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| Status |
Public on Jul 13, 2018 |
| Title |
CGND-HRA-00724 |
| Sample type |
SRA |
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| Source name |
ungrouped ALS_Cerebellum
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| Organism |
Homo sapiens |
| Characteristics |
sample group: ungrouped ALS
subject id: NEUYY221HZA
sample type: post-mortem tissue
tissue: Cerebellum
cns subregion: Cerebellum
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| Treatment protocol |
Flash frozen autopsy tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA is extracted from flash frozen post-mortem tissue using Trizol/Chloroform, followed by Qiagen RNeasy minikit column purification. RNA is quantified on a Nanodrop 2000 and Qubit™ 2.0 Fluorometer; the quality and integrity of the RNA are verified on an Agilent Bioanalyzer.
Starting from 500 ng of total RNA, rRNA are depleted and cDNA libraries prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA, Roche) and Illumina platform-compatible PCR primers (NEXTflex RNA-seq indexes, BioScientific). Libraries are 500-550bp in length and sequenced PE 125.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CGND-HRA-00724_ACCTCCAA_BCB4F2ANXX_L008_001
CGND-HRA-00724
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| Data processing |
fastq Illumina RNASeq paired-end reads were aligned using STAR (2.5.2a).
We used Leafcutter (0.2.6) to perform differential splicing analyses of each of four defined groups of ALS cases (ALSlow, ALShigh, C9, FTD grouped samples for a total of 54 samples referred to as the training set) against the Control group (all groups are described in: link to manuscript here). In each differential splicing analysis, Leafcutter outputs a file listing the set of cluster padj values, and a second file listing the splice junctions that reside within those clusters and their delta PSIs as a result of the differential analysis.
Clusters with a padj value <0.1 were selected for further analysis; we aggregated splice junctions and their corresponding delta PSIs across the 4 analyses into a single matrix. Differentially spliced events are ordered by the max delta PSI across the 4 analyses (file: sig.junctions.padj01.sorted_by_max_deltapsi_Conlon_et_al_2018.txt).
Splice junction coordinates are intersected with Gencode release 25 annotations.
PSI ratios across all samples in Conlon et al. 2018 (77 training and test samples, see link to manuscript here) were computed using the leafcutter_quantify_psi.R script starting from the splice junction counts (see https://github.com/davidaknowles/leafcutter/issues/34)
Genome_build: GRCh38
Supplementary_files_format_and_content: sig.junctions.padj01.sorted_by_max_deltapsi_Conlon_et_al_2018.txt : Differentially spliced events, coordinates and gene names are ordered by the max delta PSI across the 4 analyses of 54 ALS and Control samples.
Supplementary_files_format_and_content: DS_leafcutter.ratios_Conlon_et_al_2018.txt : PSI ratios across all samples (77 training and test samples in Conlon et al. 2018, link to manuscript here) were computed using the leafcutter_quantify_psi.R script starting from the splice junction counts (see https://github.com/davidaknowles/leafcutter/issues/34)
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| Submission date |
Jul 03, 2018 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Hemali Phatnani |
| E-mail(s) |
[email protected]
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| Organization name |
New York Genome Center
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| Street address |
101 Avenue of the Americas
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE116622 |
Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism |
| GSE137810 |
NYGC ALS Consortium data |
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| Relations |
| Reanalyzed by |
GSM4660835 |
| BioSample |
SAMN09579857 |
| SRA |
SRX4339502 |
| 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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