|
| Status |
Public on May 04, 2020 |
| Title |
KO1_P63 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
tag: C57BL/6
tissue: Back skin
age: post natal day 63
genotype/variation: LDB2-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skins were removed and dispase treated 30mins in 37℃, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
|
| |
|
| Submission date |
Jul 24, 2019 |
| Last update date |
May 04, 2020 |
| Contact name |
Jonghyo Lim |
| Organization name |
Yonsei university
|
| Department |
Biochemistry
|
| Lab |
Vascular Genomics laboratory
|
| Street address |
Yonsei-ro 50
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE134785 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and LDB2-/- skin epidermal lysates |
|
| Relations |
| BioSample |
SAMN12241857 |
| SRA |
SRX6425524 |
| SRA |
SRX6579635 |
