|
| Status |
Public on Oct 04, 2019 |
| Title |
CGND-HRA-00553 |
| Sample type |
SRA |
| |
|
| Source name |
Motor Cortex
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: post-mortem tissue
cns subregion: Motor Cortex (Medial)
subject id: JHU 73
sample group: ALS Spectrum MND
|
| 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 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
total RNA rRNA depleted
|
| Data processing |
fastq Illumina RNASeq paired-end reads were aligned to the hg19 reference genome using STAR v2.5.2b with the following configurations: --outFilterMultimapNmax 100; --outFilterMismatchNoverReadLmax 0.04
Genes and transposable elements (TE) were quantified using TEcount (from TEtranscripts v2.0.3) with the following configurations: hg19 genic GTF from refGene (Jan 2018), custom hg19 TE GTF generated from repeatMasker; --stranded reverse
Genome_build: hg19
Supplementary_files_format_and_content: Individual count tables (SampleName_counts.txt) were generated as output from TEcount
|
| |
|
| Submission date |
Dec 27, 2018 |
| 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) |
| GSE124439 |
Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia |
| GSE137810 |
NYGC ALS Consortium data |
|
| Relations |
| Reanalyzed by |
GSM4660955 |
| BioSample |
SAMN10656608 |
| SRA |
SRX5185396 |
