 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 25, 2023 |
| Title |
sheep1-MAD.RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
mesenteric adipose
|
| Organism |
Ovis aries |
| Characteristics |
breed: Small-tail Han sheep
developmental stage: Adult
age: 2-year-old
tissue: mesenteric adipose
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, total RNA was extracted from each sample using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA). Concentration and purity were quantified by Nanodrop, and integrity was evaluated using an Agilent 2000.
Then, RNA-seq libraries were generated using a rRNA depletion method (Globin-Zero Gold rRNA Removal Kit, Illumina, San Diego, CA, USA) coupled with a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). The libraries were sequenced by the HiSeq X Ten platform (Illumina) with a paired-end sequencing length of 150 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Contacts matrix were generated by using Juicer pipeline.
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Tpm and counts matrixs were generated using R vresion 3.6.1.
TADs were identified using Insulation Score.
Compartment A/B were defined by A-B index.
Assembly: Susscrofa11.1
Supplementary files format and content: Binned raw and normalized 2D contact matrices text files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Genes expression level (TPM) and counts text file
Supplementary files format and content: TAD files
Supplementary files format and content: ABindex files
|
| |
|
| Submission date |
Apr 01, 2022 |
| Last update date |
Apr 25, 2023 |
| Contact name |
jin long |
| E-mail(s) |
longjin8806@163.com
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
Hui ming
|
| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL23810 |
| Series (1) |
| GSE199968 |
Comparative 3D Genome Architectures of Adipose Tissues Provide Insight into Human-specific Regulation of Metabolic Homeostasis |
|
| Relations |
| BioSample |
SAMN26748030 |
| SRA |
SRX14491712 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
