GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4756706

Query DataSets for GSM4756706

Status

Public on Apr 01, 2021

Title

atypical endometriosis_6

Sample type

SRA

Source name

paraffin-embedded tissue

Organism

Homo sapiens

Characteristics

tissue: atypical endometriosis

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

E-mail(s)

hayeon37@naver.com

Organization name

Yonsei University

Department

Obstetrics and Gynecology