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Sample GSM7733703 Query DataSets for GSM7733703
Status Public on Dec 01, 2023
Title Serum, control 4
Sample type SRA
 
Source name serum
Organism Homo sapiens
Characteristics tissue: serum
Extracted molecule total RNA
Extraction protocol mirVanaTM PARISTM RNA and native protein purification kit (AM1556, Invitrogen, Waltham, MA) was used to extract total RNAs from 300 µl CSF or 250 µl serum samples, according to the manufacturer's protocol. 5 μl of 5 nM artificial microRNA (cel-miR-39) was spiked after denaturing endogenous ribonucleases to control extraction efficiency. At the elution step, samples were incubated on the column for 5 min at 65 ℃, and RNAs were eluted with 45 μl nuclease-free water. TRIzol reagents (Thermo Fisher Scientific, Hercules, CA) were used to extract RNAs from the hippocampus.
RNAs were treated with T4 PNK (New England Biolabs, Ipswich, MA, US) to make the 3’-end of tRFs homogenously with 3’-OH before the ligation with sequencing barcodes, as the ligation of the 3′-end of sncRNAs with sequencing barcodes requires the presence of 3′-OH and not all sncRNAs have 3-OH ends. The treated RNA was purified and concentrated using Zymo RNA Clean and Concentrator kit (D4060, Thomas Scientific, Swedesboro, NJ). Small RNA libraries were then prepared with NEB Next Multiplex Small RNA Library Prep Set for Illumina (Ipswich, MA, US).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model NextSeq 550
 
Description 7-CN_Serum
Data processing For seq data analyses, adaptor sequences were removed using Cutadpat, and RNAs with a length ≥ 15 bp were extracted. RNAs with counts of less than ten and all rRNAs were filtered out. The remaining RNA reads, also treated as cleaned input reads, were mapped to our in-house small RNA database using bowtie2 (v2.4.1), allowing two mismatches, as we previously described. In brief, our in-house small RNA database includes 1) tRF5 and tRF3 databases using the identical sequences derived from different tRNAs [sequences downloaded from tRNA genes using the Table Browser of the UCSC genome browser, 2) tRF1 sequences using genome locations of tRNAs, 3) miR/snoR sequences downloaded from the UCSC genome browser, and 4) piRNA sequences downloaded from piRBase (https://www.pirnadb.org/browse/pirna ).
Assembly: hg38
Supplementary files format and content: tab-seperated text file of read counts (matrix file)
 
Submission date Aug 24, 2023
Last update date Dec 01, 2023
Contact name Xiaoyong Bao
Organization name University of Texas Medical Branch
Department Pediatrics
Street address 301 University Boulevard
City Galveston
State/province TX
ZIP/Postal code 77555-0366
Country USA
 
Platform ID GPL21697
Series (1)
GSE241686 Diagnostic marker development of tRNA-derived fragments in cerebrospinal fluid and blood serum
Relations
BioSample SAMN37146814
SRA SRX21481283

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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