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Sample GSM3762921 Query DataSets for GSM3762921
Status Public on Dec 31, 2019
Title sample 135b
Sample type SRA
 
Source name human in vivo nucleus pulposus in young scoliotic individuals 2b
Organism Homo sapiens
Characteristics tissue: nucleus pulposus
age: 13
gender: female
ivd level: L1/L2
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_T12_L1]
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 SAMN11634452
SRA SRX5823886

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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