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Sample GSM5289659

Query DataSets for GSM5289659

Status

Public on Feb 02, 2022

Title

A014_ 22.12_2_ctrl

Sample type

SRA

Source name

E12.5 UB control 1

Organism

Mus musculus

Characteristics

cell type - genotype: UB - HoxB7Cre-GFP;Mek1fl/+;Mek2+/-
background strain: mixed C57BL6/Rcc -129/SvEv

Treatment protocol

genetic modification

Growth protocol

in vivo - normal growth

Extracted molecule

total RNA

Extraction protocol

RNA was isolated from FAC-sorted cells by a standard protocol for chloroform/isopropanol extraction (Thermo Fisher Scientific – 04/2016, rev. B.00)
NuGen Ovation Solo

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

UB samples: Demultiplexed and quality filtered reads were aligned to reference using STAR
UB samples: Gene counts were generated from alignments using featureCounts from subread-package
NP samples: Demultiplexed and quality filtered reads were aligned to reference using HISAT2
NP samples: Gene counts were generated from alignments using HTSeq.
After gene counts, both UB and NP data were normalized and differentially expressed genes were called using DESeq2 R-package.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene expression matrices for both UB and NP samples as .xlsx

Submission date

May 11, 2021

Last update date

Feb 11, 2022

Contact name

Satu kUURE

E-mail(s)

[email protected]

Organization name

University of Helsinki

Street address

Haartmaninkatu 8