GSE86227
GSE GEOHNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]
Organism:
Mus musculus
Platform:
GPL15520
Samples:
12
Experiment Types:
Non-coding RNA profiling by high throughput sequencing
Submitted:
Aug 30 2016
Last Updated:
May 15 2019
Status:
Public on Oct 20 2016
Contact:
Gene,,Yeo (UCSD)
Relations
SubSeries of: GSE86464
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA341998
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP086705
Summary
HnRNPA2B1 encodes an RNA binding protein associated with neurodegenerative disorders. However, its function in the nervous system is unclear. Transcriptome-wide cross-linking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ~2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. Loss of hnRNP A2/B1 results in alternative splicing, including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. Inclusion of the DAO exon is also reduced in transgenic ALS mice models. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells demonstrate gain-of-mutant-dependent splicing differences. Mutant motor neurons also exhibit increased hnRNP A2/B1 localization to cytoplasmic granules during stress, which are abrogated by a small molecule CA43. Our findings and cellular resource identify RNA networks affected in loss of normal and mutated hnRNP A2/B1 with broad relevance to neurodegeneration.
Overall Design
small RNA-seq in mouse spinal after injection with ASO against hnRNP A2/B1 or saline. Three or four replicates per condition
Analysis (5 steps)
View Data Processing
Processing steps for GSE86227
- 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
Supplementary Files (2)
Dataset Citations (1)
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
PMID 27773581
· 2016
· Neuron
Fernando J Martinez, Gabriel A Pratt, Eric L Van Nostrand, Ranjan Batra, Stephanie C Huelga, Katannya Kapeli, Peter Freese, Seung J Chun, Karen Ling, Chelsea Gelboin-Burkhart, Layla Fijany, Harrison C Wang, Julia K Nussbacher, Sara M Broski, Hong Joo Kim, Rea Lardelli, Balaji Sundararaman, John P Donohue, Ashkan Javaherian, Jens Lykke-Andersen, Steven Finkbeiner, C Frank Bennett, Manuel Ares, Christopher B Burge, J Paul Taylor, Frank Rigo, Gene W Yeo
SRA Experiments (12) and Runs (12)
Total: 274 MBGSM2298799: saline control 1 [mouse]; Mus musculus; ncRNA-Seq
Sample: SRS1672521
BioProject: PRJNA341998
BioSample: SAMN05731006
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Mus musculus
Sample attributes
source_name: spinal cord
strain: C57BL/6J
age: 8weeks
tissue type: spinal cord
treatment: saline
Original files (1)
spinal cord
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175377 | 1415527 | 50958972 | 24.51 | B7P80-A1_S2_L001_R1_001.fastq, SRR4175377, SRR4175377.sralite | SRA |
GSM2298800: saline control 2 [mouse]; Mus musculus; ncRNA-Seq
Sample: SRS1672522
BioProject: PRJNA341998
BioSample: SAMN05731005
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Mus musculus
Sample attributes
source_name: spinal cord
strain: C57BL/6J
age: 8weeks
tissue type: spinal cord
treatment: saline
Original files (1)
spinal cord
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175378 | 1215467 | 43756812 | 21.57 | B7P80-A2_S9_L001_R1_001.fastq, SRR4175378, SRR4175378.sralite | SRA |
