 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 10, 2015 |
| Title |
Spleen |
| Sample type |
SRA |
| |
|
| Source name |
WT spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver and spleen were removed, flash frozen in liquid nitrogen, and small RNA (10-200bp) was harvested using RNAzol RT reagent. RNA were then run on a polyacrylamide gel, and RNA with size from ~24-31 nt was purified and used for the construction of sequencing libraries.
RNA libraries were prepared using the Illumina Small RNA v1.5 Sample Preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
size-selected small RNA
|
| Data processing |
Basecalls performed using CASAVA version 1.8
The last 6 bases (Illumina indexes) were removed and added to the header line of the .fastq files.
Reads that did not pass Illumina quality control were filtered.
3' adapters were stripped using Cutadapt with the following parameters: -a -e 0.25 -n 3 -O 1 -m 15
5' adapters were removed using Cutadapt with the following parameters: -b -e 0.25 -n 3 -O 5 -m 15
Known ncRNAs were removed by aligning reads to non-coding RNA sequences using Bowtie with the following parameters: -v3 -k1 --un
Remaining small RNAs were aligned to the mm9 genome using Bowtie with the following parameters: -v1 -m1 --best -- strata
3' UTR clusters were generated by selecting 3' UTRs with at least 3 sense small RNAs and a minimum density of 7.5 reads per kilobase 3' UTR per million reads aligned. Genes where the density of sense small RNAs in the 3' UTR was less than two fold that of the density in the coding region were removed. We then set the cluster boundaries as the region of the largest 3' UTR isoform and extended the 3' boundary into intergenic sequence if there was at least 1 sense small RNA per 2 kb.
RNAs that intersected the 3' UTR clusters were isolated using BEDtools IntersectBed with the default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bam – alignments of trimmed and filtered RNAs
|
| |
|
| Submission date |
May 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dario Boffelli |
| E-mail(s) |
dario.boffelli@cshs.org
|
| Organization name |
Cedars Sinai
|
| Department |
Pediatrics
|
| Lab |
Boffelli
|
| Street address |
700 N San Vicente Blvd
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE47093 |
Somatic piRNAs in the adult mouse |
|
| Relations |
| BioSample |
SAMN02147101 |
| SRA |
SRX283444 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1144685_spleen_3UTRclusters.bed.gz |
4.9 Kb |
(ftp)(http) |
BED |
| GSM1144685_spleen_processed_RNAinClusters.txt.gz |
18.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
