|
| Status |
Public on Dec 27, 2019 |
| Title |
MS10_CD33_N2 |
| Sample type |
SRA |
| |
|
| Source name |
CD33+ LPMC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD33+ LPMC
strain: Non-IBD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from sorted cells by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I and then bound to Dynabeads Oligo(dT) EcoP magnetic beads. The double-stranded cDNA synthesized on the beads was digested with Nla III and ligated to the adaptor containing an EcoP15I restriction enzyme recognition site. The adapter-ligated cDNA was digested with EcoP15I to release the tag containing the adaptor sequence and 27 bp of unique sequence from a single transcript.
SAGE-seq libraries were prepared for sequencing using SOLiD SAGE Kit with Barcoding Adaptor Module and multiplexed by using SOLiD RNA Barcoding Kit Module 1-16 according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
library strategy: SAGE-Seq
|
| Data processing |
Sequenced reads were mapped to hg19 whole genome using LifeScope version 2.5.1 with set parameters analysis.filter.reference non coding RNA sequence.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a using a pipeline of Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.13.2; tab-delimited text files include RPKM values, count of tags, and total exon length for each gene;
|
| |
|
| Submission date |
Mar 25, 2015 |
| Last update date |
Dec 27, 2019 |
| Contact name |
noriko nishi |
| Organization name |
Axiohelix Co. Ltd.
|
| Street address |
5-11 hakozaki 5F Yunibasaru Bldg
|
| City |
tyuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
103-0015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE67280 |
Transcriptome Analysis of immune cells derived from IBD patients by using Next Generation Sequencing |
|
| Relations |
| BioSample |
SAMN03453567 |
| SRA |
SRX974474 |
