|
| Status |
Public on Oct 20, 2016 |
| Title |
saline control 1 [human] |
| Sample type |
SRA |
| |
|
| Source name |
CVBiPS
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: craig venter iPS cells
treatment: saline
|
| Treatment protocol |
ASO complementary to Hnrnpa2b1 was added to media for XXX days to deplete hnRNP A2/B1.
|
| Growth protocol |
craig venter fibroblast-derived induced pluripotent stem cells were cultured under normal conditions
|
| 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 |
C1
mature_counts_hg19.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 |
GPL15520 |
| 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 |
SAMN05730997 |
| SRA |
SRX2140604 |
