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Sample GSM6857400

Query DataSets for GSM6857400

Status

Public on Apr 01, 2023

Title

Endothelial Cell, Nuclear Localization STUB1, Replicate 2

Sample type

SRA

Source name

Pulmonary Endothelia

Organism

Homo sapiens

Characteristics

tissue: Pulmonary Endothelia
cell line: HPAEC
treatment: Stub1 NLS transfection

Treatment protocol

Cells were transfected at ~50% confluency for 24 hours with Fugene 6 transfection reagent (Fugent, Middleton, WI, USA), followed by 24 hours rest.

Growth protocol

Pulmonary-derived arterial endothelial cells or smooth muscle cells (ATCC) were generated by plating on TC-treated plastic (typically 2–3 × 106 cells into a 100mm dish) with Vasculife EC Media (Lifeline Cell Technology, Frederick, MD, USA).

Extracted molecule

total RNA

Extraction protocol

Cells were collected using trypsin and RNA was gathered using the Qiagen RNeasy kit (cat. 74004)
Libraries were prepared according to Lexogen's instruction accompanying the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Cat. 015). Briefly, total RNA was reverse transcribed by oligodT priming, RNA template was removed, and the second strand was synthesized by random priming using DNA polymerase. After bead purification, library is amplified by PCR and sequences required for cluster generation are introduced. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

stub_nls_gene_exp.diff
Stub1 FPKM data file.xlsx
ECSTUB_NLS_2

Data processing

In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner
Transcript is assembled by StringTie with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value
Assembly: UCSC hg37, GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

Submission date

Dec 19, 2022

Last update date

Apr 01, 2023

Contact name

Adeleye J. Afolayan

E-mail(s)

aafolayan@mcw.edu

Phone

4149555634

Organization name

Medical College of Wisconsin