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Sample GSM4756749 Query DataSets for GSM4756749
Status Public on Apr 01, 2021
Title endometrioid ovarian carcinoma_10
Sample type SRA
Source name paraffin-embedded tissue
Organism Homo sapiens
Characteristics tissue: endometrioid ovarian carcinoma
Extracted molecule total RNA
Extraction protocol All FFPE tissue slides were stained with hematoxylin and reviewed by an experienced gynecological pathologist. The selected lesions from whole tissues were excised by laser capture microdissection. For LCM, the FFPE tissues were sectioned and placed on slides with polyethylene terephthalate membrane (Leica Microsystems Inc., IL, USA). LCM was performed using a Leica AS LMD laser microdissection system (Leica Microsystems Inc.) according to the manufacturer’s instructions. An RNeasy FFPE kit (Qiagen, Valencia, CA, USA) was used to isolate total RNA from FFPE tissues according to the manufacturer’s instructions.
Sample emulsion PCR, emulsion breaking, and enrichment were performed using an Ion PITM Template OT2 200 Kit v3 (Life Technologies, Part #4488318 Rev. B.0) according to the manufacturer’s instructions. Multiple barcoded libraries were combined with equal molar ratios for one Ion PITM v2 chip. Two-pooled Ion AmpliSeqTM Exome libraries were loaded onto a single Ion PITM v2 chip. Five-pooled Ion AmpliSeq™ Transcriptome libraries were loaded onto a single Ion PITM v2 chip. Subsequent emulsion PCR and enrichment of the sequencing beads of the pooled libraries were performed using the Ion OneTouchTM system (Life Technologies) within approximately 7 h, according to the manufacturer’s protocol. Finally, 520 Flows sequencing was done on the Ion PITM v2 chip using Ion PITM Sequencing 200 Kit v3 (Life Technologies, Part #4488315 Rev. B.0) on the Ion ProtonTM sequencer (Life Technologies).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description endometriosis_associated.txt
Data processing FASTQ format were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using STAR and Bowtie2.
Read counts analysis were conducted using HTSeq and Picard.
Normalization and differential expression were conducted by DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: endometriosis_associated.txt: TXT file contains normalized abundance measurements for each sample.
Submission date Aug 30, 2020
Last update date Apr 01, 2021
Contact name Ha-Yeon Shin
Organization name Yonsei University
Department Obstetrics and Gynecology
Street address 237, Dogok-ro
City Seoul
ZIP/Postal code 06230
Country South Korea
Platform ID GPL17303
Series (1)
GSE157153 Gene expression profiling in endometriosis and ovarian cancer
BioSample SAMN15944644
SRA SRX9038570

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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