|
| Status |
Public on Jul 17, 2024 |
| Title |
Nucleus pulposus cells from sham operation #3, RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Nucleus pulposus tissue from sham operation
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Nucleus pulposus tissue from sham operation
cell type: Nucleus pulposus cells
treatment: Sham operation
|
| Treatment protocol |
Nucleus pulposus tissues were digested with 0.4% type II collagenase for 4-6 hours.
|
| Growth protocol |
Nucleus pulposus cells were isolated from human or rat lumbar nucleus pulposus tissues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from samples using TRIzol reagent. Illumina TruSeq RNA Sample Pre Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
Libraries were prepared according to instructions of Illumina HiSeq X ten accompanying the Ovation RNA-Seq System V2 (M01206 v9). Briefly, RNA was elutated according to the manuscription user guide. Then RNA was fragmented using fragment buffer. cDNA was synthed using dNTPs, DNA polymeraseI and RNaseH. Then cDNA was purified using AMPure XP beads. PCR Was used to amplify with Illumina primers for 15 cycles and library fragments of ~200 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X ten following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Sham_3
Sham_LSI_LSI_E_RPKM.txt
|
| Data processing |
Illumina Casava 1.7 software was used for basecalling.
Sequenced reads were qualified using FastQC and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCH38.94 whole genome and Rattus_norvegicus.Rnor_6.0.
Read Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a procotol from Feng, Jianxing et al. Bioinformatics (Oxford, England) vol. 28,21 (2012): 2782-8. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling of the meta-transcript and by the size of the library.
Assembly: Homo_sapiens.GRCh38.94; Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: IVDD_Normal_RPKM.txt
Supplementary files format and content: Sham_LSI_LSI_E_RPKM.txt
|
| |
|
| Submission date |
May 07, 2024 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Cao Yang |
| E-mail(s) |
caoyangunion@hust.edu.cn
|
| Organization name |
Wuhan Union Hospital
|
| Street address |
Jiefang average
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
000000 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (1) |
| GSE266883 |
Exercise accelerated the degeneration of lumbar IVDs from surgical lumbar instability, similar to the clinical degeneration process |
|
| Relations |
| BioSample |
SAMN41248698 |
| SRA |
SRX24482285 |
