |
SRX6664970 |