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Sample GSM6108640

Query DataSets for GSM6108640

Status

Public on May 18, 2023

Title

SCR3

Sample type

SRA

Source name

human trophoblast stem cell

Organism

Homo sapiens

Characteristics

cell type: extravillouse trophoblast
shRNA: shRNAscr

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated from cells using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped. A false discovery rate of 0.05 was used as a cutoff for significant differential expression (scr versus KD).
RACE

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

RACE

Instrument model

Illumina NovaSeq 6000

Data processing

Reads from *.fastq files were mapped to the human reference genome (GRCh37) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Assembly: human reference genome (GRCh37)

Submission date

May 05, 2022

Last update date

May 18, 2023

Contact name

Khursheed Iqbal

E-mail(s)

kiqbal@kumc.edu

Phone

913 588 5690

Organization name

University of Kansas Medical Center