|
| Status |
Public on Oct 20, 2020 |
| Title |
post-mortem tissue [CGND-HRA-00425] |
| Sample type |
SRA |
| |
|
| Source name |
Spinal Cord Cervical
|
| Organism |
Homo sapiens |
| Characteristics |
project: Target ALS PM core
tissue: Spinal Cord Cervical
subject id: NEUDT233ZZ1
group: ALS Spectrum MND
sample id alt: CGND-HRA-00425
library preparation method: Manual KAPA Total
|
| Treatment protocol |
Flash frozen autopsy tissue
|
| 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 is depleted and cDNA libraries prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (KAPA, Roche) and either i) Illumina platform-compatible PCR primers (NEXTflex RNA-seq indexes, BioScientific) for the manual library preparation protocol and sequencing on Illumina HiSeq 2500 or ii) Illumina sequencing adapters with dual indexes (IDT for Illumina – TruSeq DNA UD Indexes Cat# 20022370) and amplified with 9 cycles of PCR for sequencing on the NovaSeq 6000 (automated library preparation protocol). Libraries are ~ 500bp in length and sequenced PE 125 (HiSeq 2500) or PE 100 (NovaSeq 6000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired-end reads in raw fastq files were subject to adapter trimming with trimmomatic (v0.36) (Bolger, Lohse, and Usadel 2014; https://pubmed.ncbi.nlm.nih.gov/24695404/)
Reads were aligned to the hg38 build (GRCh38.primary_assembly) of the human reference genome using STAR (2.7.2a) (Dobin et al. 2013; https://pubmed.ncbi.nlm.nih.gov/23104886/) with indexes created from GENCODE (v30) (“GENCODE - Human Release 30” n.d.).
Gene expression was quantified using RSEM (1.3.1) (B. Li and Dewey 2011; https://pubmed.ncbi.nlm.nih.gov/21816040/) using gene models from GENCODE (v30).
A matrix of read counts per gene in each sample was generated using tximport (v1.12.0) (Soneson et al, 2015; https://pubmed.ncbi.nlm.nih.gov/26925227/).
Genome_build: hg38 (GRCh38.primary_assembly)
Supplementary_files_format_and_content: tximport (v1.12.0) generated matrix of RSEM read counts per gene in txt file format for all samples retained for analysis in Prudencio et al., 2020; Differential STMN2 gene expression (processed count data in Gene_counts_matrix_RSEM_Prudencio_et_al_2020.txt) and splicing analyses of Amyotrophic Lateral Sclerosis (ALS), ALS-FTD and Control postmortem samples in Prudencio et al. 2020 were performed on samples from this release and prior NYGC ALS Consortium releases.
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Hemali Phatnani |
| E-mail(s) |
[email protected]
|
| Organization name |
New York Genome Center
|
| Street address |
101 Avenue of the Americas
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10013 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE137810 |
NYGC ALS Consortium data |
| GSE153960 |
Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia |
|
| Relations |
| BioSample |
SAMN15465798 |
| SRA |
SRX8681341 |
