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| Status |
Public on Mar 12, 2021 |
| Title |
ALS patient_enrolment [UCH00114] |
| Sample type |
SRA |
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| Source name |
Blood plasma
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| Organism |
Homo sapiens |
| Characteristics |
disease: ALS
group: enrolment
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Plasma were isolated from blood and total RNA was extracted using the Qiagen miRNeasy micro kit (Cat# 217184)
libraries were prepared from 7.5 ng of total RNA using the QIAseq miRNA library kit and QIAseq miRNA NGS 48 Index IL (Qiagen, Cat# 331505 and 331565), by an experimenter who was blinded to the identity of samples. Samples were randomly allocated to library preparation and sequencing in batches. Libraries with different indices were multiplexed and sequenced on NextSeq 500/550 v2 flow cell or Novaseq SP100 (Illumina), with 75bp single read and 6bp index read.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
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| Description |
UCH00114
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv
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| Data processing |
Data were aligned to the genome using the GeneGlobe pipeline (https://geneglobe.qiagen.com/us/)
Data were filtered using the following specifications: >50 UMIs in >60% of the samples for longitudinal analysis, >100 UMIs on average for other analyses
Data were corrected for batch using the ComBat function in R and then normalized by DESeq2
Supplementary_files_format_and_content: txt files contain raw UMI counts, after alignment
Supplementary_files_format_and_content: xls files contain batch and DESeq2 corrected UMIs, after filtration of low-abundance miRNAs. Related R code are in the same folder
Supplementary_files_format_and_content: csv files contain categorial values for miRNAs and other clinical features, to be run by an R code for calculation of hazard ratios by COX proportional hazard analysis. Related R codes are in the same folder
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| Submission date |
Mar 11, 2021 |
| Last update date |
Mar 12, 2021 |
| Contact name |
Iddo Magen |
| E-mail(s) |
[email protected]
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| Phone |
0545727335
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| Organization name |
Weizmann Institute
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| Street address |
בן אליעזר 32, 17
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| City |
ראשון לציון |
| State/province |
Not in US |
| ZIP/Postal code |
7522679 |
| Country |
Israel |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE168714 |
Circulating miR-181 is a prognostic biomarker for amyotrophic lateral sclerosis |
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| Relations |
| BioSample |
SAMN18261677 |
| SRA |
SRX10313602 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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