GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM5460953

Query DataSets for GSM5460953

Status

Public on Oct 24, 2022

Title

Chick brachial motor neurons - RNA-seq 2 [sample_3]

Sample type

SRA

Source name

Brachial motor neurons

Organism

Gallus gallus

Characteristics

tissue: Brachial motor neurons
developmental stage: HH25

Treatment protocol

Growth protocol

Extracted molecule

total RNA

Extraction protocol

For mouse, spinal cords of Hb9-GFP (Jackson laboratory) were dissociated and GFP+ MNs were manually collected. The regions for forelimb MNs were visualized under a fluorescence dissection scope and separated from other neurons using a sharp scalpel. The spinal cords were digested with pronase for 30min at RT. For chick MN RNA sequencing, HH stage 12-13 chick embryos were electroporated with a plasmid that drives nuclear YPF expression under the control of Hb9 promoter. After 3day incubation, limb level spinal cords were isolated and dissociated. 5000-23000 YFP+ MNs were collected using a FACS sorter (BD, FACSAria III) and PicoPure RNA Isolation Kit (Arcturus, KIT0202) was used to extract total RNAs. cDNA was synthesized and amplified using Ovation RNA amplification system v2 (Nugen, 3100-12).
The sequencing library was prepared using the TruSeq RNA sample prep Kit (Illumina, CA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

Chicken_CountDf.txt
sample_3

Data processing

Quality of RNA-seq raw reads were checked with FastQC (v. 0.11.9). Next, the raw data was trimmed for low quality and illumina truseq adapter sequences using trimmomatic-0.39 with the following options: “ILLUMINACLIP:[AdapterFile]:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50”. The resulting clean reads were aligned to GRCm38 for mouse and GRCg6a for chick with STAR (v. 2.7.5a) and were quantified using featureCounts.
To account for different gene length in multiple species, RPKM normalization implemented in python bioinfokit was used.
Genome_build: GRCm38 for mouse and GRCg6a for chick
Supplementary_files_format_and_content: Tab-separated file with raw gene counts for every gene and every sample

Submission date

Jul 19, 2021

Last update date

Oct 24, 2022

Contact name

DongAhn Yoo

E-mail(s)

dongahn.yoo@gmail.com

Organization name

Seoul National University

Street address

1 Gwanak-ro, Gwanak-gu