 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 08, 2016 |
| Title |
RNASeq ABP1d 2 |
| Sample type |
SRA |
| |
|
| Source name |
ABPd
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: ABP1d
|
| Treatment protocol |
none
|
| Growth protocol |
exponentially growing cells in rich media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extraction by acid phenol protocol
total RNA was quantified by Qubit fluorometer using the Quant-iT RNA Assay Kit (Life Technologies). Using Illumina’s small RNA Sample Prep Kit v1.5, 3’ and 5’ adapters were ligated to 5 µg of total RNA, followed by reverse transcription and 12 cycles of amplification. Amplification products of 125 to 250 nucleotides size selected from a 4% agarose gel and purified. Libraries were quantified by Qubit fluorometer using the Quant-iT DNA HS Assay Kit (Life Technologies). Using Illumina’s Cluster Generation Kit, libraries were subject to cluster generation at 8 pM concentration as one sample per lane. Sequencing-by-synthesis was performed for 38 cycles.
Strand-specific RNA-Seq
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
smallRNAs_ABP1d_regions_geo.bed
smallRNAs_ABP1d_vs_WT_regions_geo.bed
|
| Data processing |
Base calling was performed with Illumina Pipeline version 1.5
Solexa Illumina strand-specific small RNA-Seq data for Saccharomyces pombe in ABP1d mutant and wild type control samples were aligned against reference genome (Sanger release 09052011) using Bowtie 0.12.5, allowing 0 mismatches in the read seed. In order to estimate enrichment and depletion in repeated regions (i.e. transposons, rRNA units) in an unbiased manner, all possible sites for multiple hits were considered.
First, significantly enriched regions in small RNA-Seq ABP1d mutant and WT were detected using the enrichedRegions function from the htSeqTools package, using the one tailed option (no control) and a Benjamini Hochbergh pvalue threshold of 0.05, and leaving the other settings as default.
Afterwards, significantly enriched and depleted regions in small RNA-Seq ABP1d mutant against WT (up and down-regulated small RNAs) were detected using the enrichedRegions function from the htSeqTools package, using the two tailed option and a Benjamini Hochbergh pvalue threshold of 0.05, and leaving the other settings as default.
Genome_build: Spombe Sanger 09052011
Supplementary_files_format_and_content: smallRNAs ABP1 and WT BED files include chromosome, start, end, rpkm abundance and BH adjusted pvalue of the identified enriched regions in each sample individually (no control).
Supplementary_files_format_and_content: smallRNAs ABP1_vs_WT BED file include chromosome, start, end, rpkm abundance in ABP1d and WT respectively, and BH adjusted pvalue of the identified regions differentially expressed in ABP1d vs WT.
|
| |
|
| Submission date |
May 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
oscar.reina@irbbarcelona.org
|
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
C/Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL9453 |
| Series (2) |
| GSE81280 |
The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [smallRNA-Seq] |
| GSE81326 |
The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat |
|
| Relations |
| BioSample |
SAMN04967261 |
| SRA |
SRX1754633 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
