|
| Status |
Public on Dec 31, 2019 |
| Title |
sample135a |
| Sample type |
SRA |
| |
|
| Source name |
human in vivo nucleus pulposus in young scoliotic individuals 2a
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: nucleus pulposus
age: 13
gender: female
ivd level: T12/L1
date of surgery: 2014-05-29
surgical procedures: discectomy
condition: scoliosis
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction from dissociated cells was done by using Ambiion RNA extraction kit (CAT#AM-1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
invivoNPC.gene.expression.tables.FPKM.txt [CDS_135_L1_L2]
|
| Data processing |
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes
|
| |
|
| Submission date |
May 12, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Peikai Chen |
| E-mail(s) |
pkchen1@hku.hk
|
| Phone |
852-258315217
|
| Organization name |
The University of Hong Kong
|
| Department |
Faculty of Medicine
|
| Street address |
Sassoon Road 5
|
| City |
Pok Fu Lam |
| ZIP/Postal code |
10000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE131065 |
bulk RNA-seq of human nucleusus pulposus from scoliosis patients |
|
| Relations |
| BioSample |
SAMN11634447 |
| SRA |
SRX5823885 |
