|
| Status |
Public on Nov 30, 2020 |
| Title |
Ribo_Plus_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Pooled-Ribo-Zero Plus rRNA Depletion
|
| Treatment protocol |
A total of 1 μg of each RNA sample was processed by four different kits to remove the globin gene (GLOBINClear Kit, NEBgr: NEBNext® Globin & rRNA Depletion Kit (NEBgr), RZr: Ribo-Zero Plus rRNA Depletion Kit (RZr), GZr: Globin-Zero Gold rRNA Removal Kit (GZr)).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was PAXgene RNA extraction kit (Qiagen)
1 ug of total RNA from each sample was used. The RNA-Seq libraries were generated using TruSeq Stranded mRNA Library Prep kit (Illumina, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
2nd set_Gene_counts.txt
Ribo_Plus_1
|
| Data processing |
The STAR (2.6.1d) aligner was used to perform alignment of reads to the hg38. After alignment, the final BAM files were quantified using Partek E/M algorithm by Ensembl annotations (Ensembl Transcripts release 92).
Genome_build: hg38, Ensembl Transcripts release 92
Supplementary_files_format_and_content: tab-delimited text files and gene counts & transcripts counts
|
| |
|
| Submission date |
May 14, 2020 |
| Last update date |
Nov 30, 2020 |
| Contact name |
Jin Sung Jang |
| Organization name |
Mayo Clinic
|
| Street address |
200 First St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE150587 |
Comparative evaluation for the globin gene depletion methods for mRNA sequencing using the whole blood-derived total RNAs |
|
| Relations |
| BioSample |
SAMN14924393 |
| SRA |
SRX8342581 |
