|
| Status |
Public on Jun 23, 2023 |
| Title |
E17.5 (embryonic day 17.5) skin, Tie1 control [skin_Tie1ECDWT_3] |
| Sample type |
SRA |
| |
|
| Source name |
E17.5 (embryonic day 17.5) skin, Tie1 control
|
| Organism |
Mus musculus |
| Characteristics |
tissue: skin
developmental stage: E17.5 (embryonic day 17.5)
genotype: control
strain background: C57BL/6N
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin tissues were harvested from Tie1 knockout and control mice (E17.5) and kept frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the manufacturer’s instruction
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented, converted into cDNA and amplified by PCR, and finally made into RNAseq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Single end 50 bases reads were generated with a target depth of 20 million reads on BGIseq500 platform (BGI-Shenzhen, China).
The sequencing data was filtered with SOAPnuke (v1.5.2), and clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set.
Gene expression level was calculated by RSEM (v1.2.12)
Assembly: Mus_musculus：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files including read count for each sample
|
| |
|
| Submission date |
Apr 06, 2023 |
| Last update date |
Jun 23, 2023 |
| Contact name |
Yulong He |
| E-mail(s) |
heyulong@suda.edu.cn
|
| Organization name |
Soochow University
|
| Street address |
199 Ren-Ai Road
|
| City |
Suzhou |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE229118 |
Endothelial TIE1 restricts angiogenic sprouting to coordinate vein assembly in synergy with its homologue TIE2 |
|
| Relations |
| BioSample |
SAMN34099320 |
| SRA |
SRX19894380 |
