|
| Status |
Public on Feb 09, 2018 |
| Title |
control immunoprecipitation |
| Sample type |
SRA |
| |
|
| Source name |
immunoprecipitation
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
ip: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol Chloroform extraction
RNA libraries from Lsm8 and control immunoprecipitations were prepared following instructions for Solexa mRNA sequencing and each sample was sequenced on a single lane of the Illumina GAIIx sequencer producing 40bp single-end unstranded reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
STAR_lsm8_all_genes.ignore_strand.SNU4EDIT.tsv
|
| Data processing |
The fastq files were aligned to the S. pombe reference genome ASM294v2 using the STAR aligner (v 2.5.2b) with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000 --outSAMtype BAM SortedByCoordinate --twopassMode Basic. The corresponding reference annotation gtf file was manually curated for snu4 using coordinates II:467,488-467,615.
A counts table for unambiguous uniquely mapped reads was generated using a custom R script.
The read counts for each gene were normalized to the median read counts per library. Genes were called enriched if the normalized counts in the IP sample exceeded the corresponding counts in the control by 10 or more and the normalized read count ratio was greater than two.
Genome_build: S. pombe ASM294v2
Supplementary_files_format_and_content: STAR_lsm8_all_genes.ignore_strand.SNU4EDIT.tsv; normalized gene counts per sample and enrichment value per gene in tab separated file.
|
| |
|
| Submission date |
Oct 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Baumann |
| E-mail(s) |
peter@baumannlab.org
|
| Organization name |
Stowers Institute for Medical Research
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL15167 |
| Series (1) |
| GSE104672 |
Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast |
|
| Relations |
| BioSample |
SAMN07757667 |
| SRA |
SRX3257820 |
