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Sample GSM2298802 Query DataSets for GSM2298802
Status Public on Oct 20, 2016
Title hnRNP A2/B1 ASO 1 [mouse]
Sample type SRA
 
Source name spinal cord
Organism Mus musculus
Characteristics strain: c57bl/6j
age: 8weeks
tissue type: spinal cord
treatment: ASO Hnrnpa2/b1
Treatment protocol Sterotactic injections of ASO complementary to Hnrnpa2b1 were performed in eight-week old female C57Bl/b mice to deplete hnRNP A2/B1. ASOs were delivered specifically to the lateral ventricle (12.5 mg) injection (300 mg). Mice were regularly monitored for 28 days until sacrificed.
Growth protocol eight-week old female C57Bl/6j mice were grown under normal coniditons
Extracted molecule total RNA
Extraction protocol RNA was extracted by standard Trizol extraction.
TruSeq small-RNA Sample Preparation Kit
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina MiSeq
 
Description D1
mature_counts_mm10.csv
Data processing Sequencing reads from small RNA-seq libraries were first trimmed adapters using cutadapt
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the mm9 or hg19 genome (UCSC assembly) using bowtie version 1.1.1 with parameters -p 8 -k 1 -m 10 -l 25 --best --chunkmbs 128
counts of reads for each gene annotated in gencode vM3 were calculated from featureCounts for mouse and v19 for human
Genome_build: mm10/hg19 for mouse and human, respectively
Supplementary_files_format_and_content: count file, csv
 
Submission date Aug 30, 2016
Last update date May 15, 2019
Contact name Gene Yeo
E-mail(s) geneyeo@ucsd.edu
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL16417
Series (2)
GSE86227 HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]
GSE86464 HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons
Relations
BioSample SAMN05730999
SRA SRX2140601

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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