GSM2298801: saline control 3 [mouse]; Mus musculus; ncRNA-Seq
Sample: SRS1672523
BioProject: PRJNA341998
BioSample: SAMN05731000
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Mus musculus
Sample attributes
source_name: spinal cord
strain: C57BL/6J
age: 8weeks
tissue type: spinal cord
treatment: saline
Original files (1)
spinal cord
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175379 | 1192450 | 42928200 | 21.14 | B7P80-A3_S11_L001_R1_001.fastq, SRR4175379, SRR4175379.sralite | SRA |
GSM2298802: hnRNP A2/B1 ASO 1 [mouse]; Mus musculus; ncRNA-Seq
Sample: SRS1672524
BioProject: PRJNA341998
BioSample: SAMN05730999
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Mus musculus
Sample attributes
source_name: spinal cord
strain: C57BL/6J
age: 8weeks
tissue type: spinal cord
treatment: ASO Hnrnpa2/b1
Original files (1)
spinal cord
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175380 | 1283095 | 46191420 | 22.57 | B7P80-D1_S12_L001_R1_001.fastq, SRR4175380, SRR4175380.sralite | SRA |
GSM2298803: hnRNP A2/B1 ASO 2 [mouse]; Mus musculus; ncRNA-Seq
Sample: SRS1672525
BioProject: PRJNA341998
BioSample: SAMN05731001
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Mus musculus
Sample attributes
source_name: spinal cord
strain: C57BL/6J
age: 8weeks
tissue type: spinal cord
treatment: ASO Hnrnpa2/b1
Original files (1)
spinal cord
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175381 | 1160057 | 41762052 | 20.32 | B7P80-D2_S13_L001_R1_001.fastq, SRR4175381, SRR4175381.sralite | SRA |
GSM2298804: hnRNP A2/B1 ASO 3 [mouse]; Mus musculus; ncRNA-Seq
Sample: SRS1672526
BioProject: PRJNA341998
BioSample: SAMN05730998
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Mus musculus
Sample attributes
source_name: spinal cord
strain: C57BL/6J
age: 8weeks
tissue type: spinal cord
treatment: ASO Hnrnpa2/b1
Original files (1)
spinal cord
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175382 | 2084468 | 75040848 | 35.77 | B7P80-D3_S8_L001_R1_001.fastq, SRR4175382, SRR4175382.sralite | SRA |
GSM2298805: saline control 1 [human]; Homo sapiens; ncRNA-Seq
Sample: SRS1672527
BioProject: PRJNA341998
BioSample: SAMN05730997
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: CVBiPS
cell type: craig venter iPS cells
treatment: saline
Original files (1)
CVBiPS
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175383 | 1132234 | 40760424 | 20.34 | B7P80-C-1_S4_L001_R1_001.fastq, SRR4175383, SRR4175383.sralite | SRA |
GSM2298806: saline control 2 [human]; Homo sapiens; ncRNA-Seq
Sample: SRS1672528
BioProject: PRJNA341998
BioSample: SAMN05731009
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: CVBiPS
cell type: craig venter iPS cells
treatment: saline
Original files (1)
CVBiPS
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175384 | 1029699 | 37069164 | 18.12 | B7P80-C-2_S5_L001_R1_001.fastq, SRR4175384, SRR4175384.sralite | SRA |
GSM2298807: saline control 3 [human]; Homo sapiens; ncRNA-Seq
Sample: SRS1672529
BioProject: PRJNA341998
BioSample: SAMN05731008
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: CVBiPS
cell type: craig venter iPS cells
treatment: saline
Original files (1)
CVBiPS
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175385 | 1194571 | 43004556 | 21.17 | B7P80-C-3_S6_L001_R1_001.fastq, SRR4175385, SRR4175385.sralite | SRA |
