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Sample GSM2410429 Query DataSets for GSM2410429
Status Public on Jul 27, 2017
Title BC1/Mmi1 IP
Sample type SRA
Source name Mmi1 immunoprecipitation
Organism Schizosaccharomyces pombe
Characteristics strain: SPV8
genotype: wild type
antibody: ant-Mmi1
Treatment protocol No treatment
Growth protocol S. pombe cells were grown in 200 ml yeast extract (YE) supplemented with Adenine at 30℃ and 220 rpm up to OD595=1.2
Extracted molecule total RNA
Extraction protocol Immunoprecipitated RNA was extracted and purified using the classical phenol-chlofororm extraction and ethanol precipitation
Immunoprecipitated RNA was subjected to 5' RACE experiments (shared RNA ligated to 5'-adapter, reverse transcribed using RT-oligo with random hexamer at the 3'-end, then PCR amplified).
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
Description Raw fastq data are not available due to computer failure
Data processing reads were extracted from the fastq files, and each unique read was assigned a count (frequency) and mapped (exact matches) to the pombe genome (from, circa 2013)
annotations from pombase as gff3 files were downloaded and used to annotate each mapped read.
These annotations and counts are provided in the processed and tabDelimited files
All the processing was done using custom software
Genome_build: Release 20 (2013)
Supplementary_files_format_and_content: tabDelimited files include all reads for the sample; processed files are mapping/annotation for the sample
Submission date Nov 30, 2016
Last update date Jul 27, 2017
Contact name Ravi Sachidanandam
Organization name Girihlet Inc.
Street address 2945 Webster St
City Oakland
State/province CA
ZIP/Postal code 94609
Country USA
Platform ID GPL13988
Series (1)
GSE90688 Genome-wide data of RNAs associated to Mmi1 in wild type Schizosaccharomyces pombe cells
BioSample SAMN06075654

Supplementary file Size Download File type/resource
GSM2410429_BC1_processed.txt.gz 8.9 Mb (ftp)(http) TXT
GSM2410429_BC1_tabDelimited.txt.gz 80.5 Mb (ftp)(http) TXT
Raw data not provided for this record
Processed data provided as supplementary file

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