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Sample GSM6509880 Query DataSets for GSM6509880
Status Public on Jan 03, 2024
Title Long-12 R3S7
Sample type SRA
 
Source name Human lymphoblastoid cell line
Organism Homo sapiens
Characteristics Sex: Female
cell line: Human lymphoblastoid cell line
Extracted molecule total RNA
Extraction protocol 100 μL LCL suspension containing approximately 6.6 x106 cells was taken through the Maxwell 16 miRNA tissue kit protocol using the Maxwell 16MDX instrument following the manufacturer’s instructions, with miRNA eluted in 60 μL RNase-free water.
RNA libraries for small RNA-seq were prepared using the Illumina TruSeq Small RNA library preparation kit following a modified protocol as described previously (Waller et al 2017 doi:10.3389/fnins.2017.00731). For cluster generation 1000 pM of each barcoded cDNA library were pooled together and loaded onto two lanes of the flow cell at 20 pM and 25 pM concentration per lane.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiScanSQ
 
Description Long-12
20 pM concentration per lane
Data processing Initial QC completed in Illumina Sequencing Analysis Viewer
Sequence data were converted from the generated image .bcl files to raw, demultiplexed sequencing data in the .fastq text file format using the Illumina developed bcl2fastq pipeline.
In OASIS 2.0, an online small RNA data analysis software package the Illumina TruSeq 3′adapter (TGGAATTCTCGGGTGCCAAGG) sequence was removed from the .fastq file of each sample’s reads and the read size filtered (15-32nt) with low abundance reads (<5 reads) discarded.
All remaining reads were mapped to the Human genome (Oasis 2.0: GRCh38 [hg38]). Differential miRNA expression using DESeq2 between patient samples with long disease duration and short disease duration were assessed.
Ingenuity Pathway Analysis (IPA) (Qiagen) was used to analyse the diseases and biological functions of the differentially expressed miRNA associated with disease duration.
Assembly: GRCh38 [hg38]
Supplementary files format and content: Tab-delimited text files include count values for each Sample
 
Submission date Aug 26, 2022
Last update date Jan 03, 2024
Contact name Rachel Waller
E-mail(s) r.waller@sheffield.ac.uk
Organization name The University of Sheffield
Department Neuroscience
Street address SITraN, 385A Glossop Road
City SHEFFIELD
State/province South Yorkshire
ZIP/Postal code S102HQ
Country United Kingdom
 
Platform ID GPL15456
Series (2)
GSE212133 Establishing mRNA and miRNA interactions driving disease heterogeneity in ALS patient survival (miRNA-Seq)
GSE212134 Establishing mRNA and microRNA interactions driving disease heterogeneity in Amyotrophic lateral sclerosis
Relations
BioSample SAMN30524852
SRA SRX17234837

Supplementary file Size Download File type/resource
GSM6509880_R3S7_CAGATC_L003_allspeciesCounts.txt.gz 210.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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