GSM2298808: hnRNP A2/B1 ASO 1 [human]; Homo sapiens; ncRNA-Seq
Sample: SRS1672530
BioProject: PRJNA341998
BioSample: SAMN05731007
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: CVBiPS
cell type: craig venter iPS cells
treatment: ASO Hnrnpa2/b1
Original files (1)
CVBiPS
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175386 | 1510692 | 54384912 | 27.57 | B7P80-501-1_S7_L001_R1_001.fastq, SRR4175386, SRR4175386.sralite | SRA |
GSM2298809: hnRNP A2/B1 ASO 2 [human]; Homo sapiens; ncRNA-Seq
Sample: SRS1672531
BioProject: PRJNA341998
BioSample: SAMN05731004
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: CVBiPS
cell type: craig venter iPS cells
treatment: ASO Hnrnpa2/b1
Original files (1)
CVBiPS
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175387 | 1177414 | 42386904 | 20.91 | B7P80-501-2_S1_L001_R1_001.fastq, SRR4175387, SRR4175387.sralite | SRA |
GSM2298810: hnRNP A2/B1 ASO 3 [human]; Homo sapiens; ncRNA-Seq
Sample: SRS1672532
BioProject: PRJNA341998
BioSample: SAMN05731003
Platform: ILLUMINA
Instrument: Illumina MiSeq
Organism: Homo sapiens
Sample attributes
source_name: CVBiPS
cell type: craig venter iPS cells
treatment: ASO Hnrnpa2/b1
Original files (1)
CVBiPS
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR4175388 | 1115399 | 40154364 | 20.48 | B7P80-501-3_S3_L001_R1_001.fastq, SRR4175388, SRR4175388.sralite | SRA |
Linked Publications (1)
Data Files (24)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | B7P80-501-1_S7_L001_R1_001.fastq | ncRNA-Seq | 27.6 MB | link | |||
| — | B7P80-501-1_S7_L001_R1_001.fastq | ncRNA-Seq | 27.6 MB | link | |||
| — | B7P80-501-2_S1_L001_R1_001.fastq | ncRNA-Seq | 20.9 MB | link | |||
| — | B7P80-501-2_S1_L001_R1_001.fastq | ncRNA-Seq | 20.9 MB | link | |||
| — | B7P80-501-3_S3_L001_R1_001.fastq | ncRNA-Seq | 20.5 MB | link | |||
| — | B7P80-501-3_S3_L001_R1_001.fastq | ncRNA-Seq | 20.5 MB | link | |||
| — | B7P80-A1_S2_L001_R1_001.fastq | ncRNA-Seq | 24.5 MB | link | |||
| — | B7P80-A1_S2_L001_R1_001.fastq | ncRNA-Seq | 24.5 MB | link | |||
| — | B7P80-A2_S9_L001_R1_001.fastq | ncRNA-Seq | 21.6 MB | link | |||
| — | B7P80-A2_S9_L001_R1_001.fastq | ncRNA-Seq | 21.6 MB | link | |||
| — | B7P80-A3_S11_L001_R1_001.fastq | ncRNA-Seq | 21.1 MB | link | |||
| — | B7P80-A3_S11_L001_R1_001.fastq | ncRNA-Seq | 21.1 MB | link | |||
| — | B7P80-C-1_S4_L001_R1_001.fastq | ncRNA-Seq | 20.3 MB | link | |||
| — | B7P80-C-1_S4_L001_R1_001.fastq | ncRNA-Seq | 20.3 MB | link | |||
| — | B7P80-C-2_S5_L001_R1_001.fastq | ncRNA-Seq | 18.1 MB | link | |||
| — | B7P80-C-2_S5_L001_R1_001.fastq | ncRNA-Seq | 18.1 MB | link | |||
| — | B7P80-C-3_S6_L001_R1_001.fastq | ncRNA-Seq | 21.2 MB | link | |||
| — | B7P80-C-3_S6_L001_R1_001.fastq | ncRNA-Seq | 21.2 MB | link | |||
| — | B7P80-D1_S12_L001_R1_001.fastq | ncRNA-Seq | 22.6 MB | link | |||
| — | B7P80-D1_S12_L001_R1_001.fastq | ncRNA-Seq | 22.6 MB | link | |||
| — | B7P80-D2_S13_L001_R1_001.fastq | ncRNA-Seq | 20.3 MB | link | |||
| — | B7P80-D2_S13_L001_R1_001.fastq | ncRNA-Seq | 20.3 MB | link | |||
| — | B7P80-D3_S8_L001_R1_001.fastq | ncRNA-Seq | 35.8 MB | link | |||
| — | B7P80-D3_S8_L001_R1_001.fastq | ncRNA-Seq | 35.8 MB | link |