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| Status |
Public on Sep 01, 2024 |
| Title |
fALS_TARDBP_3 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
cell line: Lymphoblastoid cell line
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| Growth protocol |
PBMCs were isolated from peripheral venous blood samples. Lymphocytes B were isolated from an aliquot of PBMCs and were immortalized into LCLs via Epstein-Barr Virus (EBV) infection.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized and total RNA was isolated by Trizol® reagent.
Sequencing libraries were prepared by the Illumina TruSeq RNA Library Prep, version 2, Protocol D, using 500-ng total RNA (Illumina, California, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
FastQ files were generated using the llumina bcl2fastq2 software (Version 2.17.1.14 -http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html) from raw sequencing reads gener-ated by the Illumina NextSeq 500 sequencer (Illumina, California, USA). STAR/RSEM software was used to cal-culate gene and transcript intensities using Gencode Release 19 (GRCh37.p13) as a reference and the "stranded" op-tion. The mRNA differential expression analysis was carried out using the R package EBSeq. The R package DESeq2 was used to perform differential expression analysis on lncRNAs. With |log2(disease sample/healthy con-trol)|1 and an FDR of 0.1, genes were considered differentially expressed and retained for further analysis.
Assembly: Hg19
Supplementary files format and content: fastq.gz
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| Submission date |
Jun 28, 2024 |
| Last update date |
Sep 01, 2024 |
| Contact name |
Jessica Garau |
| Organization name |
IRCCS Mondino Foundation
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| Street address |
Via Mondino 2
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| City |
Pavia |
| ZIP/Postal code |
27100 |
| Country |
Italy |
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| Platform ID |
GPL15433 |
| Series (1) |
| GSE271030 |
RNA Expression Profiling in Lymphoblastoid Cell Lines from Mutated and Non-Mutated Amyotrophic Lateral Sclerosis Patients |
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| Relations |
| BioSample |
SAMN42152240 |
| SRA |
SRX25143232 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8367542_Sample_SLA18_14_TARDBP.genes.results.gz |
691.6 Kb |
(ftp)(http) |
RESULTS |
| GSM8367542_Sample_SLA18_14_TARDBP.isoforms.results.gz |
1.2 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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